Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020701.1 Corchorus olitorius cultivar O-4 contig20734, 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: 63556
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--32 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1 AT AT 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 AT AT
33 GAGAATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1174 original size:1 final size:1
Alignment explanation
Indices: 1159--1201 Score: 50
Period size: 1 Copynumber: 43.0 Consensus size: 1
1149 ACTGGGGAAA
* * * *
1159 GGGGAGGGGGAGGGGGAGGGGGGAGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1202 TGGTCTTTTA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.09, C:0.00, G:0.91, T:0.00
Consensus pattern (1 bp):
G
Found at i:1174 original size:7 final size:7
Alignment explanation
Indices: 1159--1200 Score: 56
Period size: 6 Copynumber: 6.6 Consensus size: 7
1149 ACTGGGGAAA
1159 GGGGA-G
1 GGGGAGG
1165 GGGGA-G
1 GGGGAGG
1171 GGGGAGG
1 GGGGAGG
1178 GGGGAGG
1 GGGGAGG
1185 GGGG-GG
1 GGGGAGG
1191 GGGG-GG
1 GGGGAGG
1197 GGGG
1 GGGG
1201 GTGGTCTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 23 0.66
7 12 0.34
ACGTcount: A:0.10, C:0.00, G:0.90, T:0.00
Consensus pattern (7 bp):
GGGGAGG
Found at i:1200 original size:19 final size:19
Alignment explanation
Indices: 1159--1198 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1149 ACTGGGGAAA
1159 GGGGAGGGGGAGGGGGAGG
1 GGGGAGGGGGAGGGGGAGG
1178 GGGGAGGGGG-GGGGG-GG
1 GGGGAGGGGGAGGGGGAGG
1195 GGGG
1 GGGG
1199 GGGTGGTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.29
18 5 0.24
19 10 0.48
ACGTcount: A:0.10, C:0.00, G:0.90, T:0.00
Consensus pattern (19 bp):
GGGGAGGGGGAGGGGGAGG
Found at i:5566 original size:85 final size:85
Alignment explanation
Indices: 5423--5594 Score: 308
Period size: 85 Copynumber: 2.0 Consensus size: 85
5413 ATGTAAATCA
* *
5423 GAACCAATTTTTTATAGGCATTTACTTAATAAAGACTTAAAATTTACAGCATAATAACATCCCAA
1 GAACCAATCTATTATAGGCATTTACTTAATAAAGACTTAAAATTTACAGCATAATAACATCCCAA
*
5488 ATTTAATTCATTCATAAGAG
66 ATTCAATTCATTCATAAGAG
*
5508 GAACCAATCTATTATAGGCATTTACTTAATAAAGACTTCAAATTTACAGCATAATAACATCCCAA
1 GAACCAATCTATTATAGGCATTTACTTAATAAAGACTTAAAATTTACAGCATAATAACATCCCAA
5573 ATTCAATTCATTCATAAGAG
66 ATTCAATTCATTCATAAGAG
5593 GA
1 GA
5595 TAAATTCATT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 83 1.00
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (85 bp):
GAACCAATCTATTATAGGCATTTACTTAATAAAGACTTAAAATTTACAGCATAATAACATCCCAA
ATTCAATTCATTCATAAGAG
Found at i:23175 original size:35 final size:35
Alignment explanation
Indices: 23124--23224 Score: 193
Period size: 35 Copynumber: 2.9 Consensus size: 35
23114 TAGTTTTAAT
*
23124 TTTCTCAAGGAAGAAGAAGAAGAAAATTGCAAGAC
1 TTTCTCAAGGAGGAAGAAGAAGAAAATTGCAAGAC
23159 TTTCTCAAGGAGGAAGAAGAAGAAAATTGCAAGAC
1 TTTCTCAAGGAGGAAGAAGAAGAAAATTGCAAGAC
23194 TTTCTCAAGGAGGAAGAAGAAGAAAATTGCA
1 TTTCTCAAGGAGGAAGAAGAAGAAAATTGCA
23225 GAACCCTCTG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.47, C:0.11, G:0.25, T:0.18
