Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003061.1 Corchorus capsularis cultivar CVL-1 contig03069, 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, 700
Length: 1168
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Found at i:193 original size:22 final size:22
Alignment explanation
Indices: 168--451 Score: 121
Period size: 22 Copynumber: 13.1 Consensus size: 22
158 GAATTGTTAG
*
168 TAATCATACTCTGAAATTTTGA
1 TAATCATACTATGAAATTTTGA
*
190 TAATCACACTATGAAATTTTGA
1 TAATCATACTATGAAATTTTGA
* *
212 TAA-CCTCGCTATGAAATTTTGA
1 TAATCAT-ACTATGAAATTTTGA
* * *
234 TAAATCTTCCTATAAAATTTTGA
1 T-AATCATACTATGAAATTTTGA
* * * *
257 TAAACCTCCCTATAAAATTTTGA
1 TAATCAT-ACTATGAAATTTTGA
* * *
280 TAA-CTTTCTTATGAAATCTTGA
1 TAATCATAC-TATGAAATTTTGA
302 TAA-C-TAC----AAATTTTGA
1 TAATCATACTATGAAATTTTGA
* * * **
318 TAA-CCTCCCTAGGATTTTTTGA
1 TAATCAT-ACTATGAAATTTTGA
*
340 TAACCTCAT--TATGAAATTTTGT
1 TAA--TCATACTATGAAATTTTGA
*
362 TAATC-TCCCTATGAAATTTTGA
1 TAATCAT-ACTATGAAATTTTGA
*
384 T-CTGCATACTATGAAATTTTGA
1 TAAT-CATACTATGAAATTTTGA
* *
406 TAACCCT-CTTATGAAATTTTGA
1 TAATCATAC-TATGAAATTTTGA
* * *
428 -AAACTAAACTATAAAATTTTGA
1 TAATC-ATACTATGAAATTTTGA
450 TA
1 TA
452 TCCTCCCTGA
Statistics
Matches: 204, Mismatches: 34, Indels: 47
0.72 0.12 0.16
Matches are distributed among these distances:
16 12 0.06
17 1 0.00
18 1 0.00
19 1 0.00
20 2 0.01
21 9 0.04
22 137 0.67
23 37 0.18
24 2 0.01
25 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (22 bp):
TAATCATACTATGAAATTTTGA
Found at i:227 original size:44 final size:43
Alignment explanation
Indices: 44--946 Score: 247
Period size: 44 Copynumber: 20.9 Consensus size: 43
34 GAGACGTCAG
*
44 TATGAAATTTTGATAA-CTTCCCAATGAAATTTTGATAA-CTAACAC
1 TATGAAATTTTGATAATC-T-CCTATGAAATTTTGATAACCT--CAC
* * * * * * **
89 TATGAGATGTTGATAACCTCCATATGATATATTGATAACCACGT
1 TATGAAATTTTGATAATCTCC-TATGAAATTTTGATAACCTCAC
* * * * *
133 TATGAAAATTTAAAAACCTCCATATG-AATTGTT-AGTAATCAT-AC
1 TATGAAATTTTGATAATCTCC-TATGAAATT-TTGA-TAA-CCTCAC
* * *
177 TCTGAAATTTTGATAATCACACTATGAAATTTTGATAACCTCGC
1 TATGAAATTTTGATAATCTC-CTATGAAATTTTGATAACCTCAC
* *
221 TATGAAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AATC-TCCTATGAAATTTTGAT-AACCTCAC
* * * *
267 TATAAAATTTTGATAACTTTCTTATGAAATCTTGATAA-CT-AC
1 TATGAAATTTTGATAA-TCTCCTATGAAATTTTGATAACCTCAC
* * ** *
309 ----AAATTTTGATAACCTCCCTAGGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAATCT-CCTATGAAATTTTGATAACCTCAC
* ** *
349 TATGAAATTTTGTTAATCTCCCTATGAAATTTTGATCTGCAT-AC
1 TATGAAATTTTGATAATCT-CCTATGAAATTTTGAT-AACCTCAC
* * * *
393 TATGAAATTTTGATAACCCTCTTATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAA-TCTCCTATGAAATTTTGATAACCT-CAC
* * * *
437 TATAAAATTTTGAT-ATCCTCC-CTGAAATTTTGATATCTTC-C
1 TATGAAATTTTGATAAT-CTCCTATGAAATTTTGATAACCTCAC
* * * * *
478 ATAATAAAAGTTTAATAACCTTCC--T--AA-TTTGGTAACCAT-AC
1 -T-ATGAAATTTTGATAATC-TCCTATGAAATTTTGATAACC-TCAC
* *
