Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011750.1 Corchorus capsularis cultivar CVL-1 contig11771, whole genome shotgun sequence
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: 124499
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:6665 original size:75 final size:74
Alignment explanation
Indices: 6513--6792 Score: 352
Period size: 75 Copynumber: 3.7 Consensus size: 74
6503 AGAGGATACG
* * *
6513 ATTCATAACATCCTCGGGCAACTCGGAAATTCGATCTGTTGCACTCGAAGCATCAA-TAGGGTCT
1 ATTCATAACATCCTCCGGCAACTCGGAAATTCGATCTGTTGCACTCG--G--TGAAGCAGGGTCT
6577 AATCTCA--TATT
62 AATCTCAGTTATT
* * * *
6588 ATTCATAACATCCTCCGGTAAATCGGAAATTTGATCTGTTGCACTCGGTGAAGCCGGGTCTAATC
1 ATTCATAACATCCTCCGGCAACTCGGAAATTCGATCTGTTGCACTCGGTGAAGCAGGGTCTAATC
*
6653 TCACGTTGTT
66 TCA-GTTATT
* *
6663 ATTCATAACATCCTCCGGCAACTCGAAAATTCGATCTGTTGCACTCGGTGAAGCAGGGTATAATC
1 ATTCATAACATCCTCCGGCAACTCGGAAATTCGATCTGTTGCACTCGGTGAAGCAGGGTCTAATC
6728 TCATGTTATT
66 TCA-GTTATT
* * *
6738 ATTCATAACATCCT-CGGTCAACTCGGAAATTTGATCTGTTGCACTCAGAGAAGCA
1 ATTCATAACATCCTCCGG-CAACTCGGAAATTCGATCTGTTGCACTCGGTGAAGCA
6793 TCAGCAGGGT
Statistics
Matches: 180, Mismatches: 20, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
71 3 0.02
72 13 0.07
73 1 0.01
74 3 0.02
75 160 0.89
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (74 bp):
ATTCATAACATCCTCCGGCAACTCGGAAATTCGATCTGTTGCACTCGGTGAAGCAGGGTCTAATC
TCAGTTATT
Found at i:6791 original size:150 final size:148
Alignment explanation
Indices: 6513--6791 Score: 402
Period size: 150 Copynumber: 1.9 Consensus size: 148
6503 AGAGGATACG
* * * *
6513 ATTCATAACATCCTCGGGCAACTCGGAAATTCGATCTGTTGCACTCGAAGCATCAATAGGGTCTA
1 ATTCATAACATCCTCCGGCAACTCGAAAATTCGATCTGTTGCACTCG-AG-ATCAACAGGGTATA
* *
6578 ATCTCATATTATTCATAACATCCTCCGGTAAATCGGAAATTTGATCTGTTGCACTCGGTGAAGCC
64 ATCTCATATTATTCATAACATCCTCCGGTAAATCGGAAATTTGATCTGTTGCACTCAGAGAAGCC
6643 GGGTCTAATCTCACGTTGTT
129 GGGTCTAATCTCACGTTGTT
*
6663 ATTCATAACATCCTCCGGCAACTCGAAAATTCGATCTGTTGCACTCG-G-TGAAGCAGGGTATAA
1 ATTCATAACATCCTCCGGCAACTCGAAAATTCGATCTGTTGCACTCGAGATCAA-CAGGGTATAA
*
6726 TCTCATGTTATTATTCATAACATCCT-CGGTCAACTCGGAAATTTGATCTGTTGCACTCAGAGAA
65 TCTCA---TATTATTCATAACATCCTCCGGT-AAATCGGAAATTTGATCTGTTGCACTCAGAGAA
6790 GC
126 GC
6792 ATCAGCAGGG
Statistics
Matches: 116, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
146 3 0.03
147 13 0.11
148 1 0.01
149 4 0.03
150 95 0.82
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (148 bp):
ATTCATAACATCCTCCGGCAACTCGAAAATTCGATCTGTTGCACTCGAGATCAACAGGGTATAAT
CTCATATTATTCATAACATCCTCCGGTAAATCGGAAATTTGATCTGTTGCACTCAGAGAAGCCGG
GTCTAATCTCACGTTGTT
Found at i:15103 original size:20 final size:20
Alignment explanation
Indices: 15065--15103 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
15055 AGTTTCTAAG
**
15065 AGAAGAAAGAGGTGAGAAGT
1 AGAAGAAAGAGAAGAGAAGT
*
15085 AGAAGAAAGAGAAGGGAAG
1 AGAAGAAAGAGAAGAGAAG
15104 CAGAGGAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.41, T:0.05
Consensus pattern (20 bp):
AGAAGAAAGAGAAGAGAAGT
Found at i:19839 original size:14 final size:14
Alignment explanation
Indices: 19818--19882 Score: 59
Period size: 14 Copynumber: 5.0 Consensus size: 14
19808 GGTTTCAAGT
19818 TTTG-AGATTTTGG
1 TTTGTAGATTTTGG
19831 TTTGTAGATTTTGG
1 TTTGTAGATTTTGG
* * * *
19845 -ATGGAG-GTTTGA
1 TTTGTAGATTTTGG
19857 TTT-T-GATTTTGG
1 TTTGTAGATTTTGG
19869 TTTGTAGATTTTGG
1 TTTGTAGATTTTGG
19883 ATGGAGGTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
11 1 0.03
12 11 0.28
13 10 0.26
14 17 0.44
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (14 bp):
TTTGTAGATTTTGG
Found at i:19853 original size:21 final size:21
Alignment explanation
Indices: 19829--19893 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
19819 TTGAGATTTT
19829 GGTTTGTAGATTTTGGATGGA
1 GGTTTGTAGATTTTGGATGGA
***
19850 GG-TT-T-GATTTT-GATTTT
1 GGTTTGTAGATTTTGGATGGA
19867 GGTTTGTAGATTTTGGATGGA
1 GGTTTGTAGATTTTGGATGGA
19888 GGTTTG
1 GGTTTG
19894 ATTTTCGACA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
17 5 0.15
18 8 0.24
19 2 0.06
20 8 0.24
21 11 0.32
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.49
Consensus pattern (21 bp):
GGTTTGTAGATTTTGGATGGA
Found at i:19860 original size:18 final size:18
Alignment explanation
Indices: 19837--19898 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
19827 TTGGTTTGTA
19837 GATTTTGGATGGAGGTTT
1 GATTTTGGATGGAGGTTT
***
19855 GATTTT-GATTTTGGTTTGT
1 GATTTTGGATGGAGG-TT-T
19874 AGATTTTGGATGGAGGTTT
1 -GATTTTGGATGGAGGTTT
19893 GATTTT
1 GATTTT
19899 CGACAATAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
17 5 0.15
18 14 0.41
19 2 0.06
20 8 0.24
21 5 0.15
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (18 bp):
GATTTTGGATGGAGGTTT
Found at i:19866 original size:38 final size:38
Alignment explanation
Indices: 19823--19898 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
19813 CAAGTTTTGA
19823 GATTTTGGTTTGTAGATTTTGGATGGAGGTTTGATTTT
1 GATTTTGGTTTGTAGATTTTGGATGGAGGTTTGATTTT
19861 GATTTTGGTTTGTAGATTTTGGATGGAGGTTTGATTTT
1 GATTTTGGTTTGTAGATTTTGGATGGAGGTTTGATTTT
19899 CGACAATAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.53
Consensus pattern (38 bp):
GATTTTGGTTTGTAGATTTTGGATGGAGGTTTGATTTT
Found at i:20112 original size:20 final size:20
Alignment explanation
Indices: 20074--20112 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20064 AGTTTCTAAG
**
20074 AGAAGAAAGAGGTGAGAAGT
1 AGAAGAAAGAGAAGAGAAGT
*
20094 AGAAGAAAGAGAAGGGAAG
1 AGAAGAAAGAGAAGAGAAG
20113 CAGAGGAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.41, T:0.05
Consensus pattern (20 bp):
AGAAGAAAGAGAAGAGAAGT
Found at i:21164 original size:15 final size:15
Alignment explanation
Indices: 21144--21173 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21134 AAAACCACTG
21144 ATCGTGATGAAGAGT
1 ATCGTGATGAAGAGT
*
21159 ATCGTGATGGAGAGT
1 ATCGTGATGAAGAGT
21174 GAATTTCGAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.37, T:0.27
Consensus pattern (15 bp):
ATCGTGATGAAGAGT
Found at i:24408 original size:10 final size:10
Alignment explanation
Indices: 24393--24428 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
24383 ATCATAAATA
24393 AAATTAATTG
1 AAATTAATTG
24403 AAATTAATTG
1 AAATTAATTG
*
24413 AAATTGATTG
1 AAATTAATTG
24423 AAATTA
1 AAATTA
24429 CCTCTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (10 bp):
AAATTAATTG
Found at i:30306 original size:21 final size:21
Alignment explanation
Indices: 30282--30323 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
30272 TATGAAAAAA
30282 CTTTCAATCAAAATCAAACCC
1 CTTTCAATCAAAATCAAACCC
30303 CTTTCAATCAAAATCAAACCC
1 CTTTCAATCAAAATCAAACCC
30324 TTTTTGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.24
Consensus pattern (21 bp):
CTTTCAATCAAAATCAAACCC
