Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010456.1 Corchorus capsularis cultivar CVL-1 contig10477, 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: 54483
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1575 original size:4 final size:4
Alignment explanation
Indices: 1566--1594 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1556 AGTGTGTCTA
1566 TATC TATC TATC TATC TATC TATC TATC T
1 TATC TATC TATC TATC TATC TATC TATC T
1595 CTCTGTCTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:13005 original size:45 final size:45
Alignment explanation
Indices: 12955--13089 Score: 261
Period size: 45 Copynumber: 3.0 Consensus size: 45
12945 CGTTTGTCTC
*
12955 TTGCTATTGAAATTGAGTATAATGTGTTAGATATGAAAACCCCAA
1 TTGCTATTGAAATTAAGTATAATGTGTTAGATATGAAAACCCCAA
13000 TTGCTATTGAAATTAAGTATAATGTGTTAGATATGAAAACCCCAA
1 TTGCTATTGAAATTAAGTATAATGTGTTAGATATGAAAACCCCAA
13045 TTGCTATTGAAATTAAGTATAATGTGTTAGATATGAAAACCCCAA
1 TTGCTATTGAAATTAAGTATAATGTGTTAGATATGAAAACCCCAA
13090 AGGAGTTGAT
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
45 89 1.00
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.33
Consensus pattern (45 bp):
TTGCTATTGAAATTAAGTATAATGTGTTAGATATGAAAACCCCAA
Found at i:15554 original size:33 final size:33
Alignment explanation
Indices: 15509--15581 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
15499 CCCCAGTAGA
* *
15509 GAGGCTCCGCCGTGGTTGAGCC-TCCCTAGTGGG
1 GAGGCTCCGCCGTGGCTGAACCGT-CCTAGTGGG
*
15542 GAGGCTCTGCCGTGGCTGAACCGTCCTAGTGGG
1 GAGGCTCCGCCGTGGCTGAACCGTCCTAGTGGG
15575 GAGGCTC
1 GAGGCTC
15582 AGTGTAAAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 35 0.97
34 1 0.03
ACGTcount: A:0.11, C:0.29, G:0.40, T:0.21
Consensus pattern (33 bp):
GAGGCTCCGCCGTGGCTGAACCGTCCTAGTGGG
Found at i:15908 original size:22 final size:21
Alignment explanation
Indices: 15883--16420 Score: 177
Period size: 22 Copynumber: 24.7 Consensus size: 21
15873 ATGATCCCAT
15883 TATGAAATTTTGATAACATTCC
1 TATGAAATTTTGATAAC-TTCC
* * *
15905 TATGAAATTTTAATAACGATAC
1 TATGAAATTTTGATAAC-TTCC
* * * **
15927 TATGGAATTTCGAGAAACTTTT
1 TATGAAATTTTGA-TAACTTCC
** *
15949 TAT-AAATTTTTTTAACCTTCT
1 TATGAAATTTTGATAA-CTTCC
* *
15970 TATGAAATTTGGTTAACTTCCC
1 TATGAAATTTTGATAACTT-CC
* * * *
15992 TAAGGAATTTTGA-AGACCTCAA
1 TATGAAATTTTGATA-ACTTC-C
16014 TATGAAATTTTGATAACTTCGC
1 TATGAAATTTTGATAACTTC-C
* * *
16036 AATGAAATTTTGATGACTAACAC
1 TATGAAATTTTGATAACT-TC-C
* * *
16059 TATGAGATGTTGATAACCTCC
1 TATGAAATTTTGATAACTTCC
* * * ** *
16080 ATATGATATATTGATCACCACGT
1 -TATGAAATTTTGATAACTTC-C
*
16103 TATGAAAATTT-A-AACATCTCC
1 TATGAAATTTTGATAAC-T-TCC
* *
16124 AAATG-AATTGTT-AGTAA-TCACAC
1 -TATGAAATT-TTGA-TAACT-TC-C
* **
16147 TCTGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACTTC-C
