Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021512.1 Corchorus olitorius cultivar O-4 contig21545, 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: 17051
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31
Found at i:1895 original size:21 final size:21
Alignment explanation
Indices: 1870--1909 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1860 TTAGAAACCC
1870 TAGTACCACTTAG-ATCCAACT
1 TAGTACCACTT-GTATCCAACT
1891 TAGTACCACTTGTATCCAA
1 TAGTACCACTTGTATCCAA
1910 TATGGCTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.28, G:0.10, T:0.30
Consensus pattern (21 bp):
TAGTACCACTTGTATCCAACT
Found at i:9431 original size:33 final size:32
Alignment explanation
Indices: 9394--9507 Score: 129
Period size: 33 Copynumber: 3.5 Consensus size: 32
9384 AGAATTTATT
9394 TCATCACAAACAACACCTAAAACAGATTTAGTG
1 TCATCACAAACAACA-CTAAAACAGATTTAGTG
** * *
9427 TCATCACAAACAACACTCAAATTAGGTTTAGTA
1 TCATCACAAACAACACT-AAAACAGATTTAGTG
* *
9460 TCATCGCAAACAACATCTAAAACAGATTTCGTG
1 TCATCACAAACAACA-CTAAAACAGATTTAGTG
**
9493 TCATTGCAAACAACA
1 TCATCACAAACAACA
9508 ATCAAATTAG
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
32 2 0.03
33 64 0.94
34 2 0.03
ACGTcount: A:0.43, C:0.24, G:0.10, T:0.24
Consensus pattern (32 bp):
TCATCACAAACAACACTAAAACAGATTTAGTG
Found at i:9470 original size:66 final size:66
Alignment explanation
Indices: 9394--9520 Score: 200
Period size: 66 Copynumber: 1.9 Consensus size: 66
9384 AGAATTTATT
*
9394 TCATCACAAACAACACCTAAAACAGATTTAGTGTCATCACAAACAACACTCAAATTAGGTTTAGT
1 TCATCACAAACAACACCTAAAACAGATTTAGTGTCATCACAAACAACAATCAAATTAGGTTTAGT
9459 A
66 A
* * * **
9460 TCATCGCAAACAACATCTAAAACAGATTTCGTGTCATTGCAAACAACAATCAAATTAGGTT
1 TCATCACAAACAACACCTAAAACAGATTTAGTGTCATCACAAACAACAATCAAATTAGGTT
9521 CAGAATTACT
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:0.43, C:0.22, G:0.10, T:0.25
Consensus pattern (66 bp):
TCATCACAAACAACACCTAAAACAGATTTAGTGTCATCACAAACAACAATCAAATTAGGTTTAGT
A
Found at i:12415 original size:16 final size:15
Alignment explanation
Indices: 12379--12500 Score: 93
Period size: 16 Copynumber: 7.7 Consensus size: 15
12369 CTCGGGCGGA
**
12379 TTCGGGTTCGGGTAC
1 TTCGGGTTCGGGTTT
12394 TTCGGGTTCGGGCTTT
1 TTCGGGTTCGGG-TTT
* *
12410 TTCGGGCTCGAGTATT
1 TTCGGGTTCGGGT-TT
* *
12426 TTC-GGTCTCAGGTTAA
1 TTCGGGT-TCGGGTT-T
*
12442 GTCGGGTTCGGGTATT
1 TTCGGGTTCGGGT-TT
*
12458 TTCGGGCTCGGGTTAT
1 TTCGGGTTCGGGTT-T
*
12474 GTCGGGTTCGGGTATT
1 TTCGGGTTCGGGT-TT
12490 TTCGGGTTCGG
1 TTCGGGTTCGG
12501 TCTCGGATAG
Statistics
Matches: 83, Mismatches: 16, Indels: 15
0.73 0.14 0.13
Matches are distributed among these distances:
15 17 0.20
16 61 0.73
17 5 0.06
ACGTcount: A:0.07, C:0.17, G:0.38, T:0.38
Consensus pattern (15 bp):
TTCGGGTTCGGGTTT
Found at i:12447 original size:32 final size:32
Alignment explanation
Indices: 12411--12495 Score: 125
Period size: 32 Copynumber: 2.7 Consensus size: 32
12401 TCGGGCTTTT
* * *
12411 TCGGGCTCGAGTATTTTCGGTCTCAGGTTAAG
1 TCGGGTTCGGGTATTTTCGGGCTCAGGTTAAG
* *
