Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009157.1 Corchorus capsularis cultivar CVL-1 contig09178, 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: 28444
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:1644 original size:15 final size:16
Alignment explanation
Indices: 1624--1655 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1614 ACAACAATAA
1624 TACTTTT-TTTTAATT
1 TACTTTTCTTTTAATT
1639 TACTTTTCTTTTAATT
1 TACTTTTCTTTTAATT
1655 T
1 T
1656 TAAATTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (16 bp):
TACTTTTCTTTTAATT
Found at i:2068 original size:17 final size:16
Alignment explanation
Indices: 2046--2098 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
2036 ATATTATGGT
2046 TTCATTTCTAATTAATA
1 TTCATTT-TAATTAATA
* *
2063 TTCATTATTATTTAATG
1 TTCATT-TTAATTAATA
*
2080 TTCGTTTTAATTGAATA
1 TTCATTTTAATT-AATA
2097 TT
1 TT
2099 TCTCATTTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
16 5 0.17
17 23 0.79
18 1 0.03
ACGTcount: A:0.30, C:0.08, G:0.06, T:0.57
Consensus pattern (16 bp):
TTCATTTTAATTAATA
Found at i:3513 original size:65 final size:63
Alignment explanation
Indices: 3433--3591 Score: 223
Period size: 62 Copynumber: 2.5 Consensus size: 63
3423 ATCTATTGAC
*
3433 ATCTTTTATTTTTCTCCAATTTGATTTTAATTGAACTTAAGAAATTGGA-TCTTGGTAGATCTTA
1 ATCTTTTA-TTTTCTCCAATTTGATTTTAA---AACTTAAGAAATTCGATTCTTGGTAGATCTTA
3497 AA
62 AA
*
3499 ATCTTTTATTTTCTCCAATTTGATTTT-AAACTTAAGAAATTCGATTTTTGGTAGATCTTAAA
1 ATCTTTTATTTTCTCCAATTTGATTTTAAAACTTAAGAAATTCGATTCTTGGTAGATCTTAAA
* *
3561 ATCTTTTAATTTTCTCTAATTTGACTTTAAA
1 ATCTTTT-ATTTTCTCCAATTTGATTTTAAA
3592 CACATTCCAC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
61 15 0.17
62 23 0.27
63 18 0.21
64 3 0.03
65 19 0.22
66 8 0.09
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.49
Consensus pattern (63 bp):
ATCTTTTATTTTCTCCAATTTGATTTTAAAACTTAAGAAATTCGATTCTTGGTAGATCTTAAA
Found at i:7025 original size:49 final size:49
Alignment explanation
Indices: 6951--7326 Score: 231
Period size: 49 Copynumber: 7.8 Consensus size: 49
6941 ACTTGCCTTT
* * * *
6951 CGTCCGGAAAGGGCATTTTAAGAAAAAAGCGAGTAAAACTAACGTCTTC
1 CGTCCGGGAAGGGCATTTTAGGAAAAAAGCAAGTAAAAATAACGTCTTC
* * *
7000 CATCCGGGAAGGGCGTTTTAGG-AAAAAGCAAGTAAAAATTAGCGTCTTC
1 CGTCCGGGAAGGGCATTTTAGGAAAAAAGCAAGTAAAAA-TAACGTCTTC
* * * * * *
7049 CGTCCGGGAAGGGCACTTT-GGGAAAAAGTAGGTAAAAATAAGTGTCTCC
1 CGTCCGGGAAGGGCATTTTAGGAAAAAAGCAAGTAAAAATAA-CGTCTTC
* * *
7098 CGTCCGGGAAGGGCATTTTTGGAAAATAGCAAGT-AAAATAA-GTGTTCTC
1 CGTCCGGGAAGGGCATTTTAGGAAAAAAGCAAGTAAAAATAACGT-CT-TC
* * * * *
7147 CGTCCTGGAAGGGCATTTT-GG-GAAAA-CAGGTAAAGATTA-GTGCCTTC
1 CGTCCGGGAAGGGCATTTTAGGAAAAAAGCAAGTAAAAATAACGT--CTTC
* ** * * *
7194 CGTCCGAGAAGGGTGTTTT-GGGAAAAA-CAAGTAAAGATTA-GTGCCTTC
1 CGTCCGGGAAGGGCATTTTAGGAAAAAAGCAAGTAAAAATAACGT--CTTC
* * * * *
7242 CGTCCGGGAAGGGCGTTTTGGGGAAAAA-CATGTAAAAATTA-GTGCCTTC
1 CGTCCGGGAAGGGCATTTTAGGAAAAAAGCAAGTAAAAATAACGT--CTTC
* * * * *
7291 CGCCCGGGAAGGGCGTTTTTGGGAAAAA-CAGGTAAA
