Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014187.1 Corchorus olitorius cultivar O-4 contig14220, 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: 41524
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:2254 original size:52 final size:52
Alignment explanation
Indices: 2176--2279 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
2166 GTTATTGGTG
2176 AAACTATTTCTGTCAATGTTCTCTCTAATGAAACTAAACATAAACCTGACTC
1 AAACTATTTCTGTCAATGTTCTCTCTAATGAAACTAAACATAAACCTGACTC
2228 AAACTATTTCTGTCAATGTTCTCTCTAATGAAACTAAACATAAACCTGACTC
1 AAACTATTTCTGTCAATGTTCTCTCTAATGAAACTAAACATAAACCTGACTC
2280 TAATTTGAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.37, C:0.23, G:0.08, T:0.33
Consensus pattern (52 bp):
AAACTATTTCTGTCAATGTTCTCTCTAATGAAACTAAACATAAACCTGACTC
Found at i:3008 original size:25 final size:25
Alignment explanation
Indices: 2980--3054 Score: 98
Period size: 28 Copynumber: 2.9 Consensus size: 25
2970 TAGCAAGATC
2980 CAAAACAGAAACAGTTTGCAACTAA
1 CAAAACAGAAACAGTTTGCAACTAA
3005 CAAAACA-ACAACAGTTTGCAGCAACTAA
1 CAAAACAGA-AACAGTTT---GCAACTAA
*
3033 CAAAACAGAAACAATTTGCAAC
1 CAAAACAGAAACAGTTTGCAAC
3055 ACCCCAATTA
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
24 1 0.02
25 20 0.45
28 22 0.50
29 1 0.02
ACGTcount: A:0.52, C:0.23, G:0.11, T:0.15
Consensus pattern (25 bp):
CAAAACAGAAACAGTTTGCAACTAA
Found at i:3877 original size:38 final size:37
Alignment explanation
Indices: 3829--3900 Score: 108
Period size: 38 Copynumber: 1.9 Consensus size: 37
3819 ACGTCACTAG
*
3829 TTAGTTTCAAAACATATTGGAAAAAAACAACATCAAAT
1 TTAGTCTCAAAACATATT-GAAAAAAACAACATCAAAT
* *
3867 TTAGTCTCAAAACATATTGTAAGAAACAACATCA
1 TTAGTCTCAAAACATATTGAAAAAAACAACATCA
3901 CCTTTGACGA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
37 14 0.45
38 17 0.55
ACGTcount: A:0.50, C:0.15, G:0.08, T:0.26
Consensus pattern (37 bp):
TTAGTCTCAAAACATATTGAAAAAAACAACATCAAAT
Found at i:4512 original size:47 final size:45
Alignment explanation
Indices: 4417--4588 Score: 283
Period size: 45 Copynumber: 3.8 Consensus size: 45
4407 ATATAAGTTG
* *
4417 AAAATGAAGCAAACAAAACAGAAATTTGTCTAATAGAAATGCAAT
1 AAAATGCAGCAAACAAAACAGAAATTTGTATAATAGAAATGCAAT
4462 AAAATGCAGCAAACAAAACAGAAATTATAGTATAATAGAAATGCAAT
1 AAAATGCAGCAAACAAAACAGAAATT-T-GTATAATAGAAATGCAAT
4509 AAAATGCAGCAAACAAAACAGAAATTTGTATAATAGAAATGCAAT
1 AAAATGCAGCAAACAAAACAGAAATTTGTATAATAGAAATGCAAT
*
4554 AAAATGCAGCAAACAAAACA-ATCATTTGTATAATA
1 AAAATGCAGCAAACAAAACAGA-AATTTGTATAATA
4589 ATAATCACCA
Statistics
Matches: 121, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
44 1 0.01
45 75 0.62
46 2 0.02
47 43 0.36
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.20
Consensus pattern (45 bp):
AAAATGCAGCAAACAAAACAGAAATTTGTATAATAGAAATGCAAT
Found at i:11267 original size:83 final size:82
Alignment explanation
Indices: 11105--11267 Score: 229
Period size: 83 Copynumber: 2.0 Consensus size: 82
11095 TAAATTTTTT
11105 CCATAACGGCGTTTATGTGTCAAAAACGCCGTCATATTGCAGCGTTCATTCAGAAAAACGCCGTT
