Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007939.1 Corchorus capsularis cultivar CVL-1 contig07960, 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: 37573
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1638 original size:32 final size:31
Alignment explanation
Indices: 1602--1664 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 31
1592 GATTTTCACA
*
1602 ATTTTCTTTTCTTTCT-TTTTTGTGATTTTTTG
1 ATTTT-TTTTATTTCTATTTTTGT-ATTTTTTG
*
1634 ATTTTTTTTATTTTTACTTTTTGTATTTTTT
1 ATTTTTTTTATTTCTA-TTTTTGTATTTTTT
1665 TGCAAAATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 8 0.30
32 12 0.44
33 7 0.26
ACGTcount: A:0.10, C:0.06, G:0.06, T:0.78
Consensus pattern (31 bp):
ATTTTTTTTATTTCTATTTTTGTATTTTTTG
Found at i:2783 original size:46 final size:46
Alignment explanation
Indices: 2721--2864 Score: 261
Period size: 46 Copynumber: 3.1 Consensus size: 46
2711 GTCTCTGACT
*
2721 ACTTTTTCTCACTTTATTTGTTTCCTATCAAGTCAATCCCAACAAA
1 ACTTTTCCTCACTTTATTTGTTTCCTATCAAGTCAATCCCAACAAA
*
2767 ACTTTTCCTCAATTTATTTGTTTCCTATCAAGTCAATCCCAACAAA
1 ACTTTTCCTCACTTTATTTGTTTCCTATCAAGTCAATCCCAACAAA
*
2813 ACTTTTCCTCACTTTATTTGTTTCCTATCAAGTCAATCCCAGCAAA
1 ACTTTTCCTCACTTTATTTGTTTCCTATCAAGTCAATCCCAACAAA
2859 ACTTTT
1 ACTTTT
2865 ACCCAGATGA
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 94 1.00
ACGTcount: A:0.28, C:0.26, G:0.05, T:0.41
Consensus pattern (46 bp):
ACTTTTCCTCACTTTATTTGTTTCCTATCAAGTCAATCCCAACAAA
Found at i:13326 original size:34 final size:34
Alignment explanation
Indices: 13267--13371 Score: 180
Period size: 34 Copynumber: 3.2 Consensus size: 34
13257 GTTTCATCGG
13267 CCCTGCCCAGTGGG-T-T-ATAATAACTGGAAGA
1 CCCTGCCCAGTGGGTTGTGATAATAACTGGAAGA
*
13298 CTCTGCCCAGTGGGTTGTGATAATAACTGGAAGA
1 CCCTGCCCAGTGGGTTGTGATAATAACTGGAAGA
13332 CCCTGCCCAGTGGGTTGTGATAATAACTGGAAGA
1 CCCTGCCCAGTGGGTTGTGATAATAACTGGAAGA
13366 CCCTGC
1 CCCTGC
13372 TAACGGGTTA
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
31 13 0.19
32 1 0.01
33 1 0.01
34 54 0.78
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.24
Consensus pattern (34 bp):
CCCTGCCCAGTGGGTTGTGATAATAACTGGAAGA
Found at i:28184 original size:13 final size:13
Alignment explanation
Indices: 28168--28213 Score: 67
Period size: 13 Copynumber: 3.5 Consensus size: 13
28158 TAAAATAAAT
28168 AAGCAAAAAAAAA
1 AAGCAAAAAAAAA
28181 AAGCAAAAAAAAA
1 AAGCAAAAAAAAA
28194 AA-CAAAAAAATAA
1 AAGCAAAAAAA-AA
*
28207 AAACAAA
1 AAGCAAA
28214 CAAACAAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.26
13 19 0.61
14 4 0.13
ACGTcount: A:0.85, C:0.09, G:0.04, T:0.02
Consensus pattern (13 bp):
AAGCAAAAAAAAA
Found at i:28189 original size:14 final size:12
Alignment explanation
Indices: 28171--28259 Score: 70
Period size: 12 Copynumber: 7.2 Consensus size: 12
28161 AATAAATAAG
28171 CAAAAAAAAAAA
1 CAAAAAAAAAAA
28183 GCAAAAAAAAAAA
1 -CAAAAAAAAAAA
28196 CAAAAAAATAAAAA
1 C-AAAAAA-AAAAA
* *
28210 CAAACAAACAAA
1 CAAAAAAAAAAA
* * *
28222 CAAACAGACAAA
1 CAAAAAAAAAAA
* *
28234 CAAACAAACAAA
1 CAAAAAAAAAAA
* *
28246 CAAACAAACAAA
1 CAAAAAAAAAAA
28258 CA
1 CA
28260 TGAAGAATAA
Statistics
Matches: 70, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
12 41 0.59
13 23 0.33
14 6 0.09
ACGTcount: A:0.79, C:0.18, G:0.02, T:0.01
Consensus pattern (12 bp):
CAAAAAAAAAAA
Found at i:28200 original size:8 final size:8
Alignment explanation
Indices: 28193--28259 Score: 93
Period size: 8 Copynumber: 8.6 Consensus size: 8
28183 GCAAAAAAAA
*
28193 AAACAAAA
1 AAACAAAC
*
28201 AAATAAA-
1 AAACAAAC
28208 AA-CAAAC
1 AAACAAAC
28215 AAACAAAC
1 AAACAAAC
*
28223 AAACAGAC
1 AAACAAAC
28231 AAACAAAC
1 AAACAAAC
28239 AAACAAAC
1 AAACAAAC
28247 AAACAAAC
1 AAACAAAC
28255 AAACA
1 AAACA
28260 TGAAGAATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
6 3 0.06
7 4 0.08
8 46 0.87
ACGTcount: A:0.76, C:0.21, G:0.01, T:0.01
Consensus pattern (8 bp):
AAACAAAC
Found at i:28214 original size:4 final size:4
Alignment explanation
Indices: 28207--28259 Score: 97
Period size: 4 Copynumber: 13.2 Consensus size: 4
28197 AAAAAAATAA
*
28207 AAAC AAAC AAAC AAAC AAAC AGAC AAAC AAAC AAAC AAAC AAAC AAAC
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC
28255 AAAC A
1 AAAC A
28260 TGAAGAATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.74, C:0.25, G:0.02, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:29435 original size:43 final size:43
Alignment explanation
Indices: 29374--29457 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
29364 TTTACTAACG
* *
29374 TAAAAGAATGTATTTAATTAGTATATATG-TACGGCGTCATCGA
1 TAAAAGAATGTATATAATTAGTATATA-GATACGGCGCCATCGA
29417 TAAAAGAATGTATATAATTAGTATATAGATACGGCGCCATC
1 TAAAAGAATGTATATAATTAGTATATAGATACGGCGCCATC
29458 AAGAACAGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 1 0.03
43 37 0.97
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (43 bp):
TAAAAGAATGTATATAATTAGTATATAGATACGGCGCCATCGA
Done.