1 CGTCCGGGAAGGGCATTTTAGGAAAAAAGCAAGTAAA
7327 GATTAAAAAT
Statistics
Matches: 274, Mismatches: 43, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
46 4 0.01
47 31 0.11
48 63 0.23
49 166 0.61
50 10 0.04
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (49 bp):
CGTCCGGGAAGGGCATTTTAGGAAAAAAGCAAGTAAAAATAACGTCTTC
Found at i:7240 original size:48 final size:48
Alignment explanation
Indices: 6996--7331 Score: 354
Period size: 49 Copynumber: 6.9 Consensus size: 48
6986 AAACTAACGT
* * * *
6996 CTTCCATCCGGGAAGGGCGTTTTAGGAAAAAGCAAGTAAAAATTAGCGT
1 CTTCCGTCCGGGAAGGGCGTTTTGGGAAAAA-CAAGTAAAAATTAGTGC
** * * * *
7045 CTTCCGTCCGGGAAGGGCACTTTGGGAAAAAGTAGGTAAAAATAAGTGT
1 CTTCCGTCCGGGAAGGGCGTTTTGGGAAAAA-CAAGTAAAAATTAGTGC
* * * *
7094 CTCCCGTCCGGGAAGGGCATTTTTGGAAAATAGCAAGT-AAAATAAGTG-
1 CTTCCGTCCGGGAAGGGCGTTTTGGGAAAA-A-CAAGTAAAAATTAGTGC
* * * * *
7142 TTCTCCGTCCTGGAAGGGCATTTTGGG-AAAACAGGTAAAGATTAGTGC
1 CT-TCCGTCCGGGAAGGGCGTTTTGGGAAAAACAAGTAAAAATTAGTGC
* * *
7190 CTTCCGTCCGAGAAGGGTGTTTTGGGAAAAACAAGTAAAGATTAGTGC
1 CTTCCGTCCGGGAAGGGCGTTTTGGGAAAAACAAGTAAAAATTAGTGC
*
7238 CTTCCGTCCGGGAAGGGCGTTTTGGGGAAAAACATGTAAAAATTAGTGC
1 CTTCCGTCCGGGAAGGGCGTTTT-GGGAAAAACAAGTAAAAATTAGTGC
* * *
7287 CTTCCGCCCGGGAAGGGCGTTTTTGGGAAAAACAGGTAAAGATTA
1 CTTCCGTCCGGGAAGGGCG-TTTTGGGAAAAACAAGTAAAAATTA
7332 AAAATTGAGA
Statistics
Matches: 247, Mismatches: 33, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
46 4 0.02
47 29 0.12
48 46 0.19
49 159 0.64
50 9 0.04
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (48 bp):
CTTCCGTCCGGGAAGGGCGTTTTGGGAAAAACAAGTAAAAATTAGTGC
Found at i:10299 original size:20 final size:20
Alignment explanation
Indices: 10274--10323 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
10264 TCAAAGCTAC
10274 AACCCAAAAGCCCAAGTTTA
1 AACCCAAAAGCCCAAGTTTA
10294 AACCCAAAAGCCCAAGTTTA
1 AACCCAAAAGCCCAAGTTTA
10314 AAGCCCAAAA
1 AA-CCCAAAA
10324 TGATAGCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 22 0.76
21 7 0.24
ACGTcount: A:0.48, C:0.30, G:0.10, T:0.12
Consensus pattern (20 bp):
AACCCAAAAGCCCAAGTTTA
Found at i:11366 original size:14 final size:14
Alignment explanation
Indices: 11333--11368 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
11323 AGATAGATCT
11333 TTTCATAAACAGAA
1 TTTCATAAACAGAA
*
11347 -TTCATAAACATAA
1 TTTCATAAACAGAA
11360 TTTCATAAA
1 TTTCATAAA
11369 TTTTTATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.50, C:0.14, G:0.03, T:0.33
Consensus pattern (14 bp):
TTTCATAAACAGAA
Found at i:11393 original size:2 final size:2
Alignment explanation
Indices: 11378--11423 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
11368 ATTTTTATTC
* *
11378 TA TA TA AA TA -A TA TA TA -A TA TA TA TA TA TA TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11418 TA TA TA
1 TA TA TA
11424 GATAGAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:11490 original size:14 final size:14
Alignment explanation
Indices: 11455--11526 Score: 76
Period size: 14 Copynumber: 5.1 Consensus size: 14