1 CCATAACGGCGTTTATGTGTCAAAAACGCCGTCATATTGCAGCGTTCATTCAGAAAAACGCCGTT
11170 ACACTCTTTGGGCTTTA
66 ACACTCTTTGGGCTTTA
* * ** * * * *
11187 CCATAGCGGCGTTTATGTGAT-AGAAACGCCGTCATATTGGGGGCGTTGATTCATATAAACGCTG
1 CCATAACGGCGTTTATGTG-TCAAAAACGCCGTCATATT-GCAGCGTTCATTCAGAAAAACGCCG
11251 TTACACTCTTTGGGCTT
64 TTACACTCTTTGGGCTT
11268 CATGGTGTAA
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
82 34 0.48
83 37 0.52
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.31
Consensus pattern (82 bp):
CCATAACGGCGTTTATGTGTCAAAAACGCCGTCATATTGCAGCGTTCATTCAGAAAAACGCCGTT
ACACTCTTTGGGCTTTA
Found at i:12642 original size:15 final size:16
Alignment explanation
Indices: 12616--12645 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12606 AATCTAGACT
12616 ATAACAAATAATAAGG
1 ATAACAAATAATAAGG
12632 ATAAC-AATAATAAG
1 ATAACAAATAATAAG
12646 AAAGCATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.63, C:0.07, G:0.10, T:0.20
Consensus pattern (16 bp):
ATAACAAATAATAAGG
Found at i:14812 original size:65 final size:65
Alignment explanation
Indices: 14703--14833 Score: 217
Period size: 65 Copynumber: 2.0 Consensus size: 65
14693 CCTTTCACCT
* *
14703 TTCTTATTCTATAATCGAGCTTCATCTCTTATTTTTCTTAATTTTTCTTTGGAACTCCCATTGGG
1 TTCTTATTCTATAATCGAGCTCCATCTCCTATTTTTCTTAATTTTTCTTTGGAACTCCCATTGGG
* * *
14768 TTCTTCTTCTATAATCGAGCTCCATCTCCTATTTTTCTTGATTTTTCTTTGGAACTCCCTTTGGG
1 TTCTTATTCTATAATCGAGCTCCATCTCCTATTTTTCTTAATTTTTCTTTGGAACTCCCATTGGG
14833 T
1 T
14834 CGGTGGAGAC
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.16, C:0.22, G:0.11, T:0.50
Consensus pattern (65 bp):
TTCTTATTCTATAATCGAGCTCCATCTCCTATTTTTCTTAATTTTTCTTTGGAACTCCCATTGGG
Found at i:17254 original size:48 final size:48
Alignment explanation
Indices: 17198--17293 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
17188 TGCTTTGGAA
17198 AAGTCACAACTTGGAAGTGAATCTTCTAGAAGCTACTGAGCAGGAGAT
1 AAGTCACAACTTGGAAGTGAATCTTCTAGAAGCTACTGAGCAGGAGAT
*
17246 AAGTCACAACTTGGAAGTGAATCTTCTGGAAGCTACTGAGCAGGAGAT
1 AAGTCACAACTTGGAAGTGAATCTTCTAGAAGCTACTGAGCAGGAGAT
17294 CCATGCAACT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (48 bp):
AAGTCACAACTTGGAAGTGAATCTTCTAGAAGCTACTGAGCAGGAGAT
Found at i:25299 original size:25 final size:25
Alignment explanation
Indices: 25265--25315 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
25255 AACTTTGATG
* *
25265 ATAGAATTTTGGTGAGACAAACAAC
1 ATAGAATTTTAGTAAGACAAACAAC
25290 ATAGAATTTTAGTAAGACAAACAAC
1 ATAGAATTTTAGTAAGACAAACAAC
25315 A
1 A
25316 CGATCTGACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.49, C:0.12, G:0.16, T:0.24
Consensus pattern (25 bp):
ATAGAATTTTAGTAAGACAAACAAC
Found at i:32810 original size:3 final size:3
Alignment explanation
Indices: 32802--32836 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
32792 AAGAATTGTG
*
32802 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGG TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
