Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023454.1 Corchorus olitorius cultivar O-4 contig23487, 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: 17684
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3545 original size:51 final size:50
Alignment explanation
Indices: 3444--3545 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 50
3434 GTTCTTCATA
* **
3444 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
*
3494 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGT
3545 T
1 T
3546 CTTCATTCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
50 7 0.16
51 37 0.82
52 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
Found at i:4510 original size:108 final size:108
Alignment explanation
Indices: 4321--4537 Score: 326
Period size: 108 Copynumber: 2.0 Consensus size: 108
4311 TTGAATTTGC
* * * *
4321 TAACCACCTAATCACATATATGATAAGAACCGAGAGAAAAAAAACTCTATAACTAGAATGATTTG
1 TAACCACCTAATCACATATATGATAAGAACCGAGAGAAAAAAAACTCTAAAACTAAAATAATTTA
* * *
4386 TTAGCCACATATCAAGAATGCTCAACGTGCCAGCGCGAGCCGA
66 CTAGCCACAAATCAAGAATGCTCAACGCGCCAGCGCGAGCCGA
*
4429 TAACCACCTACTCACATATATGATAAGAACCGAGAGAAAAAAAACTCTAAAACTAAAATAATTTA
1 TAACCACCTAATCACATATATGATAAGAACCGAGAGAAAAAAAACTCTAAAACTAAAATAATTTA
* * * *
4494 CTAGGCACAAATCAAGAATGCTCAATGCGCCCGCGTGAGCCGA
66 CTAGCCACAAATCAAGAATGCTCAACGCGCCAGCGCGAGCCGA
4537 T
1 T
4538 CAACTTGTGT
Statistics
Matches: 97, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
108 97 1.00
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.20
Consensus pattern (108 bp):
TAACCACCTAATCACATATATGATAAGAACCGAGAGAAAAAAAACTCTAAAACTAAAATAATTTA
CTAGCCACAAATCAAGAATGCTCAACGCGCCAGCGCGAGCCGA
Found at i:4919 original size:18 final size:18
Alignment explanation
Indices: 4896--4931 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4886 TATATTATTG
4896 AAAAAAGTCTACAAATTA
1 AAAAAAGTCTACAAATTA
4914 AAAAAAGTCTACAAATTA
1 AAAAAAGTCTACAAATTA
4932 TTATTAGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.11, G:0.06, T:0.22
Consensus pattern (18 bp):
AAAAAAGTCTACAAATTA
Found at i:8419 original size:132 final size:132
Alignment explanation
Indices: 8254--8774 Score: 563
Period size: 132 Copynumber: 4.0 Consensus size: 132
8244 GTTTAATATC
* * * * ** *
8254 TAATTTGTCGTTTCAAACGTAATGT-TGTTTTTTGTAGCAACGTT-AATATCGCTGCAAAAATCA
1 TAATTTGTCGCTTCAAAAGTAAT-TATGTTTTTTGTAGCGACTTTCAAGGTCGCTGCGAAAATCA
* *
8317 ATTTAG-AAAATATATTAAGCAACGACTAACAGAAGGACGTTGCGAAAAGAGTAAGATTTCACAA
65 ATTT-GTAAAATATATTAAGCAACGACTAACA-AAAGACGTTGCGAAAAGAGTAAGATTTCGCAA
8381 CGACT
128 CGACT
* * *
8386 TAATTTGTCGCTTCAAAAGTAATTACGTTTTTTGTAGTGACTTTCAAGGTCGTTG-GCAAAATCA
1 TAATTTGTCGCTTCAAAAGTAATTATGTTTTTTGTAGCGACTTTCAAGGTCGCTGCG-AAAATCA
*
8450 ATTTGTAAAATATATTAAGCAACGACTAAC---A-A----GCGAAAAGAGTAAGATTTCGCAGCG
65 ATTTGTAAAATATATTAAGCAACGACTAACAAAAGACGTTGCGAAAAGAGTAAGATTTCGCAACG
8507 ACT
130 ACT
* * *
8510 TAATTTGT-GTCTTCAAAAGTATTTAT-ATTTTT-TAGCGACTTTCAAGGTCGCTGCGAAAACCA
1 TAATTTGTCG-CTTCAAAAGTAATTATGTTTTTTGTAGCGACTTTCAAGGTCGCTGCGAAAATCA
* * ***
8572 ATTTGTAAAATATATTAAGCAACGACTAACAAAAGTCGTTGCTAAAATTTTAAGATTTCGCAACG
65 ATTTGTAAAATATATTAAGCAACGACTAACAAAAGACGTTGCGAAAAGAGTAAGATTTCGCAACG
*
8637 ACC
130 ACT
* * * *
8640 TAATCTGTCG-TGTCAAAAGTAATCATGTCTTTTGTAGCGACTTTCAAGGTCGCTTCGAAAATCA
1 TAATTTGTCGCT-TCAAAAGTAATTATGTTTTTTGTAGCGACTTTCAAGGTCGCTGCGAAAATCA
* * ** * * **
8704 ATTTGTATAATATATTAAACAACGACTAACAAAACTCGTTGCGAAAAGACTATGAACTCGCAACG
65 ATTTGTAAAATATATTAAGCAACGACTAACAAAAGACGTTGCGAAAAGAGTAAGATTTCGCAACG
8769 A-T
130 ACT
8771 TAAT
1 TAAT
8775 AGAAGTCGTT
Statistics
Matches: 327, Mismatches: 44, Indels: 37
0.80 0.11 0.09
Matches are distributed among these distances:
122 55 0.17
123 7 0.02
124 48 0.15
125 1 0.00
128 1 0.00
129 1 0.00
130 41 0.13
131 10 0.03
132 121 0.37
133 42 0.13
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (132 bp):
TAATTTGTCGCTTCAAAAGTAATTATGTTTTTTGTAGCGACTTTCAAGGTCGCTGCGAAAATCAA
TTTGTAAAATATATTAAGCAACGACTAACAAAAGACGTTGCGAAAAGAGTAAGATTTCGCAACGA
CT
Found at i:15920 original size:12 final size:13
Alignment explanation
Indices: 15898--15927 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
15888 ACTAGCAATT
15898 AAAATCAATCAAG
1 AAAATCAATCAAG
15911 AAAA-CAATCAAG
1 AAAATCAATCAAG
15923 AAAAT
1 AAAAT
15928 TAAAGAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13
Consensus pattern (13 bp):
AAAATCAATCAAG
Done.