Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008657.1 Corchorus capsularis cultivar CVL-1 contig08678, 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: 27656
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:557 original size:32 final size:32
Alignment explanation
Indices: 521--584 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
511 AACTCGAAAT
* * *
521 CGAAAATACCTGAAGCCGACA-AAGTCCGAATC
1 CGAAAATACCCGAACCCGA-ATAAATCCGAATC
553 CGAAAATACCCGAACCCGAATAAATCCGAATC
1 CGAAAATACCCGAACCCGAATAAATCCGAATC
585 AGAATGAACC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 1 0.04
32 27 0.96
ACGTcount: A:0.42, C:0.30, G:0.16, T:0.12
Consensus pattern (32 bp):
CGAAAATACCCGAACCCGAATAAATCCGAATC
Found at i:2055 original size:7 final size:7
Alignment explanation
Indices: 2043--2076 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
2033 GATGGTTCGG
2043 TTGCAAT
1 TTGCAAT
2050 TTGCAAT
1 TTGCAAT
2057 TTGCAAT
1 TTGCAAT
2064 TTGCAAT
1 TTGCAAT
2071 TTGCAA
1 TTGCAA
2077 ATCCACCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (7 bp):
TTGCAAT
Found at i:6392 original size:17 final size:17
Alignment explanation
Indices: 6370--6402 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6360 GTGAGTATAA
*
6370 AATTTCATCTATATTAG
1 AATTTCATCCATATTAG
6387 AATTTCATCCATATTA
1 AATTTCATCCATATTA
6403 ATGTATAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.45
Consensus pattern (17 bp):
AATTTCATCCATATTAG
Found at i:6589 original size:111 final size:110
Alignment explanation
Indices: 6459--6679 Score: 338
Period size: 111 Copynumber: 2.0 Consensus size: 110
6449 TATTAATCGG
* * *
6459 ATATATTAATTCTTCAACAAAATAATCCGACTTTACATTATAAATTTTAAGGCTGGGATATTCGG
1 ATATATTAATTCTTCAACAAAATAATCCGACTTTACATTATAAATTATAAGGCTGAGATATTC-A
* *
6524 AAAA-AAGAAAAC-CAAAAAATTGATTTAAGGATATTGTTAATTAATT
65 AAAACAAAAAAACAAAAAAAATT-A-TTAAGGATATTGTTAATTAATT
* *
6570 ATATATTAATTCTTGAACAAAATAATCCGACTTTACATTATAAATTATAAGGTTGAGATATTCAA
1 ATATATTAATTCTTCAACAAAATAATCCGACTTTACATTATAAATTATAAGGCTGAGATATTCAA
6635 AAACAAAAAAACAAAAAAAATTATTAAGGATATTGTTAATTAATT
66 AAACAAAAAAACAAAAAAAATTATTAAGGATATTGTTAATTAATT
6680 TTTACATTAT
Statistics
Matches: 101, Mismatches: 7, Indels: 5
0.89 0.06 0.04
Matches are distributed among these distances:
110 26 0.26
111 67 0.66
112 8 0.08
ACGTcount: A:0.47, C:0.09, G:0.10, T:0.34
Consensus pattern (110 bp):
ATATATTAATTCTTCAACAAAATAATCCGACTTTACATTATAAATTATAAGGCTGAGATATTCAA
AAACAAAAAAACAAAAAAAATTATTAAGGATATTGTTAATTAATT
Found at i:7970 original size:78 final size:76
Alignment explanation
Indices: 7888--8126 Score: 337
Period size: 78 Copynumber: 3.2 Consensus size: 76
7878 TTGTTTAGGT
* * *
7888 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAACTA
1 TTTTATA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
*
7953 TTTTATTTT--A
65 TTATATTTTACA
*
7963 ----ATATTTTACTCAACTAAAAACTCTATTTTTATATGATTAAATCTAATATCCTTATAACTAT
1 TTTTATATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTAT
8024 TATATTTTACCA
66 TATATTTTA-CA
*
8036 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATTACTA
1 TTTTA-TATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
8101 TTATATTTTACCA
65 TTATATTTTA-CA
8114 TTTTACTATTTTA
1 TTTTA-TATTTTA
8127 ATTAAAAAAC
Statistics
Matches: 149, Mismatches: 7, Indels: 13
0.88 0.04 0.08
Matches are distributed among these distances:
70 61 0.41
71 3 0.02
73 1 0.01
77 1 0.01
78 83 0.56
ACGTcount: A:0.36, C:0.13, G:0.01, T:0.50
Consensus pattern (76 bp):
TTTTATATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTAT
TATATTTTACA
Found at i:7971 original size:70 final size:70
Alignment explanation
Indices: 7887--8120 Score: 297
Period size: 70 Copynumber: 3.2 Consensus size: 70
7877 ATTGTTTAGG
* * * *
