Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009324.1 Corchorus capsularis cultivar CVL-1 contig09345, 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: 43670
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2575 original size:205 final size:204
Alignment explanation
Indices: 2218--2589 Score: 620
Period size: 205 Copynumber: 1.8 Consensus size: 204
2208 TTAGAAAGGG
* *
2218 TAATTATTTGATACACCGGCGGAGTAAATTTTGGACTCCACAGGCGGGTTGTGGAGTTGACACAT
1 TAATTATTTGATACACCGGCGGAGTAAATTTTGGACTCCACAAGCGGGTTGTGGAGTTGAAACAT
*
2283 GTCCATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGGACACATGTCACC
66 GTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGGACACATGTCACC
* *
2348 TTTCAGGACCCGCTTGTGTAGTCTGCTAAACTACACTAACGGTCTATCGTGTAATTTACCTATTA
131 ATTCAGAACCCGCTTGTGTAGTCTGCTAAACTACACTAACGGTCTATCGTGTAATTTACCTATTA
2413 GAAATATGA
196 GAAATATGA
*
2422 TAATTATTTGATACACCGTC-GATGTAAATTTTGGACTCCACAAGCGGGTTGTGGAGTTGAAACA
1 TAATTATTTGATACACCGGCGGA-GTAAATTTTGGACTCCACAAGCGGGTTGTGGAGTTGAAACA
*
2486 TGTTCATTTCTTTGAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGGACACATGTCA
65 TGTCCATTT-TTTGAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGGACACATGTCA
* * * *
2551 CCATTCAGAACCCGTTTTTGTAGTCTGTTAAACTCCACT
129 CCATTCAGAACCCGCTTGTGTAGTCTGCTAAACTACACT
2590 GACGATGTAT
Statistics
Matches: 155, Mismatches: 11, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
203 2 0.01
204 66 0.43
205 87 0.56
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (204 bp):
TAATTATTTGATACACCGGCGGAGTAAATTTTGGACTCCACAAGCGGGTTGTGGAGTTGAAACAT
GTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGGACACATGTCACC
ATTCAGAACCCGCTTGTGTAGTCTGCTAAACTACACTAACGGTCTATCGTGTAATTTACCTATTA
GAAATATGA
Found at i:6209 original size:2 final size:2
Alignment explanation
Indices: 6202--6228 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6192 TCATAGGGTT
6202 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6229 CCCCGATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18577 original size:15 final size:15
Alignment explanation
Indices: 18548--18576 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18538 CACAATTCGA
18548 CTCCATATTATTTTT
1 CTCCATATTATTTTT
18563 CTCCATATT-TTTTT
1 CTCCATATTATTTTT
18577 TATCAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.17, C:0.21, G:0.00, T:0.62
Consensus pattern (15 bp):
CTCCATATTATTTTT
Found at i:32275 original size:6 final size:6
Alignment explanation
Indices: 32264--32290 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
32254 CTAGGTAGTA
32264 TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTT
32291 TCCTTATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:36303 original size:16 final size:16
Alignment explanation
Indices: 36282--36316 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
36272 ACAATTCAGA
36282 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
*
36298 AAGCAGAAAAGCTTTG
1 AAGCAGAAAAGCTCTG
36314 AAG
1 AAG
36317 TATTTCAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.14, G:0.26, T:0.14
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:39321 original size:16 final size:16
Alignment explanation
Indices: 39300--39342 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
39290 ATAAGAACAT
