Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013173.1 Corchorus olitorius cultivar O-4 contig13206, 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: 35219
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:43 original size:2 final size:2
Alignment explanation
Indices: 36--76 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
26 TGAAAACTAG
36 TA TA TA TA TA 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 TA TA TA TA TA T
77 TTGTTTATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4306 original size:36 final size:36
Alignment explanation
Indices: 4265--4354 Score: 180
Period size: 36 Copynumber: 2.5 Consensus size: 36
4255 AATGGGTATG
4265 ATATAATTGCTATTTTAATCATAACCAATTAATTGT
1 ATATAATTGCTATTTTAATCATAACCAATTAATTGT
4301 ATATAATTGCTATTTTAATCATAACCAATTAATTGT
1 ATATAATTGCTATTTTAATCATAACCAATTAATTGT
4337 ATATAATTGCTATTTTAA
1 ATATAATTGCTATTTTAA
4355 CTTAATGAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.46
Consensus pattern (36 bp):
ATATAATTGCTATTTTAATCATAACCAATTAATTGT
Found at i:5073 original size:8 final size:8
Alignment explanation
Indices: 5060--5084 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5050 AGTCATAGTC
5060 ATTGGGTT
1 ATTGGGTT
5068 ATTGGGTT
1 ATTGGGTT
5076 ATTGGGTT
1 ATTGGGTT
5084 A
1 A
5085 CAACTTACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.36, T:0.48
Consensus pattern (8 bp):
ATTGGGTT
Found at i:6571 original size:22 final size:22
Alignment explanation
Indices: 6540--6595 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
6530 TCTCCACCGC
* *
6540 TTCTTCCTCTTTCTCCTCTCCA
1 TTCTTTCTCTTCCTCCTCTCCA
*
6562 TTCTTTCTCTTCCTTCTCTCCA
1 TTCTTTCTCTTCCTCCTCTCCA
6584 TTCTTTCTCTTC
1 TTCTTTCTCTTC
6596 TCTTTTGGCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.04, C:0.41, G:0.00, T:0.55
Consensus pattern (22 bp):
TTCTTTCTCTTCCTCCTCTCCA
Found at i:18447 original size:390 final size:391
Alignment explanation
Indices: 17728--18501 Score: 1415
Period size: 390 Copynumber: 2.0 Consensus size: 391
17718 GTCTAAAACA
17728 TTAAAAGTAGCACTTACATTGCCATATTCACTAGGAAGATCTAGCTTGTATGCATTGTTGTTGAT
1 TTAAAAGTAGCACTTACATTGCCATATTCACTAGGAAGATCTAGCTTGTATGCATTGTTGTTGAT
* *
17793 CCTCTCCAAGACTTGGAATGGACCATCTCCACGAGGTAAGAGCTTAGACTTTCTCTTTTCAGGGA
66 CCTCTCCAAGACTTAGAATGGACCATCTCCACGAGGTAAGAGCTTAGACTTTCTCTTTTCAGGAA
* *
17858 ACCTTTCCTTTCTTAGATGCAACCATACCCAATTTCCAGGTTCAAAGATGACCTCTTTGCGACCC
131 ACCTTTCCTTCCTTAGATGCAACCATACCCAATCTCCAGGTTCAAAGATGACCTCTTTGCGACCC
17923 TTGTTAACATTCTTCATGTAGTGTTGTGTTTTCTTCTCAATTTGAGCTCTAACCTTTGCATGAAG
196 TTGTTAACATTCTTCATGTAGTGTTGTGTTTTCTTCTCAATTTGAGCTCTAACCTTTGCATGAAG
* *
17988 ATCCCTAACATATTCGGCCTTGCTTTGCCCATCCATGTCAACTTGCACACTCAAAGGTAAACTCA
261 ATCCCTAACATATTCGGCCTTACTTTGCCCATCCATGTCAACTTGCACACTCAAAAGTAAACTCA
*
18053 ACAAATCCAATGGGGTTAAAGGATTAAAG-CATACACACATTCAAAAGGTGAAAATCCATATTCA
326 ACAAATCCAATGGGGTTAAAGGAATAAAGCCATACACACATTCAAAAGGTGAAAATCCATATTCA
18117 C
391 C
*
18118 TTAAAAGTAGCACTTACATTGCTATATTCACTAGGAAGATCTAGCTTGTATGCATTGTTGTTGAT
1 TTAAAAGTAGCACTTACATTGCCATATTCACTAGGAAGATCTAGCTTGTATGCATTGTTGTTGAT
18183 CCTCTCCAAGACTTAGAATGGACCATCTCCACGAGGTAAGAGCTTAGACTTTCTCTTTTCAGGAA
66 CCTCTCCAAGACTTAGAATGGACCATCTCCACGAGGTAAGAGCTTAGACTTTCTCTTTTCAGGAA