* *
16169 TATGAAATTGTGATAACCTCCC
1 TATGAAATTTTGATAA-CTTCC
16191 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AA-CTTCC
* *
16214 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAAC-TTCC
*
16236 TATGAAATCTTGATAA----C
1 TATGAAATTTTGATAACTTCC
* *
16253 TA-CAAATTTTGATAACCTCC
1 TATGAAATTTTGATAACTTCC
** *
16273 ATATGATTTTTTGATAA-TCTCAT
1 -TATGAAATTTTGATAACT-TC-C
*
16296 TATGAAATTTTGTTAA-TCTCC
1 TATGAAATTTTGATAACT-TCC
* * *
16317 GTATGAAATTTTGATCTACATAC
1 -TATGAAATTTTGAT-AACTTCC
* *
16340 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAA-CTTCC
* * **
16362 TGTGAAATTTTGAAAACTAAAC
1 TATGAAATTTTGATAACT-TCC
*
16384 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAA-CTTCC
16406 TATGAAATTTTGATA
1 TATGAAATTTTGATA
16421 TCCTCCCTGA
Statistics
Matches: 378, Mismatches: 101, Indels: 74
0.68 0.18 0.13
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
20 5 0.01
21 27 0.07
22 280 0.74
23 51 0.13
24 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (21 bp):
TATGAAATTTTGATAACTTCC
Found at i:15989 original size:21 final size:20
Alignment explanation
Indices: 15942--15989 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
15932 AATTTCGAGA
* **
15942 AACTTTTTATAAATTTTTTT
1 AACTTCTTATAAATTTGGTT
15962 AACCTTCTTATGAAATTTGGTT
1 AA-CTTCTTAT-AAATTTGGTT
15984 AACTTC
1 AACTTC
15990 CCTAAGGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.09
21 11 0.48
22 10 0.43
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
AACTTCTTATAAATTTGGTT
Found at i:16702 original size:22 final size:22
Alignment explanation
Indices: 16677--16904 Score: 130
Period size: 22 Copynumber: 10.4 Consensus size: 22
16667 AATCACATTT
*
16677 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTCTA
* *
16699 TGAAATTTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTCTA
* * *
16721 T-AAAATTTTGTTGACCCCTCTA
1 TGAAAA-TTTGATAACCTCTCTA
* *
16743 TG-AAATTCTGATAATCACAT-TA
1 TGAAAATT-TGATAACCTC-TCTA
* * * *
16765 TGTAATTTTGATAACCTCGCTT
1 TGAAAATTTGATAACCTCTCTA
* ** *
16787 TGAAATTTTGATAACAACACTA
1 TGAAAATTTGATAACCTCTCTA
* * *
16809 TGAAATTTTGATAATCTTTCTA
1 TGAAAATTTGATAACCTCTCTA
*
16831 T-AAATTTTGATAATCCGATCTCTA
1 TGAAAATTTGATAA-CC--TCTCTA
* *
16855 TG-AAATTTCGATAATCACTCTA
1 TGAAAATTT-GATAACCTCTCTA
*
16877 TG-AGATTTGATAACCT-TCTA
1 TGAAAATTTGATAACCTCTCTA
16897 T-AAAATTT
1 TGAAAATTT
16905 TGGTACTCCC
Statistics
Matches: 160, Mismatches: 34, Indels: 26
0.73 0.15 0.12
Matches are distributed among these distances:
20 10 0.06
21 23 0.14
22 105 0.66
23 5 0.03
24 12 0.08
25 5 0.03
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTCTA
Found at i:16745 original size:44 final size:44
Alignment explanation
Indices: 16652--16822 Score: 139
