Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018444.1 Corchorus olitorius cultivar O-4 contig18477, 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: 44264
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:6141 original size:23 final size:21
Alignment explanation
Indices: 6115--6183 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 21
6105 GTTTTTAAGT
6115 AAAATCCCAAAAGAAGATTTTGG
1 AAAAT-CCAAAAGAAG-TTTTGG
6138 AAAAT--AAAAGAAG-TTTGG
1 AAAATCCAAAAGAAGTTTTGG
* *
6156 ATAATTCCAAAAGAGGGTTTTGG
1 A-AAATCCAAAAGA-AGTTTTGG
6179 AAAAT
1 AAAAT
6184 AAAGGTTCCC
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
18 6 0.16
19 3 0.08
20 8 0.21
21 6 0.16
22 4 0.11
23 11 0.29
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.25
Consensus pattern (21 bp):
AAAATCCAAAAGAAGTTTTGG
Found at i:6148 original size:20 final size:19
Alignment explanation
Indices: 6123--6186 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 19
6113 GTAAAATCCC
6123 AAAAGAAGATTTTGGAAAAT
1 AAAAGAAG-TTTTGGAAAAT
*
6143 AAAAGAAG-TTTGGATAATT
1 AAAAGAAGTTTTGGA-AAAT
*
6162 CCAAAAGAGGGTTTTGGAAAAT
1 --AAAAGA-AGTTTTGGAAAAT
6184 AAA
1 AAA
6187 GGTTCCCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
18 6 0.17
19 3 0.08
20 11 0.31
21 6 0.17
22 4 0.11
23 6 0.17
ACGTcount: A:0.50, C:0.03, G:0.22, T:0.25
Consensus pattern (19 bp):
AAAAGAAGTTTTGGAAAAT
Found at i:13418 original size:2 final size:2
Alignment explanation
Indices: 13411--13441 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13401 TAGTTTGTTT
13411 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
13442 TTATTTATTT
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:19758 original size:19 final size:20
Alignment explanation
Indices: 19729--19769 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
19719 CTGATGCTAT
19729 ATTTCTTAGTAAAAACAACA
1 ATTTCTTAGTAAAAACAACA
*
19749 ATTT-TTAGTAAAGACAACA
1 ATTTCTTAGTAAAAACAACA
19768 AT
1 AT
19770 ATTGAGAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (20 bp):
ATTTCTTAGTAAAAACAACA
Found at i:20794 original size:3 final size:3
Alignment explanation
Indices: 20786--20820 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
20776 GGCTGTGAGT
20786 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
20821 TTACTTTTTC
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:21095 original size:22 final size:22
Alignment explanation
Indices: 21070--21116 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
21060 TTTGTAATAT
21070 ATTCTGATATGATTATTAATGA
1 ATTCTGATATGATTATTAATGA
21092 ATTCTGATATGATTATTAATGA
1 ATTCTGATATGATTATTAATGA
21114 ATT
1 ATT
21117 TCAAGAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (22 bp):
ATTCTGATATGATTATTAATGA
Found at i:30717 original size:13 final size:13
Alignment explanation
Indices: 30701--30737 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
