Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015407.1 Corchorus olitorius cultivar O-4 contig15440, 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: 4022
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Found at i:160 original size:29 final size:29
Alignment explanation
Indices: 118--206 Score: 132
Period size: 29 Copynumber: 3.2 Consensus size: 29
108 AAAAAAAACA
118 GAGAGAGAGAGACGAGAGACCGAGAGCGC
1 GAGAGAGAGAGACGAGAGACCGAGAGCGC
147 GAGAGAGAGAGACGAGAGACCGAGA----
1 GAGAGAGAGAGACGAGAGACCGAGAGCGC
* *
172 GAGAGAGAGAGTCGAGAGACCTAGAGCGC
1 GAGAGAGAGAGACGAGAGACCGAGAGCGC
201 GAGAGA
1 GAGAGA
207 CCTTCAATAA
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
25 23 0.43
29 31 0.57
ACGTcount: A:0.39, C:0.15, G:0.44, T:0.02
Consensus pattern (29 bp):
GAGAGAGAGAGACGAGAGACCGAGAGCGC
Found at i:190 original size:2 final size:2
Alignment explanation
Indices: 117--182 Score: 60
Period size: 2 Copynumber: 32.0 Consensus size: 2
107 GAAAAAAAAC
* * * *
117 AG AG AG AG AG AG ACG AG AG AC CG AG AG CG CG AG AG AG AG AG ACG
1 AG AG AG AG AG AG A-G AG AG AG AG AG AG AG AG AG AG AG AG AG A-G
* *
161 AG AG AC CG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG
183 TCGAGAGACC
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
2 48 0.92
3 4 0.08
ACGTcount: A:0.42, C:0.12, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:197 original size:23 final size:24
Alignment explanation
Indices: 122--206 Score: 80
Period size: 25 Copynumber: 3.2 Consensus size: 24
112 AAAACAGAGA
122 GAGAGAGACGAGAGACCGAGAGCGCGAGA
1 GAGAGAGACGAGAGACC-AGA----GAGA
151 GAGAGAGACGAGAGACCGAGAGAGA
1 GAGAGAGACGAGAGACC-AGAGAGA
* * *
176 GAGAGAGTCGAGAGACCTAGAGCGC
1 GAGAGAGACGAGAGACC-AGAGAGA
201 GAGAGA
1 GAGAGA
207 CCTTCAATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
25 31 0.60
29 21 0.40
ACGTcount: A:0.39, C:0.15, G:0.44, T:0.02
Consensus pattern (24 bp):
GAGAGAGACGAGAGACCAGAGAGA
Found at i:619 original size:26 final size:26
Alignment explanation
Indices: 590--695 Score: 75
Period size: 26 Copynumber: 4.2 Consensus size: 26
580 AACAACCAGC
590 ACAATCAATGACAAGCAAAATCACAA
1 ACAATCAATGACAAGCAAAATCACAA
* *
616 ACAATCCA-G-C-A-CAAAA--AGAA
1 ACAATCAATGACAAGCAAAATCACAA
* *
636 ACAATGAAAGATCACAG-AAGAATCA-AA
1 ACAATCAATGA-CA-AGCAA-AATCACAA
*
663 TAAAATCAATGACAAGCAAAATCACAA
1 -ACAATCAATGACAAGCAAAATCACAA
690 ACAATC
1 ACAATC
696 CAGCACAAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 24
0.65 0.09 0.26
Matches are distributed among these distances:
20 9 0.15
21 1 0.02
22 5 0.08
23 2 0.03
24 1 0.02
25 4 0.07
26 21 0.35
27 8 0.13
28 9 0.15
ACGTcount: A:0.58, C:0.21, G:0.09, T:0.11
Consensus pattern (26 bp):
ACAATCAATGACAAGCAAAATCACAA
Found at i:731 original size:103 final size:99
Alignment explanation
Indices: 616--866 Score: 409
Period size: 103 Copynumber: 2.5 Consensus size: 99
606 AAAATCACAA
616 ACAATCCAGCACAAAAAGAAACAATGAAAGATCACAGAAGAATCAAATAAAATCAATGACAAGCA
1 ACAATCCAGCACAAAAAGAAACAA-GAAAGATCACAGAAGAATCAAATAAAATCAATGACAAGCA
