Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022054.1 Corchorus olitorius cultivar O-4 contig22087, 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: 107467
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:542 original size:2 final size:2
Alignment explanation
Indices: 537--584 Score: 87
Period size: 2 Copynumber: 23.5 Consensus size: 2
527 CATATTTTTT
537 AC AC AC AC ATC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC A-C AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
580 AC AC A
1 AC AC A
585 TATATATATA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 43 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.48, G:0.00, T:0.02
Consensus pattern (2 bp):
AC
Found at i:589 original size:2 final size:2
Alignment explanation
Indices: 584--619 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
574 ACACACACAC
584 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
620 GGAATTTGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:880 original size:43 final size:42
Alignment explanation
Indices: 729--1058 Score: 343
Period size: 43 Copynumber: 7.8 Consensus size: 42
719 TAAGGAGAAA
*
729 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGA
1 TGCC-CTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAGAGT
* * *
773 TGCCCCATGTGTTACATATGTGTTTGGGGACTTTG-ATATA-A-A
1 TG-CCC-TGTGTTATATATGTGTTTGAGGACTTTGTA-ATAGAGT
* * *
815 TGCCTCTGAGTTATATCTGTGTTTGAGGACTTCGTAATAGAGT
1 TGCC-CTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGT
*
858 TGCCCATGTGTTATATATGTGTTTGGGGACTTTG-ATATAGA-T
1 TGCCC-TGTGTTATATATGTGTTTGAGGACTTTGTA-ATAGAGT
* * * *
900 GGCTCTGTGTTATATATGTGTTTGAGGACTTTGTAGTAAAGT
1 TGCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGT
*
942 TGCCCCTGTGTTATATATGTGTTTGGGGACTTTG-ATATAGA-T
1 TG-CCCTGTGTTATATATGTGTTTGAGGACTTTGTA-ATAGAGT
* * *
984 T-CCTCTGTGTTATATATGTGTTTGAGGACTATGTAATAAAGG
1 TGCC-CTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGT
*
1026 TGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 TG-CCCTGTGTTATATATGTGTTTGAGGACTTT
1059 TTGGCTATTG
Statistics
Matches: 240, Mismatches: 28, Indels: 37
0.79 0.09 0.12
Matches are distributed among these distances:
40 2 0.01
41 89 0.37
42 20 0.08
43 93 0.39
44 12 0.05
45 24 0.10
ACGTcount: A:0.21, C:0.11, G:0.26, T:0.42
Consensus pattern (42 bp):
TGCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGT
Found at i:886 original size:84 final size:84
Alignment explanation
Indices: 726--1058 Score: 504
Period size: 84 Copynumber: 3.9 Consensus size: 84
716 CCATAAGGAG
* * *
726 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGATGCCCCATGTGTTACATA
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAAAGTTG-CCCATGTGTTATATA
791 TGTGTTTGGGGACTTTGATAT
64 TGTGTTTGGGGACTTTGATAT
* * * *
812 AAATGCCTCTGAGTTATATCTGTGTTTGAGGACTTCGTAATAGAGTTGCCCATGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGTTGCCCATGTGTTATATATG
877 TGTTTGGGGACTTTGATAT
66 TGTTTGGGGACTTTGATAT
* * * *
896 AGATGGCTCTGTGTTATATATGTGTTTGAGGACTTTGTAGTAAAGTTGCCCCTGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGTTGCCCATGTGTTATATATG
961 TGTTTGGGGACTTTGATAT
66 TGTTTGGGGACTTTGATAT