39300 CTTTTCTGCTTCAGAG
1 CTTTTCTGCTTCAGAG
39316 CTTTTCTGCTTCAGAG
1 CTTTTCTGCTTCAGAG
39332 CTTTTCTGCTT
1 CTTTTCTGCTT
39343 TCTGAATTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.09, C:0.26, G:0.16, T:0.49
Consensus pattern (16 bp):
CTTTTCTGCTTCAGAG
Found at i:41466 original size:28 final size:28
Alignment explanation
Indices: 41435--41491 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
41425 GATTATGGGG
41435 TTTTACTGAAATTTGATATAATGAAGGA
1 TTTTACTGAAATTTGATATAATGAAGGA
41463 TTTTACTGAAATTTGATATAATGAAGGA
1 TTTTACTGAAATTTGATATAATGAAGGA
41491 T
1 T
41492 GATATTCCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.39, C:0.04, G:0.18, T:0.40
Consensus pattern (28 bp):
TTTTACTGAAATTTGATATAATGAAGGA
Found at i:42805 original size:153 final size:154
Alignment explanation
Indices: 42516--42824 Score: 532
Period size: 153 Copynumber: 2.0 Consensus size: 154
42506 TTTAAATGAT
*
42516 ATAAATAAAAATTTAAATATTATATTTATCCTCTAATAGGTAGTTTTATTTAAGATGGGTAGTTT
1 ATAAATAAAAATTTAAATATTATATTTATCCTCTAATAGGTAGTTTTATTTAAGATGAGTAGTTT
* *
42581 TTATTTTGTTTTGAATTTTTAAAAAACTGAGTTTGTCTCCAAGTCAACTCGTGAGACAAACTCAG
66 TTATTTTGTTTTGAATTTCTAAAAAACTGAGTTTGTCTCCAAGTCAACTCGTGAGACAAACTCAA
*
42646 GGTTTGGCTTTATAATTAGTATAG
131 GGTTTGGCATTATAATTAGTATAG
*
42670 ATAAAT-AAAATTTAAATATTATATTTATTCTCTAAT-GGATAGTTTTATTTAAGATGAGTAGTT
1 ATAAATAAAAATTTAAATATTATATTTATCCTCTAATAGG-TAGTTTTATTTAAGATGAGTAGTT
*
42733 TTTATTTTGTTTTGAATTTCTAAAAAACTGAGTTTGTCTCCGAGTCAACTCGTGAGACAAACTCA
65 TTTATTTTGTTTTGAATTTCTAAAAAACTGAGTTTGTCTCCAAGTCAACTCGTGAGACAAACTCA
*
42798 AGTTTTGGCATTATAATTAGTATAG
130 AGGTTTGGCATTATAATTAGTATAG
42823 AT
1 AT
42825 TATCTTATAA
Statistics
Matches: 147, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
152 2 0.01
153 139 0.95
154 6 0.04
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (154 bp):
ATAAATAAAAATTTAAATATTATATTTATCCTCTAATAGGTAGTTTTATTTAAGATGAGTAGTTT
TTATTTTGTTTTGAATTTCTAAAAAACTGAGTTTGTCTCCAAGTCAACTCGTGAGACAAACTCAA
GGTTTGGCATTATAATTAGTATAG
Found at i:42972 original size:28 final size:27
Alignment explanation
Indices: 42934--42990 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
42924 TAAGCTTACT
42934 AAAAAAATCTTAT-AAGGTC-ATTAATAA
1 AAAAAAATCTT-TGAAGGTCAATTAA-AA
42961 AAAATAAATCTTTGAAGGTCAATTAAAA
1 AAAA-AAATCTTTGAAGGTCAATTAAAA
42989 AA
1 AA
42991 GCTCCATAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 5 0.19
28 17 0.63
29 5 0.19
ACGTcount: A:0.56, C:0.07, G:0.09, T:0.28
Consensus pattern (27 bp):
AAAAAAATCTTTGAAGGTCAATTAAAA
Found at i:43066 original size:21 final size:20
Alignment explanation
Indices: 43040--43088 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
43030 AAAAAATAAG
*
43040 GCTTATAAGATTAATAAAAAT
1 GCTTATAAG-TTAATAAAAAA
**
43061 GCTTATGAAGTTTCTAAAAAA
1 GCTTAT-AAGTTAATAAAAAA
43082 GCTTATA
1 GCTTATA
43089 TATTTTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 20 0.83
22 3 0.12
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (20 bp):
GCTTATAAGTTAATAAAAAA
Found at i:43554 original size:2 final size:2
Alignment explanation
Indices: 43547--43577 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
43537 TTTAATTACA
43547 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
43578 CAATCAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.