Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009777.1 Corchorus capsularis cultivar CVL-1 contig09798, 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: 31388
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3676 original size:22 final size:20
Alignment explanation
Indices: 3658--3693 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 20
3648 CCTTTTCCCA
3658 TTTTCTTTTCTTTTTTTTCC
1 TTTTCTTTTCTTTTTTTTCC
3678 TTTT-TTTT-TTTTTTTT
1 TTTTCTTTTCTTTTTTTT
3694 TTGGTCTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.50
19 4 0.25
20 4 0.25
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (20 bp):
TTTTCTTTTCTTTTTTTTCC
Found at i:3694 original size:10 final size:10
Alignment explanation
Indices: 3658--3695 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
3648 CCTTTTCCCA
*
3658 TTTTCTTTTC
1 TTTTTTTTTC
*
3668 TTTTTTTTCC
1 TTTTTTTTTC
3678 TTTTTTTTT-
1 TTTTTTTTTC
3687 TTTTTTTTT
1 TTTTTTTTT
3696 GGTCTTAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:12864 original size:71 final size:69
Alignment explanation
Indices: 12748--12950 Score: 280
Period size: 70 Copynumber: 2.9 Consensus size: 69
12738 TAATCAAGAA
* *
12748 TTACTAATAGCAAGAAACAGTTACAAAATCGACTTTGAGTGTTGTTCACGGCATCTATTTTCGAC
1 TTACTAATAGTAAGAAACGGTTACAAAATCGACTTTGAGTGTTGTTCACGGCATCTATTTTCGAC
*
12813 TTTGAG
66 --CGAG
* * * * * *
12819 TTACTAATAGTAAGAAACGGTTACAAAATCAACTATAATTATTGTTTCACGGCAACTATTTTCGA
1 TTACTAATAGTAAGAAACGGTTACAAAATCGACTTTGAGTGTTG-TTCACGGCATCTATTTTCGA
12884 CCGAG
65 CCGAG
* *
12889 TTACTAATAGTAAGAAACGGTTACAAAATTGACTTTGAGTGTTGTTCACAGCATCTATTTTC
1 TTACTAATAGTAAGAAACGGTTACAAAATCGACTTTGAGTGTTGTTCACGGCATCTATTTTC
12951 CCCGTTCATG
Statistics
Matches: 114, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
69 16 0.14
70 41 0.36
71 37 0.32
72 20 0.18
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (69 bp):
TTACTAATAGTAAGAAACGGTTACAAAATCGACTTTGAGTGTTGTTCACGGCATCTATTTTCGAC
CGAG
Found at i:13142 original size:71 final size:70
Alignment explanation
Indices: 13062--13344 Score: 349
Period size: 71 Copynumber: 4.0 Consensus size: 70
13052 CTTTTTGGTA
* * * * *
13062 TCGACTTTGAGTTACTAACAGTACGAAACGGTTACAAAATCAAATTTAAGTATTGTTCACAGCAA
1 TCGACTTTGAGTTACTAATAGTAAGAAACGGTTACAAAATC-GATTTGAGTATTGTTCACGGCAA
13127 CTATCTT
65 CTAT-TT
* * *
13134 T-GACTTTGAGTTACTAATAGTAAGAAATGGTTAC-AAA--GACTTTGAGTGTTGTTCACGGCAT
1 TCGACTTTGAGTTACTAATAGTAAGAAACGGTTACAAAATCGA-TTTGAGTATTGTTCACGGCAA
13195 CTATTT
65 CTATTT
* * * *
13201 TCGACTTTGAGTTACTAGTAGTAAGAAACGGTTACAAAATCGACTTTGAGTATTGATCATGGAAA
1 TCGACTTTGAGTTACTAATAGTAAGAAACGGTTACAAAATCGA-TTTGAGTATTGTTCACGGCAA
13266 CTATTT
65 CTATTT
* * * *
13272 TCGACTTTGAGTTACTAATAGTAAGAAACGGTTATAAAATCGAGTTTGAGTGTTGTTCACGACAT
1 TCGACTTTGAGTTACTAATAGTAAGAAACGGTTACAAAATCGA-TTTGAGTATTGTTCACGGCAA
13337 CTATTT
65 CTATTT
13343 TC
1 TC
13345 TCCGTTCATA
Statistics
Matches: 182, Mismatches: 24, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
67 4 0.02
68 52 0.29
69 3 0.02
70 3 0.02
71 119 0.65
72 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (70 bp):