Period size: 44 Copynumber: 3.9 Consensus size: 44
16642 AGAAATACCA
* * * *
16652 CTATGAAATTTTTG-TAATCACATTTTGAAAA-TTTGATAACCTCT
1 CTATGAAA-TTTTGATAACCACATTAT-AAAATTTTGATAACCCCG
* * * * * *
16696 TTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAACCACATTATAAAATTTTGATAACCCCG
* * ** *
16740 CTATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAACCACATTATAAAATTTTGATAACCCCG
* * * *
16784 CTTTGAAATTTTGATAACAACACTATGAAATTTTGATAA
1 CTATGAAATTTTGATAACCACATTATAAAATTTTGATAA
16823 TCTTTCTATA
Statistics
Matches: 100, Mismatches: 25, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
43 9 0.09
44 91 0.91
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.42
Consensus pattern (44 bp):
CTATGAAATTTTGATAACCACATTATAAAATTTTGATAACCCCG
Found at i:16793 original size:66 final size:66
Alignment explanation
Indices: 16696--16824 Score: 161
Period size: 66 Copynumber: 2.0 Consensus size: 66
16686 GATAACCTCT
* * * ** *
16696 TTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCTCTATGAAATTCTGATAATCAC
1 TTATGAAATTTTGATAACCTCCTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATCAC
16761 A
66 A
* * *
16762 TTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAACACTATGAAATTTTGATAATC
1 TTATGAAATTTTGATAACCTC-CTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATC
16825 TTTCTATAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
66 51 0.96
67 2 0.04
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (66 bp):
TTATGAAATTTTGATAACCTCCTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATCAC
A
Found at i:16815 original size:88 final size:88
Alignment explanation
Indices: 16652--16818 Score: 212
Period size: 88 Copynumber: 1.9 Consensus size: 88
16642 AGAAATACCA
* * * **
16652 CTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTC
1 CTATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
**
16717 TTTATAAAATTTTGTTGACCCCT
66 ACTATAAAATTTTGTTGACCCCT
* *
16740 CTATGAAA-TTCTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACA
1 CTATGAAATTTCTG-TAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACA
*
16803 ACACTATGAAATTTTG
64 ACACTATAAAATTTTG
16819 ATAATCTTTC
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
87 4 0.06
88 61 0.91
89 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (88 bp):
CTATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
ACTATAAAATTTTGTTGACCCCT
Found at i:17028 original size:22 final size:23
Alignment explanation
Indices: 17000--17060 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
16990 TATATATTTA
17000 ATGAAATTTTGT-TAACCACACT
1 ATGAAATTTTGTATAACCACACT
* * *
17022 ATGAAATTCTTATATAACCTCGCT
1 ATGAAATT-TTGTATAACCACACT
*
17046 ATGACATTTTG-ATAA
1 ATGAAATTTTGTATAA
