Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024300.1 Corchorus olitorius cultivar O-4 contig24333, 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: 14974
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Found at i:843 original size:32 final size:33
Alignment explanation
Indices: 796--859 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
786 AAAGAAAACG
*
796 GAGAAGAAAAGAATAAA-AAATAAAAAAAGTTA
1 GAGAAAAAAAGAATAAACAAATAAAAAAAGTTA
* *
828 GAGAAAAAAATAATAAATCAAGTAAAAAAAGT
1 GAGAAAAAAAGAATAAA-CAAATAAAAAAAGT
860 AGTTGATATC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 15 0.56
34 12 0.44
ACGTcount: A:0.70, C:0.02, G:0.14, T:0.14
Consensus pattern (33 bp):
GAGAAAAAAAGAATAAACAAATAAAAAAAGTTA
Found at i:2962 original size:430 final size:433
Alignment explanation
Indices: 2353--3162 Score: 1146
Period size: 430 Copynumber: 1.9 Consensus size: 433
2343 TAATTTTTTG
* * * * * * * * *
2353 TCCACATGTCCGATTGAAGTTATTGAAGTGTCGGTTAAAAGGTTATTGCATGATTTACGACTTTT
1 TCCACATGTCCAATTAAAGTTATTCAAATGTCGGTTAAAAGGTTACTGCATAATCTACGACTGTC
* * * *
2418 ATGAAAGACCCGAAAGCTAAATTTGATATACGGGTTTCGTTAAGAGTTCAAAAGGGATTTTTTAT
66 ATGAAAGACCCGAAAGCTAAATTTGATATACGAGTTTCATAAAGAGTTCAAAAGGGAATTTTTAT
* * *
2483 GTTTCAAGATCTCCATTAACAAACATTTTCTTATTTGGATTATTTATCAAATGACCCTCATACTT
131 GTTTCAAGATCTCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATACTT
* * * *
2548 TTCTACTTTATACTACTTAGTCCTTTACAAATTCTATCTTA-ATCT-A-ACTTTATTTTTTTTAT
196 TTCCACTTTATACTACATAGTCCTTTACAAATTCTATCTTACATCTAACACTTCAATTTTTTT-T
* * * * *
2610 TATTTGTTCTATTTGTCCGATTAAGTTGATTCATGTGTCTATTAAAAGGTAATTTCATGATCTAC
260 TATTTGTTCTATTTGTCCAATTAAGCTAATTCAAGTGTCTATTAAAAGGTAATTTCATAATCTAC
* *
2675 AACTTTCATGAAGGACTAAAAAGCAAATTTTTATGTTTCAATTCAAAAAAATGCTTCCTAAATTT
325 AACTTTCATGAAAGACTAAAAAGCAAATTTTTATATTTCAATTCAAAAAAATGCTTCCTAAATTT
2740 GTTCGTTTCGATTGTTGGTCTATTTAATACCATATGATTTTCGA
390 GTTCGTTTCGATTGTTGGTCTATTTAATACCATATGATTTTCGA
*
2784 TCCACATGTCCAATTAAAGTTATTCAAATGTCGGTTAAAAGGTTACTGTATAATCTACGACTGTC
1 TCCACATGTCCAATTAAAGTTATTCAAATGTCGGTTAAAAGGTTACTGCATAATCTACGACTGTC
* * * *
2849 ATG-AAGAACCCGAAAG-TTAATTTGATCTACGAGTTTTATGAAAG-GTTCAAAATGGAATTTTT
66 ATGAAAG-ACCCGAAAGCTAAATTTGATATACGAGTTTCAT-AAAGAGTTCAAAAGGGAATTTTT
*
2911 ATGTTTCAAGATCTCCATTAACAAATATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATAC
129 ATGTTTCAAGATCTCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATAC
* * * *
2976 TTTTCCATTTTATGCTACATAGTCCTTTCCAAATTCTATCTTACTCGATTTAACACTTCAATTTT
194 TTTTCCACTTTATACTACATAGTCCTTTACAAATTCTATCTTA--C-ATCTAACACTTCAATTTT
* *
3041 TTTTTCTTTGTTCTATTTGTCCAATTAAGCTAATTCAAGTGTCTATTAAAAGGTAATTTTATAAT
256 TTTTTATTTGTTCTATTTGTCCAATTAAGCTAATTCAAGTGTCTATTAAAAGGTAATTTCATAAT
* * *
3106 CTACAACTTTCATGAAAGACTCAAAAGCTAATTTTTATATTTCAATTCTAAAAAATG
321 CTACAACTTTCATGAAAGACTAAAAAGCAAATTTTTATATTTCAATTCAAAAAAATG
3163 TTTTTGAAAT
Statistics
Matches: 329, Mismatches: 42, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
430 136 0.41
431 70 0.21
434 3 0.01
435 108 0.33
436 12 0.04
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.41
Consensus pattern (433 bp):
