Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020106.1 Corchorus olitorius cultivar O-4 contig20139, 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: 44574
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:5044 original size:3 final size:3
Alignment explanation
Indices: 5036--5113 Score: 115
Period size: 3 Copynumber: 25.7 Consensus size: 3
5026 AGTAAGGAGA
5036 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
5084 TTC TTC TTTC TTTC TTTC TT- TT- TTC TTC TT
1 TTC TTC -TTC -TTC -TTC TTC TTC TTC TTC TT
5114 TCTTTTTTTT
Statistics
Matches: 73, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 4 0.05
3 58 0.79
4 11 0.15
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:5096 original size:4 final size:4
Alignment explanation
Indices: 5087--5130 Score: 53
Period size: 4 Copynumber: 12.2 Consensus size: 4
5077 CTTCTTCTTC
5087 TTCT TTCT TTCT TTCT TT-T TTC- TTCT TTCT TT-T TT-T TT-T TTCT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
5130 T
1 T
5131 AAATAGAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 15 0.41
4 22 0.59
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (4 bp):
TTCT
Found at i:5108 original size:7 final size:7
Alignment explanation
Indices: 5084--5130 Score: 60
Period size: 7 Copynumber: 6.7 Consensus size: 7
5074 CTTCTTCTTC
*
5084 TTCTTCT
1 TTCTTTT
5091 TTCTTTCT
1 TTCTTT-T
5099 TTCTTTT
1 TTCTTTT
*
5106 TTCTTCT
1 TTCTTTT
5113 TTCTTTT
1 TTCTTTT
5120 TT-TTTT
1 TTCTTTT
5126 TTCTT
1 TTCTT
5131 AAATAGAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
6 6 0.17
7 22 0.63
8 7 0.20
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
TTCTTTT
Found at i:5114 original size:18 final size:16
Alignment explanation
Indices: 5039--5130 Score: 89
Period size: 18 Copynumber: 5.5 Consensus size: 16
5029 AAGGAGATTC
5039 TTCTTCTTCTTCTTCTT
1 TTCTTCTTCTTCTT-TT
5056 CTTCTTCTTCTTCTTCTT
1 -TTCTTCTTCTTCTT-TT
*
5074 CTTCTTCTTCTTCTTCT
1 -TTCTTCTTCTTCTTTT
5091 TTC-T-TTCTTTCTTTT
1 TTCTTCTTC-TTCTTTT
*
5106 TTCTTCTTTCTTTTTTT
1 TTCTTC-TTCTTCTTTT
*
5123 TTTTTCTT
1 TTCTTCTT
5131 AAATAGAAGA
Statistics
Matches: 66, Mismatches: 4, Indels: 10
0.82 0.05 0.12
Matches are distributed among these distances:
14 3 0.05
15 10 0.15
16 6 0.09
17 12 0.18
18 35 0.53
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
TTCTTCTTCTTCTTTT
Found at i:6563 original size:22 final size:22
Alignment explanation
Indices: 6535--6580 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
6525 CGTCTTTTTC
*
6535 CTTCCACCACCGGTGAGCTTCT
1 CTTCCACCACCAGTGAGCTTCT
*
6557 CTTCCACCAGCAGTGAGCTTCT
1 CTTCCACCACCAGTGAGCTTCT
6579 CT
1 CT
6581 GCTCTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.15, C:0.39, G:0.17, T:0.28
Consensus pattern (22 bp):
CTTCCACCACCAGTGAGCTTCT
Found at i:13908 original size:27 final size:28
Alignment explanation
Indices: 13857--13909 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
13847 TTAAGTACAT
***
13857 AAAAACTTTAAGTCTTTTTGTTAAAAAA
1 AAAAACTTTAAGTCTTTTAACTAAAAAA
13885 AAAAACTTTAAGTC-TTTAACTAAAA
1 AAAAACTTTAAGTCTTTTAACTAAAA
13910 GACTTTGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 8 0.36
28 14 0.64
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.36
Consensus pattern (28 bp):
AAAAACTTTAAGTCTTTTAACTAAAAAA
Found at i:15310 original size:14 final size:14
Alignment explanation
Indices: 15262--15332 Score: 63
Period size: 14 Copynumber: 5.1 Consensus size: 14
15252 TCGTAAATTT
*
15262 TAATAT-ATATAAA
1 TAATATAATATATA
* *
15275 TAATAATATTAGATA
1 TAAT-ATAATATATA
*
15290 TATTATAATATATA
1 TAATATAATATATA
*
15304 TAATATAAAATATA
1 TAATATAATATATA
* *
15318 AAAAATAATATATA
1 TAATATAATATATA
15332 T
1 T
15333 TATTATTCGA
Statistics
Matches: 44, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
13 4 0.09
14 33 0.75
15 7 0.16
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (14 bp):
TAATATAATATATA
Found at i:27553 original size:17 final size:17
Alignment explanation
Indices: 27525--27565 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
27515 CATTCCCACC
27525 CATAAATATCAACACTT
1 CATAAATATCAACACTT
* * *
27542 CTTAAATTTCAACCCTT
1 CATAAATATCAACACTT
27559 CATAAAT
1 CATAAAT
27566 CATTTAGGCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.34
Consensus pattern (17 bp):
CATAAATATCAACACTT