681 AAATCACAAACAATCCAGCACAAAAGAAAACAAAG
65 AAATCACAAACAATCCAGCACAAAAGAAAACAAAG
716 ATCACAGTCCAGCACAAAAAGAAACAAAGAAAGATCACAGAAGAATCAAATAAAATCAATGACAA
1 A-CA-A-TCCAGCACAAAAAGAAAC-AAGAAAGATCACAGAAGAATCAAATAAAATCAATGACAA
781 GCAAAATCACAAACAATCCAGCACAAAAGAAAACAAAG
62 GCAAAATCACAAACAATCCAGCACAAAAGAAAACAAAG
* * *
819 ACAATCCAGCAC-AAAAG-AA-AACAAAGATCACAGAAGAATAAAAAAAAA
1 ACAATCCAGCACAAAAAGAAACAAGAAAGATCACAGAAGAATCAAATAAAA
867 AGTTTGGCTG
Statistics
Matches: 144, Mismatches: 3, Indels: 12
0.91 0.02 0.08
Matches are distributed among these distances:
96 26 0.18
98 2 0.01
99 5 0.03
100 9 0.06
101 3 0.02
102 3 0.02
103 94 0.65
104 2 0.01
ACGTcount: A:0.61, C:0.20, G:0.11, T:0.08
Consensus pattern (99 bp):
ACAATCCAGCACAAAAAGAAACAAGAAAGATCACAGAAGAATCAAATAAAATCAATGACAAGCAA
AATCACAAACAATCCAGCACAAAAGAAAACAAAG
Found at i:806 original size:26 final size:24
Alignment explanation
Indices: 793--845 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 24
783 AAAATCACAA
793 ACAATCCAGCACAAAAGAAAACAAAG
1 ACAATCCAGCAC--AAGAAAACAAAG
819 ACAATCCAGCACAAAAGAAAACAAAG
1 ACAATCCAGCAC--AAGAAAACAAAG
845 A
1 A
846 TCACAGAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.62, C:0.23, G:0.11, T:0.04
Consensus pattern (24 bp):
ACAATCCAGCACAAGAAAACAAAG
Found at i:3527 original size:16 final size:17
Alignment explanation
Indices: 3506--3552 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
3496 AGGGAGGAAA
3506 GAAATAGGAA-GAAAAG
1 GAAATAGGAAGGAAAAG
* *
3522 GAAATAGCAAGGGAAAG
1 GAAATAGGAAGGAAAAG
*
3539 GAAATAGGGAGGAA
1 GAAATAGGAAGGAA
3553 GGGAAAGGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 9 0.36
17 16 0.64
ACGTcount: A:0.55, C:0.02, G:0.36, T:0.06
Consensus pattern (17 bp):
GAAATAGGAAGGAAAAG
Found at i:3540 original size:17 final size:16
Alignment explanation
Indices: 3500--3545 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
3490 TTTGGTAGGG
*
3500 AGGAAA-GAAATAGGA
1 AGGAAAGGAAATAGCA
*
3515 AGAAAAGGAAATAGCA
1 AGGAAAGGAAATAGCA
3531 AGGGAAAGGAAATAG
1 A-GGAAAGGAAATAG
3546 GGAGGAAGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 5 0.19
16 9 0.35
17 12 0.46
ACGTcount: A:0.59, C:0.02, G:0.33, T:0.07
Consensus pattern (16 bp):
AGGAAAGGAAATAGCA
Found at i:3557 original size:16 final size:16
Alignment explanation
Indices: 3495--3558 Score: 67
Period size: 16 Copynumber: 4.0 Consensus size: 16
3485 GTCTGTTTGG
*
3495 TAGGGAGGAAA-GAAA
1 TAGGAAGGAAAGGAAA
*
3510 TAGGAAGAAAAGGAAA
1 TAGGAAGGAAAGGAAA
*
3526 TAGCAAGGGAAAGGAAA
1 TAGGAA-GGAAAGGAAA
* *
3543 TAGGGAGGAAGGGAAA
1 TAGGAAGGAAAGGAAA
3559 GGAAGTCACA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
15 9 0.22
16 18 0.45
17 13 0.32
ACGTcount: A:0.53, C:0.02, G:0.39, T:0.06
Consensus pattern (16 bp):
TAGGAAGGAAAGGAAA
Found at i:4001 original size:1 final size:1
Alignment explanation
Indices: 3995--4022 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
3985 GCCATTTCAC
3995 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.