Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023669.1 Corchorus olitorius cultivar O-4 contig23702, 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: 14684
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:1709 original size:15 final size:15
Alignment explanation
Indices: 1691--1724 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1681 TTTGTTGTTG
1691 GATTGTTTTTGGATT
1 GATTGTTTTTGGATT
1706 GATTGTTTTTGGATT
1 GATTGTTTTTGGATT
1721 GATT
1 GATT
1725 ATCCCCCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.59
Consensus pattern (15 bp):
GATTGTTTTTGGATT
Found at i:5950 original size:27 final size:27
Alignment explanation
Indices: 5920--5993 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 27
5910 TTCGGCATTT
5920 AAGGGCAAAACTGTAATTTAG-TCAACC
1 AAGGGCAAAACTGTAATTTAGCT-AACC
* *
5947 AAGGGTAAAA-TGGTAATTTTAGCTGACC
1 AAGGGCAAAACT-GTAA-TTTAGCTAACC
*
5975 AAGGGCAAAACAGTAATTT
1 AAGGGCAAAACTGTAATTT
5994 TGACATCTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
26 1 0.03
27 16 0.41
28 21 0.54
29 1 0.03
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.24
Consensus pattern (27 bp):
AAGGGCAAAACTGTAATTTAGCTAACC
Found at i:8940 original size:30 final size:30
Alignment explanation
Indices: 8904--8994 Score: 155
Period size: 30 Copynumber: 3.0 Consensus size: 30
8894 TATTTGCCTG
*
8904 TTACAAATTGTATGCAATGTCATGGAACTA
1 TTACAAATTATATGCAATGTCATGGAACTA
*
8934 TTACAAATTATATGCAATGTCATGGAACTC
1 TTACAAATTATATGCAATGTCATGGAACTA
8964 TTACAAATTATATGCAAATGTCATGGAACTA
1 TTACAAATTATATGC-AATGTCATGGAACTA
8995 AAACTTATAA
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 43 0.75
31 14 0.25
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (30 bp):
TTACAAATTATATGCAATGTCATGGAACTA
Found at i:10128 original size:39 final size:39
Alignment explanation
Indices: 10072--10147 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
10062 ATAAGACTTT
* * *
10072 GAAATTCACTGAGAAAACATTGACCCTGAACAGGATTTC
1 GAAATTAACTGAGAAAACAATGACCCTAAACAGGATTTC
* * *
10111 GAAATTAACTGATAAAACAATGATCCTAAATAGGATT
1 GAAATTAACTGAGAAAACAATGACCCTAAACAGGATT
10148 CAGAAAACAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (39 bp):
GAAATTAACTGAGAAAACAATGACCCTAAACAGGATTTC
Found at i:10155 original size:27 final size:27
Alignment explanation
Indices: 10124--10235 Score: 145
Period size: 27 Copynumber: 4.1 Consensus size: 27
10114 ATTAACTGAT
*
10124 AAAACAATGATCCTAAATAGGATTCAG
1 AAAACAATGATCCTGAATAGGATTCAG
* *
10151 AAAACAATGATCCTGAATAGCATTTGAG
1 AAAACAATGATCCTGAATAGGA-TTCAG
*
10179 AAAGCAATGATCCTGAATAGGATTCTA-
1 AAAACAATGATCCTGAATAGGATTC-AG
* *
10206 AAAACGATGATCCTGAATAGGATTCTG
1 AAAACAATGATCCTGAATAGGATTCAG
10233 AAA
1 AAA
10236 TTCACTTGAT
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
27 48 0.66
28 25 0.34
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.24