30691 GATACTTTTT
30701 TTTGACCCTCCAA
1 TTTGACCCTCCAA
*
30714 TTTGTCCCTCCAA
1 TTTGACCCTCCAA
*
30727 CTTGACCCTCC
1 TTTGACCCTCC
30738 TAATAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.16, C:0.43, G:0.08, T:0.32
Consensus pattern (13 bp):
TTTGACCCTCCAA
Found at i:30780 original size:40 final size:40
Alignment explanation
Indices: 30731--30816 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 40
30721 CTCCAACTTG
*
30731 ACCCTCCTAATAATTAAGGAAATAAATTAAATCCAAGTTTA
1 ACCC-CCTAATAATTAAGGAAAGAAATTAAATCCAAGTTTA
* * *
30772 GCCCCCTAATAATTAAGGTAAGAAATTAAATCCAGGTTTA
1 ACCCCCTAATAATTAAGGAAAGAAATTAAATCCAAGTTTA
30812 ACCCC
1 ACCCC
30817 TACTTATAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 37 0.93
41 3 0.08
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (40 bp):
ACCCCCTAATAATTAAGGAAAGAAATTAAATCCAAGTTTA
Found at i:31148 original size:29 final size:32
Alignment explanation
Indices: 31116--31176 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
31106 AATAAAAATA
31116 TTTTTTT-ACA-TTTCACATTAAATAGCTTCT
1 TTTTTTTGACACTTTCACATTAAATAGCTTCT
*
31146 TTTTTTTGGCATCTTTCACATTAAATAGCTT
1 TTTTTTTGACA-CTTTCACATTAAATAGCTT
31177 ATCAAACAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 7 0.26
31 2 0.07
33 18 0.67
ACGTcount: A:0.25, C:0.16, G:0.07, T:0.52
Consensus pattern (32 bp):
TTTTTTTGACACTTTCACATTAAATAGCTTCT
Found at i:34341 original size:677 final size:676
Alignment explanation
Indices: 33009--34356 Score: 2240
Period size: 677 Copynumber: 2.0 Consensus size: 676
32999 CATAAAGTAT
* * * **
33009 AAAAGTATGATGATCATTTGATAAATAATCGAACCAAAAAAATATATGTTTATGGAGATTAAACA
1 AAAAGTATGATGATCATTTGATAAATAATCCAACAAAAAAAATATATGTCTATGGAGACCAAACA
* * *
33074 TAAAAATTCCCTCTTAAACCCTCCACGAAACTCATTAATCAAATTCAGGTTTCAGGCCCTTGACG
66 TAAAAATTCCCTCTTAAACCCTCCACGAAACTCACTAATCAAATTCAGGTTTCAAGCCCTTGAAG
*
33139 AAAGTTGTAGATCATACAATAACCTTTTAACCGAAACTTGAACAACCTCAATCGGAAAAGTGGAC
131 AAAGTTGTAGATCATACAATAACCTTTTAACCGAAACTTGAAAAACCTCAATCGGAAAAGTGGAC
33204 CGAAAATTAAACAATATTAGAAAGACCGACAATCGAGACCACAAAATTTCAAAAGCATTTTTTAG
196 CGAAAATTAAACAATATTAGAAAGACCGACAATCGAGACCACAAAATTTCAAAAGCATTTTTTAG
*
33269 AATCAAAACATTAAAATTGGCTTTCGAATATTTCAGGAAAGTTGTAGATCATTAAATTACCTTTA
261 AATCAAAACATTAAAATTGGCTTTCGAATACTTCAGGAAAGTTGTAGATCATTAAATTACCTTTA
* * *
33334 AATAAACACTTGAATCACCTTGATCGGATAAGCAAAACAAAAAATAAAGGAATTAAAGCCGAAAC
326 AATAAACACTTGAATCACCTTGATCGGACAAACAAAACAAAAAATAAAAGAATTAAAGCCGAAAC
33399 GTTAAATCGTCCAACCAAGAATTTGTAAAGGATTAAATAACATAAAGCATAAAAGTATAGAGATC
391 GTTAAATCGTCCAACCAAGAATTTGTAAAGGATTAAATAACATAAAGCATAAAAGTATAGAGATC
33464 ATTTGCTAAATATTCCAAAAAAAATTAGTTTATTGAGAATGGGACTCACAAATAGTAACTTTTAA
456 ATTTGCTAAATATTCCAAAAAAAATTAGTTTATTGAGAATGGGACTCACAAATAGTAACTTTTAA
* * *
33529 TCAAAGTTCCCAAAATGCCCTTGGCTACCAACCTAAATAGCGAAAAAAACCGAATATGAAAGTAC
521 TCAAAGTTCCCAAAACGCCATTGACTACCAACCTAAATAGCGAAAAAAACCGAATATGAAAGTAC
