Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003249.1 Hibiscus syriacus cultivar Beakdansim tig00006830_pilon, 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: 55143
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:1063 original size:219 final size:219
Alignment explanation
Indices: 397--1066 Score: 968
Period size: 219 Copynumber: 3.1 Consensus size: 219
387 ATTCTACCTG
* * * *
397 GAGGTCTTATGAATAGCCCGGAGGACTTATCATCTTGCTCAGAA-CTTACAGAT-AACCAGAGGA
1 GAGGTCTTATGGATGGCCC-GAGGTCTTATCATCTTGCTCAGAAGCTTACAGATGAACCGGAGGA
* * *
460 TTTAAATATCAAG-AACCCTTG-AAATAAAACTTAGTTTCTTGGTTGTCAAGGAACCCC-TAAAG
65 TTTAAACATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGGTTGTCAAGGAACCCCTTAAAG
* *
522 GCTTAGCTTCCTTTAACAACTCTTTGAGATAA-TAACAAACCCCTGAAAACCTTATTTTCTAAAA
130 GCTTAGCTTCCTTTAACAACTCTTTGAGATAATTAACAAACCCCTGAAAAGCTTAGTTTCTAAAA
*
586 TCTCATTTGAAAACATCTTGCACTA
195 TCTCATTTGAAAACATCCTGCACTA
* *
611 GAGGTCTTATGGATTGCCCGAAGGTCTTATCATCTTGCTCGGAAGGCTTACAGATG-ACCTGGAG
1 GAGGTCTTATGGATGGCCCG-AGGTCTTATCATCTTGCTCAGAA-GCTTACAGATGAACC-GGAG
**
675 GATTTAAACATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTT-GTTGTCAAGGAGTCCCTTAA
63 GATTTAAACATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGGTTGTCAAGGAACCCCTTAA
* *
739 AGGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAATAATCCCCTGAAAAGCTTAGTTTCT-
128 AGGCTTAGCTTCCTTTAACAACTC-TTTGAGATAATTAACAAACCCCTGAAAAGCTTAGTTTCTA
803 AAATCTCATTTGAAAA-ATCCTGCACTA
192 AAATCTCATTTGAAAACATCCTGCACTA
* * * *
830 GAGGTCTTATGGATGGCCCAGAGGTCTTATCATCTTCCTTAGAAGATTAC-GATGAACCGGATGA
1 GAGGTCTTATGGATGGCCC-GAGGTCTTATCATCTTGCTCAGAAGCTTACAGATGAACCGGAGGA
*
894 TTTAAACATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGGTTGTTAAGGAACCCCTTAAAA
65 TTTAAACATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGGTTGTCAAGGAACCCCTT-AAA
* *
959 GGCTTAGCTTCCTTTCACAACTCTTTGAGATAATTAAGAAACCCCTGAAAAGCTTAGTTTCTAAA
129 GGCTTAGCTTCCTTTAACAACTCTTTGAGATAATTAACAAACCCCTGAAAAGCTTAGTTTCTAAA
**
1024 ATCTCATTTGAAAACATCCTGC-CCG
194 ATCTCATTTGAAAACATCCTGCACTA
1049 GAGGTCTTATGGATGGCC
1 GAGGTCTTATGGATGGCC
1067 GGGAGGACTT
Statistics
Matches: 411, Mismatches: 29, Indels: 27
0.88 0.06 0.06
Matches are distributed among these distances:
213 1 0.00
214 38 0.09
216 12 0.03
217 68 0.17
218 82 0.20
219 152 0.37
220 34 0.08
221 24 0.06
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Consensus pattern (219 bp):
GAGGTCTTATGGATGGCCCGAGGTCTTATCATCTTGCTCAGAAGCTTACAGATGAACCGGAGGAT
TTAAACATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGGTTGTCAAGGAACCCCTTAAAGG
CTTAGCTTCCTTTAACAACTCTTTGAGATAATTAACAAACCCCTGAAAAGCTTAGTTTCTAAAAT
CTCATTTGAAAACATCCTGCACTA
Found at i:2199 original size:54 final size:54
Alignment explanation
Indices: 2135--2289 Score: 229
Period size: 54 Copynumber: 2.9 Consensus size: 54
2125 CTGGTTCATG
* *
2135 AAACATTTGACAACATATTCATCCTTTCCAGTGGCTTCTGCACAGATGTTCGTA
1 AAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCACAGATGTTCGTA
* * * * *
2189 AAACATTTGACAACACATTTATCCTATCTTGCGGCTTCTGCCCAGATGTTCGTA
1 AAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCACAGATGTTCGTA
* *
2243 AAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTACACAGAT
1 AAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCACAGAT
2290 TTCTCGTCAG
Statistics
Matches: 87, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 87 1.00
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.34
Consensus pattern (54 bp):
AAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCACAGATGTTCGTA
Found at i:6849 original size:14 final size:15
Alignment explanation
Indices: 6827--6864 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
6817 AAATGCGAAA
6827 AATGCAAAAATG-GC
1 AATGCAAAAATGTGC
* *
6841 AATGTAAAATTGTGC
1 AATGCAAAAATGTGC
6856 AATGCAAAA
1 AATGCAAAA
6865 TGAAAATGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.50, C:0.11, G:0.18, T:0.21
Consensus pattern (15 bp):
AATGCAAAAATGTGC
Found at i:9939 original size:150 final size:143
Alignment explanation
Indices: 9757--10044 Score: 335
Period size: 146 Copynumber: 2.0 Consensus size: 143
9747 AAAATATATT
