Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006196.1 Corchorus capsularis cultivar CVL-1 contig06214, 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: 25289
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:942 original size:68 final size:71
Alignment explanation
Indices: 861--1015 Score: 201
Period size: 72 Copynumber: 2.2 Consensus size: 71
851 TAATTAAAAT
* * * *
861 AGTAAAATGGTAAAAT-ATA-AGTAATAAGGATATTAGATTTAATT-ATATAAAAATAGAGTTTT
1 AGTAAAATAGTAAAATAAAATAGTAATAAAGATATTAGATTTAATTAAAATAAAAATAGAGTTTT
*
923 TAGTTG
66 TAGTTA
* *
929 AGTAAAATAGTAAAATAAAATAGTTATAAAGATATTATATTTAATTAAAAATAAAAATAGAGTTT
1 AGTAAAATAGTAAAATAAAATAGTAATAAAGATATTAGATTTAATT-AAAATAAAAATAGAGTTT
994 TTAGTTA
65 TTAGTTA
1001 AGTAAAACTA-TAAAA
1 AGTAAAA-TAGTAAAA
1016 ACCTAAATAA
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
68 15 0.20
69 2 0.03
70 22 0.29
72 34 0.45
73 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.12, T:0.35
Consensus pattern (71 bp):
AGTAAAATAGTAAAATAAAATAGTAATAAAGATATTAGATTTAATTAAAATAAAAATAGAGTTTT
TAGTTA
Found at i:3430 original size:16 final size:16
Alignment explanation
Indices: 3411--3442 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3401 TAACGTAACG
*
3411 TACGTTGCACGTGAAC
1 TACGTTACACGTGAAC
3427 TACGTTACACGTGAAC
1 TACGTTACACGTGAAC
3443 AAATTAAATG
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:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (16 bp):
TACGTTACACGTGAAC
Found at i:8213 original size:29 final size:29
Alignment explanation
Indices: 8157--8217 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
8147 ACCTATTTCT
* * *
8157 AAATAAACAAATAAATTTTTCTCTAAAAA
1 AAATAAACAAATAAATTTATCGCAAAAAA
8186 AAATAAACAAATAAATTTAAT-GCAAAAAA
1 AAATAAACAAATAAATTT-ATCGCAAAAAA
8215 AAA
1 AAA
8218 AAATTAACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.66, C:0.08, G:0.02, T:0.25
Consensus pattern (29 bp):
AAATAAACAAATAAATTTATCGCAAAAAA
Found at i:8942 original size:16 final size:17
Alignment explanation
Indices: 8916--8961 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 17
8906 GACCCTTTTA
*
8916 ATATA-TATTATATTAT
1 ATATATTATTATATAAT
8932 AT-TATTATTAT-TAAT
1 ATATATTATTATATAAT
8947 ATATATTATTATATA
1 ATATATTATTATATA
8962 TTTCTGTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 7 0.27
16 17 0.65
17 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATATATTATTATATAAT
Found at i:8959 original size:10 final size:10
Alignment explanation
Indices: 8917--8963 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
8907 ACCCTTTTAA
8917 TATATATTA-
1 TATATATTAT
8926 TATTATATTAT
1 TA-TATATTAT
*
8937 TAT-TATTAA
1 TATATATTAT
8946 TATATATTAT
1 TATATATTAT
8956 TATATATT
1 TATATATT
8964 TCTGTTTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
9 10 0.30
10 21 0.64
11 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TATATATTAT
Found at i:9979 original size:68 final size:67
Alignment explanation
Indices: 9893--10038 Score: 256
Period size: 68 Copynumber: 2.2 Consensus size: 67
9883 AGACACACAA
*
9893 AATCTCCGTTTAGTTTTCAGAAATTTGTGTTCTGTTTTTTCTTTGGAGTTACAATTGTAATTGGA
1 AATCTCTGTTTAGTTTTCAGAAATTTGTGTTCTGTTTTTTCTTTGGAGTTACAATTGTAATTGGA
9958 CT
66 CT
*
9960 AATTCTCTGTTTAGTTTTCAGAAATTTGTGTTCTGTTTTTTCTTTGGAGTTGCAATTGTAATTGG
1 AA-TCTCTGTTTAGTTTTCAGAAATTTGTGTTCTGTTTTTTCTTTGGAGTTACAATTGTAATTGG
10025 ACT
65 ACT
*
10028 AATATCTGTTT
1 AATCTCTGTTT
10039 TTTCTTTGGG
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
67 10 0.13
68 65 0.87