33594 CGAAATACCCCTGACAATTTGTTCTTGGGTGAATGTGGTGTATCTTATAGCTAGACAAAAGGGAA
586 CGAAATACCCCTGACAATTTGTTCTTGGGTGAATGTGGTGTATCTTATAGCTAGACAAAAGGGAA
33659 ATTTCATTTTCAACTTTAATATATTA
651 ATTTCATTTTCAACTTTAATATATTA
*
33685 AAAAGTATGA-GAATCATTTGATAAATAATCCAACGAAAAAAAATATTTGTCTATGGAGACCAAA
1 AAAAGTATGATG-ATCATTTGATAAATAATCCAAC-AAAAAAAATATATGTCTATGGAGACCAAA
* *
33749 CATAAAAATTCCCTCTTGAACCCTCCACGAAACTCACTAATCAAATTCAGGTTTCAAGCCTTTGA
64 CATAAAAATTCCCTCTTAAACCCTCCACGAAACTCACTAATCAAATTCAGGTTTCAAGCCCTTGA
* * * *
33814 AGAAAGTTGTAGATTATATAATAACCTTTTAACCGACACTTGAAAAACCTCAATCGGACAAGTGG
129 AGAAAGTTGTAGATCATACAATAACCTTTTAACCGAAACTTGAAAAACCTCAATCGGAAAAGTGG
33879 ACCGAAAATTAAACAATATTAGAAAGACCGACAATCGAGACCACAAAATTTCAGAAA-CATTTTT
194 ACCGAAAATTAAACAATATTAGAAAGACCGACAATCGAGACCACAAAATTTCA-AAAGCATTTTT
* * * *
33943 TAGAATCAAACCATTAAAATTGG-TTTCTGGATACTTCATGAAAGTTGTATATCATTAAATTACC
258 TAGAATCAAAACATTAAAATTGGCTTTC-GAATACTTCAGGAAAGTTGTAGATCATTAAATTACC
* *
34007 TTTAAATAGACACTTGAATCACCTTGGTCGGACAAACAAAACAAAAAAATTAAAAGAATTAAAGC
322 TTTAAATAAACACTTGAATCACCTTGATCGGACAAACAAAAC-AAAAAA-TAAAAGAATTAAAGC
* * *
34072 CGAAACGTTAAATCGTCCAACCAAGAATTTGTGAAGGATTAAATAGCATAAAGCATAAAAGTCTA
385 CGAAACGTTAAATCGTCCAACCAAGAATTTGTAAAGGATTAAATAACATAAAGCATAAAAGTATA
* *
34137 GGGATCATTTGCTAAATATTCCAGAAAAAAATTAGTTTATTGAGAATGGGAC-CATAAATAGTAA
450 GAGATCATTTGCTAAATATTCCA-AAAAAAATTAGTTTATTGAGAATGGGACTCACAAATAGTAA
* *
34201 CTTTTAATCAAATTTCCCAAAACGCCATTGACTACCAACCTAAATAGCG-AAAAAA-CGAGTATG
514 CTTTTAATCAAAGTTCCCAAAACGCCATTGACTACCAACCTAAATAGCGAAAAAAACCGAATATG
* *
34264 AAAGTACCGAAATACCCCTGACAATTTGTTTTTGGGTGAATGTGGTGTATCTTATAGCTGGACAA
579 AAAGTACCGAAATACCCCTGACAATTTGTTCTTGGGTGAATGTGGTGTATCTTATAGCTAGACAA
*
34329 AAGGGTAATTTCATTTTCAACTTTAATA
644 AAGGGAAATTTCATTTTCAACTTTAATA
34357 CTCCCTCCGA
Statistics
Matches: 626, Mismatches: 39, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
675 1 0.00
676 35 0.06
677 393 0.63
678 15 0.02
679 154 0.25
680 28 0.04
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (676 bp):
AAAAGTATGATGATCATTTGATAAATAATCCAACAAAAAAAATATATGTCTATGGAGACCAAACA
TAAAAATTCCCTCTTAAACCCTCCACGAAACTCACTAATCAAATTCAGGTTTCAAGCCCTTGAAG
AAAGTTGTAGATCATACAATAACCTTTTAACCGAAACTTGAAAAACCTCAATCGGAAAAGTGGAC
CGAAAATTAAACAATATTAGAAAGACCGACAATCGAGACCACAAAATTTCAAAAGCATTTTTTAG
AATCAAAACATTAAAATTGGCTTTCGAATACTTCAGGAAAGTTGTAGATCATTAAATTACCTTTA
AATAAACACTTGAATCACCTTGATCGGACAAACAAAACAAAAAATAAAAGAATTAAAGCCGAAAC
GTTAAATCGTCCAACCAAGAATTTGTAAAGGATTAAATAACATAAAGCATAAAAGTATAGAGATC
ATTTGCTAAATATTCCAAAAAAAATTAGTTTATTGAGAATGGGACTCACAAATAGTAACTTTTAA
TCAAAGTTCCCAAAACGCCATTGACTACCAACCTAAATAGCGAAAAAAACCGAATATGAAAGTAC
CGAAATACCCCTGACAATTTGTTCTTGGGTGAATGTGGTGTATCTTATAGCTAGACAAAAGGGAA
ATTTCATTTTCAACTTTAATATATTA
Found at i:37630 original size:2 final size:2
Alignment explanation
Indices: 37623--37650 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