17061 TCTCTTTGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
22 12 0.38
23 5 0.16
24 15 0.47
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (23 bp):
ATGAAATTTTGTATAACCACACT
Found at i:17549 original size:22 final size:21
Alignment explanation
Indices: 17488--17607 Score: 96
Period size: 22 Copynumber: 5.4 Consensus size: 21
17478 ACACTATTAA
* * *
17488 ATAACCAACCTAAGAGATTTTA
1 ATAACC-ACCTATGAAATTTTG
17510 ATAACCTGATCCTATGAAATTTTG
1 ATAACC--A-CCTATGAAATTTTG
*
17534 GTAACCACACTATGAAATTTTG
1 ATAACCAC-CTATGAAATTTTG
* * * *
17556 GTAACCTCCTCATGAAATTATA
1 ATAACCACCT-ATGAAATTTTG
*
17578 ATAACCATCTTATGAAATTTTG
1 ATAACCA-CCTATGAAATTTTG
17600 ATAACCAC
1 ATAACCAC
17608 TTAGAGACAA
Statistics
Matches: 80, Mismatches: 13, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
21 4 0.05
22 57 0.71
23 3 0.04
24 16 0.20
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (21 bp):
ATAACCACCTATGAAATTTTG
Found at i:21371 original size:17 final size:18
Alignment explanation
Indices: 21349--21386 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
21339 GAGACAATAG
*
21349 AATATGGAGAAGAAGA-A
1 AATATGAAGAAGAAGAGA
21366 AATATGAAGAAGAAGAGA
1 AATATGAAGAAGAAGAGA
21384 AAT
1 AAT
21387 TGTTCTCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.61, C:0.00, G:0.26, T:0.13
Consensus pattern (18 bp):
AATATGAAGAAGAAGAGA
Found at i:21586 original size:11 final size:11
Alignment explanation
Indices: 21566--21609 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
21556 ATGTATATTC
*
21566 ATAATAAATTT
1 ATAATTAATTT
21577 ATAATTAATTT
1 ATAATTAATTT
21588 ATAATT-ATTT
1 ATAATTAATTT
*
21598 GATAATTTATTT
1 -ATAATTAATTT
21610 TATATAGGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 4 0.13
11 22 0.73
12 4 0.13
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (11 bp):
ATAATTAATTT
Found at i:23380 original size:21 final size:21
Alignment explanation
Indices: 23351--23391 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
23341 AGTATCAGTG
*
23351 TATTTATTCAGATAATAACTT
1 TATTCATTCAGATAATAACTT
*
23372 TATTCATTCATATAATAACT
1 TATTCATTCAGATAATAACT
23392 CATACAAGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.46
Consensus pattern (21 bp):
TATTCATTCAGATAATAACTT
Found at i:29439 original size:2 final size:2
Alignment explanation
Indices: 29432--29462 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29422 GGTTGTTATT
29432 TA TA TA TA TA 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 T
29463 TCAAATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40828 original size:15 final size:15
Alignment explanation
Indices: 40804--40842 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
40794 AGCTCGAAGC
40804 AATC-GACGAAGAAA
1 AATCAGACGAAGAAA
*
