Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008955.1 Corchorus capsularis cultivar CVL-1 contig08976, 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: 30601
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Found at i:4832 original size:19 final size:18
Alignment explanation
Indices: 4799--4834 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4789 TTGAAATAAT
4799 TCTTCAATAATCTTCAAG
1 TCTTCAATAATCTTCAAG
*
4817 TCTTCAAATTATCTTCAA
1 TCTTC-AATAATCTTCAA
4835 ATAAGTCTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATAATCTTCAAG
Found at i:4845 original size:12 final size:12
Alignment explanation
Indices: 4814--4847 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
4804 AATAATCTTC
4814 AAGTCTTCAAAT
1 AAGTCTTCAAAT
*
4826 TA-TCTTCAAAT
1 AAGTCTTCAAAT
4837 AAGTCTTCAAA
1 AAGTCTTCAAA
4848 CACGAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (12 bp):
AAGTCTTCAAAT
Found at i:10445 original size:25 final size:25
Alignment explanation
Indices: 10412--10497 Score: 102
Period size: 25 Copynumber: 3.4 Consensus size: 25
10402 TTTCTGCCAG
*
10412 CTTCCCAGCAGTGAGCGTCAGC-AA
1 CTTCCCAGCAGTGGGCGTCAGCGAA
* *
10436 GCTTCTCAGCAGTGGGCGTTAGCGAA
1 -CTTCCCAGCAGTGGGCGTCAGCGAA
* * *
10462 CTTTCTAGCAGCGGGCGTCAGCGAA
1 CTTCCCAGCAGTGGGCGTCAGCGAA
10487 CTTCCCAGCAG
1 CTTCCCAGCAG
10498 CAGGCTTCCT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
25 48 0.96
26 2 0.04
ACGTcount: A:0.21, C:0.30, G:0.29, T:0.20
Consensus pattern (25 bp):
CTTCCCAGCAGTGGGCGTCAGCGAA
Found at i:12632 original size:72 final size:72
Alignment explanation
Indices: 12538--12677 Score: 226
Period size: 72 Copynumber: 1.9 Consensus size: 72
12528 TCTCTGCTGA
* *
12538 CAATTCCATTGTCGGCCTGCTCACTATTGGAGATCTGCTGGCAACGAGCTTTGTTTGTCGAGGAT
1 CAATTCCACTGTCGGCCTGCTCACTATTGGAGATCTGCTGGCAACGAGCTTTATTTGTCGAGGAT
12603 CTGTTGG
66 CTGTTGG
* * * *
12610 CAATTCCACTGTCGGTCTGCTCACTATTGGAGGTTTGTTGGCAACGAGCTTTATTTGTCGAGGAT
1 CAATTCCACTGTCGGCCTGCTCACTATTGGAGATCTGCTGGCAACGAGCTTTATTTGTCGAGGAT
12675 CTG
66 CTG
12678 CTAGCAACGG
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.17, C:0.21, G:0.27, T:0.34
Consensus pattern (72 bp):
CAATTCCACTGTCGGCCTGCTCACTATTGGAGATCTGCTGGCAACGAGCTTTATTTGTCGAGGAT
CTGTTGG
Found at i:12685 original size:31 final size:31
Alignment explanation
Indices: 12650--12710 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
12640 AGGTTTGTTG
*
12650 GCAACGAGCTTTATTTGTCGAGGATCTGCTA
1 GCAACGAGCTTCATTTGTCGAGGATCTGCTA
* * *
12681 GCAACGGGCTTCGTTTGTCGGGGATCTGCT
1 GCAACGAGCTTCATTTGTCGAGGATCTGCT
12711 GGAGAGTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.16, C:0.21, G:0.31, T:0.31
Consensus pattern (31 bp):
GCAACGAGCTTCATTTGTCGAGGATCTGCTA
Found at i:16865 original size:54 final size:54
Alignment explanation
Indices: 16796--16937 Score: 159
Period size: 54 Copynumber: 2.6 Consensus size: 54
16786 TATTGCTGGG
* * **
16796 GAGCAAGTCATTGCTGGACA-CCCTCTCGATGTTGTCAAGACTCCTCCTGTTGTA
1 GAGCAAGTCATTGCTGGACATCCC-CTCGATGCTGACAAGACTCCTCCTGCCGTA
*
16850 GAGCAAGTC-TCTGCTGGTCATCCCCTCGATGCTGACAAGACTCCTCCTGCCGTA
1 GAGCAAGTCAT-TGCTGGACATCCCCTCGATGCTGACAAGACTCCTCCTGCCGTA
16904 GAGCAAGT--TTCCGCT-GAGCATCCCCTCGATGCTG
1 GAGCAAGTCATT--GCTGGA-CATCCCCTCGATGCTG
16938 GTCAGCCCTT
Statistics
Matches: 77, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
52 1 0.01
53 3 0.04
54 70 0.91
55 3 0.04
ACGTcount: A:0.19, C:0.32, G:0.23, T:0.26
Consensus pattern (54 bp):
GAGCAAGTCATTGCTGGACATCCCCTCGATGCTGACAAGACTCCTCCTGCCGTA
Found at i:18165 original size:2 final size:2
Alignment explanation
Indices: 18158--18206 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
18148 ATGGGACACT
18158 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