* * * * *
980 AGATTCCTCTGTGTTATATATGTGTTTGAGGACTATGTAATAAAGGTGCCCCTGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGTTGCCCATGTGTTATATATG
1045 TGTTTGGGGACTTT
66 TGTTTGGGGACTTT
1059 TTGGCTATTG
Statistics
Matches: 229, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
84 185 0.81
85 13 0.06
86 31 0.14
ACGTcount: A:0.22, C:0.11, G:0.26, T:0.41
Consensus pattern (84 bp):
AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGTTGCCCATGTGTTATATATG
TGTTTGGGGACTTTGATAT
Found at i:1821 original size:16 final size:16
Alignment explanation
Indices: 1800--1831 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1790 TAAACATAGC
1800 TCTAGATGGGCTTAAA
1 TCTAGATGGGCTTAAA
1816 TCTAGATGGGCTTAAA
1 TCTAGATGGGCTTAAA
1832 ATAACAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.31
Consensus pattern (16 bp):
TCTAGATGGGCTTAAA
Found at i:5268 original size:12 final size:12
Alignment explanation
Indices: 5253--5277 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5243 TAATTATAAA
5253 ATTTCAAAAACT
1 ATTTCAAAAACT
5265 ATTTCAAAAACT
1 ATTTCAAAAACT
5277 A
1 A
5278 ATTATAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
ATTTCAAAAACT
Found at i:5772 original size:22 final size:22
Alignment explanation
Indices: 5744--5894 Score: 96
Period size: 22 Copynumber: 6.9 Consensus size: 22
5734 TGTCTATGTG
5744 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
5766 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* * *
5789 -GGTTATCTAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
5810 TGGTTACCAAAATTTCATATGCA
1 TGGTTATCAAAATTTCATAAG-A
* **
5833 -AGTTATCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAAGA
* *
5854 AGCTTATCAAAATTTCAT-AG-
1 TGGTTATCAAAATTTCATAAGA
*
5874 TGTAGTTACCAAAATTTCATA
1 TG--GTTATCAAAATTTCATA
5895 GGATCATGTT
Statistics
Matches: 96, Mismatches: 25, Indels: 15
0.71 0.18 0.11
Matches are distributed among these distances:
20 2 0.02
21 2 0.02
22 88 0.92
23 4 0.04
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:5895 original size:22 final size:22
Alignment explanation
Indices: 5797--5895 Score: 103
Period size: 22 Copynumber: 4.5 Consensus size: 22
5787 GAGGTTATCT
* **
5797 AAATTCCATAGTGTGGTTACCA
1 AAATTTCATAGTGAAGTTACCA
*
5819 AAATTTCATA-TGCAAGTTATCA
1 AAATTTCATAGTG-AAGTTACCA
* *
5841 AAATTTCAT-GGGAAGCTTATCA
1 AAATTTCATAGTGAAG-TTACCA
*
5863 AAATTTCATAGTGTAGTTACCA
1 AAATTTCATAGTGAAGTTACCA
5885 AAATTTCATAG
1 AAATTTCATAG
5896 GATCATGTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
21 5 0.08
22 56 0.86
23 4 0.06
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (22 bp):
AAATTTCATAGTGAAGTTACCA
Found at i:5942 original size:68 final size:66
Alignment explanation
Indices: 5741--5976 Score: 201
Period size: 66 Copynumber: 3.5 Consensus size: 66
5731 TCTTGTCTAT
* * * * * * * *
5741 GTGTGGTTATCAAAATTTCATAAG-ATGGTTATTATAATTTCATGAGG-AGGTTATCTAAATTCC
1 GTGTGGTTACCAAAATTTCATAGGCA-AGTTATCAAAATTTCAT-AGGAAGCTTATCAAAATTTC
5804 ATA
64 ATA
* *
5807 GTGTGGTTACCAAAATTTCATATGCAAGTTATCAAAATTTCATGGGAAGCTTATCAAAATTTCAT
1 GTGTGGTTACCAAAATTTCATAGGCAAGTTATCAAAATTTCATAGGAAGCTTATCAAAATTTCAT
5872 A
66 A
* * * * **
