Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023196.1 Corchorus olitorius cultivar O-4 contig23229, 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: 14226
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Found at i:821 original size:12 final size:14
Alignment explanation
Indices: 800--836 Score: 53
Period size: 11 Copynumber: 2.9 Consensus size: 14
790 TCCGTTGAGG
800 AAATTGTTTTTATT
1 AAATTGTTTTTATT
814 -AA-TG-TTTTATT
1 AAATTGTTTTTATT
825 AAATTGTTTTTA
1 AAATTGTTTTTA
837 AATGATTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
11 7 0.35
12 4 0.20
13 4 0.20
14 5 0.25
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (14 bp):
AAATTGTTTTTATT
Found at i:1823 original size:18 final size:16
Alignment explanation
Indices: 1800--1841 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 16
1790 AGGCGTGACA
1800 TCCTTATTTTTACTTATC
1 TCCTTATTTTT-C-TATC
1818 TCCTTA--TTTCTATC
1 TCCTTATTTTTCTATC
1832 TCCTTATTTT
1 TCCTTATTTT
1842 CACTCCTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 10 0.45
15 1 0.05
16 5 0.23
18 6 0.27
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.62
Consensus pattern (16 bp):
TCCTTATTTTTCTATC
Found at i:1833 original size:14 final size:14
Alignment explanation
Indices: 1814--1840 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1804 TATTTTTACT
1814 TATCTCCTTATTTC
1 TATCTCCTTATTTC
1828 TATCTCCTTATTT
1 TATCTCCTTATTT
1841 TCACTCCTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.26, G:0.00, T:0.59
Consensus pattern (14 bp):
TATCTCCTTATTTC
Found at i:3464 original size:46 final size:46
Alignment explanation
Indices: 3392--3479 Score: 167
Period size: 46 Copynumber: 1.9 Consensus size: 46
3382 CCCAAATAAT
*
3392 TGTTTATTTATTTTATGGGTATATATGGACTTTTAAACATTGTTTA
1 TGTTTATTTATTTTATGGGTAGATATGGACTTTTAAACATTGTTTA
3438 TGTTTATTTATTTTATGGGTAGATATGGACTTTTAAACATTG
1 TGTTTATTTATTTTATGGGTAGATATGGACTTTTAAACATTG
3480 ATTACGGTAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.26, C:0.05, G:0.17, T:0.52
Consensus pattern (46 bp):
TGTTTATTTATTTTATGGGTAGATATGGACTTTTAAACATTGTTTA
Found at i:5714 original size:27 final size:27
Alignment explanation
Indices: 5666--5726 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
5656 ATTACCAAAA
* * *
5666 TACCCGTGATGGACAAATTTACTATAT
1 TACCCCTGATGGACAAAATTACGATAT
* * *
5693 TACCCCTGATTGATAAAATTACGATTT
1 TACCCCTGATGGACAAAATTACGATAT
5720 TACCCCT
1 TACCCCT
5727 ATAATGAGGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34
Consensus pattern (27 bp):
TACCCCTGATGGACAAAATTACGATAT
Found at i:7865 original size:21 final size:19
Alignment explanation
Indices: 7839--7877 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
7829 ATGTTATCCT
7839 TTTTAAGTGGATGTTATTAAA
1 TTTTAAGTGGA-GTT-TTAAA
7860 TTTTAAGTGGAGTTTTAA
1 TTTTAAGTGGAGTTTTAA
7878 GAAATTTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 3 0.17
21 11 0.61
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.49
Consensus pattern (19 bp):
TTTTAAGTGGAGTTTTAAA
Found at i:7882 original size:22 final size:21
Alignment explanation
Indices: 7839--7885 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
7829 ATGTTATCCT
**
7839 TTTTAAGTGGATGTTATTAAA
1 TTTTAAGTGGATGTTAAGAAA
*
7860 TTTTAAGTGGAGTTTTAAGAAA
