Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007364.1 Corchorus capsularis cultivar CVL-1 contig07385, 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: 23665
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:861 original size:330 final size:329
Alignment explanation
Indices: 8--1490 Score: 1452
Period size: 330 Copynumber: 4.5 Consensus size: 329
1 AGTACTT
* * * *
8 GATTTCGGCTAAAATTTTCCAAAATTTGACCCGAAACATTTCTCCTCAATTTTCGGCCATAATAC
1 GATTTCGGCTAAAATTTTCTAAAAATTGACCC-AAAAATTTCTCCTCAATTTTCGGCCACAATAC
** * * * * * * * *
73 AAAT-GAAAATATATAACTCAACG-CAAAAAGATTGAAGGGCCTCTCACTCATGTAATATCATTT
65 TCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGAGCTTTTCACGCTTCTAATATC--TT
* * ** *
136 TTCC-ATTTTTAT-CGAATTAGTTTCTAGATTAAATCAAAACCGGATTGAGATGCTCGTAAAAAC
128 TTCCTATTTTT-TCCGAATTAATTTCTA-ATTAAATCGAAACATGATTCAGATGCTCGTAAAAAC
* * *
199 AAATCCTT-AATCCAAGGTGGCTGAGATTTCGTTAGATAAATATAGATATTTCAATGAGTCTTGG
191 AAATCCTTAAATCCAATGTGGCTAAGATTTCGTTAGATAAATATAGATATTTCAATGAGACTTGG
* * * * * *
263 CGCCAAAAATCATGTAAAACTA-AGCCG-GAGTTCCGGAATGCATTTTTTAGCCAAAAACTGTGA
256 CGCCAAAAATCATGCAAAAC-AGAGCCGAGA-CTCAGGAACGC-GTTTTTAGCCAAAAACCGTGA
* *
326 T-ATAATCGTACAC
318 TGGT--TAGTACAC
* * * **
339 GATTTCGGCTAAAATTTTGTAAAAATTGA-CCAGATTGAATTT-TCCTCAATTTTTGGCCATGAT
1 GATTTCGGCTAAAATTTTCTAAAAATTGACCCA-A--AAATTTCTCCTCAATTTTCGGCCACAAT
*
402 ACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAA-AGACTTTTCACGCTTCTGATATCG
63 ACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGAG-CTTTTCACGCTTCTAATATC-
*
466 ATTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCTTAAAAA
126 -TTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAA
* * **
531 CAAAT-CTTCGAATCCAATGTGGTTAAGATTT-GATTAGATGGATATAGATATTTCAATGAGACT
190 CAAATCCTT-AAATCCAATGTGGCTAAGATTTCG-TTAGATAAATATAGATATTTCAATGAGACT
* * * * ** **
594 TGTCACCAAAAATCATGCAAAACAGAGCCGAGACTTAGAAACGCGTTTTTAGTTAAAAATTGTGA
253 TGGCGCCAAAAATCATGCAAAACAGAGCCGAGACTCAGGAACGCGTTTTTAGCCAAAAACCGTGA
659 TGGTTAAGTACAC
318 TGGTT-AGTACAC
* * * * *
672 AATTTCGGCTAAAATTTTCTAAAAATTGACACAAAACATTTCTCCTTAA-TTTCCGCCACCATAC
1 GATTTCGGCTAAAATTTTCTAAAAATTGACCCAAAA-ATTTCTCCTCAATTTTCGGCCACAATAC
* * * *
736 TCATAAAAAATATATAATTCAATGTCAAAATGATTGAAGAGTTTTTCACGCTTCTAATAAT-TTT
65 TCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGAGCTTTTCACGCTTCTAAT-ATCTTT
* * *
800 TTCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACCA-GATTGAGATGCTAGTAAAAACAA
129 TCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAA-CATGATTCAGATGCTCGTAAAAACAA
* * * *
864 ATCCTTAAATCCAATGTGGCTGATATTTCGTTAGATAAATATAGATATTTCAATGAGTCTTGGTG
