Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009766.1 Corchorus olitorius cultivar O-4 contig09798, 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: 7797
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Found at i:3565 original size:100 final size:103
Alignment explanation
Indices: 3418--3688 Score: 336
Period size: 111 Copynumber: 2.6 Consensus size: 103
3408 ATTTTTTGAT
* *
3418 TTTAATTTGGGCTAAACTTGGTG-AATTAGTTATATATATTTTTTTTCTAAAACCCTATAACAAT
1 TTTAATTTGGGCTAAACTTAGTGAAATTAGTT-T-TATATTTTATTTCTAAAACCCTATAACAAT
* *
3482 -ATTATTAATTATGGAATTTATCCTTAAAAT-AAA-AAAA
64 AATTATTAATTATGAAATTTACCCTTAAAATAAAATAAAA
*
3519 -TTAATTTAGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATTTCTAAAACCCTATAACAATA
1 TTTAATTT-GGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACAAT-
*
3583 AATTATTAATTTTGAAATTTACCCTTAAAATAAAAATAAAA
64 AATTATTAATTATGAAATTTACCCTTAAAAT-AAAATAAAA
* *
3624 TTTAAATTTGGGGCTAAACTTAATTAGTGAAATTAATTTTATATTTTATTTCTAAAACTCTATAA
1 TTT-AATTT-GGGCTAAAC----TTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAA
3689 TAAAAAAAAA
Statistics
Matches: 147, Mismatches: 10, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
100 35 0.24
101 15 0.10
102 35 0.24
104 3 0.02
105 4 0.03
106 2 0.01
107 14 0.10
111 39 0.27
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.42
Consensus pattern (103 bp):
TTTAATTTGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACAATAA
TTATTAATTATGAAATTTACCCTTAAAATAAAATAAAA
Found at i:4651 original size:107 final size:104
Alignment explanation
Indices: 4430--4705 Score: 394
Period size: 107 Copynumber: 2.6 Consensus size: 104
4420 AATTTTTCTA
* ** *
4430 ACCCTTAAAATAAAATTTTAATTTTAATTT-GGGCTAAACTTAGTG-AATTGGTTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTT-TATATTTTA
**
4493 TTTCTAAAACCCTATAACAATATTATTAATTATGGAATTT
65 TTTCTAAAACCCTATAACAATATTATTAATTATAAAATTT
* *
4533 ACCCTTAAAATAAAAATAAAATTTTAGTTTGGGGCTAAACTTAGTGAAATTAGTTTAGTATTTTG
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTA-TATTTTA
* *
4598 TTTCTAAAATCCTATAACAATAAATTATTAATTTTAAAATTT
65 TTTCTAAAACCCTATAACAAT--ATTATTAATTATAAAATTT
*
4640 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGTTAAACTTAGTGAAATTAGTTTTATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAG-TTTATATTTTA
4705 T
65 T
4706 ATTTTATTTC
Statistics
Matches: 154, Mismatches: 13, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
103 26 0.17
104 17 0.11
105 33 0.21
107 74 0.48
108 4 0.03
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.42
Consensus pattern (104 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTATATTTTAT
TTCTAAAACCCTATAACAATATTATTAATTATAAAATTT
Found at i:5773 original size:14 final size:14
Alignment explanation
Indices: 5754--5785 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
5744 CAAGTAAGGG
5754 AGAAAAAAAAGAAA
1 AGAAAAAAAAGAAA
*
5768 AGAAAAAAAAGAGA
1 AGAAAAAAAAGAAA
5782 AGAA
1 AGAA
5786 TAGGAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AGAAAAAAAAGAAA
Found at i:7606 original size:41 final size:43
Alignment explanation
Indices: 7517--7797 Score: 396
Period size: 41 Copynumber: 6.7 Consensus size: 43
7507 CCAATAACCA
* * * * * *
7517 AAAGTCCCCAAACACATATATAACATAGGGGCATCTCTATTCC
