Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold354
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 564417
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 1 of 4
Found at i:450 original size:155 final size:154
Alignment explanation
Indices: 48--970 Score: 727
Period size: 156 Copynumber: 5.9 Consensus size: 154
38 AGTTCAAGAA
* * * * * *
48 AAAATTACGAAAATGCCCCTATGGGATACCCTCGACAT-AAAGTACCCGA-TACCCTTAAAGGAC
1 AAAATTACGAAAATGCCCTTAAGGGATACCTTCGACGTAAAAGTATCCGACAACCCTTAAAGGAC
* * * * * * * * *
111 TTAAAAATGAATA-TAAAAGGGATGAACCTATCCTAAAGACCCACCTTTGACATAAAAGCGGACT
66 TTAAAAA-GATTAGAAAAAGGG-TGAACCTATCCTAAATATCTACCTTCGGCATAAAAGTGGACC
* *
175 TGATGATAACCTAGGAC-TCGATTCTA-
129 AG-TGATAACCTAGGACTTAG-TTCTAG
* * * * * *
201 AAAATTACCAAAATACCCCT-AGGGGTACCTTCGACGTAAAAGTA-CCCAGCAACCC-TAAAGAA
1 AAAATTACGAAAATGCCCTTAAGGGATACCTTCGACGTAAAAGTATCCGA-CAACCCTTAAAGGA
* * *
263 CTTAAAGAGGATTAG-AAAAGGGATGAAGCTATCCTAAATATCTACCTTCGGCACAAAAGTGGAC
65 CTTAAA-AAGATTAGAAAAAGGG-TGAACCTATCCTAAATATCTACCTTCGGCATAAAAGTGGAC
* *
327 CAAGTGATGA-CTAGGAGTT-GTTCTAG
128 C-AGTGATAACCTAGGACTTAGTTCTAG
* * *
353 AAAATTACGAAAAATGCTCCTTCAGGTATACCTAT-GACGTAAAAATATCTCGA-AACCCTTAAA
1 AAAATTACG-AAAATGC-CCTTAAGGGATACCT-TCGACGTAAAAGTATC-CGACAACCCTTAAA
* * ** *
416 CGACTTAAAAAGATTAGAAAATGGGTGAACCTATCCTAAATATCTACCTTCAACATAAAAGCGGA
62 GGACTTAAAAAGATTAGAAAAAGGGTGAACCTATCCTAAATATCTACCTTCGGCATAAAAGTGGA
* * * * *
481 CTCGGT-AGTAACTTAGGCCTTGGTTCTAA
127 C-CAGTGA-TAACCTAGGACTTAGTTCTAG
* ** *
510 AAAATTACGAAAATG-CCTCTAAGGGATACCTTCGACGTGAAAGTATCCCG-GTACCCCTAAAGG
1 AAAATTACGAAAATGCCCT-TAAGGGATACCTTCGACGTAAAAGTAT-CCGACAACCCTTAAAGG
** *
573 ACTTAAAAAGGATTTTAAAAAGGGATGAACCTATCCTAAATATCTACCTTTAGTG-A-AAAAGTG
64 ACTTAAAAA-GATTAGAAAAAGGG-TGAACCTATCCTAAATATCTACC-TTCG-GCATAAAAGTG
** ** * *
636 GATAAGGTGACGACCTAGGAGTTAGTTTTAG
125 GACCA-GTGATAACCTAGGACTTAGTTCTAG
* * *
667 AAAATTATGAAAATACCCTTACGGGTATACCTTCGACGTAAAAGTATCCTGACAACCC-TAAAGG
1 AAAATTACGAAAATGCCCTTAAGGG-ATACCTTCGACGTAAAAGTATCC-GACAACCCTTAAAGG
* * * **
731 ACTTAAAAAGATTAGAAAATGGGTGAACCTATGCTAAATATCTACCTTTGGCATAAAAACGGACC
64 ACTTAAAAAGATTAGAAAAAGGGTGAACCTATCCTAAATATCTACCTTCGGCATAAAAGTGGACC
* * * *
796 TGATGGTAACCTAGAACTCAGTTCT-G
129 AG-TGATAACCTAGGACTTAGTTCTAG
* * * * * **
822 AAAAATTACGAAAATG-CTTCTAAGGGATACCTTTGACATGAAAGTATCCTAGTACCCTTAAAGG
1 -AAAATTACGAAAATGCCCT-TAAGGGATACCTTCGACGTAAAAGTATCCGACAACCCTTAAAGG
* ** *
886 ACTTTAAAAGGATTTTAAAAAGGATGAACCTATCCTAAATATCTACCTTCGGCATAAAAGTGGAC
64 AC-TTAAAAAGATTAGAAAAAGGGTGAACCTATCCTAAATATCTACCTTCGGCATAAAAGTGGAC
* * *
951 TCGGTGGTTACCTAGGACTT
128 -CAGTGATAACCTAGGACTT
971 GGTTTCGTAA
Statistics
Matches: 612, Mismatches: 116, Indels: 81
0.76 0.14 0.10
Matches are distributed among these distances:
151 5 0.01
152 31 0.05
153 93 0.15
154 20 0.03
155 148 0.24
156 172 0.28
157 96 0.16
158 43 0.07
159 4 0.01
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (154 bp):
AAAATTACGAAAATGCCCTTAAGGGATACCTTCGACGTAAAAGTATCCGACAACCCTTAAAGGAC
TTAAAAAGATTAGAAAAAGGGTGAACCTATCCTAAATATCTACCTTCGGCATAAAAGTGGACCAG
TGATAACCTAGGACTTAGTTCTAG
Found at i:743 original size:313 final size:310
Alignment explanation
Indices: 48--950 Score: 1043
Period size: 313 Copynumber: 2.9 Consensus size: 310
38 AGTTCAAGAA
* * * * * *
48 AAAATTACGAAAATGCCCCTATGGG-ATACCCTCGACAT-AAAGTA-CCCGATACCCTTAAAGGA
1 AAAATTACGAAAATGCCCTTACGGGTATACCTTCGACGTAAAAGTATCCTGAAACCCTTAAAGGA
* * * * *
110 CTTAAAAATGAATATAAAA-GGGATGAACCTATCCTAAAGACCCACCTTTGACATAAAAGCGGAC
66 CTTAAAAA-GATTAGAAAATGGG-TGAACCTATCCTAAATATCTACCTTTGACATAAAAGCGGAC
* * * * * *
174 TTGATGATAACCTAGGACTCGATTCTAAAAATTACCAAAATACCCCT-AGGGGTACCTTCGACGT
129 TCGATG-TAACCTAGGACTCGGTTCTAAAAATTACGAAAATGCCTCTAAGGGATACCTTCGACGT
* * * * * *
238 AAAAGTA-CCCAGCAACCCTAAAGAACTTAAAGAGGA--TTAGAAAAGGGATGAAGCTATCCTAA
193 GAAAGTATCCCAGTACCCCTAAAGGACTTAAAAAGGATTTTA-AAAAGGGATGAACCTATCCTAA
* *
300 ATATCTACC-TTCGGCACAAAAGTGGACCAAGTGATGACTAGGAGTTGTTCTAG
257 ATATCTACCTTTAGGCACAAAAGTGGACCAAGTGACGACTAGGAGTTGTTCTAG
* *
353 AAAATTACGAAAAATGCTCCTT-CAGGTATACCTAT-GACGTAAAAATAT-CTCGAAACCCTTAA
1 AAAATTACG-AAAATGC-CCTTACGGGTATACCT-TCGACGTAAAAGTATCCT-GAAACCCTTAA
* **
415 ACGACTTAAAAAGATTAGAAAATGGGTGAACCTATCCTAAATATCTACCTTCAACATAAAAGCGG
62 AGGACTTAAAAAGATTAGAAAATGGGTGAACCTATCCTAAATATCTACCTTTGACATAAAAGCGG
* * * *
480 ACTCGGTAGTAACTTAGGCCTTGGTTCTAAAAAATTACGAAAATGCCTCTAAGGGATACCTTCGA
127 ACTCGAT-GTAACCTAGGACTCGGTTCT-AAAAATTACGAAAATGCCTCTAAGGGATACCTTCGA
*
545 CGTGAAAGTATCCCGGTACCCCTAAAGGACTTAAAAAGGATTTTAAAAAGGGATGAACCTATCCT
190 CGTGAAAGTATCCCAGTACCCCTAAAGGACTTAAAAAGGATTTTAAAAAGGGATGAACCTATCCT
* *
610 AAATATCTACCTTTAGTG-A-AAAAGTGGA-TAAGGTGACGACCTAGGAGTTAGTTTTAG
255 AAATATCTACCTTTAG-GCACAAAAGTGGACCAA-GTGACGA-CTAGGAGTT-GTTCTAG
* *
667 AAAATTATGAAAATACCCTTACGGGTATACCTTCGACGTAAAAGTATCCTGACAACCC-TAAAGG
1 AAAATTACGAAAATGCCCTTACGGGTATACCTTCGACGTAAAAGTATCCTGA-AACCCTTAAAGG
* * *
731 ACTTAAAAAGATTAGAAAATGGGTGAACCTATGCTAAATATCTACCTTTGGCATAAAAACGGAC-
65 ACTTAAAAAGATTAGAAAATGGGTGAACCTATCCTAAATATCTACCTTTGACATAAAAGCGGACT
* * * * *
795 CTGATGGTAACCTAGAACTCAGTTCTGAAAAATTACGAAAATGCTTCTAAGGGATACCTTTGACA
130 C-GAT-GTAACCTAGGACTCGGTTCT-AAAAATTACGAAAATGCCTCTAAGGGATACCTTCGACG
* * *
860 TGAAAGTATCCTAGTACCCTTAAAGGACTTTAAAAGGATTTTAAAAA-GGATGAACCTATCCTAA
192 TGAAAGTATCCCAGTACCCCTAAAGGACTTAAAAAGGATTTTAAAAAGGGATGAACCTATCCTAA
* *
924 ATATCTACC-TTCGGCATAAAAGTGGAC
257 ATATCTACCTTTAGGCACAAAAGTGGAC
951 TCGGTGGTTA
Statistics
Matches: 508, Mismatches: 63, Indels: 46
0.82 0.10 0.07
Matches are distributed among these distances:
305 9 0.02
306 9 0.02
307 12 0.02
308 69 0.14
309 43 0.08
310 23 0.05
311 30 0.06
312 86 0.17
313 205 0.40
314 22 0.04
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.24
Consensus pattern (310 bp):
AAAATTACGAAAATGCCCTTACGGGTATACCTTCGACGTAAAAGTATCCTGAAACCCTTAAAGGA
CTTAAAAAGATTAGAAAATGGGTGAACCTATCCTAAATATCTACCTTTGACATAAAAGCGGACTC
GATGTAACCTAGGACTCGGTTCTAAAAATTACGAAAATGCCTCTAAGGGATACCTTCGACGTGAA
AGTATCCCAGTACCCCTAAAGGACTTAAAAAGGATTTTAAAAAGGGATGAACCTATCCTAAATAT
CTACCTTTAGGCACAAAAGTGGACCAAGTGACGACTAGGAGTTGTTCTAG
Found at i:1848 original size:126 final size:130
Alignment explanation
Indices: 1630--1874 Score: 313
Period size: 126 Copynumber: 1.9 Consensus size: 130
1620 TAATTATTTC
** *
1630 AAAAAAATCATTTCGTACCTTAATGGATACCGAAAAGATATGAAAAGATTTTCGAAATATTCTAT
1 AAAAAAATCATTTCGTACCTTAATGGATACCGAAAAGATACAAAAAGATTTTCGAAATATTCTAG
* * * *
1695 ACCCTACAGATGCCTATAGGAATATAAAAGACTT-GAAATAATTGATATTTATTATATTTGGAAA
66 ACCCTACAGATACCTATAAGAATATAAAAGACTTAAAAATAATTAATATTTATTATATTTGGAAA
* * *
1759 AAAAAAATCATTTCGTACCTT-ATGGATACCTG-AAAGATACAAAAAG-TTTT-GATATCTTTTA
1 AAAAAAATCATTTCGTACCTTAATGGATACC-GAAAAGATACAAAAAGATTTTCGAAATATTCTA
* * *
1820 GACCCTA-TGTATACCTATAAGAATATAAAAGATTTAAAAATGATTAATATTTATT
65 GACCCTACAG-ATACCTATAAGAATATAAAAGACTTAAAAATAATTAATATTTATT
1875 GTAATTAACG
Statistics
Matches: 100, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
125 1 0.01
126 36 0.36
127 20 0.20
128 21 0.21
129 22 0.22
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.33
Consensus pattern (130 bp):
AAAAAAATCATTTCGTACCTTAATGGATACCGAAAAGATACAAAAAGATTTTCGAAATATTCTAG
ACCCTACAGATACCTATAAGAATATAAAAGACTTAAAAATAATTAATATTTATTATATTTGGAAA
Found at i:2814 original size:10 final size:10
Alignment explanation
Indices: 2799--2830 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
2789 CAAAGCTTAG
2799 CTAATGTTTT
1 CTAATGTTTT
2809 CTAATGTTTT
1 CTAATGTTTT
*
2819 CTAATTTTTT
1 CTAATGTTTT
2829 CT
1 CT
2831 CCCTTTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.19, C:0.12, G:0.06, T:0.62
Consensus pattern (10 bp):
CTAATGTTTT
Found at i:2870 original size:23 final size:23
Alignment explanation
Indices: 2834--2883 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
2824 TTTTTCTCCC
* *
2834 TTTTCTTCTATTTTCTCTTGTTT
1 TTTTCCTCTATTTTCTCTGGTTT
*
2857 TTTTCCTCTCTTTTCTCTGGTTT
1 TTTTCCTCTATTTTCTCTGGTTT
2880 TTTT
1 TTTT
2884 TTTCTAGCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.02, C:0.20, G:0.06, T:0.72
Consensus pattern (23 bp):
TTTTCCTCTATTTTCTCTGGTTT
Found at i:3962 original size:167 final size:163
Alignment explanation
Indices: 3524--3962 Score: 408
Period size: 167 Copynumber: 2.6 Consensus size: 163
3514 ACCACATTTT
* * * *
3524 GAAAAAATAAGAATTTCGAGGAGAAAAA-TCAAAAACTCATGATAATG-ATTT-TTTTTTAAATT
1 GAAAAAA-GAGAATTTC-AAGAGAAAAATTC-AAAACTCATGAAAATGAATTTATTTTTTAAAAT
* * ** *
3586 GAATTAATAGGAAATAAATATTTG-TATTTTATGCCTTTTGAAAATTGAAAACTGAGAAAAATCC
63 GAATTAACATGAAATAAATATTTGATATTTTA--AATTTTAAAAATTGAAAACTGAGAAAAATCC
* *
3650 CTTCGACAATTTTATGGAGTAAAAAACACCGTAGTTAG
126 CTTCAACAATTTTATGGAGTAAAAAACAACGTAGTTAG
* * * * * * * *
3688 GAAAAAAAGGGTATTTCAAG-GAAAAATCCAAAACACATGAAAATGAACTTATTTTTCAGAACTA
1 G-AAAAAAGAGAATTTCAAGAGAAAAATTCAAAACTCATGAAAATGAATTTATTTTTTA-AAATG
* * * * *
3752 AATTAACATGAAATAAAT-TGTAATATTTGAATGACTTTTAAAAATTTAAAATTGAGAAAAATTC
64 AATTAACATGAAATAAATATTTGATATTTTAA--A-TTTTAAAAATTGAAAACTGAGAAAAA-TC
* * *
3816 CC-TCAAAACAA-TTTATGGAGTAGAAAACAATGTATTTAG
125 CCTTC--AACAATTTTATGGAGTAAAAAACAACGTAGTTAG
*
3855 GAAAAAAGAGAATTTCAAAGAAAAAAATTCAAAACTCATGAAAATGAATTTATTTTTTAAAATGA
1 GAAAAAAGAGAATTTC-AAGAGAAAAATTCAAAACTCATGAAAATGAATTTATTTTTTAAAATGA
**
3920 ATTAACATGAAATAAATATTTGATGAATTTTAAAAATTAAAAA
65 ATTAACATGAAATAAATATTTGAT--ATTTTAAATTTTAAAAA
3963 CCAAGAAAAA
Statistics
Matches: 218, Mismatches: 40, Indels: 31
0.75 0.14 0.11
Matches are distributed among these distances:
162 20 0.09
163 6 0.03
164 15 0.07
165 31 0.14
166 38 0.17
167 60 0.28
168 42 0.19
170 6 0.03
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.31
Consensus pattern (163 bp):
GAAAAAAGAGAATTTCAAGAGAAAAATTCAAAACTCATGAAAATGAATTTATTTTTTAAAATGAA
TTAACATGAAATAAATATTTGATATTTTAAATTTTAAAAATTGAAAACTGAGAAAAATCCCTTCA
ACAATTTTATGGAGTAAAAAACAACGTAGTTAG
Found at i:5041 original size:42 final size:42
Alignment explanation
Indices: 4998--5732 Score: 309
Period size: 42 Copynumber: 17.3 Consensus size: 42
4988 AAAAGAATCC
* * * *
4998 CGGGTCTGAGCCGACAGGCAGACGAATGATGGAAAAGTCTCC
1 CGGGTCTAAGCCGACGGGCAGATGAATGATGGAAAAGTCTCT
* ** * * *
5040 CGGGCCTAAGCCGATAGGAAGATGAAAGAT-GAAGAAGTCACT
1 CGGGTCTAAGCCGACGGGCAGATGAATGATGGAA-AAGTCTCT
* * * * * **
5082 CGAGTCTAAGTCGATGGGTAGATGATTGA-CAAAGGAAGTCTCT
1 CGGGTCTAAGCCGACGGGCAGATGAATGATGGAA--AAGTCTCT
* * * * *
5125 TGGGTCTGAGCCGATGGGCAGATGAATGGTGGAAAAGTCTCC
1 CGGGTCTAAGCCGACGGGCAGATGAATGATGGAAAAGTCTCT
* ** * *
5167 CAGGTCTAAGCCGACGAACAGATGATTAATGGAAAAGTCTCT
1 CGGGTCTAAGCCGACGGGCAGATGAATGATGGAAAAGTCTCT
* * * *
5209 CGAGTCTAAGCCGACGGGCAGACGATTGATGAAAAAGTCTCT
1 CGGGTCTAAGCCGACGGGCAGATGAATGATGGAAAAGTCTCT
*** * *** *
5251 CGGGTCTAAGCCGACGAATAGA-CAATTGACAAAGAAAGTCTTT
1 CGGGTCTAAGCCGACGGGCAGATGAA-TGATGGA-AAAGTCTCT
* * * *
5294 TGGGTCTAAGTCAACGGGCAGATGATTGATGGAAAAGTCTCT
1 CGGGTCTAAGCCGACGGGCAGATGAATGATGGAAAAGTCTCT
* * * * *
5336 CGAGTCTAAGCCAACGAGCAGACGATTGATGGAAAAGTCTC-
1 CGGGTCTAAGCCGACGGGCAGATGAATGATGGAAAAGTCTCT
* * * * *
5377 CTAGGTCTAAGCCGATGGGAAGA-CAATTGAT-AAAGGAAGTCTCT
1 C-GGGTCTAAGCCGACGGGCAGATGAA-TGATGGAA--AAGTCTCT
** * * * ** *
5421 CGATTCTGAGCCGATGGGCAAATGAATGACAGAAAAGTCTCC
1 CGGGTCTAAGCCGACGGGCAGATGAATGATGGAAAAGTCTCT
** *** * *
5463 CAAGTCTAAGCCGACGGGCAGAT-AATTGACAAAAGAAGTTTCC
1 CGGGTCTAAGCCGACGGGCAGATGAA-TGATGGAA-AAGTCTCT
** * * * * * *
5506 CCCGTTTAAGCCGATGGGCAGACGATTGATTGAAAAGTCTCC
1 CGGGTCTAAGCCGACGGGCAGATGAATGATGGAAAAGTCTCT
* ** * * * * * *
5548 CAGGTCTAAGCCGATAGGCAAATGATTCAT-AAAGGAAGTATCC
1 CGGGTCTAAGCCGACGGGCAGATGAATGATGGAA--AAGTCTCT
* * * * * *** *
5591 CGAGTCTAAGCTGATGGGTAGATGATTGACAAAGAAAGTCTCC
1 CGGGTCTAAGCCGACGGGCAGATGAATGATGGA-AAAGTCTCT
* * * * ****
5634 CTGTTCTAAGCCGACGAGTAGACCTTTGATGGAAAAGTCTCT
1 CGGGTCTAAGCCGACGGGCAGATGAATGATGGAAAAGTCTCT
** *
5676 CGGGTCTAAGCCGACGGGCA-AACAATTGATAGAGAAAGTCTCT
1 CGGGTCTAAGCCGACGGGCAGATGAA-TGATGGA-AAAGTCTCT
*
5719 TGGGTCTAAGCCGA
1 CGGGTCTAAGCCGA
5733 TAGTAGACAA
Statistics
Matches: 524, Mismatches: 146, Indels: 45
0.73 0.20 0.06
Matches are distributed among these distances:
41 14 0.03
42 306 0.58
43 192 0.37
44 11 0.02
45 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.21
Consensus pattern (42 bp):
CGGGTCTAAGCCGACGGGCAGATGAATGATGGAAAAGTCTCT
Found at i:5236 original size:127 final size:126
Alignment explanation
Indices: 4998--5265 Score: 310
Period size: 127 Copynumber: 2.1 Consensus size: 126
4988 AAAAGAATCC
* *
4998 CGGGTCTGAGCCGACAGGCAGACGAATGATGGAAAAGTCTCCCGGGCCTAAGCCGATAGGAAGAT
1 CGGGTCTGAGCCGACAGGCAGACGAATGATGGAAAAGTCTCCCAGGCCTAAGCCGATAGAAAGAT
* * * *
5063 GAAAGATGAAGAAGTCACTCGAGTCTAAGTCGATGGGTAGATGATTGA-CAAAGGAAGTCTCT
66 GAAAGATGAAGAAGTCACTCGAGTCTAAGCCGACGGGCAGACGATTGATCAAA--AAGTCTCT
* ** * * * *
5125 TGGGTCTGAGCCGATGGGCAGATGAATGGTGGAAAAGTCTCCCAGGTCTAAGCCGA-CGAACAGA
1 CGGGTCTGAGCCGACAGGCAGACGAATGATGGAAAAGTCTCCCAGGCCTAAGCCGATAGAA-AGA
* * *
5189 TGATTA-ATGGAA-AAGTCTCTCGAGTCTAAGCCGACGGGCAGACGATTGATGAAAAAGTCTCT
65 TGA-AAGAT-GAAGAAGTCACTCGAGTCTAAGCCGACGGGCAGACGATTGATCAAAAAGTCTCT
*
5251 CGGGTCTAAGCCGAC
1 CGGGTCTGAGCCGAC
5266 GAATAGACAA
Statistics
Matches: 118, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
126 22 0.19
127 89 0.75
128 7 0.06
ACGTcount: A:0.31, C:0.19, G:0.31, T:0.19
Consensus pattern (126 bp):
CGGGTCTGAGCCGACAGGCAGACGAATGATGGAAAAGTCTCCCAGGCCTAAGCCGATAGAAAGAT
GAAAGATGAAGAAGTCACTCGAGTCTAAGCCGACGGGCAGACGATTGATCAAAAAGTCTCT
Found at i:5299 original size:169 final size:169
Alignment explanation
Indices: 5016--5422 Score: 428
Period size: 169 Copynumber: 2.4 Consensus size: 169
5006 AGCCGACAGG
* * * ** * * *
5016 CAGACGAATGATGGAAAAGTCTCCCG-GGCCTAAGCCGATAGGAAGATGAA-AGATGAAGAAGTC
1 CAGACGATTAATGGAAAAGTCT-CCGAGGTCTAAGCCGACGGGAAGA-CAATTGATAAAGAAGTC
* * * * ** ** * * * *
5079 ACTCGAGTCTAAGTCGATGGGTAGATGATTGACAAAGGAAGTCTCTTGGGTCTGAGCCGATGGGC
64 TCTCGGGTCTAAGCCGACGAATAGACAATTGACAAAGAAAGTCTCTTGGGTCTAAGCCAACGGGC
* *
5144 AGATGAATGGTGGAAAAGTCTCCC-AGGTCTAAGCCGACGAA
129 AGATGAATGATGGAAAAGTCTCCCGA-GTCTAAGCCAACGAA
* * *
5185 CAGATGATTAATGGAAAAGTCTCTCGA-GTCTAAGCCGACGGGCAGACGATTGATGAAA-AAGTC
1 CAGACGATTAATGGAAAAGTCTC-CGAGGTCTAAGCCGACGGGAAGACAATTGAT-AAAGAAGTC
* *
5248 TCTCGGGTCTAAGCCGACGAATAGACAATTGACAAAGAAAGTCTTTTGGGTCTAAGTCAACGGGC
64 TCTCGGGTCTAAGCCGACGAATAGACAATTGACAAAGAAAGTCTCTTGGGTCTAAGCCAACGGGC
* * *
5313 AGATGATTGATGGAAAAGTCTCTCGAGTCTAAGCCAACGAG
129 AGATGAATGATGGAAAAGTCTCCCGAGTCTAAGCCAACGAA
* * *
5354 CAGACGATTGATGGAAAAGTCTCCTAGGTCTAAGCCGATGGGAAGACAATTGATAAAGGAAGTCT
1 CAGACGATTAATGGAAAAGTCTCCGAGGTCTAAGCCGACGGGAAGACAATTGATAAA-GAAGTCT
5419 CTCG
65 CTCG
5423 ATTCTGAGCC
Statistics
Matches: 194, Mismatches: 36, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
168 7 0.04
169 174 0.90
170 13 0.07
ACGTcount: A:0.33, C:0.18, G:0.29, T:0.21
Consensus pattern (169 bp):
CAGACGATTAATGGAAAAGTCTCCGAGGTCTAAGCCGACGGGAAGACAATTGATAAAGAAGTCTC
TCGGGTCTAAGCCGACGAATAGACAATTGACAAAGAAAGTCTCTTGGGTCTAAGCCAACGGGCAG
ATGAATGATGGAAAAGTCTCCCGAGTCTAAGCCAACGAA
Found at i:5417 original size:85 final size:84
Alignment explanation
Indices: 5001--5732 Score: 375
Period size: 85 Copynumber: 8.6 Consensus size: 84
4991 AGAATCCCGG
* * * ** * ** *
5001 GTCTGAGCCGAC-AGGCAGACGAATGATGGAAAAGTCTCCCGGGCCTAAGCCGATAGGAAGATGA
1 GTCTAAGCCGACGA-GCAGACGATTGATAGAAAAGTCTCCTAGGTCTAAGCCGACGGGCAGATGA
** * *
5065 AAGATGAAGAAGTCACTCGA
