Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012201.1 Corchorus olitorius cultivar O-4 contig12234, 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: 22812
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:9762 original size:47 final size:47
Alignment explanation
Indices: 9693--9787 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 47
9683 TCATATGAAT
* *
9693 GGTAGTAAATGCGAGTGTAGATGTGAGAATATAAAAGGAATAAGAAG
1 GGTAGTAAATGCGAGTGGAGATGTGAGAATATAAAAGGAATAACAAG
*
9740 GGTAGTAAATGCGAGTGGAGATGTGAGAATATAGAAGGAATAACAAG
1 GGTAGTAAATGCGAGTGGAGATGTGAGAATATAAAAGGAATAACAAG
9787 G
1 G
9788 AAAAAAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.43, C:0.03, G:0.34, T:0.20
Consensus pattern (47 bp):
GGTAGTAAATGCGAGTGGAGATGTGAGAATATAAAAGGAATAACAAG
Found at i:10084 original size:77 final size:78
Alignment explanation
Indices: 9995--10139 Score: 265
Period size: 77 Copynumber: 1.9 Consensus size: 78
9985 GGGTGGGCAA
*
9995 AAGTTTTTCGGATTAAAAGTATGTTATTTAAAAAAAAGGCAAA-AAAAAAAGAGAACCGTAATCA
1 AAGTTTTTCGGATTAAAAGTATGTTATTTAAAAAAAAGGCAAATAAAAAAAGAGAACCGAAATCA
10059 GGCTTGGTCGCGC
66 GGCTTGGTCGCGC
*
10072 AAGTTTTTCGGATTGAAAGTATGTTATTTAAAAAAAAGGCAAATAAAAAAAGAGAACCGAAATCA
1 AAGTTTTTCGGATTAAAAGTATGTTATTTAAAAAAAAGGCAAATAAAAAAAGAGAACCGAAATCA
10137 GGC
66 GGC
10140 GCGCGCCGCT
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
77 42 0.65
78 23 0.35
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.24
Consensus pattern (78 bp):
AAGTTTTTCGGATTAAAAGTATGTTATTTAAAAAAAAGGCAAATAAAAAAAGAGAACCGAAATCA
GGCTTGGTCGCGC
Found at i:10255 original size:33 final size:33
Alignment explanation
Indices: 10134--10247 Score: 210
Period size: 33 Copynumber: 3.5 Consensus size: 33
10124 AGAACCGAAA
10134 TCAGGCGCGCGCCGCTTGCGACCAAGCCGCGGC
1 TCAGGCGCGCGCCGCTTGCGACCAAGCCGCGGC
10167 TCAGGCGCGCGCCGCTTGCGACCAAGCCGCGGC
1 TCAGGCGCGCGCCGCTTGCGACCAAGCCGCGGC
10200 TCAGGCGCGCGCCGCTTGCGACCAAGCCGCGGC
1 TCAGGCGCGCGCCGCTTGCGACCAAGCCGCGGC
* *
10233 TCAGTCGCGAGCCGC
1 TCAGGCGCGCGCCGC
10248 GCACGACCGA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.12, C:0.42, G:0.36, T:0.10
Consensus pattern (33 bp):
TCAGGCGCGCGCCGCTTGCGACCAAGCCGCGGC
Found at i:10255 original size:66 final size:66
Alignment explanation
Indices: 10134--10260 Score: 200
Period size: 66 Copynumber: 1.9 Consensus size: 66
10124 AGAACCGAAA
* ***
10134 TCAGGCGCGCGCCGCTTGCGACCAAGCCGCGGCTCAGGCGCGCGCCGCTTGCGACCAAGCCGCGG
1 TCAGGCGCGCGCCGCTTGCGACCAAGCCGCGGCTCAGGCGCGAGCCGCGCACGACCAAGCCGCGG
10199 C
66 C
* *
10200 TCAGGCGCGCGCCGCTTGCGACCAAGCCGCGGCTCAGTCGCGAGCCGCGCACGACCGAGCC
1 TCAGGCGCGCGCCGCTTGCGACCAAGCCGCGGCTCAGGCGCGAGCCGCGCACGACCAAGCC
10261 ATGGCTTGGT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.13, C:0.43, G:0.35, T:0.09
Consensus pattern (66 bp):
TCAGGCGCGCGCCGCTTGCGACCAAGCCGCGGCTCAGGCGCGAGCCGCGCACGACCAAGCCGCGG
C
Found at i:10576 original size:15 final size:14
Alignment explanation
Indices: 10534--10576 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
10524 GAAGGTTGAC
*
10534 TTGAATGATTGAGAT
1 TTGAAAGATTGA-AT
*
10549 TTGAAAGTTTGAAT
1 TTGAAAGATTGAAT
10563 TTGAAAGAATTGAA
1 TTGAAAG-ATTGAA
10577 AAGTTTAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 9 0.38
15 15 0.62
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.37
Consensus pattern (14 bp):
TTGAAAGATTGAAT
Found at i:11522 original size:11 final size:11
Alignment explanation
Indices: 11506--11540 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
11496 TTGACAACGC
11506 AACAAAAACAA
1 AACAAAAACAA
*
11517 AACAAAAACGA
1 AACAAAAACAA
11528 AACAAAAACAA
