Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019130.1 Corchorus olitorius cultivar O-4 contig19163, 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: 52037
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:312 original size:25 final size:24
Alignment explanation
Indices: 261--317 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
251 GTCAGTCTTG
*
261 AATTT-TTTAATGTTTAATTCTTA
1 AATTTATTTAATGTTTAATTATTA
*
284 AATTTATTTAATGTCTTAATTATTC
1 AATTTATTTAATGT-TTAATTATTA
309 AATTTATTT
1 AATTTATTT
318 TACAATCCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 17 0.57
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60
Consensus pattern (24 bp):
AATTTATTTAATGTTTAATTATTA
Found at i:2874 original size:54 final size:54
Alignment explanation
Indices: 2815--2922 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
2805 TTTTCGTCTC
2815 ATTATTACCCAATTTCTACAACAATTTCCTTTTTTTACTGTAGAAAGCTAGTAT
1 ATTATTACCCAATTTCTACAACAATTTCCTTTTTTTACTGTAGAAAGCTAGTAT
2869 ATTATTACCCAATTTCTACAACAATTTCCTTTTTTTACTGTAGAAAGCTAGTAT
1 ATTATTACCCAATTTCTACAACAATTTCCTTTTTTTACTGTAGAAAGCTAGTAT
2923 TTGGCTAAAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.43
Consensus pattern (54 bp):
ATTATTACCCAATTTCTACAACAATTTCCTTTTTTTACTGTAGAAAGCTAGTAT
Found at i:5310 original size:31 final size:32
Alignment explanation
Indices: 5241--5350 Score: 101
Period size: 31 Copynumber: 3.6 Consensus size: 32
5231 AAAAATGACA
*
5241 CGTGCCACGTGTC-C-TTTTT-GTGCACGA-GG
1 CGTGCCACGTGTCACTTTTTTGGTACAC-ATGG
* *
5270 CATGTCACGTGTCACTTTTTT-GTACACATGG
1 CGTGCCACGTGTCACTTTTTTGGTACACATGG
**
5301 CGT-CACACGTGT--CTTTTTTGGTACATGTGG
1 CGTGC-CACGTGTCACTTTTTTGGTACACATGG
5331 CGTGCCACGTGTCACTTTTT
1 CGTGCCACGTGTCACTTTTT
5351 GATACACGTG
Statistics
Matches: 66, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
29 18 0.27
30 20 0.30
31 22 0.33
32 6 0.09
ACGTcount: A:0.14, C:0.25, G:0.25, T:0.37
Consensus pattern (32 bp):
CGTGCCACGTGTCACTTTTTTGGTACACATGG
Found at i:5360 original size:19 final size:19
Alignment explanation
Indices: 5336--5376 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
5326 TGTGGCGTGC
5336 CACGTGTCACTTTTTGATA
1 CACGTGTCACTTTTTGATA
* *
5355 CACGTGTCGCTTTTTGGTA
1 CACGTGTCACTTTTTGATA
5374 CAC
1 CAC
5377 ATGACATGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (19 bp):
CACGTGTCACTTTTTGATA
Found at i:7236 original size:75 final size:75
Alignment explanation
Indices: 7147--7303 Score: 289
Period size: 75 Copynumber: 2.1 Consensus size: 75
7137 TCAGATTTAC
*
7147 TTTAGATTGATTCAATTAAAATACCTATTTTTCTTCGGTTCACAAAGCTCGAGCTTAAGAACTTA
1 TTTAGATTGATTCAATTAAAATACCTATTTTTCTTCGGTTCACAAAGCTCGAACTTAAGAACTTA
7212 CTTAAAAACT
66 CTTAAAAACT
7222 TTTAGATTGATTCAATTAAAATACCTATTTTTCTTCGGTTCACAAAGCTCGAACTTAAGAACTTA
1 TTTAGATTGATTCAATTAAAATACCTATTTTTCTTCGGTTCACAAAGCTCGAACTTAAGAACTTA
*
7287 TTTAAAAACT
66 CTTAAAAACT