Found at i:32819 original size:120 final size:120
Alignment explanation
Indices: 32606--32846 Score: 394
Period size: 120 Copynumber: 2.0 Consensus size: 120
32596 GACATTCAAT
* ** *
32606 AGGTTCAATATTGGGTTTCCGCTCTGTAACGCATTGAGAAATTTTAGTAAAGAAGGATTCTGAAG
1 AGGTTCAATATTGGGTTTCCGCTCTGCAAAACATAGAGAAATTTTAGTAAAGAAGGATTCTGAAG
*
32671 AAAGTTTCAATTGATAAAGGAAAAAAAATGCTACTGAGAATAAAGATGACTTGCC
66 AAAGTTTCAATTGATAAAGGAAAAAAAATGCTACTAAGAATAAAGATGACTTGCC
* *
32726 AGGTTCAATCTTGGGTTTCCGCTCTGCAAAACATAGAGAAATTTTAGTAAGGAAGGATTCTGAAG
1 AGGTTCAATATTGGGTTTCCGCTCTGCAAAACATAGAGAAATTTTAGTAAAGAAGGATTCTGAAG
*
32791 AAAGTTTCAATTGATAAAAGG-GAAAAAATGCTACTAAGAATAAAGATGACTTGCC
66 AAAGTTTCAATTGAT-AAAGGAAAAAAAATGCTACTAAGAATAAAGATGACTTGCC
32846 A
1 A
32847 TTCTCAGAGT
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
120 107 0.96
121 5 0.04
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.27
Consensus pattern (120 bp):
AGGTTCAATATTGGGTTTCCGCTCTGCAAAACATAGAGAAATTTTAGTAAAGAAGGATTCTGAAG
AAAGTTTCAATTGATAAAGGAAAAAAAATGCTACTAAGAATAAAGATGACTTGCC
Found at i:33020 original size:142 final size:140
Alignment explanation
Indices: 32726--32992 Score: 417
Period size: 142 Copynumber: 1.9 Consensus size: 140
32716 ATGACTTGCC
* *
32726 AGGTTCAATCTTGGGTTTCCGCTCTGCAAAACATAGAGAAATTTTAGTAAGGAAGGATTCTGAAG
1 AGGTT-AATCTTGGGTTTCCGCTCTGCAAAACATAGAGAAATTATAGTAAGGAAGGATTCTGAAA
* *
32791 AAAGTTTCAATTGATAAAAGGGAAAAAATGCTACTAAGAATAAAGATGACTTGCCATTCTCAGAG
65 AAAGTTTCAATTGATAAAAGGAAAAAAATGCTACTAAGAATAAAGATGACTTGCCAGTCTCAGAG
32856 TGATATGACAT
130 TGATATGACAT
*
32867 AGGTTCAATCTTGGGTTTCCGCTCTGCAAAACATTGGAGAAATTATAGTAAGGAAGGATTCTGAA
1 AGGTT-AATCTTGGGTTTCCGCTCTGCAAAACA-TAGAGAAATTATAGTAAGGAAGGATTCTGAA
*
32932 AAAAGTTTCAATTGATAAAAGGAAAAAAATGCAACTAATTAAGAATAAAGATGACTTGCCA
64 AAAAGTTTCAATTGATAAAAGGAAAAAAATG---CT-ACTAAGAATAAAGATGACTTGCCA
32993 AGGTCCATTT
Statistics
Matches: 116, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
141 33 0.28
142 58 0.50
145 2 0.02
146 23 0.20
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (140 bp):
AGGTTAATCTTGGGTTTCCGCTCTGCAAAACATAGAGAAATTATAGTAAGGAAGGATTCTGAAAA
AAGTTTCAATTGATAAAAGGAAAAAAATGCTACTAAGAATAAAGATGACTTGCCAGTCTCAGAGT
GATATGACAT
Found at i:33167 original size:19 final size:20
Alignment explanation
Indices: 33125--33168 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
33115 GAAACCTTAA
33125 AAAGATTGACAAATAAAGTT
1 AAAGATTGACAAATAAAGTT
33145 -AAGATTGACAAATAAA-TT
1 AAAGATTGACAAATAAAGTT
33163 AAAGAT
1 AAAGAT
33169 ATTGCTACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 2 0.09
19 21 0.91
ACGTcount: A:0.57, C:0.05, G:0.14, T:0.25
Consensus pattern (20 bp):
AAAGATTGACAAATAAAGTT
Found at i:34559 original size:15 final size:15
Alignment explanation
Indices: 34541--34572 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
34531 GCACCGTATA
34541 TATCCTTTTATCATG
1 TATCCTTTTATCATG
34556 TATCCTTTTATCATG
1 TATCCTTTTATCATG
34571 TA
1 TA
34573 GACTAGCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.53
Consensus pattern (15 bp):
TATCCTTTTATCATG
Found at i:35766 original size:18 final size:18
Alignment explanation
Indices: 35743--35786 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
35733 AAAGAGTAAC
*
35743 ACTTTCCTGGGAAAGTTA
1 ACTTTCCCGGGAAAGTTA
35761 ACTTTCCCGGGAAAGTTA
1 ACTTTCCCGGGAAAGTTA
35779 ACTTTCCC
1 ACTTTCCC
35787 ACCTAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (18 bp):
ACTTTCCCGGGAAAGTTA
Found at i:40260 original size:31 final size:31
Alignment explanation
Indices: 40220--40284 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
40210 TTAGAAATAC
* * ** *
40220 GTTAGATAAGGATATAATAGGTATTTTAAAA
1 GTTAAATAAGGATACAATAGACATTTCAAAA
*
40251 GTTAAATAAGGGTACAATAGACATTTCAAAA
1 GTTAAATAAGGATACAATAGACATTTCAAAA
40282 GTT
1 GTT
40285 TCTCAAAACT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (31 bp):
GTTAAATAAGGATACAATAGACATTTCAAAA
Found at i:40994 original size:23 final size:23
Alignment explanation
Indices: 40963--41009 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
40953 AAATTCTAAT
* *
40963 TTTGTTGAATATAACTCAATTGA
1 TTTGGTGAATATAACTCAACTGA
40986 TTTGGTGAATATAACTCAACTGA
1 TTTGGTGAATATAACTCAACTGA
41009 T
1 T
41010 ATTTGTGGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (23 bp):
TTTGGTGAATATAACTCAACTGA
Found at i:44937 original size:325 final size:320
Alignment explanation
Indices: 43500--46168 Score: 2784
Period size: 325 Copynumber: 8.2 Consensus size: 320
43490 CAACTTTCTG
* * * *
43500 CCACAATACTCAG-AAAAATATATAATTCAACGTCAAAAAAATTGAAGAGTTTTTCACGCTTCTA
1 CCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAAATTGACGGGTTTTTCACGCTTCTA
* * * * *
43564 ATATCGTTTTTCC-ATTTTTTCGGAATTTATTTCTAATTAAATCGAAACAAGACTCAGATGCTCA
66 ATATCGTTTTTCCTTTTTTTTC-GAATTAAATTCTAATTAAATCGAAACAAGATTCAGATGCTCG
* * *
43628 TAAAAAGAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATACTTCAAGGA
130 TAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATA-TTTAAGGA
* *
43693 GTC-TTACTACAAAAAATCATGCAAAACTGA-GCTGAGGCACC-GAAACACGTTTTTAGTCCAAA
194 GTCTTTA-TGCCAAAAATCATGCAAAACTGAGGC-GAGGC-CCTGAAACACGTTTTTAG-CCAAA
* * * * * *
43755 ACCCGTGA----T--TACACAATTTCGGCTAAAAACTTATCCGAAAATTTTTTTTCTGAA-CTTT
255 AACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCG-AAATGTTTTTTCTGAATTTTT
*
43813 TG
319 TT
* * * * * * * * * *
43815 CCAAAATACTTAGAAAAAGTATACAATTCAACGCCAAAAAGATTTACGGGCTTTTCATGTTTCTA
1 CCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAAATTGACGGGTTTTTCACGCTTCTA
* * * * *
43880 ATATCGTTTTTCCTTTTTTTACTAATTAAA-TC----GAAA-C--AATAAGATTCAGATACTCGT
66 ATATCGTTTTTCCTTTTTTTTCGAATTAAATTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
* * * *
43937 AAAAAGAAATCCTTAAATCTAATGTTGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAG
131 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTT-AAGGAG
*** * * ** * * * *
44002 TCTTTATATGAAAAACCATGCAAAACGGAGTTGAGCCCCCGAAACGCGTTTTTAGCCAAAAACCA
195 TCTTTATGCCAAAAATCATGCAAAACTGAGGCGAGGCCCTGAAACACGTTTTTAGCCAAAAACCG
* *
44067 TGATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGAAAATGTTTTTTGCTGAATTTTCTG
260 TGATGGTTAGTACACGA-TTTCGGCTAAAAACTGACCCG-AAATGTTTTTT-CTGAATTTTTTT
* * * * *
44131 CCACAATACTCAGAAAAAATATATAATTCAACGCTAAAAAAGTTGATGGGCTTTTCACGCTTCTA
1 CCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAAATTGACGGGTTTTTCACGCTTCTA
** * *
44196 ATATCGTTTTTCCAATTTTTTCTGAATTAATTTCTGATTAAATCGAAACAAGATT-AGATGCTCG
66 ATATCGTTTTTCCTTTTTTTTC-GAATTAAATTCTAATTAAATCGAAACAAGATTCAGATGCTCG
* * * *
44260 TAAAAACAAATCCTTATATCCAATATGGCTGAGAATTT-GTTCGATGAATATAAATATTTCAAGG
130 TAAAAACAAATCCTTAAATCCAATGTGGCTGAG-ATTTGGTTAGATGAATATAGATATTT-AAGG
** * * * *
44324 AGTCTTTGCGCCAAAAATCATGTAAAATTGAGCCCG-GGCTCTGAAACACGTTTTTAGCCAAAAA
193 AGTCTTTATGCCAAAAATCATGCAAAACTGAG-GCGAGGCCCTGAAACACGTTTTTAGCCAAAAA
