Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010414.1 Corchorus capsularis cultivar CVL-1 contig10435, 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: 48377
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:608 original size:35 final size:35
Alignment explanation
Indices: 534--616 Score: 103
Period size: 35 Copynumber: 2.4 Consensus size: 35
524 AACATTAGAT
*
534 ATGCTCAAACATAGTCACAAAACAAAATTAGTAAC
1 ATGCTCAAACATAGTCACAAAACAAAATTACTAAC
* * * ***
569 ATGCTCAAACATAGTCACAAAGCCAAATTTCTGTG
1 ATGCTCAAACATAGTCACAAAACAAAATTACTAAC
604 ATGCTCAAACATA
1 ATGCTCAAACATA
617 CAAAAACATA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.45, C:0.22, G:0.11, T:0.23
Consensus pattern (35 bp):
ATGCTCAAACATAGTCACAAAACAAAATTACTAAC
Found at i:919 original size:13 final size:13
Alignment explanation
Indices: 901--925 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
891 CCCAAGCAAA
901 CAATATTAACATT
1 CAATATTAACATT
914 CAATATTAACAT
1 CAATATTAACAT
926 GGCTAAATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
CAATATTAACATT
Found at i:18212 original size:21 final size:22
Alignment explanation
Indices: 18160--18212 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
18150 CCGTAATTTA
*
18160 GTTATCAAAATTTAATAGCGAT
1 GTTATCCAAATTTAATAGCGAT
*
18182 GTTATCCAAATTTTATAGCGAT
1 GTTATCCAAATTTAATAGCGAT
18204 GTT-TCCAAA
1 GTTATCCAAA
18213 CGTTAGGTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 6 0.21
22 23 0.79
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (22 bp):
GTTATCCAAATTTAATAGCGAT
Found at i:19570 original size:7 final size:7
Alignment explanation
Indices: 19558--19594 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
19548 CTGATACATG
19558 ACCACAA
1 ACCACAA
19565 ACCACAA
1 ACCACAA
19572 ACCACAA
1 ACCACAA
19579 ACCACAA
1 ACCACAA
19586 ACCACAA
1 ACCACAA
19593 AC
1 AC
19595 ATTAATTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.57, C:0.43, G:0.00, T:0.00
Consensus pattern (7 bp):
ACCACAA
Found at i:21431 original size:1 final size:1
Alignment explanation
Indices: 21425--21467 Score: 86
Period size: 1 Copynumber: 43.0 Consensus size: 1
21415 CCTTGACCTC
21425 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
21468 GATTCAAATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:29794 original size:45 final size:45
Alignment explanation
Indices: 29736--29823 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
29726 AAAATTTCAG
*
29736 CAAAAACAAAACACCATGAATAAGGAACTCAAAGGCCTAATATCA
1 CAAAAACAAAACACCATGAATAAGAAACTCAAAGGCCTAATATCA
* *
29781 CAAAATCAGAACACCATGAATAAGAAACTCAAAGGCCTAATAT
1 CAAAAACAAAACACCATGAATAAGAAACTCAAAGGCCTAATAT
29824 ATAATAATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.52, C:0.22, G:0.11, T:0.15
Consensus pattern (45 bp):
CAAAAACAAAACACCATGAATAAGAAACTCAAAGGCCTAATATCA
Found at i:30010 original size:2 final size:2
Alignment explanation
Indices: 30005--30040 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
29995 ACATTGAAAG
30005 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30041 ACATTGAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35859 original size:299 final size:299
Alignment explanation
Indices: 35321--35906 Score: 1163
Period size: 299 Copynumber: 2.0 Consensus size: 299
35311 TATCCGTTGT
35321 TGGAAATGAAATTAAGTTATAAATAAACAAGTATAGATAGAACAATAGTTTTATCTTTCGTCAAT
1 TGGAAATGAAATTAAGTTATAAATAAACAAGTATAGATAGAACAATAGTTTTATCTTTCGTCAAT
35386 CAATTCAAAGACCTCTAATATATATACTACATATTATTTGAATAAACATATGGAAATTACTAAAA
66 CAATTCAAAGACCTCTAATATATATACTACATATTATTTGAATAAACATATGGAAATTACTAAAA
35451 GATCCCTACCCCAGATTAATGAGAAGCGAGAGAACTAATTTTTTTCGTCTTTTCCCACTTGGCCG
131 GATCCCTACCCCAGATTAATGAGAAGCGAGAGAACTAATTTTTTTCGTCTTTTCCCACTTGGCCG
35516 ATTACTTAAATGCCTTAACTTTTTATTCTTGAGGTGATTAAGTAACTAGACTTTTTGGTCATTTC
196 ATTACTTAAATGCCTTAACTTTTTATTCTTGAGGTGATTAAGTAACTAGACTTTTTGGTCATTTC
35581 TCAATTGACTTTAATAGAGTAGTGTAACAAGTATACATA
261 TCAATTGACTTTAATAGAGTAGTGTAACAAGTATACATA
35620 TGGAAATGAAATTAAGTTATAAATAAACAAGTATAGATAGAACAATAGTTTTATCTTTCGTCAAT