TCCACATGTCCAATTAAAGTTATTCAAATGTCGGTTAAAAGGTTACTGCATAATCTACGACTGTC
ATGAAAGACCCGAAAGCTAAATTTGATATACGAGTTTCATAAAGAGTTCAAAAGGGAATTTTTAT
GTTTCAAGATCTCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATACTT
TTCCACTTTATACTACATAGTCCTTTACAAATTCTATCTTACATCTAACACTTCAATTTTTTTTT
ATTTGTTCTATTTGTCCAATTAAGCTAATTCAAGTGTCTATTAAAAGGTAATTTCATAATCTACA
ACTTTCATGAAAGACTAAAAAGCAAATTTTTATATTTCAATTCAAAAAAATGCTTCCTAAATTTG
TTCGTTTCGATTGTTGGTCTATTTAATACCATATGATTTTCGA
Found at i:5733 original size:10 final size:10
Alignment explanation
Indices: 5718--5752 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
5708 CTTTTTTATT
5718 TCCTTATTTC
1 TCCTTATTTC
5728 TCCTTATTT-
1 TCCTTATTTC
5737 TCCTTATTCTC
1 TCCTTATT-TC
5748 TCCTT
1 TCCTT
5753 TTCTTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 8 0.35
10 10 0.43
11 5 0.22
ACGTcount: A:0.09, C:0.31, G:0.00, T:0.60
Consensus pattern (10 bp):
TCCTTATTTC
Found at i:5736 original size:18 final size:20
Alignment explanation
Indices: 5716--5752 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
5706 TCCTTTTTTA
5716 TTTCCTTATT-TCTCCTTAT
1 TTTCCTTATTCTCTCCTTAT
5735 TTTCCTTATTCTCTCCTT
1 TTTCCTTATTCTCTCCTT
5753 TTCTTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.08, C:0.30, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTCCTTATTCTCTCCTTAT
Found at i:6803 original size:16 final size:16
Alignment explanation
Indices: 6782--6849 Score: 73
Period size: 16 Copynumber: 4.2 Consensus size: 16
6772 ATTGAATTCA
6782 GGTTTTTTCAGGTTCG
1 GGTTTTTTCAGGTTCG
**
6798 GGTTTTTTCAGGTTTT
1 GGTTTTTTCAGGTTCG
*** * *
6814 AAATTTTTCGGGTTCT
1 GGTTTTTTCAGGTTCG
6830 GGTTTTTTCAGGTTCG
1 GGTTTTTTCAGGTTCG
6846 GGTT
1 GGTT
6850 CGGACGGGTT
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.09, C:0.10, G:0.28, T:0.53
Consensus pattern (16 bp):
GGTTTTTTCAGGTTCG
Found at i:8013 original size:11 final size:11
Alignment explanation
Indices: 7993--8038 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
7983 TATTTCGGAT
7993 TCGGGCTCGGG
1 TCGGGCTCGGG
*
8004 TCGGGATCGGG
1 TCGGGCTCGGG
*
8015 CTCGGTCTCGGG
1 -TCGGGCTCGGG
*
8027 TCGGGTTCGGG
1 TCGGGCTCGGG
8038 T
1 T
8039 TGCCTTGGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
11 20 0.69
12 9 0.31
ACGTcount: A:0.02, C:0.24, G:0.50, T:0.24
Consensus pattern (11 bp):
TCGGGCTCGGG
Found at i:8019 original size:23 final size:23
Alignment explanation
Indices: 7993--8037 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
7983 TATTTCGGAT
7993 TCGGGCTCGGGTCGGGATCGGGC
1 TCGGGCTCGGGTCGGGATCGGGC
* *
8016 TCGGTCTCGGGTCGGGTTCGGG
1 TCGGGCTCGGGTCGGGATCGGG
8038 TTGCCTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.02, C:0.24, G:0.51, T:0.22
Consensus pattern (23 bp):
TCGGGCTCGGGTCGGGATCGGGC
Found at i:8062 original size:16 final size:16
Alignment explanation
Indices: 8043--8086 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
8033 TCGGGTTGCC
*
8043 TTGGGTTCGGGTATTT
1 TTGGGTTCGGGTAATT
*
8059 TTGGGCTCGGGTAATT
1 TTGGGTTCGGGTAATT
* *
8075 TCGAGTTCGGGT
1 TTGGGTTCGGGT
8087 TCGGACGGAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.09, C:0.11, G:0.39, T:0.41
