Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023033.1 Corchorus olitorius cultivar O-4 contig23066, 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: 26401
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:71 original size:25 final size:25
Alignment explanation
Indices: 43--133 Score: 137
Period size: 25 Copynumber: 3.6 Consensus size: 25
33 TAGCCTATGT
*
43 GTTTTCTAAACGCAAGCACAGGCTC
1 GTTTGCTAAACGCAAGCACAGGCTC
*
68 GTTTGCTAAACGCTAGCACAGGCTC
1 GTTTGCTAAACGCAAGCACAGGCTC
*
93 GTTTGCTAAACGCAAGCACAGACTC
1 GTTTGCTAAACGCAAGCACAGGCTC
* *
118 GTTTTCCAAACGCAAG
1 GTTTGCTAAACGCAAG
134 AACATGAGAC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 60 1.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (25 bp):
GTTTGCTAAACGCAAGCACAGGCTC
Found at i:3356 original size:7 final size:6
Alignment explanation
Indices: 3279--3358 Score: 74
Period size: 6 Copynumber: 12.7 Consensus size: 6
3269 GGCCCCAAAA
*
3279 AAAAGG AAAAGG AAAA-G AAAA-G AAAAGA AAAAGGGG AAAAGGG AAAAGG
1 AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAA--GG AAAA-GG AAAAGG
*
3328 AAAAGA AAAAGG AAAAATGG AAATAGG AAAA
1 AAAAGG AAAAGG -AAAA-GG AAA-AGG AAAA
3359 TAATAATAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
5 10 0.16
6 27 0.42
7 19 0.30
8 8 0.12
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.03
Consensus pattern (6 bp):
AAAAGG
Found at i:18189 original size:19 final size:19
Alignment explanation
Indices: 18165--18222 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
18155 ACTTTTAGCA
*
18165 ACTGTATAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
18184 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA--C
*
18205 ATTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
18223 TTAGAGCAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:22684 original size:31 final size:31
Alignment explanation
Indices: 22622--22685 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
22612 TTAGCGACGT
**
22622 TTCAAACCAGAAACGCCACTAATTGGCGGCG
1 TTCAAACCAGAAACGCCACTAATTAACGGCG
*
22653 TTCAAACCAGAAACGCCACTAATTAATGGCG
1 TTCAAACCAGAAACGCCACTAATTAACGGCG
22684 TT
1 TT
22686 TTGGGTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (31 bp):
TTCAAACCAGAAACGCCACTAATTAACGGCG
Found at i:23042 original size:44 final size:44
Alignment explanation
Indices: 22989--23204 Score: 310
Period size: 44 Copynumber: 4.9 Consensus size: 44
22979 TAATTTCTAA
* * **
22989 ACATTTATAATTTCTAGATATTATTTTCTTTTTATAATTTCATT
1 ACATATATAATTTCTAAATATTATTTTCTAATTATAATTTCATT
23033 ACATATATAATTTCTAAATATTATTTTCTAATTATAATTTCATT
1 ACATATATAATTTCTAAATATTATTTTCTAATTATAATTTCATT
*
23077 ACATATATAATTTCTAAATATTATTTTCTAAATA-ATATTTCATT
1 ACATATATAATTTCTAAATATTATTTTCTAATTATA-ATTTCATT
* * *
23121 ACATATATAATTTATAAATA-TAATTCCTAATTATAATTTCATT
1 ACATATATAATTTCTAAATATTATTTTCTAATTATAATTTCATT
* * *
23164 ACATAAATCATTTCTAAATATTATTTTCTCATTATAATTTC
1 ACATATATAATTTCTAAATATTATTTTCTAATTATAATTTC
23205 TGAACAATTT
Statistics
Matches: 154, Mismatches: 15, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
43 36 0.23
44 118 0.77
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (44 bp):
ACATATATAATTTCTAAATATTATTTTCTAATTATAATTTCATT
Found at i:23058 original size:13 final size:13
Alignment explanation
Indices: 22969--23160 Score: 89
Period size: 13 Copynumber: 13.3 Consensus size: 13
22959 CAAATTTTGT
*
22969 TTTCCAAATATAA
1 TTTCTAAATATAA
22982 TTTCTAAACATTTATAA
1 TTTCT-AA-A--TATAA
* *
22999 TTTCTAGATATTAT
1 TTTCTAAATA-TAA
***
23013 TTTCTTTTTATAA
1 TTTCTAAATATAA
23026 TTTCATTACATATATAA
