Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010985.1 Corchorus capsularis cultivar CVL-1 contig11006, 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: 29669
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Found at i:2429 original size:21 final size:22
Alignment explanation
Indices: 2384--2432 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
2374 TAAAATTGGT
*
2384 AATC-AAGAGTTTTCAAGATTT
1 AATCAAAGAGTTTTCAAGATTA
2405 AATCAAAG-GTTTTCAA-ATTCA
1 AATCAAAGAGTTTTCAAGATT-A
2426 AATCAAA
1 AATCAAA
2433 CTTAGTGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 3 0.12
21 19 0.76
22 3 0.12
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (22 bp):
AATCAAAGAGTTTTCAAGATTA
Found at i:8164 original size:183 final size:182
Alignment explanation
Indices: 7826--8172 Score: 423
Period size: 183 Copynumber: 1.9 Consensus size: 182
7816 ACTAAACCCC
* * * * *
7826 CTGATTTTTGGCTTGATTAACTAATTTTGCCTAAATCACAAAAACCCTAATTCACCAAGCGAGCT
1 CTGATTTTTGGCTTAATTAACTAACTTGGCCAAAATCACAAAAACCCTAATTCACCAAGCGAGCC
* * *
7891 AATTTGCCGCCTATGTTGCAATTTTTGCAAGGAAGGACTCGGCTCATTAGGGGTAGCTTGGTTCA
66 AATTTGCCGCCTAAGTTGCAATTTTTGCAA-GAAGGACACGGCTCATTAGGGATAGCTTGGTTCA
* * *
7956 TTAAATTGGGCTTATATTTATGTGATATAACCTAGTTATAAGGGTTTAACCTA
130 TCAAATTAGGCTTATATTCATGTGATATAACCTAGTTATAAGGGTTTAACCTA
* * * *
8009 CTGATTTTTGGCTTAATTAA-TCAACTTGGCCAAAATCACGAAAACCCTAATTTATCAAGCTAGC
1 CTGATTTTTGGCTTAATTAACT-AACTTGGCCAAAATCACAAAAACCCTAATTCACCAAGCGAGC
* * *
8073 CAATTTGCCG-CTAAGTTGCAATTTTTGCAA-AATGGGTCACGGC-CTATTAGGGATTGCTTGAT
65 CAATTTGCCGCCTAAGTTGCAATTTTTGCAAGAA--GGACACGGCTC-ATTAGGGATAGCTTG-G
* * *
8135 TTCATCAAATTAGGTTTATGTTCATGTGATATGACCTA
126 TTCATCAAATTAGGCTTATATTCATGTGATATAACCTA
8173 ATTTTACGAC
Statistics
Matches: 138, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
180 2 0.01
181 1 0.01
182 40 0.29
183 95 0.69
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (182 bp):
CTGATTTTTGGCTTAATTAACTAACTTGGCCAAAATCACAAAAACCCTAATTCACCAAGCGAGCC
AATTTGCCGCCTAAGTTGCAATTTTTGCAAGAAGGACACGGCTCATTAGGGATAGCTTGGTTCAT
CAAATTAGGCTTATATTCATGTGATATAACCTAGTTATAAGGGTTTAACCTA
Found at i:12536 original size:93 final size:91
Alignment explanation
Indices: 12435--12602 Score: 264
Period size: 91 Copynumber: 1.8 Consensus size: 91
12425 AGGCTTGAGT
***
12435 TAAAAGATTGAACTTGTGGTTAATTTATAAATAAAAATGAGATCCTTTGTGCTAAATGATTGAAC
1 TAAAAGATTGAACTTGTGGTTAATTTAT-AATAAAAATGAGAT-CTTTGAAATAAATGATTGAAC
*
12500 TTGTGATTAATTAATGAGATCCTTGAAC
64 TTGTGATCAATTAATGAGATCCTTGAAC
*