1 TTTTAAGTGGA-TGTTAAGAAA
7882 TTTT
1 TTTT
7886 GGTAACATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (21 bp):
TTTTAAGTGGATGTTAAGAAA
Found at i:7937 original size:2 final size:2
Alignment explanation
Indices: 7932--7957 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7922 TATATATTAT
7932 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
7958 GGGAAATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9730 original size:21 final size:21
Alignment explanation
Indices: 9590--9733 Score: 97
Period size: 21 Copynumber: 7.2 Consensus size: 21
9580 AATTAGCAAT
* *
9590 GTTACTAAAAGT-TTAATAAA
1 GTTACTAAAAATCTTAATAAG
*
9610 GTTACT-AAAAT-TT-ATCAG
1 GTTACTAAAAATCTTAATAAG
* *
9628 GTTATTAAAAATC-T-CTAAG
1 GTTACTAAAAATCTTAATAAG
* *
9647 ATTACTGAAAAA-CTT-ATAAA
1 GTTACT-AAAAATCTTAATAAG
* *
9667 GTTATTAAAAAGCTTAATAAG
1 GTTACTAAAAATCTTAATAAG
* * * **
9688 ATTTCTAAAATTCACAATAAG
1 GTTACTAAAAATCTTAATAAG
9709 GTTACTAAAAATCTTAATAAG
1 GTTACTAAAAATCTTAATAAG
9730 GTTA
1 GTTA
9734 GAAAAAAAAA
Statistics
Matches: 93, Mismatches: 25, Indels: 11
0.72 0.19 0.09
Matches are distributed among these distances:
18 8 0.09
19 25 0.27
20 22 0.24
21 38 0.41
ACGTcount: A:0.47, C:0.09, G:0.10, T:0.35
Consensus pattern (21 bp):
GTTACTAAAAATCTTAATAAG
Found at i:10273 original size:16 final size:16
Alignment explanation
Indices: 10248--10278 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10238 TTTACAAATT
*
10248 ATAAAGATTTAGTAAA
1 ATAAAAATTTAGTAAA
10264 ATAAAAATTTAGTAA
1 ATAAAAATTTAGTAA
10279 TATTTTTCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (16 bp):
ATAAAAATTTAGTAAA
Found at i:10484 original size:13 final size:13
Alignment explanation
Indices: 10462--10491 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
10452 TATTTATAAA
*
10462 TAAATTATAATTT
1 TAAATAATAATTT
10475 TAAATAATAATTT
1 TAAATAATAATTT
10488 TAAA
1 TAAA
10492 ATTATTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAAATAATAATTT
Found at i:13147 original size:26 final size:25
Alignment explanation
Indices: 13118--13173 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
13108 ATTTTTGAGG
*
13118 GATATTATTTCATTTA-GTAATAATTT
1 GATATT-TTT-ATTTATGAAATAATTT
*
13144 GATAATTTTTTTTTATGAAATAATTT
1 GAT-ATTTTTATTTATGAAATAATTT
13170 GATA
1 GATA
13174 AGTTTACTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 5 0.19
26 18 0.69
27 3 0.12
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.54
Consensus pattern (25 bp):
GATATTTTTATTTATGAAATAATTT
Found at i:13363 original size:18 final size:18
Alignment explanation
Indices: 13327--13370 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
13317 ATTACTTTGG
* *
13327 TTAAAATGTAATTTTTAA
1 TTAAAATGTAATGTGTAA
*
13345 TTAAAATGTACTGTGTAA
1 TTAAAATGTAATGTGTAA
13363 TTGAAAAT
1 TT-AAAAT
13371 TAGAGCTCGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.43
Consensus pattern (18 bp):
TTAAAATGTAATGTGTAA
Found at i:13702 original size:11 final size:11
Alignment explanation
Indices: 13682--13716 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
13672 TTGACAGCGC
13682 AACAAAAACAA
1 AACAAAAACAA
*
13693 AACGAAAACAA
1 AACAAAAACAA
13704 AACAAAAACAA
1 AACAAAAACAA
13715 AA
1 AA
13717 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
Done.