Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013722.1 Corchorus olitorius cultivar O-4 contig13755, 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: 13466
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Found at i:611 original size:332 final size:330
Alignment explanation
Indices: 4--994 Score: 1557
Period size: 332 Copynumber: 3.0 Consensus size: 330
1 TAA
4 AAGCGTGAAAAACCCTTCAATCTTTTTGGCTTTGAATTATATACATTTTATGAGAATTGTGGCCA
1 AAGCGTGAAAAACCCTTCAATCTTTTTGGCTTTGAATTATATACATTTTATGAGAATTGTGGCCA
* * * *
69 AAAATTGAGAAAAAAATTTTCTAATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCCA
66 AAAATTGAGGAAAAATTTTTCTGATCGA-TTTT-CAAAATTTTAGCCGAAATCGTGTACTATCCA
* * *
134 TCACGGTTTTAAGCTAAATATGTGTTTCGGGGCCCCGACTAAGTTTTGCATGATTTTTGGCACGA
129 TCACGGTTTTAAGCTAAAAATGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCACGA
* *
199 AGAATCCTTGAAATATCTATATTTATTTAACTAAATCTCAGCCACATTAAATTTAA-TGATTTGT
194 AGAATCCTTGAAATATCTATATTCATTTAACTAAATCCCAGCCACATTAAATTTAAGT-ATTTGT
* *
263 TTTTACGAGAATCTGAATCATGTTTCGATTTAATTTGAAATTAATTCAGAAAAAAGTGGATAAAC
258 TTTTACGAGCATCTGAATCATGTTTCGATTTAATTTGAAATTAATTCAGAAAAAAGTGGAAAAAC
328 GATATTAG
323 GATATTAG
336 AAGCGTGAAAAACCCTTCAATCTTTTTGGCTTTGAATTATATACATTTTATGAGAATTGTGGCCA
1 AAGCGTGAAAAACCCTTCAATCTTTTTGGCTTTGAATTATATACATTTTATGAGAATTGTGGCCA
*
401 AAAATTGAGGAAAAATTTTTCTGATCGATTTGTACAAAATTTTAGCCGAAATCGTGTATTATCCA
66 AAAATTGAGGAAAAATTTTTCTGATCGATTT-T-CAAAATTTTAGCCGAAATCGTGTACTATCCA
* ***
466 TCACGGTTTTAAGCTAAAAATGCGTTTTGGGATACCGACTCAGTTTTGCATGATTTTTGGCACGA
129 TCACGGTTTTAAGCTAAAAATGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCACGA
*
531 AGAATCCTTGAAATATCTATATTCATTTAACCAAATCCCAGCCACATTAAATTTAAGTATTTGTT
194 AGAATCCTTGAAATATCTATATTCATTTAACTAAATCCCAGCCACATTAAATTTAAGTATTTGTT
*
596 TTTACGAGCATCTGAATCATGTTTCGATTTAATTTGAAATTAATTCAGAAAAAAATGGAAAAACG
259 TTTACGAGCATCTGAATCATGTTTCGATTTAATTTGAAATTAATTCAGAAAAAAGTGGAAAAACG
661 ATATTAG
324 ATATTAG
*
668 AAGCGTGAAAAACCCTTCAATCTTTTTGGCTTTGAATTATATA-TTTTTATGAGAATTGTGGCCA
1 AAGCGTGAAAAACCCTTCAATCTTTTTGGCTTTGAATTATATACATTTTATGAGAATTGTGGCCA
732 AAAATTGAGGAAAAATTTTTC-G---GA---TC---A----AGCCGAAATCGTGTACTAT-CATC
66 AAAATTGAGGAAAAATTTTTCTGATCGATTTTCAAAATTTTAGCCGAAATCGTGTACTATCCATC
** ** *
782 ACGGTTTTAAATTAAAAACACGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCTCGAAG
131 ACGGTTTTAAGCTAAAAATGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCACGAAG
* * * * *
847 AATCCTTGAAATATCTATATTCATTTAAGTAAATCCCAGTCACAATAAATTTAAGGATATGTTTT
196 AATCCTTGAAATATCTATATTCATTTAACTAAATCCCAGCCACATTAAATTTAAGTATTTGTTTT
912 TACGAGCATCTGAATCATGTTTCGATTTAATTTGAAATTAATTCAGAAAAAAGTGGAAAAACGAT
261 TACGAGCATCTGAATCATGTTTCGATTTAATTTGAAATTAATTCAGAAAAAAGTGGAAAAACGAT
977 ATTAG
326 ATTAG
982 AAGCGTGAAAAAC
1 AAGCGTGAAAAAC
995 TCTGACTTCA
Statistics
Matches: 620, Mismatches: 37, Indels: 22