5873 GTGTAGTTACCAAAATTTCATAGGATCATGTTAAT-AAAATTTCTTAGGAAGGTTATTGAAATTT
1 GTGTGGTTACCAAAATTTCATAGG--CAAGTT-ATCAAAATTTCATAGGAAGCTTATCAAAATTT
*
5937 TATA
63 CATA
* * * *
5941 GTGTGGTTATCACAATTTTATAGAG-AGGTTATCAAA
1 GTGTGGTTACCAAAATTTCATAG-GCAAGTTATCAAA
5977 GAGATTATCA
Statistics
Matches: 140, Mismatches: 23, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
65 4 0.03
66 81 0.58
67 1 0.01
68 51 0.36
69 3 0.02
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (66 bp):
GTGTGGTTACCAAAATTTCATAGGCAAGTTATCAAAATTTCATAGGAAGCTTATCAAAATTTCAT
A
Found at i:5948 original size:22 final size:23
Alignment explanation
Indices: 5922--5972 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
5912 TTTCTTAGGA
* *
5922 AGGTTATTGA-AATTTTATAGTG
1 AGGTTATTCACAATTTTATAGAG
*
5944 TGGTTA-TCACAATTTTATAGAG
1 AGGTTATTCACAATTTTATAGAG
5966 AGGTTAT
1 AGGTTAT
5973 CAAAGAGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.31, C:0.04, G:0.22, T:0.43
Consensus pattern (23 bp):
AGGTTATTCACAATTTTATAGAG
Found at i:5973 original size:22 final size:22
Alignment explanation
Indices: 5932--5974 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5922 AGGTTATTGA
* *
5932 AATTTTATAGTGTGGTTATCAC
1 AATTTTATAGAGAGGTTATCAC
5954 AATTTTATAGAGAGGTTATCA
1 AATTTTATAGAGAGGTTATCA
5975 AAGAGATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.42
Consensus pattern (22 bp):
AATTTTATAGAGAGGTTATCAC
Found at i:6342 original size:29 final size:30
Alignment explanation
Indices: 6308--6368 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
6298 CTCCTTATAC
6308 TTTTTGAAAAC-TTTGCAGCTCTATTTTCT
1 TTTTTGAAAACTTTTGCAGCTCTATTTTCT
** *
6337 TTTTTGAATTCTTTTTGCAGCTTTATTTTCT
1 TTTTTGAAAAC-TTTTGCAGCTCTATTTTCT
6368 T
1 T
6369 CCCAAGGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 9 0.33
31 18 0.67
ACGTcount: A:0.16, C:0.15, G:0.10, T:0.59
Consensus pattern (30 bp):
TTTTTGAAAACTTTTGCAGCTCTATTTTCT
Found at i:7150 original size:29 final size:30
Alignment explanation
Indices: 7110--7170 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 30
7100 TTTCAAATAC
7110 TTTTTGAATTC-TTTGCAGCTCTATTTTCT
1 TTTTTGAATTCTTTTGCAGCTCTATTTTCT
*
7139 TTTTTGAATTCTTTTTGCAGCTTTATTTTCT
1 TTTTTGAATTC-TTTTGCAGCTCTATTTTCT
7170 T
1 T
7171 CTCAAGGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 11 0.38
31 18 0.62
ACGTcount: A:0.13, C:0.15, G:0.10, T:0.62
Consensus pattern (30 bp):
TTTTTGAATTCTTTTGCAGCTCTATTTTCT
Found at i:21429 original size:21 final size:22
Alignment explanation
Indices: 21403--21509 Score: 110
Period size: 23 Copynumber: 4.9 Consensus size: 22
21393 TCTCACAGAG
*
21403 AGGTTATCAAAA-ATCATAGGA
1 AGGTTATCAAAATTTCATAGGA
21424 AGGTTA-CAAAATTTCATAGGA
1 AGGTTATCAAAATTTCATAGGA
*
21445 AGGTTTATTAAAATTTCATAGGAA
1 AGG-TTATCAAAATTTCATAGG-A
* * **
21469 AGTTTATCAAAATTTTATAGTT
1 AGGTTATCAAAATTTCATAGGA
* *
21491 AGATTATCAAAGTTTCATA
1 AGGTTATCAAAATTTCATA
21510 TTTCATAGGT
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
20 5 0.07
21 17 0.24
22 19 0.26
23 28 0.39
24 3 0.04
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.36
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGA
Found at i:21537 original size:22 final size:22