193 ATCCTTAAATCCAATGTGGCTAAGATTTCGTTAGATAAATATAGATATTTCAATGAGACTTGGCG
* * * * **
929 CCAAAAATCATGCAAAACTGAGCTGGAGTCCCA-GAACGCGTTTTTAGCCAAAAACCGTGATAAT
258 CCAAAAATCATGCAAAACAGAGC-CGAGACTCAGGAACGCGTTTTTAGCCAAAAACCGTGATGGT
993 TAGTACAC
322 TAGTACAC
* * * *
1001 GATTTCGGCAAAAATTTTGTAAAAATTGACCCAAAATAATTT-TCCTCAATTTTTGGCCACGATA
1 GATTTCGGCTAAAATTTTCTAAAAATTGACCC-AAA-AATTTCTCCTCAATTTTCGGCCACAATA
* * * * *
1065 CTCATAAAAAATATATAATTCAACACCAAAAATATTGAA-AGGCTATTCACGCTTCTAACACCGT
64 CTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGA-GCTTTTCACGCTTCTAATATC-T
** * * *
1129 ATTTCCTATTTTTTCTAAATTAATTACTAATTGAATCGAAACATGATTCATATGCTCGTAAAAAA
127 -TTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGT-AAAAA
* * * **
1194 AAAATCCTTAAATCCAATGTATG-TAAGATTTGGTTAGATGGATATAGATA-TT---TGAGACTT
190 CAAATCCTTAAATCCAATGT-GGCTAAGATTTCGTTAGATAAATATAGATATTTCAATGAGACTT
* * * * * * * ** *
1254 GGCGCAAAAAATCTTGCAAAGCTGAGCCGGGGCTCCGGAACGCGTTTTTAGTTAAAAATCGTGAT
254 GGCGCCAAAAATCATGCAAAACAGAGCCGAGACTCAGGAACGCGTTTTTAGCCAAAAACCGTGAT
*
1319 GGTTAGTACAT
319 GGTTAGTACAC
* * * *
1330 GATTTCAGCGAAAATTTTAC-AAAAATTGACCCGAGAAATTTCTCCTCAATTTTGGGCCACAATA
1 GATTTCGGCTAAAATTTT-CTAAAAATTGACCC-AAAAATTTCTCCTCAATTTTCGGCCACAATA
* * * * **
1394 CT-ATTAAAAAATATATAACTCAACGTCAAAAAGACTGAAGTGCTTCCCACGCTTCTAATATCGC
64 CTCA-TAAAAAATATATAATTCAACGCCAAAAAGATTGAAGAGCTTTTCACGCTTCTAATAT--C
*
1458 TTTTCCTACCTTTTTCCGAATTAATTTCTAATT
126 TTTTCCTA-TTTTTTCCGAATTAATTTCTAATT
1491 TAAAAATTAT
Statistics
Matches: 954, Mismatches: 156, Indels: 85
0.80 0.13 0.07
Matches are distributed among these distances:
328 10 0.01
329 211 0.22
330 247 0.26
331 66 0.07
332 140 0.15
333 179 0.19
334 99 0.10
335 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (329 bp):
GATTTCGGCTAAAATTTTCTAAAAATTGACCCAAAAATTTCTCCTCAATTTTCGGCCACAATACT
CATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGAGCTTTTCACGCTTCTAATATCTTTTC
CTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATC
CTTAAATCCAATGTGGCTAAGATTTCGTTAGATAAATATAGATATTTCAATGAGACTTGGCGCCA
AAAATCATGCAAAACAGAGCCGAGACTCAGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGT
ACAC
Found at i:1474 original size:662 final size:659
Alignment explanation
Indices: 1--1490 Score: 1932
Period size: 662 Copynumber: 2.2 Consensus size: 659
* *
1 AGTACTTGATTTCGGCTAAAATTTTCCAAAATTTGACCCGAAACATTTCTCCTCAATTTTCGGCC
1 AGTACATGATTTCGGCTAAAATTTT-CAAAAATTGACCCGAAACATTTCTCCTCAATTTTCGGCC
* * * * * *
66 ATAATAC-A-AATGAAAATATATAACTCAACG-CAAAAAGATTGAAGGGCCTCTCACTCATGTAA
65 ACAATACTATAA--AAAATATATAACTCAACGTCAAAAAGATTGAAGAGCTTCTCACGCTTCTAA
* * * *