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.51
Consensus pattern (67 bp):
AATCTCTGTTTAGTTTTCAGAAATTTGTGTTCTGTTTTTTCTTTGGAGTTACAATTGTAATTGGA
CT
Found at i:10052 original size:40 final size:41
Alignment explanation
Indices: 9991--10067 Score: 147
Period size: 40 Copynumber: 1.9 Consensus size: 41
9981 AAATTTGTGT
9991 TCTGTTTTTTCTTTGGAGTTGCAATTGTAATTGGACTAATA
1 TCTGTTTTTTCTTTGGAGTTGCAATTGTAATTGGACTAATA
10032 TCTGTTTTTTCTTTGG-GTTGCAATTGTAATTGGACT
1 TCTGTTTTTTCTTTGGAGTTGCAATTGTAATTGGACT
10068 CGGTCTTCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
40 20 0.56
41 16 0.44
ACGTcount: A:0.18, C:0.10, G:0.21, T:0.51
Consensus pattern (41 bp):
TCTGTTTTTTCTTTGGAGTTGCAATTGTAATTGGACTAATA
Found at i:10474 original size:24 final size:25
Alignment explanation
Indices: 10426--10478 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
10416 AACTATAACT
*
10426 AACAATTGACGGCAAAAAAAAAAAA
1 AACAATTAACGGCAAAAAAAAAAAA
*
10451 AACAATTAACGGCAAAAAAGAAAAA
1 AACAATTAACGGCAAAAAAAAAAAA
10476 AAC
1 AAC
10479 TACAACTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.68, C:0.13, G:0.11, T:0.08
Consensus pattern (25 bp):
AACAATTAACGGCAAAAAAAAAAAA
Found at i:10483 original size:28 final size:27
Alignment explanation
Indices: 10422--10488 Score: 84
Period size: 25 Copynumber: 2.5 Consensus size: 27
10412 TACTAACTAT
*
10422 AACTAACAATTGACGGCAAAAAAAAAAA
1 AACT-ACAATTAACGGCAAAAAAAAAAA
10450 AA--ACAATTAACGGCAAAAAAGAAAAA
1 AACTACAATTAACGGCAAAAAA-AAAAA
*
10476 AACTACAACTAAC
1 AACTACAATTAAC
10489 AATTATTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 17 0.50
26 7 0.21
28 10 0.29
ACGTcount: A:0.64, C:0.16, G:0.09, T:0.10
Consensus pattern (27 bp):
AACTACAATTAACGGCAAAAAAAAAAA
Found at i:10669 original size:31 final size:33
Alignment explanation
Indices: 10626--10691 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 33
10616 TCTCGTCAAC
*
10626 TTGCCCTCATGAA-TGTTC-AAATTTAGGACAAT
1 TTGCCCTCATGAACT-TTCTAAATTTAAGACAAT
10658 TTGCCCT-ATGAACTTTCTAAATTTAAGACAAT
1 TTGCCCTCATGAACTTTCTAAATTTAAGACAAT
10690 TT
1 TT
10692 ACCATGACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 8 0.26
32 23 0.74
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (33 bp):
TTGCCCTCATGAACTTTCTAAATTTAAGACAAT
Found at i:12735 original size:49 final size:49
Alignment explanation
Indices: 12680--13283 Score: 709
Period size: 49 Copynumber: 12.4 Consensus size: 49
12670 AAACATTAAC
** * *
12680 GCCTTCCGTTTGGGAAGGGCGTTTTTTGGAAAAAGCAGGTAAAAA-AAGT
1 GCCTTCCGTCCGGGAAGGGCG-TTTTGGGAAAAAGCAAGTAAAAAGAAGT
* *
12729 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAACAAGTAAAAATAAGT
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAAGAAGT
* *
12778 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCATGTAAAAAGAAGT
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAAGAAGT
*
12827 GACTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAAGAAGT
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAAGAAGT
* *
12876 GCCTTCCGTCGGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAATAAGT
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAAGAAGT
* * *
12925 GCCTTCCATCCGGGAAGGGCGTTTTGGGAAATAGCATGTAAAAAGAAGT
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAAGAAGT
* * * * * *
12974 GACTTCTGTCCGGGAAGGGCATTTTGGGAAATAGCAAGTAAAAATAAAT
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAAGAAGT
*
13023 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAA-TAAGTAAAAA-AATGGT
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAAGAA--GT