** ** *
9757 AAAATAATTTTTATAAAACTAAAGTAAATATATAT-TTTTAGAGTTTTATAAATAGGGTATTTAT
1 AAAATAATTTGAATAAAACTAAAACAAATATATATATTTTAGA-TTTT-T---TAAGGTATTTAT
* * ** *
9821 TTATTTAAAAATATTAGAAAATGACATCTAGTTACTTTAAGACGACCCCTTTCTTTAATATTAAA
61 TTATTAAAAAATATCAGAAAATGACATCTAGTTAAATTAAGAC-AACCCTTTC-TTAATATTAAA
9886 AAATAAATAAATATTAATAAC
124 AAATAAAT-AATATTAATAAC
* ** *
9907 AAAATAATTTGAATAAAACTAAAACAACTATATATATTTTTTATTTTTTAAGGTTTTTATTTATT
1 AAAATAATTTGAATAAAACTAAAACAAATATATATATTTTAGATTTTTTAAGGTATTTATTTATT
* * * *
9972 AAAAAATATCGGAATATGACCTCTAGTTAAATTAAGACAACCCTTTCTTAATATTTAAAAATAAA
66 AAAAAATATCAGAAAATGACATCTAGTTAAATTAAGACAACCCTTTCTTAATATTAAAAAATAAA
10037 TAATATTA
131 TAATATTA
10045 TTATTTAATC
Statistics
Matches: 119, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
143 7 0.06
144 18 0.15
145 8 0.07
146 46 0.39
149 1 0.01
150 34 0.29
151 5 0.04
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (143 bp):
AAAATAATTTGAATAAAACTAAAACAAATATATATATTTTAGATTTTTTAAGGTATTTATTTATT
AAAAAATATCAGAAAATGACATCTAGTTAAATTAAGACAACCCTTTCTTAATATTAAAAAATAAA
TAATATTAATAAC
Found at i:11524 original size:3 final size:3
Alignment explanation
Indices: 11510--11599 Score: 171
Period size: 3 Copynumber: 30.0 Consensus size: 3
11500 TTTGGGCCTG
*
11510 TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
11558 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
11600 AAACGAATAT
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:11839 original size:42 final size:42
Alignment explanation
Indices: 11770--11871 Score: 116
Period size: 42 Copynumber: 2.5 Consensus size: 42
11760 TCCAAAATTT
*
11770 TTAAGTCCTTCGGGCCATCAGAAAGTCTTTTCAACATGATGA
1 TTAAGTCCTTCGGGCCATCAGAAAGTCTTTTCAACAAGATGA
* * * ** * *
11812 TTAAATCCTTCGGGTCATCTGTCAGTCTTTTGAGCAAGATGA
1 TTAAGTCCTTCGGGCCATCAGAAAGTCTTTTCAACAAGATGA
*
11854 -TAAGTCCTTCGGACCATC
1 TTAAGTCCTTCGGGCCATC
11872 TATAAGATCT
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
41 15 0.31
42 34 0.69
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (42 bp):
TTAAGTCCTTCGGGCCATCAGAAAGTCTTTTCAACAAGATGA
Found at i:11883 original size:42 final size:43
Alignment explanation
Indices: 11770--11883 Score: 110
Period size: 42 Copynumber: 2.7 Consensus size: 43
11760 TCCAAAATTT
* *
11770 TTAAGTCCTTCGGGCCATC-AGAA-AGTCTTTTCAACATGATGA
1 TTAAGTCCTTCGGGCCATCTATAAGA-TCTTTTCAACAAGATGA
* * * * * *
11812 TTAAATCCTTCGGGTCATCTGTCAG-TCTTTTGAGCAAGATGA
1 TTAAGTCCTTCGGGCCATCTATAAGATCTTTTCAACAAGATGA
*
11854 -TAAGTCCTTCGGACCATCTATAAGATCTTT
1 TTAAGTCCTTCGGGCCATCTATAAGATCTTT
11884 GGGCATGATG
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
41 19 0.34
42 36 0.64
43 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (43 bp):
TTAAGTCCTTCGGGCCATCTATAAGATCTTTTCAACAAGATGA
Found at i:12109 original size:259 final size:258
Alignment explanation
Indices: 11643--12982 Score: 1590
Period size: 259 Copynumber: 5.2 Consensus size: 258
11633 TCTACACACG
11643 TGATTTT-AAAAAAATGAGAAAGCA-ATTTTCAAAGTTTTCTCATTTAGTATTTTTAGAAAATGA
1 TGATTTTCAAAAAAATGAGAAAG-ATATTTTCAAAG-TTTCTCATTTAGTATTTTTAGAAAATGA
* * * * * **
11706 AATTTTTCAAAAGTAAGAAAGTGATTCCCAAGGTTTCTTACCTAGTAAACTATTTCCAAAATTTT
64 AATTTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACC-AGTAGACTATTTCCAAAATTGG
* * * *
11771 TAAGTCCTTCGGGCCATCAGAAAGTCTTTTC-AACATGATGATTAAATCCTTCGGGTCATCTGTC
128 TAAGTCCTTCGGGCCATCAGTAAG-CCTTTCGAGCATGATGATTAAATCTTTCGGGTCATCTGTC
* * * *
11835 AGTCTTTTGAGCAAGATGATAAGTCCTTCGGACCATCTATAAGATCTTTGGGCATGATGTTTTCA
192 AGTCTTTTAAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCATGATGTTTTCA
11900 CA
257 CA
* * *
11902 TGATTTTCAAAAAAAGGAGAAAGATATTTTCAAAGTTTTTCATTTAGTATTTTAAGAAAATGAAA
1 TGATTTTCAAAAAAATGAGAAAGATATTTTCAAAGTTTCTCATTTAGTATTTTTAGAAAATGAAA
* *
11967 TTTTTGGAAAGTAAGAAAATGATTTCCAAAGTTTCTTACTCAATAGACTATTTCCAAAATTGGTA
66 TTTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTAC-CAGTAGACTATTTCCAAAATTGGTA
* * * *
12032 AGTCCTTCGAGCCATCAGTAAGCCTTTTGAGCATGATGATTAAATCTTTTGGGTCATCTGTTAGT
130 AGTCCTTCGGGCCATCAGTAAGCCTTTCGAGCATGATGATTAAATCTTTCGGGTCATCTGTCAGT
* *
12097 CTTTTAAGCAAGATGATAAGTCATTCGGGCCATCTATAAGACCTTCGGGCATGATGCTTTCACA
