Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013497.1 Corchorus capsularis cultivar CVL-1 contig13518, 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: 30470
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:1355 original size:11 final size:11
Alignment explanation
Indices: 1335--1378 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
1325 TATGTTGATC
*
1335 ATAATAAATTT
1 ATAATTAATTT
1346 ATAATTAATTT
1 ATAATTAATTT
1357 ATAATT-ATTT
1 ATAATTAATTT
*
1367 GATAATTTATTT
1 -ATAATTAATTT
1379 TATATAGGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 4 0.13
11 22 0.73
12 4 0.13
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (11 bp):
ATAATTAATTT
Found at i:3940 original size:34 final size:35
Alignment explanation
Indices: 3891--3960 Score: 106
Period size: 34 Copynumber: 2.0 Consensus size: 35
3881 GGGGTTGGAG
*
3891 TCAAACCCCAGACATTTAAAAGTCAAACCAC-TTT
1 TCAAACCCCAAACATTTAAAAGTCAAACCACGTTT
* *
3925 TCAAATCCCAAACATTTGAAAGTCAAACCACGTTT
1 TCAAACCCCAAACATTTAAAAGTCAAACCACGTTT
3960 T
1 T
3961 GACCCCACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 28 0.88
35 4 0.12
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.26
Consensus pattern (35 bp):
TCAAACCCCAAACATTTAAAAGTCAAACCACGTTT
Found at i:4239 original size:21 final size:21
Alignment explanation
Indices: 4213--4379 Score: 173
Period size: 21 Copynumber: 8.0 Consensus size: 21
4203 AATGTGTCGG
4213 CTATCAAATTTTGGGGTTTGA
1 CTATCAAATTTTGGGGTTTGA
4234 CTATCAAATTTTGGAGG-TTGA
1 CTATCAAATTTTGG-GGTTTGA
* *
4255 CTACCAAACTTTGGGGTTTGA
1 CTATCAAATTTTGGGGTTTGA
*
4276 CTATC-AACTTTGGGGTTTGA
1 CTATCAAATTTTGGGGTTTGA
* *
4296 CTA-CCAATAATTGGGGTTTGA
1 CTATCAAAT-TTTGGGGTTTGA
*
4317 CTATC-AACTTTGGGGTTTGA
1 CTATCAAATTTTGGGGTTTGA
* ** *
4337 CTA-CCAATATCCGAGGTTTGA
1 CTATCAAAT-TTTGGGGTTTGA
*
4358 CTATCAAATTTTAGGGTTTGA
1 CTATCAAATTTTGGGGTTTGA
4379 C
1 C
4380 CATACATGTA
Statistics
Matches: 122, Mismatches: 16, Indels: 16
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.02
20 38 0.31
21 75 0.61
22 7 0.06
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (21 bp):
CTATCAAATTTTGGGGTTTGA
Found at i:4300 original size:41 final size:42
Alignment explanation
Indices: 4222--4379 Score: 207
Period size: 41 Copynumber: 3.8 Consensus size: 42
4212 GCTATCAAAT
*
4222 TTTGGGGTTTGACTATCAAATTTTGGAGG-TTGACTACCAA-A
1 TTTGGGGTTTGACTATCAAACTTTGG-GGTTTGACTACCAATA
4263 CTTTGGGGTTTGACTATC-AACTTTGGGGTTTGACTACCAATA
1 -TTTGGGGTTTGACTATCAAACTTTGGGGTTTGACTACCAATA
*
4305 ATTGGGGTTTGACTATC-AACTTTGGGGTTTGACTACCAATA
1 TTTGGGGTTTGACTATCAAACTTTGGGGTTTGACTACCAATA
** * * *
4346 TCCGAGGTTTGACTATCAAATTTTAGGGTTTGAC
1 TTTGGGGTTTGACTATCAAACTTTGGGGTTTGAC
4380 CATACATGTA
Statistics
Matches: 105, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
40 2 0.02
41 71 0.68
42 32 0.30
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (42 bp):
TTTGGGGTTTGACTATCAAACTTTGGGGTTTGACTACCAATA
Found at i:4375 original size:62 final size:61
Alignment explanation
Indices: 4227--4379 Score: 175
Period size: 62 Copynumber: 2.5 Consensus size: 61
4217 CAAATTTTGG
* * * *
4227 GGTTTGACTATCAAATTTTGGAGGTTGACTACCAAACTTTGGGGTTTGACTATCAACTTTGG
1 GGTTTGACTATCAAATTTTGG-GTTTGACTACCAAACTTTGGGGTTTGACTACCAACTTCGA
* * * *
4289 GGTTTGACTACCAATAATTGGGGTTTGACTATC-AACTTTGGGGTTTGACTACCAA-TATCCGA
1 GGTTTGACTATCAA-ATTTTGGGTTTGACTACCAAACTTTGGGGTTTGACTACCAACT-T-CGA
