Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006856.1 Corchorus capsularis cultivar CVL-1 contig06877, 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: 110061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2532 original size:31 final size:31
Alignment explanation
Indices: 2494--2556 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
2484 CAATCAATTC
*
2494 GTCCTGATGGAAAGCCTCTCGAT-ATTAAGTT
1 GTCCTGATGGAAAGCCTCCCGATGA-TAAGTT
*
2525 GTCCTGATGGAAAGCGTCCCGATGATAAGTT
1 GTCCTGATGGAAAGCCTCCCGATGATAAGTT
2556 G
1 G
2557 CTTTAGAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (31 bp):
GTCCTGATGGAAAGCCTCCCGATGATAAGTT
Found at i:6485 original size:24 final size:24
Alignment explanation
Indices: 6453--6501 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
6443 CAATGGAACA
**
6453 TCATGACCATCAGGACCCAAACTC
1 TCATGACCATCAAAACCCAAACTC
6477 TCATGACCATCAAAACCCAAACTC
1 TCATGACCATCAAAACCCAAACTC
6501 T
1 T
6502 TTGTCCCGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.37, G:0.08, T:0.18
Consensus pattern (24 bp):
TCATGACCATCAAAACCCAAACTC
Found at i:9114 original size:169 final size:170
Alignment explanation
Indices: 8818--9132 Score: 499
Period size: 169 Copynumber: 1.9 Consensus size: 170
8808 TCTGAAAAAA
* * * *
8818 TTACTAATTATAAATTTGTCATAAATTATTCATATAACTGATTTATTATTTATTCGTATATATAA
1 TTACTAACTATAAATTTATCAAAAATTATTCATATAACTGATTTACTATTTATTCG-ATATATAA
* * *
8883 TAAGTGTTCATATAATGAAGTCATAATAGCTAAAATTATAATAATAATATAAATTTTATTGAATA
65 TAAGTGTTCATATAATGAAATCATAATAGCTAAAATTATAACAATAATATAAATTATATTGAATA
*
8948 AATGATAATTTAGAATTTTATTCATTATGTAAAAAAACAAT
130 AATGATAAATTAGAATTTTATTCATTATGTAAAAAAACAAT
*
8989 TTACTAACTATAAATTTATCAAAAATTATTCATATATCTGATTTACTATTTATTCG-TATATAAT
1 TTACTAACTATAAATTTATCAAAAATTATTCATATAACTGATTTACTATTTATTCGATATATAAT
* *
9053 AATTGTTCGTATAATGAAATCATAATAG-TAAAAATTATAACAATAATATAAATTATATTGAATA
66 AAGTGTTCATATAATGAAATCATAATAGCT-AAAATTATAACAATAATATAAATTATATTGAATA
9117 AATGATAAATTAGAAT
130 AATGATAAATTAGAAT
9133 GGTTAAAATT
Statistics
Matches: 132, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
168 1 0.01
169 80 0.61
171 51 0.39
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (170 bp):
TTACTAACTATAAATTTATCAAAAATTATTCATATAACTGATTTACTATTTATTCGATATATAAT
AAGTGTTCATATAATGAAATCATAATAGCTAAAATTATAACAATAATATAAATTATATTGAATAA
ATGATAAATTAGAATTTTATTCATTATGTAAAAAAACAAT
Found at i:9848 original size:33 final size:32
Alignment explanation
Indices: 9796--9870 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 32
9786 TCGGTGACGC
* * * *
9796 CCCAGGAGGACGGCCTGACCACGGTAGTGCCG
1 CCCAGGGGGGCGGCCTGACCACAGTAGGGCCG
*
9828 CCCTAGGGGGGCGGCTTGACCACAGTAGGGCCG
1 CCC-AGGGGGGCGGCCTGACCACAGTAGGGCCG
9861 CCCAGGGGGG
1 CCCAGGGGGG
9871 TAGCATAAGC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 10 0.27
33 27 0.73
ACGTcount: A:0.16, C:0.32, G:0.43, T:0.09
Consensus pattern (32 bp):
CCCAGGGGGGCGGCCTGACCACAGTAGGGCCG
Found at i:9995 original size:33 final size:31
Alignment explanation
Indices: 9955--10060 Score: 106
