Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013713.1 Corchorus capsularis cultivar CVL-1 contig13734, 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: 22854
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3335 original size:22 final size:22
Alignment explanation
Indices: 3293--3333 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
3283 CTAACATTTA
3293 CTAAAAACTGAAATTTCAAAGC
1 CTAAAAACTGAAATTTCAAAGC
3315 CTAAAAA-T-AAATTTTCAAA
1 CTAAAAACTGAAA-TTTCAAA
3334 AGAATCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.17
21 8 0.44
22 7 0.39
ACGTcount: A:0.54, C:0.15, G:0.05, T:0.27
Consensus pattern (22 bp):
CTAAAAACTGAAATTTCAAAGC
Found at i:9139 original size:25 final size:25
Alignment explanation
Indices: 9105--9153 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
9095 TGTTACTTGG
9105 CCAAGACAAGGAGCCAAAATAGTGA
1 CCAAGACAAGGAGCCAAAATAGTGA
*
9130 CCAAGACAAGGAGCCACAATAGTG
1 CCAAGACAAGGAGCCAAAATAGTG
9154 GGTTGTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.45, C:0.22, G:0.24, T:0.08
Consensus pattern (25 bp):
CCAAGACAAGGAGCCAAAATAGTGA
Found at i:19067 original size:72 final size:72
Alignment explanation
Indices: 18990--19141 Score: 304
Period size: 72 Copynumber: 2.1 Consensus size: 72
18980 CGTAAAAGTC
18990 CCAGAGCCTGATATATCGGTAGAACCTGATATAGAACCCGAGGTGGTAGAAGAGCCAGAAGCGGT
1 CCAGAGCCTGATATATCGGTAGAACCTGATATAGAACCCGAGGTGGTAGAAGAGCCAGAAGCGGT
19055 AGAATCA
66 AGAATCA
19062 CCAGAGCCTGATATATCGGTAGAACCTGATATAGAACCCGAGGTGGTAGAAGAGCCAGAAGCGGT
1 CCAGAGCCTGATATATCGGTAGAACCTGATATAGAACCCGAGGTGGTAGAAGAGCCAGAAGCGGT
19127 AGAATCA
66 AGAATCA
19134 CCAGAGCC
1 CCAGAGCC
19142 AGACCCTGAT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 80 1.00
ACGTcount: A:0.34, C:0.21, G:0.29, T:0.16
Consensus pattern (72 bp):
CCAGAGCCTGATATATCGGTAGAACCTGATATAGAACCCGAGGTGGTAGAAGAGCCAGAAGCGGT
AGAATCA
Found at i:19204 original size:18 final size:18
Alignment explanation
Indices: 19181--19249 Score: 77
Period size: 18 Copynumber: 3.8 Consensus size: 18
19171 TAGAGGCTGG
* *
19181 ACTTGAAGCTGAGCCTGA
1 ACTTGAACCTGAACCTGA
*
19199 ACTTGAACCTGAATCTGA
1 ACTTGAACCTGAACCTGA
*
19217 ACTTGAACTTGAACCTGA
1 ACTTGAACCTGAACCTGA
*
19235 AGC-TGAATCTGAACC
1 A-CTTGAACCTGAACC
19250 AGTACCAGCT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 42 0.98
19 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (18 bp):
ACTTGAACCTGAACCTGA
Found at i:19268 original size:6 final size:6
Alignment explanation
Indices: 19184--19288 Score: 66
Period size: 6 Copynumber: 17.0 Consensus size: 6
19174 AGGCTGGACT
* * * * * *
19184 TGAAGC TGAGCC TGAACT TGAACC TGAATC TGAACT TGAACT TGAACC
1 TGAACC TGAACC TGAACC TGAACC TGAACC TGAACC TGAACC TGAACC
* * * * * * *
19232 TGAAGC TGAATC TGAACC AGTACCAGC TGAACT TGAACC TGAAGC TGAATC
1 TGAACC TGAACC TGAACC TG-A--ACC TGAACC TGAACC TGAACC TGAACC
19283 TGAACC
1 TGAACC
19289 AGTACCAGTT
Statistics
Matches: 75, Mismatches: 21, Indels: 6
0.74 0.21 0.06
Matches are distributed among these distances:
6 70 0.93
7 1 0.01
8 1 0.01
9 3 0.04
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (6 bp):
TGAACC
Found at i:19271 original size:39 final size:39
Alignment explanation
Indices: 19220--19296 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
19210 AATCTGAACT