* * * *
44388 CGGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAACAACTGACCTGAAATATTTTTTCCT
257 CCGTGATGGTTAGTACACGATTTCGGCT---A------AA-AACTGACCCGAAATGTTTTTT-CT
* *
44453 CAATTTTTTG
311 GAATTTTTTT
*
44463 CCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAATAA-TGAAGGGTTTTTCACGCTTCT
1 CCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAA-AATTGACGGGTTTTTCACGCTTCT
* * * * *
44527 AATATCATTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGACTCAAATGCTC
65 AATATCGTTTTTCC-TTTTTTTTCGAATTAAATTCTAATTAAATCGAAACAAGATTCAGATGCTC
* * *
44592 GTAAAAACAAATCATTAAATCCAATGTGGCTGAGATTTGGTTAGATAAATATAGACACTTTAAGG
129 GTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATA-TTTAAGG
* * *
44657 AGACTTTTTG-CAAAAATCATGCAAAACTAAGGCGAGGCCCTGAAACACGTTTTTAGCCCAAAAA
193 AGTCTTTATGCCAAAAATCATGCAAAACTGAGGCGAGGCCCTGAAACACGTTTTTAG-CCAAAAA
* * * * *
44721 CCGTGATTGTTACTACACGATTTCTGCTAGAAACTTACCCGAAATGTTTGTTT-TGAATTTTTTT
257 CCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAATGTTT-TTTCTGAATTTTTTT
* * * * * *
44785 CTACAATACTCAGAAAAACTATATAATTTAACGCCGAAAAGATTGACGGGCTTTTTCACGCTTCT
1 CCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAAATTGACGGG-TTTTTCACGCTTCT
* *
44850 AATATCGTTTTTCCTTTTTTTTTTACGAATTAAATTCTAATTAAATCGTAACAAGATTCAAGATA
65 AATATCGTTTTTCC--TTTTTTTT-CGAATTAAATTCTAATTAAATCGAAACAAGATTC-AGATG
* * *
44915 CTCGTAAAAA-GAATCCTTAAATCCAATGTTGCTAAGATTTGGTTAGATGAATATAGATATTTCA
126 CTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTT-A
* * * * * * * *
44979 AGGACTCTTTATGCCAAAAACCATGCAAAACGGAGTCGAAGCCCCGAAACTCGTGTTTAGCCAAA
190 AGGAGTCTTTATGCCAAAAATCATGCAAAACTGAGGCGAGGCCCTGAAACACGTTTTTAGCCAAA
* *
45044 AATCGTGATGGTTAGTACGCGATTTCGGCTAAAAACTGACCCGAAAATGTTTTTTGCTGAATTTT
255 AACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCG-AAATGTTTTTT-CTGAATTTT
*
45109 TTG
318 TTT
* * *
45112 CCACAATACTCA-AAAAATATATTTAAATCAATGCCAAAAAAATTGACGGGTTTTTTACGCTTCT
1 CCACAATACTCAGAAAAA-ATATATAATTCAATGCCAAAAAAATTGACGGGTTTTTCACGCTTCT
* ** * *
45176 AATATTGTTTTTCCAATTTTTTCTGAATTAATTTCTAATTAAATCGAAATAAGATTCAGATGCTC
65 AATATCGTTTTTCCTTTTTTTTC-GAATTAAATTCTAATTAAATCGAAACAAGATTCAGATGCTC
* * * * * *
45241 GTAAAAACAAATCCTTATATTCAATGTGGCTGATATTTTGTTCA-ATGAATATAAATATTCCAAG
129 GTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTT-AGATGAATATAGATATT-TAAG
** * * * *
45305 GAGTCTTTGCGTCAAAAATCATGTAAAATTGA-GC-ATGGGCTCTGAAACACGTTTTTAGCCAAA
192 GAGTCTTTATGCCAAAAATCATGCAAAACTGAGGCGA--GGCCCTGAAACACGTTTTTAGCCAAA
** * * *
45368 AATTGTGATGGTTAGTACACGATTTCGACTAAATTTTTGCAAAAACTGACCTGAAATATTTTTTC
255 AACCGTGATGGTTAGTACACGATTTCGGC--------T--AAAAACTGACCCGAAATGTTTTTT-
*
45433 CTCAATTTTTTT
309 CTGAATTTTTTT
* * * *
45445 CCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAATAGTGAAGGGGTTTTTCACGCTTTT
1 CCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAAATTG-ACGGGTTTTTCACGCTTCT
* * *
45510 AATATCGTTTTTCCATTTTTTCCGAATT-AATTCTAATTAAATCGAAACAAGACTCAGATGCTCG
65 AATATCGTTTTTCCTTTTTTTTCGAATTAAATTCTAATTAAATCGAAACAAGATTCAGATGCTCG
* * * *
45574 TAAAAACAAATCCTTAAATCCAATGTGGTTGAGATTTCGTTAGATGAATATAGACACTTCAAGGA
130 TAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATA-TTTAAGGA
* * * *
45639 GTCTTTCTG-CAAAAATCATGCAAAACTAAGGCGAGGCCCCGAAACACGTTTTTAGCCCAAAACT
194 GTCTTTATGCCAAAAATCATGCAAAACTGAGGCGAGGCCCTGAAACACGTTTTTAGCCAAAAAC-
* * *
45703 CGTGATTGTTAGTACACGATTTCTGCTAAAAACTTACCCGAAAT-TTTTTTCTTTGAATTTTTTT
258 CGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAATGTTTTTTC--TGAA-TTTTTT
45767 T
320 T
* * *
45768 CTACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGACAGGTTTTTCACGCTTCTA
1 CCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAAATTGACGGGTTTTTCACGCTTCTA
* * * *
45833 ATATCGTTATTCTTTTTTTTTTACGAATTAAATTCTAATTAAATCGAAAAAAGATTCAGATACTC
66 ATATCGTTTTTC-CTTTTTTTT-CGAATTAAATTCTAATTAAATCGAAACAAGATTCAGATGCTC
* * * * * * *
45898 GTAAAAAGAAATCCTTAAATCTAATGTTAG-TAAGATTTGATTATATGAATATAGATAATTCAAG
129 GTAAAAACAAATCCTTAAATCCAATG-TGGCTGAGATTTGGTTAGATGAATATAGAT-ATTTAAG
* * * * * *
45962 TAGTCTTTATGCCAAAAACCATGCAAAACGGAGTCGAAG-CCTCGAAACGCGTTTTTAGCCAAAA
192 GAGTCTTTATGCCAAAAATCATGCAAAACTGAGGCGAGGCCCT-GAAACACGTTTTTAGCCAAAA
*
46026 ACCGTGATTGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAATGTTTTTTGCTGAATTTTT
256 ACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCG-AAATGTTTTTT-CTGAATTTTT
46091 TT
319 TT
* * *
46093 CCACAATACTCAGAATATATATATAAATCAACT-CCAAAAAAATTGACGGGTTTTTCACGCTTCT
1 CCACAATACTCAGAAAAAATATATAATTCAA-TGCCAAAAAAATTGACGGGTTTTTCACGCTTCT
46157 AATATCGTTTTT
65 AATATCGTTTTT
46169 AGTCAAAAAC
Statistics
Matches: 1968, Mismatches: 294, Indels: 174
0.81 0.12 0.07
Matches are distributed among these distances:
307 15 0.01
308 112 0.06
309 3 0.00
310 1 0.00
311 4 0.00
313 6 0.00
314 30 0.02
315 18 0.01
316 136 0.07
317 12 0.01
318 2 0.00
320 1 0.00
321 7 0.00
322 100 0.05
323 122 0.06
324 295 0.15
325 349 0.18
326 146 0.07
327 52 0.03
328 1 0.00
330 1 0.00
331 45 0.02
332 282 0.14
333 172 0.09
334 56 0.03
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (320 bp):
CCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAAATTGACGGGTTTTTCACGCTTCTA
ATATCGTTTTTCCTTTTTTTTCGAATTAAATTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTAAGGAGT
CTTTATGCCAAAAATCATGCAAAACTGAGGCGAGGCCCTGAAACACGTTTTTAGCCAAAAACCGT
GATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAATGTTTTTTCTGAATTTTTTT
Found at i:45307 original size:982 final size:977
Alignment explanation
Indices: 43438--46168 Score: 4104
Period size: 981 Copynumber: 2.8 Consensus size: 977
43428 TCTAGAACGC
* * *
43438 GTACACGATTTCGGCTAAAATTTTGCAAAAACTTATCC-GAAA-ATTTTTTCCTCAACTTTCTGC
1 GTACACGATTTCGGCTAAAATTTTGCAAAAACTGA-CCTGAAATATTTTTTCCTCAATTTTTTGC
* * *
43501 CACAATACTCAG-AAAAATATATAATTCAACGTCAAAAA-AATTGAAGAGTTTTTCACGCTTCTA
65 CACAATACTCAGAAAAAATATATAATTCAATGCCAAAAATAA-TGAAGGGTTTTTCACGCTTCTA
* * *
43564 ATATCGTTTTTCCATTTTTTCGGAATTTATTTCTAATTAAATCGAAACAAGACTCAGATGCTCAT
129 ATATCGTTTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGACTCAGATGCTCGT
* * *
43629 AAAAAGAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATACTTCAAGGAG
194 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGACACTTCAAGGAG
* * * * *
43694 TCTTACTACAAAAAATCATGCAAAACTGA-GCTGAGGCACCGAAACACGTTTTTAGTCCAAAACC
259 TCTTTCTGC-AAAAATCATGCAAAACTAAGGC-GAGGC-CCGAAACACGTTTTTAGCCCAAAAAC
* * * *
43758 CGTGA---TTAC-ACA--ATTTCGGCTAAAAACTTATCCGAAAATTTTTTTTCTGAA-CTTTTGC
321 CGTGATTGTTACTACACGATTTCTGCTAAAAACTTACCCG-AAATTTTTTTT-TGAATTTTTTTC
* * * * * * * *
43816 CAAAATACTTAGAAAAAGTATACAATTCAACGCCAAAAAGATTTACGGGC-TTTTCATGTTTCTA
384 TACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTTCACGCTTCTA
* * *
43880 ATATCGTTTTTCC---TTTTTTTACTAATTAAA-TC----GAAA-C-AATAAGATTCAGATACTC