Period size: 33 Copynumber: 3.3 Consensus size: 31
9945 GCCGCCCTAG
9955 GGGGCGGCTTACCATGGCTCAAGCCGCCCTCCT
1 GGGGCGGCTTACCATGG-T-AAGCCGCCCTCCT
* *
9988 GGGGCGGCTCTGCCA-CGTGAAGCCGCCCTCCT
1 GGGGCGGCT-TACCATGGT-AAGCCGCCCTCCT
* *
10020 AGGGTGGCTTGAGCCATGGTAAGCCGCCCTCCT
1 GGGGCGGCTT-A-CCATGGTAAGCCGCCCTCCT
*
10053 GAGGCGGC
1 GGGGCGGC
10061 ACGGGTCATC
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
31 1 0.02
32 21 0.36
33 31 0.53
34 6 0.10
ACGTcount: A:0.12, C:0.36, G:0.35, T:0.17
Consensus pattern (31 bp):
GGGGCGGCTTACCATGGTAAGCCGCCCTCCT
Found at i:28395 original size:40 final size:40
Alignment explanation
Indices: 28340--28416 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
28330 GAGACCTTGT
28340 TAGTGTTGATTGCTAGTTAAGAAACATAATTGAAAATGGG
1 TAGTGTTGATTGCTAGTTAAGAAACATAATTGAAAATGGG
28380 TAGTGTTGATTGCTAGTTAAGAAACATAATTGAAAAT
1 TAGTGTTGATTGCTAGTTAAGAAACATAATTGAAAAT
28417 TGGAGCAAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (40 bp):
TAGTGTTGATTGCTAGTTAAGAAACATAATTGAAAATGGG
Found at i:33591 original size:442 final size:435
Alignment explanation
Indices: 32524--33564 Score: 1207
Period size: 442 Copynumber: 2.4 Consensus size: 435
32514 TCGAAATTAC
** * * *
32524 AAAATTTCAAAAGTATTTTTTAGAATTGAAACATGAAAATTAGCTTTTGAG-TCATTCAT-AAAA
1 AAAATTTCGGAAGCATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTTC-TTCATGAAAA
* * *
32587 GTTGTAGATCATAAAATTACCTTTTAATAGACACCTGAATTACCTTAAT-TGGACAAATAGAAAA
65 -TTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCACCTTAATCT-GACAAATAGAAAA
** * ** * *
32651 AAAAA-ATTAAAAGAAAAATGAAGTGTTAAATCAAATAAGATAGAATTTGTAAATGACTAAGTAT
128 AAAAATAAAAAAATAAAAACCAAGCGTTAAATC---TAAGATAGAATTTGTAAAGGACTAAGTAT
* * * * *
32715 AAAATAGAAAAGTATGAGAGTCATTTGATAACTAATTCAAATAAGAAAATATTTCTTAATGGATA
190 AAAATAGAAAAATATGAGAGTCATTTAATAAATAATTCAAATAAGAAAATATTTCTTAATGAAGA
* * *
32780 TCTTGAAATATAAAAATTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTAACTTTCAGG
255 TCTTGAAACATAAAAATTCCCTTTTAAACCCTTCATGAAACTCATAGATCAAATTAACTTTCAGG
* * * * * * * *
32845 TTCTTCATGAAAGTCGTAGATCATACAGTAATCTTTTAACCGGCACTTGAATAACTTTAGTCGGA
320 TCCTTCATGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTGAATAACTTCAATCAGA
** * * * * *
32910 CATGTGGATGGAAAATTATATGGTATTAAATAGACCAACAATCGAAACGAC
385 CATGTGGATCAAAAATTATACGATATTAAATAGACCAACAATCAAAACAAA
* * * *
32961 CAAATTTAGGAAGCATTTTTTTTTA-AATTAAAACATAAAAATTTGCTTTTGAGTCCTTCATGAA
1 AAAATTTCGGAAGCA---TTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTTCTTCATGAA
* * *
33025 AGTTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCAACTAATTAATCGGACAAATAGA
63 AATTGTAGATCATGAAATTACCTTTTAATAGACACATGAATC-AC--CTTAATCTGACAAATAGA
* * * * * *
33090 ACAAAGAATAAAAAAAT-AAATCTTAAACGTTAGAT-TAAGATAGAATTTGTAAAGGACTAAGTA
125 AAAAAAAATAAAAAAATAAAAAC-CAAGCGTTAAATCTAAGATAGAATTTGTAAAGGACTAAGTA
* * *
33153 GTATAAAGTAGAAAAATATGAGGGTCATTTAATAAATAATTCAAATAAGAAAATTTTTGTTAATG
189 -TA-AAA-TAGAAAAATATGAGAGTCATTTAATAAATAATTCAAATAAGAAAATATTTCTTAATG
* * * *
33218 AAGATCTTGAAGCATAAAAATTCCTTTTTAAATCCTTCATGAAACTCATAGATCAAATTTAGCTT