18200 TC TC TC T
1 TC TC TC T
18207 TTTTAATTCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:22328 original size:25 final size:25
Alignment explanation
Indices: 22243--22329 Score: 95
Period size: 25 Copynumber: 3.5 Consensus size: 25
22233 TCTCTGCCAG
* *
22243 CTTCCCAGCAGCGAGCGTCAAC-AA
1 CTTCCCAGCAGCGGGCGTCAGCGAA
* ** *
22267 GCTTCTCAGCAATGGGCGTTAGCGAA
1 -CTTCCCAGCAGCGGGCGTCAGCGAA
*
22293 CTTTCCAGCAGCGGGCGTCAGCGAA
1 CTTCCCAGCAGCGGGCGTCAGCGAA
22318 CTTCCCAGCAGC
1 CTTCCCAGCAGC
22330 AGGCTTCCTG
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
25 47 0.96
26 2 0.04
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.17
Consensus pattern (25 bp):
CTTCCCAGCAGCGGGCGTCAGCGAA
Found at i:22352 original size:15 final size:15
Alignment explanation
Indices: 22332--22404 Score: 68
Period size: 15 Copynumber: 5.2 Consensus size: 15
22322 CCAGCAGCAG
22332 GCTTCCT-GACAGTGA
1 GCTTCCTAG-CAGTGA
*
22347 GTTTCCTAGCAGTGA
1 GCTTCCTAGCAGTGA
*
22362 GCTTCCTAGCAGTGG
1 GCTTCCTAGCAGTGA
*
22377 GCTT-C-A--A-CGA
1 GCTTCCTAGCAGTGA
22387 GCTTCCTAGCAGTGA
1 GCTTCCTAGCAGTGA
22402 GCT
1 GCT
22405 CCTCTGTTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
10 5 0.11
11 2 0.04
12 1 0.02
13 1 0.02
14 2 0.04
15 34 0.74
16 1 0.02
ACGTcount: A:0.19, C:0.26, G:0.27, T:0.27
Consensus pattern (15 bp):
GCTTCCTAGCAGTGA
Found at i:26275 original size:18 final size:18
Alignment explanation
Indices: 26252--26287 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
26242 ATGAGGTGTA
26252 AATCGACTGGAGAGGTTC
1 AATCGACTGGAGAGGTTC
*
26270 AATCGATTGGAGAGGTTC
1 AATCGACTGGAGAGGTTC
26288 TTTGTTACTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.14, G:0.33, T:0.25
Consensus pattern (18 bp):
AATCGACTGGAGAGGTTC
Found at i:27198 original size:33 final size:33
Alignment explanation
Indices: 27143--27212 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 33
27133 CATCTAATGT
* * * *
27143 TAATGTTAACATTTACATAAATCT-TTCATCACC
1 TAATGCTAACATTGACACAAATCTACT-ATCACC
*
27176 TAATGCTAACATTGCCACAAATCTACTATCACC
1 TAATGCTAACATTGACACAAATCTACTATCACC
27209 TAAT
1 TAAT
27213 CTGAAAATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.34
Consensus pattern (33 bp):
TAATGCTAACATTGACACAAATCTACTATCACC
Found at i:27229 original size:33 final size:33
Alignment explanation
Indices: 27170--27234 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
27160 TAAATCTTTC
*
27170 ATCACCTAATGCTAACATTGCCACAAATCTACT
1 ATCACCTAATGCTAAAATTGCCACAAATCTACT
* *
27203 ATCACCTAAT-CTGAAAATTTCTACAAATCTAC
1 ATCACCTAATGCT-AAAATTGCCACAAATCTAC
27235 ATTTCCAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 2 0.07
33 26 0.93
ACGTcount: A:0.38, C:0.28, G:0.05, T:0.29
Consensus pattern (33 bp):
ATCACCTAATGCTAAAATTGCCACAAATCTACT
Found at i:27869 original size:30 final size:30
Alignment explanation
Indices: 27835--27891 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
27825 ACCCTAACTT
*
27835 TTGCTGCAGTGGAGTT-TGCAGGACCTTTGC
1 TTGCTGCAGTGG-CTTGTGCAGGACCTTTGC
27865 TTGCTGCAGTGGCTTGTGCAGGACCTT
1 TTGCTGCAGTGGCTTGTGCAGGACCTT
27892 GGGTTGCTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.12, C:0.21, G:0.33, T:0.33
Consensus pattern (30 bp):
TTGCTGCAGTGGCTTGTGCAGGACCTTTGC
Found at i:27899 original size:30 final size:30
Alignment explanation
Indices: 27835--27899 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
27825 ACCCTAACTT
* *
27835 TTGCTGCAGTGGAGTTTGCAGGACCTTTGC
1 TTGCTGCAGTGGACTTTGCAGGACCTTGGC
*
27865 TTGCTGCAGTGG-CTTGTGCAGGACCTTGGG
1 TTGCTGCAGTGGACTT-TGCAGGACCTTGGC
27895 TTGCT
1 TTGCT
27900 TGAGTTTGCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.11, C:0.20, G:0.35, T:0.34
Consensus pattern (30 bp):
TTGCTGCAGTGGACTTTGCAGGACCTTGGC
Done.