7887 TTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAACT
1 TTTTAATA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACT
7952 ATTTTA
65 ATTTTA
*
7958 TTTTAATATTTTACTCAACTAAAAACTCTATTTTTATATGATTAAATCTAATATCCTTATAACTA
1 TTTTAATATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAAC--
8023 TTATATTTTACCA
64 ---TATTTT---A
* *
8036 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATTACTA
1 TTTTAATATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
*
8101 TTATA
66 TTTTA
**
8106 TTTTACCATTTTACT
1 TTTTAATATTTTACT
8121 ATTTTAATTA
Statistics
Matches: 145, Mismatches: 10, Indels: 17
0.84 0.06 0.10
Matches are distributed among these distances:
70 66 0.46
71 7 0.05
73 5 0.03
75 6 0.04
78 61 0.42
ACGTcount: A:0.36, C:0.13, G:0.01, T:0.50
Consensus pattern (70 bp):
TTTTAATATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
TTTTA
Found at i:15697 original size:17 final size:17
Alignment explanation
Indices: 15675--15710 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
15665 GTATATTCCC
15675 ATTTCTTTATTCTTAAA
1 ATTTCTTTATTCTTAAA
15692 ATTTCTTTATTCTTAAA
1 ATTTCTTTATTCTTAAA
15709 AT
1 AT
15711 GCTTATGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.11, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTCTTTATTCTTAAA
Found at i:17239 original size:18 final size:18
Alignment explanation
Indices: 17218--17253 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
17208 GCACCTTTAG
17218 GCATTTTTGCATATTCCA
1 GCATTTTTGCATATTCCA
17236 GCATTTTTGCATATTCCA
1 GCATTTTTGCATATTCCA
17254 TGGCTTAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.44
Consensus pattern (18 bp):
GCATTTTTGCATATTCCA
Found at i:19998 original size:9 final size:9
Alignment explanation
Indices: 19978--20006 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
19968 AAGAAGAAGG
19978 AAAAGG-AA
1 AAAAGGAAA
19986 AAAAGGAAA
1 AAAAGGAAA
19995 AAAAGGAAA
1 AAAAGGAAA
20004 AAA
1 AAA
20007 TCAGAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (9 bp):
AAAAGGAAA
Found at i:20273 original size:21 final size:22
Alignment explanation
Indices: 20249--20296 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
20239 AAATGGAAGT
*
20249 TTTTAA-AGCAAAAATAAAAGA
1 TTTTAAGAACAAAAATAAAAGA
*
20270 TTTTAAGAACAAAAATAAAAGG
1 TTTTAAGAACAAAAATAAAAGA
20292 TTTTA
1 TTTTA
20297 TCACAGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.56, C:0.04, G:0.10, T:0.29
Consensus pattern (22 bp):
TTTTAAGAACAAAAATAAAAGA
Found at i:23033 original size:18 final size:18
Alignment explanation
Indices: 23010--23047 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
23000 TCAAGAAAAG
23010 GTTTTCAAAAGGTTTTGA
1 GTTTTCAAAAGGTTTTGA
23028 GTTTTCAAAAGGTTTTGA
1 GTTTTCAAAAGGTTTTGA
23046 GT
1 GT
23048 CTTTTTAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.45
Consensus pattern (18 bp):
GTTTTCAAAAGGTTTTGA
Found at i:27309 original size:12 final size:13
Alignment explanation
Indices: 27284--27317 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
27274 ATAATTATTG
27284 TTTGCTTTATTAA
1 TTTGCTTTATTAA
27297 TTTGCTTTA-TAA
1 TTTGCTTTATTAA
*
27309 TCTGCTTTA
1 TTTGCTTTA
27318 GATTTAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:27343 original size:28 final size:24
Alignment explanation
Indices: 27311--27369 Score: 64
Period size: 28 Copynumber: 2.3 Consensus size: 24
27301 CTTTATAATC
27311 TGCTTTAGATTTAGATTTAGATTTGCTT
1 TGCTTTAGATTTAG-TTTA-A-TTG-TT
**
27339 TGCTTTATTTTTAGTTTAATTGTT
1 TGCTTTAGATTTAGTTTAATTGTT
27363 TGCTTTA
1 TGCTTTA
27370 TAATTGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 9 0.31
25 3 0.10
26 1 0.03
27 4 0.14
28 12 0.41
ACGTcount: A:0.19, C:0.07, G:0.15, T:0.59
Consensus pattern (24 bp):
TGCTTTAGATTTAGTTTAATTGTT
Done.