Consensus pattern (35 bp):
TTTCTCAAGGAGGAAGAAGAAGAAAATTGCAAGAC
Found at i:36088 original size:27 final size:28
Alignment explanation
Indices: 36057--36129 Score: 85
Period size: 27 Copynumber: 2.6 Consensus size: 28
36047 ATGTGAACCT
*
36057 AAAATGACCAAAATGCCCTTAGA-CGTG
1 AAAATGACCAAAATGCCCCTAGATCGTG
* * **
36084 CAAATGACTAAAATGCCCCTAGATTTTTG
1 AAAATGACCAAAATGCCCCTAGA-TCGTG
36113 AAAATGACCAAAATGCC
1 AAAATGACCAAAATGCC
36130 TCGTAGGTGA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
27 20 0.54
29 17 0.46
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTAGATCGTG
Found at i:36934 original size:19 final size:20
Alignment explanation
Indices: 36885--36931 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
36875 AGAGAGGAAT
*
36885 ATAAATAATAATTATTCTGA
1 ATAAATAATTATTATTCTGA
36905 A-AAATAATTATTATT-T-A
1 ATAAATAATTATTATTCTGA
36922 ATAAATAATT
1 ATAAATAATT
36932 TATAAATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 2 0.08
18 9 0.36
19 13 0.52
20 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAAATAATTATTATTCTGA
Found at i:39571 original size:14 final size:14
Alignment explanation
Indices: 39532--39571 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
39522 CGAAATTAGT
**
39532 AATAATTATTGGAA
1 AATAATTATTATAA
*
39546 AATAATAATTATAA
1 AATAATTATTATAA
39560 AATAATTATTAT
1 AATAATTATTAT
39572 TATTTCAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (14 bp):
AATAATTATTATAA
Found at i:56150 original size:25 final size:25
Alignment explanation
Indices: 56113--56172 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
56103 AAGAGACTCC
56113 AGAAGATCCACGG-AGAATTATTAAA
1 AGAAGATCCACGGAAG-ATTATTAAA
* *
56138 AGAAGATCTACGGAAGATTATTGAA
1 AGAAGATCCACGGAAGATTATTAAA
56163 AGAAGATCCA
1 AGAAGATCCA
56173 AAATTATTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 29 0.94
26 2 0.06
ACGTcount: A:0.47, C:0.12, G:0.22, T:0.20
Consensus pattern (25 bp):
AGAAGATCCACGGAAGATTATTAAA
Found at i:56877 original size:24 final size:24
Alignment explanation
Indices: 56850--56896 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
56840 AATATTTTTC
*
56850 ATTAAAATTAAAAAAAAAAAGAAA
1 ATTAAAATGAAAAAAAAAAAGAAA
* * *
56874 ATTATAATGAAAAAGAAGAAGAA
1 ATTAAAATGAAAAAAAAAAAGAA
56897 GATATAGTAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (24 bp):
ATTAAAATGAAAAAAAAAAAGAAA
Found at i:58901 original size:98 final size:98
Alignment explanation
Indices: 58751--58952 Score: 260
Period size: 98 Copynumber: 2.1 Consensus size: 98
58741 CCACTTTCGA
* *
58751 TTCTTTCGACCAAACTCTTGTGCTTGGGAGATCTTAAAATTGAATAGCTTCAATTCCGACATTAG
1 TTCTTCCGACCAAACTCTTGTGCTTGGGAGATCTTAAAATTGAATAGCTTCAATTCCGACAATAG
** *
58816 AAATGCTTCATTCTCTTGAGGAGACACTTACAG
66 AAATGCCCCATTCACTTGAGGAGACACTTACAG
* * * * * * *
58849 TTCTTCCGCCCAAAGTCTTGTGTTTGGGAGATTTTGAAATTGTATAGCTTCAATTTCGACAATAG
1 TTCTTCCGACCAAACTCTTGTGCTTGGGAGATCTTAAAATTGAATAGCTTCAATTCCGACAATAG
* ** *
58914 ACATGCCCCATTCACTTGAGGAGGTACTTACGG
66 AAATGCCCCATTCACTTGAGGAGACACTTACAG
58947 TTCTTC
1 TTCTTC
58953 TGCCTTAACT
Statistics
Matches: 88, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