251 AAGATCTTGAAACATAAAAATTCCCTTTTAAACCCTTCATGAAACTCATAGATCAAA-TTAACTT
** * * *
33283 TTGGGTCCTTCATGAAAGTCGTAAATCATGCAATAACCTTTTAACTGACACTTTAATAACTTCAA
315 TCAGGTCCTTCATGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTGAATAACTTCAA
* **
33348 TCAGACATGTGGA-CAAAAACTTATACGATATTAAATTGACCGGCAATCAAAACAAA
380 TCAGACATGTGGATCAAAAA-TTATACGATATTAAATAGACCAACAATCAAAACAAA
* * *
33404 AAAATTTCGGAAGCATTTTTTAGAATCAAAACATTAAAATTGGCTTTTGAGTTCTTCATGAAAAT
1 AAAATTTCGGAAGCATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTTCTTCATGAAAAT
*
33469 TGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCACCTTAATCTGACAAATAGAAAAAAA
66 TGTAGATCATGAAATTACCTTTTAATAGACACATGAATCACCTTAATCTGACAAATAGAAAAAAA
* *
33534 AATACAAAAATAAAAGCCAATGCGTTAAATC
131 AATAAAAAAATAAAAACCAA-GCGTTAAATC
33565 GTCCAACCTA
Statistics
Matches: 502, Mismatches: 82, Indels: 37
0.81 0.13 0.06
Matches are distributed among these distances:
437 10 0.02
438 32 0.06
439 105 0.21
440 24 0.05
441 78 0.16
442 128 0.25
443 125 0.25
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.31
Consensus pattern (435 bp):
AAAATTTCGGAAGCATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTTCTTCATGAAAAT
TGTAGATCATGAAATTACCTTTTAATAGACACATGAATCACCTTAATCTGACAAATAGAAAAAAA
AATAAAAAAATAAAAACCAAGCGTTAAATCTAAGATAGAATTTGTAAAGGACTAAGTATAAAATA
GAAAAATATGAGAGTCATTTAATAAATAATTCAAATAAGAAAATATTTCTTAATGAAGATCTTGA
AACATAAAAATTCCCTTTTAAACCCTTCATGAAACTCATAGATCAAATTAACTTTCAGGTCCTTC
ATGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTGAATAACTTCAATCAGACATGTG
GATCAAAAATTATACGATATTAAATAGACCAACAATCAAAACAAA
Found at i:45033 original size:32 final size:32
Alignment explanation
Indices: 44986--45162 Score: 194
Period size: 32 Copynumber: 5.5 Consensus size: 32
44976 TATATGTAGT
* * * *
44986 TAAATATAGCGGCGTTTTATTCTCTAAAGGCCGC
1 TAAATA-AG-GGCGTTTTGTTCTATAGACGCCGC
* *
45020 TAAATAAGGGCG-TTTGCTTGTATAGACGCTGC
1 TAAATAAGGGCGTTTTG-TTCTATAGACGCCGC
* *
45052 TAAATAGGGGCGTTTTGTTCTGTAGACGCCGC
1 TAAATAAGGGCGTTTTGTTCTATAGACGCCGC
* * * *
45084 TAAATAAAGGCGTTCTGTTCTATAGATGTCGC
1 TAAATAAGGGCGTTTTGTTCTATAGACGCCGC
*
45116 TAAATAAGGGCGTTTGGTTCTATAGACGCCGC
1 TAAATAAGGGCGTTTTGTTCTATAGACGCCGC
*
45148 TAAATAAGGTCGTTT
1 TAAATAAGGGCGTTT
45163 AGGGTTCATA
Statistics
Matches: 119, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
31 3 0.03
32 104 0.87
33 6 0.05
34 6 0.05
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.32
Consensus pattern (32 bp):
TAAATAAGGGCGTTTTGTTCTATAGACGCCGC
Found at i:46881 original size:2 final size:2
Alignment explanation
Indices: 46868--46899 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
46858 CACATAAATC
46868 AT AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46900 TAAAACCATC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53855 original size:11 final size:11
Alignment explanation
Indices: 53839--53866 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
53829 ATGAATCAAA
53839 GAGAAGGAAAG
1 GAGAAGGAAAG
53850 GAGAAGGAAAG
1 GAGAAGGAAAG
53861 GAGAAG
1 GAGAAG
