Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007202.1 Corchorus capsularis cultivar CVL-1 contig07223, 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: 33478
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1581 original size:20 final size:20
Alignment explanation
Indices: 1552--1590 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1542 AGTTATGTCG
* *
1552 AAAAATATAAAAACAAATTC
1 AAAAAAATAAAAAAAAATTC
1572 AAAAAAATAAAAAAAAATT
1 AAAAAAATAAAAAAAAATT
1591 TCGACCAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (20 bp):
AAAAAAATAAAAAAAAATTC
Found at i:2642 original size:40 final size:41
Alignment explanation
Indices: 2576--2652 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 41
2566 ACATTTTCTA
* *
2576 TTAAAACAATTCCAAGAGAAGACTTTTGGAAAATAAATTTT
1 TTAAAAAAATTCCAAAAGAAGACTTTTGGAAAATAAATTTT
2617 TTAAAAAAATT-CAAAAGAAGACTTTTGGAAAATAAA
1 TTAAAAAAATTCCAAAAGAAGACTTTTGGAAAATAAA
2653 AGTATTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 24 0.71
41 10 0.29
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.29
Consensus pattern (41 bp):
TTAAAAAAATTCCAAAAGAAGACTTTTGGAAAATAAATTTT
Found at i:2661 original size:40 final size:41
Alignment explanation
Indices: 2574--2662 Score: 126
Period size: 40 Copynumber: 2.2 Consensus size: 41
2564 GAACATTTTC
* * **
2574 TATTAAAACAATTCCAAGAGAAGACTTTTGGAAAATAAATT
1 TATTAAAAAAATTCCAAAAGAAGACTTTTGGAAAATAAAAG
*
2615 TTTTAAAAAAATT-CAAAAGAAGACTTTTGGAAAATAAAAG
1 TATTAAAAAAATTCCAAAAGAAGACTTTTGGAAAATAAAAG
2655 TATTAAAA
1 TATTAAAA
2663 TACTCCCTCC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 31 0.74
41 11 0.26
ACGTcount: A:0.53, C:0.07, G:0.11, T:0.29
Consensus pattern (41 bp):
TATTAAAAAAATTCCAAAAGAAGACTTTTGGAAAATAAAAG
Found at i:19402 original size:21 final size:22
Alignment explanation
Indices: 19366--19412 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
19356 GTGCATGGGC
*
19366 ATGGCCGGGTCATGCGATGGTG
1 ATGGCCAGGTCATGCGATGGTG
19388 ATGGCCAGG-CATGCGATGGTG
1 ATGGCCAGGTCATGCGATGGTG
19409 ATGG
1 ATGG
19413 TCGAGCATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.17, C:0.17, G:0.45, T:0.21
Consensus pattern (22 bp):
ATGGCCAGGTCATGCGATGGTG
Found at i:23562 original size:10 final size:10
Alignment explanation
Indices: 23547--23572 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
23537 CTGGTCGAAA
23547 TTTTTTTTAT
1 TTTTTTTTAT
23557 TTTTTTTTAT
1 TTTTTTTTAT
23567 TTTTTT
1 TTTTTT
23573 GATATTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:24636 original size:21 final size:21
Alignment explanation
Indices: 24600--24655 Score: 94
Period size: 21 Copynumber: 2.6 Consensus size: 21
24590 GTGCATGGGC
24600 ATGGCCGGGTCATGCGATGGTG
1 ATGGCCGGG-CATGCGATGGTG
*
24622 ATGGTCGGGCATGCGATGGTG
1 ATGGCCGGGCATGCGATGGTG
24643 ATGGCCGGGCATG
1 ATGGCCGGGCATG
24656 TGGCCGGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 24 0.75
22 8 0.25
ACGTcount: A:0.14, C:0.18, G:0.46, T:0.21
Consensus pattern (21 bp):
ATGGCCGGGCATGCGATGGTG
Found at i:27113 original size:30 final size:30
Alignment explanation
Indices: 27077--27133 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
27067 AGGAGGAGGG
27077 AATGATGCGCCCAAGG-CTTATCATGGAAGA
1 AATGATGCG-CCAAGGACTTATCATGGAAGA
*
27107 AATGATGCGCCAAGGACTTATTATGGA
1 AATGATGCGCCAAGGACTTATCATGGA
27134 CTTGAAGACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (30 bp):
AATGATGCGCCAAGGACTTATCATGGAAGA
Found at i:28320 original size:17 final size:15
Alignment explanation
Indices: 28286--28321 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
28276 CGCCTCTAAA
28286 ATATATTATATTTTT
1 ATATATTATATTTTT
* *
28301 ATATATTTTATTATT
1 ATATATTATATTTTT
28316 ATATAT
1 ATATAT
28322 GTACTATATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATATATTATATTTTT
Found at i:29233 original size:10 final size:10
Alignment explanation
Indices: 29211--29249 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
29201 AAATCTCGAT
*
29211 ATATCCGTAA
1 ATATCCATAA
29221 ATATCCATAA
1 ATATCCATAA
*
29231 ATATCCGTAA
1 ATATCCATAA
*
29241 ATATGCATA
1 ATATCCATA
29250 TTAAATTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.31
Consensus pattern (10 bp):
ATATCCATAA
Found at i:29234 original size:20 final size:20
Alignment explanation
Indices: 29211--29249 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
29201 AAATCTCGAT
29211 ATATCCGTAAATATCCATAA
1 ATATCCGTAAATATCCATAA
*
29231 ATATCCGTAAATATGCATA
1 ATATCCGTAAATATCCATA
29250 TTAAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.31
Consensus pattern (20 bp):
ATATCCGTAAATATCCATAA
Found at i:30054 original size:10 final size:10
Alignment explanation
Indices: 30039--30072 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
30029 TCGCAGTACC
30039 AAAAATAAAA
1 AAAAATAAAA
30049 AAAAAT--AA
1 AAAAATAAAA
30057 AAAAATAAAA
1 AAAAATAAAA
30067 AAAAAT
1 AAAAAT
30073 GTCTACATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.36
10 14 0.64
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:30262 original size:13 final size:12
Alignment explanation
Indices: 30232--30274 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
30222 CATCGATACC
30232 TCGATATATCCG
1 TCGATATATCCG
30244 TCGATATATCCG
1 TCGATATATCCG
*
30256 TTCGATATATCGG
1 -TCGATATATCCG
30269 TCGATA
1 TCGATA
30275 CCTGTATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.35
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:33115 original size:12 final size:13
Alignment explanation
Indices: 33092--33123 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
33082 AATTATTGTT
33092 TGCTTTATTAATC
1 TGCTTTATTAATC
33105 TGCTTTA-TAATC
1 TGCTTTATTAATC
33117 TGCTTTA
1 TGCTTTA
33124 GATTTAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.22, C:0.16, G:0.09, T:0.53
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:33157 original size:28 final size:24
Alignment explanation
Indices: 33117--33177 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 24
33107 CTTTATAATC
*
33117 TGCTTTAGATTTAGATTTAGATTTGCTT
1 TGCTTTATATTTAG-TTTA-A-TTG-TT
*
33145 TGCTTTATTTTTAGTTTAATTGTT
1 TGCTTTATATTTAGTTTAATTGTT
33169 TGCTTTATA
1 TGCTTTATA
33178 ATTGTTACTC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 10 0.33
25 3 0.10
26 1 0.03
27 4 0.13
28 12 0.40
ACGTcount: A:0.20, C:0.07, G:0.15, T:0.59
Consensus pattern (24 bp):
TGCTTTATATTTAGTTTAATTGTT
Done.