195 CTTTTAAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCATGATGTTTTCACA
* * *
12161 TGATTTT-TAAAAAATGAGAAAGCA-ATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAACGAA
1 TGATTTTCAAAAAAATGAGAAAG-ATATTTTCAAAGTTTCTCATTTAGTATTTTTAGAAAATGAA
* * * * *
12224 AATTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCATGTATACTATTTACGAAATTGAT
65 ATTTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCA-GTAGACTATTTCCAAAATTGGT
* * * * * *
12289 AAGTCATTCGGGCCATCAGTAAGCCTTTCGGGCATGATGATTAAATCTTTCGAGACATTTGTCAA
129 AAGTCCTTCGGGCCATCAGTAAGCCTTTCGAGCATGATGATTAAATCTTTCGGGTCATCTGTCAG
* ** * *
12354 CCTTTCGAGCAAGATGATAAGTTCTTCGGGCCATCTATAAGACCTTCGGGCAGGATGTTTTCACA
194 TCTTTTAAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCATGATGTTTTCACA
* * * * * * *
12419 TGAATTTCTAAAAACTGAGAAA-ATGATTTCCAAAGTTTCTCACTTAATATTTTTTAGAAAATTA
1 TGATTTTCAAAAAAATGAGAAAGAT-ATTTTCAAAGTTTCTCATTTAGTA-TTTTTAGAAAATGA
* * * * *
12483 ATTTTTTGAAAAGTAAGAAAACGATTT-CAACAGTTTCTTACACAATAGACAATTTCAAAAATTG
64 AATTTTTGAAAAGTAAGAAAATGATTTCCAA-AGTTTCTTAC-CAGTAGACTATTTCCAAAATTG
* * * * *
12547 GTAAGTCATTCGGGCCATGAGTAAGCCTTTCG-GCATGATGATTAATTCCTTCGGGTCACCTGTC
127 GTAAGTCCTTCGGGCCATCAGTAAGCCTTTCGAGCATGATGATTAAATCTTTCGGGTCATCTGTC
* * * * *
12611 ATTCTTTCGAA-CAAGATGATAAGTACTTCAGACCATCTATAAGACCTTCGGGCATGATGTTTTC
192 AGTCTTT-TAAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCATGATGTTTTC
12675 ACA
256 ACA
* * * * * * * *
12678 TGATTTTCGAAAAAATGATAAAGTTATTTCCATAGTCTCTCACTTAATATTTTTAGAAAATGAAA
1 TGATTTTCAAAAAAATGAGAAAGATATTTTCAAAGTTTCTCATTTAGTATTTTTAGAAAATGAAA
* * * * * *
12743 TCTTTGAAAAGCATGAAAGTGATTTCCAATGTTTCATACCCAGTAGACTATTTCC-AAA-TGGAT
66 TTTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTA-CCAGTAGACTATTTCCAAAATTGG-T
* * * *
12806 AAGTCCTTTGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAAT-TCTCGGGTCATCTGTCAG
129 AAGTCCTTCGGGCCATCAGTAAGCCTTTCGAGCATGATGATTAAATCTTTCGGGTCATCTGTCAG
* * * * *
12870 TCTTTTAAGCAAGATGATAAGTCCTTCGGGCCATCTATAAAACCTTCAGGCAAGATGCTTTCATA
194 TCTTTTAAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCATGATGTTTTCACA
* * * *
12935 TGGTGTTTGTAAGAAAATGAG-AAGACGATTTTCAAAGTTTCTCATTTA
1 TGAT-TTT-CAAAAAAATGAGAAAGA-TATTTTCAAAGTTTCTCATTTA
12983 AAATATTTTT
Statistics
Matches: 922, Mismatches: 137, Indels: 44
0.84 0.12 0.04
Matches are distributed among these distances:
256 5 0.01
257 102 0.11
258 300 0.33
259 397 0.43
260 116 0.13
261 2 0.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (258 bp):
TGATTTTCAAAAAAATGAGAAAGATATTTTCAAAGTTTCTCATTTAGTATTTTTAGAAAATGAAA
TTTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCAGTAGACTATTTCCAAAATTGGTAA
GTCCTTCGGGCCATCAGTAAGCCTTTCGAGCATGATGATTAAATCTTTCGGGTCATCTGTCAGTC
TTTTAAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCATGATGTTTTCACA
Found at i:12628 original size:517 final size:516
Alignment explanation
Indices: 11643--12994 Score: 1671
Period size: 517 Copynumber: 2.6 Consensus size: 516
11633 TCTACACACG
11643 TGATTTTAAAAAAATGAGAAAGCAATTTTCAAAGTTTTCTCATTTAGTATTTTTAGAAAATGAAA
1 TGATTTTAAAAAAATGAGAAAGCAATTTTCAAAG-TTTCTCATTTAGTATTTTTAGAAAATGAAA
* * * * **
11708 TTTTTCAAAAGTAAGAAAGTGATTCCCAAGGTTTCTTACC-TAGTAAACTATTTCCAAAATTTTT
65 ATTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCAT-GTAAACTATTT-CAAAATTGAT
* * * *
11772 AAGTCCTTCGGGCCATCAGAAAGTCTTTTCAACATGATGATTAAATCCTTCGGGTCATCTGTCAG
128 AAGTCCTTCGGGCCATCAGTAAG-CCTTTCAGCATGATGATTAAATCTTTCGGGTCATCTGTCAG
* * * *
11837 TCTTTTGAGCAAGATGATAAGTCCTTCGGACCATCTATAAGATCTTTGGGCATGATGTTTTCACA
192 TCTTTTGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCAAGATGTTTTCACA
* * * * * *
11902 TGATTTTCAAAAAAAGGAGAAAGAT-ATTTTCAAAGTTTTTCATTTAGTA-TTTTAAGAAAATGA
257 TGAATTTCTAAAAAATGAGAAA-ATGATTTTCAAAGTTTCTCATTTAATATTTTTTAGAAAATGA
* * * * *
11965 AATTTTTGGAAAGTAAGAAAATGATTTCCAAAGTTTCTTACTCAATAGACTATTTCCAAAATTGG
321 AATTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACACAATAGACAATTTCAAAAATTGG
* * * * * *
12030 TAAGTCCTTCGAGCCATCAGTAAGCCTTTTGAGCATGATGATTAAATCTTTTGGGTCATCTGTTA
386 TAAGTCATTCGAGCCATCAGTAAGCCTTTCGAGCATGATGATTAAATCCTTCGGGTCACCTGTCA
* * *
12095 GTCTTTTAAGCAAGATGATAAGT-CATTCGGGCCATCTATAAGACCTTCGGGCATGATGCTTTCA
