Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014930.1 Corchorus capsularis cultivar CVL-1 contig14951, 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: 54784
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:60 original size:17 final size:16
Alignment explanation
Indices: 6--56 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
1 CCCCC
* *
6 AGATCACTAATGATCTA
1 AGATCACCAGTGATC-A
23 AGATCACCAGTGATGCA
1 AGATCACCAGTGAT-CA
40 AGATCACCAGTGATCA
1 AGATCACCAGTGATCA
56 A
1 A
57 AGATTACATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.22
Consensus pattern (16 bp):
AGATCACCAGTGATCA
Found at i:7190 original size:2 final size:2
Alignment explanation
Indices: 7185--7215 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7175 TTTTTTAATA
7185 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
7216 GTCTAAGACA
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
Found at i:9939 original size:26 final size:26
Alignment explanation
Indices: 9887--9940 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
9877 ATTAGAATTC
* *
9887 AAATCCATATATATTATGTTTAGAAA
1 AAATCCATATATATTATATATAGAAA
* *
9913 AAATCCGTATATATTATATATATAAA
1 AAATCCATATATATTATATATAGAAA
9939 AA
1 AA
9941 GGAGAGGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.50, C:0.07, G:0.06, T:0.37
Consensus pattern (26 bp):
AAATCCATATATATTATATATAGAAA
Found at i:11205 original size:28 final size:28
Alignment explanation
Indices: 11165--11221 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
11155 GGGGTGATTG
*
11165 TAAGGGATATAGAAGGTAAAATGCTTAA
1 TAAGGGATATAGAAGGGAAAATGCTTAA
11193 TAAGGGATATAGAAGGGAAAATGCTTAA
1 TAAGGGATATAGAAGGGAAAATGCTTAA
11221 T
1 T
11222 GGTGAAGGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.04, G:0.26, T:0.25
Consensus pattern (28 bp):
TAAGGGATATAGAAGGGAAAATGCTTAA
Found at i:17016 original size:22 final size:23
Alignment explanation
Indices: 16987--17037 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
16977 ACGTGGCCAA
*
16987 AAAATTTTTTCA-AAAAAAGAAT
1 AAAATTTTTTCAGAAAAAAAAAT
*
17009 TAAA--TTTTCAGAAAAAAAAAT
1 AAAATTTTTTCAGAAAAAAAAAT
17030 AAAATTTT
1 AAAATTTT
17038 AATTTAAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
20 6 0.26
21 12 0.52
22 3 0.13
23 2 0.09
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (23 bp):
AAAATTTTTTCAGAAAAAAAAAT
Found at i:17018 original size:20 final size:21
Alignment explanation
Indices: 16993--17037 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
16983 CCAAAAAATT
* *
16993 TTTTCA-AAAAAAGAATTAAA
1 TTTTCAGAAAAAAAAATAAAA
17013 TTTTCAGAAAAAAAAATAAAA
1 TTTTCAGAAAAAAAAATAAAA
17034 TTTT
1 TTTT
17038 AATTTAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (21 bp):
TTTTCAGAAAAAAAAATAAAA
Found at i:19848 original size:6 final size:6
Alignment explanation
Indices: 19831--19871 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
19821 GCACTTTTTA
*
19831 ATATAG -TATAG ATATAG ATATGG ATATA- A-ATAG ATATAG AT
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG AT
19872 TAATTCACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
4 3 0.10
5 7 0.23
6 20 0.67
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:21248 original size:9 final size:9
Alignment explanation
Indices: 21234--21262 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
21224 GGCTCACCTA
21234 TTTCCTTTT
1 TTTCCTTTT
21243 TTTCCTTTT
1 TTTCCTTTT
21252 TTTCCTTTT
1 TTTCCTTTT
21261 TT
1 TT
21263 GCAATTGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTCCTTTT
Found at i:21851 original size:31 final size:31
Alignment explanation
Indices: 21813--21877 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
21803 AAACTGACTA
*
21813 ACTCAAACATCCAAGATCTAAAGATCTGGAG
1 ACTCAAACATCCAAGATCTAAAAATCTGGAG
* *
21844 ACTCAAACATTCAAGATTTAAAAATCTGGAG
1 ACTCAAACATCCAAGATCTAAAAATCTGGAG
21875 ACT
1 ACT
21878 GATAACCCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (31 bp):
ACTCAAACATCCAAGATCTAAAAATCTGGAG
Found at i:25576 original size:22 final size:22