12528 TAAAAGATTGAACTTGTGGTTAATTTATGATAAAAATGAGATCTTTGAAATAAATGATTGAACTT
1 TAAAAGATTGAACTTGTGGTTAATTTATAATAAAAATGAGATCTTTGAAATAAATGATTGAACTT
*
12593 TTGATCAATT
66 GTGATCAATT
12603 TGTAATAAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
91 28 0.41
92 13 0.19
93 28 0.41
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.38
Consensus pattern (91 bp):
TAAAAGATTGAACTTGTGGTTAATTTATAATAAAAATGAGATCTTTGAAATAAATGATTGAACTT
GTGATCAATTAATGAGATCCTTGAAC
Found at i:12539 original size:41 final size:42
Alignment explanation
Indices: 12470--12557 Score: 124
Period size: 41 Copynumber: 2.1 Consensus size: 42
12460 TATAAATAAA
** *
12470 AATGAGATCCTTTGTGCTAAATGATTGAACTTGTGATTAATT
1 AATGAGATCCTTTGAACTAAAAGATTGAACTTGTGATTAATT
*
12512 AATGAGATCC-TTGAACTAAAAGATTGAACTTGTGGTTAATT
1 AATGAGATCCTTTGAACTAAAAGATTGAACTTGTGATTAATT
*
12553 TATGA
1 AATGA
12558 TAAAAATGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 31 0.76
42 10 0.24
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (42 bp):
AATGAGATCCTTTGAACTAAAAGATTGAACTTGTGATTAATT
Found at i:12603 original size:50 final size:50
Alignment explanation
Indices: 12512--12652 Score: 153
Period size: 50 Copynumber: 2.8 Consensus size: 50
12502 GTGATTAATT
* * * * *
12512 AATGAGATCCTTGAACTAAAAGATTGAACTTGTGGTTAATTTATGATAAA
1 AATGAGATCTTTGAACTAAAAGATTGAACTTTTGATAAATTTATAATAAA
* * * *
12562 AATGAGATCTTTGAAATAAATGATTGAACTTTTGATCAATTTGTAATAAA
1 AATGAGATCTTTGAACTAAAAGATTGAACTTTTGATAAATTTATAATAAA
*
12612 AGTGA-AGTCTTT-AAGCTAAAAGATT-AACTTTTGATAAATTT
1 AATGAGA-TCTTTGAA-CTAAAAGATTGAACTTTTGATAAATTT
12653 GGAATGAAAT
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
49 18 0.23
50 59 0.77
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (50 bp):
AATGAGATCTTTGAACTAAAAGATTGAACTTTTGATAAATTTATAATAAA
Found at i:13228 original size:48 final size:48
Alignment explanation
Indices: 13157--13619 Score: 574
Period size: 48 Copynumber: 9.7 Consensus size: 48
13147 ATGTCAATTC
* * * * * *
13157 CCTGTTTTGTCCTTCTCAGTCGGAAGGCGCTATATTCAGTGTTTCTTT
1 CCTGTTTTGCCCTTCCCGGTCGGAAGGTGCTATCTTCAGTGTTTATTT
* * * *
13205 CCTGTTTTGCCCTTCCCGGTCGGAAGGTGCTATTTTCCGTATCTATTT
1 CCTGTTTTGCCCTTCCCGGTCGGAAGGTGCTATCTTCAGTGTTTATTT
* * *
13253 CCCGTTTTGCCCTTCCCGGTCGGAAGGTGCTACCTTCAGTGTTTCTTT
1 CCTGTTTTGCCCTTCCCGGTCGGAAGGTGCTATCTTCAGTGTTTATTT
* * * *
13301 CCTGTTTT-CCCTTCCCGGTCGGTAGGTGCTATTTTCAGTATCTATTT
1 CCTGTTTTGCCCTTCCCGGTCGGAAGGTGCTATCTTCAGTGTTTATTT
* * * **
13348 CCCGTTTTGCCCTTCACGGTCGGAAGGTGCTACCTTCAGTGTCAATTT