37613 TCCAAATCTA
37623 AT AT 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
37651 GAGAAACTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38286 original size:20 final size:20
Alignment explanation
Indices: 38263--38306 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
38253 ACAAACACTA
38263 AAAAACTATAT-ATTGTAAAT
1 AAAAACTATATAATT-TAAAT
**
38283 AAAAGGTATATAATTTAAAT
1 AAAAACTATATAATTTAAAT
38303 AAAA
1 AAAA
38307 TTATGATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (20 bp):
AAAAACTATATAATTTAAAT
Found at i:39681 original size:17 final size:17
Alignment explanation
Indices: 39659--39713 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
39649 CAAAATATCT
39659 GTTTCAATTAAGTCTGG
1 GTTTCAATTAAGTCTGG
* **
39676 GTTTCAACTTAA-TATTT
1 GTTTCAA-TTAAGTCTGG
39693 GTTTCAATTAAGTCTGG
1 GTTTCAATTAAGTCTGG
39710 GTTT
1 GTTT
39714 TGGTCATCTC
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
16 4 0.13
17 22 0.73
18 4 0.13
ACGTcount: A:0.24, C:0.11, G:0.18, T:0.47
Consensus pattern (17 bp):
GTTTCAATTAAGTCTGG
Found at i:39736 original size:23 final size:23
Alignment explanation
Indices: 39710--39776 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
39700 TTAAGTCTGG
39710 GTTTTGGTCATCTCAAAATATCT
1 GTTTTGGTCATCTCAAAATATCT
* *
39733 G--TT--TCAAT-T--AAATCTGT
1 GTTTTGGTC-ATCTCAAAATATCT
39750 GTTTTGGTCATCTCAAAATATCT
1 GTTTTGGTCATCTCAAAATATCT
39773 GTTT
1 GTTT
39777 CAATTAACTC
Statistics
Matches: 32, Mismatches: 4, Indels: 16
0.62 0.08 0.31
Matches are distributed among these distances:
17 7 0.22
19 5 0.16
20 4 0.12
21 5 0.16
23 11 0.34
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.46
Consensus pattern (23 bp):
GTTTTGGTCATCTCAAAATATCT
Found at i:39741 original size:40 final size:40
Alignment explanation
Indices: 39686--39792 Score: 178
Period size: 40 Copynumber: 2.7 Consensus size: 40
39676 GTTTCAACTT
* *
39686 AATATTTGTTTCAATTAAGTCTGGGTTTTGGTCATCTCAA
1 AATATCTGTTTCAATTAAATCTGGGTTTTGGTCATCTCAA
*
39726 AATATCTGTTTCAATTAAATCTGTGTTTTGGTCATCTCAA
1 AATATCTGTTTCAATTAAATCTGGGTTTTGGTCATCTCAA
*
39766 AATATCTGTTTCAATTAACTCTGGGTT
1 AATATCTGTTTCAATTAAATCTGGGTT
39793 CTACATTTAA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (40 bp):
AATATCTGTTTCAATTAAATCTGGGTTTTGGTCATCTCAA
Found at i:40053 original size:12 final size:12
Alignment explanation
Indices: 40036--40115 Score: 126
Period size: 12 Copynumber: 6.6 Consensus size: 12
40026 CATCGATACC
40036 TCGATATATCCG
1 TCGATATATCCG
40048 TCGATATATCCG
1 TCGATATATCCG
*
40060 CCGATATATCCG
1 TCGATATATCCG
40072 TCGATATATCCG
1 TCGATATATCCG
40084 -CTGATATATCCG
1 TC-GATATATCCG
40096 TTCGATATATCCG
1 -TCGATATATCCG
40109 TCGATAT
1 TCGATAT
40116 CTGTATTAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
11 1 0.02
12 51 0.81
13 10 0.16
14 1 0.02
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (12 bp):
TCGATATATCCG
Done.