Alignment explanation
Indices: 21509--21583 Score: 82
Period size: 22 Copynumber: 3.4 Consensus size: 22
21499 AAAGTTTCAT
* *
21509 ATTTCATAGGTAAATTATCAAA
1 ATTTCATAAGTAAGTTATCAAA
*
21531 ATTTCATAATGT-GGTTATCAAA
1 ATTTCATAA-GTAAGTTATCAAA
*
21553 ATTTAATAAG-ATAGTTATCAAA
1 ATTTCATAAGTA-AGTTATCAAA
21575 ATTTCATAA
1 ATTTCATAA
21584 AAATATTCAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
21 1 0.02
22 41 0.93
23 2 0.05
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (22 bp):
ATTTCATAAGTAAGTTATCAAA
Found at i:29087 original size:72 final size:72
Alignment explanation
Indices: 28970--29113 Score: 270
Period size: 72 Copynumber: 2.0 Consensus size: 72
28960 GCAATTCTAA
* *
28970 ATTTTTTCTTTTGACTTTTGAGAGAGACGAGATAAGTCTTCCTGAAATCCAACGGCCCTGGTTTA
1 ATTTTTCCTTTAGACTTTTGAGAGAGACGAGATAAGTCTTCCTGAAATCCAACGGCCCTGGTTTA
29035 GCACGTC
66 GCACGTC
29042 ATTTTTCCTTTAGACTTTTGAGAGAGACGAGATAAGTCTTCCTGAAATCCAACGGCCCTGGTTTA
1 ATTTTTCCTTTAGACTTTTGAGAGAGACGAGATAAGTCTTCCTGAAATCCAACGGCCCTGGTTTA
29107 GCACGTC
66 GCACGTC
29114 GGATGGGCGT
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:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (72 bp):
ATTTTTCCTTTAGACTTTTGAGAGAGACGAGATAAGTCTTCCTGAAATCCAACGGCCCTGGTTTA
GCACGTC
Found at i:29915 original size:17 final size:17
Alignment explanation
Indices: 29893--29925 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
29883 TCAGCTCACT
29893 ATCATAACCATCAAAGC
1 ATCATAACCATCAAAGC
29910 ATCATAACCATCAAAG
1 ATCATAACCATCAAAG
29926 TCGTCATACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.27, G:0.06, T:0.18
Consensus pattern (17 bp):
ATCATAACCATCAAAGC
Found at i:33141 original size:31 final size:31
Alignment explanation
Indices: 33101--33222 Score: 145
Period size: 31 Copynumber: 3.9 Consensus size: 31
33091 GCACGAGGTC
*
33101 TGCCACGTGTCACTTTTTGGTATACATGGCG
1 TGCCACGTGTCACTTTTTGGTACACATGGCG
* ** *
33132 TGACACGTGTCACTTTTTGGTACATGTGGTG
1 TGCCACGTGTCACTTTTTGGTACACATGGCG
* * * *
33163 TGCCACGTGTCGCTTTTTGATACACGTTGCG
1 TGCCACGTGTCACTTTTTGGTACACATGGCG
* *
33194 TGCCAAGTGTCGCTTTTTGGTACACATGG
1 TGCCACGTGTCACTTTTTGGTACACATGG
33223 TATCTCATGT
Statistics
Matches: 76, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.16, C:0.21, G:0.27, T:0.36
Consensus pattern (31 bp):
TGCCACGTGTCACTTTTTGGTACACATGGCG
Found at i:33167 original size:62 final size:62
Alignment explanation
Indices: 33101--33217 Score: 162
Period size: 62 Copynumber: 1.9 Consensus size: 62
33091 GCACGAGGTC
* * *
33101 TGCCACGTGTCACTTTTTGGTATACATGGCGTGACACGTGTCACTTTTTGGTACATGTGGTG
1 TGCCACGTGTCACTTTTTGATACACATGGCGTGACAAGTGTCACTTTTTGGTACATGTGGTG
* * * * *
33163 TGCCACGTGTCGCTTTTTGATACACGTTGCGTGCCAAGTGTCGCTTTTTGGTACA
1 TGCCACGTGTCACTTTTTGATACACATGGCGTGACAAGTGTCACTTTTTGGTACA
33218 CATGGTATCT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
62 47 1.00
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.37
Consensus pattern (62 bp):
TGCCACGTGTCACTTTTTGATACACATGGCGTGACAAGTGTCACTTTTTGGTACATGTGGTG
Found at i:40277 original size:165 final size:167
Alignment explanation
Indices: 40076--40376 Score: 525
Period size: 166 Copynumber: 1.8 Consensus size: 167
40066 ATTTTACTAT