1 TTTC--TA-A-ATATAA
*
23043 TTTCTAAATATTAT
1 TTTCTAAATA-TAA
*
23057 TTTCTAATTATAA
1 TTTCTAAATATAA
23070 TTTCATTACATATATAA
1 TTTC--TA-A-ATATAA
*
23087 TTTCTAAATATTAT
1 TTTCTAAATA-TAA
23101 TTTCTAAATA-ATA
1 TTTCTAAATATA-A
23114 TTTCATTACATATATAA
1 TTTC--TA-A-ATATAA
*
23131 TTTATAAATATAA
1 TTTCTAAATATAA
* *
23144 TTCCTAATTATAA
1 TTTCTAAATATAA
23157 TTTC
1 TTTC
23161 ATTACATAAA
Statistics
Matches: 137, Mismatches: 21, Indels: 42
0.69 0.10 0.21
Matches are distributed among these distances:
12 1 0.01
13 47 0.34
14 37 0.27
15 13 0.09
16 3 0.02
17 35 0.26
18 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.51
Consensus pattern (13 bp):
TTTCTAAATATAA
Found at i:23062 original size:14 final size:14
Alignment explanation
Indices: 23043--23116 Score: 69
Period size: 14 Copynumber: 5.1 Consensus size: 14
23033 ACATATATAA
23043 TTTCTAAATATTAT
1 TTTCTAAATATTAT
* *
23057 TTTCTAATTA-TAA
1 TTTCTAAATATTAT
* *
23070 TTTCATTACATATATAA
1 TTTC--TAAATAT-TAT
23087 TTTCTAAATATTAT
1 TTTCTAAATATTAT
*
23101 TTTCTAAATAATAT
1 TTTCTAAATATTAT
23115 TT
1 TT
23117 CATTACATAT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
13 6 0.12
14 26 0.53
15 10 0.20
17 7 0.14
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (14 bp):
TTTCTAAATATTAT
Found at i:23093 original size:30 final size:29
Alignment explanation
Indices: 23057--23205 Score: 91
Period size: 30 Copynumber: 5.2 Consensus size: 29
23047 TAAATATTAT
23057 TTTCTAATTATAATTTCATTACATATATAA
1 TTTCTAATTATAATTT-ATTACATATATAA
* * *
23087 TTTCTAAATATTATTT-TCTAAATA-AT-A
1 TTTCTAATTATAATTTAT-TACATATATAA
23114 TTTCATTACATATATAATTTA-TA-A-ATATAA
1 TTTC--TA-AT-TATAATTTATTACATATATAA
* * *
23144 TTCCTAATTATAATTTCATTACATAAATCA
1 TTTCTAATTATAATTT-ATTACATATATAA
* *
23174 TTTCTAAATATTATTT-TCT-CAT-TATAA
1 TTTCTAATTATAATTTAT-TACATATATAA
23201 TTTCT
1 TTTCT
23206 GAACAATTTT
Statistics
Matches: 93, Mismatches: 13, Indels: 29
0.69 0.10 0.21
Matches are distributed among these distances:
26 8 0.09
27 16 0.17
28 12 0.13
29 12 0.13
30 38 0.41
31 7 0.08
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (29 bp):
TTTCTAATTATAATTTATTACATATATAA
Found at i:23190 original size:87 final size:88
Alignment explanation
Indices: 22995--23204 Score: 298
Period size: 87 Copynumber: 2.4 Consensus size: 88
22985 CTAAACATTT
* ** * * * *
22995 ATAATTTCTAGATATTATTTTCTTTTTATAATTTCATTACATATATAATTTCTAAATATTATTTT
1 ATAATTTCTAAATATTATTTTCTAATAATAATTTCATTACATATATAATTTATAAATATTAATTC
*
23060 CTAATTATAATTTCATTACATAT
66 CTAATTATAATTTCATTACATAA
23083 ATAATTTCTAAATATTATTTTCTAAATAAT-ATTTCATTACATATATAATTTATAAATA-TAATT
1 ATAATTTCTAAATATTATTTTCT-AATAATAATTTCATTACATATATAATTTATAAATATTAATT
23146 CCTAATTATAATTTCATTACATAA
65 CCTAATTATAATTTCATTACATAA
* * *
23170 ATCATTTCTAAATATTATTTTCTCATTATAATTTC
1 ATAATTTCTAAATATTATTTTCTAATAATAATTTC
23205 TGAACAATTT
Statistics
Matches: 109, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
86 4 0.04
87 53 0.49
88 49 0.45
89 3 0.03
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (88 bp):
ATAATTTCTAAATATTATTTTCTAATAATAATTTCATTACATATATAATTTATAAATATTAATTC
CTAATTATAATTTCATTACATAA
Found at i:23696 original size:20 final size:21
Alignment explanation
Indices: 23659--23698 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
23649 CGTTAAAGTC
* *
23659 TCGATTTGTTGTTGTAGGTCT
1 TCGATTTATAGTTGTAGGTCT
23680 TCGATTTATAGTT-TAGGTC
1 TCGATTTATAGTTGTAGGTC
23699 GAAAATCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.15, C:0.10, G:0.25, T:0.50
Consensus pattern (21 bp):
TCGATTTATAGTTGTAGGTCT
Done.