53867 CCAGAAGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (11 bp):
GAGAAGGAAAG
Found at i:54005 original size:44 final size:43
Alignment explanation
Indices: 53917--53998 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 43
53907 GCGAATCAAA
*
53917 GAAGTTT-TAGGGGAGTTAGAAATGAAAGTTAGAAAAGAGACT
1 GAAGTTTGTAGGGGAGTTAGAAAAGAAAGTTAGAAAAGAGACT
* *
53959 GAAGTTTGTGGGGAGAGTTAGAAAAGAGAG-TAGGAAAAGA
1 GAAGTTTGTAGGG-GAGTTAGAAAAGAAAGTTA-GAAAAGA
53999 TGCTGAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 7 0.21
43 6 0.18
44 21 0.62
ACGTcount: A:0.43, C:0.01, G:0.35, T:0.21
Consensus pattern (43 bp):
GAAGTTTGTAGGGGAGTTAGAAAAGAAAGTTAGAAAAGAGACT
Found at i:54188 original size:28 final size:28
Alignment explanation
Indices: 54139--54202 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 28
54129 AATTAGAAAA
54139 TAATAGTATTTACAATGAAATGAAATTAT
1 TAATAG-ATTTACAATGAAATGAAATTAT
*
54168 TAATAGATTGTA-AATGTAATGAAATTAT
1 TAATAGATT-TACAATGAAATGAAATTAT
54196 TAATAGA
1 TAATAGA
54203 AAATAATATT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 25 0.76
29 8 0.24
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (28 bp):
TAATAGATTTACAATGAAATGAAATTAT
Found at i:54256 original size:30 final size:30
Alignment explanation
Indices: 54221--54279 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
54211 TTATGATGAC
*
54221 AATTATAAATGTAATGAAATTATATTTAGG
1 AATTATAAATGTAATGAAATAATATTTAGG
*
54251 AATTATATATGTAATGAAATAATATTTAG
1 AATTATAAATGTAATGAAATAATATTTAG
54280 AAAATAATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (30 bp):
AATTATAAATGTAATGAAATAATATTTAGG
Found at i:54286 original size:14 final size:14
Alignment explanation
Indices: 54267--54340 Score: 87
Period size: 14 Copynumber: 5.1 Consensus size: 14
54257 ATATGTAATG
54267 AAATAATATTTAGA
1 AAATAATATTTAGA
*
54281 AAATAATACTTAGA
1 AAATAATATTTAGA
*
54295 AATTATATATGTTTAG-
1 AA--ATA-ATATTTAGA
*
54311 AAATTATATTTAGA
1 AAATAATATTTAGA
54325 AAATAATATTTAGA
1 AAATAATATTTAGA
54339 AA
1 AA
54341 TTATAGATGT
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
13 7 0.14
14 32 0.64
16 5 0.10
17 6 0.12
ACGTcount: A:0.53, C:0.01, G:0.08, T:0.38
Consensus pattern (14 bp):
AAATAATATTTAGA
Found at i:54339 original size:27 final size:27
Alignment explanation
Indices: 54267--54345 Score: 95
Period size: 30 Copynumber: 2.8 Consensus size: 27
54257 ATATGTAATG
*
54267 AAATAATATTTAGAAAATAATACTTAGA
1 AAATAATATTTAG-AAATTATACTTAGA
* *
54295 AATTATATATGTTTAGAAATTATATTTAGA
1 AA--ATA-ATATTTAGAAATTATACTTAGA
54325 AAATAATATTTAGAAATTATA
1 AAATAATATTTAGAAATTATA
54346 GATGTAATGC
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
27 15 0.34
28 5 0.11
30 17 0.39
31 7 0.16
ACGTcount: A:0.52, C:0.01, G:0.08, T:0.39
Consensus pattern (27 bp):
AAATAATATTTAGAAATTATACTTAGA
Found at i:54362 original size:44 final size:44
Alignment explanation
Indices: 54237--54354 Score: 166
Period size: 44 Copynumber: 2.7 Consensus size: 44
54227 AAATGTAATG
* * *
54237 AAATTATATTTAGGAATTATATATGTAATGAAATAATATTTAGA
1 AAATAATATTTAGAAATTATATATGTAATGAAATTATATTTAGA
