Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011318.1 Corchorus capsularis cultivar CVL-1 contig11339, 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: 14908
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:33 original size:20 final size:19
Alignment explanation
Indices: 4--175 Score: 131
Period size: 20 Copynumber: 8.8 Consensus size: 19
1 GCA
*
4 AAAAGGTAATCAATAAGAGT
1 AAAA-GTAATCAGTAAGAGT
*
24 AAAAGATAATCAGTAAGAAT
1 AAAAG-TAATCAGTAAGAGT
44 AAATAGTAATCAGTAAG-G-
1 AAA-AGTAATCAGTAAGAGT
*
62 ---AGTAATCAGTAAAAAGT
1 AAAAGTAATCAGT-AAGAGT
* *
79 AAAAAAGCAATCATTAAGAGT
1 --AAAAGTAATCAGTAAGAGT
*
100 GAAATAGTAGTCAGTAAGAGT
1 -AAA-AGTAATCAGTAAGAGT
121 -AAAGATAATCAGTAAGAGT
1 AAAAG-TAATCAGTAAGAGT
*
140 AAATAGTATTCAGTAAGAGT
1 AAA-AGTAATCAGTAAGAGT
*
160 AAAGAGCAATCAGTAA
1 AAA-AGTAATCAGTAA
176 AAGAGTAATC
Statistics
Matches: 122, Mismatches: 16, Indels: 28
0.73 0.10 0.17
Matches are distributed among these distances:
14 10 0.08
15 2 0.02
16 1 0.01
18 2 0.02
19 16 0.13
20 61 0.50
21 22 0.18
22 8 0.07
ACGTcount: A:0.52, C:0.06, G:0.20, T:0.22
Consensus pattern (19 bp):
AAAAGTAATCAGTAAGAGT
Found at i:153 original size:39 final size:41
Alignment explanation
Indices: 84--175 Score: 143
Period size: 39 Copynumber: 2.3 Consensus size: 41
74 AAAGTAAAAA
*
84 AGCAATCATTAAGAGTGAAATAGTAGTCAGTAAGAGTAAAG
1 AGCAATCAGTAAGAGTGAAATAGTAGTCAGTAAGAGTAAAG
* *
125 A-TAATCAGTAAGAGT-AAATAGTATTCAGTAAGAGTAAAG
1 AGCAATCAGTAAGAGTGAAATAGTAGTCAGTAAGAGTAAAG
164 AGCAATCAGTAA
1 AGCAATCAGTAA
176 AAGAGTAATC
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
39 24 0.52
40 21 0.46
41 1 0.02
ACGTcount: A:0.48, C:0.08, G:0.22, T:0.23
Consensus pattern (41 bp):
AGCAATCAGTAAGAGTGAAATAGTAGTCAGTAAGAGTAAAG
Found at i:174 original size:14 final size:14
Alignment explanation
Indices: 157--193 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
147 ATTCAGTAAG
157 AGTAAAGAGCAATC
1 AGTAAAGAGCAATC
*
171 AGTAAAAGAGTAATC
1 AGT-AAAGAGCAATC
186 AGTAAAGA
1 AGTAAAGA
194 CAAAAGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.54, C:0.08, G:0.22, T:0.16
Consensus pattern (14 bp):
AGTAAAGAGCAATC
Found at i:317 original size:19 final size:19
Alignment explanation
Indices: 279--317 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
269 AAGTATAATG
* *
279 GTAAAGAGTAAAGAGTAAA
1 GTAAAGAGTAAACAGCAAA
*
298 GTAAAGAGTAATCAGCAAA
1 GTAAAGAGTAAACAGCAAA
317 G
1 G
318 GAGATGGTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.05, G:0.26, T:0.15
Consensus pattern (19 bp):
GTAAAGAGTAAACAGCAAA
Found at i:347 original size:21 final size:21
Alignment explanation
Indices: 321--437 Score: 73
Period size: 21 Copynumber: 5.8 Consensus size: 21
311 AGCAAAGGAG
321 ATGGTAATCAGTAAAGAAAAA
1 ATGGTAATCAGTAAAGAAAAA
** *
342 ATGGTAAAGAGTAAAGTAAAA