Consensus pattern (27 bp):
AAAACAATGATCCTGAATAGGATTCAG
Found at i:10267 original size:40 final size:40
Alignment explanation
Indices: 10218--10294 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
10208 AACGATGATC
*
10218 CTGAATAGGATTCTGAAATTCACT-TGATAAAGCAATGGTT
1 CTGAATAGGATTCTGAAATT-ACTCTAATAAAGCAATGGTT
* *
10258 CTGAGTAGGATTCTGAAATTAGTCTAATAAAGCAATG
1 CTGAATAGGATTCTGAAATTACTCTAATAAAGCAATG
10295 ATCCCAAGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 2 0.06
40 31 0.94
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (40 bp):
CTGAATAGGATTCTGAAATTACTCTAATAAAGCAATGGTT
Found at i:10305 original size:40 final size:39
Alignment explanation
Indices: 10223--10318 Score: 102
Period size: 40 Copynumber: 2.4 Consensus size: 39
10213 TGATCCTGAA
* * * **
10223 TAGGATTCTGAAATTCACTTGATAAAGCAATGGTTCTGAG
1 TAGGATTCTGAAATT-ACTTAATAAAGCAATGATCCCAAG
*
10263 TAGGATTCTGAAATTAGTCTAATAAAGCAATGATCCCAAG
1 TAGGATTCTGAAATTACT-TAATAAAGCAATGATCCCAAG
* *
10303 TAGGCTTATGAAATTA
1 TAGGATTCTGAAATTA
10319 ACTGGTAAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 2 0.04
40 45 0.96
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31
Consensus pattern (39 bp):
TAGGATTCTGAAATTACTTAATAAAGCAATGATCCCAAG
Found at i:10354 original size:27 final size:27
Alignment explanation
Indices: 10324--10375 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
10314 AATTAACTGG
*
10324 TAAAGAAATGATCCTGAATAGGATTGA
1 TAAAGAAAGGATCCTGAATAGGATTGA
**
10351 TAAAGCTAGGATCCTGAATAGGATT
1 TAAAGAAAGGATCCTGAATAGGATT
10376 CCGGAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27
Consensus pattern (27 bp):
TAAAGAAAGGATCCTGAATAGGATTGA
Found at i:10404 original size:40 final size:40
Alignment explanation
Indices: 10347--10495 Score: 226
Period size: 40 Copynumber: 3.7 Consensus size: 40
10337 CTGAATAGGA
* * *
10347 TTGATAAAGCTAGGATCCTGAATAGGATTCCGGAATTTAC
1 TTGATAAAGCAATGATCCTGAATAGGATTCCAGAATTTAC
10387 TTGATAAAGCAATGATCCTGAATAGGATTCCAGAATTTAC
1 TTGATAAAGCAATGATCCTGAATAGGATTCCAGAATTTAC
* * * *
10427 TTGATAAAGCAATGATCCTGAATAGGATTCTAAAATTAAT
1 TTGATAAAGCAATGATCCTGAATAGGATTCCAGAATTTAC
*
10467 TTGATAAAACAATGATCCTGAATAGGATT
1 TTGATAAAGCAATGATCCTGAATAGGATT
10496 GATAAAGCAA
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 101 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (40 bp):
TTGATAAAGCAATGATCCTGAATAGGATTCCAGAATTTAC
Found at i:10463 original size:146 final size:147
Alignment explanation
Indices: 10179--10523 Score: 403
Period size: 146 Copynumber: 2.3 Consensus size: 147
10169 AGCATTTGAG
* * * * * *
10179 AAAGCAATGATCCTGAATAGGATT-CTAAAAACGATGATCCTGAATAGGATTCTGAAATTCACTT
1 AAAGAAATGATCCTGAATAGGATTGAT-AAAGCAAGGATCCTGAATAGGATTCCGAAATTCACTT
* * * * * *
10243 GATAAAGCAATGGTTCTGAGTAGGATTCTGAAATTAGTCTAATAAAGCAATGATCCCAAGTAGGC
65 GATAAAGCAATGATCCTGAATAGGATTCAGAAATTACTCTAATAAAGCAATGATCCCAAGTAGGA
* *