12443 TCGGGTTCGGGTATTTTCGGGCTCGGGTTATG
1 TCGGGTTCGGGTATTTTCGGGCTCAGGTTAAG
12475 TCGGGTTCGGGTATTTTCGGG
1 TCGGGTTCGGGTATTTTCGGG
12496 TTCGGTCTCG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.09, C:0.16, G:0.38, T:0.36
Consensus pattern (32 bp):
TCGGGTTCGGGTATTTTCGGGCTCAGGTTAAG
Found at i:12495 original size:48 final size:48
Alignment explanation
Indices: 12380--12500 Score: 117
Period size: 48 Copynumber: 2.5 Consensus size: 48
12370 TCGGGCGGAT
* *
12380 TCGGGTTCGGGTA-CTTCGGGTTCGGGCTTTTTCGGGCTCGAGTATTT
1 TCGGGTTCGGGTATATTCGGGTTCGGGCTTTTTCGGGCTCGAGTATTG
* * *
12427 TC-GGTCTCAGGT-TAAGTCGGGTTCGGG-TATTTTCGGGCTCGGGT-TATG
1 TCGGGT-TCGGGTAT-ATTCGGGTTCGGGCT-TTTTCGGGCTCGAGTAT-TG
*
12475 TCGGGTTCGGGTATTTTCGGGTTCGG
1 TCGGGTTCGGGTATATTCGGGTTCGG
12501 TCTCGGATAG
Statistics
Matches: 59, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
46 3 0.05
47 9 0.15
48 43 0.73
49 4 0.07
ACGTcount: A:0.07, C:0.17, G:0.38, T:0.37
Consensus pattern (48 bp):
TCGGGTTCGGGTATATTCGGGTTCGGGCTTTTTCGGGCTCGAGTATTG
Found at i:14208 original size:11 final size:11
Alignment explanation
Indices: 14188--14217 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
14178 CTAAGGGTAA
14188 AGGAAAGAGCT
1 AGGAAAGAGCT
*
14199 AGGAAGGAGCT
1 AGGAAAGAGCT
14210 AGGAAAGA
1 AGGAAAGA
14218 TCCTACTCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.40, T:0.07
Consensus pattern (11 bp):
AGGAAAGAGCT
Found at i:14620 original size:21 final size:21
Alignment explanation
Indices: 14594--14635 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
14584 GCACCTTAGG
14594 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
14615 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
14636 TTCTTTGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19
Consensus pattern (21 bp):
CAACTCCGATGAGCTTGAAAC
Found at i:15995 original size:17 final size:17
Alignment explanation
Indices: 15973--16012 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
15963 ATCACCCCCC
*
15973 AGATCACTAGTGAT-CTA
1 AGATCACCAGTGATGC-A
15990 AGATCACCAGTGATGCA
1 AGATCACCAGTGATGCA
16007 AGATCA
1 AGATCA
16013 ATGGTAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (17 bp):
AGATCACCAGTGATGCA
Found at i:16437 original size:20 final size:20
Alignment explanation
Indices: 16407--16453 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
16397 GGGCACATGA
16407 GAAAGAAAAAATGAGATGCAG
1 GAAA-AAAAAATGAGATGCAG
*
16428 GAAAAAAAAATGGGATGCAG
1 GAAAAAAAAATGAGATGCAG
16448 GAAAAA
1 GAAAAA
16454 GATATTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.60, C:0.04, G:0.28, T:0.09
Consensus pattern (20 bp):
GAAAAAAAAATGAGATGCAG
Found at i:16735 original size:19 final size:17
Alignment explanation
Indices: 16699--16733 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
16689 CCTGAAAACG
16699 TTTAACATCAGTATATA
1 TTTAACATCAGTATATA
16716 TTTAACATCAGTATATA
1 TTTAACATCAGTATATA
16733 T
1 T
16734 ATACCTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (17 bp):
TTTAACATCAGTATATA
Done.