Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005214.1 Corchorus capsularis cultivar CVL-1 contig05232, 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: 11124
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.32
Found at i:1124 original size:47 final size:47
Alignment explanation
Indices: 958--1190 Score: 331
Period size: 47 Copynumber: 4.9 Consensus size: 47
948 AAAGCCCGTT
* * * * *
958 GACCAACTCTGGTCACTAAATTGCAGACTCGCATGGAAACGAGAGAAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCATGGAAGCGAGA-AAA
* *
1006 GACCATCTTTGGTCACTAAATTGAAAACCCGCGTGGAAGCGAGAAAAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCATGGAAGCGAG-AAAA
*
1054 GACCATCTTTGGTCACTAGATTGAAAACTCGCATGGAAGCGAGAAAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCATGGAAGCGAGAAAA
* * *
1101 GACCATCTTTGGTCACCAAATTGAAAACTCGCGTGTAAGCGAGAAAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCATGGAAGCGAGAAAA
* *
1148 GACCATCTTTGGTTACTAAATTGAAAATTCGCATGGAAGCGAG
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCATGGAAGCGAG
1191 TTTGACTTAT
Statistics
Matches: 165, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
47 85 0.52
48 79 0.48
49 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (47 bp):
GACCATCTTTGGTCACTAAATTGAAAACTCGCATGGAAGCGAGAAAA
Found at i:1399 original size:69 final size:70
Alignment explanation
Indices: 1181--1486 Score: 332
Period size: 69 Copynumber: 4.4 Consensus size: 70
1171 AAAATTCGCA
* * * * ** * * *
1181 TGGAAGCGAGTTTGACTTATGGAAAAGCCTCT-CTTGCCTGGATGGAACCGAAGCTGGATCTGAA
1 TGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCCTGGATGGAACCGAAGCTGAAACTGAC
1245 TCGTG
66 TCGTG
* * * * *
1250 TGGAAACAAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAATCTGAAACTGTC
1 TGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCCTGGATGGAACCGAAGCTGAAACTGAC
*
1315 TCGCG
66 TCGTG
* * * * ** * *
1320 TGGAAGCGAGTTTGGCTTATTGAAAAGCCTCT-CTTGCCTGGATGGAACCGAAGCTGGATCTGAC
1 TGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCCTGGATGGAACCGAAGCTGAAACTGAC
1384 TCGTG
66 TCGTG
* **
1389 TGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGACAGAACC-AAGGCT-AAACTGA
1 TGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCCTGGATGGAACCGAA-GCTGAAACTGA
1452 CTCGTG
65 CTCGTG
*
1458 TGGAAATGAGTTTGGCTTGTGGAAAAGCC
1 TGGAAACGAGTTTGGCTTGTGGAAAAGCC
1487 AAAGCATTCG
Statistics
Matches: 193, Mismatches: 41, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
69 124 0.64
70 69 0.36
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (70 bp):
TGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCCTGGATGGAACCGAAGCTGAAACTGAC
TCGTG
Found at i:1431 original size:139 final size:138
Alignment explanation
Indices: 1176--1486 Score: 487
Period size: 139 Copynumber: 2.2 Consensus size: 138
1166 AATTGAAAAT
* *
1176 TCGCATGGAAGCGAGTTTGACTTATGGAAAAGCCTCTCTTGCCTGGATGGAACCGAAGCTGGATC
1 TCGCGTGGAAGCGAGTTTGGCTTATGGAAAAGCCTCTCTTGCCTGGATGGAACCGAAGCTGGATC
** *
1241 TGAATCGTGTGGAAACAAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAATCT
66 TGAATCGTGTGGAAACAAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGACAGAACCAAAGCT
*
1306 GAAACTGTC
131 -AAACTGAC
*
1315 TCGCGTGGAAGCGAGTTTGGCTTATTGAAAAGCCTCTCTTGCCTGGATGGAACCGAAGCTGGATC
1 TCGCGTGGAAGCGAGTTTGGCTTATGGAAAAGCCTCTCTTGCCTGGATGGAACCGAAGCTGGATC
* * *
1380 TGACTCGTGTGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGACAGAACCAAGGCT
66 TGAATCGTGTGGAAACAAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGACAGAACCAAAGCT
1445 AAACTGAC
131 AAACTGAC
* ** *
1453 TCGTGTGGAAATGAGTTTGGCTTGTGGAAAAGCC
1 TCGCGTGGAAGCGAGTTTGGCTTATGGAAAAGCC
1487 AAAGCATTCG
Statistics
Matches: 157, Mismatches: 15, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
138 36 0.23
139 121 0.77
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (138 bp):
TCGCGTGGAAGCGAGTTTGGCTTATGGAAAAGCCTCTCTTGCCTGGATGGAACCGAAGCTGGATC
TGAATCGTGTGGAAACAAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGACAGAACCAAAGCT
AAACTGAC
Found at i:2735 original size:11 final size:11
Alignment explanation
Indices: 2719--2744 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2709 TTCATTCTCT
2719 TTTTCTTTTTC
1 TTTTCTTTTTC
2730 TTTTCTTTTTC
1 TTTTCTTTTTC
2741 TTTT
1 TTTT
2745 TTTCCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:2753 original size:6 final size:6
Alignment explanation
Indices: 2716--2745 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
2706 TTCTTCATTC
2716 TCTTTT TCTTTT TC-TTT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT T
2746 TTCCTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TCTTTT
Found at i:3085 original size:12 final size:12
Alignment explanation
Indices: 3068--3123 Score: 69
Period size: 12 Copynumber: 4.7 Consensus size: 12
3058 TCCACTTTCA
*
3068 TTTTTTTTCCTC
1 TTTTTTTTCTTC
3080 -TTTTTTTCTTTC
1 TTTTTTTTC-TTC
*
3092 TTCTTTTTCTTC
1 TTTTTTTTCTTC
*
3104 TTTTTCTTCTTC
1 TTTTTTTTCTTC
3116 TTTTTTTT
1 TTTTTTTT
3124 TCCTTTTCTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
11 8 0.22
12 22 0.59
13 7 0.19
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTTTTCTTC
Found at i:3100 original size:9 final size:9
Alignment explanation
Indices: 3071--3114 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
3061 ACTTTCATTT
*
3071 TTTTTCCTC
1 TTTTTCTTC
3080 TTTTT-TTC
1 TTTTTCTTC
3088 --TTTCTTC
1 TTTTTCTTC
3095 TTTTTCTTC
1 TTTTTCTTC
3104 TTTTTCTTC
1 TTTTTCTTC
3113 TT
1 TT
3115 CTTTTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
6 3 0.10
7 3 0.10
8 2 0.06
9 23 0.74
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:3139 original size:24 final size:23
Alignment explanation
Indices: 3068--3141 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 23
3058 TCCACTTTCA
* * *
3068 TTTTTTTTCCTCTTTTTTTCTTTC
1 TTTTTTTTTC-CTTTTCTTCCTTC
*
3092 TTCTTTTTCTTCTTTTTCTT-CTTC
1 TT-TTTTT-TTCCTTTTCTTCCTTC
3116 TTTTTTTTTCCTTTTCTTCCCTTC
1 TTTTTTTTTCCTTTTCTT-CCTTC
3140 TT
1 TT
3142 CATCTGACTT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
22 10 0.24
23 5 0.12
24 13 0.32
25 11 0.27
26 2 0.05
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTTTTTTCCTTTTCTTCCTTC
Found at i:9356 original size:21 final size:22
Alignment explanation
Indices: 9332--9378 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
9322 TCACTAAATC
*
9332 TGATTTGAAT-TTGAAAAC-CTT
1 TGATTTAAATCTTGAAAACTC-T
9353 TGA-TTAAATCTTGAAAACTCT
1 TGATTTAAATCTTGAAAACTCT
9374 TGATT
1 TGATT
9379 ACCAATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 5 0.23
21 15 0.68
22 2 0.09
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.43
Consensus pattern (22 bp):
TGATTTAAATCTTGAAAACTCT
Found at i:10443 original size:6 final size:7
Alignment explanation
Indices: 10424--10456 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
10414 AAAAATTAAG
10424 CTAAAAA
1 CTAAAAA
10431 CTAAAAA
1 CTAAAAA
10438 CTAAAAA
1 CTAAAAA
10445 TCTAAAAA
1 -CTAAAAA
10453 CTAA
1 CTAA
10457 TCTTTAATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.18
Consensus pattern (7 bp):
CTAAAAA
Found at i:10449 original size:15 final size:14
Alignment explanation
Indices: 10424--10456 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
10414 AAAAATTAAG
10424 CTAAAAACTAAAAA
1 CTAAAAACTAAAAA
10438 CTAAAAATCTAAAAA
1 CTAAAAA-CTAAAAA
10453 CTAA
1 CTAA
10457 TCTTTAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.18
Consensus pattern (14 bp):
CTAAAAACTAAAAA
Found at i:10834 original size:18 final size:17
Alignment explanation
Indices: 10811--10848 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
10801 TTTTATCGCG
10811 CTTTTCTTCC-TCTTCTCT
1 CTTTTC-TCCTTCTTCT-T
10829 CTTTTCTCCTTCTTCTT
1 CTTTTCTCCTTCTTCTT
10846 CTT
1 CTT
10849 CCTCGAGCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (17 bp):
CTTTTCTCCTTCTTCTT
Done.