128 TATCATTTTTCC-ATTTTTATCGAATTAGTTTCTAGATTAAATCAAAACCGGATTGAGATGCTCG
128 TATC--TTTTCCTATTTTT-CCGAATTAATTTCTA-ATTAAATCAAAACCAGATTGAGATGCTAG
192 TAAAAACAAATCCTTAATCCAAGGTGGCTGAGATTTCGTTAGATAAATATAGATATTTCAATGAG
189 TAAAAACAAATCCTTAATCCAAGGTGGCTGAGATTTCGTTAGATAAATATAGATATTTCAATGAG
* * * * * *
257 TCTTGGCGCCAAAAATCATGTAAAACTAAGCCGGAGTTCCGGAATGCATTTTTTAGCCAAAAACT
254 TCTTGGCGCCAAAAATCATGCAAAACTAAGCCGGAGTCCCAGAACGCAGTTTTTAGCCAAAAACC
* * * *
322 GTGATATAATCGTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCAGATTGAATTTTCCTCA
319 GTGATATAATAGTACACGATTTCGGCAAAAATTTTGTAAAAATTGACCAAAATGAATTTTCCTCA
* * *
387 ATTTTTGGCCATGATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGACTTTTCA
384 ATTTTTGGCCACGATACTCATAAAAAATATATAATTCAACACCAAAAAGATTGAAAGACTATTCA
* * * * *
452 CGCTTCTGATATCGATTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCA
449 CGCTTCTAACACCGATTTTCCTATTTTTTCCAAATTAATTACTAATTAAATCGAAACATGATTCA
* * *
517 GATGCTCTTAAAAACAAATCTTCGAATCCAATGTGGTTAAGATTTGATTAGATGGATATAGATAT
514 GATGCTCTAAAAAAAAAATCTTCAAATCCAATGTGGTTAAGATTTGATTAGATGGATATAGATAT
* * *
582 TTCAATGAGACTTGTCACCAAAAATCATGCAAAACAGAGCCGAGACTTAGAAACGCGTTTTTAGT
579 TT--ATGAGACTTGGCACAAAAAATCATGCAAAACAGAGCCGAGACTCAGAAACGCGTTTTTAGT
*
647 TAAAAATTGTGATGGTTA
642 TAAAAATCGTGATGGTTA
** * * * *
665 AGTACACAATTTCGGCTAAAATTTTCTAAAAATTGACACAAAACATTTCTCCTTAA-TTTCCGCC
1 AGTACATGATTTCGGCTAAAATTTTC-AAAAATTGACCCGAAACATTTCTCCTCAATTTTCGGCC
* * * * * *
729 ACCATACTCATAAAAAATATATAATTCAATGTCAAAATGATTGAAGAGTTTTTCACGCTTCTAAT
65 ACAATACT-ATAAAAAATATATAACTCAACGTCAAAAAGATTGAAGAGCTTCTCACGCTTCTAAT
* *
794 AAT-TTTTTCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACCAGATTGAGATGCTAGTAA
129 -ATCTTTTCCTA-TTTTTCCGAATTAATTTCTAATTAAATCAAAACCAGATTGAGATGCTAGTAA
* *
858 AAACAAATCCTTAAATCCAATGTGGCTGATATTTCGTTAGATAAATATAGATATTTCAATGAGTC
192 AAACAAATCCTT-AATCCAAGGTGGCTGAGATTTCGTTAGATAAATATAGATATTTCAATGAGTC
* * *
923 TTGGTGCCAAAAATCATGCAAAACTGAGCTGGAGTCCCAGAACGC-GTTTTTAGCCAAAAACCGT
256 TTGGCGCCAAAAATCATGCAAAACTAAGCCGGAGTCCCAGAACGCAGTTTTTAGCCAAAAACCGT
*
987 GATA-ATTAGTACACGATTTCGGCAAAAATTTTGTAAAAATTGACCCAAAAT-AATTTTCCTCAA
321 GATATAATAGTACACGATTTCGGCAAAAATTTTGTAAAAATTGA-CCAAAATGAATTTTCCTCAA
* *
1050 TTTTTGGCCACGATACTCATAAAAAATATATAATTCAACACCAAAAATATTGAAAGGCTATTCAC
385 TTTTTGGCCACGATACTCATAAAAAATATATAATTCAACACCAAAAAGATTGAAAGACTATTCAC
* *
1115 GCTTCTAACACCG-TATTTCCTATTTTTTCTAAATTAATTACTAATTGAATCGAAACATGATTCA
450 GCTTCTAACACCGAT-TTTCCTATTTTTTCCAAATTAATTACTAATTAAATCGAAACATGATTCA
* * *
1179 TATGCTCGTAAAAAAAAAATCCTT-AAATCCAATGT-ATGTAAGATTTGGTTAGATGGATATAGA
514 GATGCTC-TAAAAAAAAAAT-CTTCAAATCCAATGTGGT-TAAGATTTGATTAGATGGATATAGA
