Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005981.1 Corchorus capsularis cultivar CVL-1 contig05999, 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: 20979
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:7863 original size:15 final size:14
Alignment explanation
Indices: 7843--7873 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
7833 CCCTGTGTCT
7843 TATTACTATTATTAC
1 TATTACTATT-TTAC
7858 TATTACTATTTTAC
1 TATTACTATTTTAC
7872 TA
1 TA
7874 CTATATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (14 bp):
TATTACTATTTTAC
Found at i:10909 original size:18 final size:18
Alignment explanation
Indices: 10886--10921 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
10876 TATAAGAGTT
10886 TAGCTACTCATGGATTGC
1 TAGCTACTCATGGATTGC
10904 TAGCTACTCATGGATTGC
1 TAGCTACTCATGGATTGC
10922 AAGCAATCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (18 bp):
TAGCTACTCATGGATTGC
Found at i:10933 original size:18 final size:18
Alignment explanation
Indices: 10891--10927 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
10881 GAGTTTAGCT
* *
10891 ACTCATGGATTGCTAGCT
1 ACTCATGGATTGCAAGCA
10909 ACTCATGGATTGCAAGCA
1 ACTCATGGATTGCAAGCA
10927 A
1 A
10928 TCCATGAGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (18 bp):
ACTCATGGATTGCAAGCA
Found at i:12169 original size:16 final size:16
Alignment explanation
Indices: 12130--12169 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
12120 TGTATTATGA
*
12130 TTATTTTTATTATTAT
1 TTATTTTTAGTATTAT
*
12146 TTACTTTTAGTATTAT
1 TTATTTTTAGTATTAT
12162 TTATTTTT
1 TTATTTTT
12170 GTTATAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (16 bp):
TTATTTTTAGTATTAT
Found at i:12179 original size:16 final size:16
Alignment explanation
Indices: 12130--12179 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
12120 TGTATTATGA
*
12130 TTATTTTTATTATTAT
1 TTATTTTTGTTATTAT
*
12146 TTACTTTTAG-TATTAT
1 TTA-TTTTTGTTATTAT
*
12162 TTATTTTTGTTATAAT
1 TTATTTTTGTTATTAT
12178 TT
1 TT
12180 TTATAAGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 5 0.18
16 19 0.68
17 4 0.14
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (16 bp):
TTATTTTTGTTATTAT
Found at i:13926 original size:23 final size:23
Alignment explanation
Indices: 13896--13944 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
13886 CTAATCGGGG
*
13896 GCCCGGTTAGGGGCT-AGGTGGGA
1 GCCCGGTT-GGGGCTCAAGTGGGA
*
13919 GCCCGGTTGGGGGTCAAGTGGGA
1 GCCCGGTTGGGGCTCAAGTGGGA
13942 GCC
1 GCC
13945 GCTTGACCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.12, C:0.20, G:0.51, T:0.16
Consensus pattern (23 bp):
GCCCGGTTGGGGCTCAAGTGGGA
Found at i:14016 original size:92 final size:90
Alignment explanation
Indices: 13758--14036 Score: 274
Period size: 92 Copynumber: 3.0 Consensus size: 90
13748 CAACTAGGAC
* * * * * *
13758 CCGCTTGACCCCTCCA-ATAGAGCAAACTCACTGTTCTAATCGGTCTCCCACTTGACCCCTAATC
1 CCGCTTGACCCCTCAAGAT-GAACAAACCCGCTGTTCTAATCGGGCTCCCGCTTGACCCC-AA-C
* *
13822 GGGGCCCCGATTTGGGGTCAAATGGGAG
63 GGGGCCCCGGTTGGGGGTCAAATGGGAG
* ** * *** * *
13850 TCCGCTTGACCCCTCAAGATGACCAAACCCGCTGTTCTAATCGGGGGCCCGGTT-AGGGGCTAGG
1 -CCGCTTGACCCCTCAAGATGAACAAACCCGCTGTTCTAATCGGGCTCCCGCTTGA-CCCCAACG
* *
13914 TGGGAGCCCGGTTGGGGGTCAAGTGGGAG
64 -GGG-CCCCGGTTGGGGGTCAAATGGGAG
*
13943 CCGCTTGACCCCTCAAGATGAACAAACCCGCTGTTCTAACCGGGCTCCCGCTTGACCACCAACCG
1 CCGCTTGACCCCTCAAGATGAACAAACCCGCTGTTCTAATCGGGCTCCCGCTTGACC-CCAA-CG
*
14008 GGGTCCCGGTTGGGGGTCAAATGGGAG
64 GGGCCCCGGTTGGGGGTCAAATGGGAG
14035 CC
1 CC
14037 CGATTTTTTT
Statistics
Matches: 149, Mismatches: 30, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
91 1 0.01
92 77 0.52
93 68 0.46
94 3 0.02
ACGTcount: A:0.20, C:0.31, G:0.29, T:0.20
Consensus pattern (90 bp):
CCGCTTGACCCCTCAAGATGAACAAACCCGCTGTTCTAATCGGGCTCCCGCTTGACCCCAACGGG