40818 AATCAGACGAAGGAA
1 AATCAGACGAAGAAA
40833 AATCAGACGA
1 AATCAGACGA
40843 TTCCAATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.54, C:0.15, G:0.23, T:0.08
Consensus pattern (15 bp):
AATCAGACGAAGAAA
Found at i:44900 original size:63 final size:62
Alignment explanation
Indices: 44801--44918 Score: 191
Period size: 63 Copynumber: 1.9 Consensus size: 62
44791 TGTGACCGAT
*
44801 TTCAACCCATTTTTAACCAAACCAGAAACTTGAGTCTTCCCATCCAAATACTCATCAGTTATG
1 TTCAACCCATTTTCAACCAAACCAGAAACTTGAGTCTTCCCA-CCAAATACTCATCAGTTATG
* * *
44864 TTCAACCCATTTTCAACCAAACCCGAAACTTGAGTCTTCCTACCAAATATTCATC
1 TTCAACCCATTTTCAACCAAACCAGAAACTTGAGTCTTCCCACCAAATACTCATC
44919 TGATATGTCA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
62 12 0.24
63 39 0.76
ACGTcount: A:0.33, C:0.31, G:0.07, T:0.30
Consensus pattern (62 bp):
TTCAACCCATTTTCAACCAAACCAGAAACTTGAGTCTTCCCACCAAATACTCATCAGTTATG
Found at i:46151 original size:63 final size:61
Alignment explanation
Indices: 46046--46170 Score: 205
Period size: 63 Copynumber: 2.0 Consensus size: 61
46036 TGTGACCGGT
* * *
46046 TTCAACCCATTTTCAACCAAAAGAAACTTGAGTTTTCCCATCCGAATATTCATCTGTTATG
1 TTCAACCCATTTTCAACCAAAAGAAACTTGAGTCTTCCCATCCAAATATTCATATGTTATG
46107 TTCAACCCATTTTCAACCAAACCAGAAACTTGAGTCTTCCCATCCAAATATTCATATGTTATG
1 TTCAACCCATTTTCAACCAAA--AGAAACTTGAGTCTTCCCATCCAAATATTCATATGTTATG
46170 T
1 T
46171 CGCATATCTC
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 21 0.36
63 38 0.64
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.34
Consensus pattern (61 bp):
TTCAACCCATTTTCAACCAAAAGAAACTTGAGTCTTCCCATCCAAATATTCATATGTTATG
Found at i:46987 original size:369 final size:368
Alignment explanation
Indices: 46107--47397 Score: 1702
Period size: 369 Copynumber: 3.6 Consensus size: 368
46097 ATCTGTTATG
* *
46107 TTCAACCCATTTTCAACCAAACCAGAAACTTGAGTCTTCCCATCCAAATATTCATATGTTATGTC
1 TTCAACCCATTTTCAACCAAACCCGAAACTTGAGTCTTCCCATCCAAATATTCATCTGTTATGTC
* * *
46172 GCATATCTCATCTATTTCCAAGTAAAACTTTTATAAGTTGAAGTAGACATTATAAAAAACAACCT
66 GCTTATCTCATCTATTTCCAAGTAAAACTTTTATAAGTTGAAATAGACATTGTAAAAAACAACCT
* * *
46237 TAATATAAAATTTCAATTTGATTGT--A----AAATTATACTTGTGATAGGTTTCAACAGTTTTT
131 TAATATAAAATTTTAACTTGATTGTAAATTTCAAATTGTACTTGTGATAGGTTTCAACA-TTTTT
* * *
46296 CAACCAAATCAGAAACTTCAATGCTTCTATCCAAATACTCATTTGTTATCTCGCTT-GCATATGT
195 CAACCAAA-CAGAAACTTCAATGCTCCTATCCAAATACTCATTTGTTATCTCGCTTAG-ATCTGC
** * *
46360 AATTTCTGAAAGAAAGTTGTATAAGTAGTGTGAAACAATGAAATTAGAAACATATATGGCCATAG
258 AATTTCCAAAAGAAAGTTGTATAAGTAGAGTGAAACAATGAAATTAGCAACATATATGGCCATAG
* * * **
46425 AACATTTTCACATGACTATTAAGAAATAATTCTACCCATGACCGAT
323 AACATTTTCACATAAATATTAAGAAAGAATTCTACCTGTGACCGAT
** * * *
46471 TTCAATTCATTATCAAACAAACCCGAAACTTGAGTATTCCCATCCAAATATTCATCTGTTATGTC