1 ATGGTAATCAGTAAAGAAAAA
* * ***
363 A--GTACTTAGTAAAGAGTGA
1 ATGGTAATCAGTAAAGAAAAA
* *
382 AGGGTAATTAGTAAAG-AAAA
1 ATGGTAATCAGTAAAGAAAAA
** *
402 ATGGTAAAGAGTAAAGTAAAA
1 ATGGTAATCAGTAAAGAAAAA
*
423 A--GTACTCAGTAAAGA
1 ATGGTAATCAGTAAAGA
438 GTGAGGGGTA
Statistics
Matches: 72, Mismatches: 21, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
19 22 0.31
20 14 0.19
21 36 0.50
ACGTcount: A:0.53, C:0.03, G:0.23, T:0.21
Consensus pattern (21 bp):
ATGGTAATCAGTAAAGAAAAA
Found at i:415 original size:60 final size:60
Alignment explanation
Indices: 286--477 Score: 280
Period size: 60 Copynumber: 3.2 Consensus size: 60
276 ATGGTAAAGA
* * * * * *
286 GTAAAGAGTAAAGTAAAGAGTAATCAGCAAAG-GAG-ATGGTAATCAGTAAAGAAAAAATG
1 GTAAAGAGTAAAGTAAAAAGTACTCAGTAAAGAGTGAAGGGTAATTAGTAAAG-AAAAATG
*
345 GTAAAGAGTAAAGTAAAAAGTACTTAGTAAAGAGTGAAGGGTAATTAGTAAAGAAAAATG
1 GTAAAGAGTAAAGTAAAAAGTACTCAGTAAAGAGTGAAGGGTAATTAGTAAAGAAAAATG
* *
405 GTAAAGAGTAAAGTAAAAAGTACTCAGTAAAGAGTGAGGGGTAATTAGTAAAGAAAAATT
1 GTAAAGAGTAAAGTAAAAAGTACTCAGTAAAGAGTGAAGGGTAATTAGTAAAGAAAAATG
465 GTAAAGAGTAAAG
1 GTAAAGAGTAAAG
478 AGTAAAGAGT
Statistics
Matches: 121, Mismatches: 10, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
59 28 0.23
60 79 0.65
61 14 0.12
ACGTcount: A:0.52, C:0.03, G:0.26, T:0.20
Consensus pattern (60 bp):
GTAAAGAGTAAAGTAAAAAGTACTCAGTAAAGAGTGAAGGGTAATTAGTAAAGAAAAATG
Found at i:477 original size:7 final size:7
Alignment explanation
Indices: 465--537 Score: 69
Period size: 7 Copynumber: 10.6 Consensus size: 7
455 AAGAAAAATT
465 GTAAAGA
1 GTAAAGA
472 GTAAAGA
1 GTAAAGA
479 GTAAAGA
1 GTAAAGA
*
486 GTAAAAA
1 GTAAAGA
*
493 GTAAAAA
1 GTAAAGA
**
500 GTAATCA
1 GTAAAGA
*
507 GTCAAGAA
1 GTAAAG-A
*
515 G-AATG-
1 GTAAAGA
520 GTAAAGA
1 GTAAAGA
527 GTAAAGA
1 GTAAAGA
534 GTAA
1 GTAA
538 TCAGTAAAGG
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
5 1 0.02
6 3 0.06
7 48 0.89
8 2 0.04
ACGTcount: A:0.56, C:0.03, G:0.25, T:0.16
Consensus pattern (7 bp):
GTAAAGA
Found at i:524 original size:34 final size:35
Alignment explanation
Indices: 486--581 Score: 104
Period size: 34 Copynumber: 2.7 Consensus size: 35
476 AGAGTAAAGA
* *
486 GTAAAAAGTAAAAAGTAATCAGTCAA-GAAGAATG
1 GTAAAAAGTAAAAAGTAATCAGTAAAGGAAAAATG
* *
520 GTAAAGAGTAAAGAGTAATCAGTAAAGGAAAAATG
1 GTAAAAAGTAAAAAGTAATCAGTAAAGGAAAAATG
** * *
555 GTAATTAGTAAAATACTAACCAGTAAA
1 GTAAAAAGTAAAA-AGTAATCAGTAAA
582 AAGTAATGGC
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
34 23 0.45
35 17 0.33
36 11 0.22
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.20
Consensus pattern (35 bp):
GTAAAAAGTAAAAAGTAATCAGTAAAGGAAAAATG
Found at i:1462 original size:19 final size:19
Alignment explanation
Indices: 1449--1499 Score: 50
Period size: 22 Copynumber: 2.6 Consensus size: 19