GCCCCGGTTGGGGGTCAAATGGGAG
Found at i:16892 original size:22 final size:21
Alignment explanation
Indices: 16858--16933 Score: 57
Period size: 22 Copynumber: 3.6 Consensus size: 21
16848 TTAATGAATT
**
16858 ATTAATATTTAATAACTCTTCA
1 ATTAATAACTAATAACTCTT-A
* *
16880 ATTAATAACTAAT--TTATTA
1 ATTAATAACTAATAACTCTTA
* *
16899 ACTAATAATTAATAACTCTTAA
1 ATTAATAACTAATAACTCTT-A
*
16921 ATTATTAACTAAT
1 ATTAATAACTAAT
16934 TTAATAATTA
Statistics
Matches: 40, Mismatches: 11, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 12 0.30
20 3 0.08
21 3 0.08
22 22 0.55
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTAATAACTAATAACTCTTA
Found at i:16913 original size:41 final size:41
Alignment explanation
Indices: 16860--16967 Score: 144
Period size: 41 Copynumber: 2.6 Consensus size: 41
16850 AATGAATTAT
* *
16860 TAATATTTAATAACTCTTCAATTAATAACTAATTTATTAAC
1 TAATAATTAATAACTCTTCAATTAATAACTAATTTAATAAC
* * *
16901 TAATAATTAATAACTCTTAAATTATTAACTAATTTAATAAT
1 TAATAATTAATAACTCTTCAATTAATAACTAATTTAATAAC
*
16942 TAAACATATTAATAACTCTTCAATTA
1 T-AATA-ATTAATAACTCTTCAATTA
16968 TTAATAAATC
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 37 0.64
42 3 0.05
43 18 0.31
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (41 bp):
TAATAATTAATAACTCTTCAATTAATAACTAATTTAATAAC
Found at i:16914 original size:26 final size:28
Alignment explanation
Indices: 16879--16940 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
16869 ATAACTCTTC
*
16879 AATTAATAA-C-TAATTTATTAACTAAT
1 AATTAATAACCTTAAATTATTAACTAAT
16905 AATTAATAACTCTTAAATTATTAACTAAT
1 AATTAATAAC-CTTAAATTATTAACTAAT
16934 --TTAATAA
1 AATTAATAA
16941 TTAAACATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
26 9 0.28
27 7 0.22
28 1 0.03
29 15 0.47
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (28 bp):
AATTAATAACCTTAAATTATTAACTAAT
Found at i:17437 original size:11 final size:11
Alignment explanation
Indices: 17423--17465 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
17413 GTTCATAACA
17423 AATTTATAATT
1 AATTTATAATT
17434 AATTTATAATT
1 AATTTATAATT
17445 -ATTTGATAATTT
1 AATTT-ATAA-TT
*
17457 ATTTTATAA
1 AATTTATAA
17466 AGGAATGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 4 0.14
11 15 0.54
12 6 0.21
13 3 0.11
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (11 bp):
AATTTATAATT
Found at i:17453 original size:22 final size:22
Alignment explanation
Indices: 17424--17465 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
17414 TTCATAACAA
17424 ATTTATAA-TTAATTTATAATT
1 ATTTATAATTTAATTTATAATT
*
17445 ATTTGATAATTTATTTTATAA
1 ATTT-ATAATTTAATTTATAA
17466 AGGAATGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 4 0.22
23 10 0.56
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
ATTTATAATTTAATTTATAATT
Found at i:17790 original size:8 final size:7
Alignment explanation
Indices: 17751--17886 Score: 68
Period size: 7 Copynumber: 18.6 Consensus size: 7
17741 ACGACGTTAT
17751 TAATTAA
1 TAATTAA
17758 TAATT-A
1 TAATTAA
*
17764 -AATTCCA
1 TAATT-AA
17771 TAATTAA
1 TAATTAA
17778 TAATTAA
1 TAATTAA
17785 TGAATTAA
1 T-AATTAA
17793 CTAATTAA
1 -TAATTAA
17801 TTTAA-TAA
1 --TAATTAA
17809 TAATTAA
1 TAATTAA
17816 -ACATTAA
1 TA-ATTAA
17823 TAACTCTTCAA
1 TAA---TT-AA
*
17834 TTATTAA
1 TAATTAA
* *
17841 TAAAATCA
1 T-AATTAA
*
17849 TAATGAA
1 TAATTAA
17856 TAATTAA
1 TAATTAA
17863 TAA--AA
1 TAATTAA
17868 TATATTAA
1 TA-ATTAA
*
17876 TACTTAA
1 TAATTAA
17883 TAAT
1 TAAT
17887 CCTAACTCTT
Statistics
Matches: 100, Mismatches: 12, Indels: 34
0.68 0.08 0.23
Matches are distributed among these distances:
5 8 0.08
6 6 0.06
7 46 0.46
8 30 0.30
9 4 0.04
10 2 0.02
11 4 0.04
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.40
Consensus pattern (7 bp):
TAATTAA