1 TTCAACCCATTTTCAACCAAACCCGAAACTTGAGTCTTCCCATCCAAATATTCATCTGTTATGTC
* * *
46536 ACTTATCTCATCTATTTCCAAGTAAAACTTTTATAAGTTGAAATTGACATTGTAAATAACAACCT
66 GCTTATCTCATCTATTTCCAAGTAAAACTTTTATAAGTTGAAATAGACATTGTAAAAAACAACCT
*
46601 TAACATAAAATTTTAACTTGATTGTAAATTTCAAATTGTACTTGTGATAGGTTTCAACAATTTTT
131 TAATATAAAATTTTAACTTGATTGTAAATTTCAAATTGTACTTGTGATAGGTTTCAAC-ATTTTT
* * *
46666 CAACCAAACAAGAGACTTCAGTGCTCCTATCCAAATACTCATTTGTTATCTTGCTTAGATCTGCA
195 CAACCAAAC-AGAAACTTCAATGCTCCTATCCAAATACTCATTTGTTATCTCGCTTAGATCTGCA
*
46731 ATTTCCAAAAGAAAGTTGTATAAGTAGAGTGAAACAATGAAATTAGCAACATATATGGCTATAGA
259 ATTTCCAAAAGAAAGTTGTATAAGTAGAGTGAAACAATGAAATTAGCAACATATATGGCCATAGA
* * * *
46796 ATATTTT-ACATAAATATTAAGAAAGAATTTTACATGTGATCGAT
324 ACATTTTCACATAAATATTAAGAAAGAATTCTACCTGTGACCGAT
* * * *
46840 TTCAACCCATTTTCAACCAAACCTGAAACTTGAGTCTGCCCATCCAAATATTCATCTATTATGTT
1 TTCAACCCATTTTCAACCAAACCCGAAACTTGAGTCTTCCCATCCAAATATTCATCTGTTATGTC
* *
46905 GCTTGTCTCATCTATTTCCAAGTAAAACTTTTATAAGTCGAAATAGACATTGTAAAAAACAACCT
66 GCTTATCTCATCTATTTCCAAGTAAAACTTTTATAAGTTGAAATAGACATTGTAAAAAACAACCT
*
46970 TAATATAAAACTTTAACTTGATTGTAAATTTCAAATTGTACTTGTGATAGG--------TTTTTC
131 TAATATAAAATTTTAACTTGATTGTAAATTTCAAATTGTACTTGTGATAGGTTTCAACATTTTTC
* * * *
47027 AA-C-ACCAGAAACTTCACTGCTCCTATCCAAATACTCATTTGTTATCTCGCTTACATCTGGAAT
196 AACCAAACAGAAACTTCAATGCTCCTATCCAAATACTCATTTGTTATCTCGCTTAGATCTGCAAT
*
47090 TTCCAAAAGAACGTTCGTATAAGTA-AGGTGAAACAATGAAATTAGCAACATATATGGCCATAGA
261 TTCCAAAAGAAAGTT-GTATAAGTAGA-GTGAAACAATGAAATTAGCAACATATATGGCCATAGA
* **
47154 ACATTTTGACATGTATAATAAAAAGAAAGAATTCTACCTGTGACCGAT
324 ACATTTTCACA--TA-AATATTAAGAAAGAATTCTACCTGTGACCGAT
* * *
47202 TTCAACCCATTTTTAACCAAACCCGAAACTTGAGTCTTCCCATCAAAATATTCATTTGTTATGTC
1 TTCAACCCATTTTCAACCAAACCCGAAACTTGAGTCTTCCCATCCAAATATTCATCTGTTATGTC
* * * **
47267 GCTTGT-ACATGCTATTTCCAAGT-AAAGTTTTATAA---G---TAGACATTG-GGAAAACAACC
66 GCTTATCTCAT-CTATTTCCAAGTAAAACTTTTATAAGTTGAAATAGACATTGTAAAAAACAACC
* * * *
47323 TTAATATAAAATTTTAACATGATTGTAAATTTCAAATTGTAGTTCTGATAGGTTTCAACACTATT
130 TTAATATAAAATTTTAACTTGATTGTAAATTTCAAATTGTACTTGTGATAGGTTTCAACA-TTTT
47388 TCAACCAAAC
194 TCAACCAAAC
47398 CAGGATTTTA
Statistics
Matches: 816, Mismatches: 84, Indels: 53
0.86 0.09 0.06
Matches are distributed among these distances:
354 57 0.07
355 9 0.01
357 67 0.08
358 54 0.07
359 4 0.00
360 8 0.01
361 16 0.02
362 103 0.13
363 7 0.01
364 140 0.17
365 2 0.00
366 1 0.00
369 195 0.24
370 151 0.19
371 2 0.00
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.34
Consensus pattern (368 bp):
TTCAACCCATTTTCAACCAAACCCGAAACTTGAGTCTTCCCATCCAAATATTCATCTGTTATGTC
GCTTATCTCATCTATTTCCAAGTAAAACTTTTATAAGTTGAAATAGACATTGTAAAAAACAACCT
TAATATAAAATTTTAACTTGATTGTAAATTTCAAATTGTACTTGTGATAGGTTTCAACATTTTTC
