Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011875.1 Corchorus olitorius cultivar O-4 contig11908, 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: 19213
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:9 original size:3 final size:3
Alignment explanation
Indices: 2--68 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
1 G
2 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
50 ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
69 ATAGTAGAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:825 original size:27 final size:26
Alignment explanation
Indices: 771--833 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
761 CTAAATTTTC
771 ATTATTTTAATAATGGAATAATTAAAAT
1 ATTA-TTTAATAATGGAAT-ATTAAAAT
799 ATTATTTAATAATGGTAAT-TTAGAAAT
1 ATTATTTAATAATGG-AATATTA-AAAT
826 ATATATTT
1 AT-TATTT
834 GAAAAAAGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 3 0.09
27 17 0.53
28 12 0.38
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (26 bp):
ATTATTTAATAATGGAATATTAAAAT
Found at i:963 original size:31 final size:31
Alignment explanation
Indices: 921--979 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
911 GTATTCAAAA
* *
921 AATAAGAGTATAATAGGTGATTCAAAAGGTT
1 AATAAGAGTATAATAGGCGAATCAAAAGGTT
*
952 AATAAGGGTATAATAGGCGAATCAAAAG
1 AATAAGAGTATAATAGGCGAATCAAAAG
980 TTTTACAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.47, C:0.05, G:0.24, T:0.24
Consensus pattern (31 bp):
AATAAGAGTATAATAGGCGAATCAAAAGGTT
Found at i:1269 original size:2 final size:2
Alignment explanation
Indices: 1215--1252 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
1205 AAATTACTTC
1215 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
1253 ATAGAGGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 31 0.91
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1834 original size:33 final size:30
Alignment explanation
Indices: 1749--1834 Score: 82
Period size: 33 Copynumber: 2.7 Consensus size: 30
1739 AGAAAGTTAC
* *
1749 AATCAAATTGAGTTTTTGTTTGTAGGCCACA
1 AATCAAATTAAGTTTTT-TTTTTAGGCCACA
* * * *
1780 AATCAAATTATGCTTTATTTTTGGGCCACATCA
1 AATCAAATTAAGTTTTTTTTTTAGG-C-CA-CA
1813 AATCAAATTAAGTTTTTTTTTT
1 AATCAAATTAAGTTTTTTTTTT
1835 TTTTTTACCG
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
30 6 0.14
31 14 0.33
32 2 0.05
33 21 0.49
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (30 bp):
AATCAAATTAAGTTTTTTTTTTAGGCCACA
Found at i:11750 original size:94 final size:96
Alignment explanation
Indices: 11559--11752 Score: 254
Period size: 98 Copynumber: 2.0 Consensus size: 96
11549 TAACTGACAA
11559 TGCATGTGATCTTCATGCTGCTAACTTGCAAAGAGAAAGTTTCTTAGGGAAAGTTATCGTGATTA
1 TGCATGTGATCTTCATGCTGCTAACTTGCAAAGAGAAAGTTTCTTAGGGAAAGTTATCG-GA-TA
* *
11624 ATGATGTAAATTTACTTGTGCTTCTGATTTATT
64 ATGATGCAAATTTACTTGTGCTTCTAATTTATT
* * * *
11657 TGCATGTGATCTTCATGGTGCTAACTTTCTAAGAG-AAGTTT-TGTAGATGAAA-TTACTC-G-T
1 TGCATGTGATCTTCATGCTGCTAACTTGCAAAGAGAAAGTTTCT-TAG-GGAAAGTTA-TCGGAT
11717 AATGATGCAAATTTACTTGTGCTTCTAATTTATT
63 AATGATGCAAATTTACTTGTGCTTCTAATTTATT
11751 TG
1 TG
11753 ATCGATTTGC
Statistics
Matches: 87, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
94 35 0.40
96 2 0.02
97 12 0.14
98 38 0.44
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (96 bp):
TGCATGTGATCTTCATGCTGCTAACTTGCAAAGAGAAAGTTTCTTAGGGAAAGTTATCGGATAAT
GATGCAAATTTACTTGTGCTTCTAATTTATT
Found at i:14084 original size:8 final size:8
Alignment explanation
Indices: 14025--14084 Score: 50
Period size: 8 Copynumber: 7.4 Consensus size: 8
14015 CTGAACGCGT
14025 TTAAATAA
1 TTAAATAA
** *
14033 AAAAATAT
1 TTAAATAA
14041 TTAAATAA
1 TTAAATAA
14049 TTGAAATTAA
1 TT-AAA-TAA
14059 TTAAA-AA
1 TTAAATAA
*
14066 TTAAAGAA
1 TTAAATAA
*
14074 TTAAATTA
1 TTAAATAA
14082 TTA
1 TTA
14085 CATTGTATTT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
7 7 0.17
8 23 0.56
9 6 0.15
10 5 0.12
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (8 bp):
TTAAATAA
Done.