Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009492.1 Corchorus capsularis cultivar CVL-1 contig09513, 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: 22456
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:2974 original size:12 final size:12
Alignment explanation
Indices: 2959--3001 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
2949 AACATCATCA
2959 TCCTCAACCTCT
1 TCCTCAACCTCT
**
2971 TCCTCTTCCTCT
1 TCCTCAACCTCT
**
2983 TCCTCTTCCTCT
1 TCCTCAACCTCT
2995 TCCTCAA
1 TCCTCAA
3002 AGTTAAGAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.09, C:0.49, G:0.00, T:0.42
Consensus pattern (12 bp):
TCCTCAACCTCT
Found at i:2975 original size:6 final size:6
Alignment explanation
Indices: 2966--2999 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
2956 TCATCCTCAA
2966 CCTCTT CCTCTT CCTCTT CCTCTT CCTCTT CCTC
1 CCTCTT CCTCTT CCTCTT CCTCTT CCTCTT CCTC
3000 AAAGTTAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (6 bp):
CCTCTT
Found at i:10934 original size:19 final size:19
Alignment explanation
Indices: 10890--10934 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
10880 AATTTCTTAT
* *
10890 AAAAAAACTACCCACTTAA
1 AAAAAAACCACCCAATTAA
* *
10909 AAGAAAACCACTCAATTAA
1 AAAAAAACCACCCAATTAA
10928 AAAAAAA
1 AAAAAAA
10935 AAAACCCGCC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.64, C:0.20, G:0.02, T:0.13
Consensus pattern (19 bp):
AAAAAAACCACCCAATTAA
Found at i:11278 original size:33 final size:32
Alignment explanation
Indices: 11218--11286 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 32
11208 CCGCCCTAGG
* *
11218 GGGGCGGCACTACCATGGCCAGGCCGCCTCCAT
1 GGGGCGGCACTACCATGGACAGACCGCC-CCAT
* * *
11251 GGGGCGGCCCTACCATGGATAGACCGCCCCCT
1 GGGGCGGCACTACCATGGACAGACCGCCCCAT
11283 GGGG
1 GGGG
11287 TGGCTAGCCG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
32 7 0.23
33 24 0.77
ACGTcount: A:0.14, C:0.38, G:0.36, T:0.12
Consensus pattern (32 bp):
GGGGCGGCACTACCATGGACAGACCGCCCCAT
Found at i:11324 original size:32 final size:32
Alignment explanation
Indices: 11282--11388 Score: 178
Period size: 32 Copynumber: 3.3 Consensus size: 32
11272 GACCGCCCCC
*
11282 TGGGGTGGCTAGCCGTGGCAGAGCCGTCCTAG
1 TGGGGAGGCTAGCCGTGGCAGAGCCGTCCTAG
*
11314 TGGGGCGGCTAGCCGTGGCAGAGCCGTCCTAG
1 TGGGGAGGCTAGCCGTGGCAGAGCCGTCCTAG
*
11346 TGGGGAGGCTCCGCCGTGGCAGAGCCGTCCTAG
1 TGGGGAGGCT-AGCCGTGGCAGAGCCGTCCTAG
11379 TGGGGAGGCT
1 TGGGGAGGCT
11389 TCGCGTGGCT
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 40 0.56
33 31 0.44
ACGTcount: A:0.12, C:0.26, G:0.45, T:0.17
Consensus pattern (32 bp):
TGGGGAGGCTAGCCGTGGCAGAGCCGTCCTAG
Found at i:11998 original size:41 final size:41
Alignment explanation
Indices: 11883--11983 Score: 163
Period size: 38 Copynumber: 2.5 Consensus size: 41
11873 CTCACAAATT
*
11883 AAATAAAAAAAAACTGCTCCCTATTAAATTAGTTACCTATGC
1 AAAT-AAAAAAAACTACTCCCTATTAAATTAGTTACCTATGC
11925 AAATAAAAAAAACTA---CCTATTAAATTAGTTACCTATGC
1 AAATAAAAAAAACTACTCCCTATTAAATTAGTTACCTATGC
11963 AAATAAAAAAAACTACTCCCT
1 AAATAAAAAAAACTACTCCCT
11984 GATGAGTTGG
Statistics
Matches: 55, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
38 38 0.69
41 13 0.24
42 4 0.07
ACGTcount: A:0.50, C:0.19, G:0.05, T:0.27
Consensus pattern (41 bp):
AAATAAAAAAAACTACTCCCTATTAAATTAGTTACCTATGC
Found at i:12866 original size:6 final size:6
Alignment explanation