* * * * * * * *
1242 TA-TT-TGAGACTTGGCGCAAAAAATCTTGCAAAGCTGAGCCGGGGCTCCGGAACGCGTTTTTAG
576 TATTTATGAGACTTGGCACAAAAAATCATGCAAAACAGAGCCGAGACTCAGAAACGCGTTTTTAG
1305 TTAAAAATCGTGATGGTT-
641 TTAAAAATCGTGATGGTTA
* * *
1323 AGTACATGATTTCAGCGAAAATTTTACAAAAATTGACCCGAGAA-ATTTCTCCTCAATTTTGGGC
1 AGTACATGATTTCGGCTAAAATTTT-CAAAAATTGACCCGA-AACATTTCTCCTCAATTTTCGGC
* * *
1387 CACAATACTATTAAAAAATATATAACTCAACGTCAAAAAGACTGAAGTGCTTCCCACGCTTCTAA
64 CACAATACTA-TAAAAAATATATAACTCAACGTCAAAAAGATTGAAGAGCTTCTCACGCTTCTAA
1452 TATCGCTTTTCCTACCTTTTTCCGAATTAATTTCTAATT
128 TAT--CTTTTCCTA--TTTTTCCGAATTAATTTCTAATT
1491 TAAAAATTAT
Statistics
Matches: 712, Mismatches: 92, Indels: 46
0.84 0.11 0.05
Matches are distributed among these distances:
658 47 0.07
659 128 0.18
661 8 0.01
662 195 0.27
663 131 0.18
664 168 0.24
665 31 0.04
666 4 0.01
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (659 bp):
AGTACATGATTTCGGCTAAAATTTTCAAAAATTGACCCGAAACATTTCTCCTCAATTTTCGGCCA
CAATACTATAAAAAATATATAACTCAACGTCAAAAAGATTGAAGAGCTTCTCACGCTTCTAATAT
CTTTTCCTATTTTTCCGAATTAATTTCTAATTAAATCAAAACCAGATTGAGATGCTAGTAAAAAC
AAATCCTTAATCCAAGGTGGCTGAGATTTCGTTAGATAAATATAGATATTTCAATGAGTCTTGGC
GCCAAAAATCATGCAAAACTAAGCCGGAGTCCCAGAACGCAGTTTTTAGCCAAAAACCGTGATAT
AATAGTACACGATTTCGGCAAAAATTTTGTAAAAATTGACCAAAATGAATTTTCCTCAATTTTTG
GCCACGATACTCATAAAAAATATATAATTCAACACCAAAAAGATTGAAAGACTATTCACGCTTCT
AACACCGATTTTCCTATTTTTTCCAAATTAATTACTAATTAAATCGAAACATGATTCAGATGCTC
TAAAAAAAAAATCTTCAAATCCAATGTGGTTAAGATTTGATTAGATGGATATAGATATTTATGAG
ACTTGGCACAAAAAATCATGCAAAACAGAGCCGAGACTCAGAAACGCGTTTTTAGTTAAAAATCG
TGATGGTTA
Found at i:1586 original size:27 final size:26
Alignment explanation
Indices: 1547--1637 Score: 91
Period size: 27 Copynumber: 3.4 Consensus size: 26
1537 AAAAATACAA
1547 AAAATTATATTTTAATAATG-GTATAGTT
1 AAAA-TATATTTTAATAATGAGTA-A-TT
1575 AAAATATATTTTAATAATGACGTAATT
1 AAAATATATTTTAATAATGA-GTAATT
*
1602 -AAA-ATATTTTAATAATGA-CAATTT
1 AAAATATATTTTAATAATGAGTAA-TT
1626 AGAAATATATTT
1 A-AAATATATTT
1638 GGAAAAATGG
Statistics
Matches: 56, Mismatches: 1, Indels: 13
0.80 0.01 0.19
Matches are distributed among these distances:
23 2 0.04
24 2 0.04
25 15 0.27
26 6 0.11
27 23 0.41
28 5 0.09
29 3 0.05
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (26 bp):
AAAATATATTTTAATAATGAGTAATT
Found at i:1614 original size:25 final size:29
Alignment explanation
Indices: 1547--1620 Score: 97
Period size: 27 Copynumber: 2.7 Consensus size: 29
1537 AAAAATACAA
1547 AAAATTATATTTTAATAATG--GTATAGTT
1 AAAA-TATATTTTAATAATGACGTATAGTT
1575 AAAATATATTTTAATAATGACGTA-A-TT
1 AAAATATATTTTAATAATGACGTATAGTT
