Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017766.1 Corchorus olitorius cultivar O-4 contig17799, 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: 35118
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2966 original size:70 final size:69
Alignment explanation
Indices: 2844--3004 Score: 268
Period size: 70 Copynumber: 2.3 Consensus size: 69
2834 ATTTCCCGCA
* *
2844 ACAACTCCTGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTTCTGCGCTCGTCA
1 ACAAGTCCTGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTTCTGCGCTCCT-A
2909 ACAGC
65 ACAGC
* *
2914 ACAAGTCCGGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTTCTGCGTTCCTAA
1 ACAAGTCCTGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTTCTGCGCTCCTAA
2979 CAGC
66 CAGC
*
2983 CCAAGTCCTGGACAGGACTTGG
1 ACAAGTCCTGGACAGGACTTGG
3005 CCAAGATCTG
Statistics
Matches: 85, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
69 26 0.31
70 59 0.69
ACGTcount: A:0.19, C:0.30, G:0.25, T:0.26
Consensus pattern (69 bp):
ACAAGTCCTGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTTCTGCGCTCCTAA
CAGC
Found at i:3298 original size:23 final size:22
Alignment explanation
Indices: 3271--3318 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
3261 TAATTTCCAT
3271 TTCTTCTAT-TATATATGTTTCAC
1 TTCTTCTATATATATAT-TTT-AC
*
3294 TTCTTCTATATCTATATTTTAC
1 TTCTTCTATATATATATTTTAC
3316 TTC
1 TTC
3319 AGCATTACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 5 0.22
23 12 0.52
24 6 0.26
ACGTcount: A:0.21, C:0.19, G:0.02, T:0.58
Consensus pattern (22 bp):
TTCTTCTATATATATATTTTAC
Found at i:6930 original size:19 final size:20
Alignment explanation
Indices: 6883--6930 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
6873 GGGATTTTTG
6883 ATAA-TAATTATTCAATAAA
1 ATAATTAATTATTCAATAAA
* *
6902 ATAATT-ATTATTTAAT-TA
1 ATAATTAATTATTCAATAAA
6920 ATAATTAATTA
1 ATAATTAATTA
6931 ATTTCAGTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 7 0.28
19 17 0.68
20 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAATTAATTATTCAATAAA
Found at i:7302 original size:13 final size:13
Alignment explanation
Indices: 7284--7309 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7274 AAGGTAACAA
7284 CAAAAATCATCAC
1 CAAAAATCATCAC
7297 CAAAAATCATCAC
1 CAAAAATCATCAC
7310 TCATGCCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Found at i:20386 original size:19 final size:20
Alignment explanation
Indices: 20339--20386 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
20329 GGGATGTTTG
20339 ATAA-TAATTATTCAATAAA
1 ATAATTAATTATTCAATAAA
* *
20358 ATAATT-ATTATTTAAT-TA
1 ATAATTAATTATTCAATAAA
20376 ATAATTAATTA
1 ATAATTAATTA
20387 ATTTCAGTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 7 0.28
19 17 0.68
20 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAATTAATTATTCAATAAA
Found at i:23752 original size:40 final size:41
Alignment explanation
Indices: 23703--23785 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 41
23693 TTTATGCGGC
* *
23703 TTAGTCCCTGATTCAAGA-TTTATTTACTATTTGATGCAAT
1 TTAGCCCCTGATTCAAGATTTTAGTTACTATTTGATGCAAT
* * * *
23743 TTAGCCCCTGGTTTAGGATTTTAGTTACTATTTGATTCAAT
1 TTAGCCCCTGATTCAAGATTTTAGTTACTATTTGATGCAAT
23784 TT
1 TT
23786 GGTCCCTAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
40 14 0.39
41 22 0.61
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.47
Consensus pattern (41 bp):
TTAGCCCCTGATTCAAGATTTTAGTTACTATTTGATGCAAT
Found at i:26172 original size:17 final size:18
Alignment explanation
Indices: 26132--26174 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
26122 TGAGATTTTT
*
26132 AGTTTGAAAGTTTCAGAG
1 AGTTTGAAAGGTTCAGAG
26150 -GATTTGAAAGGTT-AGAG
1 AG-TTTGAAAGGTTCAGAG
26167 AGTTTGAA
1 AGTTTGAA
26175 GAAAATGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.35, C:0.02, G:0.30, T:0.33
Consensus pattern (18 bp):
AGTTTGAAAGGTTCAGAG
Found at i:33798 original size:2 final size:2
Alignment explanation
Indices: 33791--33824 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
33781 TCAACAATTT
33791 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33825 CAAGGTGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34660 original size:6 final size:7
Alignment explanation
Indices: 34644--34669 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
34634 TCTTTGATGC
34644 AAAAATA
1 AAAAATA
34651 AAAAATA
1 AAAAATA
34658 AAAAATA
1 AAAAATA
34665 AAAAA
1 AAAAA
34670 GAATAAGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Done.