Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007802.1 Corchorus capsularis cultivar CVL-1 contig07823, 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: 87342
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:12874 original size:10 final size:10
Alignment explanation
Indices: 12859--12883 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12849 GAGGACTCTA
12859 GAATTTTCTG
1 GAATTTTCTG
12869 GAATTTTCTG
1 GAATTTTCTG
12879 GAATT
1 GAATT
12884 ATGCAGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:15321 original size:21 final size:21
Alignment explanation
Indices: 15297--15364 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
15287 AAGGCCGAGC
15297 ATGGCCGGGCAGGCGGCACGG
1 ATGGCCGGGCAGGCGGCACGG
* *
15318 ATGG-CGCGGCA-GTGAC-CTGG
1 ATGGCCG-GGCAGGCGGCAC-GG
*
15338 CTGGGCCGGGCAGGCGGCACGG
1 AT-GGCCGGGCAGGCGGCACGG
15360 ATGGC
1 ATGGC
15365 GCGGCAGTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
19 1 0.03
20 8 0.23
21 17 0.49
22 8 0.23
23 1 0.03
ACGTcount: A:0.13, C:0.28, G:0.50, T:0.09
Consensus pattern (21 bp):
ATGGCCGGGCAGGCGGCACGG
Found at i:15358 original size:42 final size:42
Alignment explanation
Indices: 15299--15401 Score: 206
Period size: 42 Copynumber: 2.5 Consensus size: 42
15289 GGCCGAGCAT
15299 GGCCGGGCAGGCGGCACGGATGGCGCGGCAGTGACCTGGCTG
1 GGCCGGGCAGGCGGCACGGATGGCGCGGCAGTGACCTGGCTG
15341 GGCCGGGCAGGCGGCACGGATGGCGCGGCAGTGACCTGGCTG
1 GGCCGGGCAGGCGGCACGGATGGCGCGGCAGTGACCTGGCTG
15383 GGCCGGGCAGGCGGCACGG
1 GGCCGGGCAGGCGGCACGG
15402 CATCGGCTGG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.12, C:0.29, G:0.51, T:0.08
Consensus pattern (42 bp):
GGCCGGGCAGGCGGCACGGATGGCGCGGCAGTGACCTGGCTG
Found at i:15370 original size:21 final size:21
Alignment explanation
Indices: 15304--15371 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
15294 AGCATGGCCG
15304 GGCAGGCGGCACGGATGGCGC
1 GGCAGGCGGCACGGATGGCGC
* * *
15325 GGCA-GTGAC-CTGGCTGG-GCC
1 GGCAGGCGGCAC-GGATGGCG-C
15345 GGGCAGGCGGCACGGATGGCGC
1 -GGCAGGCGGCACGGATGGCGC
15367 GGCAG
1 GGCAG
15372 TGACCTGGCT
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
19 2 0.06
20 9 0.26
21 13 0.37
22 9 0.26
23 2 0.06
ACGTcount: A:0.13, C:0.28, G:0.51, T:0.07
Consensus pattern (21 bp):
GGCAGGCGGCACGGATGGCGC
Found at i:15391 original size:21 final size:21
Alignment explanation
Indices: 15325--15392 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
15315 CGGATGGCGC
15325 GGCAGTGACCTGGCTGGGCCG
1 GGCAGTGACCTGGCTGGGCCG
* * *
15346 GGCAGGCGGCAC-GGAT-GG-CG
1 GGCA-GTGAC-CTGGCTGGGCCG
15366 CGGCAGTGACCTGGCTGGGCCG
1 -GGCAGTGACCTGGCTGGGCCG
15388 GGCAG
1 GGCAG
15393 GCGGCACGGC
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
19 1 0.03
20 8 0.23
21 17 0.49
22 8 0.23
23 1 0.03
ACGTcount: A:0.12, C:0.28, G:0.50, T:0.10
Consensus pattern (21 bp):
GGCAGTGACCTGGCTGGGCCG
Found at i:25408 original size:14 final size:14
Alignment explanation
Indices: 25389--25419 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
25379 TAGTTTTTAG
*
25389 TTTAATTGCTTTCT
1 TTTAATTGATTTCT
25403 TTTAATTGATTTCT
1 TTTAATTGATTTCT
25417 TTT
1 TTT
25420 TTATCCCCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.10, G:0.06, T:0.68
Consensus pattern (14 bp):