1 CCTGTTTTGCCCTTCCCGGTCGGAAGGTGCTATCTTCAGTGTTTATTT
*
13396 CCTGTTTTGCCCTTCCCGGTCGGAAGGTGC-AGTTTTCAGTGTTTATTT
1 CCTGTTTTGCCCTTCCCGGTCGGAAGGTGCTA-TCTTCAGTGTTTATTT
* * *
13444 CCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTATCCTCGGTGTTTATTT
1 CCTGTTTTGCCCTTCCCGGTCGGAAGGTGCTATCTTCAGTGTTTATTT
*
13492 -CTATTTTTGCCCTTCCCGGTCGGAAGGTG-TAGTCTTCAGTGTTTATTT
1 CCT-GTTTTGCCCTTCCCGGTCGGAAGGTGCTA-TCTTCAGTGTTTATTT
* * * * *
13540 CTTGTTTTGTCCTTCCCGGTCGGAAGTTGCTATTTTCAGTGTCTATTT
1 CCTGTTTTGCCCTTCCCGGTCGGAAGGTGCTATCTTCAGTGTTTATTT
*
13588 CCAGTTTTGCCCTTCCCGGTCGGAAGGTGCTA
1 CCTGTTTTGCCCTTCCCGGTCGGAAGGTGCTA
13620 GATTTGTCTT
Statistics
Matches: 354, Mismatches: 54, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
47 44 0.12
48 306 0.86
49 4 0.01
ACGTcount: A:0.11, C:0.26, G:0.23, T:0.40
Consensus pattern (48 bp):
CCTGTTTTGCCCTTCCCGGTCGGAAGGTGCTATCTTCAGTGTTTATTT
Found at i:23855 original size:30 final size:30
Alignment explanation
Indices: 23815--23873 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
23805 TGTCTTCAAG
*
23815 TCCATAATAAGTCCTT-GGCGCATCATTCCT
1 TCCATAATAAG-CCTTGGGCACATCATTCCT
*
23845 TCCATGATAAGCCTTGGGCACATCATTCC
1 TCCATAATAAGCCTTGGGCACATCATTCC
23874 CTCTCCTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.31
Consensus pattern (30 bp):
TCCATAATAAGCCTTGGGCACATCATTCCT
Found at i:24290 original size:33 final size:33
Alignment explanation
Indices: 24253--24337 Score: 125
Period size: 33 Copynumber: 2.6 Consensus size: 33
24243 TCTTTTCATT
24253 CAAAACAGAATTATTTTCAATGCTATGATCAAC
1 CAAAACAGAATTATTTTCAATGCTATGATCAAC
* *
24286 CAAAACAAAATTATTTTTAATGCTATGATCAAC
1 CAAAACAGAATTATTTTCAATGCTATGATCAAC
* * *
24319 CAAAATAGATTTGTTTTCA
1 CAAAACAGAATTATTTTCA
24338 TCACAATTAG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.34
Consensus pattern (33 bp):
CAAAACAGAATTATTTTCAATGCTATGATCAAC
Found at i:24390 original size:33 final size:32
Alignment explanation
Indices: 24353--24457 Score: 120
Period size: 33 Copynumber: 3.2 Consensus size: 32
24343 ATTAGTATCC
* *
24353 AAAACAGATTTAGTTTCATCACAAACAACACCT
1 AAAACAGATTTAGTATCATCGCAAACAACA-CT
* *
24386 AAAACAGATTTAGTGTCATTGCAAACAACACT
1 AAAACAGATTTAGTATCATCGCAAACAACACT
** *
24418 CAAATTAGGTTTAGTATCATCGCAAACAACATCT
1 -AAAACAGATTTAGTATCATCGCAAACAACA-CT
24452 AAAACA
1 AAAACA
24458 CTCTTTGCAA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
32 2 0.03
33 56 0.93
34 2 0.03
ACGTcount: A:0.45, C:0.21, G:0.10, T:0.25
Consensus pattern (32 bp):
AAAACAGATTTAGTATCATCGCAAACAACACT
Done.