0.91 0.05 0.03
Matches are distributed among these distances:
314 201 0.32
315 18 0.03
319 1 0.00
322 1 0.00
323 1 0.00
327 2 0.00
330 1 0.00
331 44 0.07
332 350 0.56
333 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (330 bp):
AAGCGTGAAAAACCCTTCAATCTTTTTGGCTTTGAATTATATACATTTTATGAGAATTGTGGCCA
AAAATTGAGGAAAAATTTTTCTGATCGATTTTCAAAATTTTAGCCGAAATCGTGTACTATCCATC
ACGGTTTTAAGCTAAAAATGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCACGAAG
AATCCTTGAAATATCTATATTCATTTAACTAAATCCCAGCCACATTAAATTTAAGTATTTGTTTT
TACGAGCATCTGAATCATGTTTCGATTTAATTTGAAATTAATTCAGAAAAAAGTGGAAAAACGAT
ATTAG
Found at i:1015 original size:14 final size:14
Alignment explanation
Indices: 996--1024 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
986 GTGAAAAACT
996 CTGACTTCACAACC
1 CTGACTTCACAACC
1010 CTGACTTCACAACC
1 CTGACTTCACAACC
1024 C
1 C
1025 ATCCCCGTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.45, G:0.07, T:0.21
Consensus pattern (14 bp):
CTGACTTCACAACC
Found at i:1169 original size:22 final size:23
Alignment explanation
Indices: 1134--1176 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1124 TGGTAAAAAA
1134 AAAACTATATTATTATATCTTTG
1 AAAACTATATTATTATATCTTTG
* *
1157 AAAA-TATTTTATTTTATCTT
1 AAAACTATATTATTATATCTT
1177 ATTGATTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.53
Consensus pattern (23 bp):
AAAACTATATTATTATATCTTTG
Found at i:1286 original size:33 final size:33
Alignment explanation
Indices: 1249--1316 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
1239 ACAATAATTA
1249 ATTTACCTTATTTAGTCCAATTAGTTTTAATAC
1 ATTTACCTTATTTAGTCCAATTAGTTTTAATAC
1282 ATTTACCTTATTTAGTCCAATTAGTTTTAATAC
1 ATTTACCTTATTTAGTCCAATTAGTTTTAATAC
1315 AT
1 AT
1317 GATTTTCATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.31, C:0.15, G:0.06, T:0.49
Consensus pattern (33 bp):
ATTTACCTTATTTAGTCCAATTAGTTTTAATAC
Found at i:1623 original size:32 final size:32
Alignment explanation
Indices: 1587--1669 Score: 157
Period size: 32 Copynumber: 2.6 Consensus size: 32
1577 TGAATTTCAT
1587 TCCCCATCCCCGTCCCCATTCCCCAAATTAAC
1 TCCCCATCCCCGTCCCCATTCCCCAAATTAAC
*
1619 TCCCCATCCCCGTCCCCGTTCCCCAAATTAAC
1 TCCCCATCCCCGTCCCCATTCCCCAAATTAAC
1651 TCCCCATCCCCGTCCCCAT
1 TCCCCATCCCCGTCCCCAT
1670 AGGGACGGGT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.18, C:0.55, G:0.05, T:0.22
Consensus pattern (32 bp):
TCCCCATCCCCGTCCCCATTCCCCAAATTAAC
Found at i:2568 original size:27 final size:27
Alignment explanation
Indices: 2530--2584 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
2520 AGATTGGGAC
*
2530 CATTACTAACCTAAGCCGGAAAACATG
1 CATTACTAACCTAAGCAGGAAAACATG
*
2557 CATTACTAACCTAAGCAGTAAAACATG
1 CATTACTAACCTAAGCAGGAAAACATG
2584 C
1 C
2585 CTTCATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.25, G:0.13, T:0.20
Consensus pattern (27 bp):
CATTACTAACCTAAGCAGGAAAACATG
Done.