Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011960.1 Corchorus olitorius cultivar O-4 contig11993, 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: 34898
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1025 original size:51 final size:47
Alignment explanation
Indices: 950--1092 Score: 173
Period size: 51 Copynumber: 2.9 Consensus size: 47
940 AAAGCAATCC
*
950 TTTACTTTTTACTGCACTTTTTCTCAATTTTTACTACAAAATTGAACT
1 TTTACTTTTTATTGCACTTTTTCTCAATTTTTA-TACAAAATTGAACT
* *
998 TTTA-TTTTTACTTGCACCCTTTTTTCTCAATTTTTAAGACAAAATTGATCT
1 TTTACTTTTTA-TTGCA--C-TTTTTCTCAATTTTT-ATACAAAATTGAACT
*
1049 TTTACTTTTTATTGCACTTTTTATCAATTTTT-TGACAAAATTGA
1 TTTACTTTTTATTGCACTTTTTCTCAATTTTTAT-ACAAAATTGA
1093 TTGGCACGCT
Statistics
Matches: 83, Mismatches: 5, Indels: 15
0.81 0.05 0.15
Matches are distributed among these distances:
47 16 0.19
48 22 0.27
49 1 0.01
50 1 0.01
51 36 0.43
52 7 0.08
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.52
Consensus pattern (47 bp):
TTTACTTTTTATTGCACTTTTTCTCAATTTTTATACAAAATTGAACT
Found at i:5984 original size:16 final size:16
Alignment explanation
Indices: 5957--5989 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5947 ATAATATACC
5957 TATTTTTCCTTCTCTCT
1 TATTTTTCCTTCT-TCT
5974 TATTTTT-CTTCTTCT
1 TATTTTTCCTTCTTCT
5989 T
1 T
5990 TACAACCCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 5 0.31
17 7 0.44
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTTTTCCTTCTTCT
Found at i:6424 original size:28 final size:28
Alignment explanation
Indices: 6393--6448 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
6383 GTAATCGTCA
**
6393 GAAAGTGGGGTGGAAATGGGTAAGGTTG
1 GAAAGTGGGGTGGAAATGGACAAGGTTG
6421 GAAAGTGGGGTGGAAATGGACAAGGTTG
1 GAAAGTGGGGTGGAAATGGACAAGGTTG
6449 CGCAGAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.30, C:0.02, G:0.48, T:0.20
Consensus pattern (28 bp):
GAAAGTGGGGTGGAAATGGACAAGGTTG
Found at i:7048 original size:19 final size:20
Alignment explanation
Indices: 7020--7060 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
7010 TTAAAGTGTG
*
7020 TTTGTGATTTT-TATTTAAT
1 TTTGTAATTTTATATTTAAT
*
7039 TTTGTAATTTTATTTTTAAT
1 TTTGTAATTTTATATTTAAT
7059 TT
1 TT
7061 CATAAATTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (20 bp):
TTTGTAATTTTATATTTAAT
Found at i:10577 original size:25 final size:25
Alignment explanation
Indices: 10543--10605 Score: 126
Period size: 25 Copynumber: 2.5 Consensus size: 25
10533 ATAGGTATTT
10543 AAATTTTATTTATTTTTTACTAAAA
1 AAATTTTATTTATTTTTTACTAAAA
10568 AAATTTTATTTATTTTTTACTAAAA
1 AAATTTTATTTATTTTTTACTAAAA
10593 AAATTTTATTTAT
1 AAATTTTATTTAT
10606 ATCATTTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (25 bp):
AAATTTTATTTATTTTTTACTAAAA
Found at i:10616 original size:25 final size:24
Alignment explanation
Indices: 10543--10622 Score: 99
Period size: 25 Copynumber: 3.2 Consensus size: 24
10533 ATAGGTATTT
*
10543 AAATTTTATTTATTTTTTACTAAAA
1 AAATTTTATTTATTATTTA-TAAAA
*
10568 AAATTTTATTTATTTTTTACTAAAA
1 AAATTTTATTTATTATTTA-TAAAA
10593 AAATTTTATTTATATCATTT-TAAAA
1 AAATTTTATTTAT-T-ATTTATAAAA
10618 AAATT
1 AAATT
10623 ATCCATTTAA
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
25 48 0.92
26 1 0.02
27 3 0.06
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (24 bp):
AAATTTTATTTATTATTTATAAAA
Found at i:12202 original size:2 final size:2
Alignment explanation
Indices: 12197--12233 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
12187 AGAATGTGTG
*
12197 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12234 GTTTTTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13832 original size:22 final size:22
Alignment explanation