65 TTGATAAAGAAGTCTCTCGA
* * * * * * * * * *
5085 GTCTAAGTCGATGGGTAGATGATTGACA-AAGGAAGTCTCTTGGGTCTGAGCCGATGGGCAGATG
1 GTCTAAGCCGACGAGCAGACGATTGATAGAA--AAGTCTCCTAGGTCTAAGCCGACGGGCAGATG
* * * *
5149 AATGGTGGAA-AAGTCTC-CCA
64 ATTGAT-AAAGAAGTCTCTCGA
* * * * * *
5169 GGTCTAAGCCGACGAACAGATGATTAATGGAAAAGTCT-CTCGAGTCTAAGCCGACGGGCAGACG
1 -GTCTAAGCCGACGAGCAGACGATTGATAGAAAAGTCTCCTAG-GTCTAAGCCGACGGGCAGATG
*
5233 ATTGATGAAA-AAGTCTCTCGG
64 ATTGAT-AAAGAAGTCTCTCGA
** * * * ** * * *
5254 GTCTAAGCCGACGAATAGACAATTGACAAAGAAAGTCTTTTGGGTCTAAGTCAACGGGCAGATGA
1 GTCTAAGCCGACGAGCAGACGATTGATAGA-AAAGTCTCCTAGGTCTAAGCCGACGGGCAGATGA
*
5319 TTGATGGAA-AAGTCTCTCGA
65 TTGAT-AAAGAAGTCTCTCGA
* * * * **
5339 GTCTAAGCCAACGAGCAGACGATTGATGGAAAAGTCTCCTAGGTCTAAGCCGATGGGAAGACAAT
1 GTCTAAGCCGACGAGCAGACGATTGATAGAAAAGTCTCCTAGGTCTAAGCCGACGGGCAGATGAT
5404 TGATAAAGGAAGTCTCTCGA
66 TGATAAA-GAAGTCTCTCGA
* * * * * * * * * * *
5424 TTCTGAGCCGATGGGCAAATGAATGACAGAAAAGTCTCCCAAGTCTAAGCCGACGGGCAGATAAT
1 GTCTAAGCCGACGAGCAGACGATTGATAGAAAAGTCTCCTAGGTCTAAGCCGACGGGCAGATGAT
* * * **
5489 TGACAAAAGAAGTTTCCCCC
66 TGA-TAAAGAAGTCTCTCGA
* * * * * ** *
5509 GTTTAAGCCGATGGGCAGACGATTGATTGAAAAGTCTCCCAGGTCTAAGCCGATAGGCAAATGAT
1 GTCTAAGCCGACGAGCAGACGATTGATAGAAAAGTCTCCTAGGTCTAAGCCGACGGGCAGATGAT
* * *
5574 TCATAAAGGAAGTATCCCGA
66 TGATAAA-GAAGTCTCTCGA
* * * * * * * * * * **
5594 GTCTAAGCTGATGGGTAGATGATTGACAAAGAAAGTCTCCCT-GTTCTAAGCCGACGAGTAGACC
1 GTCTAAGCCGACGAGCAGACGATTGATAGA-AAAGTCT-CCTAGGTCTAAGCCGACGGGCAGATG
* * *
5658 TTTGATGGAA-AAGTCTCTCGG
64 ATTGAT-AAAGAAGTCTCTCGA
* * * * *
5679 GTCTAAGCCGACGGGCAAACAATTGATAGAGAAAGTCTCTTGGGTCTAAGCCGA
1 GTCTAAGCCGACGAGCAGACGATTGATAGA-AAAGTCTCCTAGGTCTAAGCCGA
5733 TAGTAGACAA
Statistics
Matches: 492, Mismatches: 138, Indels: 35
0.74 0.21 0.05
Matches are distributed among these distances:
83 6 0.01
84 116 0.24
85 331 0.67
86 35 0.07
87 4 0.01
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.21
Consensus pattern (84 bp):
GTCTAAGCCGACGAGCAGACGATTGATAGAAAAGTCTCCTAGGTCTAAGCCGACGGGCAGATGAT
TGATAAAGAAGTCTCTCGA
Found at i:5440 original size:127 final size:127
Alignment explanation
Indices: 5170--5484 Score: 364
Period size: 127 Copynumber: 2.5 Consensus size: 127
5160 AGTCTCCCAG
* ** *
5170 GTCTAAGCCGACGAACAGATGATTAATGGAAAAGTCTCTCGAGTCTAAGCCGACGGGCAGACGAT
1 GTCTAAGCCAACGGGCAGATGATTGATGGAAAAGTCTCTCGAGTCTAAGCCGACGGGCAGACGAT
* * * *
5235 TGATGAAAAAGTCTCTCGGGTCTAAGCCGACGAATAGACAATTGACAAAGAAAGTCTTTTGG
66 TGATGAAAAAGTCTCTCAGGTCTAAGCCGACGAATAGACAATTGACAAAGAAAGTCTCTCGA
* * *
5297 GTCTAAGTCAACGGGCAGATGATTGATGGAAAAGTCTCTCGAGTCTAAGCCAACGAGCAGACGAT
1 GTCTAAGCCAACGGGCAGATGATTGATGGAAAAGTCTCTCGAGTCTAAGCCGACGGGCAGACGAT
* * * * *
5362 TGATGGAAAAGTCTC-CTAGGTCTAAGCCGATGGGA-AGACAATTGATAAAGGAAGTCTCTCGA
66 TGATGAAAAAGTCTCTC-AGGTCTAAGCCGA-CGAATAGACAATTGACAAAGAAAGTCTCTCGA
* * * * * * ** * *
5424 TTCTGAGCCGATGGGCAAATGAATGACAGAAAAGTCTCCCAAGTCTAAGCCGACGGGCAGA
1 GTCTAAGCCAACGGGCAGATGATTGATGGAAAAGTCTCTCGAGTCTAAGCCGACGGGCAGA
5485 TAATTGACAA
Statistics
Matches: 157, Mismatches: 29, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
126 1 0.01
127 154 0.98
128 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.20
Consensus pattern (127 bp):
GTCTAAGCCAACGGGCAGATGATTGATGGAAAAGTCTCTCGAGTCTAAGCCGACGGGCAGACGAT
TGATGAAAAAGTCTCTCAGGTCTAAGCCGACGAATAGACAATTGACAAAGAAAGTCTCTCGA
Found at i:5619 original size:128 final size:128
Alignment explanation
Indices: 5455--5689 Score: 294
Period size: 128 Copynumber: 1.8 Consensus size: 128
5445 AATGACAGAA
* *
5455 AAGTCTCCCAAGTCTAAGCCGACGGGCAGATAATTGACAAA-AGAAGTTTCCCCCGTT-TAAGCC
1 AAGTATCCCAAGTCTAAGCCGACGGGCAGATAATTGACAAAGA-AAGTCT-CCCCGTTCTAAGCC
* * * *
5518 GATGGGCAGACGATTGATTGAAAAGTCTCCCAGGTCTAAGCCGATAGGCAAATGATTCATAAAGG
64 GACGAGCAGACCATTGATGGAAAAGTCTCCCAGGTCTAAGCCGATAGGCAAATGATTCATAAAGG
* * * * * *
5583 AAGTATCCCGAGTCTAAGCTGATGGGTAGATGATTGACAAAGAAAGTCTCCCTGTTCTAAGCCGA
1 AAGTATCCCAAGTCTAAGCCGACGGGCAGATAATTGACAAAGAAAGTCTCCCCGTTCTAAGCCGA
* * * *
5648 CGAGTAGACCTTTGATGGAAAAGTCTCTCGGGTCTAAGCCGA
66 CGAGCAGACCATTGATGGAAAAGTCTCCCAGGTCTAAGCCGA
5690 CGGGCAAACA
Statistics
Matches: 89, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
127 6 0.07
128 82 0.92
129 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (128 bp):
AAGTATCCCAAGTCTAAGCCGACGGGCAGATAATTGACAAAGAAAGTCTCCCCGTTCTAAGCCGA
CGAGCAGACCATTGATGGAAAAGTCTCCCAGGTCTAAGCCGATAGGCAAATGATTCATAAAGG
Found at i:5744 original size:42 final size:42
Alignment explanation
Indices: 5638--5768 Score: 133
Period size: 42 Copynumber: 3.1 Consensus size: 42
5628 GTCTCCCTGT
** *
5638 TCTAAGCCGACGAGTAGACCTTTGATG-GAAAAGTCTCTCGGG
1 TCTAAGCCGACGAGTAGACAATTGATGAG-AAAGTCTCTTGGG
* * *
5680 TCTAAGCCGACGGGCAAACAATTGATAGAGAAAGTCTCTTGGG
1 TCTAAGCCGACGAGTAGACAATTGAT-GAGAAAGTCTCTTGGG
* * *
5723 TCTAAGCCGA-TAGTAGACAATTGATG-GAAAGGTCTCCTAGG
1 TCTAAGCCGACGAGTAGACAATTGATGAGAAA-GTCTCTTGGG
5764 TCTAA
1 TCTAA
5769 ACTGATGGGT
Statistics
Matches: 74, Mismatches: 12, Indels: 7
0.80 0.13 0.08
Matches are distributed among these distances:
40 4 0.05
41 14 0.19
42 32 0.43
43 23 0.31
44 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (42 bp):
TCTAAGCCGACGAGTAGACAATTGATGAGAAAGTCTCTTGGG
Found at i:6491 original size:78 final size:78
Alignment explanation
Indices: 6296--6503 Score: 247
Period size: 78 Copynumber: 2.7 Consensus size: 78
6286 ATGGCCATGT
* * * * ** * *
6296 GATGCATCAATACCATTTAGTGTTTAGGAAGGAAGGATACAAATGGGAATGTGTGAGAAATGCCC
1 GATGCACCAATATCATCTAGTATTTAGGAAGGAAGGATATGATTGGGAATGTATGAGAAATGCCC
* *
6361 CCTTTGGCTTTAT
66 CCTTTGGCCTTAG
* * * *
6374 GATGCACTAATATCATCTAGTATTCAGTAAGGAAGGATATGATTGGGAATGTATGAGAAGTG-CC
1 GATGCACCAATATCATCTAGTATTTAGGAAGGAAGGATATGATTGGGAATGTATGAGAAATGCCC
6438 CCTCTTGGCCTTAG
66 CCT-TTGGCCTTAG
* * *
6452 GATGCACCAGTATCATCTGGTATTTAGGAAGGAAGGATATGATTAGGAATGT
1 GATGCACCAATATCATCTAGTATTTAGGAAGGAAGGATATGATTGGGAATGT
6504 GTGGTTAGGC
Statistics
Matches: 109, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
77 5 0.05
78 104 0.95
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.29
Consensus pattern (78 bp):
GATGCACCAATATCATCTAGTATTTAGGAAGGAAGGATATGATTGGGAATGTATGAGAAATGCCC
CCTTTGGCCTTAG
Found at i:7223 original size:53 final size:53
Alignment explanation
Indices: 7149--7365 Score: 257
Period size: 53 Copynumber: 4.2 Consensus size: 53
7139 CATTCAGTCC
* * * *
7149 ATTTTTTTTACCTGTATGCCCTTTTGGGTTTTCATCCAAGCATTATCATTCTT
1 ATTTTTTTTACCTGAACGCCCTTTCGGGTTTTCATCCAAGCATTATCATTCTA
* *
7202 ATTTTTTTTACTTGAACGCCCTTTCGGGTTTTCATCCAAGCA-T-T--GTC--
1 ATTTTTTTTACCTGAACGCCCTTTCGGGTTTTCATCCAAGCATTATCATTCTA
* * * *
7249 ATTTTTTTTACCTAAATGCCCTTTCGAGTTTTCATCCAAGCATTGTCATTCTA
1 ATTTTTTTTACCTGAACGCCCTTTCGGGTTTTCATCCAAGCATTATCATTCTA
* * * *
7302 ATTTTTTTTACTTGAACACCCTTTCGGGTTTTCATCTAGGCATTATCATTCTAA
1 ATTTTTTTTACCTGAACGCCCTTTCGGGTTTTCATCCAAGCATTATCATTCT-A
7356 ATTTTTTTTA
1 ATTTTTTTTA
7366 ACACATAGTA
Statistics
Matches: 139, Mismatches: 18, Indels: 13
0.82 0.11 0.08
Matches are distributed among these distances:
47 38 0.27
48 1 0.01
49 3 0.02
51 3 0.02
52 1 0.01
53 82 0.59
54 11 0.08
ACGTcount: A:0.20, C:0.21, G:0.11, T:0.48
Consensus pattern (53 bp):
ATTTTTTTTACCTGAACGCCCTTTCGGGTTTTCATCCAAGCATTATCATTCTA
Found at i:7269 original size:100 final size:100
Alignment explanation
Indices: 7148--7351 Score: 318
Period size: 100 Copynumber: 2.0 Consensus size: 100
7138 TCATTCAGTC
** * * *
7148 CATTTTTTTTACCTGTATGCCCTTTTGGGTTTTCATCCAAGCATTATCATTCTTATTTTTTTTAC
1 CATTTTTTTTACCTAAATGCCCTTTCGAGTTTTCATCCAAGCATTATCATTCTAATTTTTTTTAC
* *
7213 TTGAACGCCCTTTCGGGTTTTCATCCAAGCATTGT
66 TTGAACACCCTTTCGGGTTTTCATCCAAGCATTAT
*
7248 CATTTTTTTTACCTAAATGCCCTTTCGAGTTTTCATCCAAGCATTGTCATTCTAATTTTTTTTAC
1 CATTTTTTTTACCTAAATGCCCTTTCGAGTTTTCATCCAAGCATTATCATTCTAATTTTTTTTAC
* *
7313 TTGAACACCCTTTCGGGTTTTCATCTAGGCATTAT
66 TTGAACACCCTTTCGGGTTTTCATCCAAGCATTAT
7348 CATT
1 CATT
7352 CTAAATTTTT
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
100 94 1.00
ACGTcount: A:0.19, C:0.22, G:0.12, T:0.47
Consensus pattern (100 bp):
CATTTTTTTTACCTAAATGCCCTTTCGAGTTTTCATCCAAGCATTATCATTCTAATTTTTTTTAC
TTGAACACCCTTTCGGGTTTTCATCCAAGCATTAT
Found at i:18755 original size:61 final size:61
Alignment explanation
Indices: 18672--18818 Score: 251
Period size: 61 Copynumber: 2.4 Consensus size: 61
18662 TAAGGTTTAT
* *
18672 CATTGACACTAAGGTACTCGATAACAGCTTAGGACTCGATCAAATTATCCCTAAAGCTTAC
1 CATTAACACTAAGGTACCCGATAACAGCTTAGGACTCGATCAAATTATCCCTAAAGCTTAC
18733 CATTAACACTAAGGTACCCGATAACAGCTTAGGACTCGATCAAATTATCCCTAAAGCTTAC
1 CATTAACACTAAGGTACCCGATAACAGCTTAGGACTCGATCAAATTATCCCTAAAGCTTAC
*
18794 CATTGAA-ACTAAGGCACCCGATAAC
1 CATT-AACACTAAGGTACCCGATAAC
18819 TCTAAAAGGC
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
61 80 0.98
62 2 0.02
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (61 bp):
CATTAACACTAAGGTACCCGATAACAGCTTAGGACTCGATCAAATTATCCCTAAAGCTTAC
Found at i:18792 original size:29 final size:29
Alignment explanation
Indices: 18697--18792 Score: 72
Period size: 29 Copynumber: 3.2 Consensus size: 29
18687 ACTCGATAAC
18697 AGCTTAGGACTCGATCAAATTATCCCTAA
1 AGCTTAGGACTCGATCAAATTATCCCTAA
** * **
18726 AGCTTACCATTAAC-A-CTAAGGTA-CCCGATAA
1 AGCTTAGGACT--CGATC-AAATTATCCC--TAA
18757 CAGCTTAGGACTCGATCAAATTATCCCTAA
1 -AGCTTAGGACTCGATCAAATTATCCCTAA
18787 AGCTTA
1 AGCTTA
18793 CCATTGAAAC
Statistics
Matches: 48, Mismatches: 10, Indels: 18
0.63 0.13 0.24
Matches are distributed among these distances:
29 18 0.38
30 9 0.19
31 9 0.19
32 12 0.25
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (29 bp):
AGCTTAGGACTCGATCAAATTATCCCTAA
Found at i:19457 original size:157 final size:155
Alignment explanation
Indices: 18839--19457 Score: 397
Period size: 153 Copynumber: 4.0 Consensus size: 155
18829 TAAGTTCAAG
* * *
18839 AAAAATTACAAAAATGCC-CCTA-AGGGATATCC-TCGACGTAGAAGTA-CCC-G-ATACCCTTA
1 AAAAATTACAAAAAT-CCTCTTAGAGGGATA-CCTTCAACGTAAAAGTATCCCGGCA-ACCC-TA
* * * * * * *
18898 AAAGACGTAAAAATGACTATAAAAA-GGATGAACCTATCCTAAAGACCCACCTTCGGCATAAAAG
62 AAAGACTTAAAAA-GATTA-AAAAAGGGATGAACCTATCCTAAATATCTACCTTCAGCACAAAAG
* * * * * *** *
18962 CAGACTCGATGATAACTTAGGACTCAATTCTA
125 CA-AATCGGTGATGACCTAGGAGTTGGTTTTA
* * ** * *
18994 AAAAATTACGAAAATACC-CTTAG-GGG-TACCTTCGACGTAAAAG-A-AGCGACACCCCT-AAA
1 AAAAATTACAAAAAT-CCTCTTAGAGGGATACCTTCAACGTAAAAGTATCCCGGCAACCCTAAAA
*** * * * **
19053 GAACTTGAAGTGGATCAAAAAAAGGATGAACCTATCCTAAATATCTACCTTCGGCACAAAAGCGG
65 G-ACTT-AAAAAGATTAAAAAAGGGATGAACCTATCCTAAATATCTACCTTCAGCACAAAAGCAA
* *
19118 ATCTGGTGATGACTTAGGAGTTGGTTCTA
128 ATC-GGTGATGACCTAGGAGTTGGTTTTA
* * * ** ** * *
19147 AAAAATTACGAAAATGCTCTTATAGGTTTACCTTTGACGTAAAAGTTTCCCGGCAACCCTAAAGG
1 AAAAATTACAAAAATCCTCTTAGAGGGATACCTTCAACGTAAAAGTATCCCGGCAACCCTAAAAG
* * * *
19212 ACTTAAAAAGATTAAAAAATGGG-TGAACCAATCCTAACTATCTACCTTCAACATAAAAGCAGAA
66 ACTTAAAAAGATTAAAAAA-GGGATGAACCTATCCTAAATATCTACCTTCAGCACAAAAGCA-AA
* * * * * * *
19276 ACAGTGGTAACCTAGGACTCGGTTTTG
129 TCGGTGATGACCTAGGAGTTGGTTTTA
* * * *
19303 AAAAATTACAAAAATACCTC-T-GAGGGATACCTTCAACGTGAAAGTATCTCGGTACCCCTAAAA
1 AAAAATTACAAAAAT-CCTCTTAGAGGGATACCTTCAACGTAAAAGTATCCCGGCAACCCTAAAA
* * * *
19366 GACTTAAAAAGGATTTTAAAAAGGGATGAACCTATCCTAAATATCTACCTTTAGTAGAAAAGCAA
65 GACTTAAAAA-GA-TTAAAAAAGGGATGAACCTATCCTAAATATCTACCTTCAGCACAAAAGCAA
*
19431 ACTCGGTGATGACCTAGTAGTTGGTTT
128 A-TCGGTGATGACCTAGGAGTTGGTTT
19458 CGTAACAAAT
Statistics
Matches: 358, Mismatches: 85, Indels: 40
0.74 0.18 0.08
Matches are distributed among these distances:
152 12 0.03
153 85 0.24
154 20 0.06
155 80 0.22
156 82 0.23
157 76 0.21
158 3 0.01
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.24
Consensus pattern (155 bp):
AAAAATTACAAAAATCCTCTTAGAGGGATACCTTCAACGTAAAAGTATCCCGGCAACCCTAAAAG
ACTTAAAAAGATTAAAAAAGGGATGAACCTATCCTAAATATCTACCTTCAGCACAAAAGCAAATC
GGTGATGACCTAGGAGTTGGTTTTA
Found at i:20131 original size:147 final size:151
Alignment explanation
Indices: 19962--20230 Score: 334
Period size: 147 Copynumber: 1.8 Consensus size: 151
19952 TTTTCTTTTA
*** *
19962 AAAAAATCATTTCATACCTTAATAAAAATCCGTCAAA-ATAC-AAAA-AATTTTGAAATCTTTTA
1 AAAAAATCATTTCATACCTTAATAAAAA-CCCAAAAAGATACGAAAAGAATTTTGAAATATTTT-
* *
20024 ATACC-CCTATAGATACCCA-AGGAATATAAAAGA-TTGAAAACGATTAATATTTATTTTAGCAA
64 ATACCTCCTACAGATACCCATAGGAATATAAAAGACTTGAAAACAATTAATATTTATTTTAGCAA
20086 GGAGGGTTAATTTAATTATTTCT
129 GGAGGGTTAATTTAATTATTTCT
* * ** * **
20109 AAAAAATCATTTCGTACTTTAATGGATACCCAAAAAGATACGAAAAGTTTTTTGAAATATTTTAT
1 AAAAAATCATTTCATACCTTAATAAAAACCCAAAAAGATACGAAAAGAATTTTGAAATATTTTAT
* * *
20174 ACCTCCTACGGATACCCATAGGAATATAAAAGACTTGAAAATAATTGATATTTATTT
66 ACCTCCTACAGATACCCATAGGAATATAAAAGACTTGAAAACAATTAATATTTATTT
20231 ATATTTGGAA
Statistics
Matches: 100, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
146 5 0.05
147 27 0.27
148 9 0.09
149 25 0.25
150 14 0.14
151 20 0.20
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (151 bp):
AAAAAATCATTTCATACCTTAATAAAAACCCAAAAAGATACGAAAAGAATTTTGAAATATTTTAT
ACCTCCTACAGATACCCATAGGAATATAAAAGACTTGAAAACAATTAATATTTATTTTAGCAAGG
AGGGTTAATTTAATTATTTCT
Found at i:22254 original size:164 final size:164
Alignment explanation
Indices: 21973--22528 Score: 622
Period size: 165 Copynumber: 3.4 Consensus size: 164
21963 GGCATTTTGA
* * * ** **
21973 AAAAAGGAAAATTTCGAGGAAAAAAATAAAAAACTCATGAAAATAAATTTATTTTTCAAAACAAA
1 AAAAATGAGAATTTCAAGG-AAAAAATCTAAAACTCATGAAAATAAATTTATTTTT-AAAACTGA
* * * *
22038 ATTAATATGGAATAAATAATAGTATTTTATGACTTTTAAAAATTGAAAACTGAGAAAAATCCCCT
64 ATTAACATGAAATAAATAATAATATTTGATGACTTTTAAAAATTGAAAACTGAGAAAAAT-CCCT
* *
22103 CGAAAAAATTTATAGAGTAGAAAACACTATATTTAGG
128 CAAAAAAAATTATAGAGTAGAAAACACTATATTTAGG
* *
22140 AAAAATG-GTATTTCAAGGAAAAAATCTAAAACTC-TCGAAAATAAATTTATTTTTAAAATTGAA
1 AAAAATGAGAATTTCAAGGAAAAAATCTAAAACTCAT-GAAAATAAATTTATTTTTAAAACTGAA
*
22203 TTAACATGAAATAAATTATAATATTTGATGACTTTTAAAAATTGAAAACTGAGAAAAATTCCCT-
65 TTAACATGAAATAAATAATAATATTTGATGACTTTTAAAAATTGAAAACTGAGAAAAA-TCCCTC
* * * *
22267 AAAAAAAATTACATAGTAGAAAATACTATATTTAGT
129 AAAAAAAATTATAGAGTAGAAAACACTATATTTAGG
*
22303 AAAAATGAGAATTTCAAGGAAAAAATCTAAAACTCATGAAAATGAATTTATTTTTTAAAACTGAA
1 AAAAATGAGAATTTCAAGGAAAAAATCTAAAACTCATGAAAATAAATTTA-TTTTTAAAACTGAA
* * * * ** * *
22368 TTAACATGAAATAAATAATAATATTTGATTAATTTTACAAATTAAAAACCAAAAAAAAGTCTCTC
65 TTAACATGAAATAAATAATAATATTTGATGACTTTTAAAAATTGAAAACTGAGAAAAA-TCCCTC
* ** *
22433 AAAAAAAATCATAGAGTAGAAAACTTTGA-ATTT-CG
129 AAAAAAAATTATAGAGTAGAAAACACT-ATATTTAGG
* * * *
22468 AAAAAAGAAAAATTTTAAGGAAAAAAT-TAAAAAACTAATGAAAATGAAA-TTATTTTTAAAA
1 AAAAATG-AGAATTTCAAGGAAAAAATCT--AAAACTCATGAAAAT-AAATTTATTTTTAAAA
22529 ATTGATTTGA
Statistics
Matches: 332, Mismatches: 46, Indels: 23
0.83 0.11 0.06
Matches are distributed among these distances:
163 37 0.11
164 102 0.31
165 108 0.33
166 59 0.18
167 24 0.07
168 2 0.01
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.30
Consensus pattern (164 bp):
AAAAATGAGAATTTCAAGGAAAAAATCTAAAACTCATGAAAATAAATTTATTTTTAAAACTGAAT
TAACATGAAATAAATAATAATATTTGATGACTTTTAAAAATTGAAAACTGAGAAAAATCCCTCAA
AAAAAATTATAGAGTAGAAAACACTATATTTAGG
Found at i:23574 original size:51 final size:52
Alignment explanation
Indices: 23514--23623 Score: 150
Period size: 51 Copynumber: 2.1 Consensus size: 52
23504 ATTTAACTAG
* * *
23514 ATGTATCAATACATTGAAGAATGTATCGATACATTTAGGT-TAAAACCCAAA