* *
54281 AAATAATACTTAGAAATTATATATGT-TTAGAAATTATATTTAGA
1 AAATAATATTTAGAAATTATATATGTAAT-GAAATTATATTTAGA
*
54325 AAATAATATTTAGAAATTATAGATGTAATG
1 AAATAATATTTAGAAATTATATATGTAATG
54355 CTATTATAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
43 1 0.02
44 62 0.97
45 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.11, T:0.40
Consensus pattern (44 bp):
AAATAATATTTAGAAATTATATATGTAATGAAATTATATTTAGA
Found at i:54750 original size:32 final size:32
Alignment explanation
Indices: 54655--54762 Score: 101
Period size: 32 Copynumber: 3.4 Consensus size: 32
54645 AGACGCGAAC
* * * *
54655 TTAGTGGCGTTTTCTTCAATAGACGCCGCTAA
1 TTAGCGGCATTTTATTCAATAGACGCCGCTAT
* * * ** *
54687 ATAGCGGCGTTTTGTTCTTTGGACGCCGCTAT
1 TTAGCGGCATTTTATTCAATAGACGCCGCTAT
*
54719 TTAGCGGCATTTTATTCAATAGATGCCGCTAT
1 TTAGCGGCATTTTATTCAATAGACGCCGCTAT
*
54751 TT-GCTGCATTTT
1 TTAGCGGCATTTT
54763 CCACAGATGT
Statistics
Matches: 61, Mismatches: 15, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
31 9 0.15
32 52 0.85
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (32 bp):
TTAGCGGCATTTTATTCAATAGACGCCGCTAT
Found at i:56269 original size:27 final size:27
Alignment explanation
Indices: 56239--56318 Score: 115
Period size: 27 Copynumber: 3.0 Consensus size: 27
56229 GCATTAGGGT
*
56239 CGCCCAAGGGTATTTTGGTCATTTTCG
1 CGCCCAGGGGTATTTTGGTCATTTTCG
56266 CGCCCAGGGGTATTTTGGTCATTTTCG
1 CGCCCAGGGGTATTTTGGTCATTTTCG
** * *
56293 CATCCAGGGGCATTTTGGTAATTTTC
1 CGCCCAGGGGTATTTTGGTCATTTTC
56319 ACACTCGGGG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (27 bp):
CGCCCAGGGGTATTTTGGTCATTTTCG
Found at i:56329 original size:27 final size:27
Alignment explanation
Indices: 56250--56335 Score: 84
Period size: 27 Copynumber: 3.2 Consensus size: 27
56240 GCCCAAGGGT
* * ** *
56250 ATTTTGGTCATTTTCGCGCCCAGGGGT
1 ATTTTGGTAATTTTCACATCCAGGGGC
* *
56277 ATTTTGGTCATTTTCGCATCCAGGGGC
1 ATTTTGGTAATTTTCACATCCAGGGGC
*
56304 ATTTTGGTAATTTTCACA-CTCGGGGGC
1 ATTTTGGTAATTTTCACATC-CAGGGGC
56331 ATTTT
1 ATTTT
56336 AGTGATTCTT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
26 1 0.02
27 51 0.98
ACGTcount: A:0.15, C:0.20, G:0.26, T:0.40
Consensus pattern (27 bp):
ATTTTGGTAATTTTCACATCCAGGGGC
Found at i:59866 original size:39 final size:39
Alignment explanation
Indices: 59805--59908 Score: 111
Period size: 39 Copynumber: 2.6 Consensus size: 39
59795 ATCAGTAATT
**
59805 AAGTAAAAAGAGATTAATCAGTAATTTGATAATTAAGAGTCA-
1 AAGTAAAAA-AG--TAATCAGTAAAATGATAATTAAGAGT-AG
* *
59847 AAGTAAAAAAGTAATCAGTAAAATGGTAATTGAGAGTAG
1 AAGTAAAAAAGTAATCAGTAAAATGATAATTAAGAGTAG
*
59886 GAGTAAAAGAAGTAATCAGTAAA
1 AAGTAAAA-AAGTAATCAGTAAA
59909 TCGGTAAAGA
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
38 1 0.02
39 29 0.53
40 14 0.25
41 2 0.04
42 9 0.16
ACGTcount: A:0.52, C:0.04, G:0.20, T:0.24
Consensus pattern (39 bp):
AAGTAAAAAAGTAATCAGTAAAATGATAATTAAGAGTAG
Found at i:59945 original size:15 final size:16
Alignment explanation
Indices: 59906--59946 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
59896 AGTAATCAGT
