Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018918.1 Corchorus olitorius cultivar O-4 contig18951, 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: 23496
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Found at i:578 original size:124 final size:126
Alignment explanation
Indices: 450--687 Score: 347
Period size: 125 Copynumber: 1.9 Consensus size: 126
440 CTTATATTTC
* ** *
450 AAATATATTTCTTAAATGCCATT-TTTAAACTTTTACAATTTTA-CTCAATTAAAAACTCTATTT
1 AAATATATTTCTTAAATGACATTATTTAAACTTTTACAATTTTATCTC-ACCAAAAAATCTATTT
*
513 TTATTTAATCAAA-TCAATATATTTATAACTATTTTATTTTTACCATTTTACTATTTTAATT
65 TTATTTAATCAAATTCAATATATTTATAACTATTTTATCTTTACCATTTTACTATTTTAATT
* * *
574 AAATATATTTCTTAAATGACATTATTTAAACTTTTACAGTTTTATTTCACCAAAAAATTTATTTT
1 AAATATATTTCTTAAATGACATTATTTAAACTTTTACAATTTTATCTCACCAAAAAATCTATTTT
* * *
639 TATTTAATTAAATTCAATATTTTTATAACTATTTTATCTTTATCATTTT
66 TATTTAATCAAATTCAATATATTTATAACTATTTTATCTTTACCATTTT
688 TTTAGGGAAT
Statistics
Matches: 100, Mismatches: 11, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
124 22 0.22
125 43 0.43
126 35 0.35
ACGTcount: A:0.36, C:0.11, G:0.01, T:0.52
Consensus pattern (126 bp):
AAATATATTTCTTAAATGACATTATTTAAACTTTTACAATTTTATCTCACCAAAAAATCTATTTT
TATTTAATCAAATTCAATATATTTATAACTATTTTATCTTTACCATTTTACTATTTTAATT
Found at i:971 original size:30 final size:31
Alignment explanation
Indices: 840--961 Score: 182
Period size: 31 Copynumber: 4.1 Consensus size: 31
830 ACTAAATACT
*
840 AAAAAATCCCTAATG-TTTTC-TTTGGGAC-
1 AAAAAATCCCTTATGTTTTTCTTTTGGGACA
868 AAAAAAT-CCTTAATGTTTTTCTTTTGGGACA
1 AAAAAATCCCTT-ATGTTTTTCTTTTGGGACA
*
899 AAAAAATCCCTTATGTTTTTCTTATGGGACA
1 AAAAAATCCCTTATGTTTTTCTTTTGGGACA
930 AAAAAATCCCTTATGTTTTT-TTTTGGGACA
1 AAAAAATCCCTTATGTTTTTCTTTTGGGACA
960 AA
1 AA
962 TTAGTCCCTT
Statistics
Matches: 86, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
27 3 0.03
28 10 0.12
29 5 0.06
30 19 0.22
31 45 0.52
32 4 0.05
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (31 bp):
AAAAAATCCCTTATGTTTTTCTTTTGGGACA
Found at i:1147 original size:29 final size:30
Alignment explanation
Indices: 1105--1178 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 30
1095 CTCATTTTTG
*
1105 AAACATAAGGGATTAATTTGTCCCGAAA-A
1 AAACATAAGGGATTAATTTGTCCCAAAACA
*
1134 AAACATAAGGGATTATTTTGTCCCAAAAGCA
1 AAACATAAGGGATTAATTTGTCCCAAAA-CA
*
1165 AAACATAAGAGATT
1 AAACATAAGGGATT
1179 TTTTTGGGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 26 0.65
31 14 0.35
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.24
Consensus pattern (30 bp):
AAACATAAGGGATTAATTTGTCCCAAAACA
Found at i:3357 original size:29 final size:29
Alignment explanation
Indices: 3298--3362 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
3288 ACCAAACCGT
* *****
3298 CAAATAAGCCCCTGAACTTTTATTTCGGC
1 CAAATAAGCCCCTGAACTCTTAAAAAAGC
3327 CAAATAAGCCCCTGAACTCTTAAAAAAGC
1 CAAATAAGCCCCTGAACTCTTAAAAAAGC
3356 CAAATAA
1 CAAATAA
3363 ACTCTGTTGC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.23
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTCTTAAAAAAGC
Found at i:4167 original size:22 final size:22
Alignment explanation
Indices: 4142--4185 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
4132 CTTTGGAGGT
* *
4142 TCGAACCTGAATGTCTTCCACC
1 TCGAACCCGAATGCCTTCCACC
4164 TCGAACCCGAATGCCTTCCACC
1 TCGAACCCGAATGCCTTCCACC
4186 ACAAATTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.41, G:0.14, T:0.23
Consensus pattern (22 bp):
TCGAACCCGAATGCCTTCCACC
Found at i:12650 original size:19 final size:18
Alignment explanation
Indices: 12626--12661 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
12616 TGAAGACTTA
12626 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
12645 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
12662 ATGGAGCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:14931 original size:15 final size:16
Alignment explanation
Indices: 14911--14950 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
14901 AGAGGTTGAA
14911 AGAAAACAATTAAAC-
1 AGAAAACAATTAAACT
*
14926 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
14942 AGAAAACAA
1 AGAAAACAA
14951 AGCAAAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.65, C:0.12, G:0.07, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:19115 original size:11 final size:11
Alignment explanation
Indices: 19082--19115 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
19072 TGCCGGTTTC
19082 TATCGAAGATT
1 TATCGAAGATT
* *
19093 CATCAAAGATT
1 TATCGAAGATT
19104 TATCGAAGATT
1 TATCGAAGATT
19115 T
1 T
19116 CAGCACCAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (11 bp):
TATCGAAGATT
Found at i:21073 original size:3 final size:3
Alignment explanation
Indices: 21065--21095 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
21055 ATTTTAATTA
21065 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
21096 ATTTGTACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Done.