4351 GGTTTGACTATCAAATTTTAGGGTTTGAC
1 GGTTTGACTATCAAATTTT-GGGTTTGAC
4380 CATACATGTA
Statistics
Matches: 76, Mismatches: 11, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
60 1 0.01
61 25 0.33
62 45 0.59
63 5 0.07
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.37
Consensus pattern (61 bp):
GGTTTGACTATCAAATTTTGGGTTTGACTACCAAACTTTGGGGTTTGACTACCAACTTCGA
Found at i:7897 original size:20 final size:22
Alignment explanation
Indices: 7857--7897 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
7847 ATGACAAAAC
*
7857 CTTTTATTTTTGTTCTTGAAAT
1 CTTTTATTTTTGCTCTTGAAAT
7879 CTTTTA-TTTTGCT-TTGAAA
1 CTTTTATTTTTGCTCTTGAAA
7898 ACTTCCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 6 0.33
22 6 0.33
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.61
Consensus pattern (22 bp):
CTTTTATTTTTGCTCTTGAAAT
Found at i:8939 original size:30 final size:30
Alignment explanation
Indices: 8845--9094 Score: 156
Period size: 30 Copynumber: 8.6 Consensus size: 30
8835 GTCCAATAAT
* * *
8845 TAAAGTCCTCAAGCAGAAGGGCAT-T-CA-
1 TAAAGTCCTCAAACACAAGGGCATCTATAC
*
8872 T-AAGTCC-CTAAACAC-AGAGGCATCCATATC
1 TAAAGTCCTC-AAACACAAG-GGCATCTATA-C
* *
8902 AAAAGTCCTCAAACACAAGGGCATTTATAC
1 TAAAGTCCTCAAACACAAGGGCATCTATAC
** * *
8932 TAAAGTCC-CTAAACACAAATGCAACTCT-C
1 TAAAGTCCTC-AAACACAAGGGCATCTATAC
* *
8961 TACAAGTCCTCAAATACAAGGGCAT-T-CA-
1 TA-AAGTCCTCAAACACAAGGGCATCTATAC
*
8989 T-AAGTCC-CTAAACAC-AGAGGCATCTCT-C
1 TAAAGTCCTC-AAACACAAG-GGCATCTATAC
*
9017 TCAAAGTCCTCAAGCACAAGGGCATCTATAC
1 T-AAAGTCCTCAAACACAAGGGCATCTATAC
*
9048 TAAAGTCC-CTAAACAC-AGATGCATCTATAC
1 TAAAGTCCTC-AAACACAAG-GGCATCTATAC
9078 TAAAGTCCTCAAACACA
1 TAAAGTCCTCAAACACA
9095 TATAACACAG
Statistics
Matches: 172, Mismatches: 24, Indels: 50
0.70 0.10 0.20
Matches are distributed among these distances:
25 6 0.03
26 31 0.18
27 2 0.01
28 3 0.02
29 8 0.05
30 92 0.53
31 27 0.16
32 3 0.02
ACGTcount: A:0.39, C:0.28, G:0.13, T:0.20
Consensus pattern (30 bp):
TAAAGTCCTCAAACACAAGGGCATCTATAC
Found at i:8980 original size:60 final size:60
Alignment explanation
Indices: 8873--9094 Score: 260
Period size: 60 Copynumber: 3.8 Consensus size: 60
8863 GGGCATTCAT
* * *
8873 AAGTCCCTAAACACAGAGGCATC-CATATCAAAAGTCCTCAAACACAAGGGCATTTATACTA
1 AAGTCCCTAAACACAGATGCATCTC-TCT-ACAAGTCCTCAAACACAAGGGCATTTATACTA
* * * *
8934 AAGTCCCTAAACACAAATGCAACTCTCTACAAGTCCTCAAATACAAGGGCA-TT-CA-T-
1 AAGTCCCTAAACACAGATGCATCTCTCTACAAGTCCTCAAACACAAGGGCATTTATACTA
* * *
8990 AAGTCCCTAAACACAGAGGCATCTCTCT-CAAAGTCCTCAAGCACAAGGGCATCTATACTA
1 AAGTCCCTAAACACAGATGCATCTCTCTAC-AAGTCCTCAAACACAAGGGCATTTATACTA
*
9050 AAGTCCCTAAACACAGATGCATCTATACTA-AAGTCCTCAAACACA
1 AAGTCCCTAAACACAGATGCATCTCT-CTACAAGTCCTCAAACACA
9095 TATAACACAG
Statistics
Matches: 136, Mismatches: 17, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
55 1 0.01
56 44 0.32
57 2 0.01
58 2 0.01
59 3 0.02
60 59 0.43
61 24 0.18
62 1 0.01
ACGTcount: A:0.39, C:0.28, G:0.12, T:0.20
Consensus pattern (60 bp):
AAGTCCCTAAACACAGATGCATCTCTCTACAAGTCCTCAAACACAAGGGCATTTATACTA
Found at i:9084 original size:116 final size:116
Alignment explanation
Indices: 8845--9094 Score: 378
Period size: 116 Copynumber: 2.1 Consensus size: 116
8835 GTCCAATAAT
* *
8845 TAAAGTCCTCAAGCAGAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCCATATCAAAAGTCC
1 TAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCCATATCAAAAGTCC
* *