519 TATGAAATTTTGATAACCTTCCCA-G-AA-----AT-A--TCAC
1 TATGAAATTTTGATAATC-TCCTATGAAATTTTGATAACCTCAC
* * * * **
553 TATGAAATTTTTG-TAATCACATTCTGAAAATTTGATAACCTCTT
1 TATGAAA-TTTTGATAATCTC-CTATGAAATTTTGATAACCTCAC
* * * * * * *
597 TCTGAAATTTTGATAACCTCTTTATAAAATTTTGTTGATCC-C-T
1 TATGAAATTTTGATAATCTC-CTATGAAATTTTGAT-AACCTCAC
* * * * * *
640 TAATGAAATTCTGATAATCACATTATGTAATTTTGATAACATCGC
1 T-ATGAAATTTTGATAATCTC-CTATGAAATTTTGATAACCTCAC
* * *
685 TTTCG-AATTTTGATAATCTTCCTAT-AAATTTTGATAATCTGATCTC
1 TAT-GAAATTTTGATAATC-TCCTATGAAATTTTGATAA-C--CTCAC
* * * * *
731 TATGGAATTTCGATAATCACTCTATGAGA-TTTGATAACCT-TC
1 TATGAAATTTTGATAATCTC-CTATGAAATTTTGATAACCTCAC
* * *
773 TATCAAATTTTGGT-A-CTCCTTATGAAACTGAGACTTTTATAACCTTCA-
1 TATGAAATTTTGATAATCTCC-TATGAAA-T-----TTTGATAACC-TCAC
* * * *
821 TATGAAATTTTGATAACCACGCTATAAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAATCTC-CTATGAAATTTTGATAACCTCAC
* * * * * *
865 CATGAAATATT-ACTAACCTCCTAATGAAATTTTGTTGACCACAC
1 TATGAAATTTTGA-TAATCTCCT-ATGAAATTTTGATAACCTCAC
* *
909 TATGAAATTCTT-ATAACCTCGCTATGACATTTTGATAA
1 TATGAAATT-TTGATAATCTC-CTATGAAATTTTGATAA
947 TCTCTTTGAT
Statistics
Matches: 634, Mismatches: 144, Indels: 161
0.68 0.15 0.17
Matches are distributed among these distances:
33 2 0.00
34 13 0.02
35 6 0.01
36 3 0.00
37 2 0.00
38 25 0.04
39 21 0.03
40 17 0.03
41 10 0.02
42 27 0.04
43 52 0.08
44 280 0.44
45 87 0.14
46 54 0.09
47 11 0.02
48 13 0.02
49 2 0.00
50 8 0.01
51 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.39
Consensus pattern (43 bp):
TATGAAATTTTGATAATCTCCTATGAAATTTTGATAACCTCAC
Found at i:302 original size:45 final size:46
Alignment explanation
Indices: 181--304 Score: 148
Period size: 45 Copynumber: 2.8 Consensus size: 46
171 TCATACTCTG
* * *
181 AAATTTTGAT-AATC-ACACTATGAAATTTTGAT-AACCTCGCTATG
1 AAATTTTGATAAATCTTC-CTATGAAATTTTGATAAACCTCCCTATA
*
225 AAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCCTATGAAATTTTGATAAACCTCCCTATA
* * *
271 AAATTTTGATAACT-TTCTTATGAAATCTTGATAA
1 AAATTTTGATAAATCTTCCTATGAAATTTTGATAA
305 CTACAAATTT
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
44 10 0.14
45 35 0.51
46 24 0.35
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.40
Consensus pattern (46 bp):
AAATTTTGATAAATCTTCCTATGAAATTTTGATAAACCTCCCTATA
Found at i:581 original size:22 final size:23
Alignment explanation
Indices: 555--614 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
545 AATATCACTA
*
555 TGAAATTTTTG-TAATCACATTC
1 TGAAATTTTTGATAACCACATTC
* * *
577 TGAAA-ATTTGATAACCTCTTTC
1 TGAAATTTTTGATAACCACATTC
599 TGAAA-TTTTGATAACC
1 TGAAATTTTTGATAACC
615 TCTTTATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 4 0.12
22 28 0.88
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (23 bp):
TGAAATTTTTGATAACCACATTC
Found at i:615 original size:22 final size:22
Alignment explanation
Indices: 574--630 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
564 TGTAATCACA
*