7297 TTT-GATT
1 TTTAGATT
7304 TTTAACCCTT
Statistics
Matches: 80, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
74 4 0.05
75 76 0.95
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.39
Consensus pattern (75 bp):
TTTAGATTGATTCAATTAAAATACCTATTTTTCTTCGGTTCACAAAGCTCGAACTTAAGAACTTA
CTTAAAAACT
Found at i:7343 original size:23 final size:24
Alignment explanation
Indices: 7311--7362 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
7301 ATTTTTAACC
*
7311 CTTACAT-AAAACTAAAGACAAAT
1 CTTACATAAAAAATAAAGACAAAT
*
7334 CTTACCTAAAAAAAATAAAGACAAAT
1 CTTA-C-ATAAAAAATAAAGACAAAT
7360 CTT
1 CTT
7363 TGATTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.17
24 1 0.04
25 1 0.04
26 18 0.75
ACGTcount: A:0.56, C:0.17, G:0.04, T:0.23
Consensus pattern (24 bp):
CTTACATAAAAAATAAAGACAAAT
Found at i:14792 original size:237 final size:241
Alignment explanation
Indices: 14505--14949 Score: 645
Period size: 237 Copynumber: 1.9 Consensus size: 241
14495 ACAGAGCATG
14505 AAAACAGAGAGAGAGAGAGAGAGATTATAGGCAAATTTCAGTAGAAAATCAATCAAAATTGGGGT
1 AAAACAGAGAGAGAGAGAGAGAGATTATAGGCAAATTTCAGTAGAAAATCAATCAAAATTGGGGT
* ***
14570 CGGAAAATGTGAAATCAATAAAAATTAATTTTCAAATAAATTTCAACCAAAAAT-ATTCCA-TC-
66 CGGAAAATGTGAAATCAATAAAAATTAATTTTCAAAGAAATTTCAACCAAAAATAAGAACATTCG
** *
14632 ATAAAACAAGATTGTTGAAACA-AAGTCAAAATAAAAAACAAAAGGCGCAAGTTGAA-AATGGAT
131 ATAAAACAAGATCATTGAAACAGAA-TCAAAAGAAAAAACAAAAGGCGCAAGTT-AAGAATGGAT
14695 ACAGAAACAAGCGAAAAAACAGAGCATTCTATAGAACTATTGGAAGTA
194 ACAGAAACAAGCGAAAAAACAGAGCATTCTATAGAACTATTGGAAGTA
*
14743 AAAACAGAGAGAG-GA-AGAGAGATT-TAGAAGCAAATTTTAGTAGAAAATCAATCAAAATTGGG
1 AAAACAGAGAGAGAGAGAGAGAGATTATAG--GCAAATTTCAGTAGAAAATCAATCAAAATTGGG
* *
14805 GTCGGAAAATGTGAAATCAATCAAAATTCATTTTCAAAGAAATTTCAACCAAAAATAAGAACATT
64 GTCGGAAAATGTGAAATCAATAAAAATTAATTTTCAAAGAAATTTCAACCAAAAATAAGAACATT
* * *
14870 CTGAGATAAAACAAGATCATTGAAACAGAATCAAAAGCAAAAGCAAAAGGCGGAAGTTAAGAATG
129 C---GATAAAACAAGATCATTGAAACAGAATCAAAAGAAAAAACAAAAGGCGCAAGTTAAGAATG
*
14935 GATACAGAAATAAGC
191 GATACAGAAACAAGC
14950 TTAGAAAAAG
Statistics
Matches: 183, Mismatches: 14, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
235 3 0.02
236 9 0.05
237 87 0.48
238 16 0.09
239 2 0.01
242 2 0.01
243 62 0.34
244 2 0.01
ACGTcount: A:0.51, C:0.11, G:0.18, T:0.20
Consensus pattern (241 bp):
AAAACAGAGAGAGAGAGAGAGAGATTATAGGCAAATTTCAGTAGAAAATCAATCAAAATTGGGGT
CGGAAAATGTGAAATCAATAAAAATTAATTTTCAAAGAAATTTCAACCAAAAATAAGAACATTCG
ATAAAACAAGATCATTGAAACAGAATCAAAAGAAAAAACAAAAGGCGCAAGTTAAGAATGGATAC
AGAAACAAGCGAAAAAACAGAGCATTCTATAGAACTATTGGAAGTA
Found at i:18175 original size:30 final size:30
Alignment explanation
Indices: 18135--18195 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
18125 ACACCCGCAG
* *
18135 GAGGCGGAGGAATACAGGCCTCCGGCGGAA
1 GAGGAGGAGGAATACAGACCTCCGGCGGAA
* * *
18165 GAGGAGGAGGAGTTCAGACCTCCGGTGGAA