10308 TTATGAAATTAA-CTGGT
130 TTATAAAATTAATCTGAT
* * *
10325 AAAGAAATGATCCTGAATAGGATTGATAAAGCTAGGATCCTGAATAGGATTCCGGAATTTACTTG
1 AAAGAAATGATCCTGAATAGGATTGATAAAGCAAGGATCCTGAATAGGATTCCGAAATTCACTTG
* * *
10390 ATAAAGCAATGATCCTGAATAGGATTCCAGAATTTACT-TGATAAAGCAATGATCCTGAA-TAGG
66 ATAAAGCAATGATCCTGAATAGGATT-CAGAAATTACTCTAATAAAGCAATGATCC-CAAGTAGG
* *
10453 ATTCTAAAATTAATTTGAT
129 ATTATAAAATTAATCTGAT
*
10472 AAA-ACAATGATCCTGAATAGGATTGATAAAGCAATGGATCCTGAATAAGATT
1 AAAGA-AATGATCCTGAATAGGATTGATAAAGCAA-GGATCCTGAATAGGATT
10524 GAGAAAGCAA
Statistics
Matches: 170, Mismatches: 23, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
146 109 0.64
147 45 0.26
148 16 0.09
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (147 bp):
AAAGAAATGATCCTGAATAGGATTGATAAAGCAAGGATCCTGAATAGGATTCCGAAATTCACTTG
ATAAAGCAATGATCCTGAATAGGATTCAGAAATTACTCTAATAAAGCAATGATCCCAAGTAGGAT
TATAAAATTAATCTGAT
Found at i:10523 original size:28 final size:28
Alignment explanation
Indices: 10467--10592 Score: 173
Period size: 28 Copynumber: 4.5 Consensus size: 28
10457 TAAAATTAAT
* *
10467 TTGATAAAACAAT-GATCCTGAATAGGA
1 TTGAGAAAGCAATGGATCCTGAATAGGA
* *
10494 TTGATAAAGCAATGGATCCTGAATAAGA
1 TTGAGAAAGCAATGGATCCTGAATAGGA
10522 TTGAGAAAGCAATGGATCCTGAATAGGA
1 TTGAGAAAGCAATGGATCCTGAATAGGA
* * * *
10550 TTGAGAAAGTAATAGATCTTGAACAGGA
1 TTGAGAAAGCAATGGATCCTGAATAGGA
10578 TTGAGAAAGCAATGG
1 TTGAGAAAGCAATGG
10593 TAAGGAAATG
Statistics
Matches: 88, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
27 12 0.14
28 76 0.86
ACGTcount: A:0.42, C:0.10, G:0.25, T:0.24
Consensus pattern (28 bp):
TTGAGAAAGCAATGGATCCTGAATAGGA
Found at i:10677 original size:27 final size:27
Alignment explanation
Indices: 10599--10677 Score: 99
Period size: 27 Copynumber: 2.9 Consensus size: 27
10589 ATGGTAAGGA
*
10599 AATGATCCTGAATAGGATTGGTG-AAGC
1 AATGATCCTGAATAGGATT-GTGAAACC
*
10626 AATGATCCT-ATATAGGATTGAGAAACC
1 AATGATCCTGA-ATAGGATTGTGAAACC
*
10653 AATGATCCTGAATAGGATTTTGAAA
1 AATGATCCTGAATAGGATTGTGAAA
10678 TTAACCGGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 3 0.07
27 41 0.91
28 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (27 bp):
AATGATCCTGAATAGGATTGTGAAACC
Found at i:10688 original size:93 final size:94
Alignment explanation
Indices: 10498--10737 Score: 256
Period size: 93 Copynumber: 2.6 Consensus size: 94
10488 ATAGGATTGA
* * **
10498 TAAAGCAATGGATCCTGAATAAGATTGAGAAAGCAATGGATCCTGAATAGGATTGAGAAAGTAAT
1 TAAAGAAAT-GATCCTGAATAGGATTGAGAAAGCAATGGATCCTGAATAGGATTGAGAAACCAAT
* *
10563 AGATCTTGAACAGGATTGAGAAAGCAATGG
65 AGATCCTGAACAGGATTGAGAAAGCAACGG
* *
10593 TAAGGAAATGATCCTGAATAGGATTG-GTGAAGCAAT-GATCCT-ATATAGGATTGAGAAACCAA
1 TAAAGAAATGATCCTGAATAGGATTGAG-AAAGCAATGGATCCTGA-ATAGGATTGAGAAACCAA
* ** **
10655 T-GATCCTGAATAGGATTTTGAAATTAACCGG
64 TAGATCCTGAACAGGATTGAGAAAGCAA-CGG
* * * *
10686 TAAAGAAATGATCATGAATAGGATTGATAAAGCTA-GGATCTTGAATAGGATT
