Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012553.1 Corchorus olitorius cultivar O-4 contig12586, 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: 24471
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Found at i:7362 original size:14 final size:14
Alignment explanation
Indices: 7343--7370 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
7333 TTTTGCACTT
7343 ATTCAAGACATTTA
1 ATTCAAGACATTTA
7357 ATTCAAGACATTTA
1 ATTCAAGACATTTA
7371 GTTAGACAAC
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):
ATTCAAGACATTTA
Found at i:9260 original size:30 final size:32
Alignment explanation
Indices: 9226--9286 Score: 90
Period size: 34 Copynumber: 1.9 Consensus size: 32
9216 TTGTTTGATG
9226 GACTG-TTTTT-TTTAGATTATCTTATATGCA
1 GACTGTTTTTTGTTTAGATTATCTTATATGCA
9256 GACTGTTTTTTTGGTTTAGATTATCTTATAT
1 GACTG-TTTTTT-GTTTAGATTATCTTATAT
9287 TCTTGTTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 5 0.19
32 5 0.19
34 17 0.63
ACGTcount: A:0.21, C:0.08, G:0.15, T:0.56
Consensus pattern (32 bp):
GACTGTTTTTTGTTTAGATTATCTTATATGCA
Found at i:9498 original size:175 final size:174
Alignment explanation
Indices: 9193--9647 Score: 797
Period size: 173 Copynumber: 2.6 Consensus size: 174
9183 TAATTCATTA
9193 GATTCTAGTAAGATAATATAATCTTGTTTGATGGACTGTTTTTTTTAGATTATCTTATATGCAGA
1 GATTCTAGTAAGATAATATAATCTTGTTTGATGGACTGTTTTTTTTAGATTATCTTATATGCAGA
9258 CTGTTTTTTTGGTTTAGATTATCTTATATTCTTGTTAAGATTTGGATATATGCAGCCTGTTTTTT
66 CTGTTTTTTTGGTTTA-ATTATCTTATATTCTTGTTAAGATTTGGATATATGCAGCCTGTTTTTT
9323 TTTTGGCTTCGTCCTTTGAGTAATGAGTTTTTTTTTGCTGGATTT
130 TTTTGGCTTCGTCCTTTGAGTAATGAGTTTTTTTTTGCTGGATTT
9368 GATTCTAGTAAGATAATATAATCTTGTTTGATGGACTG-TTTTTTTAGATTATCTTATATGCAGA
1 GATTCTAGTAAGATAATATAATCTTGTTTGATGGACTGTTTTTTTTAGATTATCTTATATGCAGA
*
9432 CTGTTTTTTTGGTTT-CTCTATCTTATATTCTTGTTAAGATTTGGATATATGCAGCCTGTTTTTT
66 CTGTTTTTTTGGTTTAAT-TATCTTATATTCTTGTTAAGATTTGGATATATGCAGCCTGTTTTTT
** **
9496 TTTTGGCTTCGTCCTTTGTTTCTTGAGTTTTTTTTTGCTGGATTT
130 TTTTGGCTTCGTCCTTTGAGTAATGAGTTTTTTTTTGCTGGATTT
*
9541 GATTCTAGTAAGATAATATAATCTTGTTTGGTGGACTGTTTTTTTTAGATTATCTTATATGCAGA
1 GATTCTAGTAAGATAATATAATCTTGTTTGATGGACTGTTTTTTTTAGATTATCTTATATGCAGA
* *
9606 CTGTTTTTTTGTTTTAGATTATCTTATATTCTTGTTTAGATT
66 CTGTTTTTTTGGTTTA-ATTATCTTATATTCTTGTTAAGATT
9648 ATCTTATATG
Statistics
Matches: 267, Mismatches: 9, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
172 1 0.00
173 124 0.46
174 81 0.30
175 60 0.22
176 1 0.00
ACGTcount: A:0.20, C:0.09, G:0.17, T:0.53
Consensus pattern (174 bp):
GATTCTAGTAAGATAATATAATCTTGTTTGATGGACTGTTTTTTTTAGATTATCTTATATGCAGA
CTGTTTTTTTGGTTTAATTATCTTATATTCTTGTTAAGATTTGGATATATGCAGCCTGTTTTTTT
TTTGGCTTCGTCCTTTGAGTAATGAGTTTTTTTTTGCTGGATTT
Found at i:9608 original size:30 final size:32
Alignment explanation
Indices: 9574--9634 Score: 90
Period size: 34 Copynumber: 1.9 Consensus size: 32
9564 TTGTTTGGTG
9574 GACTG-TTTT-TTTTAGATTATCTTATATGCA
1 GACTGTTTTTGTTTTAGATTATCTTATATGCA
9604 GACTGTTTTTTTGTTTTAGATTATCTTATAT
1 GACTG--TTTTTGTTTTAGATTATCTTATAT
9635 TCTTGTTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 5 0.19
33 4 0.15
34 18 0.67
ACGTcount: A:0.21, C:0.08, G:0.13, T:0.57
Consensus pattern (32 bp):
GACTGTTTTTGTTTTAGATTATCTTATATGCA
Found at i:10466 original size:17 final size:17
Alignment explanation
Indices: 10444--10480 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
10434 AGCTTAATAC
10444 TGATGTTATACTTTTGT
1 TGATGTTATACTTTTGT
*
10461 TGATGTTATTCTTTTGT
1 TGATGTTATACTTTTGT
10478 TGA
1 TGA