451 GTCTTTGAAGCAAGATGATAAGTAC-TTCAGACCATCTATAAGACCTTCGGGCATGATGCTTTCA
12159 CA
515 CA
* * *
12161 TGATTTTTAAAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAACGAAAA
1 TGATTTTAAAAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAGTATTTTTAGAAAATGAAAA
* * *
12226 TTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCATGTATACTATTTACGAAATTGATAA
66 TTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCATGTAAACTATTT-CAAAATTGATAA
* * * * * **
12291 GTCATTCGGGCCATCAGTAAGCCTTTCGGGCATGATGATTAAATCTTTCGAGACATTTGTCAACC
130 GTCCTTCGGGCCATCAGTAAGCCTTTC-AGCATGATGATTAAATCTTTCGGGTCATCTGTCAGTC
* * *
12356 TTTCGAGCAAGATGATAAGTTCTTCGGGCCATCTATAAGACCTTCGGGCAGGATGTTTTCACATG
194 TTTTGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCAAGATGTTTTCACATG
* * * * *
12421 AATTTCTAAAAACTGAGAAAATGATTTCCAAAGTTTCTCACTTAATATTTTTTAGAAAATTAATT
259 AATTTCTAAAAAATGAGAAAATGATTTTCAAAGTTTCTCATTTAATATTTTTTAGAAAATGAAAT
12486 TTTTGAAAAGTAAGAAAACGATTT-CAACAGTTTCTTACACAATAGACAATTTCAAAAATTGGTA
324 TTTTGAAAAGTAAGAAAACGATTTCCAA-AGTTTCTTACACAATAGACAATTTCAAAAATTGGTA
* * * *
12550 AGTCATTCGGGCCATGAGTAAGCCTTTCG-GCATGATGATTAATTCCTTCGGGTCACCTGTCATT
388 AGTCATTCGAGCCATCAGTAAGCCTTTCGAGCATGATGATTAAATCCTTCGGGTCACCTGTCAGT
*
12614 CTTTCGAA-CAAGATGATAAGTACTTCAGACCATCTATAAGACCTTCGGGCATGATGTTTTCACA
453 CTTT-GAAGCAAGATGATAAGTACTTCAGACCATCTATAAGACCTTCGGGCATGATGCTTTCACA
* * ** * * * * *
12678 TGATTTTCGAAAAAATGATAAAGTTATTTCCATAGTCTCTCACTTAATATTTTTAGAAAATG-AA
1 TGATTTT-AAAAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAGTATTTTTAGAAAATGAAA
* * * * * * *
12742 ATCTTTGAAAAGCATGAAAGTGATTTCCAATGTTTCATACCCA-GTAGACTATTTCCAAATGGAT
65 AT-TTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTA-CCATGTAAACTATTTCAAAATTGAT
* * *
12806 AAGTCCTTTGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAAT-TCTCGGGTCATCTGTCAG
128 AAGTCCTTCGGGCCATCAGTAAGCCTTTC-AGCATGATGATTAAATCTTTCGGGTCATCTGTCAG
* * * * *
12870 TCTTTTAAGCAAGATGATAAGTCCTTCGGGCCATCTATAAAACCTTCAGGCAAGATGCTTTCATA
192 TCTTTTGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCAAGATGTTTTCACA
** * * *
12935 TGGTGTTTGTAAGAAAATGAGAAGACGATTTTCAAAGTTTCTCATTTAAAATATTTTTTA
257 T-GAATTTCTAA-AAAATGAGAAAATGATTTTCAAAGTTTCTCATTT--AATATTTTTTA
12995 AAGAAAAAAA
Statistics
Matches: 714, Mismatches: 106, Indels: 26
0.84 0.13 0.03
Matches are distributed among these distances:
516 77 0.11
517 379 0.53
518 244 0.34
519 3 0.00
520 11 0.02
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (516 bp):
TGATTTTAAAAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAGTATTTTTAGAAAATGAAAA
TTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCATGTAAACTATTTCAAAATTGATAAG
TCCTTCGGGCCATCAGTAAGCCTTTCAGCATGATGATTAAATCTTTCGGGTCATCTGTCAGTCTT
TTGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCAAGATGTTTTCACATGAA
TTTCTAAAAAATGAGAAAATGATTTTCAAAGTTTCTCATTTAATATTTTTTAGAAAATGAAATTT
TTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACACAATAGACAATTTCAAAAATTGGTAAGT
CATTCGAGCCATCAGTAAGCCTTTCGAGCATGATGATTAAATCCTTCGGGTCACCTGTCAGTCTT
TGAAGCAAGATGATAAGTACTTCAGACCATCTATAAGACCTTCGGGCATGATGCTTTCACA
Found at i:12899 original size:41 final size:41
Alignment explanation
Indices: 12803--12905 Score: 118
Period size: 41 Copynumber: 2.5 Consensus size: 41
12793 TTTCCAAATG
* * *
12803 GATAAGTCCTTTGGGCCATCAGTAAGTCTTTCAAGCATGAT
1 GATAAGTCCTTCGGGCCATCTGTAAGTCTTTCAAGCAAGAT
* * * * *
12844 GATTAAATTC-TCGGGTCATCTGTCAGTCTTTTAAGCAAGAT
1 GA-TAAGTCCTTCGGGCCATCTGTAAGTCTTTCAAGCAAGAT
12885 GATAAGTCCTTCGGGCCATCT
1 GATAAGTCCTTCGGGCCATCT
12906 ATAAAACCTT
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
40 5 0.10
41 39 0.80
42 5 0.10
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.33
Consensus pattern (41 bp):
GATAAGTCCTTCGGGCCATCTGTAAGTCTTTCAAGCAAGAT
Found at i:13880 original size:132 final size:131
Alignment explanation
Indices: 13730--14080 Score: 356
Period size: 132 Copynumber: 2.7 Consensus size: 131
13720 CAAATCCTTC
* * * * *
13730 TTCTTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCAATTCCGATTTAATCTTCCCGGA
1 TTCTTTCATATTTGGTCTTCCTGGAGAGCAGCGAAGCAAATCAATTCCGATTCAATCTTCCCAGA
* * * *
13795 AGAGAAGCGAAGTGGATCAAAATTTA-TATGTCC-GATCTCCCCTAAAGAGTAGTAGAGGAGACC