1 AACAAAAACAA
11539 AA
1 AA
11541 AACAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:12970 original size:17 final size:16
Alignment explanation
Indices: 12930--12972 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
12920 CATGTAATCT
*
12930 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
12946 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
12963 TTAGATCACT
1 TT-GATCACT
12973 AGTAATGTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 20 0.83
18 1 0.04
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:13804 original size:105 final size:105
Alignment explanation
Indices: 13637--13825 Score: 333
Period size: 105 Copynumber: 1.8 Consensus size: 105
13627 GGTCGTCTGC
* *
13637 AAATCATAAAATTAATTTATAAGTCAACCAACTAGAAATTATGAAATTTAAAACTTGCAAGTGGC
1 AAATCATAAAAATAATTTATAAATCAACCAACTAGAAATTATGAAATTTAAAACTTGCAAGTGGC
*
13702 AAGTTAAGTCGAACCCACAAAAAAATTATCGGTGGTTTAG
66 AAGTTAAGTCGAAACCACAAAAAAATTATCGGTGGTTTAG
* *
13742 AAATCATAAAAATAATTTCTAAATCAACTAACTAGAAATTATGAAATTTAAAACTTGCAAGTGGC
1 AAATCATAAAAATAATTTATAAATCAACCAACTAGAAATTATGAAATTTAAAACTTGCAAGTGGC
13807 AAGTTAAGTCGAAACCACA
66 AAGTTAAGTCGAAACCACA
13826 GGAAAAAAAA
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
105 79 1.00
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.27
Consensus pattern (105 bp):
AAATCATAAAAATAATTTATAAATCAACCAACTAGAAATTATGAAATTTAAAACTTGCAAGTGGC
AAGTTAAGTCGAAACCACAAAAAAATTATCGGTGGTTTAG
Found at i:13859 original size:105 final size:104
Alignment explanation
Indices: 13644--13859 Score: 265
Period size: 105 Copynumber: 2.1 Consensus size: 104
13634 TGCAAATCAT
* *
13644 AAAATTAATTTATAAGTCAACCAACTAGAAATTATGAAATTTAAAACTTGCAAGTGGCAAGTTAA
1 AAAAATAATTTATAAATCAACCAACTAGAAATTATGAAATTTAAAACTTGCAAGTGGCAAGTTAA
* ** ** ** * *
13709 GTCGAACCCACAAAAAAATTATCGGTGGTTTAGAAATCAT
66 GTCGAAACCACAAAAAAAAAATCGGTAATCCACAAA-CAG
* *
13749 AAAAATAATTTCTAAATCAACTAACTAGAAATTATGAAATTTAAAACTTGCAAGTGGCAAGTTAA
1 AAAAATAATTTATAAATCAACCAACTAGAAATTATGAAATTTAAAACTTGCAAGTGGCAAGTTAA
13814 GTCGAAACCACAGGAAAAAAAAATC-GTAATCCACAAA-AG
66 GTCGAAACCACA--AAAAAAAAATCGGTAATCCACAAACAG
13853 AGAAAAT
1 A-AAAAT
13860 TAGAAAATAT
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
104 2 0.02
105 77 0.81
106 7 0.07
107 9 0.09
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (104 bp):
AAAAATAATTTATAAATCAACCAACTAGAAATTATGAAATTTAAAACTTGCAAGTGGCAAGTTAA
GTCGAAACCACAAAAAAAAAATCGGTAATCCACAAACAG
Found at i:15864 original size:20 final size:21
Alignment explanation
Indices: 15834--15872 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
15824 AAAATCTTTT
*
15834 CAATATTTACTATATCAATCC
1 CAATATTTACTAAATCAATCC
15855 CAAT-TTTACTAAATCAAT
1 CAATATTTACTAAATCAAT
15873 TAGCAAGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (21 bp):
CAATATTTACTAAATCAATCC
Found at i:17545 original size:19 final size:19
Alignment explanation
Indices: 17521--17561 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
17511 TAGTTTCTGT
17521 TAGGCCCTTGATAATGTGC
1 TAGGCCCTTGATAATGTGC
17540 TAGGCCCTTGATAATGTGC
1 TAGGCCCTTGATAATGTGC
17559 TAG
1 TAG
17562 AGGGGGGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.32
Consensus pattern (19 bp):
TAGGCCCTTGATAATGTGC
Found at i:17976 original size:17 final size:18
Alignment explanation
Indices: 17936--17977 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
17926 TCTCCCAAAG
17936 ATCTCAAGTACAAATTTT
1 ATCTCAAGTACAAATTTT
*
17954 AGCTCAA-TACAAATTTT
1 ATCTCAAGTACAAATTTT
*
17971 CTCTCAA
1 ATCTCAA
17978 AACTAGTAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (18 bp):
ATCTCAAGTACAAATTTT
Done.