32837 GTGGTGGCCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.29, G:0.37, T:0.34
Consensus pattern (3 bp):
TGC
Found at i:34529 original size:1 final size:1
Alignment explanation
Indices: 34523--34547 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
34513 TCTTAGCATG
34523 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
34548 CCTTATGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:35081 original size:4 final size:4
Alignment explanation
Indices: 35058--35136 Score: 83
Period size: 4 Copynumber: 20.5 Consensus size: 4
35048 GGATTATCAT
* *
35058 TATA TA-A TATA -ATA -ATA TATA TATA TATG TATA TATG TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * *
35103 TATA TATG TATA TATG TATG TATG TATA TATA TA
1 TATA TATA TATA TATA TATA TATA TATA TATA TA
35137 GGTATAGACT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
3 9 0.14
4 56 0.86
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (4 bp):
TATA
Found at i:35142 original size:8 final size:8
Alignment explanation
Indices: 35072--35133 Score: 97
Period size: 8 Copynumber: 7.8 Consensus size: 8
35062 TAATATAATA
*
35072 ATATATAT
1 ATATATGT
35080 ATATATGT
1 ATATATGT
35088 ATATATGT
1 ATATATGT
*
35096 ATATATAT
1 ATATATGT
35104 ATATATGT
1 ATATATGT
35112 ATATATGT
1 ATATATGT
*
35120 ATGTATGT
1 ATATATGT
35128 ATATAT
1 ATATAT
35134 ATAGGTATAG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 49 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (8 bp):
ATATATGT
Found at i:36150 original size:2 final size:2
Alignment explanation
Indices: 36143--36167 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
36133 GAAGATTAAA
36143 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
36168 AAAGAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:37614 original size:30 final size:30
Alignment explanation
Indices: 37580--37650 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 30
37570 GTTAATTTAG
* *
37580 ACTTATTATTATTATTATAATAATTATTAA
1 ACTTATTATTAGTAGTATAATAATTATTAA
* *
37610 ACTTATTATTAGTGGTATTATAATTATTAA
1 ACTTATTATTAGTAGTATAATAATTATTAA
37640 ACTTATTATTA
1 ACTTATTATTA
37651 CAATAATTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (30 bp):
ACTTATTATTAGTAGTATAATAATTATTAA
Found at i:37660 original size:30 final size:29
Alignment explanation
Indices: 37580--37668 Score: 97
Period size: 30 Copynumber: 3.0 Consensus size: 29
37570 GTTAATTTAG
* *
37580 ACTTATTATTATTATTATAATAATTATTAA
1 ACTTATTATTA-TAATATTATAATTATTAA
**
37610 ACTTATTATTAGTGGTATTATAATTATTAA
1 ACTTATTATTA-TAATATTATAATTATTAA
* *
37640 ACTTATTATTACAATAATTATTATTATTA
1 ACTTATTATTATAAT-ATTATAATTATTA
37669 GTGGTATGTA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.52
Consensus pattern (29 bp):
ACTTATTATTATAATATTATAATTATTAA
Found at i:39519 original size:816 final size:820
Alignment explanation
Indices: 38382--40273 Score: 3706
Period size: 816 Copynumber: 2.3 Consensus size: 820
38372 TTTTTAAATT
38382 TTCATTAATGTAAGCTTAAATCACATAAATCCTTCATTAATTAATTAATACCCAAAAAATTGGTA