66 AGA-AAGCGAAGTGGATCAAAATTTACGA--ACCAAATCTCCCCTAAAGAGTAGTAGAGCAGACC
13858 CGCA
128 CGCA
* * * *
13862 TTC-TTCTATATTTCGTCTTCCCGGAGAAG-AACAAAGCAAATC-ATGTCCGATTCAATCTTCCC
1 TTCTTTC-ATATTTGGTCTTCCTGGAG-AGCAGCGAAGCAAATCAAT-TCCGATTCAATCTTCCC
*
13924 AGAAGATCAA-CGAAGTGGATCAAAATTTACGAACCAAATCTCCCCTAAAGAGTAGTGGAGCAGA
63 AGAAGA--AAGCGAAGTGGATCAAAATTTACGAACCAAATCTCCCCTAAAGAGTAGTAGAGCAGA
* *
13988 CTCGCT
126 CCCGCA
* * * * *
13994 TTCTTTCATATTTGGTCTTCCTGGAGAACAGCGAAACAAATCAAGTTCTG-TTCAACCTTCCCTG
1 TTCTTTCATATTTGGTCTTCCTGGAGAGCAGCGAAGCAAATCAA-TTCCGATTCAATCTTCCCAG
* *
14058 AAGAACAGTGAAGTGAATCAAAA
65 AAGAA-AGCGAAGTGGATCAAAA
14081 AATTTCAAGA
Statistics
Matches: 179, Mismatches: 28, Indels: 24
0.77 0.12 0.10
Matches are distributed among these distances:
130 1 0.01
131 9 0.05
132 156 0.87
133 12 0.07
134 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.26
Consensus pattern (131 bp):
TTCTTTCATATTTGGTCTTCCTGGAGAGCAGCGAAGCAAATCAATTCCGATTCAATCTTCCCAGA
AGAAAGCGAAGTGGATCAAAATTTACGAACCAAATCTCCCCTAAAGAGTAGTAGAGCAGACCCGC
A
Found at i:14381 original size:2 final size:2
Alignment explanation
Indices: 14374--14411 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
14364 TGCATGTGTC
* *
14374 TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14412 TATTGTTAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16489 original size:2 final size:2
Alignment explanation
Indices: 16482--16538 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
16472 AGTCATAAAT
16482 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16524 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
16539 GTATGATTGT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18370 original size:183 final size:184
Alignment explanation
Indices: 18062--18448 Score: 638
Period size: 183 Copynumber: 2.1 Consensus size: 184
18052 TTTTCTAATT
* * * *
18062 TATATAA-AAATTAAATATTTTTTAATTCAAAAAAAGATTATAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAGATTACAAATAATTTAAATAATATATAAT
*
18126 TATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
66 TATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
* *
18191 GGATCTTAAATTATTAATTGGGTTTTAAATGGTTT-GGTCTTAGCCCATATGTTA
131 GGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGT-TGAGCCCATATGTTA
*
18245 TATATAATATATTTAATATTTTTTAATT-AAAAAACAGTTTACAAATAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAA-AGATTACAAATAATTTAAATAATATATAA
*
18309 TTATAAAATAAAAAATTTATAT-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
65 TTATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
18373 TGGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
130 TGGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
*
18428 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
18449 AAAATTTAAT
Statistics
Matches: 191, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
183 124 0.65
184 67 0.35
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.45
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAGATTACAAATAATTTAAATAATATATAAT
TATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
GGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
Found at i:22171 original size:9 final size:9
Alignment explanation
Indices: 22157--22185 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
22147 GGGTTAAGTC
22157 CCTAAACTT
1 CCTAAACTT
22166 CCTAAACTT
1 CCTAAACTT
22175 CCTAAACTT
1 CCTAAACTT
22184 CC
1 CC
22186 CATAGGTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.38, G:0.00, T:0.31
Consensus pattern (9 bp):
CCTAAACTT
Found at i:32451 original size:42 final size:42
Alignment explanation
Indices: 32371--32842 Score: 405
Period size: 42 Copynumber: 11.4 Consensus size: 42
32361 TGAGAATATG
*
32371 AGTCAATC-TTCTAATGTTATTCTTGGCTTCCTCGTGAAGAGA
1 AGTCAATCTTTC-AATGTTATTCTTGACTTCCTCGTGAAGAGA
* * * * *
32413 AGTAAATCATTCAATGTTATTATTGACTTTCTCATGAAGAGA
1 AGTCAATCTTTCAATGTTATTCTTGACTTCCTCGTGAAGAGA
* *
32455 AGTCAATCGTTCAATATTTTTATTCTTGACTTCCTCGTGAAGTAGA
1 AGTCAATCTTTC-A-A-TGTTATTCTTGACTTCCTCGTGAAG-AGA
* * *
32501 A-TCAATCTTTCAATGTTATTCTTGACTCCCTCATGAAGAGG
