Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015514.1 Corchorus olitorius cultivar O-4 contig15547, 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: 39154
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:3530 original size:32 final size:32
Alignment explanation
Indices: 3472--3588 Score: 121
Period size: 32 Copynumber: 3.7 Consensus size: 32
3462 TAAAAGGCCA
** **
3472 AAATAGCGGCGTTTAAA-GATAGAAACGTTGCT
1 AAATAGCGGCGTTTAAATTTTA-AAACGCCGCT
** *
3504 ATTTAGCGGCGTTTAAATTTTAAAACGCCACT
1 AAATAGCGGCGTTTAAATTTTAAAACGCCGCT
*
3536 AAATAGCGGCGTTT-AATTTTCCAAACGCCGCT
1 AAATAGCGGCGTTTAAATTTT-AAAACGCCGCT
*
3568 AAATAGCGGCGTCTAAATTTT
1 AAATAGCGGCGTTTAAATTTT
3589 TAAATATCGA
Statistics
Matches: 70, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
31 6 0.09
32 56 0.80
33 8 0.11
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (32 bp):
AAATAGCGGCGTTTAAATTTTAAAACGCCGCT
Found at i:20253 original size:44 final size:47
Alignment explanation
Indices: 20203--20298 Score: 135
Period size: 50 Copynumber: 2.0 Consensus size: 47
20193 TCATCAAAAA
20203 CACATTAA-AAT-A-GTTATGGGCATAGTAATTTTGAACAGGAGGTT
1 CACATTAATAATAATGTTATGGGCATAGTAATTTTGAACAGGAGGTT
*
20247 CACATTAATTAATAAGTTGTTATGGGCATAGTAATTTTGAATAGGAGGTT
1 CACATTAA-TAATAA--TGTTATGGGCATAGTAATTTTGAACAGGAGGTT
20297 CA
1 CA
20299 TTAAATAAGA
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
44 8 0.18
46 3 0.07
47 1 0.02
50 33 0.73
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.34
Consensus pattern (47 bp):
CACATTAATAATAATGTTATGGGCATAGTAATTTTGAACAGGAGGTT
Found at i:26882 original size:19 final size:18
Alignment explanation
Indices: 26858--26893 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
26848 TGAAGACTTA
26858 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
26877 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
26894 ATAATTTCAA
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:26900 original size:30 final size:30
Alignment explanation
Indices: 26846--26905 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
26836 GAAGTTCATG
* *
26846 TTTGAAGACTTATTGAAGACAATTTGAAGA
1 TTTGAAGACTCATTGAAGACAATTTCAAGA
*
26876 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
1 TTTGAAGACTCATTGAAG-ACAATTTCAAGA
26906 GCAAGAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (30 bp):
TTTGAAGACTCATTGAAGACAATTTCAAGA
Found at i:28185 original size:19 final size:20
Alignment explanation
Indices: 28144--28185 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
28134 TCTTAATTAT
*
28144 TTTCTCAATTTATTTTTTGC
1 TTTCTCAATTAATTTTTTGC
28164 TTTCT-AATTAATTGTTTT-C
1 TTTCTCAATTAATT-TTTTGC
28183 TTT
1 TTT
28186 AATTTTCTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.17, C:0.12, G:0.05, T:0.67
Consensus pattern (20 bp):
TTTCTCAATTAATTTTTTGC
Found at i:36119 original size:16 final size:15
Alignment explanation
Indices: 36091--36132 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
36081 TATCGACTTA
36091 AAGGATCAAGTCGAT
1 AAGGATCAAGTCGAT
36106 AAGGATCAAAGTCGAT
1 AAGGATC-AAGTCGAT
*
36122 AAGGAGCAAGT
1 AAGGATCAAGT
36133 GTCGACTAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.43, C:0.12, G:0.29, T:0.17
Consensus pattern (15 bp):
AAGGATCAAGTCGAT
Found at i:36206 original size:22 final size:21
Alignment explanation
Indices: 36180--36278 Score: 72
Period size: 22 Copynumber: 4.5 Consensus size: 21
36170 GTCGACTAAG
36180 AATTGTCGACTTCAAGGAAAGA
1 AATTGTCGAC-TCAAGGAAAGA
* *
36202 AATTGTCGACTCTGAGGAAAGC
1 AATTGTCGACTC-AAGGAAAGA
* * * *
36224 AATAGTCGACTAAAAGGAGATA
1 AATTGTCGACT-CAAGGAAAGA
* *
36246 AATTTTCGACTCAAGAGGAAGCA
1 AATTGTCGACTCAAG-GAAAG-A
*
36269 AATCGTCGAC
1 AATTGTCGAC
36279 AAGAAGGCAA
Statistics
Matches: 57, Mismatches: 16, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
21 5 0.09
22 43 0.75
23 9 0.16
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.21
Consensus pattern (21 bp):
AATTGTCGACTCAAGGAAAGA
Found at i:36210 original size:36 final size:37
Alignment explanation
Indices: 36132--36212 Score: 98
Period size: 36 Copynumber: 2.2 Consensus size: 37
36122 AAGGAGCAAG
*
36132 TGTCGACTAGGGAATTGTCGACTTAAGGAAGGAGTAAA
1 TGTCGACTAGAGAATTGTCGACTTAAGGAA-GAGTAAA
36170 -GTCGACTA-AGAATTGTCGACTTCAAGGAA-AG-AAA
1 TGTCGACTAGAGAATTGTCGACTT-AAGGAAGAGTAAA
36204 TTGTCGACT
1 -TGTCGACT
36213 CTGAGGAAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
34 3 0.08
35 2 0.05
36 20 0.51
37 14 0.36
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.25
Consensus pattern (37 bp):
TGTCGACTAGAGAATTGTCGACTTAAGGAAGAGTAAA
Done.