Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015525.1 Corchorus capsularis cultivar CVL-1 contig15546, 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: 48731
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:3570 original size:22 final size:22
Alignment explanation
Indices: 3163--3571 Score: 185
Period size: 22 Copynumber: 18.4 Consensus size: 22
3153 AGATTATACG
* * *
3163 AATTTCATAGTGTGGTTAACAA
1 AATTTCATAGAGAGGTTATCAA
3185 AATTTCATTAG-GAGGTTA-CTAA
1 AATTTCA-TAGAGAGGTTATC-AA
* * *
3207 TATTTCATTGGGAGGTTATCAA
1 AATTTCATAGAGAGGTTATCAA
* * *
3229 AATTTTATA-ATGTGGTAATCAA
1 AATTTCATAGA-GAGGTTATCAA
*
3251 AACTTCATATGA-AGGTTAT-AA
1 AATTTCATA-GAGAGGTTATCAA
* * * * *
3272 AAGTCTCAATTTGATAAGGAATACCAA
1 AA-TTTC-A-TAGA-GAGG-TTATCAA
*
3299 AATTTGATAGA-AGGTTATC-A
1 AATTTCATAGAGAGGTTATCAA
* * * * *
3319 AATCTCTTAGAGTGATTATCGA
1 AATTTCATAGAGAGGTTATCAA
* *
3341 AATTTCAAAAAGATCGGATTATCAA
1 AATTTCATAGAGA--GG-TTATCAA
**
3366 AATTT-ATATGA-AAATTATCAA
1 AATTTCATA-GAGAGGTTATCAA
* ** *
3387 AATTTCATAGTGTTGTCATCAA
1 AATTTCATAGAGAGGTTATCAA
* *
3409 AATTTCAAAGCGAGGTTATCAA
1 AATTTCATAGAGAGGTTATCAA
* * *
3431 AATTACATA-ATATGATTATCAA
1 AATTTCATAGAGA-GGTTATCAA
* * *
3453 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAGAGAGGTTATCAA
* *
3475 AATTTTATAAAGAGGTTATCAA
1 AATTTCATAGAGAGGTTATCAA
*
3497 AATTTCATAAAGAGGTTATCAA
1 AATTTCATAGAGAGGTTATCAA
* * * *
3519 ATTTTCA-AAATGTGATTA-CAAA
1 AATTTCATAGA-GAGGTTATC-AA
*
3541 AATTTCATAGAGAGGTTATCAT
1 AATTTCATAGAGAGGTTATCAA
3563 AATTTCATA
1 AATTTCATA
3572 TGAATATTTT
Statistics
Matches: 285, Mismatches: 74, Indels: 56
0.69 0.18 0.13
Matches are distributed among these distances:
20 9 0.03
21 34 0.12
22 198 0.69
23 11 0.04
24 9 0.03
25 16 0.06
26 4 0.01
27 4 0.01
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (22 bp):
AATTTCATAGAGAGGTTATCAA
Found at i:3713 original size:13 final size:13
Alignment explanation
Indices: 3683--3727 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
3673 GAATTTTTTA
*
3683 ATTTCATTTATTT
1 ATTTTATTTATTT
3696 ATTTTATTTATTT
1 ATTTTATTTATTT
3709 ATTTTAAATTT-TTT
1 ATTTT--ATTTATTT
3723 ATTTT
1 ATTTT
3728 TAAAAAGTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 17 0.59
14 8 0.28
15 4 0.14
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (13 bp):
ATTTTATTTATTT
Found at i:3731 original size:15 final size:15
Alignment explanation
Indices: 3688--3727 Score: 59
Period size: 13 Copynumber: 2.9 Consensus size: 15
3678 TTTTAATTTC
3688 ATTTATTTATTTT--
1 ATTTATTTATTTTAA
3701 ATTTATTTATTTTAA
1 ATTTATTTATTTTAA
3716 ATTT-TTTATTTT
1 ATTTATTTATTTT
3728 TAAAAAGTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.52
14 8 0.32
15 4 0.16
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
ATTTATTTATTTTAA
Found at i:3770 original size:11 final size:11
Alignment explanation
Indices: 3734--3776 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
3724 TTTTTAAAAA
3734 GTCCACGTGGC
1 GTCCACGTGGC
* *
3745 G-CCTACATAGC
1 GTCC-ACGTGGC
3756 GTCCACGTGGC
1 GTCCACGTGGC
3767 GTCCACGTGG
1 GTCCACGTGG
3777 TGTCTACATC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 2 0.08
11 22 0.85
12 2 0.08
ACGTcount: A:0.14, C:0.35, G:0.33, T:0.19
Consensus pattern (11 bp):
GTCCACGTGGC
Found at i:13193 original size:15 final size:14
Alignment explanation
Indices: 13168--13206 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
13158 AAAACGTAAT
13168 TTTTTTA-AATTTA
1 TTTTTTATAATTTA
13181 TTTTTATATAATTT-
1 TTTTT-TATAATTTA
13195 TTTTTTATAATT
1 TTTTTTATAATT
13207 AAAGGTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 7 0.29
15 5 0.21
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTTATAATTTA
Found at i:17444 original size:12 final size:12
Alignment explanation
Indices: 17419--17455 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
17409 AAGAGACCCC
17419 CAAAATCA-AAA
1 CAAAATCAGAAA
17430 CAAAATCAGAAA
1 CAAAATCAGAAA
*
17442 C-AAATCAGCAA
1 CAAAATCAGAAA
17453 CAA
1 CAA
17456 TAAAGAATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 18 0.78
12 5 0.22