449 ATATCGTTTTTCCTTTTTTTTTTACGAATTAAATTCTAATTAAATCGAAAAAGATTCAGATACTC
43935 GTAAAAAGAAATCCTTAAATCTAATGTTGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGG
514 GTAAAAAGAAATCCTTAAATCTAATGTTGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGG
*** *
44000 AGTCTTTATATGAAAAACCATGCAAAACGGAGTTG-AGCCCCCGAAACGCGTTTTTAGCCAAAAA
579 AGTCTTTATGCCAAAAACCATGCAAAACGGAGTCGAAG-CCCCGAAACGCGTTTTTAGCCAAAAA
* *
44064 CCATGATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGAAAATGTTTTTTGCTGAATTTTC
643 CCGTGATGGTTAGTACACGA-TTTCGGCTAAAAACTGACCCGAAAATGTTTTTTGCTGAATTTTT
* * * * * *
44129 TGCCACAATACTCAGAAAAA-ATATATAATTCAACGCTAAAAAAGTTGATGGGCTTTTCACGCTT
707 TGCCACAATACTCA-AAAAATATATATAAATCAATGCCAAAAAAATTGACGGGTTTTTCACGCTT
*
44193 CTAATATCGTTTTTCCAATTTTTTCTGAATTAATTTCTGATTAAATCGAAACAAGATTAGATGCT
771 CTAATATCGTTTTTCCAATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTAGATGCT
* *
44258 CGTAAAAACAAATCCTTATATCCAATATGGCTGAGAATTTGTTCGATGAATATAAATATTTCAAG
836 CGTAAAAACAAATCCTTATATCCAATATGGCTGAGAATTTGTTCAATGAATATAAATATTCCAAG
*
44323 GAGTCTTTGCGCCAAAAATCATGTAAAATTGAGCCCGGGCTCTGAAACACGTTTTTAGCCAAAAA
901 GAGTCTTTGCGCCAAAAATCATGTAAAATTGAGCACGGGCTCTGAAACACGTTTTTAGCCAAAAA
44388 CGGTGATGGTTA
966 CGGTGATGGTTA
* *
44400 GTACATGATTTCGGCTAAAATTTTGCAACAACTGACCTGAAATATTTTTTCCTCAATTTTTTGCC
1 GTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCTGAAATATTTTTTCCTCAATTTTTTGCC
44465 ACAATACTCAGAAAAAATATATAATTCAATGCCAAAAATAATGAAGGGTTTTTCACGCTTCTAAT
66 ACAATACTCAGAAAAAATATATAATTCAATGCCAAAAATAATGAAGGGTTTTTCACGCTTCTAAT
* *
44530 ATCATTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGACTCAAATGCTCGTA
131 ATCGTTTTTCCA-TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGACTCAGATGCTCGTA
* * * *
44595 AAAACAAATCATTAAATCCAATGTGGCTGAGATTTGGTTAGATAAATATAGACACTTTAAGGAGA
195 AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGACACTTCAAGGAGT
*
44660 CTTTTTGCAAAAATCATGCAAAACTAAGGCGAGGCCCTGAAACACGTTTTTAGCCCAAAAACCGT
260 CTTTCTGCAAAAATCATGCAAAACTAAGGCGAGGCCC-GAAACACGTTTTTAGCCCAAAAACCGT
* *
44725 GATTGTTACTACACGATTTCTGCTAGAAACTTACCCGAAATGTTTGTTTTGAATTTTTTTCTACA
324 GATTGTTACTACACGATTTCTGCTAAAAACTTACCCGAAAT-TTTTTTTTGAATTTTTTTCTACA
* * *
44790 ATACTCAGAAAAACTATATAATTTAACGCCGAAAAGATTGACGGGCTTTTTCACGCTTCTAATAT
388 ATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTTCACGCTTCTAATAT
*
44855 CGTTTTTCCTTTTTTTTTTACGAATTAAATTCTAATTAAATCGTAACAAGATTCAAGATACTCGT
453 CGTTTTTCCTTTTTTTTTTACGAATTAAATTCTAATTAAATCG-AAAAAGATTC-AGATACTCGT
* *
44920 AAAAAG-AATCCTTAAATCCAATGTTGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAC
516 AAAAAGAAATCCTTAAATCTAATGTTGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAG
* * *
44984 TCTTTATGCCAAAAACCATGCAAAACGGAGTCGAAGCCCCGAAACTCGTGTTTAGCCAAAAATCG
581 TCTTTATGCCAAAAACCATGCAAAACGGAGTCGAAGCCCCGAAACGCGTTTTTAGCCAAAAACCG
*
45049 TGATGGTTAGTACGCGATTTCGGCTAAAAACTGACCCGAAAATGTTTTTTGCTGAATTTTTTGCC
646 TGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAATGTTTTTTGCTGAATTTTTTGCC
* *
45114 ACAATACTCAAAAAATATATTTAAATCAATGCCAAAAAAATTGACGGGTTTTTTACGCTTCTAAT
711 ACAATACTCAAAAAATATATATAAATCAATGCCAAAAAAATTGACGGGTTTTTCACGCTTCTAAT
* *
45179 ATTGTTTTTCCAATTTTTTCTGAATTAATTTCTAATTAAATCGAAATAAGATTCAGATGCTCGTA
776 ATCGTTTTTCCAATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATT-AGATGCTCGTA
* * * *
45244 AAAACAAATCCTTATATTCAATGTGGCTGATATTTTGTTCAATGAATATAAATATTCCAAGGAGT
840 AAAACAAATCCTTATATCCAATATGGCTGAGAATTTGTTCAATGAATATAAATATTCCAAGGAGT
* * **
45309 CTTTGCGTCAAAAATCATGTAAAATTGAGCATGGGCTCTGAAACACGTTTTTAGCCAAAAATTGT
905 CTTTGCGCCAAAAATCATGTAAAATTGAGCACGGGCTCTGAAACACGTTTTTAGCCAAAAACGGT
45374 GATGGTTA
970 GATGGTTA
* * *
45382 GTACACGATTTCGACTAAATTTTTGCAAAAACTGACCTGAAATATTTTTTCCTCAATTTTTTTCC
1 GTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCTGAAATATTTTTTCCTCAATTTTTTGCC
* *
45447 ACAATACTCAGAAAAAATATATAATTCAATGCCAAAAATAGTGAAGGGGTTTTTCACGCTTTTAA
66 ACAATACTCAGAAAAAATATATAATTCAATGCCAAAAATAATGAA-GGGTTTTTCACGCTTCTAA
45512 TATCGTTTTTCCATTTTTTCCGAATTAA-TTCTAATTAAATCGAAACAAGACTCAGATGCTCGTA
130 TATCGTTTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGACTCAGATGCTCGTA
* *
45576 AAAACAAATCCTTAAATCCAATGTGGTTGAGATTTCGTTAGATGAATATAGACACTTCAAGGAGT
195 AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGACACTTCAAGGAGT
45641 CTTTCTGCAAAAATCATGCAAAACTAAGGCGAGGCCCCGAAACACGTTTTTAGCCC-AAAACTCG
260 CTTTCTGCAAAAATCATGCAAAACTAAGGCGAGG-CCCGAAACACGTTTTTAGCCCAAAAAC-CG
*
45705 TGATTGTTAGTACACGATTTCTGCTAAAAACTTACCCGAAATTTTTTTCTTTGAATTTTTTTTCT
323 TGATTGTTACTACACGATTTCTGCTAAAAACTTACCCGAAA-TTTTTT-TTTGAA-TTTTTTTCT
* *
45770 ACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGACAGG-TTTTTCACGCTTCTAA
385 ACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTTCACGCTTCTAA
*
45834 TATCGTTATT-CTTTTTTTTTTACGAATTAAATTCTAATTAAATCGAAAAAAGATTCAGATACTC
450 TATCGTTTTTCCTTTTTTTTTTACGAATTAAATTCTAATTAAATCG-AAAAAGATTCAGATACTC
* * *
45898 GTAAAAAGAAATCCTTAAATCTAATGTTAG-TAAGATTTGATTATATGAATATAGATAATTCAAG
514 GTAAAAAGAAATCCTTAAATCTAATGTT-GCTAAGATTTGGTTAGATGAATATAGATATTTCAAG
* *
45962 TAGTCTTTATGCCAAAAACCATGCAAAACGGAGTCGAAGCCTCGAAACGCGTTTTTAGCCAAAAA
578 GAGTCTTTATGCCAAAAACCATGCAAAACGGAGTCGAAGCCCCGAAACGCGTTTTTAGCCAAAAA
*
46027 CCGTGATTGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAATGTTTTTTGCTGAATTTTTT
643 CCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAATGTTTTTTGCTGAATTTTTT
* * *
46092 TCCACAATACTCAGAATATATATATAAATCAACT-CCAAAAAAATTGACGGGTTTTTCACGCTTC
708 GCCACAATACTCAAAAAATATATATAAATCAA-TGCCAAAAAAATTGACGGGTTTTTCACGCTTC
46156 TAATATCGTTTTT
772 TAATATCGTTTTT
46169 AGTCAAAAAC
Statistics
Matches: 1605, Mismatches: 124, Indels: 61
0.90 0.07 0.03
Matches are distributed among these distances:
961 2 0.00
962 36 0.02
963 33 0.02
964 108 0.07
965 115 0.07
967 4 0.00
968 3 0.00
969 8 0.00
970 72 0.04
971 25 0.02
974 16 0.01
975 2 0.00
979 3 0.00
980 27 0.02
981 622 0.39
982 429 0.27
983 100 0.06
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Consensus pattern (977 bp):
GTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCTGAAATATTTTTTCCTCAATTTTTTGCC
ACAATACTCAGAAAAAATATATAATTCAATGCCAAAAATAATGAAGGGTTTTTCACGCTTCTAAT
ATCGTTTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGACTCAGATGCTCGTAA
AAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGACACTTCAAGGAGTC
TTTCTGCAAAAATCATGCAAAACTAAGGCGAGGCCCGAAACACGTTTTTAGCCCAAAAACCGTGA
TTGTTACTACACGATTTCTGCTAAAAACTTACCCGAAATTTTTTTTTGAATTTTTTTCTACAATA
CTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTTCACGCTTCTAATATCGT
TTTTCCTTTTTTTTTTACGAATTAAATTCTAATTAAATCGAAAAAGATTCAGATACTCGTAAAAA
GAAATCCTTAAATCTAATGTTGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTT
ATGCCAAAAACCATGCAAAACGGAGTCGAAGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATG
GTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAATGTTTTTTGCTGAATTTTTTGCCACAAT
