Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012760.1 Corchorus olitorius cultivar O-4 contig12793, 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: 44884
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1905 original size:30 final size:29
Alignment explanation
Indices: 1866--1922 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 29
1856 GTTTATTAAT
1866 GAAACTTGAAAATTAAAGACATAAGATAAAG
1 GAAACTTGAAAATTAAAG-CATAA-ATAAAG
1897 GAAA-TTGAAAATTAAAGCATAAATAA
1 GAAACTTGAAAATTAAAGCATAAATAA
1923 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:7344 original size:19 final size:18
Alignment explanation
Indices: 7311--7346 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
7301 TGGAAATAAT
7311 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
7329 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
7347 TAAATCTTCA
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:7801 original size:14 final size:15
Alignment explanation
Indices: 7775--7805 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
7765 CTAAGTCCAA
7775 TCCTTGTTTATTTAT
1 TCCTTGTTTATTTAT
7790 TCCTTG-TTATTTAT
1 TCCTTGTTTATTTAT
7804 TC
1 TC
7806 TTCCTATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.13, C:0.16, G:0.06, T:0.65
Consensus pattern (15 bp):
TCCTTGTTTATTTAT
Found at i:8823 original size:75 final size:75
Alignment explanation
Indices: 8744--8985 Score: 367
Period size: 75 Copynumber: 3.2 Consensus size: 75
8734 TCAGGAAAAA
* * * * *
8744 CACTTATGGCTACGATTCTTGTTGAGCATGAAATTTTGATGGGCTACATAGGCCAGAAGCATCAA
1 CACTTATGGCTACGATCCTTGCTGAGAATGGAATCTTGATGGGCTACATAGGCCAGAAGCATCAA
8809 CAAGGAAAGG
66 CAAGGAAAGG
*
8819 CACTTATGGCTACGATCCTTGCTGAGAATGGAATCTTGATGGGCTACATAGGTCAGAAGCATCAA
1 CACTTATGGCTACGATCCTTGCTGAGAATGGAATCTTGATGGGCTACATAGGCCAGAAGCATCAA
*
8884 TAAGGAAAGG
66 CAAGGAAAGG
* * * * * *
8894 CACTTATGGCTACAATCCTTGCTAAGTATGGAATCTTGATGGGCTAGAAAGGCTAGAAGCATCAA
1 CACTTATGGCTACGATCCTTGCTGAGAATGGAATCTTGATGGGCTACATAGGCCAGAAGCATCAA
8959 CAAGGAAAGG
66 CAAGGAAAGG
8969 CACTTATGGCTACGATC
1 CACTTATGGCTACGATC
8986 AGTAGCAGAG
Statistics
Matches: 151, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 151 1.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (75 bp):
CACTTATGGCTACGATCCTTGCTGAGAATGGAATCTTGATGGGCTACATAGGCCAGAAGCATCAA
CAAGGAAAGG
Found at i:30074 original size:42 final size:42
Alignment explanation
Indices: 30015--30095 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
30005 GCTAAGTCTT
* *
30015 GAAAATTCTCTGTAAATTAAGAACTACTCAACTCAAATCATA
1 GAAAATTCTCTGCAAATTAAGAAATACTCAACTCAAATCATA
*
30057 GAAAATTCTTTGCAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTCTCTGCAAATTAAGAAATACTCAACTCAAATC
30096 TTGATCCTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.46, C:0.19, G:0.07, T:0.28
Consensus pattern (42 bp):
GAAAATTCTCTGCAAATTAAGAAATACTCAACTCAAATCATA
Found at i:30093 original size:21 final size:21
Alignment explanation
Indices: 30028--30094 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