1 TGGAAATGAAATTAAGTTATAAATAAACAAGTATAGATAGAACAATAGTTTTATCTTTCGTCAAT
35685 CAATTCAAAGACCTCTAATATATATACTACATATTATTTGAATAAACATATGGAAATTACTAAAA
66 CAATTCAAAGACCTCTAATATATATACTACATATTATTTGAATAAACATATGGAAATTACTAAAA
*
35750 GATCCCTACCCCAGATTAATGAGGAGCGAGAGAACTAATTTTTTTCGTCTTTTCCCACTTGGCCG
131 GATCCCTACCCCAGATTAATGAGAAGCGAGAGAACTAATTTTTTTCGTCTTTTCCCACTTGGCCG
35815 ATTACTTAAATGCCTTAACTTTTTATTCTTGAGGTGATTAAGTAACTAGACTTTTTGGTCATTTC
196 ATTACTTAAATGCCTTAACTTTTTATTCTTGAGGTGATTAAGTAACTAGACTTTTTGGTCATTTC
35880 TCAATTGACTTTAATAGAGTAGTGTAA
261 TCAATTGACTTTAATAGAGTAGTGTAA
35907 TTATTAAAAG
Statistics
Matches: 286, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
299 286 1.00
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Consensus pattern (299 bp):
TGGAAATGAAATTAAGTTATAAATAAACAAGTATAGATAGAACAATAGTTTTATCTTTCGTCAAT
CAATTCAAAGACCTCTAATATATATACTACATATTATTTGAATAAACATATGGAAATTACTAAAA
GATCCCTACCCCAGATTAATGAGAAGCGAGAGAACTAATTTTTTTCGTCTTTTCCCACTTGGCCG
ATTACTTAAATGCCTTAACTTTTTATTCTTGAGGTGATTAAGTAACTAGACTTTTTGGTCATTTC
TCAATTGACTTTAATAGAGTAGTGTAACAAGTATACATA
Found at i:36209 original size:66 final size:67
Alignment explanation
Indices: 36098--36229 Score: 221
Period size: 66 Copynumber: 2.0 Consensus size: 67
36088 CTCTAAAATT
* * *
36098 TAAACTATATTTTAAATTTTATTTATTTATATATAATAAAAACATATATAATAT-ATTTATAATA
1 TAAAATATATTTTAAAATTTATTTATTTATATATAATAAAAACATATATAATATAATATATAATA
36162 TA
66 TA
*
36164 TAAAATATATTTTAAAATTTATTTATTTGTATATAATAAAAACATATATAATATAATATATAATA
1 TAAAATATATTTTAAAATTTATTTATTTATATATAATAAAAACATATATAATATAATATATAATA
36229 T
66 T
36230 GTTTTAAATA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
66 51 0.84
67 10 0.16
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (67 bp):
TAAAATATATTTTAAAATTTATTTATTTATATATAATAAAAACATATATAATATAATATATAATA
TA
Found at i:37055 original size:17 final size:17
Alignment explanation
Indices: 37035--37068 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
37025 TTTTTTCCCG
37035 TCGATTATTTGTTGAAA
1 TCGATTATTTGTTGAAA
*
37052 TCGATTATTTTTTGAAA
1 TCGATTATTTGTTGAAA
37069 AATCTGTACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.06, G:0.15, T:0.50
Consensus pattern (17 bp):
TCGATTATTTGTTGAAA
Found at i:40564 original size:29 final size:29
Alignment explanation
Indices: 40524--40581 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
40514 TAACTATCCA
40524 TTTTGGGACAAATTGGCCCATTAACTTTT
1 TTTTGGGACAAATTGGCCCATTAACTTTT
*
40553 TTTTGGGACAAATTGGCCCCTTAACTTTT
1 TTTTGGGACAAATTGGCCCATTAACTTTT
40582 AAAAATGAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.41
Consensus pattern (29 bp):
TTTTGGGACAAATTGGCCCATTAACTTTT
Found at i:41617 original size:34 final size:34
Alignment explanation
Indices: 41573--41640 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
41563 ATTTGAATAA
*
41573 AATAATTTTACAAAAAAATTAAAATGGAATCATT
1 AATAAGTTTACAAAAAAATTAAAATGGAATCATT
41607 AATAAGTTTACAAAAAAATTAAAATGGAATCATT
1 AATAAGTTTACAAAAAAATTAAAATGGAATCATT
41641 CTAAAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.56, C:0.06, G:0.07, T:0.31
Consensus pattern (34 bp):
AATAAGTTTACAAAAAAATTAAAATGGAATCATT
Found at i:41913 original size:27 final size:28
Alignment explanation
Indices: 41868--41923 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
41858 TTACCATCCC
41868 AACATTCATTAACATATTTAGAATTTTAA
1 AACATTCATTAACA-ATTTAGAATTTTAA
*
41897 AACATTCTTTAAC-ATTTAGAATTTTAA
1 AACATTCATTAACAATTTAGAATTTTAA
41924 TGTTTAGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 14 0.54
29 12 0.46
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.43
Consensus pattern (28 bp):
AACATTCATTAACAATTTAGAATTTTAA
Found at i:41929 original size:15 final size:15
Alignment explanation
Indices: 41911--41941 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
41901 TTCTTTAACA
41911 TTTAGAATTTTAATG
1 TTTAGAATTTTAATG
41926 TTTAGAATTTTAATG
1 TTTAGAATTTTAATG
41941 T
1 T
41942 GATGCAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (15 bp):
TTTAGAATTTTAATG
Done.