59906 AAATCGGTAAAGAGCAA
1 AAAT-GGTAAAGAGCAA
*
59923 AAATGGTAAAGAGTAA
1 AAATGGTAAAGAGCAA
59939 AAA-GGTAA
1 AAATGGTAA
59947 TCAATGAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.22
16 14 0.61
17 4 0.17
ACGTcount: A:0.56, C:0.05, G:0.24, T:0.15
Consensus pattern (16 bp):
AAATGGTAAAGAGCAA
Found at i:60046 original size:21 final size:21
Alignment explanation
Indices: 60020--60101 Score: 103
Period size: 21 Copynumber: 3.9 Consensus size: 21
60010 TAGTAAAAGG
*
60020 TAATCAGTAAGAGTAAAACAA
1 TAATCAGTAAGAGTAAAATAA
* * *
60041 TAATCAGTAAGAGCAAAGTGA
1 TAATCAGTAAGAGTAAAATAA
60062 TAATTC-GTAAGAGTAAAATAA
1 TAA-TCAGTAAGAGTAAAATAA
60083 TAATCAGTAAAGAGTAAAA
1 TAATCAGT-AAGAGTAAAA
60102 GGGTGATCAG
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
20 2 0.04
21 37 0.73
22 12 0.24
ACGTcount: A:0.54, C:0.07, G:0.17, T:0.22
Consensus pattern (21 bp):
TAATCAGTAAGAGTAAAATAA
Found at i:60205 original size:28 final size:27
Alignment explanation
Indices: 60152--60218 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
60142 AAGAAAAAGG
**
60152 AAGAGTAA-AAAGTAGTAATAAATAAA
1 AAGAGTAAGAAAAAAGTAATAAATAAA
* *
60178 AGAGAGTAAGAAAAAAGTAATTAGTAAA
1 A-AGAGTAAGAAAAAAGTAATAAATAAA
60206 AAGAGTAAGAAAA
1 AAGAGTAAGAAAA
60219 GAGAAAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.03
27 19 0.54
28 15 0.43
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.16
Consensus pattern (27 bp):
AAGAGTAAGAAAAAAGTAATAAATAAA
Found at i:61421 original size:17 final size:17
Alignment explanation
Indices: 61411--61447 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
61401 TATTATTTAT
61411 TATTATCTATTTATTAC
1 TATTATCTATTTATTAC
*
61428 TATTATCTATTTAATAC
1 TATTATCTATTTATTAC
61445 TAT
1 TAT
61448 CATTTATCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (17 bp):
TATTATCTATTTATTAC
Found at i:61431 original size:27 final size:27
Alignment explanation
Indices: 61387--61438 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
61377 TTTACTTCCC
* * *
61387 TATCTATTTGTAATTATTATTTATTAT
1 TATCTATTTATAACTATTATCTATTAT
*
61414 TATCTATTTATTACTATTATCTATT
1 TATCTATTTATAACTATTATCTATT
61439 TAATACTATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.62
Consensus pattern (27 bp):
TATCTATTTATAACTATTATCTATTAT
Found at i:86285 original size:45 final size:45
Alignment explanation
Indices: 86221--86322 Score: 168
Period size: 45 Copynumber: 2.3 Consensus size: 45
86211 GCTTTGTTCC
*
86221 AGCTTTGTTCCAGATTGGGGACTCAATAGTGAACACACAGGTCAT
1 AGCTTTGTTCCAGATTGGGGACTCAATAATGAACACACAGGTCAT
* * *
86266 AGCTTTATTCCAGATTGGGGACTCAATAATGAACGCACAGGTCCT
1 AGCTTTGTTCCAGATTGGGGACTCAATAATGAACACACAGGTCAT
86311 AGCTTTGTTCCA
1 AGCTTTGTTCCA
86323 ACTGCTTCTT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (45 bp):
AGCTTTGTTCCAGATTGGGGACTCAATAATGAACACACAGGTCAT
Found at i:89697 original size:12 final size:12
Alignment explanation
Indices: 89679--89717 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
89669 ATGAAGATAT
89679 AGATGATGAAGA
1 AGATGATGAAGA
* *
89691 AGTTGATGATGA
1 AGATGATGAAGA
*
89703 GGATGATGAAGA