98 88 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.35
Consensus pattern (98 bp):
TTCTTCCGACCAAACTCTTGTGCTTGGGAGATCTTAAAATTGAATAGCTTCAATTCCGACAATAG
AAATGCCCCATTCACTTGAGGAGACACTTACAG
Found at i:61458 original size:58 final size:58
Alignment explanation
Indices: 61359--61468 Score: 150
Period size: 58 Copynumber: 1.9 Consensus size: 58
61349 ATTAATGAAA
* *
61359 TATCAAGTGACATGTTCTTTATTAGGTGTATAAAAAAAGACGTTTTCGGACCAAGGCT
1 TATCAAGTGACATGTTCTTTATTAGATGTATAAAAAAAGACGTTTTAGGACCAAGGCT
* * * *
61417 TATCTAGTGACATGTTTTTTTATTAGATGTCT-AAAACAGACGTTTTAGGACC
1 TATCAAGTGACATG-TTCTTTATTAGATGTATAAAAAAAGACGTTTTAGGACC
61469 GAGACATGAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
58 31 0.69
59 14 0.31
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGTATAAAAAAAGACGTTTTAGGACCAAGGCT
Found at i:62994 original size:297 final size:297
Alignment explanation
Indices: 62460--63054 Score: 964
Period size: 297 Copynumber: 2.0 Consensus size: 297
62450 TTTTTAGTGA
*
62460 CTATGGAAATTACTTAAAGGCTAAATTGGGTATTAATGTGGAGCGTCCTTTTGTTTTTTTTTTTT
1 CTATGGAAATTACTTAAAGGCTAAATTGGGTATTAATGTGGAGCCTCCTTTTGTTTTTTTTTTTT
* * *
62525 GGTCTTTTCTCACTTTTCGAGTGACTAAAAAGGCCCTTGATGAATTTACTCCCTTACTTTTCCTC
66 GGTCTTTTCTCACTTTCCGAGTGACTAAAAAGGCACTCGATGAATTTACTCCCTTACTTTTCCTC
* *
62590 CTACCCTTTTTATGTAATTTACTATTTTTGTATTTATGATTAAGTGTGTTTTAATTACGTATTAA
131 CTACCCTTTTTATGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTAA
* *
62655 TTGTGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCGGAATTCCAAAGGATTGGTGTTA
196 TTGTGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCGGAATTCCAAAGGATTAGTGCTA
62720 TAAATGTATCTACCCGAGTTCATTAATTTAACAATTG
261 TAAATGTATCTACCCGAGTTCATTAATTTAACAATTG
* *
62757 CTATGGAAATTACTTAAAAGG-TCAAATTGAGG-ATTGATGTGGTGCCTCCTTTTGTTTTTTTGT
1 CTATGGAAATTACTT-AAAGGCT-AAATTG-GGTATTAATGTGGAGCCTCCTTTTGTTTTTTT-T
* * *
62820 TTTT-GTCTTTTCTCACTTTCCGGGTGACTAAAAAGGCACTCGATGAGTTTCCTCCCTTACTTTT
62 TTTTGGTCTTTTCTCACTTTCCGAGTGACTAAAAAGGCACTCGATGAATTTACTCCCTTACTTTT
* *
62884 CCTGCTGCCCTTTTT-TGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATA
127 CCTCCTACCCTTTTTATGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATA
*
62948 TTGATTGTGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCGGAATTCCAAAGGATTAGT
192 TTAATTGTGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCGGAATTCCAAAGGATTAGT
* *
63013 GCTGTAAATGTGTCTACCCGAGTTCATTAATTTAACAATTG
257 GCTATAAATGTATCTACCCGAGTTCATTAATTTAACAATTG
63054 C
1 C
63055 AATCAAGATT
Statistics
Matches: 276, Mismatches: 18, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
297 165 0.60
298 104 0.38
299 7 0.03
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.43
Consensus pattern (297 bp):
CTATGGAAATTACTTAAAGGCTAAATTGGGTATTAATGTGGAGCCTCCTTTTGTTTTTTTTTTTT
GGTCTTTTCTCACTTTCCGAGTGACTAAAAAGGCACTCGATGAATTTACTCCCTTACTTTTCCTC
CTACCCTTTTTATGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTAA
TTGTGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCGGAATTCCAAAGGATTAGTGCTA
TAAATGTATCTACCCGAGTTCATTAATTTAACAATTG
Done.