Found at i:17799 original size:16 final size:15
Alignment explanation
Indices: 17772--17815 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
17762 TAAATTCCAT
17772 AATTAATAATTAATG
1 AATTAATAATTAATG
*
17787 AATTAACTAATTAATTT
1 AATTAA-TAATTAA-TG
17804 AA-TAATAATTAA
1 AATTAATAATTAA
17816 ACATTAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 13 0.50
16 10 0.38
17 3 0.12
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (15 bp):
AATTAATAATTAATG
Found at i:17882 original size:20 final size:22
Alignment explanation
Indices: 17836--17885 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 22
17826 CTCTTCAATT
17836 ATTAATAAAATCATAATGAATA
1 ATTAATAAAATCATAATGAATA
*
17858 ATTAATAAAAT-AT-ATTAATA
1 ATTAATAAAATCATAATGAATA
*
17878 CTTAATAA
1 ATTAATAA
17886 TCCTAACTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 13 0.50
21 2 0.08
22 11 0.42
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (22 bp):
ATTAATAAAATCATAATGAATA
Found at i:18051 original size:29 final size:32
Alignment explanation
Indices: 18019--18086 Score: 79
Period size: 30 Copynumber: 2.2 Consensus size: 32
18009 TAAATCATTC
* *
18019 AATAATTTAA-ACAATTATCTAAAA-A-TAAT
1 AATAATTTAATAAAATAATCTAAAATAGTAAT
**
18048 AATAAAATAATAAAATAATCTAAAATAGTAAT
1 AATAATTTAATAAAATAATCTAAAATAGTAAT
18080 AATAATT
1 AATAATT
18087 AATCATTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
29 8 0.27
30 12 0.40
31 1 0.03
32 9 0.30
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.32
Consensus pattern (32 bp):
AATAATTTAATAAAATAATCTAAAATAGTAAT
Found at i:18064 original size:19 final size:18
Alignment explanation
Indices: 18040--18085 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
18030 CAATTATCTA
18040 AAAATAATAATAAAATAAT
1 AAAATAAT-ATAAAATAAT
* *
18059 AAAATAATCTAAAATAGT
1 AAAATAATATAAAATAAT
18077 AATAATAAT
1 AA-AATAAT
18086 TAATCATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (18 bp):
AAAATAATATAAAATAAT
Found at i:18066 original size:16 final size:17
Alignment explanation
Indices: 18042--18085 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
18032 ATTATCTAAA
18042 AATAATAATAAAATAAT
1 AATAATAATAAAATAAT
*
18059 AA-AATAATCTAAAATAGT
1 AATAATAA--TAAAATAAT
18077 AATAATAAT
1 AATAATAAT
18086 TAATCATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
16 5 0.22
17 3 0.13
18 10 0.43
19 5 0.22
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (17 bp):
AATAATAATAAAATAAT
Found at i:18097 original size:35 final size:31
Alignment explanation
Indices: 18026--18104 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 31
18016 TTCAATAATT
*
18026 TAAACAATTATCTAAAAATAATAATAAAATAA
1 TAAA-AATAATCTAAAAATAATAATAAAATAA
*
18058 T-AAAATAATCTAAAATAGTAATAATAATTAATCAT
1 TAAAAATAATCTAAAA-A-TAATAATAA--AAT-AA
18093 TAAAAATAATCT
1 TAAAAATAATCT
18105 TTTTTAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
30 11 0.28
31 3 0.08
32 10 0.26
34 3 0.08
35 2 0.05
36 10 0.26
ACGTcount: A:0.61, C:0.06, G:0.01, T:0.32
Consensus pattern (31 bp):
TAAAAATAATCTAAAAATAATAATAAAATAA
Found at i:18275 original size:59 final size:61
Alignment explanation
Indices: 18166--18298 Score: 153
Period size: 59 Copynumber: 2.2 Consensus size: 61
18156 TCGGCTCGTC
* * * ** * *
18166 GTCGCGCGCGACCCAGGCCAATGGTGGAGCGCGACTGGATTGCGTTCCACCGTCGGCCTGG
1 GTCGCGCGCGACCCAGGCCAACGGTGGAGCGCGACTGAATCGCGACCCACCCTCGGCCTAG
* * *
18227 GTCGCGAGCGACCCA-GCC-ACGGTGGATCGCGACTGAATCGTGACCCACCCTCGGCCTAG
1 GTCGCGCGCGACCCAGGCCAACGGTGGAGCGCGACTGAATCGCGACCCACCCTCGGCCTAG
*
18286 GTTGCGCGCGACC
1 GTCGCGCGCGACC
18299 TGCCGTCGAA
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
59 43 0.72
60 3 0.05
61 14 0.23
ACGTcount: A:0.15, C:0.35, G:0.35, T:0.15
Consensus pattern (61 bp):
GTCGCGCGCGACCCAGGCCAACGGTGGAGCGCGACTGAATCGCGACCCACCCTCGGCCTAG
Done.