TTTAATTGATTTCT
Found at i:26487 original size:21 final size:21
Alignment explanation
Indices: 26436--26487 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
26426 AACTCATCTT
* *
26436 GATGATATGAAGTCCTTTGAA
1 GATGATTTGAAGACCTTTGAA
* * *
26457 GATCAATTGAAGACCTTTGGA
1 GATGATTTGAAGACCTTTGAA
26478 GATGATTTGA
1 GATGATTTGA
26488 GTAAGAAAGC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.33
Consensus pattern (21 bp):
GATGATTTGAAGACCTTTGAA
Found at i:29712 original size:20 final size:19
Alignment explanation
Indices: 29687--29730 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
29677 TTTCAAAGAA
*
29687 ATCATGCTACATCACGTTGC
1 ATCATGCTACAACACGTT-C
* *
29707 ATCATGTTACAACATGTTC
1 ATCATGCTACAACACGTTC
29726 ATCAT
1 ATCAT
29731 ATTGCACCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (19 bp):
ATCATGCTACAACACGTTC
Found at i:29907 original size:26 final size:26
Alignment explanation
Indices: 29867--29954 Score: 131
Period size: 26 Copynumber: 3.4 Consensus size: 26
29857 CTCCAGAAGC
*
29867 TTTCAGCAATTGCCCCTAGTTCGGCA
1 TTTCAGCAATCGCCCCTAGTTCGGCA
29893 TTTCAGCAATCGCCCCTAGTTCGGCA
1 TTTCAGCAATCGCCCCTAGTTCGGCA
** *
29919 TTTCTTCAGTCGCCCCTAGTTCGGCA
1 TTTCAGCAATCGCCCCTAGTTCGGCA
*
29945 TCTCAGCAAT
1 TTTCAGCAAT
29955 TTTCATTTCA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.18, C:0.33, G:0.18, T:0.31
Consensus pattern (26 bp):
TTTCAGCAATCGCCCCTAGTTCGGCA
Found at i:30120 original size:15 final size:15
Alignment explanation
Indices: 30100--30132 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
30090 TTCCAGCAGT
30100 TTTTCAGTTCAGTAG
1 TTTTCAGTTCAGTAG
30115 TTTTCAGTTCAGTAG
1 TTTTCAGTTCAGTAG
30130 TTT
1 TTT
30133 CTGGTTGCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (15 bp):
TTTTCAGTTCAGTAG
Found at i:30154 original size:64 final size:64
Alignment explanation
Indices: 29997--30194 Score: 204
Period size: 63 Copynumber: 3.1 Consensus size: 64
29987 GTAGGCACTC
* * * * ** *
29997 CAGCAGTTTTTGGTTGCACGCACGGGGGAATTCCATTAGTTTTTCAGTTCAGCA-TTTTCAATT
1 CAGCAGTTTCTGGTTGCCCGCACGAGGGCATTCCAACAGTTTTTCAGTTCAGTAGTTTTCAATT
* * * * *
30060 CAACAATTTTTGGTTGCCCGCACGAGGGCATTCCAGCAGTTTTTCAGTTCAGTAGTTTTCAGTT
1 CAGCAGTTTCTGGTTGCCCGCACGAGGGCATTCCAACAGTTTTTCAGTTCAGTAGTTTTCAATT
* * * * * *
30124 CAGTAGTTTCTGGTTGCCCGCATGTA-GGCATTCTAACAG-TATTCAGTTCAATAGTTTTCATTT
1 CAGCAGTTTCTGGTTGCCCGCACG-AGGGCATTCCAACAGTTTTTCAGTTCAGTAGTTTTCAATT
30187 CAGCAGTT
1 CAGCAGTT
30195 CAGAGGTTTC
Statistics
Matches: 113, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
63 74 0.65
64 38 0.34
65 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.37
Consensus pattern (64 bp):
CAGCAGTTTCTGGTTGCCCGCACGAGGGCATTCCAACAGTTTTTCAGTTCAGTAGTTTTCAATT
Found at i:39649 original size:15 final size:15
Alignment explanation
Indices: 39617--39660 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
39607 ACTCACGACA
39617 AAAAC-AGTTAT-A-
1 AAAACAAGTTATAAT
39629 AAAACAAGTTATAAT
1 AAAACAAGTTATAAT
39644 AAAACAA-TTAGTAAT
1 AAAACAAGTTA-TAAT
39659 AA
1 AA
39661 TAAATCCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 5 0.18
13 6 0.21
14 4 0.14
15 13 0.46
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.25
Consensus pattern (15 bp):