19220 TGAACTTGAACCTGAAGCTGAATCTGAACCAGTACCAGC
1 TGAACTTGAACCTGAAGCTGAATCTGAACCAGTACCAGC
19259 TGAACTTGAACCTGAAGCTGAATCTGAACCAGTACCAG
1 TGAACTTGAACCTGAAGCTGAATCTGAACCAGTACCAG
19297 TTTGATCCGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.21
Consensus pattern (39 bp):
TGAACTTGAACCTGAAGCTGAATCTGAACCAGTACCAGC
Found at i:19672 original size:57 final size:58
Alignment explanation
Indices: 19604--19724 Score: 192
Period size: 60 Copynumber: 2.1 Consensus size: 58
19594 CTGAACCTGA
*
19604 TGAACTTGAAGAGTC-ATA-ACCCGATGAGCTAGAAGAACCCATAGGAGCGCTTGAGTC
1 TGAACTTGAAGAGTCTA-AGACCCGACGAGCTAGAAGAACCCATAGGAGCGCTTGAGTC
19661 TGAACTTGAAGAGTCTGAAGTACCCGACGAGCTAGAAGAACCCATAGGAGCGCTTGAGTC
1 TGAACTTGAAGAGTCT-AAG-ACCCGACGAGCTAGAAGAACCCATAGGAGCGCTTGAGTC
19721 TGAA
1 TGAA
19725 TCTGAATTTG
Statistics
Matches: 59, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
57 15 0.25
58 1 0.02
59 1 0.02
60 42 0.71
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.19
Consensus pattern (58 bp):
TGAACTTGAAGAGTCTAAGACCCGACGAGCTAGAAGAACCCATAGGAGCGCTTGAGTC
Found at i:19895 original size:24 final size:24
Alignment explanation
Indices: 19850--19897 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
19840 TACCTGAAGG
* *
19850 GCTAGGACCCATAGAAGGACTTGA
1 GCTAGGACCAATAGAACGACTTGA
* *
19874 GCTAGGACTAATAGAACTACTTGA
1 GCTAGGACCAATAGAACGACTTGA
19898 TCCTGAAACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (24 bp):
GCTAGGACCAATAGAACGACTTGA
Found at i:20294 original size:7 final size:6
Alignment explanation
Indices: 20278--20312 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
20268 ATTTCAAAGA
*
20278 TTTTTC TTTTTC TTTTTC TTTTT- TCTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
20313 GCTTTGAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:20317 original size:12 final size:12
Alignment explanation
Indices: 20280--20317 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
20270 TTCAAAGATT
*
20280 TTTCTTTTTCTT
1 TTTCTTTTTCTC
20292 TTTCTTTTT-TC
1 TTTCTTTTTCTC
*
20303 TTTCTTTTTCGC
1 TTTCTTTTTCTC
20315 TTT
1 TTT
20318 GAGTTGTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (12 bp):
TTTCTTTTTCTC
Found at i:21390 original size:28 final size:29
Alignment explanation
Indices: 21321--21400 Score: 83
Period size: 28 Copynumber: 2.7 Consensus size: 29
21311 TAAAAGTACA
*
21321 AAATTGGTCCCTCAAGTGGAGCGAACATAGC
1 AAATTAGTCCCTCAAGTGGA--GAACATAGC
*
21352 AAATTGGTCCCTCAAGTGGA-AA-ATATGC
1 AAATTAGTCCCTCAAGTGGAGAACATA-GC
* *
21380 AATTTAGTCCCTGAAGTGGAG
1 AAATTAGTCCCTCAAGTGGAG
21401 TTAACTAAGC
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
27 3 0.07
28 21 0.48
31 20 0.45
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.24
Consensus pattern (29 bp):
AAATTAGTCCCTCAAGTGGAGAACATAGC
Found at i:22386 original size:31 final size:30
Alignment explanation
Indices: 22318--22387 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
22308 AATGTGCAAA
*
22318 TGGGTCCCTGAAGTGAACTTAGTGAGCAAT
1 TGGGTCCCTGAAGTGAACTTAGTGAACAAT
* * *
22348 TGAGTCCCTGAAGTTG-AGTTAATTGAACAAT
1 TGGGTCCCTGAAG-TGAACTT-AGTGAACAAT
22379 TGGGTCCCT
1 TGGGTCCCT
22388 CACCAATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
30 15 0.45
31 18 0.55
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (30 bp):
TGGGTCCCTGAAGTGAACTTAGTGAACAAT
Done.