11445 TCTATAAATA
11455 ATAGAATAAATAGAATT
1 ATAGAAT-AA-AGAA-T
11472 ATAGAATAAAGAAT
1 ATAGAATAAAGAAT
*
11486 ATAGAATAAATAA-
1 ATAGAATAAAGAAT
* *
11499 ATAGAATATAGAAA
1 ATAGAATAAAGAAT
11513 ATAGAATAAA-AAT
1 ATAGAATAAAGAAT
11526 A
1 A
11527 AATTTCGAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
13 14 0.29
14 22 0.45
15 4 0.08
16 2 0.04
17 7 0.14
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.24
Consensus pattern (14 bp):
ATAGAATAAAGAAT
Found at i:11807 original size:31 final size:31
Alignment explanation
Indices: 11769--11830 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
11759 CTAAATTTAT
* *
11769 CCAATTTTGAAACATTTAGTACTTATTTGAG
1 CCAATTTTAAAACATTTAGTACCTATTTGAG
*
11800 CCAATTTTAAAACGTTTAGTACCTATTTGAG
1 CCAATTTTAAAACATTTAGTACCTATTTGAG
11831 TTGGTTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (31 bp):
CCAATTTTAAAACATTTAGTACCTATTTGAG
Found at i:11860 original size:11 final size:11
Alignment explanation
Indices: 11846--11883 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
11836 TTTAAAAAAA
11846 TAAAAAAATAT
1 TAAAAAAATAT
11857 T--AAAAA-AT
1 TAAAAAAATAT
11865 TAAAAAAATAT
1 TAAAAAAATAT
11876 TAAAAAAA
1 TAAAAAAA
11884 GCCACGTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
8 3 0.12
9 5 0.21
10 5 0.21
11 11 0.46
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
TAAAAAAATAT
Found at i:11861 original size:19 final size:19
Alignment explanation
Indices: 11837--11883 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
11827 TGAGTTGGTT
11837 TTAAAAAAATAAAAAAATA
1 TTAAAAAAATAAAAAAATA
*
11856 TTAAAAAATTAAAAAAATA
1 TTAAAAAAATAAAAAAATA
11875 TTAAAAAAA
1 TTAAAAAAA
11884 GCCACGTAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (19 bp):
TTAAAAAAATAAAAAAATA
Found at i:16554 original size:27 final size:24
Alignment explanation
Indices: 16524--16587 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 24
16514 ATAAACTTAA
*
16524 ATATAATTATATCTTATTTATATACAT
1 ATATAAATATATCTTA--TATATA-AT
*
16551 ATATAAATATTTCTTATATATAAT
1 ATATAAATATATCTTATATATAAT
16575 ATATAAAATATAT
1 ATAT-AAATATAT
16588 AAAATTAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 6 0.18
25 13 0.39
27 14 0.42
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (24 bp):
ATATAAATATATCTTATATATAAT
Found at i:20048 original size:225 final size:225
Alignment explanation
Indices: 19657--20106 Score: 891
Period size: 225 Copynumber: 2.0 Consensus size: 225
19647 AAGACAAGAA
19657 ATATTGGAGTCAAATAAGAATTTTATTGATTGATGAATGCATGTACAATCTTTGGAAATTCTAAT
1 ATATTGGAGTCAAATAAGAATTTTATTGATTGATGAATGCATGTACAATCTTTGGAAATTCTAAT
19722 AATAAGAAATTGTCCTCTGATCCTTCTCCTTATGCTTCAAGATTTGCTTCAAGGGTCGAATGACT
66 AATAAGAAATTGTCCTCTGATCCTTCTCCTTATGCTTCAAGATTTGCTTCAAGGGTCGAATGACT
*
19787 TGATCTTGAACTTGATGATAATTTGATAATTTGAGAACTTGAGAACTTGATTTGATTAAAGGGTC
131 TAATCTTGAACTTGATGATAATTTGATAATTTGAGAACTTGAGAACTTGATTTGATTAAAGGGTC
19852 GAATGACTTGGTCTTCAAATTCAAGTGTCT
196 GAATGACTTGGTCTTCAAATTCAAGTGTCT