* * *
18248 ACCTTTCCTTCCTTAGATGCAACCATACCCAATCTCTAGGTTCAAAGATGAGCTCTTTGCGCCCC
131 ACCTTTCCTTCCTTAGATGCAACCATACCCAATCTCCAGGTTCAAAGATGACCTCTTTGCGACCC
* *
18313 TTGTTAGCATTCTTCTTGTAGTGTTGTGTTTTCTTCTCAATTTGAGCTCTAACCTTTGCATGAAG
196 TTGTTAACATTCTTCATGTAGTGTTGTGTTTTCTTCTCAATTTGAGCTCTAACCTTTGCATGAAG
*
18378 ATCCCTAACATATTCGGCCTTACTTTTCCCATCCATGTCAACTTGCACACTCAAAAGTAAACTCA
261 ATCCCTAACATATTCGGCCTTACTTTGCCCATCCATGTCAACTTGCACACTCAAAAGTAAACTCA
18443 ACAAATCCAATGGGGTTAAAGGAATAAAGCCATACACACATTCAAAAGGTGAAAATCCA
326 ACAAATCCAATGGGGTTAAAGGAATAAAGCCATACACACATTCAAAAGGTGAAAATCCA
18502 GTTGTACTAT
Statistics
Matches: 369, Mismatches: 14, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
390 340 0.92
391 29 0.08
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.32
Consensus pattern (391 bp):
TTAAAAGTAGCACTTACATTGCCATATTCACTAGGAAGATCTAGCTTGTATGCATTGTTGTTGAT
CCTCTCCAAGACTTAGAATGGACCATCTCCACGAGGTAAGAGCTTAGACTTTCTCTTTTCAGGAA
ACCTTTCCTTCCTTAGATGCAACCATACCCAATCTCCAGGTTCAAAGATGACCTCTTTGCGACCC
TTGTTAACATTCTTCATGTAGTGTTGTGTTTTCTTCTCAATTTGAGCTCTAACCTTTGCATGAAG
ATCCCTAACATATTCGGCCTTACTTTGCCCATCCATGTCAACTTGCACACTCAAAAGTAAACTCA
ACAAATCCAATGGGGTTAAAGGAATAAAGCCATACACACATTCAAAAGGTGAAAATCCATATTCA
C
Found at i:19829 original size:33 final size:31
Alignment explanation
Indices: 19756--19860 Score: 120
Period size: 33 Copynumber: 3.2 Consensus size: 31
19746 GCTATGATCA
** *
19756 ACCAAAACAGATTTGTTTTCATCACAATTAGC
1 ACCAAAACAGATTTG-TTTCATCACAAACAAC
19788 ATCCAAAACAGAATTTGTTTCATCACAAACAAC
1 A-CCAAAACAG-ATTTGTTTCATCACAAACAAC
*
19821 ACCTAAAACAGATTTAGTGTCATCACAAACAAC
1 ACC-AAAACAGATTT-GTTTCATCACAAACAAC
19854 ACTCAAA
1 AC-CAAA
19861 TTAGTTAATA
Statistics
Matches: 64, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
32 7 0.11
33 51 0.80
34 6 0.09
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.25
Consensus pattern (31 bp):
ACCAAAACAGATTTGTTTCATCACAAACAAC
Found at i:29068 original size:16 final size:16
Alignment explanation
Indices: 29047--29092 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
29037 TGTAATTTTG
29047 AATTCAGTTCCTTCAT
1 AATTCAGTTCCTTCAT
* *
29063 AATTCAGCTCAC-TCTT
1 AATTCAGTTC-CTTCAT
29079 AATTCAGTTCCTTC
1 AATTCAGTTCCTTC
29093 TAAATTCCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 1 0.04
16 23 0.92
17 1 0.04
ACGTcount: A:0.24, C:0.28, G:0.07, T:0.41
Consensus pattern (16 bp):
AATTCAGTTCCTTCAT
Found at i:29098 original size:16 final size:16
Alignment explanation
Indices: 29047--29099 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
29037 TGTAATTTTG
29047 AATTCAGTTCCTTC-A
1 AATTCAGTTCCTTCTA
* *
29062 TAATTCAGCTCAC-TCTT
1 -AATTCAGTTC-CTTCTA
29079 AATTCAGTTCCTTCTA
1 AATTCAGTTCCTTCTA
29095 AATTC
1 AATTC
29100 CCCCTTAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 1 0.03
16 28 0.93
17 1 0.03
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.42
Consensus pattern (16 bp):
AATTCAGTTCCTTCTA
Found at i:30352 original size:13 final size:13
Alignment explanation
Indices: 30334--30359 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30324 TAGTTATATT
30334 TGATATGATTATC
1 TGATATGATTATC
30347 TGATATGATTATC
1 TGATATGATTATC
30360 GGATGGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