TCGACTTTGAGTTACTAATAGTAAGAAACGGTTACAAAATCGATTTGAGTATTGTTCACGGCAAC
TATTT
Found at i:13390 original size:64 final size:64
Alignment explanation
Indices: 13310--13437 Score: 238
Period size: 64 Copynumber: 2.0 Consensus size: 64
13300 CGGTTATAAA
13310 ATCGAGTTTGAGTGTTGTTCACGACATCTATTTTCTCCGTTCATAATAATTGAACTGGAAACCT
1 ATCGAGTTTGAGTGTTGTTCACGACATCTATTTTCTCCGTTCATAATAATTGAACTGGAAACCT
* *
13374 ATCGAGTTTGAGTGTTGTTCACGGCATCTATTTTCTCCGTTCATAATATTTGAACTGGAAACCT
1 ATCGAGTTTGAGTGTTGTTCACGACATCTATTTTCTCCGTTCATAATAATTGAACTGGAAACCT
13438 TACTTAAAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (64 bp):
ATCGAGTTTGAGTGTTGTTCACGACATCTATTTTCTCCGTTCATAATAATTGAACTGGAAACCT
Found at i:18833 original size:29 final size:29
Alignment explanation
Indices: 18768--18843 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
18758 GGTCTAATAT
*
18768 CCAAATT-AGGTCTAAACCTTTACAAACTTG
1 CCAAATTGA-GTCTAAACCTTTA-AAACATG
18798 CTCAAATTGAGTCTAAACCTTT-AAACATG
1 C-CAAATTGAGTCTAAACCTTTAAAACATG
*
18827 ACCAAATTGGGTCTAAA
1 -CCAAATTGAGTCTAAA
18844 AGTTAGCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
29 20 0.49
30 2 0.05
31 18 0.44
32 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (29 bp):
CCAAATTGAGTCTAAACCTTTAAAACATG
Found at i:19000 original size:29 final size:29
Alignment explanation
Indices: 18967--19043 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
18957 ATTTGCTAAC
* *
18967 GTTTAGGCTCAATTTGGTCATGTTT-AAAG
1 GTTTAGACTCAATTTGGT-AAGTTTAAAAG
*
18996 GTTTAGACTCAAATTGAGTAAGTTTGAAAAG
1 GTTTAGACTCAATTTG-GTAAGTTT-AAAAG
19027 GTTTAGACTCAATTTGG
1 GTTTAGACTCAATTTGG
19044 ACATTAGGCC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 19 0.46
30 3 0.07
31 19 0.46
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (29 bp):
GTTTAGACTCAATTTGGTAAGTTTAAAAG
Found at i:19461 original size:38 final size:38
Alignment explanation
Indices: 19392--19464 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 38
19382 GGTGGTGTGT
* *
19392 AAACTAATTAATGTTGTTTTACTGCAAAAAAAAAAAAA
1 AAACTAACTAATGTTGTTTCACTGCAAAAAAAAAAAAA
* * *
19430 AAACTAACTAATGTTGTTTCATTGTAGAAAAAAAA
1 AAACTAACTAATGTTGTTTCACTGCAAAAAAAAAA
19465 TTAAATGTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (38 bp):
AAACTAACTAATGTTGTTTCACTGCAAAAAAAAAAAAA
Found at i:28835 original size:24 final size:24
Alignment explanation
Indices: 28803--28855 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
28793 TTAGTATATT
28803 TAGTTGTCCAAGAATGGATCTGTG
1 TAGTTGTCCAAGAATGGATCTGTG
*
28827 TAGTTGTCCTAGAATGGATCTGTG
1 TAGTTGTCCAAGAATGGATCTGTG
28851 TAGTT
1 TAGTT
28856 ATTCATTGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.23, C:0.11, G:0.28, T:0.38
Consensus pattern (24 bp):
TAGTTGTCCAAGAATGGATCTGTG
Found at i:30942 original size:6 final size:6
Alignment explanation
Indices: 30933--30965 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
30923 TCTCTCTCCA
30933 ATATCT ATATCT ATATCT ATATCT ATA-CT ATAT
1 ATATCT ATATCT ATATCT ATATCT ATATCT ATAT