1 ATGTATCAATACAATGAAGAATCTATCGATACATTTAGGTCAAAAACCCAAA
* * * *
23565 ATGTATCAATACAATGAATAATCTATCGATACATTTGGGTCAAAAACCTAGA
1 ATGTATCAATACAATGAAGAATCTATCGATACATTTAGGTCAAAAACCCAAA
23617 ATGTATC
1 ATGTATC
23624 GATATAAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
51 36 0.71
52 15 0.29
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.30
Consensus pattern (52 bp):
ATGTATCAATACAATGAAGAATCTATCGATACATTTAGGTCAAAAACCCAAA
Found at i:23657 original size:49 final size:49
Alignment explanation
Indices: 23533--23698 Score: 167
Period size: 49 Copynumber: 3.3 Consensus size: 49
23523 TACATTGAAG
* * * * * *
23533 AATGTATCGATACATTTAGGTTAAAACCCAAAATGTATCAATACAATGAAT
1 AATGTATCGATACATTT-GGATCAAACCCAGAATGTATCGATATAAT-AAA
* * *
23584 AATCTATCGATACATTTGGGTCAAAAACCTAGAATGTATCGATAT-A-AAA
1 AATGTATCGATACATTTGGATC--AAACCCAGAATGTATCGATATAATAAA
*
23633 AATGTATCGATACACTTT-GATCAAACCCAGAATGTATTGATATAATAAA
1 AATGTATCGATACA-TTTGGATCAAACCCAGAATGTATCGATATAATAAA
*
23682 AATGTATTGATACATTT
1 AATGTATCGATACATTT
23699 TTTTTTCCAG
Statistics
Matches: 97, Mismatches: 13, Indels: 13
0.79 0.11 0.11
Matches are distributed among these distances:
47 19 0.20
48 4 0.04
49 34 0.35
50 6 0.06
51 17 0.18
52 17 0.18
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (49 bp):
AATGTATCGATACATTTGGATCAAACCCAGAATGTATCGATATAATAAA
Found at i:23778 original size:20 final size:20
Alignment explanation
Indices: 23736--23795 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
23726 GATATGGTCT
**
23736 TGTATCGATACATTTCAAATA
1 TGTATCGATACA-TTCACTTA
23757 TGTATCGATACATTCACTTA
1 TGTATCGATACATTCACTTA
*
23777 TGTATCAATACATTCACTT
1 TGTATCGATACATTCACTT
23796 GTTATATCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
20 24 0.67
21 12 0.33
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTCACTTA
Found at i:28158 original size:60 final size:60
Alignment explanation
Indices: 28044--28171 Score: 159
Period size: 60 Copynumber: 2.1 Consensus size: 60
28034 TTAAAGATGA
* * * * *
28044 TAAAGATGAGAAGAGTGATAAAGATGCCAATTGCTGATTCAAGGCCAATGATATTAGGCT
1 TAAAGATGAAAAAAATGATAAAGATGCCAATTGCTGATTCAAAGCCAATAATATTAGGCT
* * * *
28104 TAAAGATGAAAAAAATGATAAAGGTGCCAATATGTTGATTCAAAG-CAGTAATATTGGGCT
1 TAAAGATGAAAAAAATGATAAAGATGCCAAT-TGCTGATTCAAAGCCAATAATATTAGGCT
28164 TAAAGATG
1 TAAAGATG
28172 CGAAGAATGT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 47 0.81
61 11 0.19
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.26
Consensus pattern (60 bp):
TAAAGATGAAAAAAATGATAAAGATGCCAATTGCTGATTCAAAGCCAATAATATTAGGCT
Found at i:28243 original size:43 final size:43
Alignment explanation
Indices: 28182--28588 Score: 393
Period size: 43 Copynumber: 8.9 Consensus size: 43
28172 CGAAGAATGT
28182 CAATGTGCTGATTCAAGGCCAACGACATTAGACTTAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAACGACATTAGACTTAAAGGTGC
*
28225 CAATGTGCAGATTCAAGGCCAACGACATTAGACTTAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAACGACATTAGACTTAAAGGTGC
* * * *
28268 TAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAATATGACAAAGGCGC
1 CAATGTGCTGATTCAAGGCCAACGACATTAGAC-----T-T---AAAGGTGC
* * * *
28320 CAATATGCTGATTCAAAGCCAACGATATTGGACTTAAAGGTGCC
1 CAATGTGCTGATTCAAGGCCAACGACATTAGACTTAAAGGTG-C
28364 AATGATGTCAATGTGCTGATTCAAGGCCAACGACATTAGACTTAAAGGTGC
1 --------CAATGTGCTGATTCAAGGCCAACGACATTAGACTTAAAGGTGC
*
28415 CAATATGCTGATTCAAGGCCAACGACATTAGACTTAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAACGACATTAGACTTAAAGGTGC
* * * *
28458 CAATATGCTGATTCAAGGCCAGA-GACATTCTTAATAATGACAAAGGTGC
1 CAATGTGCTGATTCAAGGCCA-ACGACA---TT-AGACT--TAAAGGTGC
* * *
28507 CAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAACGACATTAGACTTAAAGGTGC
* * * *
28550 CAATGTGCTGATTCAAGTCCAATGACATTGGACATAAAG
1 CAATGTGCTGATTCAAGGCCAACGACATTAGACTTAAAG
28589 ATGACAAAGG
Statistics
Matches: 308, Mismatches: 30, Indels: 52
0.79 0.08 0.13
Matches are distributed among these distances:
43 186 0.60
44 2 0.01
45 2 0.01
46 5 0.02
47 4 0.01
48 2 0.01
49 33 0.11
51 1 0.00
52 73 0.24
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.24
Consensus pattern (43 bp):
CAATGTGCTGATTCAAGGCCAACGACATTAGACTTAAAGGTGC
Found at i:28342 original size:95 final size:95
Alignment explanation
Indices: 28217--28733 Score: 495
Period size: 95 Copynumber: 5.4 Consensus size: 95
28207 CATTAGACTT
* * * *
28217 AAAGGTGCCAATGTGCAGATTCAAGGCCAACGACATTAGACTTAAAGGTGCTAATGTGCTGATTC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGGTGCTAATGTGCTGATTC
28282 AAGGCCAGCGACATTGGACTTAAATATGAC
66 AAGGCCAGCGACATTGGACTTAAATATGAC
* *
28312 AAAGGCGCCAATATGCTGATTCAAAGCCAACGATATTGGACTTAAAGGTGCCAATGATGTCAATG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGGTG-C-------T-AATG
* *
28377 TGCTGATTCAAGGCCAACGACATTAGAC-----T-T---
57 TGCTGATTCAAGGCCAGCGACATTGGACTTAAATATGAC
* * * *
28407 AAAGGTGCCAATATGCTGATTCAAGGCCAACGACATTAGACTTAAAGGTGCCAATATGCTGATTC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGGTGCTAATGTGCTGATTC
*
28472 AAGGCCAGAGACATT---CTT-AATAATGAC
66 AAGGCCAGCGACATTGGACTTAAAT-ATGAC
*
28499 AAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGGTGCTAATGTGCTGATTC
* ** * *
28564 AAGTCCAATGACATTGGACATAAAGATGAC
66 AAGGCCAGCGACATTGGACTTAAATATGAC
* * * * *
28594 AAAGGTACCAATATGTTGATTCAAGGCCAGCGATATTGGACTTAAAGGT-TTCAATGTGCTAATT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGGTGCT-AATGTGCTGATT
* * *
28658 CAAGGCTAGCGACGTTGGGCTTAAAGATGCGAAGAATGAC
65 CAAGGCCAGCGACATTGGACTT-AA-AT-------ATGAC
* *
28698 AAAGGTGCCAATATGCTGATTCACGGCCAACAATAT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAACGATAT
28734 CAGGCTTGAA
Statistics
Matches: 347, Mismatches: 43, Indels: 55
0.78 0.10 0.12
Matches are distributed among these distances:
83 1 0.00
86 25 0.07
87 1 0.00
89 1 0.00
92 74 0.21
94 1 0.00
95 169 0.49
96 5 0.01
97 1 0.00
98 1 0.00
99 1 0.00
103 1 0.00
104 66 0.19
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (95 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGGTGCTAATGTGCTGATTC
AAGGCCAGCGACATTGGACTTAAATATGAC
Found at i:28350 original size:52 final size:49
Alignment explanation
Indices: 28182--28638 Score: 307
Period size: 43 Copynumber: 9.8 Consensus size: 49
28172 CGAAGAATGT
* *
28182 CAATGTGCTGATTCAAGGCCAACGACATTAGAC----TT--AAAGGTGC
1 CAATATGCTGATTCAAGGCCAACGACATTGGACTTAATTGCAAAGGTGC
* * *
28225 CAATGTGCAGATTCAAGGCCAACGACATTAGAC----TT--AAAGGTGC
1 CAATATGCTGATTCAAGGCCAACGACATTGGACTTAATTGCAAAGGTGC
* * * *
28268 TAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAATATGACAAAGGCGC
1 CAATATGCTGATTCAAGGCCAACGACATTGGACTT-AAT-TG-CAAAGGTGC
* * * * * *
28320 CAATATGCTGATTCAAAGCCAACGATATTGGACTTAAAGGTGCCAATGATGT
1 CAATATGCTGATTCAAGGCCAACGACATTGGACTT-AA-TTG-CAAAGGTGC
* *
28372 CAATGTGCTGATTCAAGGCCAACGACATTAGAC----TT--AAAGGTGC
1 CAATATGCTGATTCAAGGCCAACGACATTGGACTTAATTGCAAAGGTGC
*
28415 CAATATGCTGATTCAAGGCCAACGACATTAGAC----TT--AAAGGTGC
1 CAATATGCTGATTCAAGGCCAACGACATTGGACTTAATTGCAAAGGTGC
28458 CAATATGCTGATTCAAGGCCAGA-GACATT---CTTAATAATGACAAAGGTGC
1 CAATATGCTGATTCAAGGCCA-ACGACATTGGACTTAAT--TG-CAAAGGTGC
*
28507 CAATATGCTGATTCAAGGCCAACGATATTGGAC----TT--AAAGGTGC
1 CAATATGCTGATTCAAGGCCAACGACATTGGACTTAATTGCAAAGGTGC
* * * * * *
28550 CAATGTGCTGATTCAAGTCCAATGACATTGGACATAAAGATGACAAAGGTAC
1 CAATATGCTGATTCAAGGCCAACGACATTGGAC-TTAA-TTG-CAAAGGTGC
* * *
28602 CAATATGTTGATTCAAGGCCAGCGATATTGGACTTAA
1 CAATATGCTGATTCAAGGCCAACGACATTGGACTTAA
28639 AGGTTTCAAT
Statistics
Matches: 341, Mismatches: 40, Indels: 58
0.78 0.09 0.13
Matches are distributed among these distances:
40 1 0.00
43 182 0.53
44 2 0.01
46 3 0.01
48 3 0.01
49 36 0.11
51 3 0.01
52 111 0.33
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.24
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAACGACATTGGACTTAATTGCAAAGGTGC
Found at i:28379 original size:190 final size:188
Alignment explanation
Indices: 28117--28554 Score: 677
Period size: 190 Copynumber: 2.3 Consensus size: 188
28107 AGATGAAAAA
* * *** * * *
28117 AATGATAAAGGTGCCAATATGTTGATTCAAAG-CAGTAATATTGGGCTTAAAGATGCGAA-GAAT
1 AATGACAAAGGTGCCAATATGCTGATTCAAAGCCAACGATATTGGACTTAAAGGTGCCAATGAAT
*
28180 GTCAATGTGCTGATTCAAGGCCAACGACATTAGACTTAAAGGTGCCAATGTGCAGATTCAAGGCC
66 GTCAATGTGCTGATTCAAGGCCAACGACATTAGACTTAAAGGTGCCAATATGCAGATTCAAGGCC
* * *
28245 AACGACATTAGACTTAAAGGTGCTAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAA-
131 AACGACATTAGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGAGACATT---CTTAAT
*
28305 ATATGACAAAGGCGCCAATATGCTGATTCAAAGCCAACGATATTGGACTTAAAGGTGCCAATG-A
1 A-ATGACAAAGGTGCCAATATGCTGATTCAAAGCCAACGATATTGGACTTAAAGGTGCCAATGAA
*
28369 TGTCAATGTGCTGATTCAAGGCCAACGACATTAGACTTAAAGGTGCCAATATGCTGATTCAAGGC
65 TGTCAATGTGCTGATTCAAGGCCAACGACATTAGACTTAAAGGTGCCAATATGCAGATTCAAGGC
28434 CAACGACATTAGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGAGACATTCTTAAT
130 CAACGACATTAGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGAGACATTCTTAAT
*
28493 AATGACAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGGTGCCAATG
1 AATGACAAAGGTGCCAATATGCTGATTCAAAGCCAACGATATTGGACTTAAAGGTGCCAATG
28555 TGCTGATTCA
Statistics
Matches: 230, Mismatches: 16, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
187 64 0.28
188 2 0.01
189 28 0.12
190 135 0.59
191 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (188 bp):
AATGACAAAGGTGCCAATATGCTGATTCAAAGCCAACGATATTGGACTTAAAGGTGCCAATGAAT
GTCAATGTGCTGATTCAAGGCCAACGACATTAGACTTAAAGGTGCCAATATGCAGATTCAAGGCC
AACGACATTAGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGAGACATTCTTAAT
Found at i:28416 original size:24 final size:24
Alignment explanation
Indices: 28389--28460 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
28379 CTGATTCAAG
28389 GCCAACGACATTAGACTTAAAGGT
1 GCCAACGACATTAGACTTAAAGGT
* *** *
28413 GCCAA-TATGCT-GA-TTCAA-G-
1 GCCAACGACATTAGACTTAAAGGT
28432 GCCAACGACATTAGACTTAAAGGT
1 GCCAACGACATTAGACTTAAAGGT
28456 GCCAA
1 GCCAA
28461 TATGCTGATT
Statistics
Matches: 33, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
19 5 0.15
20 3 0.09
21 6 0.18
22 6 0.18
23 3 0.09
24 10 0.30
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (24 bp):
GCCAACGACATTAGACTTAAAGGT
Found at i:28525 original size:92 final size:93
Alignment explanation
Indices: 28407--28663 Score: 358
Period size: 92 Copynumber: 2.8 Consensus size: 93
28397 CATTAGACTT
* * *
28407 AAAGGTGCCAATATGCTGATTCAAGGCCAACGACATTAGACTTAAAGGTGCCAATATGCTGATTC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
*
28472 AAGGCCAGA-GACATT-CTTAATA-ATGAC
66 AAGGCCA-ATGACATTGCATAA-AGATGAC
28499 AAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
*
28564 AAGTCCAATGACATTGGACATAAAGATGAC
66 AAGGCCAATGACATT-G-CATAAAGATGAC
* * * ** *
28594 AAAGGTACCAATATGTTGATTCAAGGCCAGCGATATTGGACTTAAAGGTTTCAATGTGCTAATTC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
28659 AAGGC
66 AAGGC
28664 TAGCGACGTT
Statistics
Matches: 148, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
91 1 0.01
92 74 0.50
94 1 0.01
95 72 0.49
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (93 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
AAGGCCAATGACATTGCATAAAGATGAC
Found at i:28640 original size:52 final size:52
Alignment explanation
Indices: 28542--28640 Score: 126
Period size: 52 Copynumber: 1.9 Consensus size: 52
28532 TATTGGACTT
* * * *
28542 AAAGGTGCCAATGTGCTGATTCAAGTCCAATGACATTGGACATAAAGATGAC
1 AAAGGTACCAATATGCTGATTCAAGGCCAACGACATTGGACATAAAGATGAC
* * * *
28594 AAAGGTACCAATATGTTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 AAAGGTACCAATATGCTGATTCAAGGCCAACGACATTGGACATAAAG
28641 GTTTCAATGT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 39 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.24
Consensus pattern (52 bp):
AAAGGTACCAATATGCTGATTCAAGGCCAACGACATTGGACATAAAGATGAC
Found at i:29161 original size:32 final size:30
Alignment explanation
Indices: 29133--29226 Score: 109
Period size: 31 Copynumber: 3.0 Consensus size: 30
29123 CAGGCTTTTG
*
29133 AAAGGGTTACCACTGACTTGTGTGGGCTTT
1 AAAGGGTTGCCACTGACTTGTGTGGGCTTT
**
29163 AAGAAGGGTTGCCACT-AGCTTGTACGGGCTTT
1 -A-AAGGGTTGCCACTGA-CTTGTGTGGGCTTT
*
29195 AAAGGGGTTGCCACCGACTTGTGTGGGCTTT
1 AAA-GGGTTGCCACTGACTTGTGTGGGCTTT
29226 A
1 A
29227 CGAAGGATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
30 2 0.04
31 26 0.49
32 25 0.47
ACGTcount: A:0.20, C:0.18, G:0.32, T:0.30
Consensus pattern (30 bp):
AAAGGGTTGCCACTGACTTGTGTGGGCTTT
Found at i:29206 original size:31 final size:30
Alignment explanation
Indices: 29108--29226 Score: 98
Period size: 32 Copynumber: 3.8 Consensus size: 30
29098 TAGAAGAAGA
* *
29108 TGCCACCAGCTTGTGCAGGCTTTTGAAAGGGT
1 TGCCACTAGCTTGTGCGGGC-TTT-AAAGGGT
* *
29140 TACCACT-GACTTGTGTGGGCTTTAAGAAGGGT
1 TGCCACTAG-CTTGTGCGGGCTTT-A-AAGGGT
*
29172 TGCCACTAGCTTGTACGGGCTTTAAAGGGGT
1 TGCCACTAGCTTGTGCGGGCTTTAAA-GGGT
* *
29203 TGCCAC-CGACTTGTGTGGGCTTTA
1 TGCCACTAG-CTTGTGCGGGCTTTA
29227 CGAAGGATTT
Statistics
Matches: 71, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
30 3 0.04
31 29 0.41
32 38 0.54
33 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.31, T:0.30
Consensus pattern (30 bp):
TGCCACTAGCTTGTGCGGGCTTTAAAGGGT
Found at i:29223 original size:63 final size:64
Alignment explanation
Indices: 29108--29232 Score: 173
Period size: 63 Copynumber: 2.0 Consensus size: 64
29098 TAGAAGAAGA
* *
29108 TGCCACCAGCTTGTGCAGGCTTTTGAAAGGGTTACCACTGACTTGTGTGGGCTTTAAGAAGGGT
1 TGCCACCAGCTTGTACAGGCTTTTGAAAGGGTTACCACCGACTTGTGTGGGCTTTAAGAAGGGT
* * * *
29172 TGCCACTAGCTTGTACGGGC-TTT-AAAGGGGTTGCCACCGACTTGTGTGGGCTTTACGAAGG
1 TGCCACCAGCTTGTACAGGCTTTTGAAA-GGGTTACCACCGACTTGTGTGGGCTTTAAGAAGG
29233 ATTTCTCCAT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
62 3 0.06
63 34 0.63
64 17 0.31
ACGTcount: A:0.19, C:0.20, G:0.32, T:0.29
Consensus pattern (64 bp):
TGCCACCAGCTTGTACAGGCTTTTGAAAGGGTTACCACCGACTTGTGTGGGCTTTAAGAAGGGT
Found at i:29470 original size:28 final size:28
Alignment explanation
Indices: 29434--29489 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
29424 TCCGAAAGGA
*
29434 TGCCATTAACTTGTGGACTTTGAAGAGG
1 TGCCATTAACTAGTGGACTTTGAAGAGG
* * *
29462 TGCCCTTAACTAGTGGGCTTTGAGGAGG
1 TGCCATTAACTAGTGGACTTTGAAGAGG
29490 GATTCGTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.30
Consensus pattern (28 bp):
TGCCATTAACTAGTGGACTTTGAAGAGG
Found at i:29574 original size:14 final size:14
Alignment explanation
Indices: 29532--29575 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
29522 TTCTAACACG
* *
29532 TTCTCGACAAAAAG
1 TTCTTGACAAAAAT
29546 TTCTTGACAAAAAT
1 TTCTTGACAAAAAT
*
29560 TTCTTGACAACAAT
1 TTCTTGACAAAAAT
29574 TT
1 TT
29576 TGTTGACAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (14 bp):
TTCTTGACAAAAAT
Found at i:29583 original size:15 final size:15
Alignment explanation
Indices: 29532--29585 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 15
29522 TTCTAACACG
* *
29532 TTCTCGACAA-AAAG
1 TTCTTGACAACAAAT
29546 TTCTTGACAA-AAAT
1 TTCTTGACAACAAAT
*
29560 TTCTTGACAACAATT
1 TTCTTGACAACAAAT
*
29575 TTGTTGACAAC
1 TTCTTGACAAC
29586 GGCAAATTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
14 22 0.63
15 13 0.37
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (15 bp):
TTCTTGACAACAAAT
Found at i:45371 original size:52 final size:52
Alignment explanation
Indices: 45315--45677 Score: 195