1 GAGGAGGAGGAATACAGACCTCCGGCGGAA
18195 G
1 G
18196 TAATGCCAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.26, C:0.20, G:0.44, T:0.10
Consensus pattern (30 bp):
GAGGAGGAGGAATACAGACCTCCGGCGGAA
Found at i:20343 original size:19 final size:19
Alignment explanation
Indices: 20319--20356 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
20309 CCTACTTAAT
20319 CGTGGAACACTATTCGTGC
1 CGTGGAACACTATTCGTGC
20338 CGTGGAACACTATTCGTGC
1 CGTGGAACACTATTCGTGC
20357 ATATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (19 bp):
CGTGGAACACTATTCGTGC
Found at i:31594 original size:30 final size:30
Alignment explanation
Indices: 31558--31619 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
31548 GATCCGTTTG
31558 TTTAATCTGCTAAATTACATAACCGGTGTA
1 TTTAATCTGCTAAATTACATAACCGGTGTA
31588 TTTAATCTGCTAAATTACATAACCGGTGTA
1 TTTAATCTGCTAAATTACATAACCGGTGTA
31618 TT
1 TT
31620 ATATGATATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (30 bp):
TTTAATCTGCTAAATTACATAACCGGTGTA
Found at i:39414 original size:2 final size:2
Alignment explanation
Indices: 39407--39446 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
39397 AATCACTAAA
39407 AT AT AT AT AT AT AT AGT AT AT AT AT A- AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A
39447 GAGATTGACT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 31 0.89
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:39428 original size:11 final size:10
Alignment explanation
Indices: 39407--39446 Score: 57
Period size: 9 Copynumber: 4.1 Consensus size: 10
39397 AATCACTAAA
39407 ATATATATAT
1 ATATATATAT
39417 ATATAGTATAT
1 ATATA-TATAT
39428 ATATA-ATAT
1 ATATATATAT
39437 ATATAT-TAT
1 ATATATATAT
39446 A
1 A
39447 GAGATTGACT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 13 0.46
10 5 0.18
11 10 0.36
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (10 bp):
ATATATATAT
Found at i:40891 original size:14 final size:14
Alignment explanation
Indices: 40872--40899 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40862 GCACTGTAAG
40872 GTGCAAGTTACAGA
1 GTGCAAGTTACAGA
40886 GTGCAAGTTACAGA
1 GTGCAAGTTACAGA
40900 ACAAAACAAA
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:0.36, C:0.14, G:0.29, T:0.21
Consensus pattern (14 bp):
GTGCAAGTTACAGA
Found at i:51409 original size:32 final size:33
Alignment explanation
Indices: 51359--51446 Score: 117
Period size: 32 Copynumber: 2.7 Consensus size: 33
51349 ATCTCCGTTA
*
51359 GAGGTAAAATGTCTTGAATTTGAAAAGTT-TAG
1 GAGGCAAAATGTCTTGAATTTGAAAAGTTATAG
* * *
51391 GAGGCTAATTGTCTTGAATTTGAAAATTTATAG
1 GAGGCAAAATGTCTTGAATTTGAAAAGTTATAG
*
51424 GAGGCAAAATGTCCTG-ATTTGAA
1 GAGGCAAAATGTCTTGAATTTGAA
51447 GTTCAAGCAT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 32 0.67
33 16 0.33
ACGTcount: A:0.35, C:0.07, G:0.24, T:0.34
Consensus pattern (33 bp):
GAGGCAAAATGTCTTGAATTTGAAAAGTTATAG
Done.