* * * * *
40076 TTTTCATTAAAAACTTGGATATATTAAAATTTTTTAATATATAGTTTGATTCTATTAAAAACTCT
1 TTTTCATTAAAAACTTGAATATATGAAAAATTTTTAATATATAATTTGATTCTACTAAAAACTCT
*
40141 ATTTTT-ATTTAATTAAATTCAATATTTTTATAATTATTTTATTTTTACTATTTTAATTTAAAAG
66 ATTTTTCATTTAATTAAATTCAATATTTTTATAATTATTTTATTTTTACCATTTTAATTTAAAAG
40205 TTTATTTTTACCATTTTACTATTTTTCAATAAAAAAC
131 TTTATTTTTACCATTTTACTATTTTTCAATAAAAAAC
40242 TTTTCA-TAAAAACTTGAATATATGAAAAATTTTTAATATATAATTTGATTCTACTAAAAACTCT
1 TTTTCATTAAAAACTTGAATATATGAAAAATTTTTAATATATAATTTGATTCTACTAAAAACTCT
*
40306 ATTTTTCATTTAATTAAATTCAATATTTTTATAATTATTTTATTTTTACCATTTTAATTTAGAAG
66 ATTTTTCATTTAATTAAATTCAATATTTTTATAATTATTTTATTTTTACCATTTTAATTTAAAAG
40371 TTTATT
131 TTTATT
40377 GTGATTGACC
Statistics
Matches: 127, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
165 59 0.46
166 68 0.54
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.52
Consensus pattern (167 bp):
TTTTCATTAAAAACTTGAATATATGAAAAATTTTTAATATATAATTTGATTCTACTAAAAACTCT
ATTTTTCATTTAATTAAATTCAATATTTTTATAATTATTTTATTTTTACCATTTTAATTTAAAAG
TTTATTTTTACCATTTTACTATTTTTCAATAAAAAAC
Found at i:41221 original size:31 final size:31
Alignment explanation
Indices: 41183--41243 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
41173 GAGTTTTGTA
* *
41183 AAACTTTTGAATCGGCTATTATACCCTTATC
1 AAACTTTTGAATCGCCTATCATACCCTTATC
41214 AAACTTTTGAATCGCCTATCATACCCTTAT
1 AAACTTTTGAATCGCCTATCATACCCTTAT
41244 TTTTCGAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.38
Consensus pattern (31 bp):
AAACTTTTGAATCGCCTATCATACCCTTATC
Found at i:41382 original size:93 final size:93
Alignment explanation
Indices: 41280--41449 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
41270 TTGTTTAAAT
*
41280 TTTTATAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTAT-CACT
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAC-CT
41344 ATTTTATTTTTACCATTTTATTATTTTAC
65 ATTTTATTTTTACCATTTTATTATTTTAC
*
41373 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTT
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTA
41438 TTTTATTTTTAC
66 TTTTATTTTTAC
41450 GATATTACTA
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
93 73 0.99
94 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.02, T:0.54
Consensus pattern (93 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTA
TTTTATTTTTACCATTTTATTATTTTAC
Found at i:41476 original size:93 final size:93
Alignment explanation
Indices: 41286--41476 Score: 276
Period size: 93 Copynumber: 2.1 Consensus size: 93
41276 AAATTTTTAT
*
41286 AGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATCACTATTTTAT
1 AGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATCACTATTTTAT
* * * * ** *
41351 TTTTACCATTTTATTATTTTACTTTTAT
66 TTTTACCATATTACTAATTTAATTAAAA
*
41379 AGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTAT-ACCTTTTTTA
1 AGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATCA-CTATTTTA
*
41443 TTTTTACGATATTACTAATTTAATTAAAA
65 TTTTTACCATATTACTAATTTAATTAAAA
41472 AGTTT
1 AGTTT
41477 AGATATATTA
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
92 1 0.01
93 86 0.99
ACGTcount: A:0.34, C:0.13, G:0.03, T:0.51
Consensus pattern (93 bp):
AGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATCACTATTTTAT
TTTTACCATATTACTAATTTAATTAAAA
Found at i:42400 original size:17 final size:17
Alignment explanation
Indices: 42378--42410 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42368 TCATTACATC
42378 AATTAA-AATTATAAGTT
1 AATTAATAA-TATAAGTT
42395 AATTAATAATATAAGT
1 AATTAATAATATAAGT
42411 ATCCATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (17 bp):
AATTAATAATATAAGTT
Found at i:44729 original size:113 final size:102
Alignment explanation
Indices: 44606--44869 Score: 288
Period size: 113 Copynumber: 2.5 Consensus size: 102
44596 TTATCATCGA
44606 GTTTTAGAAATAAAATATAAAAATAATTGCACTAAGTTTAGCTCCAAATTAAAATTTTATTTTTA
1 GTTTTAGAAATAAAATATAAAAATAATT-CACTAAGTTTAGC-CCAAATTAAAATTTT-TTTTTA
*
44671 TTTTAAGGGTAAATTTTAAAATTAATAATTTATTGTTATTGTTATAGG
63 TTTTAAGGGTAAA-TTT--AATTAATAA--TA---ATATTGTTATAGG
* * * *
44719 GTTTTAGAAATAAAATACAAAACTAATTTCACTAAATTTAGCCC------CAATTTTTTTTTATT
1 GTTTTAGAAATAAAATATAAAAATAA-TTCACTAAGTTTAGCCCAAATTAAAATTTTTTTTTATT
* *
44778 TTAAGGGTAAATTTCATTATTAATAATATTGTTATAGG
65 TTAAGGGTAAATTTAATTAATAATAATATTGTTATAGG
* * *
44816 GTTTTAGAAATAAAATATATAAGTAATTCACCAAGTTTAGCCCAAATTAAAATT
1 GTTTTAGAAATAAAATATAAAAATAATTCACTAAGTTTAGCCCAAATTAAAATT
44870 AAAATTTTAT
Statistics
Matches: 131, Mismatches: 13, Indels: 25
0.78 0.08 0.15
Matches are distributed among these distances:
96 15 0.11
97 35 0.27
100 2 0.02
102 11 0.08
104 3 0.02
105 19 0.15
106 6 0.05
112 2 0.02
113 36 0.27
114 2 0.02
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.42
Consensus pattern (102 bp):
GTTTTAGAAATAAAATATAAAAATAATTCACTAAGTTTAGCCCAAATTAAAATTTTTTTTTATTT
TAAGGGTAAATTTAATTAATAATAATATTGTTATAGG
Found at i:50011 original size:46 final size:47
Alignment explanation
Indices: 49950--50039 Score: 155
Period size: 46 Copynumber: 1.9 Consensus size: 47
49940 ATCCTGGTAT
*
49950 GGTACCCAAAGGTGAATTGTTAAAGGCCTAGCAAAAACCCATTACCA
1 GGTACCCAAAGGTGAATTGTTAAAGGCCTACCAAAAACCCATTACCA
*
49997 GGTA-CCAAATGTGAATTGTTAAAGGCCTACCAAAAACCCATTA
1 GGTACCCAAAGGTGAATTGTTAAAGGCCTACCAAAAACCCATTA
50040 TTAATATAGC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
46 37 0.90
47 4 0.10
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (47 bp):
GGTACCCAAAGGTGAATTGTTAAAGGCCTACCAAAAACCCATTACCA
Found at i:64120 original size:125 final size:124
Alignment explanation
Indices: 63856--64228 Score: 620
Period size: 124 Copynumber: 3.0 Consensus size: 124
63846 AAATTATAAT
* *
63856 TGATGTTAGGAATAGCCTTTTAGATGAAGAGGTTATATTTTTAAAACTCTAACAAATAATATATA
1 TGATGTTAGGAGTAGCCTTTTAGATGAAGAGGTTATATTTTTAAAACTCTAACAAATAATATATG
*
63921 AGTTAGTTAGACAAGTAATATTATGAGTTAGCTCGTTATGATGATCATATAGGGAAAAA
66 AGTTAGTTAGACAAGTAATATTATGAGTTAGCTCATTATGATGATCATATAGGGAAAAA
* * * * * *
63980 TGATGTTAGGAGTAGCCTTTTAGATAAAGAGGTTATATTTTTAAAACTTTGACAAGTAATTTGTG
1 TGATGTTAGGAGTAGCCTTTTAGATGAAGAGGTTATATTTTTAAAACTCTAACAAATAATATATG
* * *
64045 AGTTAGTTAGACAAGTAAATATTATGAGTTAGCTCATTCTGATGACCATATAGGGAACAA
66 AGTTAGTTAGACAAGT-AATATTATGAGTTAGCTCATTATGATGATCATATAGGGAAAAA
*
64105 TGATGTTAGGAGTAGCCTTTTAGATGAAGAGGTTATATTTTTAAAGCTCTAACAAATAATATATG
1 TGATGTTAGGAGTAGCCTTTTAGATGAAGAGGTTATATTTTTAAAACTCTAACAAATAATATATG