TGATATGATTATC
Found at i:32379 original size:11 final size:11
Alignment explanation
Indices: 32353--32388 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
32343 CTTAACACGG
32353 GAAAAAAGAAA
1 GAAAAAAGAAA
32364 -AAAAAAGAAA
1 GAAAAAAGAAA
*
32374 GGAAAAAGAAA
1 GAAAAAAGAAA
32385 GAAA
1 GAAA
32389 CCCAGTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:32904 original size:105 final size:105
Alignment explanation
Indices: 32795--33004 Score: 348
Period size: 105 Copynumber: 2.0 Consensus size: 105
32785 CTTATCTTAC
* * *
32795 TACTATATAAAATCACGAACTCAAAAATTTTAATTGGAAAATTTCTAAAATACCCTTAGTGTTAT
1 TACTATATAAAATCACGAACTCAAAAATCTTAATTGGAAAATTTCTAAAATACCCTCAGTATTAT
32860 AGTATAATAATTTTTTAATTAATATTCTTATTAGTCATTA
66 AGTATAATAATTTTTTAATTAATATTCTTATTAGTCATTA
* ***
32900 TACTATATAAAATCACGAACTCAAAAATCTTAATTGGGAAATTTCTAAAATTTTCTCAGTATTAT
1 TACTATATAAAATCACGAACTCAAAAATCTTAATTGGAAAATTTCTAAAATACCCTCAGTATTAT
*
32965 AGTATAATAATTTTTTAATTAATATTCTTTTTAGTCATTA
66 AGTATAATAATTTTTTAATTAATATTCTTATTAGTCATTA
33005 AATTTTTTAT
Statistics
Matches: 97, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
105 97 1.00
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (105 bp):
TACTATATAAAATCACGAACTCAAAAATCTTAATTGGAAAATTTCTAAAATACCCTCAGTATTAT
AGTATAATAATTTTTTAATTAATATTCTTATTAGTCATTA
Found at i:33459 original size:121 final size:118
Alignment explanation
Indices: 33218--33568 Score: 504
Period size: 121 Copynumber: 3.0 Consensus size: 118
33208 TGGAAGAATA
* * *
33218 TCCACCACAACCATGAATATTATTTTGAGGAATTTCAAGTCCTTC-ATTTTTCCATTTCAAACC-
1 TCCACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCC-TCAAATTTTCCACTTCAAACCA
* *
33281 ACTCTTCCAATAAAAACTAGTATAAATTACTCCTTAATTCTTA-GATCTCAAAGGC
65 ACTCTTCCAATAAAAA-TAGTATAAATTACTCCTTAATTCTTAGGTTC-CAAACGC
33336 TCCACCACAACCATCGAATATTGTTTTGAGGAATTTCTACAAGTCCTCAAATTTTCCACTTCAAA
1 TCCACCACAACCAT-GAATATTGTTTTGAGGAA-TT-T-CAAGTCCTCAAATTTTCCACTTCAAA
33401 CCAACTCTTCC-ATAAAAATAGTATAAATTACTCCTTAATTCTTAGGTTCCAAACGC
62 CCAACTCTTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGGTTCCAAACGC
*
33457 TCCACCACAACCATGAATATTGTTTTGAGG-----CAAGTCCTTAAATTTTCCACTTCAAACCAA
1 TCCACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTCAAATTTTCCACTTCAAACCAA
* *
33517 CTCTTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCCCAAACG
66 CTCTTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGGTTCCAAACG
33569 TGTTAACAAT
Statistics
Matches: 217, Mismatches: 8, Indels: 21
0.88 0.03 0.09
Matches are distributed among these distances:
112 36 0.17
113 42 0.19
118 14 0.06
119 17 0.08
120 18 0.08
121 49 0.23
122 33 0.15
123 8 0.04
ACGTcount: A:0.34, C:0.25, G:0.08, T:0.33
Consensus pattern (118 bp):
TCCACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTCAAATTTTCCACTTCAAACCAA
CTCTTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGGTTCCAAACGC
Found at i:34359 original size:2 final size:2
Alignment explanation
Indices: 34352--34572 Score: 379
Period size: 2 Copynumber: 110.5 Consensus size: 2
34342 TGCAAGCATA
34352 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
34394 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
34436 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