Indices: 13805--13849 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
13795 GATTCATACT
13805 CTGTTTTTTTCATTGTTCAACA
1 CTGTTTTTTTCATTGTTCAACA
13827 CTGTTTTTTTCATTGTTCAACA
1 CTGTTTTTTTCATTGTTCAACA
13849 C
1 C
13850 ATAATATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.20, G:0.09, T:0.53
Consensus pattern (22 bp):
CTGTTTTTTTCATTGTTCAACA
Found at i:21689 original size:22 final size:22
Alignment explanation
Indices: 21664--21709 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
21654 AGGTTTCTGC
21664 TAATTTAATGCCTTAAAATTCA
1 TAATTTAATGCCTTAAAATTCA
*
21686 TAATTTAATGTCTTAAAATTCA
1 TAATTTAATGCCTTAAAATTCA
21708 TA
1 TA
21710 TTATTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.43
Consensus pattern (22 bp):
TAATTTAATGCCTTAAAATTCA
Found at i:27583 original size:3 final size:3
Alignment explanation
Indices: 27575--27612 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
27565 TTAACAAATA
27575 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT T
27613 TATCTTTACT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:29354 original size:6 final size:6
Alignment explanation
Indices: 29337--29380 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
29327 ATTATTTTCT
* *
29337 TAAAAA TGAAAA TCAAAA TCAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA T-AAAAA TAAAAA TAAAAA TAAAAA T
29381 CAACCCCTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
6 29 0.85
7 5 0.15
ACGTcount: A:0.75, C:0.05, G:0.02, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:29362 original size:19 final size:18
Alignment explanation
Indices: 29337--29380 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
29327 ATTATTTTCT
* *
29337 TAAAAATGAAAATCAAAA
1 TAAAAATAAAAATAAAAA
29355 TCAAAAATAAAAATAAAAA
1 T-AAAAATAAAAATAAAAA
29374 TAAAAAT
1 TAAAAAT
29381 CAACCCCTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.75, C:0.05, G:0.02, T:0.18
Consensus pattern (18 bp):
TAAAAATAAAAATAAAAA
Found at i:30560 original size:131 final size:131
Alignment explanation
Indices: 30155--30805 Score: 905
Period size: 131 Copynumber: 5.0 Consensus size: 131
30145 AATTAAAAGT
* * * * * *
30155 CGTTGTCTTAGTGATTTTGATGGTATTTTACCCAACGAATTTTTTAATTGTTGCCAATGCTTACA
1 CGTTGCCTAAGTGATTTTGATGGTATTTTACACAAC-ACTTTTTTAGTTGTTGCCAATGTTTACA
* ** * * * * *
30220 GT-TCTCGTAACAACAAAAAC-AAAGTCGTTGCGAAATCACAATCTATTCGTAACAATTTTATAA
65 ATAT-TCGTAACAACAAATTCTTAAGTTGTTGCGAAATCATAAACTATTCGTAACAACTTTATAA
**
30283 AGT
129 AAA
* * *
30286 CGTTGCCTAAATGATTTTGATGGTATTTTACACAACACTTTTTTAGTCGTTAG-CAATGCTTACA
1 CGTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTT-GCCAATGTTTACA
* ** * *
30350 ATTTTCGTAACAACAAAAAC-AAAGTCGTTGCGAAATCATAAACTATTCGTAACAACTTTATAAA
65 ATATTCGTAACAACAAATTCTTAAGTTGTTGCGAAATCATAAACTATTCGTAACAACTTTATAAA
30414 AA
130 AA
* * *
30416 CGGTGGCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTTGTCAATGTTTACAA
1 CGTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTTGCCAATGTTTACAA
* *
30481 TATTCGTAATAACAAATTCTTAAGTTGTTGCGAAATCATAAACTATTCGTAACAATTTTATAAAA
66 TATTCGTAACAACAAATTCTTAAGTTGTTGCGAAATCATAAACTATTCGTAACAACTTTATAAAA
30546 A
131 A
*
30547 CGTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTTGCCAATGTTTACAG
1 CGTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTTGCCAATGTTTACAA
* * * *
30612 TATTCGTAACAACAACTTCTTAAGTTGCTGCGAAATCATACACTTTTCGTAACAACTTTATAAAA
66 TATTCGTAACAACAAATTCTTAAGTTGTTGCGAAATCATAAACTATTCGTAACAACTTTATAAAA
30677 A
131 A
* *
30678 CGTTGCCTAAGTGATTTTGATGGTATTTTACACTACACTTTTTTAGTTGTTGCCAATATTTACAA
1 CGTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTTGCCAATGTTTACAA
* *
30743 TATTCGTAACAACAAATTCTTAAGTTGTTGCGACATCATAATCTATTCGTAACAACTTTATAA