1602 -AAA-ATATTTTAATAATGAC
1 AAAATATATTTTAATAATGAC
1621 AATTTAGAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
25 16 0.36
26 3 0.07
27 17 0.39
28 5 0.11
29 3 0.07
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (29 bp):
AAAATATATTTTAATAATGACGTATAGTT
Found at i:1631 original size:25 final size:23
Alignment explanation
Indices: 1553--1633 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 23
1543 ACAAAAAATT
* *
1553 ATATTTTAATAATGGTATAGTTAAAA
1 ATATTTTAATAAT-G-ACAATT-AAA
1579 TATATTTTAATAATGACGTAATTAAA
1 -ATATTTTAATAATGAC--AATTAAA
1605 ATATTTTAATAATGACAATTTAGAA
1 ATATTTTAATAATGACAA-TTA-AA
1630 ATAT
1 ATAT
1634 ATTTGGAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
23 2 0.04
24 3 0.06
25 23 0.48
26 4 0.08
27 16 0.33
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (23 bp):
ATATTTTAATAATGACAATTAAA
Found at i:1906 original size:37 final size:37
Alignment explanation
Indices: 1865--1960 Score: 113
Period size: 38 Copynumber: 2.6 Consensus size: 37
1855 TCTAAAGCCC
* *
1865 AAATAAGACGTTGGAGACGAAGACAAAAAGCAAAATT
1 AAATAAGACGTTGGAAACAAAGACAAAAAGCAAAATT
* * *
1902 AAATACA-ATGATTGGAAACAAAGACAAAAGGTAAAATT
1 AAATA-AGACG-TTGGAAACAAAGACAAAAAGCAAAATT
*
1940 AAATAGGACGTTGGAAACAAA
1 AAATAAGACGTTGGAAACAAA
1961 AAGGCAAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
37 18 0.37
38 31 0.63
ACGTcount: A:0.55, C:0.09, G:0.20, T:0.16
Consensus pattern (37 bp):
AAATAAGACGTTGGAAACAAAGACAAAAAGCAAAATT
Found at i:2028 original size:15 final size:15
Alignment explanation
Indices: 2008--2058 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
1998 TATATTATCT
2008 AATAATTAATAATGG
1 AATAATTAATAATGG
* * *
2023 AATAATTTATGATTG
1 AATAATTAATAATGG
2038 AA-AA--AATAATGG
1 AATAATTAATAATGG
2050 AATAATTAA
1 AATAATTAA
2059 AATATTATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
12 7 0.26
13 2 0.07
14 2 0.07
15 16 0.59
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (15 bp):
AATAATTAATAATGG
Found at i:2139 original size:31 final size:31
Alignment explanation
Indices: 2084--2179 Score: 149
Period size: 31 Copynumber: 3.1 Consensus size: 31
2074 TGGCAATTTA
* *
2084 GAAATATGTTTTAAAAA-AAAGGTACAATTG
1 GAAATATATTTTAAAAATAAGGGTACAATTG
2114 GAAATATATTTTAAAAATAAGGGTACAATTG
1 GAAATATATTTTAAAAATAAGGGTACAATTG
* *
2145 GAAATATTTTTTAAAAATAAGGGTACAATCG
1 GAAATATATTTTAAAAATAAGGGTACAATTG
2176 GAAA
1 GAAA
2180 ACATAAAGTT
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 16 0.26
31 45 0.74
ACGTcount: A:0.49, C:0.04, G:0.17, T:0.30
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGGGTACAATTG
Found at i:5242 original size:128 final size:129