64170 AGTTAGTTAGACAAGTAATATTATGAGTTAGCTCATTATGATGATCATATAGGGAAAAA
66 AGTTAGTTAGACAAGTAATATTATGAGTTAGCTCATTATGATGATCATATAGGGAAAAA
64229 AGTATACATT
Statistics
Matches: 226, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
124 113 0.50
125 113 0.50
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.35
Consensus pattern (124 bp):
TGATGTTAGGAGTAGCCTTTTAGATGAAGAGGTTATATTTTTAAAACTCTAACAAATAATATATG
AGTTAGTTAGACAAGTAATATTATGAGTTAGCTCATTATGATGATCATATAGGGAAAAA
Found at i:66436 original size:13 final size:13
Alignment explanation
Indices: 66418--66453 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
66408 TTATATGTGT
66418 ATTATCCCCAAAA
1 ATTATCCCCAAAA
66431 ATTATCCCCAAAA
1 ATTATCCCCAAAA
66444 ATTATCCCCA
1 ATTATCCCCA
66454 GGTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.25
Consensus pattern (13 bp):
ATTATCCCCAAAA
Found at i:67031 original size:13 final size:13
Alignment explanation
Indices: 67013--67048 Score: 65
Period size: 12 Copynumber: 2.8 Consensus size: 13
67003 AGATATCCAT
67013 GGATATATCGAAC
1 GGATATATCGAAC
67026 GGATATATCG-AC
1 GGATATATCGAAC
67038 GGATATATCGA
1 GGATATATCGA
67049 GGTATTGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (13 bp):
GGATATATCGAAC
Found at i:68246 original size:10 final size:10
Alignment explanation
Indices: 68231--68256 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
68221 AATTTAATAT
68231 GGATATTTAC
1 GGATATTTAC
68241 GGATATTTAC
1 GGATATTTAC
68251 GGATAT
1 GGATAT
68257 ATCGAGGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (10 bp):
GGATATTTAC
Found at i:72011 original size:22 final size:22
Alignment explanation
Indices: 71970--72011 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
71960 GACAAACCTG
*
71970 TAACCCGAATGACCCGAGAAGT
1 TAACCCGAATGACCCAAGAAGT
* *
71992 TAACCCGGATGATCCAAGAA
1 TAACCCGAATGACCCAAGAA
72012 TACTGTAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.14
Consensus pattern (22 bp):
TAACCCGAATGACCCAAGAAGT
Found at i:73046 original size:105 final size:102
Alignment explanation
Indices: 72897--73088 Score: 285
Period size: 105 Copynumber: 1.9 Consensus size: 102
72887 TAAAAAAAAT
** *
72897 TAGTAAAATGATAAAAATAAAATATGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTT
1 TAGTAAAATGATAAAAATAAAATATGTATAAAAATATTAGATTTAATCAAATAAAAATAGAGTTT
*
72962 TTAATTGAGTAAAACTATAAAAGTATTTTAATTAAGA
66 TTAATTAAGTAAAACTATAAAAGTATTTTAATTAAGA
* *
72999 TAGTAAAATGGTAAAAATAAAATAGTACTTATAAAAATATTAGATTTAATCAAATAAAAATAGAG
1 TAGTAAAATGATAAAAATAAAATA-T--GTATAAAAATATTAGATTTAATCAAATAAAAATAGAG
* *
73064 TTTTTAGTTAAGTAAAATTATAAAA
63 TTTTTAATTAAGTAAAACTATAAAA
73089 ATTTAAGTAA
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
102 23 0.29
103 1 0.01
105 55 0.70
ACGTcount: A:0.53, C:0.02, G:0.11, T:0.34
Consensus pattern (102 bp):
TAGTAAAATGATAAAAATAAAATATGTATAAAAATATTAGATTTAATCAAATAAAAATAGAGTTT
TTAATTAAGTAAAACTATAAAAGTATTTTAATTAAGA
Found at i:73894 original size:16 final size:16
Alignment explanation
Indices: 73873--73905 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
73863 TATTTTTATT
73873 TCATTTAAATTAATTA
1 TCATTTAAATTAATTA
*
73889 TCATTTAGATTAATTA