* * * * **
13072 GCCTTCCGTCCGAGAAGGGCGTTTTAGGAAAAA-CAGGTAAAGATTAGT
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAAGAAGT
* * * * **
13120 GCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAA-TAGGTAAAGATTAGT
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAAGAAGT
* * * * **
13168 GCTTTCCGTCCGGGAAGGGCGTTTTAGGAAAAA-CAGGTAAAGATTAGT
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAAGAAGT
* * * * * **
13216 GTCTTCCGTCCGGGAAGAGCGTTTTAGGAAAAA-CAGGTAAAGACTAGT
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAAGAAGT
*
13264 GCCTTCCGTCTGGGAAGGGC
1 GCCTTCCGTCCGGGAAGGGC
13284 ACTTTTGGAA
Statistics
Matches: 501, Mismatches: 50, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
47 2 0.00
48 184 0.37
49 314 0.63
50 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (49 bp):
GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAAGAAGT
Found at i:15006 original size:22 final size:22
Alignment explanation
Indices: 14978--15046 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
14968 TCAATCCCCT
14978 GCAGGAAGGCTTTGGTGACATG
1 GCAGGAAGGCTTTGGTGACATG
* * *
15000 GCAGGAAGACCTTGGTAACATG
1 GCAGGAAGGCTTTGGTGACATG
* *
15022 GCAGG-AGAGCTCTAGTGACATG
1 GCAGGAAG-GCTTTGGTGACATG
15044 GCA
1 GCA
15047 TGTGCAGACA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
21 2 0.05
22 36 0.95
ACGTcount: A:0.28, C:0.17, G:0.36, T:0.19
Consensus pattern (22 bp):
GCAGGAAGGCTTTGGTGACATG
Found at i:16064 original size:13 final size:13
Alignment explanation
Indices: 16044--16075 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
16034 ATGATTATGC
16044 ATAA-TGCAATTT
1 ATAAGTGCAATTT
16056 ATAAGTGCAATTT
1 ATAAGTGCAATTT
16069 ATAAGTG
1 ATAAGTG
16076 ATATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.38
Consensus pattern (13 bp):
ATAAGTGCAATTT
Found at i:16083 original size:2 final size:2
Alignment explanation
Indices: 16076--16103 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16066 TTTATAAGTG
16076 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16104 TACTAATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24345 original size:8 final size:8
Alignment explanation
Indices: 24332--24377 Score: 56
Period size: 8 Copynumber: 5.2 Consensus size: 8
24322 TGAAGATATT
24332 TTGAAGAA
1 TTGAAGAA
24340 TTGAAGACAA
1 TTGAAG--AA
24350 TTGAAGAA
1 TTGAAGAA
24358 TTGAAGACAA
1 TTGAAG--AA
24368 TTGAAGAA
1 TTGAAGAA
24376 TT
1 TT
24378 AATTTAAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
8 18 0.53
10 16 0.47
ACGTcount: A:0.48, C:0.04, G:0.22, T:0.26
Consensus pattern (8 bp):
TTGAAGAA
Found at i:24351 original size:10 final size:10
Alignment explanation
Indices: 24338--24374 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
24328 TATTTTGAAG
24338 AATTGAAGAC
1 AATTGAAGAC
24348 AATTGAAG--
1 AATTGAAGAC
24356 AATTGAAGAC
1 AATTGAAGAC
24366 AATTGAAGA
1 AATTGAAGA
24375 ATTAATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 8 0.32
10 17 0.68
ACGTcount: A:0.51, C:0.05, G:0.22, T:0.22
Consensus pattern (10 bp):
AATTGAAGAC
Found at i:24355 original size:18 final size:18
Alignment explanation
Indices: 24332--24377 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
24322 TGAAGATATT
24332 TTGAAGAATTGAAGACAA
1 TTGAAGAATTGAAGACAA
24350 TTGAAGAATTGAAGACAA
1 TTGAAGAATTGAAGACAA
24368 TTGAAGAATT
1 TTGAAGAATT
24378 AATTTAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.48, C:0.04, G:0.22, T:0.26
Consensus pattern (18 bp):
TTGAAGAATTGAAGACAA
Done.