1 AGTCAATCTTTCAATGTTATTCTTGACTTCCTCGTGAAGAGA
* * * *
32542 AGTCAATCCTTCAATGTTA-TCATTGACTCCCTCATGAAGAGG
1 AGTCAATCTTTCAATGTTATTC-TTGACTTCCTCGTGAAGAGA
*
32584 AGTCAATCTTTC-ATAGTTATTCTTGAC-TCCTTCGTGAAGATA
1 AGTCAATCTTTCAAT-GTTATTCTTGACTTCC-TCGTGAAGAGA
* * * *
32626 TA-TCAATCTTTCAATGTCATTCTTGACTCCCTCGTGAAGGGG
1 -AGTCAATCTTTCAATGTTATTCTTGACTTCCTCGTGAAGAGA
* * *
32668 AGTCAATCTTTCAATGTTATTCTTGACTTTCTCATGAAGAGG
1 AGTCAATCTTTCAATGTTATTCTTGACTTCCTCGTGAAGAGA
* * *
32710 AGT---T-TTTCAGTGTTATTCTTAACTTCCTCATGAAGAGA
1 AGTCAATCTTTCAATGTTATTCTTGACTTCCTCGTGAAGAGA
* * * * *
32748 AGTTAATC-TT---TGTTATTATTGACTCCCTCGTGAAAAGT
1 AGTCAATCTTTCAATGTTATTCTTGACTTCCTCGTGAAGAGA
* * * * ** *
32786 AGTTAATATTTCAATGTTATTATTAACTTTATTGTGAAGAGA
1 AGTCAATCTTTCAATGTTATTCTTGACTTCCTCGTGAAGAGA
* *
32828 ATTCAATCGTTCAAT
1 AGTCAATCTTTCAAT
32843 ATAGTCATTC
Statistics
Matches: 354, Mismatches: 54, Indels: 44
0.78 0.12 0.10
Matches are distributed among these distances:
38 62 0.18
39 3 0.01
41 13 0.04
42 228 0.64
43 12 0.03
44 2 0.01
45 30 0.08
46 4 0.01
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (42 bp):
AGTCAATCTTTCAATGTTATTCTTGACTTCCTCGTGAAGAGA
Found at i:32653 original size:126 final size:128
Alignment explanation
Indices: 32373--32863 Score: 478
Period size: 126 Copynumber: 3.9 Consensus size: 128
32363 AGAATATGAG
* * * * *
32373 TCAATC-TTCTAATGTTATTCTTGGCTTCCTCGTGAAGAGAAGTAAATCATTCAATGTTATTATT
1 TCAATCTTTC-AATGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATCATTCAATGTTATCATT
* *
32437 GACTTTCTCATGAAGAGAAGTCAATCGTTCAATATTTTTATTCTTGACTTCCTCGTGAAGTAGAA
65 GACTTTCTCATGAAGAGGAGTCAATCGTTCAATA-TGTTATTCTTGACTTCCTCGTGAAGTAGAA
* *
32502 TCAATCTTTCAATGTTATTCTTGACTCCCTCATGAAGAGGAGTCAATCCTTCAATGTTATCATTG
1 TCAATCTTTCAATGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATCATTCAATGTTATCATTG
** * *
32567 ACTCCCTCATGAAGAGGAGTCAATCTTTC-ATA-GTTATTCTTGAC-TCCTTCGTGAAGATA-TA
66 ACTTTCTCATGAAGAGGAGTCAATCGTTCAATATGTTATTCTTGACTTCC-TCGTGAAG-TAGAA
* * *
32628 TCAATCTTTCAATGTCATTCTTGACTCCCTCGTGAAGGGGAGTCAATCTTTCAATGTTATTC-TT
1 TCAATCTTTCAATGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATCATTCAATGTTA-TCATT
* * * *
32692 GACTTTCTCATGAAGAGGAGT---T-TTTC-A-GTGTTATTCTTAACTTCCTCATGAAG-AGAA
65 GACTTTCTCATGAAGAGGAGTCAATCGTTCAATATGTTATTCTTGACTTCCTCGTGAAGTAGAA
* * * * * *
32749 GTTAATC-TT---TGTTATTATTGACTCCCTCGTGAAAAGTAGTTAAT-ATTTCAATGTTATTAT
1 -TCAATCTTTCAATGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATCA-TTCAATGTTATCAT
* * ** * * * *
32809 TAACTTTATTGTGAAGAGAATTCAATCGTTCAATATAGTCATTCTTGAATTCCTC
64 TGACTTTCTCATGAAGAGGAGTCAATCGTTCAATAT-GTTATTCTTGACTTCCTC
32864 ATTAAGATGA
Statistics
Matches: 302, Mismatches: 43, Indels: 38
0.79 0.11 0.10
Matches are distributed among these distances:
117 1 0.00
118 56 0.19
120 1 0.00
121 4 0.01
122 31 0.10
123 5 0.02
124 1 0.00
125 18 0.06
126 96 0.32
127 4 0.01
128 3 0.01
129 79 0.26
130 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (128 bp):
TCAATCTTTCAATGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATCATTCAATGTTATCATTG
ACTTTCTCATGAAGAGGAGTCAATCGTTCAATATGTTATTCTTGACTTCCTCGTGAAGTAGAA
Found at i:32727 original size:38 final size:38
Alignment explanation
Indices: 32676--32751 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
32666 GGAGTCAATC
* * *
32676 TTTCAATGTTATTCTTGACTTTCTCATGAAGAGGAGTT
1 TTTCAATGTTATTCTTAACTTCCTCATGAAGAGAAGTT
*
32714 TTTCAGTGTTATTCTTAACTTCCTCATGAAGAGAAGTT
1 TTTCAATGTTATTCTTAACTTCCTCATGAAGAGAAGTT
32752 AATCTTTGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.43
Consensus pattern (38 bp):
TTTCAATGTTATTCTTAACTTCCTCATGAAGAGAAGTT
Found at i:32762 original size:38 final size:38
Alignment explanation
Indices: 32682--32792 Score: 114
Period size: 38 Copynumber: 2.9 Consensus size: 38
32672 AATCTTTCAA
* * **
32682 TGTTATTCTTGACTTTCTCATGAAGAGGAGTTTTTCAG
1 TGTTATTCTTGACTTCCTCATGAAGAGAAGTTAATCAG
* **
32720 TGTTATTCTTAACTTCCTCATGAAGAGAAGTTAATCTT
1 TGTTATTCTTGACTTCCTCATGAAGAGAAGTTAATCAG
* * * * *
32758 TGTTATTATTGACTCCCTCGTGAAAAGTAGTTAAT
1 TGTTATTCTTGACTTCCTCATGAAGAGAAGTTAAT
32793 ATTTCAATGT
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
38 60 1.00