1 TCATTTAAATTAATTA
73905 T
1 T
73906 TTTATTTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (16 bp):
TCATTTAAATTAATTA
Found at i:75449 original size:8 final size:8
Alignment explanation
Indices: 75438--75463 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
75428 TATACGCATA
75438 AATAAAAT
1 AATAAAAT
75446 AATAAAAT
1 AATAAAAT
75454 AATAAAAT
1 AATAAAAT
75462 AA
1 AA
75464 AACTCCCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AATAAAAT
Found at i:77116 original size:3 final size:3
Alignment explanation
Indices: 77108--77142 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
77098 GGATGAGGAT
77108 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
77143 TTTTACTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:81708 original size:21 final size:20
Alignment explanation
Indices: 81683--81721 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
81673 CAATTCTTGC
*
81683 TCTTCAAATATTTCTTCAAGG
1 TCTTCAAAT-TATCTTCAAGG
81704 TCTTCAAATTATCTTCAA
1 TCTTCAAATTATCTTCAA
81722 ACACGAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.44
Consensus pattern (20 bp):
TCTTCAAATTATCTTCAAGG
Found at i:84911 original size:13 final size:13
Alignment explanation
Indices: 84893--84930 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
84883 TCCAGCACTT
*
84893 ACCTTACCTTGTA
1 ACCTTATCTTGTA
84906 ACCTTATCTTGTA
1 ACCTTATCTTGTA
84919 ACCTTATCTTGT
1 ACCTTATCTTGT
84931 TGGTACAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.21, C:0.26, G:0.08, T:0.45
Consensus pattern (13 bp):
ACCTTATCTTGTA
Found at i:86731 original size:29 final size:28
Alignment explanation
Indices: 86698--86753 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
86688 ATTAAAGACA
86698 GAAAATAAAAGAAA-ATATTTTTTTTTTCT
1 GAAAAT-AAAGAAACA-ATTTTTTTTTTCT
**
86727 GAAAATGCAGAAACAATTTTTTTTTTC
1 GAAAATAAAGAAACAATTTTTTTTTTC
86754 AAGAAAACGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (28 bp):
GAAAATAAAGAAACAATTTTTTTTTTCT
Found at i:86769 original size:29 final size:28
Alignment explanation
Indices: 86714--86779 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
86704 AAAAGAAAAT
* * *
86714 ATTTTTTTTTTCTGAAAATGCAGAAACA
1 ATTTTTTTTTTCAGAAAACGCAAAAACA
* *
86742 ATTTTTTTTTTCAAGAAAACGTAAAAACC
1 ATTTTTTTTTTC-AGAAAACGCAAAAACA
*
86771 CTTTTTTTT
1 ATTTTTTTT
86780 CAAAATCGCA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
28 12 0.39
29 19 0.61
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (28 bp):
ATTTTTTTTTTCAGAAAACGCAAAAACA
Found at i:86838 original size:13 final size:14
Alignment explanation
Indices: 86814--86841 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
86804 AAACGGAAAA
86814 TCAAATTTTTTTTT
1 TCAAATTTTTTTTT
86828 TCAAATTTTTTTTT
1 TCAAATTTTTTTTT
86842 AAAGAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (14 bp):
TCAAATTTTTTTTT
Found at i:101447 original size:12 final size:12
Alignment explanation
Indices: 101430--101454 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
101420 GTTATCACTT
101430 AAAAAAAAAACA
1 AAAAAAAAAACA
101442 AAAAAAAAAACA
1 AAAAAAAAAACA
101454 A
1 A
101455 CAACAACAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAACA
Done.