1 TAAAGAAATGATCCTGAATAGGATTGAGAAAGCAATGGATCCTGAATAGGATT
10738 TCGGAATTTA
Statistics
Matches: 120, Mismatches: 19, Indels: 14
0.78 0.12 0.09
Matches are distributed among these distances:
92 21 0.17
93 68 0.57
94 24 0.20
95 7 0.06
ACGTcount: A:0.40, C:0.10, G:0.25, T:0.25
Consensus pattern (94 bp):
TAAAGAAATGATCCTGAATAGGATTGAGAAAGCAATGGATCCTGAATAGGATTGAGAAACCAATA
GATCCTGAACAGGATTGAGAAAGCAACGG
Found at i:10712 original size:66 final size:67
Alignment explanation
Indices: 10637--10777 Score: 167
Period size: 66 Copynumber: 2.1 Consensus size: 67
10627 ATGATCCTAT
* * *
10637 ATAGGATTGAGAAACCAATGATCCTGAATAGGATTTTGAAATTAAC-CGGTAAAGAAATGATCAT
1 ATAGGATTGAGAAACCAAGGATCCTGAATAGGATTTCGAAATTAACTCGATAAAGAAATGATCAT
10701 GA
66 GA
* * * * * * * * *
10703 ATAGGATTGATAAAGCTAGGATCTTGAATAGGATTTCGGAATTTACTTGATAAAGCAATGATCCT
1 ATAGGATTGAGAAACCAAGGATCCTGAATAGGATTTCGAAATTAACTCGATAAAGAAATGATCAT
10768 GA
66 GA
10770 ATAGGATT
1 ATAGGATT
10778 CTGAAATTAA
Statistics
Matches: 62, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
66 38 0.61
67 24 0.39
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (67 bp):
ATAGGATTGAGAAACCAAGGATCCTGAATAGGATTTCGAAATTAACTCGATAAAGAAATGATCAT
GA
Found at i:10716 original size:27 final size:27
Alignment explanation
Indices: 10686--10737 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
10676 AATTAACCGG
*
10686 TAAAGAAATGATCATGAATAGGATTGA
1 TAAAGAAAGGATCATGAATAGGATTGA
** *
10713 TAAAGCTAGGATCTTGAATAGGATT
1 TAAAGAAAGGATCATGAATAGGATT
10738 TCGGAATTTA
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:0.42, C:0.06, G:0.23, T:0.29
Consensus pattern (27 bp):
TAAAGAAAGGATCATGAATAGGATTGA
Found at i:10771 original size:40 final size:40
Alignment explanation
Indices: 10709--10801 Score: 116
Period size: 40 Copynumber: 2.3 Consensus size: 40
10699 ATGAATAGGA
* * * * *
10709 TTGATAAAGCTAGGATCTTGAATAGGATT-TCGGAATTTAC
1 TTGATAAAGCAATGATCCTGAATAGGATTCT-GAAATTAAC
*
10749 TTGATAAAGCAATGATCCTGAATAGGATTCTGAAATTAAT
1 TTGATAAAGCAATGATCCTGAATAGGATTCTGAAATTAAC
10789 TTGATAAAGCAAT
1 TTGATAAAGCAAT
10802 TGATTGAGCC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 45 0.98
41 1 0.02
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (40 bp):
TTGATAAAGCAATGATCCTGAATAGGATTCTGAAATTAAC
Found at i:13551 original size:26 final size:27
Alignment explanation
Indices: 13495--13566 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 27
13485 TCAAGAATCT
**
13495 AGGGGCATTTTGGTCATTTTTACACTA
1 AGGGGCATTTTGGTCATTTGCACACTA
* * *
13522 A-GGGCATTTTGGTCATTTGCATATTC
1 AGGGGCATTTTGGTCATTTGCACACTA
* *
13548 AGGGGGATGTTGGTCATTT
1 AGGGGCATTTTGGTCATTT
13567 TAAGTCCACC
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
26 21 0.57
27 16 0.43
ACGTcount: A:0.19, C:0.12, G:0.28, T:0.40
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTGCACACTA
Done.