ACTCAAAAAATATATATAAATCAATGCCAAAAAAATTGACGGGTTTTTCACGCTTCTAATATCGT
TTTTCCAATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTAGATGCTCGTAAAAACA
AATCCTTATATCCAATATGGCTGAGAATTTGTTCAATGAATATAAATATTCCAAGGAGTCTTTGC
GCCAAAAATCATGTAAAATTGAGCACGGGCTCTGAAACACGTTTTTAGCCAAAAACGGTGATGGT
TA
Found at i:46298 original size:149 final size:151
Alignment explanation
Indices: 46011--46316 Score: 388
Period size: 149 Copynumber: 2.0 Consensus size: 151
46001 CCTCGAAACG
* * * * *
46011 CGTTTTTAGCCAAAAACCGTGATTGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAATGTT
1 CGTTTTTAGCCAAAAACAGTGATTGTAAGTACACGATTTCGGCTAAAAACTGACACGAAAATATA
* * * * *
46076 TTTTGCTGAATTTTTTTCCACAATACTCAGAATATATATATAAATCAACTCCAAAAAAATTGACG
66 TTTTGCTCAATTTTTTACCACAATACTCAAAAAATATATATAAATCAACTCCAAAAAAATTGAAG
46141 GGTTTTTCACGCTTCTAATAT
131 GGTTTTTCACGCTTCTAATAT
* * * *
46162 CGTTTTTAGTCAAAAACAGTGA-TGTAACGTATACGATTTCGGCTAAGAACTTACACGAAAA-AT
1 CGTTTTTAGCCAAAAACAGTGATTGTAA-GTACACGATTTCGGCTAAAAACTGACACGAAAATAT
* * *
46225 ATTTT-CTCAATTTTTTACTACAATACTCATAAAAAT-TATATAATTCAA-TGCCAAAAATATTG
65 ATTTTGCTCAATTTTTTACCACAATACTCA-AAAAATATATATAAATCAACT-CCAAAAAAATTG
*
46287 AAGGGTTTTTCATGCTTCTAATAT
128 AAGGGTTTTTCACGCTTCTAATAT
46311 CGTTTT
1 CGTTTT
46317 CCTATTTATT
Statistics
Matches: 134, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
148 1 0.01
149 71 0.53
150 13 0.10
151 49 0.37
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (151 bp):
CGTTTTTAGCCAAAAACAGTGATTGTAAGTACACGATTTCGGCTAAAAACTGACACGAAAATATA
TTTTGCTCAATTTTTTACCACAATACTCAAAAAATATATATAAATCAACTCCAAAAAAATTGAAG
GGTTTTTCACGCTTCTAATAT
Found at i:48501 original size:166 final size:165
Alignment explanation
Indices: 48199--48602 Score: 553
Period size: 166 Copynumber: 2.4 Consensus size: 165
48189 ATTTTGTTTT
* * * * * *
48199 CAGATTACTTAAATATCTTAACCTTTAATTCTTGA-GGGATTAAATAACTAGACTTTTTGGTTAT
1 CAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTA-ACTTTTTAGTCAT
* * * * * * *
48263 TTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAAGATCCCTACCAACGCTTGCTTCTGGAG
65 TTCTCAATGGACTTGAATAGAGTAGTGGAATTAATAAAGATCCCCACCAACGATTGATGCTGGAG
* * *
48328 TTAGAGAACTTAT-TTTTTCCGTCTTTTCCTACTTGA
130 CTAGAGAACTAATCTTTTT-CGTCTTTACCTACTTGA
* *
48364 CAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAAGTAATTTTTTTAGTCAT
1 CAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAA-CTTTTTAGTCAT
* * *
48429 TTCTCAATGGACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCATCAAGGATTGATGGT-GA
65 TTCTCAATGGACTTGAATAGAGTAGTGGAATTAAT-AAAGATCCCCACCAACGATTGATGCTGGA
48493 GCTAGAGAACTAATCTTTTTCGTCTTTACCTACTTGA
129 GCTAGAGAACTAATCTTTTTCGTCTTTACCTACTTGA
48530 CAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAACTTTTTAGTCAT
1 CAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACT-AACTTTTTAGTCAT
48595 TTCTCAAT
65 TTCTCAAT
48603 TGACAAATGA
Statistics
Matches: 211, Mismatches: 23, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
165 32 0.15
166 153 0.73
167 26 0.12
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (165 bp):
CAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAACTTTTTAGTCATT
TCTCAATGGACTTGAATAGAGTAGTGGAATTAATAAAGATCCCCACCAACGATTGATGCTGGAGC
TAGAGAACTAATCTTTTTCGTCTTTACCTACTTGA
Found at i:50934 original size:30 final size:29
Alignment explanation
Indices: 50867--50939 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 29
50857 GTAGTATTTG
* * *
50867 GACGTTTTGCCTCTTGAACTTTAATTTTA
1 GACGTTTTGCCCCCTGAACTTCAATTTTA
** *
50896 GATATTTTGCCCCCTGAACTCTCAATTTTC
1 GACGTTTTGCCCCCTGAACT-TCAATTTTA
50926 GACGTTTTGCCCCC
1 GACGTTTTGCCCCC
50940 CTTTCAAGGG
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 16 0.46
30 19 0.54
ACGTcount: A:0.18, C:0.27, G:0.14, T:0.41
Consensus pattern (29 bp):
GACGTTTTGCCCCCTGAACTTCAATTTTA
Found at i:50938 original size:29 final size:28
Alignment explanation
Indices: 50867--50938 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
50857 GTAGTATTTG
* *
50867 GACGTTTTGCCTCTTGAACTTTAATTTTA
1 GACGTTTTGCC-CCTGAACTTCAATTTTA
** *
50896 GATATTTTGCCCCCTGAACTCTCAATTTTC
1 GACGTTTTG-CCCCTGAACT-TCAATTTTA
50926 GACGTTTTGCCCC
1 GACGTTTTGCCCC
50939 CCTTTCAAGG
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
29 18 0.53
30 16 0.47
ACGTcount: A:0.18, C:0.26, G:0.14, T:0.42
Consensus pattern (28 bp):
GACGTTTTGCCCCTGAACTTCAATTTTA
Found at i:51184 original size:30 final size:31
Alignment explanation
Indices: 51131--51203 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 31
51121 TGAGAGGGGG
* *
51131 CAAAATGTCC-AAAGTTGAGAGTTCAGGAGC
1 CAAAATGTCCAAAAATCGAGAGTTCAGGAGC
* *
51161 CAAAATGTCCAAAAATCGA-AGTTCAGGGGG
1 CAAAATGTCCAAAAATCGAGAGTTCAGGAGC
*
51191 CAAAACGTCCAAA
1 CAAAATGTCCAAA
51204 CGCTACAAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 31 0.84
31 6 0.16
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.16
Consensus pattern (31 bp):
CAAAATGTCCAAAAATCGAGAGTTCAGGAGC
Found at i:53880 original size:45 final size:44
Alignment explanation
Indices: 53816--53909 Score: 163
Period size: 45 Copynumber: 2.1 Consensus size: 44
53806 CTGCTAGCCA
53816 AATGTTCATATCTTCTACTAATTTTTAAGAAACATGAACAAACTT
1 AATGTTCATATCTTCTACTAATTTTTAAG-AACATGAACAAACTT
*
53861 AATGTTCATATCTTCTACTAATTTTTAAGAACATGAATAAACTT
1 AATGTTCATATCTTCTACTAATTTTTAAGAACATGAACAAACTT
53905 -ATGTT
1 AATGTT
53910 ATTGTGTTGA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
43 5 0.10
44 14 0.29
45 29 0.60
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (44 bp):
AATGTTCATATCTTCTACTAATTTTTAAGAACATGAACAAACTT
Found at i:68236 original size:27 final size:28
Alignment explanation
Indices: 68205--68263 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
68195 TGGTTATTTG
68205 ACTTTTTTTAAGGGT-TTCTATTTAGTA
1 ACTTTTTTTAAGGGTATTCTATTTAGTA
***
68232 ACTTTTTTTTTTGGTAATTCTATTTAGTA
1 ACTTTTTTTAAGGGT-ATTCTATTTAGTA
68261 ACT
1 ACT
68264 AAACTATGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 12 0.44
29 15 0.56
ACGTcount: A:0.22, C:0.08, G:0.12, T:0.58
Consensus pattern (28 bp):
ACTTTTTTTAAGGGTATTCTATTTAGTA
Found at i:69056 original size:13 final size:13
Alignment explanation
Indices: 69038--69062 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
69028 TTATAAATAC
69038 TAAAGAATTGTAT
1 TAAAGAATTGTAT
69051 TAAAGAATTGTA
1 TAAAGAATTGTA
69063 ATCACACTAT
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:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (13 bp):
TAAAGAATTGTAT
Found at i:71081 original size:2 final size:2
Alignment explanation
Indices: 71069--71109 Score: 57
Period size: 2 Copynumber: 20.0 Consensus size: 2
71059 TGTATTGAAC
71069 TA TA TA T- TA TA TA TA TA TA TA TA TA TA CTA TA CTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA
71110 ATTTATGTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 1 0.03
