Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017928.1 Corchorus olitorius cultivar O-4 contig17961, 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: 22555
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Found at i:1053 original size:19 final size:18
Alignment explanation
Indices: 1020--1055 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1010 TGGAAATAAT
1020 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
1038 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
1056 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:2609 original size:30 final size:29
Alignment explanation
Indices: 2570--2626 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 29
2560 GTTTATTAAT
2570 GAAACTTGAAAATTAAAGACATAAGATAAAG
1 GAAACTTGAAAATTAAAG-CATAA-ATAAAG
2601 GAAA-TTGAAAATTAAAGCATAAATAA
1 GAAACTTGAAAATTAAAGCATAAATAA
2627 CTAATCCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 4 0.15
29 5 0.19
30 13 0.50
31 4 0.15
ACGTcount: A:0.60, C:0.05, G:0.14, T:0.21
Consensus pattern (29 bp):
GAAACTTGAAAATTAAAGCATAAATAAAG
Found at i:7746 original size:19 final size:18
Alignment explanation
Indices: 7713--7748 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
7703 TGGAAATAAT
7713 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
7731 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
7749 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:9308 original size:21 final size:21
Alignment explanation
Indices: 9270--9314 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
9260 GGCGCCCACA
* *
9270 TGGTTTGTCTGAAGACCCATG
1 TGGTTTGTCTGAACACCCAGG
* *
9291 TGGTTTGTTTGATCACCCAGG
1 TGGTTTGTCTGAACACCCAGG
9312 TGG
1 TGG
9315 GCAATGTCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.18, G:0.31, T:0.36
Consensus pattern (21 bp):
TGGTTTGTCTGAACACCCAGG
Found at i:10635 original size:24 final size:24
Alignment explanation
Indices: 10598--10647 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
10588 TGGGCTTCGA
*
10598 ATGTTGGGCCTTCCATTGTTAGAC
1 ATGTTAGGCCTTCCATTGTTAGAC
*
10622 ATGTTAGGCTTTCCATTGTTAGAC
1 ATGTTAGGCCTTCCATTGTTAGAC
10646 AT
1 AT
10648 TTTTACTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (24 bp):
ATGTTAGGCCTTCCATTGTTAGAC
Found at i:14253 original size:36 final size:38
Alignment explanation
Indices: 14165--14268 Score: 142
Period size: 36 Copynumber: 2.8 Consensus size: 38
14155 ATCCATAAAT
14165 CAGT-AAAGACTTAATTCAGGGTAATTAAGTAAAACCCAG
1 CAGTCAAAGACTTAATTCAGGGTAATTAAGTAAAA--CAG
*
14204 CAGTCAAAGACTTAATTCAGGGGAATTAAGT-AAA-AG
1 CAGTCAAAGACTTAATTCAGGGTAATTAAGTAAAACAG
* *
14240 CAGTCAAATACTTAATCCAGGGTAATTAA
1 CAGTCAAAGACTTAATTCAGGGTAATTAA
14269 ACTGAAAGGT
Statistics
Matches: 60, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
36 28 0.47
39 7 0.12
40 25 0.42
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.24
Consensus pattern (38 bp):
CAGTCAAAGACTTAATTCAGGGTAATTAAGTAAAACAG
Found at i:14408 original size:47 final size:47
Alignment explanation
Indices: 14339--14833 Score: 713
Period size: 47 Copynumber: 10.4 Consensus size: 47
14329 ATAGTAAGAG
14339 AAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTAATTAAACT
1 AAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTAATTAAACT
