Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013493.1 Corchorus capsularis cultivar CVL-1 contig13514, 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: 5742
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Found at i:433 original size:27 final size:27
Alignment explanation
Indices: 403--478 Score: 69
Period size: 27 Copynumber: 3.1 Consensus size: 27
393 AATCGGAGTC
403 AAAGTGATGGTAATCAGTAAATCAGTA
1 AAAGTGATGGTAATCAGTAAATCAGTA
* * *
430 AAAGAGAT--TAATC-G-----GAGTC
1 AAAGTGATGGTAATCAGTAAATCAGTA
449 AAAGTGATGGTAATCAGTAAATCAGTA
1 AAAGTGATGGTAATCAGTAAATCAGTA
476 AAA
1 AAA
479 AGAGATTAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 16
0.61 0.11 0.28
Matches are distributed among these distances:
19 10 0.29
21 5 0.14
22 1 0.03
24 1 0.03
25 5 0.14
27 13 0.37
ACGTcount: A:0.46, C:0.08, G:0.22, T:0.24
Consensus pattern (27 bp):
AAAGTGATGGTAATCAGTAAATCAGTA
Found at i:448 original size:93 final size:94
Alignment explanation
Indices: 320--524 Score: 333
Period size: 93 Copynumber: 2.2 Consensus size: 94
310 GTAAAAAGAA
320 AATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAAGTGATGGTAATCAGTAAATCAGTAAA
1 AATCAGTAAATCAGT-AAAAGAGATTAATCAGAGTCAAAGTGATGGTAATCAGTAAATCAGTAAA
** * *
385 AAGAGATTAATC-GGAGTCAA-AGTGATGGT
65 AAGAGATTAATCAAAAGTCAAGA-TAATAGT
*
414 AATCAGTAAATCAGTAAAAGAGATTAATCGGAGTCAAAGTGATGGTAATCAGTAAATCAGTAAAA
1 AATCAGTAAATCAGTAAAAGAGATTAATCAGAGTCAAAGTGATGGTAATCAGTAAATCAGTAAAA
479 AGAGATTAATCAAAAGTCAAGATAATAGT
66 AGAGATTAATCAAAAGTCAAGATAATAGT
508 AATCAGTAAATCAGTAA
1 AATCAGTAAATCAGTAA
525 TCAAGTAAAA
Statistics
Matches: 104, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
93 60 0.58
94 43 0.41
95 1 0.01
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.23
Consensus pattern (94 bp):
AATCAGTAAATCAGTAAAAGAGATTAATCAGAGTCAAAGTGATGGTAATCAGTAAATCAGTAAAA
AGAGATTAATCAAAAGTCAAGATAATAGT
Found at i:450 original size:46 final size:47
Alignment explanation
Indices: 320--524 Score: 333
Period size: 47 Copynumber: 4.4 Consensus size: 47
310 GTAAAAAGAA
320 AATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAAGTGATGGT
1 AATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAAGTGATGGT
*
367 AATCAGTAAATCAGTAAAAAGAGATTAATCGGAGTCAAAGTGATGGT
1 AATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAAGTGATGGT
*
414 AATCAGTAAATCAGT-AAAAGAGATTAATCGGAGTCAAAGTGATGGT
1 AATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAAGTGATGGT
* * *
460 AATCAGTAAATCAGTAAAAAGAGATTAATCAAAAGTC-AAGATAATAGT
1 AATCAGTAAATCAGTAAAAAGAGATTAATC-AGAGTCAAAG-TGATGGT
508 AATCAGTAAATCAGTAA
1 AATCAGTAAATCAGTAA
525 TCAAGTAAAA
Statistics
Matches: 150, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
46 46 0.31
47 78 0.52
48 26 0.17
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.23
Consensus pattern (47 bp):
AATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAAGTGATGGT
Found at i:621 original size:32 final size:31
Alignment explanation
Indices: 556--621 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
546 AGTAAATTGA
* *
556 TAATTACGAGTCAAGGTAAGAGATTAATCAG
1 TAATTAAGAGTCAAGGTAAGAAATTAATCAG
587 TAATTAAGAGTCAAGGTAA-AAATAGTAATCAG
1 TAATTAAGAGTCAAGGTAAGAAAT--TAATCAG
619 TAA
1 TAA
622 ATCAGTGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 3 0.10
31 18 0.58
32 10 0.32
ACGTcount: A:0.47, C:0.08, G:0.20, T:0.26
Consensus pattern (31 bp):
TAATTAAGAGTCAAGGTAAGAAATTAATCAG
Found at i:639 original size:71 final size:71
Alignment explanation
Indices: 485--640 Score: 158
Period size: 71 Copynumber: 2.2 Consensus size: 71
475 AAAAAGAGAT
* * *
485 TAATCAAAAGTCAAGATAATAGTAATCAGTAAATCAGTAATCAAGTAAAAACATAGTAATCAGTA
1 TAATTAAAAGTCAAGATAAGAGTAATCAGTAAATAAGTAATCAAGTAAAAACATAGTAATCAGTA
*
550 AATTGA
66 AATAGA
** * * *
556 TAATTACGAGTCAAGGTAAGAGATTAATCAGTAATTAAG-AGTCAAGGT-AAAA-ATAGTAATCA
1 TAATTAAAAGTCAAGATAAGAG--TAATCAGTAAATAAGTAATCAA-GTAAAAACATAGTAATCA
618 GTAAATCAG-
63 GTAAAT-AGA