8910 TCAAACACAAGGGCATTTATACTAAAGTCCCTAAACACAAATGCAACTCTC
66 TCAAACACAAGGGCATCTATACTAAAGTCCCTAAACACAAATGCAACTATC
* *
8961 TACAAGTCCTCAAATACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTC-TCTC-AAAGT
1 TA-AAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATC-CATATCAAAAGT
* * *
9024 CCTCAAGCACAAGGGCATCTATACTAAAGTCCCTAAACACAGATGCATCTATAC
64 CCTCAAACACAAGGGCATCTATACTAAAGTCCCTAAACACAAATGCAACTAT-C
9078 TAAAGTCCTCAAACACA
1 TAAAGTCCTCAAACACA
9095 TATAACACAG
Statistics
Matches: 121, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
116 68 0.56
117 52 0.43
118 1 0.01
ACGTcount: A:0.39, C:0.28, G:0.13, T:0.20
Consensus pattern (116 bp):
TAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCCATATCAAAAGTCC
TCAAACACAAGGGCATCTATACTAAAGTCCCTAAACACAAATGCAACTATC
Found at i:22538 original size:2 final size:2
Alignment explanation
Indices: 22531--22563 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
22521 GTTATCATGA
22531 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22564 ATTTATCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23092 original size:3 final size:3
Alignment explanation
Indices: 23079--23113 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
23069 CCACAATTGA
23079 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
23114 CAATAATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:30352 original size:4 final size:4
Alignment explanation
Indices: 30338--30396 Score: 73
Period size: 4 Copynumber: 14.2 Consensus size: 4
30328 ATAACAGACA
* * *
30338 AAAG CAAG AAAG AAAAG AAAG AAAG AAAG AAAG AAAAG AAAG AAAT ATAG
1 AAAG AAAG AAAG -AAAG AAAG AAAG AAAG AAAG -AAAG AAAG AAAG AAAG
30388 AAAG AAAG A
1 AAAG AAAG A
30397 TCAATCAAGA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
4 39 0.83
5 8 0.17
ACGTcount: A:0.73, C:0.02, G:0.22, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:30363 original size:17 final size:17
Alignment explanation
Indices: 30337--30396 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 17
30327 CATAACAGAC
*
30337 AAAAGCAAGAAAGAAA-
1 AAAAGAAAGAAAGAAAG
30353 AGAAAGAAAGAAAGAAAG
1 A-AAAGAAAGAAAGAAAG
* *
30371 AAAAGAAAGAAATATAG
1 AAAAGAAAGAAAGAAAG
30388 -AAAGAAAGA
1 AAAAGAAAGA
30397 TCAATCAAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
16 10 0.26
17 28 0.72
18 1 0.03
ACGTcount: A:0.73, C:0.02, G:0.22, T:0.03
Consensus pattern (17 bp):
AAAAGAAAGAAAGAAAG
Found at i:30367 original size:21 final size:21
Alignment explanation
Indices: 30338--30394 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
30328 ATAACAGACA
*
30338 AAAGCAAGAAAGAAAAGAAAG
1 AAAGAAAGAAAGAAAAGAAAG
30359 AAAGAAAGAAAGAAAAGAAAG
1 AAAGAAAGAAAGAAAAGAAAG
* *
30380 AAATATAGAAAGAAA
1 AAAGAAAGAAAGAAA
30395 GATCAATCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.74, C:0.02, G:0.21, T:0.04
Consensus pattern (21 bp):
AAAGAAAGAAAGAAAAGAAAG
Found at i:30415 original size:25 final size:25
Alignment explanation
Indices: 30338--30396 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
30328 ATAACAGACA
*
30338 AAAGCAAG-AAAGAAAAGAAAGAAAG
1 AAAGAAAGAAAAG-AAAGAAAGAAAG
* *
30363 AAAGAAAGAAAAGAAAGAAATATAG
1 AAAGAAAGAAAAGAAAGAAAGAAAG
30388 AAAGAAAGA
1 AAAGAAAGA
30397 TCAATCAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 26 0.87
26 4 0.13
ACGTcount: A:0.73, C:0.02, G:0.22, T:0.03
Consensus pattern (25 bp):
AAAGAAAGAAAAGAAAGAAAGAAAG
Done.