2 31 0.86
3 4 0.11
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:72965 original size:30 final size:30
Alignment explanation
Indices: 72929--73014 Score: 172
Period size: 30 Copynumber: 2.9 Consensus size: 30
72919 ATCACATTTT
72929 TAAAAAAAAATAATTATCACAAAGCATTCC
1 TAAAAAAAAATAATTATCACAAAGCATTCC
72959 TAAAAAAAAATAATTATCACAAAGCATTCC
1 TAAAAAAAAATAATTATCACAAAGCATTCC
72989 TAAAAAAAAATAATTATCACAAAGCA
1 TAAAAAAAAATAATTATCACAAAGCA
73015 CGGGCCATAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.22
Consensus pattern (30 bp):
TAAAAAAAAATAATTATCACAAAGCATTCC
Found at i:91018 original size:112 final size:112
Alignment explanation
Indices: 90821--91046 Score: 335
Period size: 112 Copynumber: 2.0 Consensus size: 112
90811 ATTCTATATG
* * * *
90821 ATCTTTTTGAAGACTTTACTAAATCAATTAATAGTTTGCTTCAAAGACTTAAATCAAGTAATAAC
1 ATCTTTTTAAAGACATTACTAAATCAATTAATAGTTTGCTTCAAAGACTAAAACCAAGTAATAAC
* * * *
90886 ATATCCATTATAATCCAATACGGTATCAAGTGTTTACGTCATTCTAC
66 AAATCCATTATAATCCAATACGGAATCAAGTGATTAAGTCATTCTAC
* * *
90933 ATCTTTTTAAAGACATTACTAATTCTATTAATAGTTTGCTTCATAGACTAAAACCAAGTAATAAC
1 ATCTTTTTAAAGACATTACTAAATCAATTAATAGTTTGCTTCAAAGACTAAAACCAAGTAATAAC
* *
90998 AAATCCATTCTAGTCCAATACGGAATCAAGTGATTAAGTCATTCTAC
66 AAATCCATTATAATCCAATACGGAATCAAGTGATTAAGTCATTCTAC
91045 AT
1 AT
91047 TTCTACTAAA
Statistics
Matches: 101, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
112 101 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (112 bp):
ATCTTTTTAAAGACATTACTAAATCAATTAATAGTTTGCTTCAAAGACTAAAACCAAGTAATAAC
AAATCCATTATAATCCAATACGGAATCAAGTGATTAAGTCATTCTAC
Found at i:102636 original size:21 final size:21
Alignment explanation
Indices: 102610--102654 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
102600 CTTTTCTGGA
102610 TTGCTAAACACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
**
102631 TTGCTATTCACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
102652 TTG
1 TTG
102655 ACGCTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.36, G:0.11, T:0.36
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCATTT
Found at i:103066 original size:33 final size:34
Alignment explanation
Indices: 103024--103099 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 34
103014 AATTTGGTCT
**
103024 AGCCGCCCCAACCGGGGCGGCCTG-CTGTGGCGA
1 AGCCGCCCCAACCGGGGCGGCCTGCCCATGGCGA
** *
103057 AGCCGCCCC-AGTGGGGCGGCCTGCCCATGGTGA
1 AGCCGCCCCAACCGGGGCGGCCTGCCCATGGCGA
103090 AGCCGCCCCA
1 AGCCGCCCCA
103100 GTGGGGAGGC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
32 12 0.33
33 24 0.67
ACGTcount: A:0.13, C:0.41, G:0.37, T:0.09
Consensus pattern (34 bp):
AGCCGCCCCAACCGGGGCGGCCTGCCCATGGCGA
Found at i:103100 original size:33 final size:33
Alignment explanation
Indices: 103037--103139 Score: 120
Period size: 33 Copynumber: 3.1 Consensus size: 33
103027 CGCCCCAACC
* *
103037 GGGGCGGCCTG-CTGTGGCGAAGCCGCCCCAGT
1 GGGGCGGCCTGCCCGTGGTGAAGCCGCCCCAGT
*
103069 GGGGCGGCCTGCCCATGGTGAAGCCGCCCCAGT
1 GGGGCGGCCTGCCCGTGGTGAAGCCGCCCCAGT
* * *
103102 GGGGAGG-CTCCGCCGTGGCTGAACCCGCCCCAGT
1 GGGGCGGCCTGC-CCGTGG-TGAAGCCGCCCCAGT
103136 GGGG
1 GGGG
103140 AGGCTCCGCC
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
32 14 0.23
33 29 0.48
34 18 0.30
ACGTcount: A:0.11, C:0.35, G:0.43, T:0.12
Consensus pattern (33 bp):
GGGGCGGCCTGCCCGTGGTGAAGCCGCCCCAGT
Found at i:103135 original size:34 final size:34
Alignment explanation
Indices: 103050--103178 Score: 158
Period size: 33 Copynumber: 3.9 Consensus size: 34
103040 GCGGCCTGCT
* *
103050 GTGGC-GAAGCCGCCCCAGTGGGGCGGC-CTGCCC
1 GTGGCTGAAGCCGCCCCAGTGGGGAGGCTCCG-CC
*
103083 ATGG-TGAAGCCGCCCCAGTGGGGAGGCTCCGCC
1 GTGGCTGAAGCCGCCCCAGTGGGGAGGCTCCGCC
*
103116 GTGGCTGAACCCGCCCCAGTGGGGAGGCTCCGCC
1 GTGGCTGAAGCCGCCCCAGTGGGGAGGCTCCGCC
* * *
103150 GTGGCTGAA-CCGTCCTAGTGAGGAGGCTC
1 GTGGCTGAAGCCGCCCCAGTGGGGAGGCTC
103179 AGTGCAAAAA
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
33 46 0.54
34 39 0.46
ACGTcount: A:0.13, C:0.34, G:0.40, T:0.13
Consensus pattern (34 bp):
GTGGCTGAAGCCGCCCCAGTGGGGAGGCTCCGCC
Found at i:103175 original size:67 final size:66
Alignment explanation
Indices: 103050--103178 Score: 154
Period size: 67 Copynumber: 1.9 Consensus size: 66
103040 GCGGCCTGCT
* * * *
103050 GTGGCGAAGCCGCCCCAGTGGGGCGGCCTGCCCATGGTGAAGCCGCCCCAGTGGGGAGGCTCCGC
1 GTGGCGAACCCGCCCCAGTGGGGAGGCCCGCCCATGGTGAAGCCGCCCCAGTGAGGAGGCTCCGC
103115 C
66 C
* * *
103116 GTGGCTGAACCCGCCCCAGTGGGGAGGCTCCG-CCGTGGCTGAA-CCGTCCTAGTGAGGAGGCTC
1 GTGGC-GAACCCGCCCCAGTGGGGAGGC-CCGCCCATGG-TGAAGCCGCCCCAGTGAGGAGGCTC
103179 AGTGCAAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
66 5 0.09
67 42 0.79
68 6 0.11
ACGTcount: A:0.13, C:0.34, G:0.40, T:0.13
Consensus pattern (66 bp):
GTGGCGAACCCGCCCCAGTGGGGAGGCCCGCCCATGGTGAAGCCGCCCCAGTGAGGAGGCTCCGC
C
Found at i:107304 original size:2 final size:2
Alignment explanation
Indices: 107297--107321 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
107287 AATAATCATG
107297 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
107322 AAATTTAACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:108934 original size:33 final size:31
Alignment explanation
Indices: 108897--108982 Score: 111
Period size: 33 Copynumber: 2.7 Consensus size: 31
108887 TTTTTGTACT
108897 AGTAAAGGAATGTAAATAACTTTTTTTTTTTGA
1 AGTAAAGGAATGTAAATAA-TTTTTTTTTTT-A
*
108930 AGT-AAGAAATGTAAATAATTTTTTTTTTTA
1 AGTAAAGGAATGTAAATAATTTTTTTTTTTA
*
108960 GGTCAGAAGGAATGTAAATAATT
1 AGT-A-AAGGAATGTAAATAATT
108983 GACATAACCA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
30 3 0.06
31 11 0.23
32 14 0.30
33 19 0.40
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.42
Consensus pattern (31 bp):
AGTAAAGGAATGTAAATAATTTTTTTTTTTA
Found at i:109410 original size:30 final size:31
Alignment explanation
Indices: 109356--109420 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
109346 AACTTTATGT
*
109356 TTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
*
109387 TTTCCAATTGTATCCTT-TTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
109417 TTTC
1 TTTC
109421 TAAATTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.49
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTTAAAACATA
Found at i:109427 original size:31 final size:31
Alignment explanation
Indices: 109362--109427 Score: 98
Period size: 30 Copynumber: 2.1 Consensus size: 31
109352 ATGTTTTCCG
*
109362 ATTGTACCCTTATTTTTAAAACATATTTCCA
1 ATTGTACCCTTATTTTTAAAACATATTTCAA
*
109393 ATTGTATCCTT-TTTTTAAAACATATTTCTAA
1 ATTGTACCCTTATTTTTAAAACATATTTC-AA
109424 ATTG
1 ATTG
109428 CCATTACTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.32, C:0.15, G:0.05, T:0.48
Consensus pattern (31 bp):
ATTGTACCCTTATTTTTAAAACATATTTCAA
Found at i:109479 original size:18 final size:19