30018 AATTCTCTGT
*
30028 AAATTAAGAACTACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * **
30049 AAATCATAGAAA-ATTC-TTTGC
1 AAATTA-AGAAATACTCAACT-C
30070 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
30091 AAAT
1 AAAT
30095 CTTGATCCTT
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
20 6 0.18
21 22 0.67
22 5 0.15
ACGTcount: A:0.49, C:0.18, G:0.06, T:0.27
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:30233 original size:56 final size:57
Alignment explanation
Indices: 30161--30275 Score: 205
Period size: 57 Copynumber: 2.0 Consensus size: 57
30151 TTTATTTTGT
* *
30161 AGAATAATTAAGTAGAGAT-AGGGGGATATGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAAGGGGGATAGGATTTATTATAACATTTATTATGTGAA
30217 AGAATAATTAAGTAGAGATAAGGGGGATAGGATTTATTATAACATTTATTATGTGAA
1 AGAATAATTAAGTAGAGATAAGGGGGATAGGATTTATTATAACATTTATTATGTGAA
30274 AG
1 AG
30276 GAAACTGATA
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
56 19 0.34
57 37 0.66
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.34
Consensus pattern (57 bp):
AGAATAATTAAGTAGAGATAAGGGGGATAGGATTTATTATAACATTTATTATGTGAA
Found at i:30469 original size:2 final size:2
Alignment explanation
Indices: 30462--30486 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30452 TAATATGTAG
30462 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 T
30487 GTGGTTGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31891 original size:43 final size:43
Alignment explanation
Indices: 31843--31927 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
31833 TATAACATTG
*
31843 TTTTTAGTAAAAAACAGACATGTACAAATCATAGAATGTATAT
1 TTTTTAGTAAAAAACAGACATGCACAAATCATAGAATGTATAT
31886 TTTTTAGTAAAAAACAGACATGCACAAATCATAGAATGTATA
1 TTTTTAGTAAAAAACAGACATGCACAAATCATAGAATGTATA
31928 AATATATATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.31
Consensus pattern (43 bp):
TTTTTAGTAAAAAACAGACATGCACAAATCATAGAATGTATAT
Found at i:32956 original size:46 final size:46
Alignment explanation
Indices: 32903--32992 Score: 162
Period size: 46 Copynumber: 2.0 Consensus size: 46
32893 TTAATTCTCG
32903 TGTCTCCTTTATTCTTGTACTAGAACTATTGGATTGTGATTTTGAA
1 TGTCTCCTTTATTCTTGTACTAGAACTATTGGATTGTGATTTTGAA
* *
32949 TGTCTCCTTTATTCTTGTACTAGAACTGTTGGTTTGTGATTTTG
1 TGTCTCCTTTATTCTTGTACTAGAACTATTGGATTGTGATTTTG
32993 GTGAAATTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.18, C:0.13, G:0.19, T:0.50
Consensus pattern (46 bp):
TGTCTCCTTTATTCTTGTACTAGAACTATTGGATTGTGATTTTGAA
Found at i:39650 original size:16 final size:16
Alignment explanation
Indices: 39629--39659 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39619 TTGAAAAATA
39629 TTACTAAATATTTATT
1 TTACTAAATATTTATT
*
39645 TTACTAAATCTTTAT
1 TTACTAAATATTTAT
39660 AATATGTAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (16 bp):
TTACTAAATATTTATT
Found at i:40730 original size:200 final size:198
Alignment explanation
Indices: 39994--40893 Score: 1262