Alignment explanation
Indices: 25545--25588 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
25535 GATGAGAAAG
* *
25545 TCTTGACCGAAGCCAAGTCTAA
1 TCTTGACCGAAACCAAGCCTAA
*
25567 TCTTGGCCGAAACCAAGCCTAA
1 TCTTGACCGAAACCAAGCCTAA
25589 AGAAGGGGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.20
Consensus pattern (22 bp):
TCTTGACCGAAACCAAGCCTAA
Found at i:26819 original size:51 final size:51
Alignment explanation
Indices: 26758--26859 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
26748 GAAATACCCG
*
26758 TATATCGCTACATGATTAGCTACATTACCGAAACGCTAATCTATGAGCCAA
1 TATACCGCTACATGATTAGCTACATTACCGAAACGCTAATCTATGAGCCAA
26809 TATACCGCTACATGATTAGCTACATTACCGAAACGCTAATCTATGAGCCAA
1 TATACCGCTACATGATTAGCTACATTACCGAAACGCTAATCTATGAGCCAA
26860 CAAACCAGTA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (51 bp):
TATACCGCTACATGATTAGCTACATTACCGAAACGCTAATCTATGAGCCAA
Found at i:29013 original size:13 final size:13
Alignment explanation
Indices: 28995--29021 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28985 GGGCCGCCAC
28995 CCTGAAACCACAA
1 CCTGAAACCACAA
29008 CCTGAAACCACAA
1 CCTGAAACCACAA
29021 C
1 C
29022 AACTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.41, G:0.07, T:0.07
Consensus pattern (13 bp):
CCTGAAACCACAA
Found at i:33554 original size:7 final size:8
Alignment explanation
Indices: 33532--33561 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
33522 TTCAATCTCT
33532 TTTTCTTTC
1 TTTT-TTTC
33541 TTTTTTTC
1 TTTTTTTC
33549 TTTTTTTC
1 TTTTTTTC
33557 TTTTT
1 TTTTT
33562 CTCCAATAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTTC
Found at i:41852 original size:2 final size:2
Alignment explanation
Indices: 41839--41872 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
41829 TTATACGAAG
41839 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA T
41873 GAAACTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42232 original size:4 final size:4
Alignment explanation
Indices: 42215--42247 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
42205 GGAGAAATAA
*
42215 AAAG AAAA AAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG A
42248 GTACATTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:51491 original size:5 final size:5
Alignment explanation
Indices: 51483--51523 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
51473 GATCAAAGAT
* *
51483 TTTTC TTTTT TTCTTC TTTTC TTTTC TTTTC CTTTC TTTTC
1 TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC TTTTC TTTTC
51524 CTTCCTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 27 0.87
6 4 0.13
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:51518 original size:15 final size:16
Alignment explanation
Indices: 51484--51531 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 16
51474 ATCAAAGATT
* *
51484 TTTCTTTTTTTCTTCT
1 TTTCTTTTCTTCTTCC
51500 TTTCTTTTCTT-TTCC
1 TTTCTTTTCTTCTTCC
51515 TTTCTTTTC--CTTCC
1 TTTCTTTTCTTCTTCC
51529 TTT
1 TTT
51532 TTCTATGCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 7 0.24
15 12 0.41
16 10 0.34
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTCTTTTCTTCTTCC
Found at i:51524 original size:10 final size:10
Alignment explanation
Indices: 51496--51532 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
51486 TCTTTTTTTC
*
51496 TTCTTTTCTT
1 TTCTTTTCCT
51506 TTCTTTTCCT
1 TTCTTTTCCT
51516 TTCTTTTCCT
1 TTCTTTTCCT
*
51526 TCCTTTT
1 TTCTTTT
51533 TCTATGCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (10 bp):
TTCTTTTCCT
Found at i:52839 original size:16 final size:16
Alignment explanation
Indices: 52796--52850 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
52786 CGAAATGACC
*
52796 CGACCTCAAATCCTTAAT
1 CGACC-CAAA-CCTGAAT
*
52814 -GACCCGAACCTGAAT
1 CGACCCAAACCTGAAT
52829 CGACCCAAACCTGAAT
1 CGACCCAAACCTGAAT
*
52845 CAACCC
1 CGACCC
52851 GAATCGGATC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 6 0.19
16 22 0.69
17 4 0.12
ACGTcount: A:0.35, C:0.38, G:0.11, T:0.16
Consensus pattern (16 bp):
CGACCCAAACCTGAAT
Done.