Indices: 12855--12933 Score: 61
Period size: 6 Copynumber: 12.2 Consensus size: 6
12845 CGGGTTTAGG
*
12855 CGGGTT CGGGTT CGGGTACTT CGGGTT CCGGTATTT TCGGGTT CGGGTT
1 CGGGTT CGGGTT CGGG---TT CGGGTT -CGG--GTT -CGGGTT CGGGTT
* *
12904 CGGGTC CGGGTC CGGG-T CGGGTT CGGGTT C
1 CGGGTT CGGGTT CGGGTT CGGGTT CGGGTT C
12934 ACTTAGAGTA
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
5 4 0.07
6 41 0.67
7 5 0.08
9 11 0.18
ACGTcount: A:0.03, C:0.22, G:0.44, T:0.32
Consensus pattern (6 bp):
CGGGTT
Found at i:12879 original size:15 final size:16
Alignment explanation
Indices: 12859--12902 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
12849 TTTAGGCGGG
12859 TTCGGGTTCGGGTA-C
1 TTCGGGTTCGGGTATC
* *
12874 TTCGGGTTCCGGTATT
1 TTCGGGTTCGGGTATC
12890 TTCGGGTTCGGGT
1 TTCGGGTTCGGGT
12903 TCGGGTCCGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.05, C:0.18, G:0.39, T:0.39
Consensus pattern (16 bp):
TTCGGGTTCGGGTATC
Found at i:13708 original size:16 final size:16
Alignment explanation
Indices: 13687--13758 Score: 65
Period size: 16 Copynumber: 4.5 Consensus size: 16
13677 GCTCGGGTCA
*
13687 GGTTCGGGTTCAGGCG
1 GGTTCGGGTTCTGGCG
* **
13703 GGTTCGGGTTGTCTCG
1 GGTTCGGGTTCTGGCG
**
13719 GGTTCGGGTAT-TTTCG
1 GGTTCGGGT-TCTGGCG
*
13735 GGTTCGGGTTCGGGCG
1 GGTTCGGGTTCTGGCG
13751 GGTTCGGG
1 GGTTCGGG
13759 CGGATTTCGG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
15 1 0.02
16 44 0.96
17 1 0.02
ACGTcount: A:0.03, C:0.17, G:0.49, T:0.32
Consensus pattern (16 bp):
GGTTCGGGTTCTGGCG
Found at i:14076 original size:102 final size:102
Alignment explanation
Indices: 13917--14120 Score: 320
Period size: 102 Copynumber: 2.0 Consensus size: 102
13907 TTTTTTTTTC
* *
13917 TTTGTTAATCTATACTAATTTCATAATTGATTTCTCAAGCTTGACGTCTTTTGTTGGCTATTCTT
1 TTTGTTAATCTATACTAATTTCATAATTGATTTCACAAGCTTGACGTCTTTTATTGGCTATTCTT
*
13982 TATTTGATTTATGA-TTAATTAAAGCTTGGAGCCTTT
66 TATTTGATTGATGATTTAATTAAAGCTTGGAGCCTTT
* *
14018 TTTGTTAATCTATACTAATTTCAATATTTGATTTCACAAGTTTGACGTCTTTTATTGGCTATTCT
1 TTTGTTAATCTATACTAATTTC-ATAATTGATTTCACAAGCTTGACGTCTTTTATTGGCTATTCT
* * *
14083 TTGTTTGATTGATGATTTACTTAAAGCTTGGCGCCTTT
65 TTATTTGATTGATGATTTAATTAAAGCTTGGAGCCTTT
14121 GAACGGTGTT
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 22 0.24
102 51 0.55
103 20 0.22
ACGTcount: A:0.23, C:0.13, G:0.14, T:0.50
Consensus pattern (102 bp):
TTTGTTAATCTATACTAATTTCATAATTGATTTCACAAGCTTGACGTCTTTTATTGGCTATTCTT
TATTTGATTGATGATTTAATTAAAGCTTGGAGCCTTT
Found at i:18761 original size:29 final size:30
Alignment explanation
Indices: 18686--18763 Score: 122
Period size: 30 Copynumber: 2.6 Consensus size: 30
18676 AAGCTCTAAA
18686 TGATATGCTATTAGTATCTACCAACTATGTT
1 TGAT-TGCTATTAGTATCTACCAACTATGTT
18717 TGATTGCTATTAGTATCTACCAACTATG-T
1 TGATTGCTATTAGTATCTACCAACTATGTT
* *
18746 TGATTGCTGTTTGTATCT
1 TGATTGCTATTAGTATCT
18764 TATGCATCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 17 0.38
30 24 0.53
31 4 0.09
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.45
Consensus pattern (30 bp):
TGATTGCTATTAGTATCTACCAACTATGTT
Found at i:22437 original size:2 final size:2
Alignment explanation
Indices: 22430--22456 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
22420 AATATTGTTA
22430 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 A
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.