AAAACAAGTTATAAT
Found at i:40132 original size:26 final size:27
Alignment explanation
Indices: 40079--40138 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
40069 TAATGCACCC
* * *
40079 AAAACATTTTAATAAAAATCATTTATA
1 AAAACAATTTAATAAAAATCAGTGATA
*
40106 AAAACAATTTATTAAAAAT-AGTGATA
1 AAAACAATTTAATAAAAATCAGTGATA
40132 AAAACAA
1 AAAACAA
40139 GTCCCTCAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 12 0.41
27 17 0.59
ACGTcount: A:0.60, C:0.07, G:0.03, T:0.30
Consensus pattern (27 bp):
AAAACAATTTAATAAAAATCAGTGATA
Found at i:49416 original size:10 final size:10
Alignment explanation
Indices: 49401--49425 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
49391 GTTCCTGCAC
49401 AATTCCAGAA
1 AATTCCAGAA
49411 AATTCCAGAA
1 AATTCCAGAA
49421 AATTC
1 AATTC
49426 TAGAGTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:56612 original size:10 final size:10
Alignment explanation
Indices: 56597--56621 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
56587 GTTCCTGCAC
56597 AATTCCAGAA
1 AATTCCAGAA
56607 AATTCCAGAA
1 AATTCCAGAA
56617 AATTC
1 AATTC
56622 TAGCATCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:57566 original size:6 final size:6
Alignment explanation
Indices: 57555--57581 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
57545 TATATTCTGC
57555 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
57582 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:62220 original size:6 final size:6
Alignment explanation
Indices: 62204--62235 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
62194 CAAGGCAAAG
62204 TAAAT- TAAATC TAAATC TAAATC TAAAT- TAAA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TAAA
62236 AGGAATACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 9 0.35
6 17 0.65
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.34
Consensus pattern (6 bp):
TAAATC
Found at i:67488 original size:190 final size:189
Alignment explanation
Indices: 67162--67541 Score: 697
Period size: 190 Copynumber: 2.0 Consensus size: 189
67152 AAGATTGCAG
67162 CAGGCAGACTGCAGCCATGAATCAGTATCTTCGAAGCAAAAAATAAACAAACAGAACTTAACCAA
1 CAGGCAGACTGCAGCCATGAATCAGTATCTTCGAAGCAAAAAATAAACAAACAGAACTTAACCAA
*
67227 GCACAAAGAAAGAGCAACGAAGGGATGAATTCGATCTCACACAACACATAACTTAACAACAGTAA
66 GCACAAAGAAAGAGCAACGAAGAGATGAATTCGATCTCACACAACACATAACTTAACAACAGTAA
67292 ACATTGATTCTATTGTGAACAAACACTCATTTTTCGTTCATATCTGAAAACTATTATCA
131 ACATTGATTCTATTGTGAACAAACACTCATTTTTCGTTCATATCTGAAAACTATTATCA
*
67351 CAGGCAGACTGCAGTCATGAATCAGTATCTTCGAAGCAAAAAAATAAACAAACAGAACTTAACCA
1 CAGGCAGACTGCAGCCATGAATCAGTATCTTCGAAGC-AAAAAATAAACAAACAGAACTTAACCA
* *
67416 AGCACAAAGAAAGAGCAACGAAGAGATGAATTCGATCTCACACAACACATAACTTAACAACATTG
65 AGCACAAAGAAAGAGCAACGAAGAGATGAATTCGATCTCACACAACACATAACTTAACAACAGTA
* *
67481 GACATTGATTCTATTGTGAACAAATACTCATTTTTCGTTCATATCTGAAAACTATTATCA
130 AACATTGATTCTATTGTGAACAAACACTCATTTTTCGTTCATATCTGAAAACTATTATCA
67541 C
1 C
67542 TCTGCCTATA
Statistics
Matches: 184, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
189 36 0.20
190 148 0.80
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.23
Consensus pattern (189 bp):
CAGGCAGACTGCAGCCATGAATCAGTATCTTCGAAGCAAAAAATAAACAAACAGAACTTAACCAA