1439 GGAAAAGGGG
*
1449 AAAAAAGAAAGAAAATGAA
1 AAAAAAGAAAGAAAAGGAA
*
1468 AAAAAAGAAAAAGGAAAATGAA
1 AAAAAAG--AAA-GAAAAGGAA
1490 AAAAAA-AAAG
1 AAAAAAGAAAG
1500 CCATGTCACG
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 1 0.03
19 10 0.34
21 3 0.10
22 15 0.52
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (19 bp):
AAAAAAGAAAGAAAAGGAA
Found at i:1485 original size:15 final size:16
Alignment explanation
Indices: 1450--1495 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1440 GAAAAGGGGA
*
1450 AAAAAGAAAGAAAATG
1 AAAAAGAAAGAAAAAG
1466 AAAAA-AAAGAAAAAGG
1 AAAAAGAAAGAAAAA-G
*
1482 AAAATGAAA-AAAAA
1 AAAAAGAAAGAAAAA
1496 AAAGCCATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 8 0.31
16 15 0.58
17 3 0.12
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.04
Consensus pattern (16 bp):
AAAAAGAAAGAAAAAG
Found at i:4863 original size:36 final size:36
Alignment explanation
Indices: 4789--4884 Score: 124
Period size: 36 Copynumber: 2.7 Consensus size: 36
4779 TTATCACCAC
**
4789 CCAACAAGCATCATGGAAAGCTT-AGTTAATAAAGG
1 CCAACAAGCATCATGGAAAGCTTAAGCCAATAAAGG
*
4824 CCAACAAGCATCATGGAAAGCTTAAGCCAATAAGGG
1 CCAACAAGCATCATGGAAAGCTTAAGCCAATAAAGG
* *
4860 CCAATAAGCA-CAATGGAATGCTTAA
1 CCAACAAGCATC-ATGGAAAGCTTAA
4885 TAAACATAAG
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
35 24 0.44
36 30 0.56
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.18
Consensus pattern (36 bp):
CCAACAAGCATCATGGAAAGCTTAAGCCAATAAAGG
Found at i:5911 original size:19 final size:19
Alignment explanation
Indices: 5880--5923 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
5870 AAATTAATCC
5880 AAAAAA-GTAAAGAATAAA
1 AAAAAAGGTAAAGAATAAA
* *
5898 AAAAAAGGTTAAGAATGAA
1 AAAAAAGGTAAAGAATAAA
*
5917 TAAAAAG
1 AAAAAAG
5924 AATTTATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14
Consensus pattern (19 bp):
AAAAAAGGTAAAGAATAAA
Found at i:7305 original size:32 final size:32
Alignment explanation
Indices: 7264--7328 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
7254 CCACGAGAGC
7264 TTCCATCCACATTGATCTTAACACACTGACCT
1 TTCCATCCACATTGATCTTAACACACTGACCT
7296 TTCCATCCACATTGATCTTAACACACTGACCT
1 TTCCATCCACATTGATCTTAACACACTGACCT
7328 T
1 T
7329 GAGGCATTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.28, C:0.34, G:0.06, T:0.32
Consensus pattern (32 bp):
TTCCATCCACATTGATCTTAACACACTGACCT
Found at i:10128 original size:30 final size:31
Alignment explanation
Indices: 10089--10163 Score: 89
Period size: 34 Copynumber: 2.4 Consensus size: 31
10079 GACAAGACGA
* *
10089 ATTCTGATTGGA-ATTTTTGACAATTGAGAC
1 ATTCAGATTGGATATTTTTGACAAGTGAGAC
*
10119 ATTCAGATTGGATTTTTTTTTTGACAAGTGAGAC
1 ATTCAGATTGGA---TATTTTTGACAAGTGAGAC
10153 ATTCAGATTGG
1 ATTCAGATTGG
10164 GTTTTATCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 11 0.29