Period size: 52 Copynumber: 6.8 Consensus size: 52
45305 ACGATGCTGG
* *
45315 ACTTAGAGATGATAAGGGTGCCAATGTGCTGATTCAAGGCCACCGCCATTAA
1 ACTTAAAGATGATAAGGGTGCCAATGTGCTGATTCAAGGCCACCGACATTAA
* * * * * * * *
45367 ACTTAAATATGATAAAGGTTCCAATCTGTTGATTCAAAGCCAGCGACATTAT
1 ACTTAAAGATGATAAGGGTGCCAATGTGCTGATTCAAGGCCACCGACATTAA
* ** * * * **
45419 ACTTAAAGGTGATAAGGAAGCCAATGCGCTGATTCATGGCCAACGACATTGG
1 ACTTAAAGATGATAAGGGTGCCAATGTGCTGATTCAAGGCCACCGACATTAA
* * * ** * * * * * *
45471 GCTTTGGAAAGAAGGTTTTGGCAAGTGCCAATGTGCTAATTCAAGGCTAGCGATAGTGA
1 AC-TT--AAAG-ATGATAAGG---GTGCCAATGTGCTGATTCAAGGCCACCGACATTAA
* ** * * * **
45530 ACTTAAAGATGATAAGGGTGCGCCAATATATTGATTCAAGGTCAGCAACATTGG
1 ACTTAAAGATGATAAGGGT--GCCAATGTGCTGATTCAAGGCCACCGACATTAA
* * * * * * ** * *
45584 ACTTAAATATGATAAAGGTTCTAATGAGCTGATTTAAGGCCTGCGATATTAG
1 ACTTAAAGATGATAAGGGTGCCAATGTGCTGATTCAAGGCCACCGACATTAA
* * *
45636 ACTTAAAGATGACAAGAGTGCCAATGTGCTGAGTCAAGGCCA
1 ACTTAAAGATGATAAGGGTGCCAATGTGCTGATTCAAGGCCA
45678 GGGACATTGG
Statistics
Matches: 223, Mismatches: 79, Indels: 18
0.70 0.25 0.06
Matches are distributed among these distances:
52 136 0.61
53 2 0.01
54 40 0.18
55 9 0.04
56 8 0.04
58 2 0.01
59 26 0.12
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (52 bp):
ACTTAAAGATGATAAGGGTGCCAATGTGCTGATTCAAGGCCACCGACATTAA
Found at i:46019 original size:30 final size:30
Alignment explanation
Indices: 45985--46096 Score: 129
Period size: 30 Copynumber: 3.8 Consensus size: 30
45975 GGTGCTATGT
**
45985 AGTTGTGGACCGTAAAAAGAGGTGACACAA
1 AGTTGTGGACTTTAAAAAGAGGTGACACAA
* * **
46015 AGTTGTGAACTTTAAAAA-AGGTGCCACTG
1 AGTTGTGGACTTTAAAAAGAGGTGACACAA
* **
46044 ACTCATGGACTTTAAAAAGAGGTGACACAA
1 AGTTGTGGACTTTAAAAAGAGGTGACACAA
46074 AGTTGTGGACTTTAAAAAG-GGTG
1 AGTTGTGGACTTTAAAAAGAGGTG
46097 CTACTGAGTC
Statistics
Matches: 65, Mismatches: 16, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
29 26 0.40
30 39 0.60
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.23
Consensus pattern (30 bp):
AGTTGTGGACTTTAAAAAGAGGTGACACAA
Found at i:46112 original size:29 final size:28
Alignment explanation
Indices: 46023--46115 Score: 87
Period size: 29 Copynumber: 3.2 Consensus size: 28
46013 AAAGTTGTGA
* *
46023 ACTTTAAAAAAGGTGCCACTGACTCATGG
1 ACTTTAAAAAGGGTG-CACTGAGTCATGG
** **
46052 ACTTTAAAAAGAGGTGACACAAAGTTGTGG
1 ACTTTAAAAAG-GGTG-CACTGAGTCATGG
*
46082 ACTTTAAAAAGGGTGCTACTGAGTCACGG
1 ACTTTAAAAAGGGTGC-ACTGAGTCATGG
46111 ACTTT
1 ACTTT
46116 GAGAAAGTTA
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
28 1 0.02
29 26 0.52
30 23 0.46
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (28 bp):
ACTTTAAAAAGGGTGCACTGAGTCATGG
Found at i:46113 original size:59 final size:59
Alignment explanation
Indices: 45997--46115 Score: 193
Period size: 59 Copynumber: 2.0 Consensus size: 59
45987 TTGTGGACCG
*
45997 TAAAAAGAGGTGACACAAAGTTGTGAACTTTAAAAAAGGTGCCACTGACTCATGGACTT
1 TAAAAAGAGGTGACACAAAGTTGTGAACTTTAAAAAAGGTGCCACTGACTCACGGACTT
* * * *
46056 TAAAAAGAGGTGACACAAAGTTGTGGACTTTAAAAAGGGTGCTACTGAGTCACGGACTT
1 TAAAAAGAGGTGACACAAAGTTGTGAACTTTAAAAAAGGTGCCACTGACTCACGGACTT
46115 T
1 T
46116 GAGAAAGTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24
Consensus pattern (59 bp):
TAAAAAGAGGTGACACAAAGTTGTGAACTTTAAAAAAGGTGCCACTGACTCACGGACTT
Found at i:47278 original size:14 final size:15
Alignment explanation
Indices: 47261--47292 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
47251 CATCTGGACC
47261 TTTTT-TTCTCTT-T
1 TTTTTCTTCTCTTGT
47274 TTTTTCTTCTCTTGT
1 TTTTTCTTCTCTTGT
47289 TTTT
1 TTTT
47293 GACTTTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 5 0.29
14 7 0.41
15 5 0.29
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (15 bp):
TTTTTCTTCTCTTGT
Found at i:47354 original size:24 final size:24
Alignment explanation
Indices: 47327--47375 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
47317 TTTCTGAAAA
47327 TTTTTTACTTT-TTTTATTTTGATT
1 TTTTTTACTTTCTTTTA-TTTGATT
**
47351 TTTTTTGTTTTCTTTTATTTGATT
1 TTTTTTACTTTCTTTTATTTGATT
47375 T
1 T
47376 GATTTGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.10, C:0.04, G:0.06, T:0.80
Consensus pattern (24 bp):
TTTTTTACTTTCTTTTATTTGATT
Found at i:47381 original size:24 final size:25
Alignment explanation
Indices: 47335--47391 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
47325 AATTTTTTAC
**
47335 TTTTTTTATTTTGATTTTTTTTG-T
1 TTTTTTTATTTTGATTTGATTTGAT
47359 TTTCTTTTA-TTTGATTTGATTTGAT
1 TTT-TTTTATTTTGATTTGATTTGAT
47384 TTTTTTTA
1 TTTTTTTA
47392 CATAGGATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 20 0.69
25 9 0.31
ACGTcount: A:0.12, C:0.02, G:0.09, T:0.77
Consensus pattern (25 bp):
TTTTTTTATTTTGATTTGATTTGAT
Found at i:66089 original size:73 final size:74
Alignment explanation
Indices: 65969--66184 Score: 224
Period size: 73 Copynumber: 2.9 Consensus size: 74
65959 CACGTCACGA
* * * *
65969 CAAAGAGCATGACA-CTTTTTCTTTTTATTCAAAGCCTACATAAGCTGGTGGCACCCTTTATCCT
1 CAAAGAGCAAGATACCTTCTTCTTTTT-TTCAAAGCCAACATAAGCTGGTGGCACCCTTTATCCT
*
66033 TTTCAATCCT
65 TTTCAATACT
* * * *
66043 CAAAGAGTAGGATGCC-TCTTCTTTTCTTT-AAAGCCAACATAAGCTGGTGGCA-CCTTTATCTT
1 CAAAGAGCAAGATACCTTCTTCTTTT-TTTCAAAGCCAACATAAGCTGGTGGCACCCTTTATCCT
* *
66105 TTTTAGTACT
65 TTTCAATACT
* * ** * * *
66115 CTAAGAGCAAGATACCTTTTTCTTTTTTTCAAAGCCCTCAGAAGCTGGTGGCACCATTTATACTT
1 CAAAGAGCAAGATACCTTCTTCTTTTTTTCAAAGCCAACATAAGCTGGTGGCACCCTTTATCCTT
66180 TTCAA
66 TTCAA
66185 AGAGCAGGAT
Statistics
Matches: 114, Mismatches: 23, Indels: 10
0.78 0.16 0.07
Matches are distributed among these distances:
72 31 0.27
73 50 0.44
74 31 0.27
75 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (74 bp):
CAAAGAGCAAGATACCTTCTTCTTTTTTTCAAAGCCAACATAAGCTGGTGGCACCCTTTATCCTT
TTCAATACT
Found at i:66662 original size:13 final size:13
Alignment explanation
Indices: 66644--66668 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
66634 ATATTGCTTA
66644 GTATCGATACATT
1 GTATCGATACATT
66657 GTATCGATACAT
1 GTATCGATACAT
66669 GTTTTTGGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:68360 original size:3 final size:3
Alignment explanation
Indices: 68352--68377 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
68342 AACCATCAAA
68352 GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GA
68378 AGTTGACTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:68838 original size:15 final size:16
Alignment explanation
Indices: 68802--68839 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
68792 AGAGATAAAT
68802 AAAAAATTATTGAGAA
1 AAAAAATTATTGAGAA
*
68818 AAAAAATTCTTGA-AA
1 AAAAAATTATTGAGAA
*
68833 AGAAAAT
1 AAAAAAT
68840 AGTTGAACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.63, C:0.03, G:0.11, T:0.24
Consensus pattern (16 bp):
AAAAAATTATTGAGAA
Found at i:69875 original size:19 final size:19
Alignment explanation
Indices: 69831--69886 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
69821 CTGCCAGTTT
**
69831 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
69851 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
69870 CATGTATCGATACAATG
1 CATGTATCGATACAATG
69887 TCTCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:70439 original size:22 final size:22
Alignment explanation
Indices: 70414--70455 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
70404 AGATAAACAT
70414 ATTTCTCCCCATTTATCAAAGC
1 ATTTCTCCCCATTTATCAAAGC
*
70436 ATTTCTCCCCCTTTATCAAA
1 ATTTCTCCCCATTTATCAAA
70456 TCAAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.33, G:0.02, T:0.38
Consensus pattern (22 bp):
ATTTCTCCCCATTTATCAAAGC
Found at i:72347 original size:13 final size:13
Alignment explanation
Indices: 72329--72353 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
72319 AGTAACCCAT
72329 GTATCGATACAAC
1 GTATCGATACAAC
72342 GTATCGATACAA
1 GTATCGATACAA
72354 GGAATGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (13 bp):
GTATCGATACAAC
Found at i:78540 original size:13 final size:13
Alignment explanation
Indices: 78500--78551 Score: 62
Period size: 13 Copynumber: 4.5 Consensus size: 13
78490 CTGTTATAAG
78500 CAATGTATCGATA
1 CAATGTATCGATA
78513 CAA--T-TC-AT-
1 CAATGTATCGATA
78521 C-ATGTATCGATA
1 CAATGTATCGATA
78533 CAATGTATCGATA
1 CAATGTATCGATA
78546 CAATGT
1 CAATGT
78552 CCTATGTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.09
10 4 0.12
11 3 0.09
12 1 0.03
13 20 0.61
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:78542 original size:33 final size:33
Alignment explanation
Indices: 78500--78568 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
78490 CTGTTATAAG
78500 CAATGTATCGATACAAT-TCATCATGTATCGATA
1 CAATGTATCGATACAATGTCAT-ATGTATCGATA
*
78533 CAATGTATCGATACAATGTCCTATGTATCGATA
1 CAATGTATCGATACAATGTCATATGTATCGATA
78566 CAA
1 CAA
78569 ACAGTGATAG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 31 0.91
34 3 0.09
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (33 bp):
CAATGTATCGATACAATGTCATATGTATCGATA
Found at i:78641 original size:19 final size:19
Alignment explanation
Indices: 78597--78652 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
78587 TTGCCGGTTT
**
78597 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
*
78617 CATGTATTGATACAATGAA
1 CATGTATCGATACAATGAA
78636 CATGTATCGATACAATG
1 CATGTATCGATACAATG
78653 CATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:80893 original size:33 final size:33
Alignment explanation
Indices: 80836--80899 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
80826 GCCAAGGAAA
*
80836 TGTATCGATACATTATTCAATGTATTGATACAG
1 TGTATCGATACATTATTCAATGTATCGATACAG
**
80869 TGTATCGATACATTGA-TCTTTGTATCGATAC
1 TGTATCGATACATT-ATTCAATGTATCGATAC
80900 CTCTGGGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATTATTCAATGTATCGATACAG
Found at i:84535 original size:10 final size:10
Alignment explanation
Indices: 84520--84552 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
84510 AGTAAGATGT
84520 GGACTAAATG
1 GGACTAAATG
84530 GGACTAAATGG
1 GGACTAAAT-G
84541 GGACTAAATG
1 GGACTAAATG
84551 GG
1 GG
84553 TGTTTAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.36, C:0.09, G:0.36, T:0.18
Consensus pattern (10 bp):
GGACTAAATG
Found at i:84545 original size:11 final size:11
Alignment explanation
Indices: 84520--84552 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
84510 AGTAAGATGT
84520 GGACTAAAT-G
1 GGACTAAATGG
84530 GGACTAAATGG
1 GGACTAAATGG
84541 GGACTAAATGG
1 GGACTAAATGG
84552 G
1 G
84553 TGTTTAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.36, C:0.09, G:0.36, T:0.18
Consensus pattern (11 bp):
GGACTAAATGG
Found at i:86502 original size:10 final size:10
Alignment explanation
Indices: 86471--86504 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
86461 CAATCCTTAT
86471 TTTCTTCAAA
1 TTTCTTCAAA
86481 TCTTCTTCAAA
1 T-TTCTTCAAA
*
86492 TTTCATCAAA
1 TTTCTTCAAA
86502 TTT
1 TTT
86505 AAATCATTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (10 bp):
TTTCTTCAAA
Found at i:89065 original size:13 final size:13
Alignment explanation
Indices: 89047--89071 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
89037 ATATTGCTTA
89047 GTATCGATACATT
1 GTATCGATACATT
89060 GTATCGATACAT
1 GTATCGATACAT
89072 GTTTTTGGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:90014 original size:74 final size:74
Alignment explanation
Indices: 89906--90455 Score: 470
Period size: 74 Copynumber: 7.5 Consensus size: 74
89896 TACAACATCT
* * * * * * *
89906 TTTTCTTTATCTTTAAAGCACACACAAGCAGGTGGCACCCTTTATCTTTTTCAGTCCTTAAAAAA
1 TTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCACCCTTTATCTTTTTCAGTCCTCAAAGAG
* * *
89971 TAGGACGTC
66 CAGGATGCC
* * * * * * * *
89980 TTTTCTTTTTCTTGAAAGTCCACAAAAGTTGGTGGCACCTTTTATCGTTTTCAATTCTCAAAGA-
1 TTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCACCCTTTATCTTTTTCAGTCCTCAAAGAG
**
90044 CTAGGACACC
66 C-AGGATGCC
* * * * * **
90054 --TT-TTTTTCTTTAAAGTCCATACAAGTTGGTGGTACTTTTTATCTTTTTCAGTCCTCAAAGTA
1 TTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCACCCTTTATCTTTTTCAGTCCTCAAAG-A
90116 -CAGGATGCC
65 GCAGGATGCC
* * * *
90125 TTTT-TTTTTTTTCAAAACCCACACAAGCTAGTGGCAGCCTTTATCCTTTTT-AGTCCTCAATA-
1 TTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCACCCTTTAT-CTTTTTCAGTCCTCAA-AG
* * *
90187 AGTAAGATACC
64 AGCAGGATGCC
* * * ** *
90198 TTTTATTTTTCTTTAAAACTTA-ACAAGCTGGTGGCACCCTTTATCTTTTTCACTCCTCAAAGAG
1 TTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCACCCTTTATCTTTTTCAGTCCTCAAAGAG
90262 CAGGATGCC
66 CAGGATGCC
* * * * *
90271 TTTTCTTTTTCTTCAAAGCCCACACAAGCTGATGACAACCTTTATCTTTTTAAGTCATCAAAGAG
1 TTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCACCCTTTATCTTTTTCAGTCCTCAAAGAG
*
90336 CAGTATGCC
66 CAGGATGCC
* * * * * * * *
90345 TTTTCTTTGTCTTCAGAGCCCATACAAGCTAGTGGCACCTTTTAGCTTTTTCAATCCTTAAAGAG
1 TTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCACCCTTTATCTTTTTCAGTCCTCAAAGAG
* * *
90410 CAAGACGCT
66 CAGGATGCC
* *
90419 TTTTCTTTTTCTTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCA
90456 TTTATCTAGG
Statistics
Matches: 380, Mismatches: 85, Indels: 22
0.78 0.17 0.05
Matches are distributed among these distances:
71 56 0.15
72 12 0.03
73 103 0.27
74 209 0.55
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.38
Consensus pattern (74 bp):
TTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGGCACCCTTTATCTTTTTCAGTCCTCAAAGAG
CAGGATGCC
Found at i:90094 original size:71 final size:71
Alignment explanation
Indices: 89985--90131 Score: 188
Period size: 71 Copynumber: 2.1 Consensus size: 71
89975 ACGTCTTTTC
*
89985 TTTTTCTTGAAAGTCCACAAAAGTTGGTGGCACCTTTTATCGTTTTCAATTCTCAAAG-ACTAGG
1 TTTTTCTTGAAAGTCCACAAAAGTTGGTGGCACCTTTTATCGTTTTCAATCCTCAAAGTAC-AGG
90049 ACACCTT
65 ACACCTT
* * * * * * *
90056 TTTTTCTTTAAAGTCCATACAAGTTGGTGGTACTTTTTATCTTTTTCAGTCCTCAAAGTACAGGA
1 TTTTTCTTGAAAGTCCACAAAAGTTGGTGGCACCTTTTATCGTTTTCAATCCTCAAAGTACAGGA
**
90121 TGCCTT
66 CACCTT
90127 TTTTT
1 TTTTT
90132 TTTTTCAAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
71 63 0.97
72 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.42
Consensus pattern (71 bp):
TTTTTCTTGAAAGTCCACAAAAGTTGGTGGCACCTTTTATCGTTTTCAATCCTCAAAGTACAGGA
CACCTT
Found at i:93944 original size:174 final size:175
Alignment explanation
Indices: 93610--93946 Score: 482
Period size: 174 Copynumber: 1.9 Consensus size: 175
93600 GAAGGGATAC
* * * *
93610 TCTAACCCTGTTCTAACAAAAATTCAAATTTACTTCATGGAATTTTACCTTTAGGGAAACTCTAT
1 TCTAACCCCGTTCTAACAAAAATTCAAATTTACTTCATGAAATTTCACCTTTAGGGAAACTCCAT
* **
93675 CCCTACTCCTTCTAAGGAACACTCCAACCTCGCTCTAACAAAAATTCAAATATTTTTTTGTGGAA
66 CCCTACTCCTTCTAAGGAACACTCCAACCTCGCTCTAACAAAAATTCAAATATTTCTTTGTAAAA
* * ** *
93740 TTTTGTATTTTGGGAAACTCCATTCTCACTATTTTGAGGGGACAT
131 TTATATATTCGGGGAAACTCCATCCTCACTATTTTGAGGGGACAT
*
93785 TCTAACCCCGTTCTAACAAAAATTCAAATTTACTTCATGAAATTTCACCTTTGGGGAAACTCCAT
1 TCTAACCCCGTTCTAACAAAAATTCAAATTTACTTCATGAAATTTCACCTTTAGGGAAACTCCAT
* * *
93850 CCC-ACTCCTT-TGAGGGGACACTCTAACC-CTGCTCTAACAAAAATTCAAATATTTCTTTGTAA
66 CCCTACTCCTTCT-AAGGAACACTCCAACCTC-GCTCTAACAAAAATTCAAATATTTCTTTGTAA
*
93912 AATTATATCTTCGGGGAAACTCCATCCTCACTATT
129 AATTATATATTCGGGGAAACTCCATCCTCACTATT
93947 CCAAGGGGAT
Statistics
Matches: 143, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
173 2 0.01
174 78 0.55
175 63 0.44
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.34
