Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009160.1 Corchorus capsularis cultivar CVL-1 contig09181, 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: 27873
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:278 original size:21 final size:21
Alignment explanation
Indices: 245--293 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
235 AAGAATTTTA
**
245 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
265 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
286 GCATTCCT
1 GC-TTCCT
294 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:7919 original size:17 final size:17
Alignment explanation
Indices: 7899--7933 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
7889 AAAGGGTAGT
7899 TAAAAAAAATCTTTTCA
1 TAAAAAAAATCTTTTCA
* *
7916 TAAAAAAAGTGTTTTCA
1 TAAAAAAAATCTTTTCA
7933 T
1 T
7934 GCAAGAGGAG
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:0.49, C:0.09, G:0.06, T:0.37
Consensus pattern (17 bp):
TAAAAAAAATCTTTTCA
Found at i:8794 original size:11 final size:11
Alignment explanation
Indices: 8778--8819 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
8768 GAAGTTCGTG
8778 TTTGAAGATTA
1 TTTGAAGATTA
8789 TTTGAAGA-TA
1 TTTGAAGATTA
8799 TTTTGAAGAATTA
1 -TTTGAAG-ATTA
*
8812 TTTCAAGA
1 TTTGAAGA
8820 AGCAATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 2 0.07
11 16 0.59
12 7 0.26
13 2 0.07
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.43
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:9671 original size:33 final size:33
Alignment explanation
Indices: 9633--9739 Score: 135
Period size: 33 Copynumber: 3.2 Consensus size: 33
9623 GGCGCGAGTG
* *
9633 ACCGGCCATGCGACTTGGAGAAGCCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGATGCCCGGCCAAC
* *
9666 ACCGGCCACGCGACTCGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACTTGGAGATGCCCGGCCAAC
* * *
9699 ACCGGCCACGCGACATGGACATGTCCGGCC-AC
1 ACCGGCCACGCGACTTGGAGATGCCCGGCCAAC
9731 AACCGGCCA
1 -ACCGGCCA
9740 TCGCTTAACG
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
32 1 0.02
33 63 0.98
ACGTcount: A:0.22, C:0.40, G:0.29, T:0.08
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGATGCCCGGCCAAC
Found at i:12364 original size:22 final size:22
Alignment explanation
Indices: 12322--12365 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
12312 GCAGGGTGTT
* *
12322 TGGGGGTTGTTATGTGTGTGGG
1 TGGGGGTTGGTATGTGGGTGGG
12344 TGGGGGTTAGGTAT-TGGGTGGG
1 TGGGGGTT-GGTATGTGGGTGGG
12366 CTTATTGGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.07, C:0.00, G:0.57, T:0.36
Consensus pattern (22 bp):
TGGGGGTTGGTATGTGGGTGGG
Found at i:15638 original size:26 final size:26
Alignment explanation
Indices: 15617--15666 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
15607 TTCCTGAAGT
*
15617 AAAAATGACTAAAATGCCCCTGGCTA
1 AAAAATGACGAAAATGCCCCTGGCTA
*
15643 AAAAATGACGAAAATGCCCTTGGC
1 AAAAATGACGAAAATGCCCCTGGC
15667 AATTTCTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (26 bp):
AAAAATGACGAAAATGCCCCTGGCTA
Found at i:27652 original size:39 final size:39
Alignment explanation
Indices: 27598--27868 Score: 327
Period size: 39 Copynumber: 6.8 Consensus size: 39
27588 ATGTGCCTCG
* *
27598 GTCTTTCTTTACCTAATATCCTTCCTTGAAATTAAGTCA
1 GTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAGCCA
*
27637 GTCTTTCTTTGCCTAATTTCCTTCCTTGAAATTAAGCCA
1 GTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAGCCA
*
27676 GTCTTTTTTTTACCTAATTTCCTTCCTTGAAATTAAGCCA
1 GTC-TTTCTTTACCTAATTTCCTTCCTTGAAATTAAGCCA
* *
27716 GTATATCTTTACCTAA--T--TTCCTTGAAATTAAGCCA
1 GTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAGCCA
*
27751 GTCTTCTTTTTACCTAATTTCCTTTCC-TGAAATTAAGCCTGTGCCTTA
1 GTCTT-TCTTTACCTAATTTCC-TTCCTTGAAATTAA------GCC--A
*
27799 GTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCA
1 GTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAGCCA
*
27838 GTCTTTCTTTGCCTAATTTCCTTCCTTGAAA
1 GTCTTTCTTTACCTAATTTCCTTCCTTGAAA
27869 CTAAT
Statistics
Matches: 202, Mismatches: 14, Indels: 32
0.81 0.06 0.13
Matches are distributed among these distances:
35 21 0.10
36 10 0.05
37 1 0.00
38 1 0.00
39 81 0.40
40 45 0.22
41 6 0.03
46 7 0.03
47 24 0.12
48 6 0.03
ACGTcount: A:0.23, C:0.24, G:0.09, T:0.45
Consensus pattern (39 bp):
GTCTTTCTTTACCTAATTTCCTTCCTTGAAATTAAGCCA
Found at i:27752 original size:75 final size:77
Alignment explanation
Indices: 27605--27868 Score: 284
Period size: 75 Copynumber: 3.3 Consensus size: 77
27595 TCGGTCTTTC
* * * * *
27605 TTTACCTAATATCCTTCCTTGAAATTAAGTCAGTCTTTCTTTGCCTAATTTCCTTCCTTGAAATT
1 TTTACCTAATTTCCTTCCTTGAAATTAAGCCAGTATATCTTTACCTAA-TT-CTTCCTTGAAATT
*
27670 AAGCCAGTCTTTTT
64 AAGCCAGTCTTCTT
27684 TTTACCTAATTTCCTTCCTTGAAATTAAGCCAGTATATCTTTACCTAA-T-TTCCTTGAAATTAA
1 TTTACCTAATTTCCTTCCTTGAAATTAAGCCAGTATATCTTTACCTAATTCTTCCTTGAAATTAA
27747 GCCAGTCTTCTT
66 GCCAGTCTTCTT
* *
27759 TTTACCTAATTTCCTTTCC-TGAAATTAAGCCTGTGCCTTAGTCTTTCTTTACCTAATTTCCTTC
1 TTTACCTAATTTCC-TTCCTTGAAATTAA------GCC--AGTATATCTTTACCTAA-TT-CTTC
* *
27823 CTTGAAATTAAGTCAGTCTT-TC
55 CTTGAAATTAAGCCAGTCTTCTT
*
27845 TTTGCCTAATTTCCTTCCTTGAAA
1 TTTACCTAATTTCCTTCCTTGAAA
27869 CTAAT
Statistics
Matches: 160, Mismatches: 11, Indels: 21
0.83 0.06 0.11
Matches are distributed among these distances:
75 48 0.30
76 4 0.03
77 1 0.01
79 43 0.27
81 3 0.02
83 15 0.09
85 5 0.03
86 19 0.12
87 22 0.14
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (77 bp):
TTTACCTAATTTCCTTCCTTGAAATTAAGCCAGTATATCTTTACCTAATTCTTCCTTGAAATTAA
GCCAGTCTTCTT
Done.