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.42
Consensus pattern (38 bp):
TGTTATTCTTGACTTCCTCATGAAGAGAAGTTAATCAG
Found at i:32947 original size:45 final size:43
Alignment explanation
Indices: 32872--33022 Score: 149
Period size: 45 Copynumber: 3.4 Consensus size: 43
32862 TCATTAAGAT
* * *
32872 GAGTCAACCTTTTAGTGGTGTTGTTTTTGACATTCTCGTGAAAA
1 GAGTCAACCTTTTAGTGGTGTTATTCTTGAC-TTCTCGCGAAAA
* * * * *
32916 GAAGTCAACCTTTTAGCGTTGTAATTCTTGACTTTCTCACGAAGAG
1 G-AGTCAACCTTTTAGTGGTGTTATTCTTGAC-TTCTCGCGAA-AA
* * *
32962 GAGTCAACCTTATAATGGTGTTATTCTTGACTCTCTTGCGAAAA
1 GAGTCAACCTTTTAGTGGTGTTATTCTTGACT-TCTCGCGAAAA
33006 TGAGTCAACCTTTTAGT
1 -GAGTCAACCTTTTAGT
33023 AGTATCCTTC
Statistics
Matches: 84, Mismatches: 19, Indels: 7
0.76 0.17 0.06
Matches are distributed among these distances:
44 3 0.04
45 79 0.94
46 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (43 bp):
GAGTCAACCTTTTAGTGGTGTTATTCTTGACTTCTCGCGAAAA
Found at i:32992 original size:90 final size:90
Alignment explanation
Indices: 32849--33021 Score: 215
Period size: 90 Copynumber: 1.9 Consensus size: 90
32839 CAATATAGTC
** * * * * * *
32849 ATTCTTGAATTCCTCATTAAGATGAGTCAACCTTTTAGTGGTGTTGTTTTTGACAT-TCTCGTGA
1 ATTCTTGAATTCCTCACGAAGAGGAGTCAACCTTATAATGGTGTTATTCTTGAC-TCTCTCGCGA
32913 AAA-GAAGTCAACCTTTTAGCGTTGTA
65 AAATG-AGTCAACCTTTTAGCGTTGTA
* * *
32939 ATTCTTGACTTTCTCACGAAGAGGAGTCAACCTTATAATGGTGTTATTCTTGACTCTCTTGCGAA
1 ATTCTTGAATTCCTCACGAAGAGGAGTCAACCTTATAATGGTGTTATTCTTGACTCTCTCGCGAA
33004 AATGAGTCAACCTTTTAG
66 AATGAGTCAACCTTTTAG
33022 TAGTATCCTT
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
89 1 0.01
90 68 0.97
91 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.38
Consensus pattern (90 bp):
ATTCTTGAATTCCTCACGAAGAGGAGTCAACCTTATAATGGTGTTATTCTTGACTCTCTCGCGAA
AATGAGTCAACCTTTTAGCGTTGTA
Found at i:35753 original size:32 final size:32
Alignment explanation
Indices: 35716--35781 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
35706 ATTCTATTAC
35716 TTTTAATTTAG-TCCCTT-ATTTAAATGTTTTTG
1 TTTTAATTTAGAT-CCTTGATTT-AATGTTTTTG
* *
35748 TTTTAATTTTGATCCTTGATTTATTGTTTTTG
1 TTTTAATTTAGATCCTTGATTTAATGTTTTTG
35780 TT
1 TT
35782 GCATTTTGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 25 0.83
33 5 0.17
ACGTcount: A:0.18, C:0.08, G:0.11, T:0.64
Consensus pattern (32 bp):
TTTTAATTTAGATCCTTGATTTAATGTTTTTG
Found at i:36090 original size:9 final size:9
Alignment explanation
Indices: 36067--36095 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
36057 TGCCTTTTGT
36067 TTTATTTTA
1 TTTATTTTA
36076 -TTATTTTA
1 TTTATTTTA
36084 TTTATTTTA
1 TTTATTTTA
36093 TTT
1 TTT
36096 TTATATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTATTTTA
Found at i:41843 original size:25 final size:25
Alignment explanation
Indices: 41785--41912 Score: 116
Period size: 25 Copynumber: 5.1 Consensus size: 25
41775 GGTCAAAGAA
* * * *
41785 TATTAATTATGAACATTAATTGTTT
1 TATTAATTGTGAATATTAAGTGTGT
41810 TATTAATTGTGAATATTAAGTGTGT
1 TATTAATTGTGAATATTAAGTGTGT
* * **
41835 TATTAATTGTTAGTATTATCTGTGT
1 TATTAATTGTGAATATTAAGTGTGT
41860 TATTAATT-TGTAATATT-AGTTGTGT
1 TATTAATTGTG-AATATTAAG-TGTGT
* * * *
41885 TAGTAATTGTTACTATTAATTGTGT
1 TATTAATTGTGAATATTAAGTGTGT
41910 TAT
1 TAT
41913 GCTAGTTAAT
Statistics
Matches: 82, Mismatches: 17, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
24 1 0.01
25 79 0.96
26 2 0.02
ACGTcount: A:0.30, C:0.02, G:0.15, T:0.53
Consensus pattern (25 bp):
TATTAATTGTGAATATTAAGTGTGT
Found at i:41865 original size:50 final size:50
Alignment explanation
Indices: 41799--41912 Score: 153
Period size: 50 Copynumber: 2.3 Consensus size: 50
41789 AATTATGAAC
* * *
41799 ATTAATTGTTTTATTAA-TTGTGAATATTAAG-TGTGTTATTAATTGTTAGT
1 ATTAATTGTGTTATTAATTTGT-AATATT-AGTTGTGTTAGTAATTGTTACT
41849 ATT-ATCTGTGTTATTAATTTGTAATATTAGTTGTGTTAGTAATTGTTACT
1 ATTAAT-TGTGTTATTAATTTGTAATATTAGTTGTGTTAGTAATTGTTACT
41899 ATTAATTGTGTTAT
1 ATTAATTGTGTTAT
41913 GCTAGTTAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
49 4 0.07
50 47 0.82
51 6 0.11
ACGTcount: A:0.28, C:0.02, G:0.16, T:0.54
Consensus pattern (50 bp):
ATTAATTGTGTTATTAATTTGTAATATTAGTTGTGTTAGTAATTGTTACT