*
627 TGATTAAAAGTCAA
1 TAATTAAAAGTCAA
641 TAGATTGATC
Statistics
Matches: 69, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
71 44 0.64
72 10 0.14
73 15 0.22
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.26
Consensus pattern (71 bp):
TAATTAAAAGTCAAGATAAGAGTAATCAGTAAATAAGTAATCAAGTAAAAACATAGTAATCAGTA
AATAGA
Found at i:849 original size:35 final size:35
Alignment explanation
Indices: 808--902 Score: 136
Period size: 35 Copynumber: 2.7 Consensus size: 35
798 AAAATGATAA
*
808 AAAAAGTAAAGAGTAATCAGCAAAAGAAGAATGGT
1 AAAAAGTAAAGAGTAATCAGCAAAAGAAGAACGGT
* * *
843 AAAAAGTAAAGAATAATCAGTAAAGGAAGAACGGT
1 AAAAAGTAAAGAGTAATCAGCAAAAGAAGAACGGT
* *
878 AAAGAGTAAAGGGTAATCAGCAAAA
1 AAAAAGTAAAGAGTAATCAGCAAAA
903 AGTAAAAAGA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.57, C:0.06, G:0.23, T:0.14
Consensus pattern (35 bp):
AAAAAGTAAAGAGTAATCAGCAAAAGAAGAACGGT
Found at i:1020 original size:21 final size:21
Alignment explanation
Indices: 996--1207 Score: 124
Period size: 21 Copynumber: 9.6 Consensus size: 21
986 ATCAGTAGAA
* *
996 AGTAATCATTAAGAGTAAAAC
1 AGTAATCAGTAAGAGTAAAAT
* * * *
1017 AGTAACCAGTGAGAGCAAAGT
1 AGTAATCAGTAAGAGTAAAAT
* * *
1038 GGTAATTAGTAAGAGTCAAAT
1 AGTAATCAGTAAGAGTAAAAT
*
1059 AGTAATCAGTAAGAAGTAAAAG
1 AGTAATCAGTAAG-AGTAAAAT
*
1081 AGTAATCAGTAAAAAAGGAGCAGAAAAT
1 AGTAATCAGT----AA-GAG--TAAAAT
1109 AGTAATCAGTAAAAGAGTAAAAT
1 AGTAATCAGT--AAGAGTAAAAT
* * *
1132 GGTAATCAGTAAAAAGTAAGA-
1 AGTAATCAGT-AAGAGTAAAAT
**
1153 AGCTAATCAACAAGAGTAAAAT
1 AG-TAATCAGTAAGAGTAAAAT
*
1175 AGTAATCAGTACAAAGTAAAGA-
1 AGTAATCAGTA-AGAGTAAA-AT
1197 A-TAATCAGTAA
1 AGTAATCAGTAA
1208 AATAATGATG
Statistics
Matches: 148, Mismatches: 31, Indels: 25
0.73 0.15 0.12
Matches are distributed among these distances:
20 1 0.01
21 65 0.44
22 41 0.28
23 15 0.10
25 3 0.02
26 8 0.05
27 1 0.01
28 14 0.09
ACGTcount: A:0.52, C:0.08, G:0.20, T:0.20
Consensus pattern (21 bp):
AGTAATCAGTAAGAGTAAAAT
Found at i:1091 original size:15 final size:15
Alignment explanation
Indices: 1073--1128 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
1063 ATCAGTAAGA
1073 AGTAAAAGAGTAATC
1 AGTAAAAGAGTAATC
* * *
1088 AGTAAAAAAG-GAGC
1 AGTAAAAGAGTAATC
*
1102 AG-AAAATAGTAATC
1 AGTAAAAGAGTAATC
1116 AGTAAAAGAGTAA
1 AGTAAAAGAGTAA
1129 AATGGTAATC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 6 0.19
14 8 0.25
15 18 0.56
ACGTcount: A:0.57, C:0.05, G:0.21, T:0.16
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:5118 original size:20 final size:20
Alignment explanation
Indices: 5090--5143 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
5080 AAATAGGATA
*
5090 TTTGGCTAAAAGATGTAACC
1 TTTGACTAAAAGATGTAACC
*
5110 TTTGACTAAAAGATTTAACC
1 TTTGACTAAAAGATGTAACC
*
5130 TTTGAATAAAAGAT
1 TTTGACTAAAAGAT
5144 TGAATTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (20 bp):
TTTGACTAAAAGATGTAACC
Found at i:5314 original size:101 final size:101
Alignment explanation
Indices: 5118--5322 Score: 236
Period size: 101 Copynumber: 2.0 Consensus size: 101
5108 CCTTTGACTA
* *
5118 AAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAATAATTGGTAAATAAAAATGTCGTCTTT
1 AAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAATAATTAGTAAATAAAAATGTCGACTTT
* * **
5183 GGGTAAAAGATTGAATCTTTAGAGTGATTAGTAAAT
66 GAGTAAAAGATTAAATCTTTAGAGCCATTAGTAAAT
* * * *
5219 AAAGCTTTAACCTTTGAATGAAAGATTGAATTTTTAAGTAATTAGTAGAT-AAAATGTC-ACATT
1 AAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAATAATTAGTAAATAAAAATGTCGAC-TT
* * * *
5282 TGAATTAGAAGTTTAAACTTTTTAG-GCCATTAGTAAAT
65 TG-AGTAAAAGATTAAA-TCTTTAGAGCCATTAGTAAAT
5320 AAA
1 AAA
5323 TTGATTAGTT
Statistics
Matches: 87, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
99 1 0.01
100 12 0.14
101 68 0.78
102 6 0.07
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (101 bp):
AAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAATAATTAGTAAATAAAAATGTCGACTTT
GAGTAAAAGATTAAATCTTTAGAGCCATTAGTAAAT
Done.