AACCAAACAGAAACTTCAATGCTCCTATCCAAATACTCATTTGTTATCTCGCTTAGATCTGCAAT
TTCCAAAAGAAAGTTGTATAAGTAGAGTGAAACAATGAAATTAGCAACATATATGGCCATAGAAC
ATTTTCACATAAATATTAAGAAAGAATTCTACCTGTGACCGAT
Found at i:47764 original size:260 final size:252
Alignment explanation
Indices: 47178--47768 Score: 893
Period size: 260 Copynumber: 2.3 Consensus size: 252
47168 ATAATAAAAA
* *
47178 GAAAGAATTCTACCTGTGACCGATTTCAACCCATTTTTAACCAAACCCGAAACTTGAGTCTTCCC
1 GAAAGAATTCTACCTGTGACCG-TTTCAACCCATTTTCAACCAAACCAGAAACTTGAGTCTTCCC
* * *
47243 ATCAAAATATTCATTTGTTATGTCGCTTGTACATGCTATTTCCAAGTAAAGTTTTATAAGTAGAC
65 ATCCAAATATTCATCTGTTAGGTCGCTTGTACATGCTATTTCCAAGTAAAGTTTTATAAGTAGAC
* *
47308 ATTGGGAAAACAACCTTAATATAAAATTTTAACATGATTGTAAATTTCAAATTGTAGTTCTGATA
130 ATTCGGAAAACAACCTTAATATAAAATTTTAACATGATTGTAAATTTCAAATTGTAGCTCTGATA
**
47373 GGTTTCAACACTATTTCAACCAAACCAGGATTTTAGAACATTTTGACATGAATTTTAG
195 GGTTTCAACACTATTTCAACCAAACCAAAATTTTAGAACATTTTGACATGAATTTTAG
* *
47431 GAAAGAATTCTAACTGTGACCAGTTTCAACTCATTTTCAACCAAACCAGAAACTTGAGTCTTCCC
1 GAAAGAATTCTACCTGTGACC-GTTTCAACCCATTTTCAACCAAACCAGAAACTTGAGTCTTCCC
*
47496 ATCCAAATATTCATCTGTTAGGTCGCTT-TCCTCAT-CTATTTCCAAGTAAAAGTTTTATAAGTT
65 ATCCAAATATTCATCTGTTAGGTCGCTTGT--ACATGCTATTTCCAAGT-AAAGTTTTATAA---
47559 GAAATAGACATTCGGAAAAGCAACCTTAATATAAAATTTTAACATGATTGTAAATTTCAAATTGT
124 G---TAGACATTCGGAAAA-CAACCTTAATATAAAATTTTAACATGATTGTAAATTTCAAATTGT
* *
47624 -GCCTGTGATAGGTTTCAACACTTTTTCAACCAAACCAAAATTTTAGAACA-TTTGACATGAATT
185 AG-CTCTGATAGGTTTCAACACTATTTCAACCAAACCAAAATTTTAGAACATTTTGACATGAATT
47687 TTAG
249 TTAG
*
47691 GAAAGAATTCTACCTGTGACCGTTGTCAACCCATTTTCAACCAAACCAGAAATTTGAGTCTTCCC
1 GAAAGAATTCTACCTGTGACCGTT-TCAACCCATTTTCAACCAAACCAGAAACTTGAGTCTTCCC
47756 ATCCAAATATTCA
65 ATCCAAATATTCA
47769 CATGTTATGT
Statistics
Matches: 308, Mismatches: 17, Indels: 19
0.90 0.05 0.06
Matches are distributed among these distances:
252 1 0.00
253 96 0.31
254 16 0.05
257 1 0.00
259 3 0.01
260 103 0.33
261 88 0.29
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.34
Consensus pattern (252 bp):
GAAAGAATTCTACCTGTGACCGTTTCAACCCATTTTCAACCAAACCAGAAACTTGAGTCTTCCCA
TCCAAATATTCATCTGTTAGGTCGCTTGTACATGCTATTTCCAAGTAAAGTTTTATAAGTAGACA
TTCGGAAAACAACCTTAATATAAAATTTTAACATGATTGTAAATTTCAAATTGTAGCTCTGATAG
GTTTCAACACTATTTCAACCAAACCAAAATTTTAGAACATTTTGACATGAATTTTAG
Found at i:47799 original size:64 final size:63
Alignment explanation
Indices: 47716--47842 Score: 186
Period size: 64 Copynumber: 2.0 Consensus size: 63
47706 GTGACCGTTG
* *
47716 TCAACCCATTTTCAACCAAA-CCAGAAATTTGAGTCTTCCCATCCAAATATTCA-CATGTTATGT
1 TCAACCCATTTTCAACCAAAGCC-GAAACTTGAGTCTTCCCATCCAAATATACATC-TGTTATGT
*
47779 TCAACCCCATTTTCATCCAAAGCCGAAACTTGAGTCTTCCCATCCAAATATACATCTGTTATGT
1 TCAA-CCCATTTTCAACCAAAGCCGAAACTTGAGTCTTCCCATCCAAATATACATCTGTTATGT