1 TTCATTAATGTAAGCTTAAATCACATAAATCCTTCATTAATTAATTAATACCCAAAAAATTGGTA
38447 GATTAAAAATGACAAATCAAGTTCTATCTTTGGTTTAAACTGTCAAAAATATGTATATGTAGCAT
66 GATTAAAAATGACAAATCAAGTTCTATCTTTGGTTTAAACTGTCAAAAATATGTATATGTAGCAT
*
38512 ATTAAATTTAATTTCTCAACCGTAAAAAAAGTTAAGGAC--ATGATTAATAATTAGGACATTTTT
131 ATTAAATTTAATTTCTCAACCGTAAAAAAAGTTAAGGACATATGATTAGTAATTAGGACATTTTT
38575 ATTTATCAATCCAATTTGTATATCAACTTTTATAGTTCCTCACGTTGCATTAAGTTTAGTTACAA
196 ATTTATCAATCCAATTTGTATATCAACTTTTATAGTTCCTCACGTTGCATTAAGTTTAGTTACAA
38640 TTTTATACAAATATAATTTATATAAAGGTAAGAGTATGTTTGATTGAACTGTGAGAACAAATATT
261 TTTTATACAAATATAATTTATATAAAGGTAAGAGTATGTTTGATTGAACTGTGAGAACAAATATT
38705 AAAAATTAGTTATGTAGCTAATATTAAAAAGTTTAAGTTTATGTAGTTTATTTAGTATTATTATA
326 AAAAATTAGTTATGTAGCTAATATTAAAAAGTTTAAGTTTATGTAGTTTATTTAGTATTATTATA
38770 TATTAAAAAGTTCAATTCAATTTAATATTTCTTTGAAATATATCAATAGATCATTACTTATTTTG
391 TATTAAAAAGTTCAATTCAATTTAATATTTCTTTGAAATATATCAATAGATCATTACTTATTTTG
*
38835 CTTTAATAGCTTCAATCACATTAATCTTTAATTAATATGCACAATAGCATATAAATTCAATTTCT
456 CTTCAATAGCTTCAATCACATTAATCTTTAATTAATATGCACAATAGCATATAAATTCAATTTCT
38900 CGATCGC-AAAAAGGAAGGAACTATAAATTGGTGAATAGGAAATATTATTTCTCAAACCAATTTG
521 CGATCGCAAAAAAGGAAGGAACTATAAATTGGTGAATAGGAAATATTATTTCTCAAACCAATTTG
38964 TATACAAATTTTACAAATTTGATTTACAGATAAGGGTGTTTGGTTGTGTTGTGAGATTTGTTTTG
586 TATACAAATTTTACAAATTTGATTTACAGATAAGGGTGTTTGGTTGTGTTGTGAGATTTGTTTTG
39029 GAAAGATTAAAATGGTGAATACTAAAATTAGATACTATATAGTGTGACATTAGAATGGCAGCAAT
651 GAAAGATTAAAATGGTGAATACTAAAATTAGATACTATATAGTGTGACATTAGAATGGCAGCAAT
39094 AATTACCT-AAAAAAATAATGGCAATAATAAAAATAAAACAGATTGAAAATTC-AAAAAAAAATA
716 AATTACCTAAAAAAAATAATGGCAATAATAAAAATAAAACAGATTGAAAATTCAAAAAAAAAATA
39157 GCTAGAAGAGAATAAAAGGCAAAAAGAAAATTGACTGAAA
781 GCTAGAAGAGAATAAAAGGCAAAAAGAAAATTGACTGAAA
39197 TTCATTAATGTAAGCTTAAATCACATAAATCCTTCATTAATTAATTAATACCCAAAAAATTGGTA
1 TTCATTAATGTAAGCTTAAATCACATAAATCCTTCATTAATTAATTAATACCCAAAAAATTGGTA
39262 GATTAAAAATGACAAATCAAGTTCTATCTTTGGTTTAAACTGTCAAAAATATGTATATGTAGCAT
66 GATTAAAAATGACAAATCAAGTTCTATCTTTGGTTTAAACTGTCAAAAATATGTATATGTAGCAT
39327 ATTAAATTTAATTTCTCAACCGT-AAAAAAGTTAAGGACATATGATTAGTAATTAGGACATTTTT
131 ATTAAATTTAATTTCTCAACCGTAAAAAAAGTTAAGGACATATGATTAGTAATTAGGACATTTTT
39391 ATTTATCAATCCAATTTGTATATCAACTTTTATAGTTCCTCACGTTGCATTAAGTTTAGTTACAA
196 ATTTATCAATCCAATTTGTATATCAACTTTTATAGTTCCTCACGTTGCATTAAGTTTAGTTACAA
39456 TTTTATACAAATATAATTTATATAAAGGTAAGAGTATGTTTGATTGAACTGTGAGAACAAATATT
261 TTTTATACAAATATAATTTATATAAAGGTAAGAGTATGTTTGATTGAACTGTGAGAACAAATATT
39521 AAAAATTAGTTATGTAGCTAATATTAAAAAGTTTAAGTTTATGTAGTTTATTTAGTATTATTATA
326 AAAAATTAGTTATGTAGCTAATATTAAAAAGTTTAAGTTTATGTAGTTTATTTAGTATTATTATA
*
39586 TATTAAAAAGTTCAATTCAATTTAATATTTCTTTGAAATATATCAATAGATCATTATTTATTTTG
391 TATTAAAAAGTTCAATTCAATTTAATATTTCTTTGAAATATATCAATAGATCATTACTTATTTTG
39651 CTTCAATAGCTTCAATCACATTAATCTTTAATTAATATGCACAATAGCATATAAATTCAATTTCT
456 CTTCAATAGCTTCAATCACATTAATCTTTAATTAATATGCACAATAGCATATAAATTCAATTTCT
39716 CGATCGCAAAAAAGGAAGGAACTATAAATTGGTGAATAGGAAATATTATTTCTCAAACCAATTTG