ACGTcount: A:0.65, C:0.22, G:0.05, T:0.08
Consensus pattern (12 bp):
CAAAATCAGAAA
Found at i:18791 original size:25 final size:25
Alignment explanation
Indices: 18757--18806 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
18747 CAAAAAATGA
*
18757 CATGATATGAAACCCAAACCCTAAC
1 CATGACATGAAACCCAAACCCTAAC
* *
18782 CATGACATGAAAGCCAAACTCTAAC
1 CATGACATGAAACCCAAACCCTAAC
18807 ATGTCATCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.44, C:0.30, G:0.10, T:0.16
Consensus pattern (25 bp):
CATGACATGAAACCCAAACCCTAAC
Found at i:29200 original size:3 final size:3
Alignment explanation
Indices: 29192--29246 Score: 94
Period size: 3 Copynumber: 18.7 Consensus size: 3
29182 AAGCTTCCAA
29192 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
29239 AGT AAT AA
1 AAT AAT AA
29247 AATCGGACGA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:32187 original size:24 final size:24
Alignment explanation
Indices: 32154--32201 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
32144 CCGCTATCCC
*
32154 TATAACGGCGTCTAAACGCCGTCA
1 TATAAAGGCGTCTAAACGCCGTCA
* *
32178 TATAAAGGCGTTTAGACGCCGTCA
1 TATAAAGGCGTCTAAACGCCGTCA
32202 CACACTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (24 bp):
TATAAAGGCGTCTAAACGCCGTCA
Found at i:33948 original size:42 final size:42
Alignment explanation
Indices: 33889--33972 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
33879 AAGCGAGCTT
33889 ATTGCAGAATCATGTGCAGGCCACCCGGTGATTTGTAGACCA
1 ATTGCAGAATCATGTGCAGGCCACCCGGTGATTTGTAGACCA
*
33931 ATTGCAGAATCATGTGCAGGCCACCTGGTGATTTGTAGACCA
1 ATTGCAGAATCATGTGCAGGCCACCCGGTGATTTGTAGACCA
33973 GCAGACATGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (42 bp):
ATTGCAGAATCATGTGCAGGCCACCCGGTGATTTGTAGACCA
Found at i:36894 original size:16 final size:15
Alignment explanation
Indices: 36871--36907 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
36861 GATCATCGGT
36871 TCGGTTTCGGAGTAG
1 TCGGTTTCGGAGTAG
*
36886 TCAGGTTTCGGTGTAG
1 TC-GGTTTCGGAGTAG
36902 TCGGTT
1 TCGGTT
36908 GGTGACTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.11, C:0.14, G:0.38, T:0.38
Consensus pattern (15 bp):
TCGGTTTCGGAGTAG
Found at i:43059 original size:16 final size:16
Alignment explanation
Indices: 43038--43068 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43028 TTGTTCCCAT
*
43038 TCGAAGCATTTTGAGA
1 TCGAAGCATATTGAGA
43054 TCGAAGCATATTGAG
1 TCGAAGCATATTGAG
43069 GTTTTGGATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (16 bp):
TCGAAGCATATTGAGA
Found at i:45126 original size:2 final size:2
Alignment explanation
Indices: 45121--45220 Score: 184
Period size: 2 Copynumber: 50.5 Consensus size: 2
45111 ATATATATAT
45121 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
45163 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
45204 AG AG AG AG AG AA AG AG A
1 AG AG AG AG AG AG AG AG A
45221 ATTAGAATGC
Statistics
Matches: 95, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 94 0.99
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:46087 original size:19 final size:17
Alignment explanation
Indices: 46039--46088 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 17
46029 AACGTTGAAG
*
46039 TTATAACCTTATTTTTT
1 TTATAACCTTATGTTTT
46056 TTATAACCTCTTATAGTTTT
1 TTATAA-C-CTTAT-GTTTT
46076 TTAGTAACCTTAT
1 TTA-TAACCTTAT
46089 TAGATGTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 6 0.21
18 1 0.04
19 10 0.36
20 8 0.29
21 3 0.11
ACGTcount: A:0.26, C:0.14, G:0.04, T:0.56
Consensus pattern (17 bp):
TTATAACCTTATGTTTT
Found at i:47306 original size:44 final size:44
Alignment explanation
Indices: 47257--47347 Score: 173
Period size: 44 Copynumber: 2.1 Consensus size: 44
47247 TCTTGGGATA
*
47257 TTCCTAATCAGTTTTTGTTAGATTATTAGATTAGTTTTCAATTT
1 TTCCTAATCAATTTTTGTTAGATTATTAGATTAGTTTTCAATTT
47301 TTCCTAATCAATTTTTGTTAGATTATTAGATTAGTTTTCAATTT
1 TTCCTAATCAATTTTTGTTAGATTATTAGATTAGTTTTCAATTT
47345 TTC
1 TTC
47348 AAATAGTATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.55
Consensus pattern (44 bp):
TTCCTAATCAATTTTTGTTAGATTATTAGATTAGTTTTCAATTT
Done.