Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017974.1 Corchorus olitorius cultivar O-4 contig18007, 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: 5436
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Found at i:621 original size:329 final size:330
Alignment explanation
Indices: 1--783 Score: 829
Period size: 330 Copynumber: 2.4 Consensus size: 330
* * *
1 AATTTTTACGAAATTTTAGCCGAAATCGTGTACTAACTATCACGGTTTTTGGCTAAAAACGCGTT
1 AATTTTTACGAAATTTTAGACGAAATCGTGTACT-ACCATTACGGTTTTTGGCTAAAAACGCGTT
* * * * *
66 CTGGGATCCCGTCTCAGTTTTGCAT-AATGTTTAGCGCCAAGTCTCATTGAAATATCTATATTCA
65 CCGGGA-CCCGACTCAGTTTTGCATGATTTTTTAGCGCCAAGACTCATTGAAATATCTATATTCA
* * * *
130 TATAATTAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTATGACCTTCAGAAATTGGTTTC
129 TATAATCAAATCTCAGCAACAATGAATTTAAGGATTTGTTTTTACGACCTTCAGAAATTGGTTTC
* * * * *
195 AATTTAATTAGAAATTAATAATAAAAAAAAAGAAAACGATATTAGAAGCGCGGAAAGCCCTTCAG
194 AATTTAATTAAAAATAAATAATAAAAAAAAAGAAAACGATATTAGAAGCGCGGAAACCCCTTAAA
* * * * * *
260 TCTTTTTGGCGTTGAACTATATATTATTTTATGAGTATTCTGCCCAAAACTTGAGG-AAAATCTT
259 CCTTTTCGGCGTTGAACTATATATTATTTTATGAGTATTCTGACAAAAAATTGAGGAAAAAACTT
* *
324 TCTGGTC
324 ACGGGTC
* * * *
331 AATTTTTTCAAAATTTTAGACGAAATCGTATACTATCCATTACGGTTTTTGGCTAAAAACGTGTT
1 AATTTTTACGAAATTTTAGACGAAATCGTGTACTA-CCATTACGGTTTTTGGCTAAAAACGCGTT
* * *
396 CCGGG-CCCTGGCTCAGTTTTGCATGATTTTTTA-CGCCGAGACTCCTTGAAATATCTATATTCA
65 CCGGGACCC-GACTCAGTTTTGCATGATTTTTTAGCGCCAAGACTCATTGAAATATCTATATTCA
* * * * * *
459 TCTGATCAAATCTTAGCAACATTGAATTTAAAGG-TTTGTTTTTACGATCC-TCTG-AATCTTGT
129 TATAATCAAATCTCAGCAACAATGAATTT-AAGGATTTGTTTTTACGA-CCTTCAGAAAT-TGGT
* * * *
521 TTCGATTTAATTAAAAATAAAT-TTAGAAAAAATAAGAAAAATGATATTAGAAGCG-TGAACACC
191 TTCAATTTAATTAAAAATAAATAATA-AAAAAA-AAG-AAAACGATATTAGAAGCGCGGAA-ACC
* * *
584 CCTTAAACCTTTTCGGCTTTGAATTATATA-T-TTTTATGAGTATTTTGACAAAAAATTGAGGAA
252 CCTTAAACCTTTTCGGCGTTGAACTATATATTATTTTATGAGTATTCTGACAAAAAATTGAGGAA
647 AAAACTTACGGGTC
317 AAAACTTACGGGTC
* * * * * *
661 TATTTTTGCGAAATTTTA-ACCAAAATCGTGTACTAACTTTCACGGGTTTTGGCTAAAAACGCGT
1 AATTTTTACGAAATTTTAGA-CGAAATCGTGTACTACCATT-ACGGTTTTTGGCTAAAAACGCGT
* * * * *
725 TCCGGGATCCCGATTCAATTTTGCATGA--TTTTAGGCGCCAAGAATCATAGAATTATCTA
64 TCCGGGA-CCCGACTCAGTTTTGCATGATTTTTTA-GCGCCAAGACTCATTGAAATATCTA
784 GGGATGCAAC
Statistics
Matches: 375, Mismatches: 61, Indels: 33
0.80 0.13 0.07
Matches are distributed among these distances:
328 8 0.02
329 142 0.38
330 146 0.39
331 76 0.20
332 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (330 bp):
AATTTTTACGAAATTTTAGACGAAATCGTGTACTACCATTACGGTTTTTGGCTAAAAACGCGTTC
CGGGACCCGACTCAGTTTTGCATGATTTTTTAGCGCCAAGACTCATTGAAATATCTATATTCATA
TAATCAAATCTCAGCAACAATGAATTTAAGGATTTGTTTTTACGACCTTCAGAAATTGGTTTCAA
TTTAATTAAAAATAAATAATAAAAAAAAAGAAAACGATATTAGAAGCGCGGAAACCCCTTAAACC
TTTTCGGCGTTGAACTATATATTATTTTATGAGTATTCTGACAAAAAATTGAGGAAAAAACTTAC
GGGTC
Found at i:1138 original size:20 final size:20