521 CGATCGCAAAAAAGGAAGGAACTATAAATTGGTGAATAGGAAATATTATTTCTCAAACCAATTTG
39781 TATACAAATTTTACAAATTTGATTTACAGATAAGGGTGTTTGGTTGTGTTGTGAGATTTGTTTTG
586 TATACAAATTTTACAAATTTGATTTACAGATAAGGGTGTTTGGTTGTGTTGTGAGATTTGTTTTG
39846 GAAAGATTAAAATGGTGAATACTAAAATTAGATACTATATAGTGTGACATTAGAATGGCAGCAAT
651 GAAAGATTAAAATGGTGAATACTAAAATTAGATACTATATAGTGTGACATTAGAATGGCAGCAAT
39911 AATTACCTAAAAAAAATAATGGCAATAATAAAAATAAAACAGATTGAAAATTCAAAAAAAAAATA
716 AATTACCTAAAAAAAATAATGGCAATAATAAAAATAAAACAGATTGAAAATTCAAAAAAAAAATA
39976 GCTAGAAGAGAATAAAAGGCAAAAAGAAAATTGACTGAAA
781 GCTAGAAGAGAATAAAAGGCAAAAAGAAAATTGACTGAAA
40016 TTCATTAATGTAAGCTTAAATCACATAAATCCTTCATTAATTAATTAATACCCAAAAAATTGGTA
1 TTCATTAATGTAAGCTTAAATCACATAAATCCTTCATTAATTAATTAATACCCAAAAAATTGGTA
40081 GATTAAAAATGACAAATCAAGTTCTATCTTTGGTTTAAACTGTCAAAAATATGTATATGTAGCAT
66 GATTAAAAATGACAAATCAAGTTCTATCTTTGGTTTAAACTGTCAAAAATATGTATATGTAGCAT
40146 ATTAAATTTAATTTCTCAACCGTAAAAAAAGTTAAGGACATATGATTAGTAATTAGGACATTTTT
131 ATTAAATTTAATTTCTCAACCGTAAAAAAAGTTAAGGACATATGATTAGTAATTAGGACATTTTT
*
40211 ATTTATCAATCCAATTTGTATATCAACTTTCATAGTTCCTCACGTTGCATTAAGTTTAGTTAC
196 ATTTATCAATCCAATTTGTATATCAACTTTTATAGTTCCTCACGTTGCATTAAGTTTAGTTAC
40274 TATATACTAT
Statistics
Matches: 1067, Mismatches: 4, Indels: 7
0.99 0.00 0.01
Matches are distributed among these distances:
814 15 0.01
815 153 0.14
816 353 0.33
817 195 0.18
818 44 0.04
819 204 0.19
820 103 0.10
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.36
Consensus pattern (820 bp):
TTCATTAATGTAAGCTTAAATCACATAAATCCTTCATTAATTAATTAATACCCAAAAAATTGGTA
GATTAAAAATGACAAATCAAGTTCTATCTTTGGTTTAAACTGTCAAAAATATGTATATGTAGCAT
ATTAAATTTAATTTCTCAACCGTAAAAAAAGTTAAGGACATATGATTAGTAATTAGGACATTTTT
ATTTATCAATCCAATTTGTATATCAACTTTTATAGTTCCTCACGTTGCATTAAGTTTAGTTACAA
TTTTATACAAATATAATTTATATAAAGGTAAGAGTATGTTTGATTGAACTGTGAGAACAAATATT
AAAAATTAGTTATGTAGCTAATATTAAAAAGTTTAAGTTTATGTAGTTTATTTAGTATTATTATA
TATTAAAAAGTTCAATTCAATTTAATATTTCTTTGAAATATATCAATAGATCATTACTTATTTTG
CTTCAATAGCTTCAATCACATTAATCTTTAATTAATATGCACAATAGCATATAAATTCAATTTCT
CGATCGCAAAAAAGGAAGGAACTATAAATTGGTGAATAGGAAATATTATTTCTCAAACCAATTTG
TATACAAATTTTACAAATTTGATTTACAGATAAGGGTGTTTGGTTGTGTTGTGAGATTTGTTTTG
GAAAGATTAAAATGGTGAATACTAAAATTAGATACTATATAGTGTGACATTAGAATGGCAGCAAT
AATTACCTAAAAAAAATAATGGCAATAATAAAAATAAAACAGATTGAAAATTCAAAAAAAAAATA
GCTAGAAGAGAATAAAAGGCAAAAAGAAAATTGACTGAAA
Found at i:40598 original size:30 final size:30
Alignment explanation
Indices: 40564--40652 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 30
40554 GTTAATTTAG
* *
40564 ACTTATTATTATTATAATAATAATTATTAA
1 ACTTATTATTATAATAATTATAATTATTAA
**
40594 ACTTATTATTAGTGGT-ATTATAATTATTAA
1 ACTTATTATTA-TAATAATTATAATTATTAA
*
40624 ACTTATTATTATAATAATTATTATTATTA
1 ACTTATTATTATAATAATTATAATTATTA
40653 GTGGTATGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
29 2 0.04
30 47 0.92
31 2 0.04
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (30 bp):
ACTTATTATTATAATAATTATAATTATTAA
Done.