1 AAAGTCCTCAAACACATATATAACACAGAGGCACCTATATTAC
7560 AAAGTCCTCAAACACATATATAACACAGAGGCACCTATATT-C
1 AAAGTCCTCAAACACATATATAACACAGAGGCACCTATATTAC
* *
7602 -AAGTCCCCAAACACATATATAACACATG-GGCACCTCTATTAC
1 AAAGTCCTCAAACACATATATAACACA-GAGGCACCTATATTAC
*
7644 AAAGTCCTCAAACACATATATAACACAGAGACACC--TATTAC
1 AAAGTCCTCAAACACATATATAACACAGAGGCACCTATATTAC
7685 AAAGTCCTCAAACACATATATAACACAGAGGCACCTATATT-C
1 AAAGTCCTCAAACACATATATAACACAGAGGCACCTATATTAC
* * *
7727 -AAGTCCCCAAACACATATATAACACAGGGGCACCTTTATTAC
1 AAAGTCCTCAAACACATATATAACACAGAGGCACCTATATTAC
7769 AAAGTCCTCAAACACATATATAACACAGA
1 AAAGTCCTCAAACACATATATAACACAGA
Statistics
Matches: 215, Mismatches: 15, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
41 113 0.53
42 6 0.03
43 96 0.45
ACGTcount: A:0.42, C:0.27, G:0.10, T:0.21
Consensus pattern (43 bp):
AAAGTCCTCAAACACATATATAACACAGAGGCACCTATATTAC
Found at i:7613 original size:84 final size:84
Alignment explanation
Indices: 7517--7796 Score: 404
Period size: 84 Copynumber: 3.3 Consensus size: 84
7507 CCAATAACCA
* *
7517 AAAGTCCCCAAACACATATATAACATAGGGGCATCTCTATTCCAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATT-CAAAGTCCTCAAACACATATATA
7582 ACACAGAGGCACCTATATTC
65 ACACAGAGGCACCTATATTC
*
7602 -AAGTCCCCAAACACATATATAACACATGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATT-CAAAGTCCTCAAACACATATATA
* *
7666 ACACAGAGACACCTAT-TAC
65 ACACAGAGGCACCTATATTC
* * * *
7685 AAAGTCCTCAAACACATATATAACACAGAGGCACCTATATTC-AAGTCCCCAAACACATATATAA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTCAAAGTCCTCAAACACATATATAA
* *
7749 CACAGGGGCACCTTTATTAC
66 CACAGAGGCACCTATATT-C
*
7769 AAAGTCCTCAAACACATATATAACACAG
1 AAAGTCCCCAAACACATATATAACACAG
7797 A
Statistics
Matches: 177, Mismatches: 15, Indels: 7
0.89 0.08 0.04
Matches are distributed among these distances:
82 33 0.19
83 4 0.02
84 140 0.79
ACGTcount: A:0.42, C:0.28, G:0.10, T:0.21
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTCAAAGTCCTCAAACACATATATAA
CACAGAGGCACCTATATTC
Found at i:7702 original size:125 final size:127
Alignment explanation
Indices: 7517--7797 Score: 485
Period size: 125 Copynumber: 2.2 Consensus size: 127
7507 CCAATAACCA
* * * * *
7517 AAAGTCCCCAAACACATATATAACATAGGGGCATCTCTATTCCAAAGTCCTCAAACACATATATA
1 AAAGTCCTCAAACACATATATAACACAGAGACATCTCTATTACAAAGTCCTCAAACACATATATA
*
7582 ACACAGAGGCACCTATATTCAAGTCCCCAAACACATATATAACACATGGGCACCTCTATTAC
66 ACACAGAGGCACCTATATTCAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTAC
7644 AAAGTCCTCAAACACATATATAACACAGAGACA-C-CTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCTCAAACACATATATAACACAGAGACATCTCTATTACAAAGTCCTCAAACACATATATA
*
7707 ACACAGAGGCACCTATATTCAAGTCCCCAAACACATATATAACACAGGGGCACCTTTATTAC
66 ACACAGAGGCACCTATATTCAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTAC
7769 AAAGTCCTCAAACACATATATAACACAGA
1 AAAGTCCTCAAACACATATATAACACAGA
Statistics
Matches: 147, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
125 117 0.80
126 1 0.01
127 29 0.20
ACGTcount: A:0.42, C:0.27, G:0.10, T:0.21
Consensus pattern (127 bp):
AAAGTCCTCAAACACATATATAACACAGAGACATCTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCACCTATATTCAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTAC
Done.