574 TTCTGAAAATTTGATAACCTCT
1 TTCTGAAATTTTGATAACCTCT
596 TTCTGAAATTTTGATAACCTCT
1 TTCTGAAATTTTGATAACCTCT
* *
618 TTATAAAATTTTG
1 TTCTGAAATTTTG
631 TTGATCCCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.46
Consensus pattern (22 bp):
TTCTGAAATTTTGATAACCTCT
Found at i:739 original size:25 final size:21
Alignment explanation
Indices: 663--748 Score: 66
Period size: 22 Copynumber: 3.8 Consensus size: 21
653 ATAATCACAT
*
663 TATGTAATTTTGATAA-CATCGC
1 TATG-AATTTTGATAATCTTC-C
*
685 TTTCGAATTTTGATAATCTTCC
1 TAT-GAATTTTGATAATCTTCC
*
707 TATAAATTTTGATAATCTGATCTC
1 TATGAATTTTGATAATCT--TC-C
*
731 TATGGAATTTCGATAATC
1 TAT-GAATTTTGATAATC
749 ACTCTATGAG
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
21 14 0.27
22 16 0.31
23 6 0.12
24 4 0.08
25 12 0.23
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (21 bp):
TATGAATTTTGATAATCTTCC
Found at i:836 original size:22 final size:21
Alignment explanation
Indices: 807--1168 Score: 150
Period size: 22 Copynumber: 16.5 Consensus size: 21
797 AAACTGAGAC
*
807 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCCTATGAAA
* *
828 TTTTGATAACCACGCTATAAAA
1 TTTTGATAACCTC-CTATGAAA
*
850 TTTTGATAACCTCCCCATGAAA
1 TTTTGATAACCT-CCTATGAAA
*
872 TATT-ACTAACCTCCTAATGAAA
1 TTTTGA-TAACCTCCT-ATGAAA
* * *
894 TTTTGTTGACCACACTATGAAA
1 TTTTGATAACCTC-CTATGAAA
*
916 TTCTT-ATAACCTCGCTATGACA
1 TT-TTGATAACCTC-CTATGAAA
* *
938 TTTTGATAATCT-CTTTGATAA
1 TTTTGATAACCTCCTATGA-AA
** *
959 CCTTTCT-ATAAAAT--TGTGAAA
1 --TTT-TGATAACCTCCTATGAAA
* *
980 -ATT--TAACCACCCTATTGAAA
1 TTTTGATAACC-TCCTA-TGAAA
** * *
1000 TTTCAATAACCCAACCTAAGAAA
1 TTTTGATAA-CC-TCCTATGAAA
*
1023 TTTTAATAACCTGATCCTATGAAA
1 TTTTGATAACC---TCCTATGAAA
* *
1047 TTTTGGTAACCACACTATGAAA
1 TTTTGATAACCTC-CTATGAAA
**
1069 TTTTGATAAGTTCCATATGAAA
1 TTTTGATAACCTCC-TATGAAA
* * *
1091 TTTTGGTAACCACGCTATGGAAT
1 TTTTGATAACCTC-CTAT-GAAA
1114 TTTTGATAACCTCCTCATGAAA
1 TTTTGATAACCTCCT-ATGAAA
* * *
1136 TTATAATAACCATCTTATGAAA
1 TTTTGATAACC-TCCTATGAAA
1158 TTTTGATAACC
1 TTTTGATAACC
Statistics
Matches: 257, Mismatches: 55, Indels: 57
0.70 0.15 0.15
Matches are distributed among these distances:
16 3 0.01
17 1 0.00
18 1 0.00
19 1 0.00
20 10 0.04
21 16 0.06
22 151 0.59
23 48 0.19
24 26 0.10
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (21 bp):
TTTTGATAACCTCCTATGAAA
Found at i:1046 original size:24 final size:23
Alignment explanation
Indices: 990--1077 Score: 72
Period size: 24 Copynumber: 3.8 Consensus size: 23
980 ATTTAACCAC
*
990 CCTATTGAAATTTCAATAACCCAA
1 CCTA-TGAAATTTTAATAACCCAA
* * *
1014 CCTAAGAAATTTTAATAACCTGAT
1 CCTATGAAATTTTAATAACC-CAA
**
1038 CCTATGAAATTTTGGTAA-CC-A
1 CCTATGAAATTTTAATAACCCAA
*
1059 CACTATGAAATTTTGATAA
1 C-CTATGAAATTTTAATAA
1078 GTTCCATATG
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
21 1 0.02
22 16 0.31
23 15 0.29
24 20 0.38
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (23 bp):
CCTATGAAATTTTAATAACCCAA
Done.