30966 TAAAAAGTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATCT
Found at i:31135 original size:70 final size:70
Alignment explanation
Indices: 31053--31189 Score: 204
Period size: 70 Copynumber: 2.0 Consensus size: 70
31043 TTGTTTAGGT
* * * *
31053 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTGTTTAATTAAATATAATATCTTTATAATTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
31118 TTTTA
66 TTTTA
* *
31123 TTTTACTA-TTTTACTCAACTAAAAACTCTTTTTTTATATAATTAAATCTAATATCCTTATAACT
1 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACT
31187 ATT
65 ATT
31190 ATCGCCTATT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
70 58 0.97
71 2 0.03
ACGTcount: A:0.36, C:0.12, G:0.01, T:0.51
Consensus pattern (70 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
TTTTA
Found at i:31326 original size:193 final size:193
Alignment explanation
Indices: 30997--31384 Score: 740
Period size: 193 Copynumber: 2.0 Consensus size: 193
30987 AAACTTTTGA
* *
30997 ATCGCCTATTATACCTTTATTTGTCAAATATATTTCTAAATTGCCATTGTTTAGGTTTTTATAGT
1 ATCGCCTATTATACCCTTATTTATCAAATATATTTCTAAATTGCCATTGTTTAGGTTTTTATAGT
31062 TTTACTCAACTAAAAACTCTATTTTTGTTTAATTAAATATAATATCTTTATAATTATTTTATTTT
66 TTTACTCAACTAAAAACTCTATTTTTGTTTAATTAAATATAATATCTTTATAATTATTTTATTTT
**
31127 ACTATTTTACTCAACTAAAAACTCTTTTTTTATATAATTAAATCTAATATCCTTATAACTATT
131 ACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTATT
31190 ATCGCCTATTATACCCTTATTTATCAAATATATTTCTAAATTGCCATTGTTTAGGTTTTTATAGT
1 ATCGCCTATTATACCCTTATTTATCAAATATATTTCTAAATTGCCATTGTTTAGGTTTTTATAGT
31255 TTTACTCAACTAAAAACTCTATTTTTGTTTAATTAAATATAATATCTTTATAATTATTTTATTTT
66 TTTACTCAACTAAAAACTCTATTTTTGTTTAATTAAATATAATATCTTTATAATTATTTTATTTT
31320 ACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTATT
131 ACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTATT
31383 AT
1 AT
31385 ATTT
Statistics
Matches: 191, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
193 191 1.00
ACGTcount: A:0.34, C:0.13, G:0.04, T:0.49
Consensus pattern (193 bp):
ATCGCCTATTATACCCTTATTTATCAAATATATTTCTAAATTGCCATTGTTTAGGTTTTTATAGT
TTTACTCAACTAAAAACTCTATTTTTGTTTAATTAAATATAATATCTTTATAATTATTTTATTTT
ACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTATT
Found at i:31331 original size:70 final size:70
Alignment explanation
Indices: 31246--31388 Score: 207
Period size: 70 Copynumber: 2.0 Consensus size: 70
31236 TTGTTTAGGT
* * * * *
31246 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTGTTTAATTAAATATAATATCTTTATAATTA
1 TTTTATAGTTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATATAATATCCTTATAACTA
*
31311 TTTTA
66 TTATA
*
31316 TTTTACTA-TTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACT
1 TTTTA-TAGTTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATATAATATCCTTATAACT
31380 ATTATA
65 ATTATA
31386 TTT
1 TTT
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
70 63 0.97
71 2 0.03
ACGTcount: A:0.37, C:0.11, G:0.01, T:0.50
Consensus pattern (70 bp):
TTTTATAGTTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATATAATATCCTTATAACTA
TTATA
Done.