Alignment explanation
Indices: 1098--1134 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1088 ATTTTTAAGT
1098 AAAAATATAATATATAAATA
1 AAAAATATAATATATAAATA
*
1118 AAAAATTTAATAT-TAAA
1 AAAAATATAATATATAAA
1135 ATAATTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAATATAATATATAAATA
Found at i:3905 original size:62 final size:62
Alignment explanation
Indices: 3828--4053 Score: 400
Period size: 62 Copynumber: 3.6 Consensus size: 62
3818 ATACGACAGA
*
3828 CACGAAGGGACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
1 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
*
3890 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGG
1 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
* *
3952 CACGAAGGTACACGAGAAGACAGAGGAAGGGAGAGGCCTCTGCAGGAGGCGAGGCCAGCAGG
1 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
4014 CACGAAGGTACACGAGAAGACAGAGGAA-GAGAGAGGCCTC
1 CACGAAGGTACACGAGAAGACAGAGGAAGGA-AGAGGCCTC
4054 GGAAGACAGA
Statistics
Matches: 157, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
61 1 0.01
62 156 0.99
ACGTcount: A:0.35, C:0.22, G:0.40, T:0.04
Consensus pattern (62 bp):
CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
Found at i:4092 original size:34 final size:34
Alignment explanation
Indices: 4054--4119 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
4044 GAGAGGCCTC
4054 GGAAGACAGACACGAAGGTACACGAGAAGACAGA
1 GGAAGACAGACACGAAGGTACACGAGAAGACAGA
4088 GGAAGACAGACACGAAGGTACACGAGAAGACA
1 GGAAGACAGACACGAAGGTACACGAGAAGACA
4120 CAGTGGTGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.47, C:0.18, G:0.32, T:0.03
Consensus pattern (34 bp):
GGAAGACAGACACGAAGGTACACGAGAAGACAGA
Found at i:4988 original size:44 final size:45
Alignment explanation
Indices: 4938--5045 Score: 128
Period size: 45 Copynumber: 2.4 Consensus size: 45
4928 GAAAACGAGC
* * *
4938 AGGAGATCAAGGAAAG-TTAGAATCCATGACTGCCAAATGCTTTA
1 AGGAGATCAAAGAAAGCTTAGAACCCAAGACTGCCAAATGCTTTA
* * ** *
4982 AGGAGATCAAAGAGAGCTTTGGCCCCAAGATTGCCAAATGCTTTA
1 AGGAGATCAAAGAAAGCTTAGAACCCAAGACTGCCAAATGCTTTA
*
5027 AGGAGATCAAAGAGAGCTT
1 AGGAGATCAAAGAAAGCTT
5046 TGGCTCCATG
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 14 0.25
45 41 0.75
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (45 bp):
AGGAGATCAAAGAAAGCTTAGAACCCAAGACTGCCAAATGCTTTA
Found at i:5022 original size:45 final size:45
Alignment explanation
Indices: 4968--5061 Score: 170
Period size: 45 Copynumber: 2.1 Consensus size: 45
4958 AATCCATGAC
4968 TGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCCCCAAGAT
1 TGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCCCCAAGAT
* *
5013 TGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCTCCATGAT
1 TGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCCCCAAGAT
5058 TGCC
1 TGCC
5062 GAGTGCACAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (45 bp):
TGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCCCCAAGAT
Done.