Consensus pattern (175 bp):
TCTAACCCCGTTCTAACAAAAATTCAAATTTACTTCATGAAATTTCACCTTTAGGGAAACTCCAT
CCCTACTCCTTCTAAGGAACACTCCAACCTCGCTCTAACAAAAATTCAAATATTTCTTTGTAAAA
TTATATATTCGGGGAAACTCCATCCTCACTATTTTGAGGGGACAT
Found at i:96667 original size:155 final size:155
Alignment explanation
Indices: 96277--96707 Score: 470
Period size: 154 Copynumber: 2.8 Consensus size: 155
96267 TAAGTTCAAG
* * * * * *
96277 AAAAATTATGAAAATACTCTTAGGGGATACCTTCGACATGAAAGTACATGATACCCTTAAAGGAC
1 AAAAATTACGAAAATGCTCCTAGGGGATACCTTTGACATAAAAGTACATGGTACCCTTAAAGGAC
* * * * * ** *
96342 TTAAAAAAGATTATAAAATGGATGAACCTATCCTAAATACCCACTTTTGGCATGAAAGTGGACTC
66 TTAAAAAAGATTTTAAAAGGGATGAACCTATCCTAAATACCTACTTTCGGCATAAAAGCAGACCC
** *
96407 GGTGACAACCTAGGACTTGATTCTA
131 AATGACAACCTAGGACTAGATTCTA
* * ** * *
96432 AAAAATTAC-AAAATGC-CTCTAGGGGATGCTTTTGACATAAAAGTACCCGGTACCCCTAAAGGG
1 AAAAATTACGAAAATGCTC-CTAGGGGATACCTTTGACATAAAAGTACATGGTACCCTTAAAGGA
* * * * *
96495 CCTAAAAAGGATTTTAAAAGGGATGAACCTATCCTAAATATCTACCTTCGACATAAAAGCAGACC
65 CTTAAAAAAGATTTTAAAAGGGATGAACCTATCCTAAATACCTACTTTCGGCATAAAAGCAGACC
* * * *
96560 CAATGACAACTTAGGACTAGGTTTTG
130 CAATGACAACCTAGGACTAGATTCTA
** * * * * **
96586 GGAAATTACGAAAATGCTCCTAAGAGATATCTTTGACATAAAAGTACTTGGTACCCTTAAAAAAC
1 AAAAATTACGAAAATGCTCCTAGGGGATACCTTTGACATAAAAGTACATGGTACCCTTAAAGGAC
*
96651 TTAAAAAAGATTTTAAAAGGGATGAACCTATCCTAAATACCTTCTTTCGGCATAAAA
66 TTAAAAAAGATTTTAAAAGGGATGAACCTATCCTAAATACCTACTTTCGGCATAAAA
96708 ACGGACCTAG
Statistics
Matches: 222, Mismatches: 51, Indels: 6
0.80 0.18 0.02
Matches are distributed among these distances:
153 1 0.00
154 119 0.54
155 101 0.45
156 1 0.00
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (155 bp):
AAAAATTACGAAAATGCTCCTAGGGGATACCTTTGACATAAAAGTACATGGTACCCTTAAAGGAC
TTAAAAAAGATTTTAAAAGGGATGAACCTATCCTAAATACCTACTTTCGGCATAAAAGCAGACCC
AATGACAACCTAGGACTAGATTCTA
Found at i:98233 original size:20 final size:19
Alignment explanation
Indices: 98196--98239 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
98186 TTCCATTTCC
**
98196 TTTTATTATTTTTTATGCCA
1 TTTTATTATTTTCCATG-CA
*
98216 TTTTTTTATTTTCCATGCA
1 TTTTATTATTTTCCATGCA
98235 TTTTA
1 TTTTA
98240 ATTTGATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.18, C:0.11, G:0.05, T:0.66
Consensus pattern (19 bp):
TTTTATTATTTTCCATGCA
Found at i:98915 original size:166 final size:165
Alignment explanation
Indices: 98644--99046 Score: 445
Period size: 166 Copynumber: 2.4 Consensus size: 165
98634 GTTCAATGAT
* * *
98644 AATATTAGATG-AATTCTAAAAATTTTAAATCAA-AGAAAATTCTCCTGAAAAATTTATGGAGTA
1 AATATTAGATGAAATT-TAAAAATTTTAAACCAAGA-AAAATCCCCCTGAAAAATTTATGGAGTA
** * * **
98707 GAAAACTCAATTTTTTGGGAAAATAAGCATTTCAAAGAAAAAATAAAAAACTTGCGAAAATAAAT
64 GAAAACTCAATTTTTTCAGAAAATAAGAATTGCAAAGAAAAAATAAAAAACTCACGAAAATAAAT
* **
98772 AAATTTTTCAAAACTGATTTAATGAAAATTTAATAAC
129 AAATTTTTCAAAAATGATTTAATGAAAATCAAATAAC
*
98809 AATATTAGATGAAATTTAAAAATTTTAAACCAAGAAAAATCCCCCCGAAAATATTTATGGAGTAG
1 AATATTAGATGAAATTTAAAAATTTTAAACCAAGAAAAATCCCCCTGAAAA-ATTTATGGAGTAG
* * *
98874 AAAACTCTA-TTTTTCAG-AAATAGAGGAATTGCAAAGAAAAAATTAAAAACTCATGAAAATAAA
65 AAAACTCAATTTTTTCAGAAAATA-A-GAATTGCAAAGAAAAAATAAAAAACTCACGAAAATAAA
* *** * *
98937 TTAATTTTTCAAAAATGATTTAATTTGAATCAAATGAT
128 TAAATTTTTCAAAAATGATTTAATGAAAATCAAATAAC
* * * ** * * * *
98975 AATATTTGATGAATTTTAAAAGTTAAAAACCAAGAAAAATCTCCCTGAAAACATTTACGGTGTAA
1 AATATTAGATGAAATTTAAAAATTTTAAACCAAGAAAAATCCCCCTGAAAA-ATTTATGGAGTAG
99040 AAAACTC
65 AAAACTC
99047 CGTATTTCCA
Statistics
Matches: 200, Mismatches: 33, Indels: 9
0.83 0.14 0.04
Matches are distributed among these distances:
164 5 0.03
165 47 0.23
166 148 0.74
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (165 bp):
AATATTAGATGAAATTTAAAAATTTTAAACCAAGAAAAATCCCCCTGAAAAATTTATGGAGTAGA
AAACTCAATTTTTTCAGAAAATAAGAATTGCAAAGAAAAAATAAAAAACTCACGAAAATAAATAA
ATTTTTCAAAAATGATTTAATGAAAATCAAATAAC
Found at i:99208 original size:155 final size:154
Alignment explanation
Indices: 98910--99201 Score: 356
Period size: 155 Copynumber: 1.9 Consensus size: 154
98900 AATTGCAAAG
* ** *
98910 AAAAAATTAAAAACTCATGAAAATAAATTAATTTTTCAAAAATGATTTAATTTGAATCAAATGAT
1 AAAAAATCAAAAACTCATGAAAATAAATTAATTTTTCAAAAATGATTTAACATGAATCAAATAAT
* * ** *
98975 AATATTTGATGAATTTTAAAAGTTAAAAACCAAGAAAAATCTCCCTGAAAACATTTACGGTGTAA
66 AATATTTGATAAATTTTAAAAATTAAAAACCAAGAAAAATCTCCCCAAAAACATTTACGGAGTAA
99040 AAAACTCCGTATTTCCAAAATAGA
131 AAAACTCCGTATTTCCAAAATAGA
* * * * * *
99064 AAAAAATCAAAAACTCATGAAGATGAGTTCAA-TTTTGAAAATTGATTTAACATGAAATTAAATA
1 AAAAAATCAAAAACTCATGAAAATAAATT-AATTTTTCAAAAATGATTTAACATG-AATCAAATA
** *
99128 ATAATATTTGATAAATTTTAAAAATTAAAAAGTAA-AAGAAATC-CCCACAAAAATATTTACGGA
64 ATAATATTTGATAAATTTTAAAAATTAAAAACCAAGAA-AAATCTCCC-CAAAAACATTTACGGA
*
99191 GTAGAAAACTC
127 GTAAAAAACTC
99202 TTTATTTAGT
Statistics
Matches: 115, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
154 48 0.42
155 67 0.58
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (154 bp):
AAAAAATCAAAAACTCATGAAAATAAATTAATTTTTCAAAAATGATTTAACATGAATCAAATAAT
AATATTTGATAAATTTTAAAAATTAAAAACCAAGAAAAATCTCCCCAAAAACATTTACGGAGTAA
AAAACTCCGTATTTCCAAAATAGA
Found at i:101179 original size:87 final size:87
Alignment explanation
Indices: 100988--101409 Score: 383
Period size: 87 Copynumber: 4.9 Consensus size: 87
100978 AACATCAAAA
* * * **
100988 AATTTTAT-TTTGGGGAAACTCCATCCCCA-TTATTCTGAGGGGATGCTCCAA-CCCATTCTAAC
1 AATTTTATCTTTAGGGAAACTCCATCCCCACTT-TTCTGAAGGGATACTCCAACCCCGCTCTAAC
* *
101050 AAAAATTTAAAT-TTGCTTTGTAG
65 AAAAATTCAAATCTT-CTTTGTGG
* * * * *
101073 AATTTTACCTTTAGGGAAACTACATCCCCACTTTTCTGAAGGGATACTACAACCCCACCCTAACA
1 AATTTTATCTTTAGGGAAACTCCATCCCCACTTTTCTGAAGGGATACTCCAACCCCGCTCTAACA
* *
101138 AAAATTCAAATCTTCATCGTGG
66 AAAATTCAAATCTTCTTTGTGG
* * * * * * * * *
101160 AATTTTATCTTTAGAGAAACCCCGTCCCTACTATTCT-AAGGGGATATTCCAACCTCGTTCTAGC
1 AATTTTATCTTTAGGGAAACTCCATCCCCACTTTTCTGAA-GGGATACTCCAACCCCGCTCTAAC
* *
101224 AAAAATTCAAATTTTCTTTGTGC
65 AAAAATTCAAATCTTCTTTGTGG
* * * * ** * ** **
101247 AATTTTACCTTTAAGGAAACTCTATCCTCACTCCTC-CAAGGAGGCACTCCAACCTTGCTCTAA-
1 AATTTTATCTTTAGGGAAACTCCATCCCCACTTTTCTGAAGG-GATACTCCAACCCCGCTCTAAC
101310 AAAAATTCAAATCTTCTTTTGTGG
65 AAAAATTCAAATCTTC-TTTGTGG
* * *
101334 AATTTTATCTTTGGGGAAACTCCATCCCTACTGTTT-TGAAGGGGTACTCCAACCCCGCTCTAAC
1 AATTTTATCTTTAGGGAAACTCCATCCCCACT-TTTCTGAAGGGATACTCCAACCCCGCTCTAAC
101398 AAAAATTCAAAT
65 AAAAATTCAAAT
101410 TTTCCTTCAT
Statistics
Matches: 266, Mismatches: 60, Indels: 19
0.77 0.17 0.06
Matches are distributed among these distances:
85 7 0.03
86 54 0.20
87 186 0.70
88 19 0.07
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.32
Consensus pattern (87 bp):
AATTTTATCTTTAGGGAAACTCCATCCCCACTTTTCTGAAGGGATACTCCAACCCCGCTCTAACA
AAAATTCAAATCTTCTTTGTGG
Found at i:101336 original size:174 final size:173
Alignment explanation
Indices: 100988--101413 Score: 450
Period size: 174 Copynumber: 2.5 Consensus size: 173
100978 AACATCAAAA
* * * * * * * *
100988 AATTTTAT-TTTGGGGAAACTCCATCCCCATTATTCTGAGGGGATGCTCCAACCCATTCTAACAA
1 AATTTTATCTTTAGAGAAACCCCATCCCTACTATTCTAAGGGGATACTCCAACCCGTTCTAACAA
* * * ** *
101052 AAATTTAAATTTGCTTTGTAGAATTTTACCTTTAGGGAAACTACATCCCCACTTTTCTGAAGGGA
66 AAATTCAAATTTTCTTTGTAGAATTTTACCTTTAAGGAAACTACATCCCCACTCCTCTCAAGGGA
*
101117 TACTACAACCCCACCCTAACAAAAATTCAAATCTTCATCGTGG
131 CACTACAACCCCACCCTAACAAAAATTCAAATCTTCATCGTGG
* * *
101160 AATTTTATCTTTAGAGAAACCCCGTCCCTACTATTCTAAGGGGATATTCCAACCTCGTTCTAGCA
1 AATTTTATCTTTAGAGAAACCCCATCCCTACTATTCTAAGGGGATACTCCAACC-CGTTCTAACA
*
101225 AAAATTCAAATTTTCTTTGT-GCAATTTTACCTTTAAGGAAACT-CTATCCTCACTCCTC-CAAG
65 AAAATTCAAATTTTCTTTGTAG-AATTTTACCTTTAAGGAAACTAC-ATCCCCACTCCTCTCAAG
* * *** * * *
101287 GAGGCACTCCAACCTTGCTCTAA-AAAAATTCAAATCTTCTTTTGTGG
128 G-GACACTACAACCCCACCCTAACAAAAATTCAAATCTTC-ATCGTGG
* * * * * *
101334 AATTTTATCTTTGGGGAAACTCCATCCCTACTGTTTTGAAGGGG-TACTCCAACCCCGCTCTAAC
1 AATTTTATCTTTAGAGAAACCCCATCCCTACTATTCT-AAGGGGATACTCCAA-CCCGTTCTAAC
101398 AAAAATTCAAATTTTC
64 AAAAATTCAAATTTTC
101414 CTTCATATAA
Statistics
Matches: 210, Mismatches: 36, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
172 8 0.04
173 58 0.28
174 136 0.65
175 8 0.04
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (173 bp):
AATTTTATCTTTAGAGAAACCCCATCCCTACTATTCTAAGGGGATACTCCAACCCGTTCTAACAA
AAATTCAAATTTTCTTTGTAGAATTTTACCTTTAAGGAAACTACATCCCCACTCCTCTCAAGGGA
CACTACAACCCCACCCTAACAAAAATTCAAATCTTCATCGTGG
Found at i:101438 original size:87 final size:87
Alignment explanation
Indices: 101000--101534 Score: 319
Period size: 87 Copynumber: 6.1 Consensus size: 87
100990 TTTTATTTTG
* * ** *
101000 GGGAAACTCCATCCCCA-TTATTCTG-AGGGGATGCTCCAA-CCCATTCTAACAAAAATTTAAA-
1 GGGAAACTCCATCCCTACTT-TT-TGAAGGGG-TACTCCAACCCCGCTCTAACAAAAATTCAAAT
* *
101061 TTTGCTTTGTAGAATTTTA-CCTTTA
63 TTTCCTTCGTAGAATTTTATCC-TTA
* * * * * * *
101086 GGGAAACTACATCCCCACTTTTCTGAAGGGATACTACAACCCCACCCTAACAAAAATTCAAATCT
1 GGGAAACTCCATCCCTACTTTT-TGAAGGGGTACTCCAACCCCGCTCTAACAAAAATTCAAATTT
* * *
101151 T-CATCGTGGAATTTTATCTTTA
65 TCCTTCGTAGAATTTTATCCTTA
* * * * * * * *
101173 GAGAAACCCCGTCCCTACTATTCT-AAGGGGATATTCCAACCTCGTTCTAGCAAAAATTCAAATT
1 GGGAAACTCCATCCCTACT-TTTTGAAGGGG-TACTCCAACCCCGCTCTAACAAAAATTCAAATT
*
101237 TT-CTTTGT-GCAATTTTA-CCTTTA
64 TTCCTTCGTAG-AATTTTATCC-TTA
* * ** ** * ** *
101260 AGGAAACTCTAT-CCTCACTCCTCCAAGGAGGCACTCCAACCTTGCTCTAA-AAAAATTCAAATC
1 GGGAAACTCCATCCCT-ACTTTTTGAAGG-GGTACTCCAACCCCGCTCTAACAAAAATTCAAATT
* * * * *
101323 TTCTTTTGTGGAATTTTATCTTTG
64 TTCCTTCGTAGAATTTTATCCTTA
101347 GGGAAACTCCATCCCTACTGTTTTGAAGGGGTACTCCAACCCCGCTCTAACAAAAATTCAAATTT
1 GGGAAACTCCATCCCTACT-TTTTGAAGGGGTACTCCAACCCCGCTCTAACAAAAATTCAAATTT
* *
101412 TCCTTCATATAATTTTATCCTT-
65 TCCTTCGTAGAATTTTATCCTTA
** * ** * ** *
101434 GGGAAAACTTTATCCCTACTCCTTTGAAGGAATACTCCAACCTCGCT-TTTCAAAAAATTAAATA
1 GGG-AAACTCCATCCCTACT-TTTTGAAGGGGTACTCCAACCCCGCTCTAAC-AAAAATTCAA-A
* *
101498 TTTTCTTTC--ATAATTTTATCCTTA
62 TTTTCCTTCGTAGAATTTTATCCTTA
*
101522 AGGAAACTCCATC
1 GGGAAACTCCATC
101535 TTCACTATTT
Statistics
Matches: 349, Mismatches: 78, Indels: 43
0.74 0.17 0.09
Matches are distributed among these distances:
86 51 0.15
87 196 0.56
88 93 0.27
89 9 0.03
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.33
Consensus pattern (87 bp):
GGGAAACTCCATCCCTACTTTTTGAAGGGGTACTCCAACCCCGCTCTAACAAAAATTCAAATTTT
CCTTCGTAGAATTTTATCCTTA
Found at i:103816 original size:38 final size:39
Alignment explanation
Indices: 103756--103831 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 39
103746 TAGATTCTAT
* *
103756 TTTTCACAAATTAAGCAGTTGATCTCTAGTTTAAATTTC
1 TTTTCACAAATTAAACACTTGATCTCTAGTTTAAATTTC
*
103795 TTTT-ACAAATTAAACACTTGATCTCTAGTTTAGATTT
1 TTTTCACAAATTAAACACTTGATCTCTAGTTTAAATTT
103832 ACATTGTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 30 0.88
39 4 0.12
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (39 bp):
TTTTCACAAATTAAACACTTGATCTCTAGTTTAAATTTC
Found at i:105380 original size:21 final size:21
Alignment explanation
Indices: 105343--105402 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
105333 AAAGATGCAG
*
105343 TTGGATGGAGTGATGC-ATTT
1 TTGGATGGAATGATGCAATTT
*
105363 ATTGGATGGAATGGTGCAATTT
1 -TTGGATGGAATGATGCAATTT
*
105385 TTAGATGGAAAT-ATGCAA
1 TTGGATGG-AATGATGCAA
105403 CTTGTATATC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 26 0.79
22 7 0.21
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (21 bp):
TTGGATGGAATGATGCAATTT
Found at i:108119 original size:13 final size:13
Alignment explanation
Indices: 108101--108127 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
108091 TACAGTGAAC
108101 ATGTATCGATACA
1 ATGTATCGATACA
108114 ATGTATCGATACA
1 ATGTATCGATACA
108127 A
1 A
108128 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:110505 original size:22 final size:21
Alignment explanation
Indices: 110470--110519 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
110460 TTTGTTGATG
*
110470 ATTTTG-A-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAAT-AAGA
110490 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
110511 AATTTGAAG
1 ATTTTGAAG
110520 AAAATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:110516 original size:21 final size:22
Alignment explanation
Indices: 110477--110519 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
110467 ATGATTTTGA
* *
110477 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
110499 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
110520 AAAATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:115099 original size:3 final size:3
Alignment explanation
Indices: 115091--115124 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
115081 TCCGAGTCAC
*
115091 CAT CAT CAT CAT CAT CAT CAT CAT CAT CTT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
115125 GTCTTTGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:122139 original size:272 final size:272
Alignment explanation
Indices: 121653--122198 Score: 1076
Period size: 272 Copynumber: 2.0 Consensus size: 272
121643 GGAAGTGAGC
121653 TATCTGCCTTCGTGAGTAACCCTCCGCACAGGCATAGCAATAACTTCCAGGATGTAAATTACCTA
1 TATCTGCCTTCGTGAGTAACCCTCCGCACAGGCATAGCAATAACTTCCAGGATGTAAATTACCTA
121718 TGTCTCTCATGAGTAACCCTCCGTATTTGCATAGGGAAATACATCCACCGAATCGAACCCGATTC
66 TGTCTCTCATGAGTAACCCTCCGTATTTGCATAGGGAAATACATCCACCGAATCGAACCCGATTC
121783 GCCAAACCCGCGATGGGCCTAGATTCGGGGTGCCTCGGTTGCTCTTACCGAGCAGAGGAACGATT
131 GCCAAACCCGCGATGGGCCTAGATTCGGGGTGCCTCGGTTGCTCTTACCGAGCAGAGGAACGATT
121848 CGGATACCTATGTAGGTGTCATCTTAACCCTCATATAGTGAACCTTACGAGCTAAACCTGGTCAA
196 CGGATACCTATGTAGGTGTCATCTTAACCCTCATATAGTGAACCTTACGAGCTAAACCTGGTCAA
121913 GCCATACCGAAA
261 GCCATACCGAAA
121925 TATCTGCCTTCGTGAGTAACCCTCCGCACAGGCATAGCAATAACTTCCAGGATGTAAATTACCTA
1 TATCTGCCTTCGTGAGTAACCCTCCGCACAGGCATAGCAATAACTTCCAGGATGTAAATTACCTA
121990 TGTCTCTCATGAGTAACCCTCCGTATTTGCATAGGGAAATACATCCACCGAATCGAACCCGATTC
66 TGTCTCTCATGAGTAACCCTCCGTATTTGCATAGGGAAATACATCCACCGAATCGAACCCGATTC
122055 GCCAAACCCGCGATGGGCCTAGATTCGGGGTGCCTCGGTTGCTCTTACCGAGCAGAGGAACGATT
131 GCCAAACCCGCGATGGGCCTAGATTCGGGGTGCCTCGGTTGCTCTTACCGAGCAGAGGAACGATT
122120 CAGG-TACCTATGTAGGTGTCATCTTAACCCTCATATAGTGAACCTTACGAGCTAAACCTGGTCA
196 C-GGATACCTATGTAGGTGTCATCTTAACCCTCATATAGTGAACCTTACGAGCTAAACCTGGTCA
122184 AGCCATACCGAAA
260 AGCCATACCGAAA
122197 TA
1 TA
122199 CTACTAGAAT
Statistics
Matches: 273, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
272 271 0.99
273 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (272 bp):
TATCTGCCTTCGTGAGTAACCCTCCGCACAGGCATAGCAATAACTTCCAGGATGTAAATTACCTA
TGTCTCTCATGAGTAACCCTCCGTATTTGCATAGGGAAATACATCCACCGAATCGAACCCGATTC
GCCAAACCCGCGATGGGCCTAGATTCGGGGTGCCTCGGTTGCTCTTACCGAGCAGAGGAACGATT
CGGATACCTATGTAGGTGTCATCTTAACCCTCATATAGTGAACCTTACGAGCTAAACCTGGTCAA
GCCATACCGAAA
Found at i:133230 original size:20 final size:20
Alignment explanation
Indices: 133188--133241 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
133178 TTTTACCTAG
***
133188 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATAGATCA
*
133208 ATGTATCGATACATAGATGA
1 ATGTATCGATACATAGATCA
*
133228 ATGTATTGATACAT
1 ATGTATCGATACAT
133242 TCTACCCAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATAGATCA
Found at i:133477 original size:32 final size:32
Alignment explanation
Indices: 133401--134324 Score: 807