34478 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * * * * *
34520 AC AC AC AC AC AC AT AT AT AC AC AC AC AT AT AC AC AC AC AT AT
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
34562 AC AC AC AC AC A
1 AC AC AC AC AC A
34573 TATACATATA
Statistics
Matches: 213, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 213 1.00
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:35032 original size:43 final size:45
Alignment explanation
Indices: 34984--35087 Score: 117
Period size: 43 Copynumber: 2.4 Consensus size: 45
34974 TCATAGTGTA
*
34984 GTTATCAAAATTTTATACAGG-CGTT-ACCAAATTTCATAAAAAG
1 GTTATCAAAATTTTATACAGGTCGTTAACAAAATTTCATAAAAAG
* * * **
35027 GTTATC-AAATTTTCT-TAGGTCGTTAACAAAATTTTATACGAAG
1 GTTATCAAAATTTTATACAGGTCGTTAACAAAATTTCATAAAAAG
*
35070 GTTAACAAAATTTTATAC
1 GTTATCAAAATTTTATAC
35088 GAAGGTTATC
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
41 3 0.06
42 12 0.25
43 25 0.52
44 8 0.17
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (45 bp):
GTTATCAAAATTTTATACAGGTCGTTAACAAAATTTCATAAAAAG
Found at i:35033 original size:65 final size:65
Alignment explanation
Indices: 34960--35125 Score: 176
Period size: 65 Copynumber: 2.6 Consensus size: 65
34950 TTTTATATGG
* * *
34960 AGGTTATCAAAACGTCATAGTGTAGTTATCAAAATTTTATAC-AGGCGTT-ACCAAATTTCATAA
1 AGGTTATCAAAA-TTCATAGTGTAGTTATCAAAATTTTATACGAAG-GTTAACAAAATTTCATAA
35023 AA
64 AA
* * * * * **
35025 AGGTTATCAAATTTTCTTAG-GTCGTTAACAAAATTTTATACGAAGGTTAACAAAATTTTATACG
1 AGGTTATCAAA-ATTCATAGTGTAGTTATCAAAATTTTATACGAAGGTTAACAAAATTTCATAAA
35089 A
65 A
* *
35090 AGGTTATCAAAATTTATAGTGTGGTTATCAAAATTT
1 AGGTTATCAAAATTCATAGTGTAGTTATCAAAATTT
35126 CATGGGGGGA
Statistics
Matches: 82, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
64 27 0.33
65 55 0.67
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (65 bp):
AGGTTATCAAAATTCATAGTGTAGTTATCAAAATTTTATACGAAGGTTAACAAAATTTCATAAAA
Found at i:35144 original size:24 final size:22
Alignment explanation
Indices: 34909--35189 Score: 128
Period size: 22 Copynumber: 12.9 Consensus size: 22
34899 ACCAATATTA
* * *
34909 CATAGGAAGGTTATGAAATTTT
1 CATAGGGAGGTTATCAAAATTT
* *
34931 CATAGTGTGGTTA-CTAAAATTT
1 CATAGGGAGGTTATC-AAAATTT
* * **
34953 TATATGGAGGTTATCAAAACGT
1 CATAGGGAGGTTATCAAAATTT
*
34975 CATAGTGTA-GTTATCAAAATTT
1 CATAG-GGAGGTTATCAAAATTT
* * * *
34997 TATACAGG-CGTTA-CCAAATTT
1 CATA-GGGAGGTTATCAAAATTT
*** *
35018 CATAAAAAGGTTATCAAATTTT
1 CATAGGGAGGTTATCAAAATTT
* ** *
35040 CTTA-GGTCGTTAACAAAATTT
1 CATAGGGAGGTTATCAAAATTT
* * * *
35061 TATACGAAGGTTAACAAAATTT
1 CATAGGGAGGTTATCAAAATTT
* * *
35083 TATACGAAGGTTATCAAAATTT
1 CATAGGGAGGTTATCAAAATTT
* *
35105 -ATAGTGTGGTTATCAAAATTT
1 CATAGGGAGGTTATCAAAATTT
* *
35126 CATGGGGGGAGGTTATCAAAGTTTT
1 CAT--AGGGAGGTTATCAAA-ATTT
*
35151 C-TAGGGAGGTTAACAAAATTT
1 CATAGGGAGGTTATCAAAATTT
* *
35172 CATTGGAAGGTTA-CAAAA
1 CATAGGGAGGTTATCAAAA
35190 ATTTTGTGGA
Statistics
Matches: 194, Mismatches: 52, Indels: 27
0.71 0.19 0.10
Matches are distributed among these distances:
20 1 0.01
21 53 0.27
22 120 0.62
23 3 0.02
24 13 0.07
25 4 0.02
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.35
Consensus pattern (22 bp):
CATAGGGAGGTTATCAAAATTT
Done.