Period size: 198 Copynumber: 4.5 Consensus size: 198
39984 CTTTATAATA
* *
39994 AGGATTATTATACAATATACTGTCAATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
40059 ACATACCCTATTTCATAATTAATTAAATATTTATAATATTTAATATTAATACATATTCCCTAAGG
66 ACATACCCTATTTCATAATTAATT-AA-A--TAT-A-A---AATATTAATACATATTCCCTAAGG
* * * *
40124 GGACACATGTCAATCCTTAAACCATGCACGTGCAGTCTGTTAAACTCCACTGACGGTGTATTGTA
122 GGACACATGTCAACCCTTAAGCCATGCACGTGCAGTCTGCTAAACTCCACTGACGATGTATTGTA
40189 TAATTTTTTTAT
187 TAATTTTTTTAT
* **
40201 AGGATTGTTATACAATACACTGTCAGTGTAAATTTTCAACTCCATAAGCGGGTTAAGAAGTTGAC
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
* *
40266 ACATACTCTATTTCATAATTAATTAAATATAAAATATTAATACATATTCCCTAAGGGGACATATG
66 ACATACCCTATTTCATAATTAATTAAATATAAAATATTAATACATATTCCCTAAGGGGACACATG
* *
40331 TCAACCCTTAAGCCATGCGCGTGCAGTCTGCTAAACTCCACTGACGATGTATTGTATATTTTTTT
131 TCAACCCTTAAGCCATGCACGTGCAGTCTGCTAAACTCCACTGACGATGTATTGTATAATTTTTT
40396 TAT
196 TAT
* * * * *
40399 AGGATTGTCATACAATACACTATCAGTGTAAATTTTGAACTCTATAAGCGGGTTAAGAAGTTGAC
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
*
40464 ACATACCCTGTTTCATAATTAATTAAATATAAAATATTAATACATATTCCCTAAGGGGACACATG
66 ACATACCCTATTTCATAATTAATTAAATATAAAATATTAATACATATTCCCTAAGGGGACACATG
* * * * *
40529 TCAACCCTTAAGCC-TGCGCGTGCAGTCTGCTAAAATCCACTAACGGTGTATTGTATAATTCTTT
131 TCAACCCTTAAGCCATGCACGTGCAGTCTGCTAAACTCCACTGACGATGTATTGTATAATTTTTT
40593 TAT
196 TAT
* *
40596 ATGATATTATTATACAATACACTGTCAGTATAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTG
1 A-G-GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTG
* * * ** *
40661 ACAATATACCCCATTTAATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGATAC
64 AC-ACATACCCTATTTCATAATTAATTAAATATAAAATATTAATACATATTCCCTAAGGGGACAC
* ** * * * * *
40726 ATGTCAACCCTTAAACCCCGCACATGTAGTATGCTAAACTCCACTGACAATGTATTGCATAATTT
128 ATGTCAACCCTTAAGCCATGCACGTGCAGTCTGCTAAACTCCACTGACGATGTATTGTATAATTT
40791 TTCTTAT
193 TT-TTAT
* * * * *
40798 AGGATTATTATACAATACACTGTCAGTATAAAATTTGGACTCCATAAGTGGGTTATGAAGTTGAA
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
*
40863 ACATACCCTATTTCATAATTACTTAAATATA
66 ACATACCCTATTTCATAATTAATTAAATATA
40894 TATACTAAAT
Statistics
Matches: 627, Mismatches: 61, Indels: 18
0.89 0.09 0.03
Matches are distributed among these distances:
197 49 0.08
198 232 0.37
199 82 0.13
200 129 0.21
201 40 0.06
202 6 0.01
203 3 0.00
205 1 0.00
206 2 0.00
207 83 0.13
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (198 bp):
AGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
ACATACCCTATTTCATAATTAATTAAATATAAAATATTAATACATATTCCCTAAGGGGACACATG
TCAACCCTTAAGCCATGCACGTGCAGTCTGCTAAACTCCACTGACGATGTATTGTATAATTTTTT
TAT
Found at i:40769 original size:398 final size:399
Alignment explanation
Indices: 39994--40897 Score: 1294
Period size: 398 Copynumber: 2.3 Consensus size: 399
39984 CTTTATAATA
* *
39994 AGGATTATTATACAATATACTGTCAATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
40059 ACATACCCTATTTCATAATTAATTAAATATTTATAATATTTAATATTAATACATATTCCCTAAGG