Period size: 32 Copynumber: 28.8 Consensus size: 32
133391 TCTCTTTCCA
* ** **
133401 AAGTCCACGACTTTGTGGCACCTTGTTCCCTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTCTTTTT
*
133434 AAGTCCACGACTCCGTGGCACCTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTTT
* * *
133466 ATGTCCACGACTCCTTGGCACCTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTTT
* * * *
133498 AAGTCCACGACTTCATGGCACCCTTTTCCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCTTTT-CTTTTT
* *
133532 AAGCCCACAACTCCGTGGCACCTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTTT
133564 AAGTCCACAACTCCGTGGCACCTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTTT
* *
133596 AAGTCCACGACTCCGTGGCACCCTTTTCCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCTTTT-CTTTTT
** **
133630 AAGTCCATGACTTTGTGGCACCTTGTTCTTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTCTTTTT
*
133663 AAGTCCACAACTCCGTGGCACCTTTTCTTTAT
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTTT
* * *
133695 AAGTCCACGATTCCGTAGCACCTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTTT
** **
133727 AAGTCCATGACTTTGTGGCACCTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTTT
*
133759 AAGTCCACGACTCCGTGGCACCTTATTCCTTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TT-CTTTTT
* * * *
133793 AAGCCCACACCTCCGTGGCATCTGTTT-TTCCTGT
1 AAGTCCACAACTCCGTGGCACCT-TTTCTT--TTT
* * * *
133827 AAGTACATAACTCCGTGGCACC----CCTGTT
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTTT
*
133855 -AGTCCACAACTCCGTGGCACCTTGTTCCTTTTA
1 AAGTCCACAACTCCGTGGCACCTT-TT-CTTTTT
* * *
133888 AAGCCCACAACTCCATGGCACTCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCAC-C-TTTTCTTTTT
*
133922 AAGTCCACAACTCCATGGCACC----C-TTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTTT
* * *
133949 AAGTCCACAACTCTGTGGCATCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCTTTTCTTTTT
*
133982 AAGTCCACAACTCTGTGGCACCTTGTTCTTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTCTTTTT
134015 AAGTCCACAACTCCGTGGCACCTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTTT
* *
134047 AAGTCCACAACT-AGTTG-ACAC----CTTTTT
1 AAGTCCACAACTCCGTGGCAC-CTTTTCTTTTT
* * *
134074 AAGTCCACAACTCCATGGCATCTTTTTCATTTT
1 AAGTCCACAACTCCGTGGCA-CCTTTTCTTTTT
* *
134107 AAGTCCATAACTCTGTGGCACC----C-TTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTTT
* * *
134134 AAGTCCACAACTTCGTGGCATCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCTTTTCTTTTT
* * *
134167 AAGTCTACAACTCTGTGGCACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTCTTTTT
* *
134200 AAGTCTACAACTCCGTGGCACCTTTTATTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTTT
* * * *
134232 AAGTCCACGACTCCATAGCACCCTTTTCCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCTTTT-CTTTTT
* * * *
134266 AAG-CCTACACCTCCATGGCATCCCTTTT-TCCTGT
1 AAGTCC-ACAACTCCGTGGCA--CCTTTTCT-TTTT
134300 AAGTCCACAACTCCGTGGCACCTTT
1 AAGTCCACAACTCCGTGGCACCTTT
134325 AAGTCCAATA
Statistics
Matches: 739, Mismatches: 104, Indels: 97
0.79 0.11 0.10
Matches are distributed among these distances:
27 80 0.11
28 7 0.01
29 1 0.00
30 4 0.01
31 4 0.01
32 249 0.34
33 211 0.29
34 168 0.23
35 13 0.02
36 2 0.00
ACGTcount: A:0.19, C:0.31, G:0.14, T:0.36
Consensus pattern (32 bp):
AAGTCCACAACTCCGTGGCACCTTTTCTTTTT
Found at i:133557 original size:98 final size:97
Alignment explanation
Indices: 133401--134324 Score: 872
Period size: 98 Copynumber: 9.6 Consensus size: 97
133391 TCTCTTTCCA
* ** * * *
133401 AAGTCCACGACTTTGTGGCACCTTGTTCCCTTTAAGTCCACGACTCCGTGGCACCTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTCTTTTT
* * *
133466 ATGTCCACGACTCCTTGGCACCTTTTCTTTTT
66 AAGTCCACAACTCCGTGGCACCTTTTCTTTTT
* * * * * *
133498 AAGTCCACGACTTCATGGCACCCTTTTCCCTTTTAAGCCCACAACTCCGTGGCACCTTTTCCTTT
1 AAGTCCACAACTCCGTGGCA-CCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTCTTTT
133563 TAAGTCCACAACTCCGTGGCACCTTTTCTTTTT
65 TAAGTCCACAACTCCGTGGCACCTTTTCTTTTT
* * ** **
133596 AAGTCCACGACTCCGTGGCACCCTTTTCCCTTTTAAGTCCATGACTTTGTGGCACCTTGTTCTTT
1 AAGTCCACAACTCCGTGGCA-CCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTT-TTCTTT
*
133661 TTAAGTCCACAACTCCGTGGCACCTTTTCTTTAT
64 TTAAGTCCACAACTCCGTGGCACCTTTTCTTTTT
* * * * ** **
133695 AAGTCCACGATTCCGTAGCACC-TTTTCTTTTTAAGTCCATGACTTTGTGGCACCTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTCTTTTT
*
133759 AAGTCCACGACTCCGTGGCACCTTATTCCTTTTT
66 AAGTCCACAACTCCGTGGCACCTT-TT-CTTTTT
* * * * * * * *
133793 AAGCCCACACCTCCGTGGCATCTGTTTTTCC-TGTAAGTACATAACTCCGTGGCACC----CCTG
1 AAGTCCACAACTCCGTGGCA-C-CTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTCTTT
*
133853 TT-AGTCCACAACTCCGTGGCACCTTGTTCCTTTTA
64 TTAAGTCCACAACTCCGTGGCACCTT-TT-CTTTTT
* * *
133888 AAGCCCACAACTCCATGGCACTCTTTTTCCTTTTAAGTCCACAACTCCATGGCACC----C-TTT
1 AAGTCCACAACTCCGTGGCAC-CTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTCTTTT
* * *
133948 TAAGTCCACAACTCTGTGGCATCTTTTTCCTTTT
65 TAAGTCCACAACTCCGTGGCA-CCTTTTCTTTTT
* * *
133982 AAGTCCACAACTCTGTGGCACCTTGTTCTTTTTAAGTCCACAACTCCGTGGCACCTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTCTTTTT
* *
134047 AAGTCCACAACT-AGTTG-ACAC----CTTTTT
66 AAGTCCACAACTCCGTGGCAC-CTTTTCTTTTT
* * * * *
134074 AAGTCCACAACTCCATGGCATCTTTTTCATTTTAAGTCCATAACTCTGTGGCACC----C-TTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTCTTTTT
* * *
134134 AAGTCCACAACTTCGTGGCATCTTTTTCCTTTT
66 AAGTCCACAACTCCGTGGCA-CCTTTTCTTTTT
* * * * *
134167 AAGTCTACAACTCTGTGGCACCTTGTTCCTTTTAAGTCTACAACTCCGTGGCACCTTTTATTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTCTTTTT
* * * *
134232 AAGTCCACGACTCCATAGCACCCTTTTCCCTTTT
66 AAGTCCACAACTCCGTGGCA-CCTTTT-CTTTTT
* * *
134266 AAG-CCTACACCTCCATGGCATCCCTTTTTCC-TGTAAGTCCACAACTCCGTGGCACCTTT
1 AAGTCC-ACAACTCCGTGGCA--CCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTT
134325 AAGTCCAATA
Statistics
Matches: 696, Mismatches: 99, Indels: 61
0.81 0.12 0.07
Matches are distributed among these distances:
87 16 0.02
88 4 0.01
89 1 0.00
90 1 0.00
92 53 0.08
93 82 0.12
94 34 0.05
95 91 0.13
96 39 0.06
97 56 0.08
98 183 0.26
99 77 0.11
100 46 0.07
101 13 0.02
ACGTcount: A:0.19, C:0.31, G:0.14, T:0.36
Consensus pattern (97 bp):
AAGTCCACAACTCCGTGGCACCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTCTTTTT
AAGTCCACAACTCCGTGGCACCTTTTCTTTTT
Found at i:133982 original size:60 final size:60
Alignment explanation
Indices: 133881--134258 Score: 395
Period size: 60 Copynumber: 6.1 Consensus size: 60
133871 GCACCTTGTT
* * **
133881 CCTTTTAAAGCCCACAACTCCATGGCACTCTTTTTCCTTTTAAGTCCACAACTCCATGGCAC
1 CCTTTT-AAGTCCACAACTCCGTGGCA-TCTTTTTCCTTTTAAGTCCACAACTCTGTGGCAC
*
133943 CCTTTTAAGTCCACAACTCTGTGGCATCTTTTTCCTTTTAAGTCCACAACTCTGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTTCCTTTTAAGTCCACAACTCTGTGGCAC
* * * *
134003 CTTGTTCTTTTTAAGTCCACAACTCCGTGGCA-CCTTTTCTTTTTAAGTCCACAACT-AGTTGAC
1 C-----C-TTTTAAGTCCACAACTCCGTGGCATCTTTTTCCTTTTAAGTCCACAACTCTG-TGGC
134066 AC
59 AC
* * * *
134068 CTTTTTAAGTCCACAACTCCATGGCATCTTTTTCATTTTAAGTCCATAACTCTGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTTCCTTTTAAGTCCACAACTCTGTGGCAC
* *
134128 CCTTTTAAGTCCACAACTTCGTGGCATCTTTTTCCTTTTAAGTCTACAACTCTGTGGCACC
1 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTTCCTTTTAAGTCCACAACTCTGTGGCA-C
* * * ** *
134189 TTGTTCCTTTTAAGTCTACAACTCCGTGGCACCTTTTAT--TTTTAAGTCCACGACTCCATAGCA
1 -----CCTTTTAAGTCCACAACTCCGTGGCATCTTTT-TCCTTTTAAGTCCACAACTCTGTGGCA
134252 C
60 C
134253 CCTTTT
1 CCTTTT
134259 CCCTTTTAAG
Statistics
Matches: 269, Mismatches: 31, Indels: 35
0.80 0.09 0.10
Matches are distributed among these distances:
59 29 0.11
60 112 0.42
61 19 0.07
62 6 0.02
64 2 0.01
65 48 0.18
66 52 0.19
67 1 0.00
ACGTcount: A:0.21, C:0.30, G:0.12, T:0.37
Consensus pattern (60 bp):
CCTTTTAAGTCCACAACTCCGTGGCATCTTTTTCCTTTTAAGTCCACAACTCTGTGGCAC
Found at i:134487 original size:49 final size:48
Alignment explanation
Indices: 134321--135148 Score: 618
Period size: 49 Copynumber: 17.9 Consensus size: 48
134311 TCCGTGGCAC
* * * *
134321 CTTTAAGTCCAATATTGCTGGCCTTGAATCAACATATTGGCACCTT-AT
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCA-CTTCAT
* * *
134369 CTTTAAGACCAATGTCACTAGCCTTGAATCAGCACATTGGCA---C--
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACTTCAT
* * * * *
134412 CTTTAAGTCCAATATCGTTAGCCTTGAATCAGCATATTGGCACTTTTAT
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCAC-TTCAT
* * *
134461 CTTTAAGAACAATGTCGCTGGCCTTGAACCAGCACATTGG-----CA-
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACTTCAT
* * * * * *
134503 ---TAAGTCCAATATTGCGGGCCGTGAATCAGCATATTGGCACCTT-GT
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCA-CTTCAT
* *
134548 CTTTAAGACCCATGTCGCTGGCCTTGAATCAGCACATTGGCA---C--
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACTTCAT
*
134591 C----AG-CCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
1 CTTTAAGACC-AATGTCGCTGGCCTTGAATCAGCATATTGGCA-CTTCAT
* *
134636 CTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGG-----CA-
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACTTCAT
* * *
134678 ---TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTAGCACCTTGC--
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCA-CTT-CAT
* *
134723 CTCTATGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCA-CTTCAT
** *
134772 CTTTAAGACCAATGTCATTGGCCTTGAATCAGCACATTGG-----CA-
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACTTCAT
* * *
134814 ---TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-AC
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCA-CTTCAT
* *
134859 CTCTAAGACCAATGTTGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCA-CTTCAT
* * * *
134908 CTTTAAGACCGATGTTGTTGGCCTTGAATCAGCACATTGGCACCTTAACCAT
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCA-CTT---CAT
* *
134960 CTTTAAGTCCAATGTCG-TCGGCCTTGAATCAGCACATTGGCATCTTCAT
1 CTTTAAGACCAATGTCGCT-GGCCTTGAATCAGCATATTGGCA-CTTCAT
* * * * * *
135009 CTTTAAGTCCGATATCGTTGGCCTTGAATCAGCATATTAGCATCTTTAT
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCA-CTTCAT
* *
135058 CTTTAAGACCAATGTCGCTGGCCTTGCATCAGCACATTGGCACCTTCAT
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCA-CTTCAT
* ** * ** *
135107 CTTTAAGTCTGATATCATTGGCCTTGAATTAGCATATTGGCA
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCA
135149 TCCTTAACAT
Statistics
Matches: 625, Mismatches: 97, Indels: 115
0.75 0.12 0.14
Matches are distributed among these distances:
38 2 0.00
39 124 0.20
43 44 0.07
44 1 0.00
45 1 0.00
46 1 0.00
47 1 0.00
48 146 0.23
49 258 0.41
50 3 0.00
51 1 0.00
52 43 0.07
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (48 bp):
CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACTTCAT
Found at i:134581 original size:87 final size:87
Alignment explanation
Indices: 134324--134949 Score: 597
Period size: 87 Copynumber: 7.0 Consensus size: 87
134314 GTGGCACCTT
* * * *
134324 TAAGTCCAATATTGCTGGCCTTGAATCAACATATTGGCACCTTATCTTTAAGACCAATGTCACTA
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGCTG
134389 GCCTTGAATCAGCACATTGGCA
66 GCCTTGAATCAGCACATTGGCA
* * * *
134411 CCTTTAAGTCCAATATCGTTAGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGAACAATGT
1 ----TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC-CTTATCTTTAAGACCAATGT
*
134476 CGCTGGCCTTGAACCAGCACATTGGCA
61 CGCTGGCCTTGAATCAGCACATTGGCA
* * * * *
134503 TAAGTCCAATATTGCGGGCCGTGAATCAGCATATTGGCACCTTGTCTTTAAGACCCATGTCGCTG
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGCTG
134568 GCCTTGAATCAGCACATTGGCA
66 GCCTTGAATCAGCACATTGGCA
** *
134590 CCAG-CCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCGT
1 TAAGTCC-AATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-ATCTTTAAGACCAATGTCGC
134654 TGGCCTTGAATCAGCACATTGGCA
64 TGGCCTTGAATCAGCACATTGGCA
* * ** * *
134678 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTAGCACCTTGCCTCTATGACCAATGTCGCTG
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGCTG
*
134743 GCCTTGAATCAGCATATTGGCACCTTCA
66 GCCTTGAATCAGCACATTGG------CA
* * ** * * *
134771 TCTTTAAGACCAATGTCATTGGCCTTGAATCAGCACATTGG---C--A----TAAGCCCAATATC
1 ----TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTC
*
134827 GCTGGCCTTGAATCAGCATATTGGCACCTTA
62 GCTGGCCTTGAATCAGCACATTGG---C--A
* * * *
134858 CCTCTAAGACCAATGTTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCGATGT
1 ----TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-ATCTTTAAGACCAATGT
* *
134923 TGTTGGCCTTGAATCAGCACATTGGCA
61 CGCTGGCCTTGAATCAGCACATTGGCA
134950 CCTTAACCAT
Statistics
Matches: 449, Mismatches: 60, Indels: 51
0.80 0.11 0.09
Matches are distributed among these distances:
85 2 0.00
86 2 0.00
87 149 0.33
88 147 0.33
89 2 0.00
90 1 0.00
91 36 0.08
92 43 0.10
93 3 0.01
94 2 0.00
97 62 0.14
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (87 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGCTG
GCCTTGAATCAGCACATTGGCA
Found at i:134616 original size:39 final size:39
Alignment explanation
Indices: 134562--134854 Score: 147
Period size: 39 Copynumber: 6.8 Consensus size: 39
134552 AAGACCCATG
*
134562 TCGCTGGCCTTGAATCAGCACATTGGCACCAGCCTAATA
1 TCGCTGGCCTTGAATCAGCATATTGGCACCAGCCTAATA
*
134601 TCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACC-AATG
1 TCGCTGGCCTTGAATCAGCATATTGGCA----C--C----AG-CCTAATA
* * ** *
134650 TCGTTGGCCTTGAATCAGCACATTGGCATAAGCCCAATA
1 TCGCTGGCCTTGAATCAGCATATTGGCACCAGCCTAATA
* * *
134689 TCGCTGGCCTTGAATCAGCATATTAGCACCTTGCCTCTATGACCAATG
1 TCGCTGGCCTTGAATCAGCATATTGGCACC-AG-C-C--T----AATA
* * *
134737 TCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGA
1 TCGCTGGCCTTGAATCAGCATATTGGCA-C--CAGC-CTAATA
* * ** *
134780 CCAATGTCATTGGCCTTGAATCAGCACATTGGCATAAGCCCAATA
1 TC---G-C--TGGCCTTGAATCAGCATATTGGCACCAGCCTAATA
134825 TCGCTGGCCTTGAATCAGCATATTGGCACC
1 TCGCTGGCCTTGAATCAGCATATTGGCACC
134855 TTACCTCTAA
Statistics
Matches: 191, Mismatches: 33, Indels: 60
0.67 0.12 0.21
Matches are distributed among these distances:
38 2 0.01
39 80 0.42
40 1 0.01
41 2 0.01
42 2 0.01
43 4 0.02
45 5 0.03
46 3 0.02
47 2 0.01
48 30 0.16
49 57 0.30
50 2 0.01
51 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (39 bp):
TCGCTGGCCTTGAATCAGCATATTGGCACCAGCCTAATA
Found at i:134675 original size:136 final size:138
Alignment explanation
Indices: 134519--135148 Score: 564
Period size: 136 Copynumber: 4.5 Consensus size: 138
134509 CAATATTGCG
* * *
134519 GGCCGTGAATCAGCATATTGGCACCTTGTCTTTAAGACCC-ATGTCGCTGGCCTTGAATCAGCAC
1 GGCCTTGAATCAGCACATTGGCACCTT-TCTTTAAG-CCCAATATCGCTGGCCTTGAATCAGCAC
134583 ATTGGCACC-AGC-CT-AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGAC
64 ATTGGCACCTAGCTCTAAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGAC
134645 CAATGTCGTT
129 CAATGTCGTT
*
134655 GGCCTTGAATCAGCACATTGGCA--------TAAGCCCAATATCGCTGGCCTTGAATCAGCATAT
1 GGCCTTGAATCAGCACATTGGCACCTTTCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCACAT
* * *
134712 TAGCACCTTGCCTCTATGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTA
66 TGGCACCTAG-CTC--T-A--AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTA
*
134777 AGACCAATGTCATT
125 AGACCAATGTCGTT
*
134791 GGCCTTGAATCAGCACATTGGCA--------TAAGCCCAATATCGCTGGCCTTGAATCAGCATAT
1 GGCCTTGAATCAGCACATTGGCACCTTTCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCACAT
* * *