66 TATTCGTAACAACAAATTCTTAAGTTGTTGCGAAATCATAAACTATTCGTAACAACTTTATAA
30806 GTCGTTGCGC
Statistics
Matches: 472, Mismatches: 44, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
129 1 0.00
130 154 0.33
131 317 0.67
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (131 bp):
CGTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTTGCCAATGTTTACAA
TATTCGTAACAACAAATTCTTAAGTTGTTGCGAAATCATAAACTATTCGTAACAACTTTATAAAA
A
Found at i:32839 original size:40 final size:38
Alignment explanation
Indices: 32792--32910 Score: 104
Period size: 40 Copynumber: 3.1 Consensus size: 38
32782 TACTTTTACG
32792 CAACAATACTGAGTTGTTGCGTAAAATACAATTCTTTTAT
1 CAACAATA-TGAGTTGTTGCGTAAAATA-AATTCTTTTAT
** * *
32832 CAACAATAAAATGTCGTTG-TTAAAAT--A-T-TTTTAT
1 CAACAATATGA-GTTGTTGCGTAAAATAAATTCTTTTAT
*
32866 GCAACAATATTGAGTTGTTGCGTAAAATATAATTCTTTTAA
1 -CAACAATA-TGAGTTGTTGCGTAAAATA-AATTCTTTTAT
32907 CAAC
1 CAAC
32911 GATAAAATAG
Statistics
Matches: 61, Mismatches: 9, Indels: 18
0.69 0.10 0.20
Matches are distributed among these distances:
34 6 0.10
35 15 0.25
36 8 0.13
39 8 0.13
40 19 0.31
41 5 0.08
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.38
Consensus pattern (38 bp):
CAACAATATGAGTTGTTGCGTAAAATAAATTCTTTTAT
Found at i:32874 original size:75 final size:75
Alignment explanation
Indices: 32751--32918 Score: 241
Period size: 75 Copynumber: 2.2 Consensus size: 75
32741 TACATTAGCA
*
32751 TTTTAACAACGAATATATAT-T-GTTGTTAAAATACTTTTACGCAACAATACTGAGTTGTTGCGT
1 TTTTAACAAC-AATA-AAATGTCGTTGTTAAAATACTTTTACGCAACAATACTGAGTTGTTGCGT
32814 AAAATACAATTC
64 AAAATACAATTC
* * * *
32826 TTTTATCAACAATAAAATGTCGTTGTTAAAATATTTTTATGCAACAATATTGAGTTGTTGCGTAA
1 TTTTAACAACAATAAAATGTCGTTGTTAAAATACTTTTACGCAACAATACTGAGTTGTTGCGTAA
*
32891 AATATAATTC
66 AATACAATTC
*
32901 TTTTAACAACGATAAAAT
1 TTTTAACAACAATAAAAT
32919 AGCGTAACAA
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
73 3 0.04
74 5 0.06
75 75 0.90
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (75 bp):
TTTTAACAACAATAAAATGTCGTTGTTAAAATACTTTTACGCAACAATACTGAGTTGTTGCGTAA
AATACAATTC
Found at i:32895 original size:36 final size:35
Alignment explanation
Indices: 32777--32895 Score: 98
Period size: 36 Copynumber: 3.2 Consensus size: 35
32767 ATATTGTTGT
* *
32777 TAAAATACTTTTACGCAACAATACTGAGTTGTTGCG
1 TAAAATATTTTTATGCAACAATA-TGAGTTGTTGCG
** * *
32813 TAAAATACAATTCTTTTAT-CAACAATAAAATGTCGTTG-T
1 TAAAAT---A-T-TTTTATGCAACAATATGA-GTTGTTGCG
32852 TAAAATATTTTTATGCAACAATATTGAGTTGTTGCG
1 TAAAATATTTTTATGCAACAATA-TGAGTTGTTGCG
32888 TAAAATAT
1 TAAAATAT
32896 AATTCTTTTA
Statistics
Matches: 64, Mismatches: 10, Indels: 18
0.70 0.11 0.20
Matches are distributed among these distances:
34 6 0.09
35 15 0.23
36 16 0.25
39 8 0.12
40 14 0.22
41 5 0.08
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.38
Consensus pattern (35 bp):
TAAAATATTTTTATGCAACAATATGAGTTGTTGCG
Found at i:32937 original size:75 final size:75
Alignment explanation
Indices: 32785--32949 Score: 206
Period size: 75 Copynumber: 2.2 Consensus size: 75
32775 GTTAAAATAC
* * *
32785 TTTTACGCAACAATACTGAGTTGTTGCGTAAAATACAATTCTTTTATCAACAATAAAATGTCGTT
1 TTTTATGCAACAATACTGAGTTGTTGCGTAAAATACAATTCTTTTAACAACAATAAAATGTCGTA
*** *
32850 GTTAAAATAT
66 ACAAAAAAAT
* * *
32860 TTTTATGCAACAATATTGAGTTGTTGCGTAAAATATAATTCTTTTAACAACGATAAAATAG-CGT
1 TTTTATGCAACAATACTGAGTTGTTGCGTAAAATACAATTCTTTTAACAACAATAAAAT-GTCGT
32924 AACAAAAAAAT
65 AACAAAAAAAT
*
32935 TTTTTTAGCAACAAT
1 TTTTAT-GCAACAAT
32950 CACCTTAAGT
Statistics
Matches: 77, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
75 68 0.88
76 9 0.12
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (75 bp):
TTTTATGCAACAATACTGAGTTGTTGCGTAAAATACAATTCTTTTAACAACAATAAAATGTCGTA
ACAAAAAAAT
Done.