Found at i:28203 original size:22 final size:22
Alignment explanation
Indices: 28175--28244 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
28165 ATATATACTA
*
28175 TTAAATAAATAATTAATATATT
1 TTAAATAAATAAATAATATATT
*
28197 TTAAAT-AATAAATAATGA-GTT
1 TTAAATAAATAAATAAT-ATATT
*
28218 TAAAATAAATAAATAATATATAT
1 TTAAATAAATAAATAATATAT-T
28241 TTAA
1 TTAA
28245 TTACTAAACG
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
21 17 0.44
22 18 0.46
23 4 0.10
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (22 bp):
TTAAATAAATAAATAATATATT
Found at i:30882 original size:12 final size:12
Alignment explanation
Indices: 30865--30889 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30855 ATTCCCATCC
30865 GTTGGATTTGCA
1 GTTGGATTTGCA
30877 GTTGGATTTGCA
1 GTTGGATTTGCA
30889 G
1 G
30890 GCTCCGAGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.36, T:0.40
Consensus pattern (12 bp):
GTTGGATTTGCA
Found at i:32232 original size:27 final size:28
Alignment explanation
Indices: 32169--32236 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 28
32159 CACGTTTTGT
*
32169 AAACAT-TTTTTTTTTTAGTTTTCAGTA
1 AAACATATTTTTTTTTTAGTTATCAGTA
* * *
32196 AAACTTTATTTTTTTTTTGGTTAT-GGTA
1 AAAC-ATATTTTTTTTTTAGTTATCAGTA
32224 AAACATATTTTTT
1 AAACATATTTTTT
32237 GCTGCATAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
27 12 0.35
28 8 0.24
29 14 0.41
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.59
Consensus pattern (28 bp):
AAACATATTTTTTTTTTAGTTATCAGTA
Found at i:32646 original size:14 final size:14
Alignment explanation
Indices: 32627--32665 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
32617 TTTTAACTTA
32627 TTTCTTTCTTCTCT
1 TTTCTTTCTTCTCT
*
32641 TTTCTTTCTTTTCT
1 TTTCTTTCTTCTCT
*
32655 TCTCTTCTCTT
1 TTTCTT-TCTT
32666 TTTCCCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTCTTTCTTCTCT
Found at i:32655 original size:19 final size:18
Alignment explanation
Indices: 32627--32666 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
32617 TTTTAACTTA
*
32627 TTTCTTTCTTCTCTTTTC
1 TTTCTTTCTTCTCTTCTC
32645 TTTCTTTTCTTCTCTTCTC
1 TTTC-TTTCTTCTCTTCTC
32664 TTT
1 TTT
32667 TTCCCTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTCTTTCTTCTCTTCTC
Found at i:33447 original size:27 final size:28
Alignment explanation
Indices: 33406--33460 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
33396 TCTCCATATT
* *
33406 TTCTTTTTCTCCATA-TTCTATCTCTCTA
1 TTCTCTTTCTCCATACTTCAAT-TCTCTA
33434 TTCTCTTT-TCCATACTTCAATTCTCTA
1 TTCTCTTTCTCCATACTTCAATTCTCTA
33461 CTCCCTTGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.16, C:0.29, G:0.00, T:0.55
Consensus pattern (28 bp):
TTCTCTTTCTCCATACTTCAATTCTCTA
Found at i:33679 original size:32 final size:33
Alignment explanation
Indices: 33633--33705 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
33623 TACAAAGTTT
* * *
33633 TTTAACATGCATAATCT-CTTCTTCTACCTTTC
1 TTTATCATGCATAATCTCCTCCTGCTACCTTTC
*
33665 TTTATCATGCATAATCTCCTCCTGCTACTTTTC
1 TTTATCATGCATAATCTCCTCCTGCTACCTTTC
33698 TTTATCAT
1 TTTATCAT
33706 TAAAAAAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 16 0.44
33 20 0.56
ACGTcount: A:0.21, C:0.27, G:0.04, T:0.48
Consensus pattern (33 bp):
TTTATCATGCATAATCTCCTCCTGCTACCTTTC
Found at i:34917 original size:14 final size:14
Alignment explanation
Indices: 34898--34925 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
34888 TCGTTCTATG
34898 TGTTCAAATCAATA
1 TGTTCAAATCAATA
34912 TGTTCAAATCAATA
1 TGTTCAAATCAATA
34926 GATGATTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
TGTTCAAATCAATA
Found at i:39397 original size:14 final size:14
Alignment explanation
Indices: 39378--39405 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39368 TATTTAAGTC
39378 AAAAATGAAAAAAG
1 AAAAATGAAAAAAG
39392 AAAAATGAAAAAAG
1 AAAAATGAAAAAAG
39406 TAATTTGCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (14 bp):
AAAAATGAAAAAAG
Found at i:42014 original size:12 final size:12
Alignment explanation
Indices: 41993--42029 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
41983 ATATTCCTCG
41993 TACATATAACCA
1 TACATATAACCA
*
42005 TACGTATAACCA
1 TACATATAACCA
42017 TACATATAACCA
1 TACATATAACCA
42029 T
1 T
42030 TCTCCTGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.46, C:0.24, G:0.03, T:0.27
Consensus pattern (12 bp):
TACATATAACCA
Done.