Consensus pattern (16 bp):
TTGGGTTCGGGTAATT
Found at i:8473 original size:93 final size:93
Alignment explanation
Indices: 8370--8549 Score: 299
Period size: 93 Copynumber: 1.9 Consensus size: 93
8360 TTTTTAAAAT
* *
8370 TTTTATAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATCAAATCTAATATCCTTATAA-CT
1 TTTTATAGTTTTACTCAACTAAAAACCCTATTTTTATTTAATCAAATCTAATATCCTTA-AACCT
*
8434 ATTTTATTTTTACCATTTTACTATTCTAC
65 ATTTTATTTTTACCATATTACTATTCTAC
*
8463 TTTTATAGTTTTACTCAACTAAAAACCCTATTTTTATTTAATTAAATCTAATATCCTTAAACCTA
1 TTTTATAGTTTTACTCAACTAAAAACCCTATTTTTATTTAATCAAATCTAATATCCTTAAACCTA
*
8528 TTTTATTTTTACGATATTACTA
66 TTTTATTTTTACCATATTACTA
8550 ATTTAATTAA
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
92 2 0.02
93 79 0.98
ACGTcount: A:0.33, C:0.15, G:0.02, T:0.49
Consensus pattern (93 bp):
TTTTATAGTTTTACTCAACTAAAAACCCTATTTTTATTTAATCAAATCTAATATCCTTAAACCTA
TTTTATTTTTACCATATTACTATTCTAC
Found at i:13986 original size:74 final size:74
Alignment explanation
Indices: 13865--14014 Score: 282
Period size: 74 Copynumber: 2.0 Consensus size: 74
13855 TATACTAATT
*
13865 ATCTATATTAATTATAAAGCCAAGTCCTGAGTTTGTGTCACGAGTTGACTCGGACACAAACTCAG
1 ATCTATACTAATTATAAAGCCAAGTCCTGAGTTTGTGTCACGAGTTGACTCGGACACAAACTCAG
13930 TTTATAAAA
66 TTTATAAAA
*
13939 ATCTATACTAATTATAAAGCCAAGTCCTGAGTTTGTGTTACGAGTTGACTCGGACACAAACTCAG
1 ATCTATACTAATTATAAAGCCAAGTCCTGAGTTTGTGTCACGAGTTGACTCGGACACAAACTCAG
14004 TTTATAAAA
66 TTTATAAAA
14013 AT
1 AT
14015 TCAAAACAAA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Consensus pattern (74 bp):
ATCTATACTAATTATAAAGCCAAGTCCTGAGTTTGTGTCACGAGTTGACTCGGACACAAACTCAG
TTTATAAAA
Found at i:14390 original size:105 final size:101
Alignment explanation
Indices: 14265--14472 Score: 292
Period size: 105 Copynumber: 2.0 Consensus size: 101
14255 TTGTTTAAAT
* * **
14265 TTTTATAGTTTTATTCAACTAAAAACTCTATTTTTATTTGATTAAATCTAATATTTTTATAAGAA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCATTAT--G-A
*
14330 CTATTTTATTTTTACCATTTTACT-ATTTAAATTAAAATAC
63 CTATTTTA-TTTTACCATTTTACTAATTT-AATTAAAAAAC
*
14370 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCATTATGCCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCATTATGACTA
* *
14435 TTTTATTTTATCATTTTACTAATTTTATTAAAAAAC
66 TTTTATTTTACCATTTTACTAATTTAATTAAAAAAC
14471 TT
1 TT
14473 AGATATATTA
Statistics
Matches: 94, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
101 25 0.27
102 12 0.13
103 1 0.01
105 56 0.60
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.51
Consensus pattern (101 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCATTATGACTA
TTTTATTTTACCATTTTACTAATTTAATTAAAAAAC
Found at i:14607 original size:17 final size:17
Alignment explanation
Indices: 14587--14633 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
14577 TTTATTTAAT
14587 TAAATTTAATATTTTTA
1 TAAATTTAATATTTTTA
*
14604 TAAATATT-TTATTTTTA
1 TAAAT-TTAATATTTTTA
* *
14621 TCATTTTAATATT
1 TAAATTTAATATT
14634 AAAAAATTGG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 2 0.08
17 20 0.83
18 2 0.08
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TAAATTTAATATTTTTA
Done.