Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011510.1 Corchorus capsularis cultivar CVL-1 contig11531, 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: 16892
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:687 original size:40 final size:41
Alignment explanation
Indices: 543--680 Score: 224
Period size: 41 Copynumber: 3.4 Consensus size: 41
533 ATGGATTAAT
* *
543 GAAGTAATCAGTGAAATCAGTAATTAAAGAGTCAAAGTAAAA
1 GAAGTAATCAGTAAAAT-GGTAATTAAAGAGTCAAAGTAAAA
585 GAAGTAATCAGTAAAATGGTAATTAAAGAGTCAAAGTAAAA
1 GAAGTAATCAGTAAAATGGTAATTAAAGAGTCAAAGTAAAA
*
626 GAAGTAATCAGTAAAATGGTAATT-AAGAGTAAAAGTAAAA
1 GAAGTAATCAGTAAAATGGTAATTAAAGAGTCAAAGTAAAA
*
666 GAAGTGATCAGTAAA
1 GAAGTAATCAGTAAA
681 TCGGTAAAGA
Statistics
Matches: 92, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
40 29 0.32
41 47 0.51
42 16 0.17
ACGTcount: A:0.53, C:0.05, G:0.20, T:0.22
Consensus pattern (41 bp):
GAAGTAATCAGTAAAATGGTAATTAAAGAGTCAAAGTAAAA
Found at i:783 original size:32 final size:33
Alignment explanation
Indices: 729--792 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
719 CAGTAAAGGG
729 TAAAATGGTAAAATGGTAATTAAATTCAAAGAA
1 TAAAATGGTAAAATGGTAATTAAATTCAAAGAA
* * *
762 TAAAATGG-CAAATGGTGATTAAGTTCAAAGA
1 TAAAATGGTAAAATGGTAATTAAATTCAAAGA
793 GCGAAAATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 20 0.71
33 8 0.29
ACGTcount: A:0.50, C:0.05, G:0.19, T:0.27
Consensus pattern (33 bp):
TAAAATGGTAAAATGGTAATTAAATTCAAAGAA
Found at i:808 original size:26 final size:26
Alignment explanation
Indices: 779--832 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
769 GCAAATGGTG
*
779 ATTAAGTTCAA-AGAGCGAAAATAGTA
1 ATTAAATTCAAGAGAG-GAAAATAGTA
*
805 ATTAAATTCAAGAGAGTAAAATAGTA
1 ATTAAATTCAAGAGAGGAAAATAGTA
831 AT
1 AT
833 CAGTAAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.52, C:0.06, G:0.17, T:0.26
Consensus pattern (26 bp):
ATTAAATTCAAGAGAGGAAAATAGTA
Found at i:933 original size:22 final size:22
Alignment explanation
Indices: 886--997 Score: 108
Period size: 22 Copynumber: 5.2 Consensus size: 22
876 AATAGTAATT
886 AGTAAAA--GTAATCAGT-AAG
1 AGTAAAATGGTAATCAGTAAAG
**
905 AACAAAATGGTAATCAGTAAAG
1 AGTAAAATGGTAATCAGTAAAG
** *
927 AGTAAAATATTAATCAGTAAAA
1 AGTAAAATGGTAATCAGTAAAG
*
949 AGTAAGAA-GGTAAACAGTAAAG
1 AGTAA-AATGGTAATCAGTAAAG
*
971 AGTAAAATGATAATCAGTAGAAG
1 AGTAAAATGGTAATCAGTA-AAG
994 -GTAA
1 AGTAA
998 TTAGTAAGAG
Statistics
Matches: 74, Mismatches: 13, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
19 5 0.07
21 11 0.15
22 53 0.72
23 5 0.07
ACGTcount: A:0.54, C:0.05, G:0.20, T:0.21
Consensus pattern (22 bp):
AGTAAAATGGTAATCAGTAAAG
Found at i:1018 original size:21 final size:22
Alignment explanation
Indices: 994--1034 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
984 TCAGTAGAAG
*
994 GTAATTAGT-AAGAGTAAAATA
1 GTAATCAGTAAAGAGTAAAATA
1015 GTAATCAGTAAAGAGTAAAA
1 GTAATCAGTAAAGAGTAAAA
1035 GGTGGTCAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.54, C:0.02, G:0.20, T:0.24
Consensus pattern (22 bp):
GTAATCAGTAAAGAGTAAAATA
Found at i:1020 original size:35 final size:36
Alignment explanation
Indices: 953--1033 Score: 105
Period size: 35 Copynumber: 2.3 Consensus size: 36
943 GTAAAAAGTA