GCACAAAGAAAGAGCAACGAAGAGATGAATTCGATCTCACACAACACATAACTTAACAACAGTAA
ACATTGATTCTATTGTGAACAAACACTCATTTTTCGTTCATATCTGAAAACTATTATCA
Found at i:73749 original size:33 final size:33
Alignment explanation
Indices: 73699--73822 Score: 151
Period size: 33 Copynumber: 3.7 Consensus size: 33
73689 CCGCGCAACA
*
73699 CCGGCCACAAGACCGGCCACGCGACATGGACATGT
1 CCGGCCAC-A-ACCGGCCACGCGACATGGACATGC
*
73734 CCGGCCATC-ACCGGCCACGCGACATGGACATGG
1 CCGGCCA-CAACCGGCCACGCGACATGGACATGC
* ** * *
73767 CCGGCTACAACCGGCCAAACGACTTGGCCATGC
1 CCGGCCACAACCGGCCACGCGACATGGACATGC
73800 CCGGCCACAACCGGCCACGCGAC
1 CCGGCCACAACCGGCCACGCGAC
73823 CCTTTGTCTA
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
32 1 0.01
33 68 0.88
35 7 0.09
36 1 0.01
ACGTcount: A:0.23, C:0.41, G:0.27, T:0.08
Consensus pattern (33 bp):
CCGGCCACAACCGGCCACGCGACATGGACATGC
Found at i:75222 original size:14 final size:15
Alignment explanation
Indices: 75186--75223 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
75176 GGTTGTCAGG
*
75186 AAAGCAATTAAATAA
1 AAAGCAATAAAATAA
*
75201 AAAACAATAAAAT-A
1 AAAGCAATAAAATAA
75215 AAAGCAATA
1 AAAGCAATA
75224 CTTCCCACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.71, C:0.08, G:0.05, T:0.16
Consensus pattern (15 bp):
AAAGCAATAAAATAA
Found at i:78591 original size:26 final size:26
Alignment explanation
Indices: 78559--78611 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
78549 TTTTTAAATT
78559 TGGATGTTATTTGGGTTGGGTCTTGG
1 TGGATGTTATTTGGGTTGGGTCTTGG
78585 TGGATGTTATTTGGGTTGGGTCTTGG
1 TGGATGTTATTTGGGTTGGGTCTTGG
78611 T
1 T
78612 TGACTAAGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.08, C:0.04, G:0.42, T:0.47
Consensus pattern (26 bp):
TGGATGTTATTTGGGTTGGGTCTTGG
Found at i:84232 original size:15 final size:15
Alignment explanation
Indices: 84212--84240 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
84202 CTTATCATCT
84212 TGTTGGATTTGAATC
1 TGTTGGATTTGAATC
84227 TGTTGGATTTGAAT
1 TGTTGGATTTGAAT
84241 TGGAATTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.03, G:0.28, T:0.48
Consensus pattern (15 bp):
TGTTGGATTTGAATC
Found at i:85958 original size:16 final size:16
Alignment explanation
Indices: 85937--85986 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
85927 GAGAACAATC
85937 TGGGAAGCAATATCAG
1 TGGGAAGCAATATCAG
85953 TGGGAA-C-A-ATC--
1 TGGGAAGCAATATCAG
*
85964 TGGGAAGCAATATTAG
1 TGGGAAGCAATATCAG
85980 TGGGAAG
1 TGGGAAG
85987 AATGGAATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 10
0.72 0.03 0.26
Matches are distributed among these distances:
11 6 0.21
12 1 0.04
13 4 0.14
14 3 0.11
15 1 0.04
16 13 0.46
ACGTcount: A:0.36, C:0.10, G:0.34, T:0.20
Consensus pattern (16 bp):
TGGGAAGCAATATCAG
Found at i:85982 original size:27 final size:27
Alignment explanation
Indices: 85915--85985 Score: 124
Period size: 27 Copynumber: 2.6 Consensus size: 27
85905 TTCTCTGAGG
*
85915 AGCAATATTAGTGAGAACAATCTGGGA
1 AGCAATATTAGTGGGAACAATCTGGGA
*
85942 AGCAATATCAGTGGGAACAATCTGGGA
1 AGCAATATTAGTGGGAACAATCTGGGA
85969 AGCAATATTAGTGGGAA
1 AGCAATATTAGTGGGAA
85986 GAATGGAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.39, C:0.11, G:0.28, T:0.21
Consensus pattern (27 bp):
AGCAATATTAGTGGGAACAATCTGGGA
Done.