134848 TGGCACCTTACCTCTAAGACCAATGTTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTA
66 TGGCACC-TAGCTCT---A--AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTA
* *
134913 AGACCGATGTTGTT
125 AGACCAATGTCGTT
* *
134927 GGCCTTGAATCAGCACATTGGCACCTTAACCATCTTTAAGTCCAATGTCG-TCGGCCTTGAATCA
1 GGCCTTGAATCAGCACATTGGCACCTT-----TCTTTAAGCCCAATATCGCT-GGCCTTGAATCA
* * * * * * *
134991 GCACATTGGCATCTTCATCTTTAAGTCCGATATCGTTGGCCTTGAATCAGCATATTAGCATCTTT
60 GCACATTGGCA-CCT-AGCTCTAA-----ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTC
*
135056 ATCTTTAAGACCAATGTCGCT
118 ATCTTTAAGACCAATGTCGTT
* * ** ** * *
135077 GGCCTTGCATCAGCACATTGGCACCTTCATCTTTAAGTCTGATATCATTGGCCTTGAATTAGCAT
1 GGCCTTGAATCAGCACATTGGCACCTT--TCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCAC
135142 ATTGGCA
64 ATTGGCA
135149 TCCTTAACAT
Statistics
Matches: 422, Mismatches: 37, Indels: 59
0.81 0.07 0.11
Matches are distributed among these distances:
126 3 0.01
127 34 0.08
128 1 0.00
129 1 0.00
130 1 0.00
132 1 0.00
134 1 0.00
136 224 0.53
137 1 0.00
145 1 0.00
147 38 0.09
148 2 0.00
149 35 0.08
150 79 0.19
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (138 bp):
GGCCTTGAATCAGCACATTGGCACCTTTCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCACAT
TGGCACCTAGCTCTAAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCA
ATGTCGTT
Found at i:134677 original size:175 final size:176
Alignment explanation
Indices: 134324--134767 Score: 649
Period size: 175 Copynumber: 2.5 Consensus size: 176
134314 GTGGCACCTT
* * * *
134324 TAAGTCCAATATTGCTGGCCTTGAATCAACATATTGGCACCTTATCTTTAAGACCAATGTCACTA
1 TAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTG
*
134389 GCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGTTAGCCTTGAATCAGCATATTGGCA
66 GCCTTGAATCAGCACATTGGCACC--T-AGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCA
* *
134454 CTTTTATCTTTAAGAACAATGTCGCTGGCCTTGAACCAGCACATTGGCA
128 CCTTCATCTTTAAGAACAATGTCGCTGGCCTTGAACCAGCACATTGGCA
* * *
134503 TAAGTCCAATATTGCGGGCCGTGAATCAGCATATTGGCACCTTGTCTTTAAGACCCATGTCGCTG
1 TAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTG
*
134568 GCCTTGAATCAGCACATTGGCACC-AG-CCTAATATCGCTGGCCTTGAATCAGCATATTGGCACC
66 GCCTTGAATCAGCACATTGGCACCTAGTCC-AATATCGCTAGCCTTGAATCAGCATATTGGCACC
* * *
134631 TTCATCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCA
130 TTCATCTTTAAGAACAATGTCGCTGGCCTTGAACCAGCACATTGGCA
* * * * * *
134678 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTAGCACCTTGCCTCTATGACCAATGTCGCTG
1 TAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTG
*
134743 GCCTTGAATCAGCATATTGGCACCT
66 GCCTTGAATCAGCACATTGGCACCT
134768 TCATCTTTAA
Statistics
Matches: 239, Mismatches: 24, Indels: 7
0.89 0.09 0.03
Matches are distributed among these distances:
174 2 0.01
175 155 0.65
179 82 0.34
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (176 bp):
TAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTG
GCCTTGAATCAGCACATTGGCACCTAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCT
TCATCTTTAAGAACAATGTCGCTGGCCTTGAACCAGCACATTGGCA
Found at i:135000 original size:101 final size:99
Alignment explanation
Indices: 134822--135200 Score: 455
Period size: 101 Copynumber: 3.8 Consensus size: 99
134812 CATAAGCCCA
* * *
134822 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTAC--CTCTAAGACCAATGTTGCTGGCCTTG
1 ATATCGTTGGCCTTGAATCAGCATATTGGCACCTTACATCTTTAAGACCAATGTCGCTGGCCTTG
* *
134885 AATCAGCATATTGGCACCTTCATCTTTAAGACCG
66 AATCAGCACATTGGCACCTTCATCTTTAAGTCCG
* * * *
134919 ATGTTGTTGGCCTTGAATCAGCACATTGGCACCTTAACCATCTTTAAGTCCAATGTCG-TCGGCC
1 ATATCGTTGGCCTTGAATCAGCATATTGGCACCTT-A-CATCTTTAAGACCAATGTCGCT-GGCC
*
134983 TTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCG
63 TTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCG
* * *
135020 ATATCGTTGGCCTTGAATCAGCATATTAGCATCTT-TATCTTTAAGACCAATGTCGCTGGCCTTG
1 ATATCGTTGGCCTTGAATCAGCATATTGGCACCTTACATCTTTAAGACCAATGTCGCTGGCCTTG
* *
135084 CATCAGCACATTGGCACCTTCATCTTTAAGTCTG
66 AATCAGCACATTGGCACCTTCATCTTTAAGTCCG
* * * * *
135118 ATATCATTGGCCTTGAATTAGCATATTGGCATCCTTAACAT-TCCTAAGCCCAATGTC-ATGGGC
1 ATATCGTTGGCCTTGAATCAGCATATTGGCA-CCTT-ACATCT-TTAAGACCAATGTCGCT-GGC
**
135181 CTTGTCTCAGCACATTGGCA
62 CTTGAATCAGCACATTGGCA
135201 TTCTTCTTCA
Statistics
Matches: 241, Mismatches: 30, Indels: 18
0.83 0.10 0.06
Matches are distributed among these distances:
97 31 0.13
98 85 0.35
99 5 0.02
100 3 0.01
101 117 0.49
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (99 bp):
ATATCGTTGGCCTTGAATCAGCATATTGGCACCTTACATCTTTAAGACCAATGTCGCTGGCCTTG
AATCAGCACATTGGCACCTTCATCTTTAAGTCCG
Found at i:135173 original size:199 final size:199
Alignment explanation
Indices: 134822--135206 Score: 533
Period size: 199 Copynumber: 1.9 Consensus size: 199
134812 CATAAGCCCA
* *
134822 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTACCTCTAAGACCAATGTTGCTGGCCTTGAA
1 ATATCGCTGGCCTTGAATCAGCATATTAGCACCTTACCTCTAAGACCAATGTCGCTGGCCTTGAA
* * **
134887 TCAGCATATTGGCACCTTCATCTTTAAGACCGATGTTGTTGGCCTTGAATCAGCACATTGGCACC
66 TCAGCACATTGGCACCTTCATCTTTAAGACCGATATCATTGGCCTTGAATCAGCACATTGGCACC
* * *
134952 TTAACCATCTTTAAGTCCAATGTCGTCGGCCTTGAATCAGCACATTGGCA-TCTTCATCTTTAAG
131 TTAACCATCTCTAAGCCCAATGTCATCGGCCTTGAATCAGCACATTGGCATTCTTCATCTTTAAG
135016 TCCG
196 TCCG
* * * * *
135020 ATATCGTTGGCCTTGAATCAGCATATTAGCATCTTTATCTTTAAGACCAATGTCGCTGGCCTTGC
1 ATATCGCTGGCCTTGAATCAGCATATTAGCA-CCTTACCTCTAAGACCAATGTCGCTGGCCTTGA
* * * *
135085 ATCAGCACATTGGCACCTTCATCTTTAAGTCTGATATCATTGGCCTTGAATTAGCATATTGGCAT
65 ATCAGCACATTGGCACCTTCATCTTTAAGACCGATATCATTGGCCTTGAATCAGCACATTGGCA-
* **
135150 CCTTAA-CAT-TCCTAAGCCCAATGTCATGGGCCTTGTCTCAGCACATTGGCATTCTTC
129 CCTTAACCATCT-CTAAGCCCAATGTCATCGGCCTTGAATCAGCACATTGGCATTCTTC
135207 TTCAATTCTA
Statistics
Matches: 162, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
198 30 0.19
199 121 0.75
200 11 0.07
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.33
Consensus pattern (199 bp):
ATATCGCTGGCCTTGAATCAGCATATTAGCACCTTACCTCTAAGACCAATGTCGCTGGCCTTGAA
TCAGCACATTGGCACCTTCATCTTTAAGACCGATATCATTGGCCTTGAATCAGCACATTGGCACC
TTAACCATCTCTAAGCCCAATGTCATCGGCCTTGAATCAGCACATTGGCATTCTTCATCTTTAAG
TCCG
Found at i:138506 original size:75 final size:75
Alignment explanation
Indices: 138419--138569 Score: 302
Period size: 75 Copynumber: 2.0 Consensus size: 75
138409 TTACGACTGT
138419 TACGTTTTCTTTCTTCTTCCTTGTTCGGCCTAGATAATTCATTTGTATGAAATATCATATGCTTT
1 TACGTTTTCTTTCTTCTTCCTTGTTCGGCCTAGATAATTCATTTGTATGAAATATCATATGCTTT
138484 TATCGCCTTA
66 TATCGCCTTA
138494 TACGTTTTCTTTCTTCTTCCTTGTTCGGCCTAGATAATTCATTTGTATGAAATATCATATGCTTT
1 TACGTTTTCTTTCTTCTTCCTTGTTCGGCCTAGATAATTCATTTGTATGAAATATCATATGCTTT
138559 TATCGCCTTA
66 TATCGCCTTA
138569 T
1 T
138570 CAGTATGCTT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.48
Consensus pattern (75 bp):
TACGTTTTCTTTCTTCTTCCTTGTTCGGCCTAGATAATTCATTTGTATGAAATATCATATGCTTT
TATCGCCTTA
Found at i:142060 original size:26 final size:25
Alignment explanation
Indices: 142023--142071 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
142013 GGGATTATAT
* *
142023 TGAAATAATATTGTGTCGAAACAAA
1 TGAAATAATATTGAGTCAAAACAAA
142048 TGAAATCAATATTGAGTCAAAACA
1 TGAAAT-AATATTGAGTCAAAACA
142072 TATCTAGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (25 bp):
TGAAATAATATTGAGTCAAAACAAA
Found at i:145769 original size:1 final size:1
Alignment explanation
Indices: 145765--145821 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
145755 TCCTTTTTCT
* * * * * * *
145765 AAAAAAAACAAAAAAACAAAATAAAAAAAAGAAAAAAAAGAAAAAAAGAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
145822 GAACCTTCTT
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.88, C:0.04, G:0.07, T:0.02
Consensus pattern (1 bp):
A
Found at i:145779 original size:9 final size:9
Alignment explanation
Indices: 145767--145824 Score: 64
Period size: 10 Copynumber: 6.2 Consensus size: 9
145757 CTTTTTCTAA
*
145767 AAAAAACAAA
1 AAAAAA-AAG
*
145777 AAAACAAAAT
1 AAAA-AAAAG
145787 AAAAAAAAG
1 AAAAAAAAG
145796 AAAAAAAAG
1 AAAAAAAAG
145805 -AAAAAAAG
1 AAAAAAAAG
145813 AAAAGAAAAG
1 AAAA-AAAAG
145823 AA
1 AA
145825 CCTTCTTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
8 8 0.19
9 16 0.37
10 17 0.40
11 2 0.05
ACGTcount: A:0.86, C:0.03, G:0.09, T:0.02
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:145816 original size:22 final size:23
Alignment explanation
Indices: 145764--145821 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
145754 TTCCTTTTTC
*
145764 TAAAAAAAA-CAAAAAAACAAAA
1 TAAAAAAAAGAAAAAAAACAAAA
*
145786 TAAAAAAAAGAAAAAAAAGAAAA
1 TAAAAAAAAGAAAAAAAACAAAA
*
145809 -AAAGAAAAGAAAA
1 TAAAAAAAAGAAAA
145822 GAACCTTCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
22 21 0.66
23 11 0.34
ACGTcount: A:0.86, C:0.03, G:0.07, T:0.03
Consensus pattern (23 bp):
TAAAAAAAAGAAAAAAAACAAAA
Found at i:146829 original size:61 final size:60
Alignment explanation
Indices: 146729--147039 Score: 293
Period size: 61 Copynumber: 5.0 Consensus size: 60
146719 ATCCTTTCAA
*
146729 TCCTCAAAGAGTAGGACGCCTTCTCCTCTCAAAGCCCACACAAGTTGGTGGCACCTTCCAG
1 TCCTCAAAGAGTAGGACGCCTTCTCCT-TTAAAGCCCACACAAGTTGGTGGCACCTTCCAG
* * *
146790 TCCTTAAAGAGCAGGACGCCTTCTCCGTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAG
1 TCCTCAAAGAGTAGGACGCCTTCTCC-TTTAAAGCCCACACAAGTTGGTGGCACCTTCCAG
* * * *
146851 TCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACA-AGGGTTGGTAGCACCTTCTAG
1 TCCTCAAAGAGTAGGACGCCTTCTCC-TTTAAAGCCCACACA-AGTTGGTGGCACCTTCCAG
* * * *
146912 TCCTCAAAAAGCAGGACACC-TCTCGCTTTTTTTTTTTTTAAAACCCACACAAGTTGGTGGCACC
1 TCCTCAAAGAGTAGGACGCCTTCTC-C----------TTTAAAGCCCACACAAGTTGGTGGCACC
*
146976 TTTCAG
55 TTCCAG
* * * * * *
146982 TCCTTAAAGAGTAGGACGTCTTTTTCTTTCAAAGTCTACACAAGTTGGTGGCACCTTC
1 TCCTCAAAGAGTAGGACGCCTTCTCCTTT-AAAGCCCACACAAGTTGGTGGCACCTTC
147040 TGTTCCCAAA
Statistics
Matches: 203, Mismatches: 32, Indels: 30
0.77 0.12 0.11
Matches are distributed among these distances:
60 7 0.03
61 148 0.73
62 1 0.00
70 44 0.22
71 3 0.01
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (60 bp):
TCCTCAAAGAGTAGGACGCCTTCTCCTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAG
Found at i:147090 original size:131 final size:130
Alignment explanation
Indices: 146820--147133 Score: 347
Period size: 131 Copynumber: 2.4 Consensus size: 130
146810 TTCTCCGTTT
*
146820 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAG
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTCAAAG
* ****
146885 CCCACAAGGGTTGGTAGCACCTTCTAGTCCTCAAAAAGCAGGACACCTCTCGCTTTTTTTTTTTT
66 CACACAA-GGTTGGTAGCACCTTCTAGTCCTCAAAAAGCAGGACACCTCTC-CTTTTTTTTAAAA
*
146950 TA
129 AA
* * *
146952 AAA-CCCACACAAGTTGGTGGCACCTTTCAGTCCTTAAAGAGTAGGACGTCTTTTTCTTTCAAAG
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTCAAAG
* * *
147016 TCTACACAA-GTTGGTGGCACCTTCT-GTTCC-CAAAGAGCAGTACA-CT-T-CTTTTTTTTAAA
66 -C-ACACAAGGTTGGTAGCACCTTCTAG-TCCTCAAAAAGCAGGACACCTCTCCTTTTTTTT---
147075 AAAAAAA
125 -AAAAAA
* *
147082 AAAGCCCACACAAGCTGGTGGCACC-TTCTAGTTCTCAAAGAGTAGGACGCCT
1 AAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGTAGGACGCCT
147134 CTCTCTTTTT
Statistics
Matches: 156, Mismatches: 17, Indels: 19
0.81 0.09 0.10
Matches are distributed among these distances:
126 9 0.06
128 1 0.01
129 2 0.01
130 20 0.13
131 115 0.74
132 4 0.03
133 5 0.03
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (130 bp):
AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTCAAAG
CACACAAGGTTGGTAGCACCTTCTAGTCCTCAAAAAGCAGGACACCTCTCCTTTTTTTTAAAAAA
Found at i:147760 original size:50 final size:51
Alignment explanation
Indices: 147694--147789 Score: 158
Period size: 50 Copynumber: 1.9 Consensus size: 51
147684 TGATACATCA
* *
147694 TTCATTATATCGATACATTATGGGTTTT-ACCTAGATGTATCGATATATTT
1 TTCATTATATCAATACATTATGGGTTTTAACCCAGATGTATCGATATATTT
*
147744 TTCATTGTATCAATACATTATGGGTTTTAACCCAGATGTATCGATA
1 TTCATTATATCAATACATTATGGGTTTTAACCCAGATGTATCGATA
147790 CATTCAGGCA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
50 26 0.62
51 16 0.38
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.43
Consensus pattern (51 bp):
TTCATTATATCAATACATTATGGGTTTTAACCCAGATGTATCGATATATTT
Found at i:150222 original size:79 final size:79
Alignment explanation
Indices: 150117--150665 Score: 524
Period size: 79 Copynumber: 6.9 Consensus size: 79
150107 CCATTCATGT
* * * * * *
150117 TTTTGTTTCTAAAACATCGATTTTTCACAATCGAGGATACTCCAACCTCGTTATTTCTGAGGGGG
1 TTTTATTTCCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCTCGTTATTTCTGAGGGGA
150182 TACTCCAACCCGAG
66 TACTCCAACCCGAG
***
150196 TTTTATTTTTGAAACACCAATTTTTCACAATCGGGGATACTCCAACC-CTGTTATTTCTGAGGGG
1 TTTTATTTCCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCTC-GTTATTTCTGAGGGG
150260 ATACTCCAACTCCGA-
65 ATACTCCAAC-CCGAG
* * * * * * **
150275 TTTTATTTCCAAAACACTGATTTTTTCACAACCGAGGATATTCCAACCTTGTTATTT-TCGATAG
1 TTTTATTTCCAAAACAC-CAATTTTTCACAATCGGGGATACTCCAACCTCGTTATTTCT-GAGGG
* *
150339 GATACTCTAACCCTAG
64 GATACTCCAACCCGAG
* * * * * * **
150355 TTTTATTTCTAAAACATCGATTTTCCACCATCGGGGATACTCCAACCTTGTTATTTCTGAACGGA
1 TTTTATTTCCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCTCGTTATTTCTGAGGGGA
*
150420 TACTCCAACCTTG-G
66 TACTCCAACC-CGAG
* * * * *
150434 TTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATGCTCCAACCCCGTTATTTTTGAGGGAA
1 TTTTATTTCCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCTCGTTATTTCTGAGGGGA
*
150499 TACTTCAACCCCG-G
66 TACTCCAA-CCCGAG
* * * * *
150513 CTTTATTTCTAAAACATCAATTTTTCATAATCGAGGATACTCCAACC-CTGTTATTT-TCGAGGG
1 TTTTATTTCCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCTC-GTTATTTCT-GAGGG
150576 GATACTCCAACCTCGA-
64 GATACTCCAACC-CGAG
* * * * * *
150592 TTTTACTTT-CAAAACATCAATTTCT-ACCATCGGGGATACTCTAACCTCGTTATTTTTTAGGGG
1 TTTTA-TTTCCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCTCGTTATTTCTGAGGGG
*
150655 ATACTCTAACC
65 ATACTCCAACC
150666 TCGTTTTTAT
Statistics
Matches: 386, Mismatches: 68, Indels: 33
0.79 0.14 0.07
Matches are distributed among these distances:
78 44 0.11
79 272 0.70
80 70 0.18
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (79 bp):
TTTTATTTCCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCTCGTTATTTCTGAGGGGA
TACTCCAACCCGAG
Found at i:150565 original size:158 final size:159
Alignment explanation
Indices: 150117--150697 Score: 640
Period size: 158 Copynumber: 3.7 Consensus size: 159
150107 CCATTCATGT
* * * *
150117 TTTTGTTTCTAAAACA-TCGATTTTTCACAATCGAGGATACTCCAACCTCGTTATTTCTGAGGGG
1 TTTTATTTCCAAAACACTCAATTTTTCACAATCGAGGATACTCCAACCTCGTTATTTTTGAGGGG
* * * * * *
150181 GTACTCCAA-CCCGAGTTTTATTTTTGAAACACCAATTTTTCACAATCGGGGATACTCCAACCCT
66 ATACTCTAACCCCG-GTTTTATTTCTAAAACATCAATTTTTCACAATCGAGGATACTCCAACCCT
150245 GTTATTTCTGAGGGGATACTCCAA-CTCCGA
130 GTTATTTCTGAGGGGATACTCCAACCT-CGA
* * * * * * **
150275 TTTTATTTCCAAAACACTGATTTTTTCACAACCGAGGATATTCCAACCTTGTTATTTTCGATAGG
1 TTTTATTTCCAAAACACTCAATTTTTCACAATCGAGGATACTCCAACCTCGTTATTTTTGAGGGG
** * * * * *
150340 ATACTCTAACCCTAGTTTTATTTCTAAAACATCGATTTTCCACCATCGGGGATACTCCAACCTTG
66 ATACTCTAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGAGGATACTCCAACCCTG
** * *
150405 TTATTTCTGAACGGATACTCCAACCTTGG
131 TTATTTCTGAGGGGATACTCCAACCTCGA
* * * *
150434 TTTTATTTCCAAAACACT-AATTTTTCACAATCGGGGATGCTCCAACCCCGTTATTTTTGAGGGA