Alignment explanation
Indices: 5031--5291 Score: 364
Period size: 128 Copynumber: 2.0 Consensus size: 129
5021 AAATCAACAC
* * * *
5031 TTGCAACAAAATTTTCAGATTTTGTTTCCCCAACAAATTTTCAAGGCGGTGAAGAGAATGCAGTG
1 TTGCAACAAAATTTTCAGATTTTGGTTCCCAAACAAATATTCAAGGCAGTGAAGAGAATGCAGTG
*
5096 TTTGCAACAAATTTTTCAGATTCGGTTTCCTCAAGAAATATT-GCGGTGAAGAGGATGCAGTGT
66 TTTGCAACAAATTTTTCAGATTCGGTTTCCTCAAGAAATATTAGCGGTGAAGAGAATGCAGTGT
** * *
5159 TTGCAACAAGTTTTTCAGA-TTTGGTTCCCTAAAGAAATATTCAGGGCAGTGAAGAGAATGCAGT
1 TTGCAACAAAATTTTCAGATTTTGGTTCCC-AAACAAATATTCAAGGCAGTGAAGAGAATGCAGT
* * *
5223 TTTTGCAACAAGTTTTTCAGATTTGGTTTCCTCAAGAAATATTCAAGGCGGTGAAGAGAATGCAG
65 GTTTGCAACAAATTTTTCAGATTCGGTTTCCTCAAGAAATATT--A-GCGGTGAAGAGAATGCAG
5288 TGT
127 TGT
5291 T
1 T
5292 CGAATCAATG
Statistics
Matches: 116, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
127 9 0.08
128 86 0.74
132 21 0.18
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.32
Consensus pattern (129 bp):
TTGCAACAAAATTTTCAGATTTTGGTTCCCAAACAAATATTCAAGGCAGTGAAGAGAATGCAGTG
TTTGCAACAAATTTTTCAGATTCGGTTTCCTCAAGAAATATTAGCGGTGAAGAGAATGCAGTGT
Found at i:5312 original size:66 final size:66
Alignment explanation
Indices: 5031--5291 Score: 368
Period size: 66 Copynumber: 4.0 Consensus size: 66
5021 AAATCAACAC
** * * * *
5031 TTGCAACAAAATTTTCAGATTTTGTTTCCCCAACAAATTTTCAAGGCGGTGAAGAGAATGCAGTG
1 TTGCAACAAGTTTTTCAGATTTGGTTTCCTCAAGAAATATTCAAGGCGGTGAAGAGAATGCAGTG
5096 T
66 T
* * *
5097 TTGCAACAAATTTTTCAGATTCGGTTTCCTCAAGAAATATT----GCGGTGAAGAGGATGCAGTG
1 TTGCAACAAGTTTTTCAGATTTGGTTTCCTCAAGAAATATTCAAGGCGGTGAAGAGAATGCAGTG
5158 T
66 T
* * * * *
5159 TTGCAACAAGTTTTTCAGATTTGGTTCCCTAAAGAAATATTCAGGGCAGTGAAGAGAATGCAGTT
1 TTGCAACAAGTTTTTCAGATTTGGTTTCCTCAAGAAATATTCAAGGCGGTGAAGAGAATGCAGTG
5224 T
66 T
5225 TTGCAACAAGTTTTTCAGATTTGGTTTCCTCAAGAAATATTCAAGGCGGTGAAGAGAATGCAGTG
1 TTGCAACAAGTTTTTCAGATTTGGTTTCCTCAAGAAATATTCAAGGCGGTGAAGAGAATGCAGTG
5290 T
66 T
5291 T
1 T
5292 CGAATCAATG
Statistics
Matches: 172, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
62 57 0.33
66 115 0.67
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.32
Consensus pattern (66 bp):
TTGCAACAAGTTTTTCAGATTTGGTTTCCTCAAGAAATATTCAAGGCGGTGAAGAGAATGCAGTG
T
Found at i:9223 original size:20 final size:20
Alignment explanation
Indices: 9180--9224 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
9170 AATTGAAATG
*
9180 ACCCGTTGAAAACCGATGTG
1 ACCCGTTGAAAACCGATGTA
*
9200 ACCCGTTGAAATCCGGAT-TA
1 ACCCGTTGAAAACC-GATGTA
9220 ACCCG
1 ACCCG
9225 ATGACCCGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (20 bp):
ACCCGTTGAAAACCGATGTA