953 AGAAGGTAAACAGTAAAGAGTAAAATGATAATCAGT
1 AGAAGGTAAACAGTAAAGAGTAAAATGATAATCAGT
**
989 AGAAGGTAATTAGT-AAGAGTAAAAT-AGTAATCAGT
1 AGAAGGTAAACAGTAAAGAGTAAAATGA-TAATCAGT
1024 A-AAGAGTAAA
1 AGAAG-GTAAA
1034 AGGTGGTCAG
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
34 4 0.10
35 24 0.60
36 12 0.30
ACGTcount: A:0.53, C:0.04, G:0.22, T:0.21
Consensus pattern (36 bp):
AGAAGGTAAACAGTAAAGAGTAAAATGATAATCAGT
Found at i:1165 original size:29 final size:29
Alignment explanation
Indices: 1104--1167 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 29
1094 GTGGTAATCA
*
1104 ATAAAAGAGAGTAAGAAAAGAGTAAATAT
1 ATAAAAGAGAGTAAGAAAAGAGTAAAAAT
*
1133 -TAAAA-AGAGTGAGAAAAGAGTAAAAAT
1 ATAAAAGAGAGTAAGAAAAGAGTAAAAAT
1160 GATAAAAG
1 -ATAAAAG
1168 TAGCATGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
27 20 0.67
28 5 0.17
29 5 0.17
ACGTcount: A:0.62, C:0.00, G:0.22, T:0.16
Consensus pattern (29 bp):
ATAAAAGAGAGTAAGAAAAGAGTAAAAAT
Found at i:3118 original size:2 final size:2
Alignment explanation
Indices: 3111--3137 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3101 AGGCCTGGTA
3111 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 A
3138 CTCAATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8411 original size:19 final size:19
Alignment explanation
Indices: 8380--8421 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
8370 CTACTTTGGG
8380 CTTTCTTGTTTGGACTTTC
1 CTTTCTTGTTTGGACTTTC
*
8399 CTTTACTTG-TTGGACTTTG
1 CTTT-CTTGTTTGGACTTTC
8418 CTTT
1 CTTT
8422 GGGTCATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.07, C:0.19, G:0.17, T:0.57
Consensus pattern (19 bp):
CTTTCTTGTTTGGACTTTC
Found at i:11177 original size:35 final size:35
Alignment explanation
Indices: 11136--11575 Score: 580
Period size: 35 Copynumber: 12.5 Consensus size: 35
11126 AGTAATAAGT
* *
11136 AACTTAATTCAGGGTAATTAAGTCAGTCAGTAATT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* * * *
11171 AACTTAATTCAGGGTAATTAAGTAATTTAGTTATT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* *
11206 AATTTAATTCAGGGTAATTAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* *
11241 AACTTCATTCAGGGTAATTAAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* *
11276 AACTTAATTCAGGGTAATTAAGTAATTCAGTTATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
11311 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* *
11346 AACTTAATTCTGGGTAATTAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
11381 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* *
11416 AACTTAATTCAGGGTAAATAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
11451 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
** * * * *
11486 AACTTTAATTTGGGGTAATTAAGTGAGGT-AATGATT
1 AAC-TTAATTCAGGGTAATTAAGT-AAGTCAGTAATC
*
11522 AACTTAATTCAGGGTAATTAAGT-AGTTCAATAAGT-
1 AACTTAATTCAGGGTAATTAAGTAAG-TCAGTAA-TC
*
11557 AACTTAATTCAAGGTAATT
1 AACTTAATTCAGGGTAATT
11576 TAGTTTAGTA
Statistics
Matches: 357, Mismatches: 43, Indels: 10
0.87 0.10 0.02
Matches are distributed among these distances:
33 1 0.00
34 1 0.00
35 327 0.92
36 26 0.07
37 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (35 bp):
AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
Done.