19882 ATATTGGAGTCAAATAAGAATTTTATTGATTGATGAATGCATGTACAATCTTTGGAAATTCTAAT
1 ATATTGGAGTCAAATAAGAATTTTATTGATTGATGAATGCATGTACAATCTTTGGAAATTCTAAT
19947 AATAAGAAATTGTCCTCTGATCCTTCTCCTTATGCTTCAAGATTTGCTTCAAGGGTCGAATGACT
66 AATAAGAAATTGTCCTCTGATCCTTCTCCTTATGCTTCAAGATTTGCTTCAAGGGTCGAATGACT
20012 TAATCTTGAACTTGATGATAATTTGATAATTTGAGAACTTGAGAACTTGATTTGATTAAAGGGTC
131 TAATCTTGAACTTGATGATAATTTGATAATTTGAGAACTTGAGAACTTGATTTGATTAAAGGGTC
20077 GAATGACTTGGTCTTCAAATTCAAGTGTCT
196 GAATGACTTGGTCTTCAAATTCAAGTGTCT
20107 TGACGACTTG
Statistics
Matches: 224, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
225 224 1.00
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.37
Consensus pattern (225 bp):
ATATTGGAGTCAAATAAGAATTTTATTGATTGATGAATGCATGTACAATCTTTGGAAATTCTAAT
AATAAGAAATTGTCCTCTGATCCTTCTCCTTATGCTTCAAGATTTGCTTCAAGGGTCGAATGACT
TAATCTTGAACTTGATGATAATTTGATAATTTGAGAACTTGAGAACTTGATTTGATTAAAGGGTC
GAATGACTTGGTCTTCAAATTCAAGTGTCT
Found at i:20316 original size:24 final size:24
Alignment explanation
Indices: 20289--20338 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
20279 AGAAAAATAA
20289 TCCTCCACATACGTGAATCTTCTT
1 TCCTCCACATACGTGAATCTTCTT
*
20313 TCCTCCACATACGTGGATCTTCTT
1 TCCTCCACATACGTGAATCTTCTT
20337 TC
1 TC
20339 AATAATTTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.18, C:0.34, G:0.10, T:0.38
Consensus pattern (24 bp):
TCCTCCACATACGTGAATCTTCTT
Found at i:20387 original size:16 final size:16
Alignment explanation
Indices: 20366--20399 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
20356 TCTAAAATAT
20366 TTCAGAGCTTTTCTGC
1 TTCAGAGCTTTTCTGC
20382 TTCAGAGCTTTTCTGC
1 TTCAGAGCTTTTCTGC
20398 TT
1 TT
20400 TCTGAATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.47
Consensus pattern (16 bp):
TTCAGAGCTTTTCTGC
Found at i:25284 original size:12 final size:12
Alignment explanation
Indices: 25269--25305 Score: 56
Period size: 12 Copynumber: 2.9 Consensus size: 12
25259 AAAATTAACC
25269 AAAAAAAAAAAG
1 AAAAAAAAAAAG
25281 AAAAAAAAAAAG
1 AAAAAAAAAAAG
25293 AAAGAAAAGAAAA
1 AAA-AAAA-AAAA
25306 CAATGAGCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 15 0.65
13 4 0.17
14 4 0.17
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:25288 original size:16 final size:16
Alignment explanation
Indices: 25269--25305 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
25259 AAAATTAACC
25269 AAAAAAAAAAAGAAAA
1 AAAAAAAAAAAGAAAA
*
25285 AAAAAAAGAAAGAAAA
1 AAAAAAAAAAAGAAAA
*
25301 GAAAA
1 AAAAA
25306 CAATGAGCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAGAAAA
Found at i:27799 original size:23 final size:25
Alignment explanation
Indices: 27769--27814 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
27759 GTTTAATAAT
*
27769 TATATATATCT-AATAT-TATTTTA
1 TATATATATATAAATATATATTTTA
27792 TATATATATATAAATATATATTT
1 TATATATATATAAATATATATTT
27815 AATTATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 5 0.25
25 5 0.25
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
TATATATATATAAATATATATTTTA
Done.