66 ACATACCCTATTTCATAATTAATT-AA-A--TAT-ATA--TAATATTAATACATATTCCCTAAGG
* * * *
40124 GGACACATGTCAATCCTTAAACCATGCACGTGCAGTCTGTTAAACTCCACTGACGGTGTATTGTA
124 GGACACATGTCAACCCTTAAACCATGCACGTGCAGTCTGCTAAAATCCACTAACGGTGTATTGTA
* * *
40189 TAATTTTTTTATAGGATTGTTATACAATACACTGTCAGTGTAAATTTTCAACTCCATAAGCGGGT
189 TAATTCTTTTATAGGATTATTATACAATACACTGTCAGTATAAATTTTCAACTCCATAAGCGGGT
* * *
40254 TAAGAAGTTGACACATACTCTATTTCATAATTAATTAAATATAAAATATTAATACATATTCCCTA
254 TAAGAAGTTGACACATACCCCATTTAATAATTAATTAAATATAAAATATTAATACATATTCCCTA
* * * * * * *
40319 AGGGGACATATGTCAACCCTTAAGCCATGCGCGTGCAGTCTGCTAAACTCCACTGACGATGTATT
319 AGGGGACACATGTCAACCCTTAAACCACGCACATGCAGTATGCTAAACTCCACTGACAATGTATT
* *
40384 GTAT-ATTTTTTTTAT
384 GCATAATTTTTCTTAT
* * * * *
40399 AGGATTGTCATACAATACACTATCAGTGTAAATTTTGAACTCTATAAGCGGGTTAAGAAGTTGAC
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
*
40464 ACATACCCTGTTTCATAATTAATTAAATATA-A-AATATTAATACATATTCCCTAAGGGGACACA
66 ACATACCCTATTTCATAATTAATTAAATATATATAATATTAATACATATTCCCTAAGGGGACACA
* *
40527 TGTCAACCCTTAAGCC-TGCGCGTGCAGTCTGCTAAAATCCACTAACGGTGTATTGTATAATTCT
131 TGTCAACCCTTAAACCATGCACGTGCAGTCTGCTAAAATCCACTAACGGTGTATTGTATAATTCT
* **
40591 TTTATATGATATTATTATACAATACACTGTCAGTATAAATTTTGGACTCCATAAGCGGGTTAAGA
196 TTTATA-G-GATTATTATACAATACACTGTCAGTATAAATTTTCAACTCCATAAGCGGGTTAAGA
* **
40656 AGTTGACAATATACCCCATTTAATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGG
259 AGTTGAC-ACATACCCCATTTAATAATTAATTAAATATAAAATATTAATACATATTCCCTAAGGG
* * *
40721 GATACATGTCAACCCTTAAACCCCGCACATGTAGTATGCTAAACTCCACTGACAATGTATTGCAT
323 GACACATGTCAACCCTTAAACCACGCACATGCAGTATGCTAAACTCCACTGACAATGTATTGCAT
40786 AATTTTTCTTAT
388 AATTTTTCTTAT
* * * * *
40798 AGGATTATTATACAATACACTGTCAGTATAAAATTTGGACTCCATAAGTGGGTTATGAAGTTGAA
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
*
40863 ACATACCCTATTTCATAATTACTTAAATATATATA
66 ACATACCCTATTTCATAATTAATTAAATATATATA
40898 CTAAATGTTA
Statistics
Matches: 443, Mismatches: 50, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
395 49 0.11
396 46 0.10
397 58 0.13
398 105 0.24
399 95 0.21
400 2 0.00
401 4 0.01
403 1 0.00
404 2 0.00
405 81 0.18
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (399 bp):
AGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
ACATACCCTATTTCATAATTAATTAAATATATATAATATTAATACATATTCCCTAAGGGGACACA
TGTCAACCCTTAAACCATGCACGTGCAGTCTGCTAAAATCCACTAACGGTGTATTGTATAATTCT
TTTATAGGATTATTATACAATACACTGTCAGTATAAATTTTCAACTCCATAAGCGGGTTAAGAAG
TTGACACATACCCCATTTAATAATTAATTAAATATAAAATATTAATACATATTCCCTAAGGGGAC
ACATGTCAACCCTTAAACCACGCACATGCAGTATGCTAAACTCCACTGACAATGTATTGCATAAT
TTTTCTTAT
Found at i:42592 original size:21 final size:21
Alignment explanation
Indices: 42566--42606 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42556 TTTAAACCCT
42566 ATTGGAGAC-AAGTGGTACTAA
1 ATTGGA-ACTAAGTGGTACTAA
*
42587 ATTGGATCTAAGTGGTACTA
1 ATTGGAACTAAGTGGTACTA
42607 GGGTTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (21 bp):
ATTGGAACTAAGTGGTACTAA
Done.