***
14386 AAATAGTAAAAGAAGAAGAGGTTAGTTTAATTACCCAG-AATTAAACT
1 AAATAGTAAAAGAAGAAGAGGTTAGTTTAATT-CTGGGTAATTAAACT
* *
14433 AAATTGTAAAAGAAGAAGAGGTTTGTTTAATTCTGGGTAATTAAACT
1 AAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTAATTAAACT
* *
14480 AAATAGTAAAAGAAGAGGAGGTTAGTTTAATTCTGGGTAATCAAACT
1 AAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTAATTAAACT
* * *
14527 AAATAATAAAAGAAGAAGAGGTTAGTTTAATTCTAGGCAATTAAACT
1 AAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTAATTAAACT
*
14574 AAATAGTAAAAGAAGAAGATGTTAGTTTAATTCTGGGTAATTAAACT
1 AAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTAATTAAACT
*
14621 AAATAGTAAAAGAAGAAGATGTTAGTTTAATTCTGGGTAATTAAACT
1 AAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTAATTAAACT
* * *
14668 AAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCAGGGCAATTAAACC
1 AAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTAATTAAACT
* * *
14715 AAATAGTAAAAGAAGAAGAGGTTAGTTGAATTCTAGCTAATTAAACT
1 AAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTAATTAAACT
* *
14762 AAAGAGTAAAAGAAGAAGTAAATAGAGGCTAGTTTAATTCTGGGTAATTAAACT
1 AAATAGT--AA-AAGAAG---A-AGAGGTTAGTTTAATTCTGGGTAATTAAACT
* *
14816 AAAGATTAAAAGAAGAAG
1 AAATAGTAAAAGAAGAAG
14834 TAAACATTTA
Statistics
Matches: 402, Mismatches: 37, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
46 2 0.00
47 347 0.86
48 3 0.01
49 2 0.00
50 6 0.01
51 6 0.01
52 2 0.00
53 1 0.00
54 33 0.08
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.28
Consensus pattern (47 bp):
AAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTAATTAAACT
Found at i:14849 original size:54 final size:53
Alignment explanation
Indices: 14736--14919 Score: 225
Period size: 54 Copynumber: 3.5 Consensus size: 53
14726 GAAGAAGAGG
* * * * * *
14736 TTAGTTGAATTCTAGCTAATTAAACTAAAGAGTAAAAGAAGAAGTAAATA-GAGG
1 TTAGTTTAATTCTGGGTAATTAAACTAAAGA-TAAAAGAAGAAGTAAACATTA-A
* *
14790 CTAGTTTAATTCTGGGTAATTAAACTAAAGATTAAAAGAAGAAGTAAACATTTA
1 TTAGTTTAATTCTGGGTAATTAAACTAAAGA-TAAAAGAAGAAGTAAACATTAA
*
14844 TTAGTTTAATTCTGGGTAATTAAA-T--AG-TAAAAGAAGGAGTAAACATTAA
1 TTAGTTTAATTCTGGGTAATTAAACTAAAGATAAAAGAAGAAGTAAACATTAA
14893 TTAGTTTAATTCTGGGTAATTAAACTA
1 TTAGTTTAATTCTGGGTAATTAAACTA
14920 GGTAGTAAAA
Statistics
Matches: 115, Mismatches: 12, Indels: 9
0.85 0.09 0.07
Matches are distributed among these distances:
49 44 0.38
50 1 0.01
51 2 0.02
53 1 0.01
54 67 0.58
ACGTcount: A:0.45, C:0.06, G:0.17, T:0.32
Consensus pattern (53 bp):
TTAGTTTAATTCTGGGTAATTAAACTAAAGATAAAAGAAGAAGTAAACATTAA
Found at i:14896 original size:49 final size:52
Alignment explanation
Indices: 14501--14919 Score: 222
Period size: 47 Copynumber: 8.5 Consensus size: 52
14491 GAAGAGGAGG
* * **
14501 TTAGTTTAATTCTGGGTAATCAAACTAA-ATAATAA-AAGAAG--AAGA--GG
1 TTAGTTTAATTCTGGGTAATTAAACTAAGATAA-AAGAAGAAGTAAACATTAA
* * * * *
14548 TTAGTTTAATTCTAGGCAATTAAACTAA-ATAGTAA-AAGAAG--AAGA-T-G
1 TTAGTTTAATTCTGGGTAATTAAACTAAGATA-AAAGAAGAAGTAAACATTAA
* * *
14595 TTAGTTTAATTCTGGGTAATTAAACTAA-ATAGTAA-AAGAAG--AAGA-T-G
1 TTAGTTTAATTCTGGGTAATTAAACTAAGATA-AAAGAAGAAGTAAACATTAA
* * **
14642 TTAGTTTAATTCTGGGTAATTAAACTAA-ATAGTAA-AAGAAG--AAGA--GG
1 TTAGTTTAATTCTGGGTAATTAAACTAAGATA-AAAGAAGAAGTAAACATTAA
* * * * * **
14689 TTAGTTTAATTCAGGGCAATTAAACCAA-ATAGTAA-AAGAAG--AAGA--GG