Alignment explanation
Indices: 109430--109482 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
109420 CTAAATTGCC
*
109430 ATTACTAAATAATGTTTTTA
1 ATTACTAAATTAT-TTTTTA
* **
109450 ATTATTCCATTATTTTTTA
1 ATTACTAAATTATTTTTTA
109469 ATTA-TAAATTATTT
1 ATTACTAAATTATTT
109483 CATTATATCA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
18 8 0.30
19 10 0.37
20 9 0.33
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.57
Consensus pattern (19 bp):
ATTACTAAATTATTTTTTA
Found at i:109544 original size:22 final size:22
Alignment explanation
Indices: 109530--109616 Score: 122
Period size: 22 Copynumber: 4.0 Consensus size: 22
109520 ATTCCATGAG
*
109530 GAGGTTACCAAAATTTCTTAGT
1 GAGGTTACCAAAATTTCATAGT
*
109552 GTGGTTACCAAAATTTCATAGT
1 GAGGTTACCAAAATTTCATAGT
*
109574 GTA-GTTACCAAAATTTCATAGA
1 G-AGGTTACCAAAATTTCATAGT
*
109596 GTGGTTACCAAAATTTCATAG
1 GAGGTTACCAAAATTTCATAG
109617 GATCAAGTTA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (22 bp):
GAGGTTACCAAAATTTCATAGT
Found at i:109582 original size:44 final size:44
Alignment explanation
Indices: 109533--109616 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
109523 CCATGAGGAG
* *
109533 GTTACCAAAATTTCTTAGTGTGGTTACCAAAATTTCATAGTGTA
1 GTTACCAAAATTTCATAGAGTGGTTACCAAAATTTCATAGTGTA
109577 GTTACCAAAATTTCATAGAGTGGTTACCAAAATTTCATAG
1 GTTACCAAAATTTCATAGAGTGGTTACCAAAATTTCATAG
109617 GATCAAGTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (44 bp):
GTTACCAAAATTTCATAGAGTGGTTACCAAAATTTCATAGTGTA
Found at i:109647 original size:46 final size:43
Alignment explanation
Indices: 109533--109663 Score: 140
Period size: 44 Copynumber: 3.0 Consensus size: 43
109523 CCATGAGGAG
109533 GTTACCAAAATTTCTTA-GTGTGGTTACCAAAATTTCATAGTGTA
1 GTTACCAAAATTTCTTAGGT-TGGTTACCAAAATTTCATAG-GTA
*
109577 GTTACCAAAATTTCATAGAG-TGGTTACCAAAATTTCATAGGATCAA
1 GTTACCAAAATTTCTTAG-GTTGGTTACCAAAATTTCATAGG-T--A
** ***
109623 GTTATTAAAATTTCTTAGGTTGGTTATTGAAATTTCATAGG
1 GTTACCAAAATTTCTTAGGTTGGTTACCAAAATTTCATAGG
109664 GTGGTTAATT
Statistics
Matches: 74, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
43 1 0.01
44 37 0.50
45 1 0.01
46 35 0.47
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (43 bp):
GTTACCAAAATTTCTTAGGTTGGTTACCAAAATTTCATAGGTA
Found at i:109655 original size:22 final size:22
Alignment explanation
Indices: 109539--109670 Score: 102
Period size: 22 Copynumber: 5.9 Consensus size: 22
109529 GGAGGTTACC
* * **
109539 AAAATTTCTTAGTGTGGTTACC
1 AAAATTTCATAGGGTGGTTATT
* * **
109561 AAAATTTCATAGTGTAGTTACC
1 AAAATTTCATAGGGTGGTTATT
* **
109583 AAAATTTCATAGAGTGGTTACC
1 AAAATTTCATAGGGTGGTTATT
* *
109605 AAAATTTCATAGGATCAAGTTATT
1 AAAATTTCATAGGGT--GGTTATT
* *
109629 AAAATTTCTTAGGTTGGTTATT
1 AAAATTTCATAGGGTGGTTATT
*
109651 GAAATTTCATAGGGTGGTTA
1 AAAATTTCATAGGGTGGTTA
109671 ATTATCACAA
Statistics
Matches: 93, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
22 76 0.82
24 17 0.18
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (22 bp):
AAAATTTCATAGGGTGGTTATT
Found at i:109759 original size:22 final size:21
Alignment explanation
Indices: 109709--109839 Score: 68
Period size: 22 Copynumber: 6.0 Consensus size: 21
109699 AAAAAGATTT
*
109709 CAAAATGTCATAGCGAGGTTATA
1 CAAAATTTCATAG-GAGGTTA-A
* *
109732 C-GAATTTCATAGTGTGGTTAA
1 CAAAATTTCATAG-GAGGTTAA
*
109753 CAAAATTTCATTAGAAGGTT-A
1 CAAAATTTCA-TAGGAGGTTAA
* * * *
109774 CTAATACTTCATCGGAAGGTTAT
1 C-AAAATTTCATAGG-AGGTTAA
* * *
109797 CAAAATTTTATAGTGTGGTTAT
1 CAAAATTTCATAG-GAGGTTAA
*
109819 CAAAATTTCATATGAAGGTTA
1 CAAAATTTCATA-GGAGGTTA
109840 TAAAAGTCTC
Statistics
Matches: 81, Mismatches: 20, Indels: 15
0.70 0.17 0.13
Matches are distributed among these distances:
21 6 0.07
22 68 0.84
23 7 0.09
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (21 bp):
CAAAATTTCATAGGAGGTTAA
Found at i:109840 original size:22 final size:22
Alignment explanation
Indices: 109734--110096 Score: 121
Period size: 22 Copynumber: 16.3 Consensus size: 22
109724 AGGTTATACG
* *
109734 AATTTCATAGTG-TGGTTAACAA
1 AATTTCATA-TGAAGGTTATCAA
109756 AATTTCAT-TAGAAGGTTA-CTAA
1 AATTTCATAT-GAAGGTTATC-AA
* * **
109778 TACTTCATCGGAAGGTTATCAA
1 AATTTCATATGAAGGTTATCAA
* *
109800 AATTTTATAGTG-TGGTTATCAA
1 AATTTCATA-TGAAGGTTATCAA
109822 AATTTCATATGAAGGTTAT-AA
1 AATTTCATATGAAGGTTATCAA
* * *
109843 AAGTCTCAATTTCAT-AAGGAGTACCAA
1 AA-TTTC-A--T-ATGAAGG-TTATCAA
*
109870 AATTTGATA-GAAGGTTATC-A
1 AATTTCATATGAAGGTTATCAA
* * *
109890 AATCTCATA-GAGTGGTTATCGA
1 AATTTCATATGA-AGGTTATCAA
* *
109912 AATTTCATAAAGATATGATTATCAA
1 AATTTCAT-ATGA-A-GGTTATCAA
*
109937 AATTT-ATATGAAGATTATCAA
1 AATTTCATATGAAGGTTATCAA
** *
109958 AATTTCATAGTG-TTGTCATCAA
1 AATTTCATA-TGAAGGTTATCAA
* *
109980 AATTTCAAAGCGAA-GTTATCAA
1 AATTTCATA-TGAAGGTTATCAA
* * *
110002 AATTACATAATG-TGATTATCAA
1 AATTTCAT-ATGAAGGTTATCAA
* * * *
110024 AATTTCCTA-GAGGGGTCAACAA
1 AATTTCATATGA-AGGTTATCAA
*
110046 AATTT--TATAAAGATGTTATCAA
1 AATTTCATATGAAG--GTTATCAA
*
110068 AATTTCATA-AAGAGGTTATCAA
1 AATTTCATATGA-AGGTTATCAA
*
110090 ATTTTCA
1 AATTTCA
110097 AAATCTGATT
Statistics
Matches: 256, Mismatches: 52, Indels: 66
0.68 0.14 0.18
Matches are distributed among these distances:
20 15 0.06
21 34 0.13
22 158 0.62
23 13 0.05
24 8 0.03
25 18 0.07
26 6 0.02
27 4 0.02
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (22 bp):
AATTTCATATGAAGGTTATCAA
Found at i:109947 original size:18 final size:19
Alignment explanation
Indices: 109924--109962 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
109914 TTTCATAAAG
109924 ATAT-GATTATCAAAATTT
1 ATATAGATTATCAAAATTT
109942 ATATGAAGATTATCAAAATTT
1 ATAT--AGATTATCAAAATTT
109963 CATAGTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
21 14 0.78
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (19 bp):
ATATAGATTATCAAAATTT
Found at i:110028 original size:66 final size:66
Alignment explanation
Indices: 109884--110096 Score: 173
Period size: 66 Copynumber: 3.2 Consensus size: 66
109874 TGATAGAAGG
* * * * * * *
109884 TTATC-AAATCTCATAGAGTGGTTATCGAAATTTCATAAAGATATGATTATCAAAATT-TAT-AT
1 TTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGA-A-G-TTATCAAAATTACATAAA
109946 GAAGA
63 G-AGA
* ** * * * *
109951 TTATCAAAATTTCATAGTGTTGTCATCAAAATTTCA-AAGCGAAGTTATCAAAATTACATAATGT
1 TTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAA-AGAAGTTATCAAAATTACATAAAGA
110015 GA
65 GA
* * * *
110017 TTATCAAAATTTCCTAGAGGGGTCAACAAAATTTTATAAAGATGTTATCAAAATTTCATAAAGAG
1 TTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAAGTTATCAAAATTACATAAAGAG
*
110082 G
66 A
*
110083 TTATCAAATTTTCA
1 TTATCAAAATTTCA
110097 AAATCTGATT
Statistics
Matches: 119, Mismatches: 22, Indels: 11
0.78 0.14 0.07
Matches are distributed among these distances:
65 11 0.09
66 68 0.57
67 13 0.11
68 27 0.23