1 TTTTATTTCCAAAACACTCAATTTTTCACAATCGAGGATACTCCAACCTCGTTATTTTTGAGGGG
* *
150498 ATACT-TCAACCCCGGCTTTATTTCTAAAACATCAATTTTTCATAATCGAGGATACTCCAACCCT
66 ATACTCT-AACCCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGAGGATACTCCAACCCT
150562 GTTATTT-TCGAGGGGATACTCCAACCTCGA
130 GTTATTTCT-GAGGGGATACTCCAACCTCGA
* * * * *
150592 TTTTACTTT-CAAAACA-TCAATTTCT-ACCATCGGGGATACTCTAACCTCGTTATTTTTTAGGG
1 TTTTA-TTTCCAAAACACTCAATTTTTCACAATCGAGGATACTCCAACCTCGTTATTTTTGAGGG
* * * * *
150654 GATACTCTAACCTCGTTTTTATCTCTAAAATATTGAATTTTTCA
65 GATACTCTAACCCCGGTTTTATTTCTAAAACA-TCAATTTTTCA
150698 TATGGAGGAT
Statistics
Matches: 350, Mismatches: 64, Indels: 18
0.81 0.15 0.04
Matches are distributed among these distances:
157 59 0.17
158 155 0.44
159 132 0.38
160 4 0.01
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (159 bp):
TTTTATTTCCAAAACACTCAATTTTTCACAATCGAGGATACTCCAACCTCGTTATTTTTGAGGGG
ATACTCTAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGAGGATACTCCAACCCTG
TTATTTCTGAGGGGATACTCCAACCTCGA
Found at i:152900 original size:33 final size:33
Alignment explanation
Indices: 152863--152939 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 33
152853 CTACCACTGT
152863 TATCGATACATGGCACATTATATCGAAACAATG
1 TATCGATACATGGCACATTATATCGAAACAATG
* * *
152896 TATCGATATATGGCACATTGTATCGATACAATG
1 TATCGATACATGGCACATTATATCGAAACAATG
152929 TATCGATACAT
1 TATCGATACAT
152940 AACGAATTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (33 bp):
TATCGATACATGGCACATTATATCGAAACAATG
Found at i:152932 original size:13 final size:13
Alignment explanation
Indices: 152914--152938 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
152904 TATGGCACAT
152914 TGTATCGATACAA
1 TGTATCGATACAA
152927 TGTATCGATACA
1 TGTATCGATACA
152939 TAACGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:152949 original size:33 final size:33
Alignment explanation
Indices: 152863--152958 Score: 113
Period size: 33 Copynumber: 2.9 Consensus size: 33
152853 CTACCACTGT
** * *
152863 TATCGATACATGGCACATTATATCGAAACAATG
1 TATCGATACATAACACATTGTATCGATACAATG
* **
152896 TATCGATATATGGCACATTGTATCGATACAATG
1 TATCGATACATAACACATTGTATCGATACAATG
152929 TATCGATACATAACGA-ATTGTATCGATACA
1 TATCGATACATAAC-ACATTGTATCGATACA
152959 TTGTCCTAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
33 55 0.98
34 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.30
Consensus pattern (33 bp):
TATCGATACATAACACATTGTATCGATACAATG
Found at i:154575 original size:15 final size:15
Alignment explanation
Indices: 154555--154589 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
154545 AACCATTAAA
154555 GATGATGAAGATAAT
1 GATGATGAAGATAAT
*
154570 GATGATGATGATAAT
1 GATGATGAAGATAAT
154585 GATGA
1 GATGA
154590 AGTTGACTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:161854 original size:52 final size:52
Alignment explanation
Indices: 161706--161830 Score: 241
Period size: 52 Copynumber: 2.4 Consensus size: 52
161696 CGAAATATGA
161706 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
*
161758 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
161810 AAATTTGCCTGCATGTATCGA
1 AAATTTGCCTGCATGTATCGA
161831 CACAAAGATC
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
Found at i:161861 original size:13 final size:13
Alignment explanation
Indices: 161843--161867 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
161833 CAAAGATCAG
161843 TGTATCGATACAA
1 TGTATCGATACAA
161856 TGTATCGATACA
1 TGTATCGATACA
161868 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:161949 original size:13 final size:13
Alignment explanation
Indices: 161931--161957 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
161921 AAAATTTATG
161931 TATCGATACAATA
1 TATCGATACAATA
161944 TATCGATACAATA
1 TATCGATACAATA
161957 T
1 T
161958 TTTATGTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.33
Consensus pattern (13 bp):
TATCGATACAATA
Found at i:161951 original size:32 final size:33
Alignment explanation
Indices: 161910--161974 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
161900 TAGCTTAAAT
161910 TATATCGATACAA-AATTTATGTATCGATACAA
1 TATATCGATACAATAATTTATGTATCGATACAA
*
161942 TATATCGATACAATATTTTATGTATCGATACAA
1 TATATCGATACAATAATTTATGTATCGATACAA
161975 ATCATTGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 13 0.42
33 18 0.58
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (33 bp):
TATATCGATACAATAATTTATGTATCGATACAA
Found at i:162727 original size:13 final size:13
Alignment explanation
Indices: 162709--162733 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
162699 CAATGTTCTT
162709 TGTATCGATACAG
1 TGTATCGATACAG
162722 TGTATCGATACA
1 TGTATCGATACA
162734 TGGGTTACTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:165235 original size:20 final size:19
Alignment explanation
Indices: 165209--165264 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
165199 AAAACCCTTG
165209 TATGTATCGATACATAT-C
1 TATGTATCGATACATATGC
*
165227 TAGATGTATCAATACATTATGC
1 T--ATGTATCGATACA-TATGC
*
165249 TTTGTATCGATACATA
1 TATGTATCGATACATA
165265 GGTATTTGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 1 0.03
19 2 0.06
20 23 0.74
21 3 0.10
22 2 0.06
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.39
Consensus pattern (19 bp):
TATGTATCGATACATATGC
Found at i:165335 original size:111 final size:111
Alignment explanation
Indices: 165141--165374 Score: 450
Period size: 111 Copynumber: 2.1 Consensus size: 111
165131 ATAAACCAAA
165141 GTATCGATACATAGGTATTTGTAATGATACATTAAGGTTGACTTAAGCTACAAAGGTCAAAACCC
1 GTATCGATACATAGGTATTTGTAATGATACATTAAGGTTGACTTAAGCTACAAAGGTCAAAACCC
*
165206 TTGTATGTATCGATACATATCTAGATGTATCAATACATTATGCTTT
66 TTGTATGTATCGATACATATCCAGATGTATCAATACATTATGCTTT
165252 GTATCGATACATAGGTATTTGTAATGATACATTAAGGTTGACTTAAGCTACAAAGGTCAAAACCC
1 GTATCGATACATAGGTATTTGTAATGATACATTAAGGTTGACTTAAGCTACAAAGGTCAAAACCC
*
165317 TTGTATGTATCGATACATATCCAGATGTATCAATGCATTATGCTTT
66 TTGTATGTATCGATACATATCCAGATGTATCAATACATTATGCTTT
165363 GTATCGATACAT
1 GTATCGATACAT
165375 GTTCATTGTA
Statistics
Matches: 121, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 121 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (111 bp):
GTATCGATACATAGGTATTTGTAATGATACATTAAGGTTGACTTAAGCTACAAAGGTCAAAACCC
TTGTATGTATCGATACATATCCAGATGTATCAATACATTATGCTTT
Found at i:165385 original size:19 final size:20
Alignment explanation
Indices: 165361--165414 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
165351 GCATTATGCT
**
165361 TTGTATCGATACATGTTC-A
1 TTGTATCGATACATGCACAA
*
165380 TTGTATCGATGCATGCACAA
1 TTGTATCGATACATGCACAA
165400 TTGTATCGATACATG
1 TTGTATCGATACATG
165415 AAACTGGTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGCACAA
Found at i:165486 original size:33 final size:33
Alignment explanation
Indices: 165444--165508 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
165434 TACCACTGTT
**
165444 TGTATCAATACATGGC-ACATTGTATCGATACAA
1 TGTATCAATACATAACGA-ATTGTATCGATACAA
165477 TGTATCAATACATAACGAATTGTATCGATACA
1 TGTATCAATACATAACGAATTGTATCGATACA
165509 TTATCCCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (33 bp):
TGTATCAATACATAACGAATTGTATCGATACAA
Found at i:167357 original size:40 final size:40
Alignment explanation
Indices: 167312--167391 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
167302 TATTCTGTAG
*
167312 GAGAAAATCAAATTTTAATATTTTTAAAAATCAAAATCTC
1 GAGAAAATCAAATTTTAATATTTTCAAAAATCAAAATCTC
* *
167352 GAGAAAATTAATTTTTAATATTTTCAAAAATCAAAATCTC
1 GAGAAAATCAAATTTTAATATTTTCAAAAATCAAAATCTC
167392 TTACATACTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (40 bp):
GAGAAAATCAAATTTTAATATTTTCAAAAATCAAAATCTC
Found at i:169642 original size:16 final size:16
Alignment explanation
Indices: 169621--169652 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
169611 ATAACAATTA
169621 AAATAAAATTATAAAT
1 AAATAAAATTATAAAT
169637 AAATAAAATTATAAAT
1 AAATAAAATTATAAAT
169653 TATAAACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATAAAATTATAAAT
Found at i:171463 original size:65 final size:66
Alignment explanation
Indices: 171324--171465 Score: 171
Period size: 65 Copynumber: 2.2 Consensus size: 66
171314 CAGGAAGTGA
* * * *
171324 CCTAGGTCGAAAGGGTTAACCAGGGTGAAATCGATACAATCAAATAAAGGTGACCAGGATATAAT
1 CCTAGGTCTAAAGGGTTAACCAAGGTGAAATCGATACAATCAAAAAAAGATGACCAGGATATAAT
171389 T
66 T
* * * * * * *
171390 CTTA-GTCTAGAGGGTTGACCAAGGTGAAATTGATATAGTCAAAAAAAGATGACTAGGATATAA-
1 CCTAGGTCTAAAGGGTTAACCAAGGTGAAATCGATACAATCAAAAAAAGATGACCAGGATATAAT
171453 T
66 T
171454 CCTAGGTCTAAA
1 CCTAGGTCTAAA
171466 ATGGTTGACA
Statistics
Matches: 62, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
64 4 0.06
65 55 0.89
66 3 0.05
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.24
Consensus pattern (66 bp):
CCTAGGTCTAAAGGGTTAACCAAGGTGAAATCGATACAATCAAAAAAAGATGACCAGGATATAAT
T
Found at i:171682 original size:40 final size:41
Alignment explanation
Indices: 171635--171833 Score: 205
Period size: 40 Copynumber: 5.0 Consensus size: 41
171625 TAAGCCAAGG
*
171635 AATGGGAAGAGTTGATCGA-GATAAAACTTATAAGTCAATGA
1 AATGGGAAGAGTTGA-CGAGGATAAAACCTATAAGTCAATGA
* * **
171676 TA-GGGAAGAGTTGACTAGGATAAAACCTGCAAGTCAAT-A
1 AATGGGAAGAGTTGACGAGGATAAAACCTATAAGTCAATGA
* * * *
171715 AATGAGAAGGGATGATC-AGGATGAAACCTATAAGTCAATG-
1 AATGGGAAGAGTTGA-CGAGGATAAAACCTATAAGTCAATGA
* *
171755 AATGGGAAGAGTTGACCGA-GATAAAACCTACAAGTCAA-CA
1 AATGGGAAGAGTTGA-CGAGGATAAAACCTATAAGTCAATGA
* *
171795 AATGGGAAAAGTTGACTAGGATAAAACCTATAAGTCAAT
1 AATGGGAAGAGTTGACGAGGATAAAACCTATAAGTCAAT
171834 AGATGAAAAG
Statistics
Matches: 128, Mismatches: 22, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
39 6 0.05
40 119 0.93
41 3 0.02
ACGTcount: A:0.44, C:0.12, G:0.24, T:0.21
Consensus pattern (41 bp):
AATGGGAAGAGTTGACGAGGATAAAACCTATAAGTCAATGA
Found at i:171764 original size:120 final size:120
Alignment explanation
Indices: 171584--171845 Score: 337
Period size: 120 Copynumber: 2.2 Consensus size: 120
171574 GATGAAATCA
* * * *
171584 ACAAGTCAACAAATGAGAAGGGCTAACCAGGACGAAACTTCTAAGCCAAGGAATGGGAAGAGTTG
1 ACAAGTCAATAAATGAGAAGGGATAACCAGGACGAAACCTATAAGCCAAGGAATGGGAAGAGTTG
* * * ** *
171649 ATCGAGATAAAACTTATAAGTCAA-TGATAGGGAAGAGTTGACTAGGATAAAACCT
66 ACCGAGATAAAACCTACAAGTCAACAAAT-GGGAAAAGTTGACTAGGATAAAACCT
* * * * * *
171704 GCAAGTCAATAAATGAGAAGGGATGATCAGGATGAAACCTATAAGTCAATGAATGGGAAGAGTTG
1 ACAAGTCAATAAATGAGAAGGGATAACCAGGACGAAACCTATAAGCCAAGGAATGGGAAGAGTTG
171769 ACCGAGATAAAACCTACAAGTCAACAAATGGGAAAAGTTGACTAGGATAAAACCT
66 ACCGAGATAAAACCTACAAGTCAACAAATGGGAAAAGTTGACTAGGATAAAACCT
* * *
171824 ATAAGTCAATAGATGAAAAGGG
1 ACAAGTCAATAAATGAGAAGGG
171846 TTGACCGAGA
Statistics
Matches: 121, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
120 119 0.98
121 2 0.02
ACGTcount: A:0.44, C:0.13, G:0.25, T:0.18
Consensus pattern (120 bp):
ACAAGTCAATAAATGAGAAGGGATAACCAGGACGAAACCTATAAGCCAAGGAATGGGAAGAGTTG
ACCGAGATAAAACCTACAAGTCAACAAATGGGAAAAGTTGACTAGGATAAAACCT
Found at i:171780 original size:80 final size:80
Alignment explanation
Indices: 171654--171871 Score: 246
Period size: 80 Copynumber: 2.7 Consensus size: 80
171644 AGTTGATCGA
* * * *
171654 GATAAAACTTATAAGTCAATG-ATAGGGAAGAGTTGA-CTAGGATAAAACCTGCAAGTCAATAAA
1 GATAAAACCTATAAGTCAATGAAT-GGGAAGAGTTGACCGA-GATAAAACCTACAAGTCAACAAA
**
171717 TGAGAAGGGATGA-TCAG
64 TGAGAAAAGATGACT-AG
*
171734 GATGAAACCTATAAGTCAATGAATGGGAAGAGTTGACCGAGATAAAACCTACAAGTCAACAAATG
1 GATAAAACCTATAAGTCAATGAATGGGAAGAGTTGACCGAGATAAAACCTACAAGTCAACAAATG
* *
171799 GGAAAAGTTGACTAG
66 AGAAAAGATGACTAG
** * * *
171814 GATAAAACCTATAAGTCAAT-AGATGAAAAGGGTTGACCGAGACAAAACGTACAAGTCA
1 GATAAAACCTATAAGTCAATGA-ATGGGAAGAGTTGACCGAGATAAAACCTACAAGTCA
171872 CTGAGTAGAA
Statistics
Matches: 119, Mismatches: 15, Indels: 8
0.84 0.11 0.06
Matches are distributed among these distances:
79 1 0.01
80 113 0.95
81 5 0.04
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.19
Consensus pattern (80 bp):
GATAAAACCTATAAGTCAATGAATGGGAAGAGTTGACCGAGATAAAACCTACAAGTCAACAAATG
AGAAAAGATGACTAG
Found at i:171861 original size:40 final size:39
Alignment explanation
Indices: 171645--171871 Score: 124
Period size: 40 Copynumber: 5.7 Consensus size: 39
171635 AATGGGAAGA
* * * **
171645 GTTGATCGAGATAAAACTTATAAGTCAAT-GATAGGGAAG
1 GTTGACCGAGATAAAACCTACAAGTCAATAGAT-GAAAAG
* * * *
171684 AGTTGA-CTAGGATAAAACCTGCAAGTCAATAAATGAGAAGG
1 -GTTGACCGA-GATAAAACCTACAAGTCAATAGATGA-AAAG
* * * * **
171725 GATGATC-AGGATGAAACCTATAAGTCAAT-GAATGGGAAG
1 GTTGACCGA-GATAAAACCTACAAGTCAATAG-ATGAAAAG
* *
171764 AGTTGACCGAGATAAAACCTACAAGTCAACAAATGGGAAAA-
1 -GTTGACCGAGATAAAACCTACAAGTCAATAGAT--GAAAAG
* *
171805 GTTGA-CTAGGATAAAACCTATAAGTCAATAGATGAAAAGG
1 GTTGACCGA-GATAAAACCTACAAGTCAATAGATGAAAA-G
* *
171845 GTTGACCGAGACAAAACGTACAAGTCA
1 GTTGACCGAGATAAAACCTACAAGTCA
171872 CTGAGTAGAA
Statistics
Matches: 141, Mismatches: 32, Indels: 28
0.70 0.16 0.14
Matches are distributed among these distances:
38 5 0.04
39 6 0.04
40 119 0.84
41 8 0.06
42 3 0.02
ACGTcount: A:0.44, C:0.13, G:0.24, T:0.20
Consensus pattern (39 bp):
GTTGACCGAGATAAAACCTACAAGTCAATAGATGAAAAG
Found at i:172439 original size:75 final size:75
Alignment explanation
Indices: 172353--172639 Score: 263
Period size: 75 Copynumber: 3.8 Consensus size: 75
172343 CAAAATGATA
* * ** *
172353 TGATAACAAGCTAGAGAAGAAAAACACAATGGGAATATGTAGTTTCTAAAATTTCCATCAACAGT
1 TGATAACAAGCTAAAAAAGAAAAACATGATGGGAATATGTAGTTTCTAAAATTTCCATCAATAGT
172418 TGAAATAAAC
66 TGAAATAAAC
* * * * * * **
172428 TGATAATAAGCTGAAGAAGAAGAACATGATGAGGAATATCT-GTTTCTATAATTTTCC-TTTATA
1 TGATAACAAGCTAAAAAAGAAAAACATGATG-GGAATATGTAGTTTCTA-AAATTTCCATCAATA
**
172491 GTCAAAATAAAC
64 GTTGAAATAAAC
* * * * * * * * *
172503 TAATAATAAACTAAAAAATAATAACATGATAGGGAATACGTGGTTTCTACAGTTTCCCATCAATA
1 TGATAACAAGCTAAAAAAGAAAAACATGAT-GGGAATATGTAGTTTCTAAAATTT-CCATCAATA
*
172568 GTTGAAACAAAC
64 GTTGAAATAAAC
* * *
172580 TGATAACAAGCTAAAAAAGAAAATCATGATGGAGAATATGTAATTTCTACAATTTCCATC
1 TGATAACAAGCTAAAAAAGAAAAACATGATGG-GAATATGTAGTTTCTAAAATTTCCATC
172640 GACAACCTGT
Statistics
Matches: 167, Mismatches: 38, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
75 80 0.48
76 32 0.19
77 55 0.33
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.28
Consensus pattern (75 bp):
TGATAACAAGCTAAAAAAGAAAAACATGATGGGAATATGTAGTTTCTAAAATTTCCATCAATAGT
TGAAATAAAC
Found at i:173015 original size:40 final size:40
Alignment explanation
Indices: 172951--173167 Score: 226
Period size: 40 Copynumber: 5.4 Consensus size: 40
172941 GACCAGGACG
* * *
172951 AAACTTATAAGCCAAGGAATGGGAAGAGTTGATCGA-GATA
1 AAACCTATAAGTCAATGAATGGGAAGAGTTGA-CGAGGATA
* *
172991 AAACTTATAAGTCAATG-ATAGGGAAGAGTTGACTAGGATA
1 AAACCTATAAGTCAATGAAT-GGGAAGAGTTGACGAGGATA
* * * * * *
173031 AAACCTACAAGTCAATAAATGAGAAGGGATGATC-AGGATG
1 AAACCTATAAGTCAATGAATGGGAAGAGTTGA-CGAGGATA
173071 AAACCTATAAGTCAATGAATGGGAAGAGTTGACCGA-GATA
1 AAACCTATAAGTCAATGAATGGGAAGAGTTGA-CGAGGATA
* ** * *
173111 AAACCTACAAGTCAACAAATGGGAAAAGTTGACTAGGATA
1 AAACCTATAAGTCAATGAATGGGAAGAGTTGACGAGGATA
173151 AAACCTATAAGTCAATG
1 AAACCTATAAGTCAATG
173168 GATGAAAAGG
Statistics
Matches: 146, Mismatches: 25, Indels: 12
0.80 0.14 0.07
Matches are distributed among these distances:
39 6 0.04
40 136 0.93
41 4 0.03
ACGTcount: A:0.44, C:0.12, G:0.24, T:0.20
Consensus pattern (40 bp):
AAACCTATAAGTCAATGAATGGGAAGAGTTGACGAGGATA
Done.