1 TTAGTTTAATTCTGGGTAATTAAACTAAGATA-AAAGAAGAAGTAAACATTAA
* * * * * *
14736 TTAGTTGAATTCTAGCTAATTAAACTAAAGAGTAAAAGAAGAAGTAAATA-GAGG
1 TTAGTTTAATTCTGGGTAATTAAACT-AAGA-TAAAAGAAGAAGTAAACATTA-A
* *
14790 CTAGTTTAATTCTGGGTAATTAAACTAAAGATTAAAAGAAGAAGTAAACATTTA
1 TTAGTTTAATTCTGGGTAATTAAACT-AAGA-TAAAAGAAGAAGTAAACATTAA
*
14844 TTAGTTTAATTCTGGGTAATTAAA-T-AG-TAAAAGAAGGAGTAAACATTAA
1 TTAGTTTAATTCTGGGTAATTAAACTAAGATAAAAGAAGAAGTAAACATTAA
14893 TTAGTTTAATTCTGGGTAATTAAACTA
1 TTAGTTTAATTCTGGGTAATTAAACTA
14920 GGTAGTAAAA
Statistics
Matches: 328, Mismatches: 30, Indels: 24
0.86 0.08 0.06
Matches are distributed among these distances:
47 196 0.60
48 2 0.01
49 47 0.14
50 9 0.03
51 2 0.01
52 3 0.01
53 1 0.00
54 68 0.21
ACGTcount: A:0.45, C:0.06, G:0.19, T:0.30
Consensus pattern (52 bp):
TTAGTTTAATTCTGGGTAATTAAACTAAGATAAAAGAAGAAGTAAACATTAA
Found at i:14950 original size:54 final size:53
Alignment explanation
Indices: 14791--14939 Score: 193
Period size: 49 Copynumber: 2.8 Consensus size: 53
14781 AAATAGAGGC
* *
14791 TAGTTTAATTCTGGGTAATTAAACTAAAG-ATTAAAAG-AAGAAGTAAACATTTAT
1 TAGTTTAATTCTGGGTAATTAAACT--AGTAGTAAAAGAAAG-AGTAAACATTAAT
*
14845 TAGTTTAATTCTGGGTAATT-AA--A-TAGTAAAAGAAGGAGTAAACATTAAT
1 TAGTTTAATTCTGGGTAATTAAACTAGTAGTAAAAGAAAGAGTAAACATTAAT
14894 TAGTTTAATTCTGGGTAATTAAACTAGGTAGTAAAAGAAAGAGTAA
1 TAGTTTAATTCTGGGTAATTAAACTA-GTAGTAAAAGAAAGAGTAA
14940 GTAGTAATTA
Statistics
Matches: 84, Mismatches: 4, Indels: 14
0.82 0.04 0.14
Matches are distributed among these distances:
49 40 0.48
50 4 0.05
52 1 0.01
53 2 0.02
54 37 0.44
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (53 bp):
TAGTTTAATTCTGGGTAATTAAACTAGTAGTAAAAGAAAGAGTAAACATTAAT
Found at i:17884 original size:21 final size:21
Alignment explanation
Indices: 17860--17899 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
17850 ATAGGTTTGG
* *
17860 ATTGGAGATGGGTGTTGGGGA
1 ATTGAAGATGGGTGATGGGGA
17881 ATTGAAGATGGGTGATGGG
1 ATTGAAGATGGGTGATGGG
17900 TGGTACTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.50, T:0.28
Consensus pattern (21 bp):
ATTGAAGATGGGTGATGGGGA
Found at i:18176 original size:24 final size:24
Alignment explanation
Indices: 18144--18189 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
18134 TAATATATAG
18144 CGGCGTCTAGACGCCACTATTTAA
1 CGGCGTCTAGACGCCACTATTTAA
*
18168 CGGCGTCTAGACGCCGCTATTT
1 CGGCGTCTAGACGCCACTATTT
18190 GGACACGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (24 bp):
CGGCGTCTAGACGCCACTATTTAA
Found at i:18358 original size:32 final size:32
Alignment explanation
Indices: 18311--18456 Score: 220
Period size: 32 Copynumber: 4.5 Consensus size: 32
18301 TAAAAGCAAT
** *
18311 TAAATATAGCGGCGTTTTGTAATGTAGACGCCGC
1 TAAATA-AG-GGCGTTTTGTTCTATAGACGCCGC
*
18345 TAAATAAGGGCGTTTTGTTCTGTAGACGCCGC
1 TAAATAAGGGCGTTTTGTTCTATAGACGCCGC
18377 TAAATAAGGGCGTTTTGTTCTATAGACGCCGC
1 TAAATAAGGGCGTTTTGTTCTATAGACGCCGC
*
18409 TAAATAAGGGTGTTTTGTTCTATAGACGCCGC
1 TAAATAAGGGCGTTTTGTTCTATAGACGCCGC
*
18441 TAAATAAAGGCGTTTT
1 TAAATAAGGGCGTTTT
18457 CTTTTCACAC
Statistics
Matches: 106, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
32 98 0.92
33 2 0.02
34 6 0.06
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.32
Consensus pattern (32 bp):
TAAATAAGGGCGTTTTGTTCTATAGACGCCGC
Done.