Found at i:11756 original size:22 final size:22
Alignment explanation
Indices: 11737--11780 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
11727 AAATTAATTT
11737 TTAATTAATTAGTATTTAATTAC
1 TTAATTAATTAGT-TTTAATTAC
* *
11760 TTAGTTTATTAGTTTTAATTA
1 TTAATTAATTAGTTTTAATTA
11781 GTTTATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.57
Consensus pattern (22 bp):
TTAATTAATTAGTTTTAATTAC
Found at i:12036 original size:21 final size:20
Alignment explanation
Indices: 11996--12039 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
11986 AAAATTATGA
*
11996 AAAAGGGGGCGGTATTTAGC
1 AAAAGGGGGCGGTATATAGC
12016 AAAAGGGAGGCGGTGA-ATAGC
1 AAAAGGG-GGCGGT-ATATAGC
12037 AAA
1 AAA
12040 CCCCTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 13 0.62
22 1 0.05
ACGTcount: A:0.39, C:0.09, G:0.39, T:0.14
Consensus pattern (20 bp):
AAAAGGGGGCGGTATATAGC
Found at i:14394 original size:14 final size:15
Alignment explanation
Indices: 14372--14406 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
14362 TAAAATAATT
*
14372 TATAGTATATATA-A
1 TATAATATATATATA
14386 TATAATATATATATA
1 TATAATATATATATA
14401 TATAAT
1 TATAAT
14407 CATCAATTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (15 bp):
TATAATATATATATA
Found at i:15715 original size:55 final size:55
Alignment explanation
Indices: 15655--15767 Score: 217
Period size: 55 Copynumber: 2.1 Consensus size: 55
15645 AAATCGTTAA
*
15655 TTGAAATTGAGGATTAAGGTTCTTTAATTTTAGTTGTTTTATAGTGGTTTTAGGG
1 TTGAAATTGAGGATTAAGGTTCTTTAATTTTAGTTGTTTTATAGTGCTTTTAGGG
15710 TTGAAATTGAGGATTAAGGTTCTTTAATTTTAGTTGTTTTATAGTGCTTTTAGGG
1 TTGAAATTGAGGATTAAGGTTCTTTAATTTTAGTTGTTTTATAGTGCTTTTAGGG
15765 TTG
1 TTG
15768 GTCATTGGAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.23, C:0.03, G:0.25, T:0.50
Consensus pattern (55 bp):
TTGAAATTGAGGATTAAGGTTCTTTAATTTTAGTTGTTTTATAGTGCTTTTAGGG
Found at i:21742 original size:2 final size:2
Alignment explanation
Indices: 21735--21772 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
21725 ACTGACAGTC
21735 TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21773 GATGATCATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22410 original size:19 final size:18
Alignment explanation
Indices: 22367--22413 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
22357 TATAAAACAT
*
22367 TAAAATTAAAAACTTATA
1 TAAAATTATAAACTTATA
22385 TATAAATTATAAA-TTATAA
1 TA-AAATTATAAACTTAT-A
22404 CTAAAATTAT
1 -TAAAATTAT
22414 TAATCTTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 6 0.24
19 17 0.68
20 2 0.08
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAATTATAAACTTATA
Done.