10481 CAAGGGAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.16, C:0.05, G:0.19, T:0.59
Consensus pattern (17 bp):
TGATGTTATACTTTTGT
Found at i:14753 original size:17 final size:17
Alignment explanation
Indices: 14727--14761 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
14717 AAGAAAAACC
14727 TTAACCCTTTTATTTCT
1 TTAACCCTTTTATTTCT
* *
14744 TTAACTCTTTTTTTTCT
1 TTAACCCTTTTATTTCT
14761 T
1 T
14762 CCATCTTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.20, G:0.00, T:0.66
Consensus pattern (17 bp):
TTAACCCTTTTATTTCT
Found at i:15905 original size:29 final size:33
Alignment explanation
Indices: 15865--15931 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 33
15855 AAAATTAAAG
15865 GGGC-AACGTGGCAC-AATTTT-T-A-GTTCAGA
1 GGGCAAACGTGGC-CTAATTTTGTAACGTTCAGA
*
15894 GGGCAAAC-TGGCCTAATTTTGTAACGTTCAGG
1 GGGCAAACGTGGCCTAATTTTGTAACGTTCAGA
15926 GGGCAA
1 GGGCAA
15932 TGGGGCTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
28 1 0.03
29 14 0.44
30 4 0.12
31 1 0.03
32 12 0.38
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (33 bp):
GGGCAAACGTGGCCTAATTTTGTAACGTTCAGA
Found at i:18474 original size:19 final size:20
Alignment explanation
Indices: 18433--18473 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
18423 TTCACTTAGG
18433 TTTGAAAACTCTTCTTATTT
1 TTTGAAAACTCTTCTTATTT
*
18453 TTTGAAAA-TTTTCTT-TTT
1 TTTGAAAACTCTTCTTATTT
18471 TTT
1 TTT
18474 TATTTGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 6 0.30
20 8 0.40
ACGTcount: A:0.22, C:0.10, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTGAAAACTCTTCTTATTT
Found at i:19011 original size:20 final size:20
Alignment explanation
Indices: 18986--19029 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
18976 ACAATAGATG
18986 TCCAAATCCCAATCATACAT
1 TCCAAATCCCAATCATACAT
19006 TCCAAATCCCAATCATACAT
1 TCCAAATCCCAATCATACAT
19026 TCCA
1 TCCA
19030 CTTAATATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (20 bp):
TCCAAATCCCAATCATACAT
Found at i:19787 original size:19 final size:19
Alignment explanation
Indices: 19759--19801 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
19749 GAAATGGAGG
19759 GGAAAAGATACTAGCAAAA
1 GGAAAAGATACTAGCAAAA
* *
19778 GGAAATGATACTAGCCAAA
1 GGAAAAGATACTAGCAAAA
19797 GGAAA
1 GGAAA
19802 GGGGTGAGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.53, C:0.12, G:0.23, T:0.12
Consensus pattern (19 bp):
GGAAAAGATACTAGCAAAA
Found at i:23092 original size:2 final size:2
Alignment explanation
Indices: 23085--23122 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
23075 GTAAGTATGG
23085 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
23123 ATACAGGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:23152 original size:16 final size:15
Alignment explanation
Indices: 23127--23158 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
23117 TCTCTCATAC
23127 AGGAAATGAATGATG
1 AGGAAATGAATGATG
23142 AGGACAATGAATGATG
1 AGGA-AATGAATGATG
23158 A
1 A
23159 AGATTATGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.47, C:0.03, G:0.31, T:0.19
Consensus pattern (15 bp):
AGGAAATGAATGATG
Found at i:23194 original size:20 final size:20
Alignment explanation
Indices: 23169--23211 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
23159 AGATTATGCC
*
23169 TTTAGGA-AGCTATTGTTCTA
1 TTTAGGAGA-CTATTGATCTA
23189 TTTAGGAGACTATTGATCTA
1 TTTAGGAGACTATTGATCTA
23209 TTT
1 TTT
23212 TGTGTGTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.26, C:0.09, G:0.19, T:0.47
Consensus pattern (20 bp):
TTTAGGAGACTATTGATCTA
Done.