Found at i:45258 original size:2 final size:2
Alignment explanation
Indices: 45251--45290 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
45241 GGAAATATCA
* * *
45251 AT AT AT AT AT AT AT AT AT AT GT AT GT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45291 GTATGTATGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45283 original size:20 final size:20
Alignment explanation
Indices: 45260--45307 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
45250 AATATATATA
45260 TATATATATATGTATGTATG
1 TATATATATATGTATGTATG
45280 TATATATATATGTATGTATG
1 TATATATATATGTATGTATG
45300 TAT-TATAT
1 TATATATAT
45308 TTTAAAGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 5 0.18
20 23 0.82
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.52
Consensus pattern (20 bp):
TATATATATATGTATGTATG
Found at i:45295 original size:4 final size:4
Alignment explanation
Indices: 45268--45302 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
45258 TATATATATA
* *
45268 TATG TATG TATG TATA TATA TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
45303 TATATTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:45320 original size:13 final size:13
Alignment explanation
Indices: 45302--45326 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45292 TATGTATGTA
45302 TTATATTTTAAAG
1 TTATATTTTAAAG
45315 TTATATTTTAAA
1 TTATATTTTAAA
45327 CGTTTTGTAA
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:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
TTATATTTTAAAG
Found at i:45371 original size:19 final size:19
Alignment explanation
Indices: 45347--45384 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
45337 AAAAAGGGTT
45347 TATATATGGTATTT-TATAA
1 TATATAT-GTATTTATATAA
45366 TATATATGTATTTATATAA
1 TATATATGTATTTATATAA
45385 AAAGGATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (19 bp):
TATATATGTATTTATATAA
Found at i:45661 original size:14 final size:15
Alignment explanation
Indices: 45634--45674 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
45624 AATAGTTTTT
45634 TAGTTATATTATATA
1 TAGTTATATTATATA
45649 TAGTTAT-TTATATA
1 TAGTTATATTATATA
45663 TATGTATATATT
1 TA-GT-TATATT
45675 TATTAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 9 0.39
15 9 0.39
16 3 0.13
17 2 0.09
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (15 bp):
TAGTTATATTATATA
Found at i:45664 original size:23 final size:24
Alignment explanation
Indices: 45625--45673 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
45615 AAAAAGGAAA
*
45625 ATAGTTTTTTAGTTATAT-TATAT
1 ATAGTTATTTAGTTATATGTATAT
45648 ATAGTTATTTA-TATATATGTATAT
1 ATAGTTATTTAGT-TATATGTATAT
45672 AT
1 AT
45674 TTATTAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 1 0.04
23 15 0.65
24 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (24 bp):
ATAGTTATTTAGTTATATGTATAT
Found at i:45788 original size:17 final size:18
Alignment explanation
Indices: 45756--45793 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
45746 TTCATGCATC
*
45756 TTTATTTAATTGTTTT-G
1 TTTATTTAATTATTTTAG
*
45773 TTTATTTACTTATTTTAG
1 TTTATTTAATTATTTTAG
45791 TTT
1 TTT
45794 TATTGTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.18, C:0.03, G:0.08, T:0.71
Consensus pattern (18 bp):
TTTATTTAATTATTTTAG
Found at i:51834 original size:17 final size:17
Alignment explanation
Indices: 51814--51866 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
51804 TTTAGGGAAG
51814 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
51831 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
*
51848 TAGTTCATTTATTAAAC
1 TAGTTCATTAATTAAAC
51865 TA
1 TA
51867 ACTCTTAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:51838 original size:34 final size:34
Alignment explanation
Indices: 51796--51866 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
51786 TTTAAATCAT
* ** *
51796 CTAGTTCATTTAGGGAAGTAGTTCATTAATTAAA
1 CTAGTTCATTCAGCAAACTAGTTCATTAATTAAA
* *
51830 CTAGTTCATTCATCAAACTAGTTCATTTATTAAA
1 CTAGTTCATTCAGCAAACTAGTTCATTAATTAAA
51864 CTA
1 CTA
51867 ACTCTTAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.39
Consensus pattern (34 bp):
CTAGTTCATTCAGCAAACTAGTTCATTAATTAAA
Done.