1 AGATGATGAAGA
89715 AGA
1 AGA
89718 GTTGGGATCT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.36, T:0.21
Consensus pattern (12 bp):
AGATGATGAAGA
Found at i:90381 original size:68 final size:67
Alignment explanation
Indices: 90247--90373 Score: 200
Period size: 68 Copynumber: 1.9 Consensus size: 67
90237 AACCTTGAAT
* * *
90247 GCAATGAAAATTCAAAAGGGAGTCAAAAATTTTAGTCTAGAAATTGGACTTCAAAATAAACGGGT
1 GCAATGAAAATTCAAAAGGGAGTCAAAAATTTTAGTCTAAAAACTGGACTCCAAAATAAACGGGT
90312 AA
66 AA
* *
90314 GCAATGAAAAATTCAAAAGGGAGTCAAAATTTTTAGTCTAAAAACTGGGCTCCAAAATAA
1 GCAATG-AAAATTCAAAAGGGAGTCAAAAATTTTAGTCTAAAAACTGGACTCCAAAATAA
90374 GGGGGTAATC
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
67 6 0.11
68 48 0.89
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.24
Consensus pattern (67 bp):
GCAATGAAAATTCAAAAGGGAGTCAAAAATTTTAGTCTAAAAACTGGACTCCAAAATAAACGGGT
AA
Found at i:90621 original size:10 final size:10
Alignment explanation
Indices: 90606--90638 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
90596 TCTAGTTCAT
90606 CTTCTTCAAC
1 CTTCTTCAAC
*
90616 CTTCTTC-AT
1 CTTCTTCAAC
90625 CTTCTTCAAC
1 CTTCTTCAAC
90635 CTTC
1 CTTC
90639 AAAGCCGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.15, C:0.39, G:0.00, T:0.45
Consensus pattern (10 bp):
CTTCTTCAAC
Found at i:90625 original size:19 final size:19
Alignment explanation
Indices: 90601--90638 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
90591 CCTATTCTAG
90601 TTCATCTTCTTCAACCTTC
1 TTCATCTTCTTCAACCTTC
90620 TTCATCTTCTTCAACCTTC
1 TTCATCTTCTTCAACCTTC
90639 AAAGCCGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.37, G:0.00, T:0.47
Consensus pattern (19 bp):
TTCATCTTCTTCAACCTTC
Found at i:91702 original size:72 final size:72
Alignment explanation
Indices: 91580--91723 Score: 270
Period size: 72 Copynumber: 2.0 Consensus size: 72
91570 GGACGAGCAA
* *
91580 CTTCTGCTAATGTGGCTAACCCACTAGCACCTCCCTGTGTGCAAAGGAGCAAGAGACCAGGCTCT
1 CTTCTGCTAATGTGGCTAACCCACCAGCACCTCCCTGTGTGCAAAAGAGCAAGAGACCAGGCTCT
91645 GTTGGTG
66 GTTGGTG
91652 CTTCTGCTAATGTGGCTAACCCACCAGCACCTCCCTGTGTGCAAAAGAGCAAGAGACCAGGCTCT
1 CTTCTGCTAATGTGGCTAACCCACCAGCACCTCCCTGTGTGCAAAAGAGCAAGAGACCAGGCTCT
91717 GTTGGTG
66 GTTGGTG
91724 GTGTAGACTT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.23, C:0.28, G:0.26, T:0.23
Consensus pattern (72 bp):
CTTCTGCTAATGTGGCTAACCCACCAGCACCTCCCTGTGTGCAAAAGAGCAAGAGACCAGGCTCT
GTTGGTG
Found at i:98198 original size:24 final size:24
Alignment explanation
Indices: 98172--98239 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
98162 ACTAACAGTC
* *
98172 TTTTCTTTTTCCTGTTGCTCATTCT
1 TTTTC-TTCTCCTGTTGCTCACTCT
*
98197 TTTTCTTCTGCTGTTGCTCACTCT
1 TTTTCTTCTCCTGTTGCTCACTCT
* * *
98221 TTTACTTCTTCTGCTGCTC
1 TTTTCTTCTCCTGTTGCTC
98240 TTTTGTTTTC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
24 32 0.86
25 5 0.14
ACGTcount: A:0.04, C:0.28, G:0.10, T:0.57
Consensus pattern (24 bp):
TTTTCTTCTCCTGTTGCTCACTCT
Found at i:101694 original size:31 final size:31
Alignment explanation