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (66 bp):
TTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAAGTTATCAAAATTACATAAAGAG
A
Found at i:110237 original size:19 final size:19
Alignment explanation
Indices: 110202--110268 Score: 91
Period size: 19 Copynumber: 3.5 Consensus size: 19
110192 TGATGTAGTA
*
110202 ATCAAAATTTTAAGGAGGAT
1 ATCAAAA-TTCAAGGAGGAT
*
110222 ACCAAAATTCAAGGAGGAT
1 ATCAAAATTCAAGGAGGAT
110241 ATCAAAATTC-AGTGAGGAT
1 ATCAAAATTCAAG-GAGGAT
110260 ATCAAAATT
1 ATCAAAATT
110269 TCATATGAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
18 2 0.05
19 35 0.81
20 6 0.14
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.25
Consensus pattern (19 bp):
ATCAAAATTCAAGGAGGAT
Found at i:110330 original size:22 final size:22
Alignment explanation
Indices: 110259--110551 Score: 110
Period size: 22 Copynumber: 13.5 Consensus size: 22
110249 TCAGTGAGGA
* *
110259 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATAAGAGGGT
* * ***
110281 TATCATATTTTCAT-AGTTTAGT
1 TATCAAAATTTCATAAG-AGGGT
*
110303 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATAAGAGGGT
*
110325 TATCAAAATTTCAT-AGCA-TGT
1 TATCAAAATTTCATAAG-AGGGT
* * *
110346 AGATCAAAATTTCAT-AGTGAGAT
1 -TATCAAAATTTCATAAGAG-GGT
*
110369 TAACAAAATTTCATAATGA-GGT
1 TATCAAAATTTCATAA-GAGGGT
** *
110391 TATCAAAAAATCATAAG-GAGCT
1 TATCAAAATTTCATAAGAG-GGT
*
110413 TATCAAAATTT-GT---A--GT
1 TATCAAAATTTCATAAGAGGGT
* **
110429 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATAAGAGGGT
* * *
110451 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATA-AGAGGGT
* * * **
110474 TATTAAAATTTTATAGAAAGATT
1 TATCAAAATTTCATA-AGAGGGT
*
110497 TATCAAAATTTCAT-AGCGAGGT
1 TATCAAAATTTCATAAGAG-GGT
* * *
110519 TATCACAATTTCAT-AGTGTGAT
1 TATCAAAATTTCATAAGAG-GGT
110541 TATCAAAATTT
1 TATCAAAATTT
110552 TAAAGTGTGA
Statistics
Matches: 199, Mismatches: 53, Indels: 38
0.69 0.18 0.13
Matches are distributed among these distances:
16 11 0.06
17 1 0.01
20 1 0.01
21 9 0.05
22 138 0.69
23 38 0.19
24 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATAAGAGGGT
Found at i:110353 original size:44 final size:43
Alignment explanation
Indices: 110259--110466 Score: 128
Period size: 44 Copynumber: 4.9 Consensus size: 43
110249 TCAGTGAGGA
* * * * *
110259 TATCAAAATTTCATATGAAGGTTATCATATTTTCATAGTTTAG
1 TATCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTGTAG
*
110302 TTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGCATGTAG
1 -TATCAAAATTTCATAAGAGGGTTATCAAAATTTCATAG--TGTAG
* * * *
110348 -ATCAAAATTTCAT-AGTGAGATTAACAAAATTTCATAATG-AGG
1 TATCAAAATTTCATAAGAG-GGTTATCAAAATTTCATAGTGTA-G
** * *
110390 TTATCAAAAAATCATAAG-GAGCTTATCAAAATTT-GTA--GT--
1 -TATCAAAATTTCATAAGAG-GGTTATCAAAATTTCATAGTGTAG
* ** *
110429 TATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAG
1 TATCAAAATTTCATAAGAGGGTTATCAAAATTTCATAG
110467 GGAGGTTTAT
Statistics
Matches: 130, Mismatches: 23, Indels: 26
0.73 0.13 0.15
Matches are distributed among these distances:
38 26 0.20
39 2 0.02
41 2 0.02
42 3 0.02
43 5 0.04
44 86 0.66
45 2 0.02
46 4 0.03
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.37
Consensus pattern (43 bp):
TATCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTGTAG
Found at i:110481 original size:23 final size:23
Alignment explanation
Indices: 110450--110553 Score: 95
Period size: 23 Copynumber: 4.6 Consensus size: 23
110440 CATAAGAAAG
*
110450 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGAGAGGT
* * *
110473 TTATTAAAATTTTATAGAAAGAT
1 TTATCAAAATTTTATAGAGAGGT
* *
110496 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAGAGAGGT
* * * * *
110518 TTATCACAATTTCATAGTG-TGA
1 TTATCAAAATTTTATAGAGAGGT
110540 TTATCAAAATTTTA
1 TTATCAAAATTTTA
110554 AAGTGTGATT
Statistics
Matches: 66, Mismatches: 14, Indels: 3
0.80 0.17 0.04
Matches are distributed among these distances:
21 1 0.02
22 29 0.44
23 36 0.55
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGAGAGGT
Found at i:110558 original size:22 final size:22
Alignment explanation
Indices: 110496--110564 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
110486 ATAGAAAGAT
* * * *
110496 TTATCAAAATTTCATAGCGAGG
1 TTATCAAAATTTCAAAGTGTGA
* *
110518 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCAAAGTGTGA
*
110540 TTATCAAAATTTTAAAGTGTGA
1 TTATCAAAATTTCAAAGTGTGA
110562 TTA
1 TTA
110565 CTAACAATTC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCAAAGTGTGA
Found at i:110656 original size:23 final size:22
Alignment explanation
Indices: 110602--110657 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
110592 TTTTTATAAA
*
110602 GTGGTTATCAATATATCATATG
1 GTGGTTATCAACATATCATATG
* *
110624 GAGGTTATCAACATCTCATAGTG
1 GTGGTTATCAACATATCATA-TG
*
110647 TTGGTTATCAA
1 GTGGTTATCAA
110658 AATTTTATTG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 17 0.61
23 11 0.39
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (22 bp):
GTGGTTATCAACATATCATATG
Found at i:110797 original size:22 final size:21
Alignment explanation
Indices: 110766--110818 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
110756 AGGATTCTTG
* *
110766 AAATTCCATAGTACCGTTATCA
1 AAATTTCATAGGA-CGTTATCA
*
110788 AAATTTCATAGGAGGTTATCA
1 AAATTTCATAGGACGTTATCA
110809 AAATTTCATA
1 AAATTTCATA
110819 ATGGGATCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (21 bp):
AAATTTCATAGGACGTTATCA
Found at i:112483 original size:32 final size:30
Alignment explanation
Indices: 112428--112488 Score: 77
Period size: 32 Copynumber: 2.0 Consensus size: 30
112418 TTCTTGTCAT
*
112428 ATGAACTTCAAGTCAGGACATTTTGCCCCC
1 ATGAACTTCAAGTCAGGACATTTTACCCCC
* *
112458 ATGAACTTCCAAATTCAGGATATTTTACCCC
1 ATGAACTT-C-AAGTCAGGACATTTTACCCC
112489 TGACGGAGCG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 8 0.31
31 1 0.04
32 17 0.65
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.30
Consensus pattern (30 bp):
ATGAACTTCAAGTCAGGACATTTTACCCCC
Found at i:121404 original size:31 final size:31
Alignment explanation
Indices: 121360--121421 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
121350 TATGTTAGAC
*
121360 AAATAAGAATATAATAGGTGTTTCAAAAGTT
1 AAATAAGAATATAATAGGCGTTTCAAAAGTT
**
121391 AAATAAGGGTATAATAGGCGTTTCAAAAGTT
1 AAATAAGAATATAATAGGCGTTTCAAAAGTT
121422 TCACAAAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.45, C:0.05, G:0.19, T:0.31
Consensus pattern (31 bp):
AAATAAGAATATAATAGGCGTTTCAAAAGTT
Found at i:121940 original size:20 final size:21
Alignment explanation
Indices: 121901--121942 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
121891 TTACAAAGAA
121901 AACTCACAATTACATGAGAGT
1 AACTCACAATTACATGAGAGT
* *
121922 AACTCAC-ATTCCGTGAGAGT
1 AACTCACAATTACATGAGAGT
121942 A
1 A
121943 GAATCTAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (21 bp):
AACTCACAATTACATGAGAGT
Done.