47843 CTCTTGTACA
Statistics
Matches: 58, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
63 4 0.07
64 51 0.88
65 3 0.05
ACGTcount: A:0.31, C:0.28, G:0.09, T:0.31
Consensus pattern (63 bp):
TCAACCCATTTTCAACCAAAGCCGAAACTTGAGTCTTCCCATCCAAATATACATCTGTTATGT
Found at i:48661 original size:63 final size:63
Alignment explanation
Indices: 48569--48687 Score: 152
Period size: 63 Copynumber: 1.9 Consensus size: 63
48559 GTTTCAAACA
* * *
48569 ATTTTCTACCAAACCAGAAACTTGGGTCTTCCCATCAAAATATTCATCTGTTATGTTCAACTC
1 ATTTTCAACCAAACCAGAAACTTGAGTCTTCCCATCAAAATATTCATCTATTATGTTCAACTC
* * *
48632 ATTTTCAACCAAACCCA-AAACTCT-AGTCTTCCCATCCAAGTATTCATTTATTATGT
1 ATTTTCAACCAAA-CCAGAAACT-TGAGTCTTCCCATCAAAATATTCATCTATTATGT
48688 CGCTTGTCTC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
63 44 0.92
64 4 0.08
ACGTcount: A:0.31, C:0.26, G:0.08, T:0.35
Consensus pattern (63 bp):
ATTTTCAACCAAACCAGAAACTTGAGTCTTCCCATCAAAATATTCATCTATTATGTTCAACTC
Found at i:49036 original size:29 final size:29
Alignment explanation
Indices: 48994--49055 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
48984 AGACAATCTT
*
48994 AATATAAAATTTTAATAACTGGGAATAGC
1 AATATAAAATTTTAAGAACTGGGAATAGC
* * *
49023 AATATTAAATTTTAAGAATTGTGAATAGC
1 AATATAAAATTTTAAGAACTGGGAATAGC
49052 AATA
1 AATA
49056 GGTAAAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.05, G:0.13, T:0.34
Consensus pattern (29 bp):
AATATAAAATTTTAAGAACTGGGAATAGC
Found at i:50171 original size:2 final size:2
Alignment explanation
Indices: 50164--50194 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
50154 TATTAATAGA
50164 AT AT AT 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 AT AT AT A
50195 CTAGTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53618 original size:36 final size:36
Alignment explanation
Indices: 53577--53664 Score: 167
Period size: 36 Copynumber: 2.4 Consensus size: 36
53567 TAAAAATTAT
53577 AATTGATTTTAATATTGATTTATGAAATATATAATA
1 AATTGATTTTAATATTGATTTATGAAATATATAATA
53613 AATTGATTTTAATATTGATTTATGAAATATATAATA
1 AATTGATTTTAATATTGATTTATGAAATATATAATA
*
53649 AATTTATTTTAATATT
1 AATTGATTTTAATATT
53665 TTGATTATAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (36 bp):
AATTGATTTTAATATTGATTTATGAAATATATAATA
Found at i:54102 original size:13 final size:12
Alignment explanation
Indices: 54079--54121 Score: 77
Period size: 12 Copynumber: 3.5 Consensus size: 12
54069 TTAATACAGG
54079 TATCGACGGATA
1 TATCGACGGATA
54091 TATCGAACGGATA
1 TATCG-ACGGATA
54104 TATCGACGGATA
1 TATCGACGGATA
54116 TATCGA
1 TATCGA
54122 GGTATCGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 18 0.60
13 12 0.40
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (12 bp):
TATCGACGGATA
Done.