Indices: 101656--101723 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
101646 CACCTGCTAT
* *
101656 AGGTAATACCTCACGTGGTTACACATGTTAC
1 AGGTAATACCTCACGTGATTACACACGTTAC
* * *
101687 AGGTAATACCTCACTTGATTAGACACGTTGC
1 AGGTAATACCTCACGTGATTACACACGTTAC
101718 AGGTAA
1 AGGTAA
101724 CACCCTGTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (31 bp):
AGGTAATACCTCACGTGATTACACACGTTAC
Found at i:101756 original size:16 final size:17
Alignment explanation
Indices: 101733--101782 Score: 59
Period size: 16 Copynumber: 3.0 Consensus size: 17
101723 ACACCCTGTA
101733 ACTGGTAATACATGTTG
1 ACTGGTAATACATGTTG
* *
101750 A-TGGTAATTCCT-TGTG
1 ACTGGTAATACATGT-TG
101766 ACTGGTAATACATGTTG
1 ACTGGTAATACATGTTG
101783 GTAACACCCT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
15 1 0.04
16 12 0.46
17 12 0.46
18 1 0.04
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (17 bp):
ACTGGTAATACATGTTG
Found at i:102476 original size:23 final size:23
Alignment explanation
Indices: 102450--102526 Score: 59
Period size: 23 Copynumber: 3.2 Consensus size: 23
102440 TATCAACCAT
102450 ATTATCCATATATATTAGAGATA
1 ATTATCCATATATATTAGAGATA
** * *
102473 ATTAT-GGTGATTATATTATCA-ACCA
1 ATTATCCAT-A-TATATTA-GAGA-TA
102498 TATTATCCATATATATTAGAGATA
1 -ATTATCCATATATATTAGAGATA
102522 ATTAT
1 ATTAT
102527 GGTGATTATA
Statistics
Matches: 39, Mismatches: 8, Indels: 14
0.64 0.13 0.23
Matches are distributed among these distances:
22 1 0.03
23 11 0.28
24 10 0.26
25 10 0.26
26 6 0.15
27 1 0.03
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (23 bp):
ATTATCCATATATATTAGAGATA
Found at i:102476 original size:49 final size:49
Alignment explanation
Indices: 102393--102587 Score: 293
Period size: 49 Copynumber: 3.9 Consensus size: 49
102383 TACCCCTATT
102393 AACCATATTATCCATACATATATT-GTAGATAATTATGGTGATTATATTATC
1 AACCATATTATCCAT--ATATATTAG-AGATAATTATGGTGATTATATTATC
102444 AACCATATTATCCATATATATTAGAGATAATTATGGTGATTATATTATC
1 AACCATATTATCCATATATATTAGAGATAATTATGGTGATTATATTATC
102493 AACCATATTATCCATATATATTAGAGATAATTATGGTGATTATATTTATC
1 AACCATATTATCCATATATATTAGAGATAATTATGGTGATTATA-TTATC
* * * *
102543 AATCATATTATCTTTATATATATTGGAGATAATTATGGTAATTAT
1 AACCATATTATC--CATATATATTAGAGATAATTATGGTGATTAT
102588 CAAAACTCCT
Statistics
Matches: 136, Mismatches: 4, Indels: 7
0.93 0.03 0.05
Matches are distributed among these distances:
49 76 0.56
50 17 0.12
51 15 0.11
52 28 0.21
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.43
Consensus pattern (49 bp):
AACCATATTATCCATATATATTAGAGATAATTATGGTGATTATATTATC
Found at i:105009 original size:21 final size:21
Alignment explanation
Indices: 104979--105032 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
104969 ACTAGCGCTG
*
104979 GGCG-CCCATGTGGTATGCTT
1 GGCGCCCCATGTGGTATGCCT
*
104999 GGCGCCCCATGTGGTTTGCCT
1 GGCGCCCCATGTGGTATGCCT
*
105020 CGCGCCCCATGTG
1 GGCGCCCCATGTG
105033 CTCCAGTGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 4 0.13
21 26 0.87
ACGTcount: A:0.07, C:0.33, G:0.33, T:0.26
Consensus pattern (21 bp):
GGCGCCCCATGTGGTATGCCT
Done.