34 27 0.71
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.41
Consensus pattern (31 bp):
ATTCAGATTGGATATTTTTGACAAGTGAGAC
Found at i:10145 original size:34 final size:34
Alignment explanation
Indices: 10102--10168 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
10092 CTGATTGGAA
*
10102 TTTTTGACAATTGAGACATTCAGATTGGATTTTT
1 TTTTTGACAAGTGAGACATTCAGATTGGATTTTT
*
10136 TTTTTGACAAGTGAGACATTCAGATTGGGTTTT
1 TTTTTGACAAGTGAGACATTCAGATTGGATTTT
10169 ATCTTGACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.25, C:0.09, G:0.21, T:0.45
Consensus pattern (34 bp):
TTTTTGACAAGTGAGACATTCAGATTGGATTTTT
Found at i:10188 original size:33 final size:34
Alignment explanation
Indices: 10105--10177 Score: 103
Period size: 34 Copynumber: 2.2 Consensus size: 34
10095 ATTGGAATTT
* * * *
10105 TTGACAATTGAGACATTCAGATTGGATTTTTTTT
1 TTGACAAGTGAGACATTCAGATTGGAGTTTTATC
10139 TTGACAAGTGAGACATTCAGATTGG-GTTTTATC
1 TTGACAAGTGAGACATTCAGATTGGAGTTTTATC
10172 TTGACA
1 TTGACA
10178 TGTGGCACAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
33 11 0.31
34 24 0.69
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.41
Consensus pattern (34 bp):
TTGACAAGTGAGACATTCAGATTGGAGTTTTATC
Found at i:11767 original size:30 final size:30
Alignment explanation
Indices: 11726--11796 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
11716 ACCCCCCTCT
* * *
11726 CCCATTTCCAAAATCTCTTCTTGTTACTTC
1 CCCATTACCAAAATCTCTTCTTCTCACTTC
*
11756 CCCATTACCAAAATTTCTTCTTCTCACTTC
1 CCCATTACCAAAATCTCTTCTTCTCACTTC
11786 CCCA-TACCAAA
1 CCCATTACCAAA
11797 CTTTAGCGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 7 0.19
30 30 0.81
ACGTcount: A:0.25, C:0.37, G:0.01, T:0.37
Consensus pattern (30 bp):
CCCATTACCAAAATCTCTTCTTCTCACTTC
Found at i:14011 original size:43 final size:44
Alignment explanation
Indices: 13928--14017 Score: 137
Period size: 43 Copynumber: 2.0 Consensus size: 44
13918 ACATTATTAA
*
13928 AATATATTTTAATTATGCCATTATTATTAAAACATATAAAATTGCC
1 AATATATTTTAATTATG-C-TCATTATTAAAACATATAAAATTGCC
*
13974 AATATATTTTAATTATG-TCATTATTAAAATATATAAAATTGCC
1 AATATATTTTAATTATGCTCATTATTAAAACATATAAAATTGCC
14017 A
1 A
14018 TTATTAAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
43 25 0.60
46 17 0.40
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.42
Consensus pattern (44 bp):
AATATATTTTAATTATGCTCATTATTAAAACATATAAAATTGCC
Found at i:14630 original size:16 final size:16
Alignment explanation
Indices: 14609--14640 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
14599 AAACCTCGGG
*
14609 TTTTCGGGTTTGGGTC
1 TTTTCGGGTTCGGGTC
14625 TTTTCGGGTTCGGGTC
1 TTTTCGGGTTCGGGTC
14641 GTAACAATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.16, G:0.38, T:0.47
Consensus pattern (16 bp):
TTTTCGGGTTCGGGTC
Done.