Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015291.1 Corchorus olitorius cultivar O-4 contig15324, 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: 38719
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:67 original size:25 final size:26
Alignment explanation
Indices: 15--68 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
5 TTTTATGGCA
*
15 ATTATTATTAGTTAGGGTCAATCAAT
1 ATTATTATTAGTTAGGGCCAATCAAT
*
41 ATTATTATTA-TTGGGGCCAATCAAT
1 ATTATTATTAGTTAGGGCCAATCAAT
66 ATT
1 ATT
69 TTTTTTAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (26 bp):
ATTATTATTAGTTAGGGCCAATCAAT
Found at i:498 original size:35 final size:35
Alignment explanation
Indices: 452--520 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
442 AAAAGACCAG
452 CTTAGACCCAAAATTTGGGCTTTTCGTTCGCTGAC
1 CTTAGACCCAAAATTTGGGCTTTTCGTTCGCTGAC
*
487 CTTAGGCCCAAAATTTGGGCTTTTCGTTCGCTGA
1 CTTAGACCCAAAATTTGGGCTTTTCGTTCGCTGA
521 TCAAGGTCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.35
Consensus pattern (35 bp):
CTTAGACCCAAAATTTGGGCTTTTCGTTCGCTGAC
Found at i:713 original size:25 final size:25
Alignment explanation
Indices: 679--728 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
669 GCGCCTCCAA
679 ATCCTCCACTCTCCTTACAGATCCC
1 ATCCTCCACTCTCCTTACAGATCCC
704 ATCCTCCACTCTCCTTACAGATCCC
1 ATCCTCCACTCTCCTTACAGATCCC
729 CGAAAATGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.48, G:0.04, T:0.28
Consensus pattern (25 bp):
ATCCTCCACTCTCCTTACAGATCCC
Found at i:2678 original size:147 final size:147
Alignment explanation
Indices: 2411--2705 Score: 536
Period size: 147 Copynumber: 2.0 Consensus size: 147
2401 TGAAGTAGTA
*
2411 GATGATTCTGTCTGTAAGACCTAGGCCCAAAGAAGTGAAAAGCCATCTGGGTATTGTCTTTATGG
1 GATGATTCTGTCTGTAAGACCTAGGCCCAAAGAAGTGAAAAGCCAACTGGGTATTGTCTTTATGG
*
2476 AAGTGAAAAGGTTCTCGATTTAGGTTTCAAGCCACCTTAATGATCATGGGAGTTGCAAATTTTTG
66 AAGTGAAAAGGTTCTCAATTTAGGTTTCAAGCCACCTTAATGATCATGGGAGTTGCAAATTTTTG
*
2541 AATGAATTCTGGATTTT
131 AATGAATTCTGGAATTT
2558 GATGATTCTGTCTGTAAGACCTAGGCCCAAAGAAGTGAAAAGCCAACTGGGTATTGTCTTTATGG
1 GATGATTCTGTCTGTAAGACCTAGGCCCAAAGAAGTGAAAAGCCAACTGGGTATTGTCTTTATGG
* * *
2623 AAGTGTAAAGGTTCTCAATTTAGGTTTTAAGCCACCTTGATGATCATGGGAGTTGCAAATTTTTG
66 AAGTGAAAAGGTTCTCAATTTAGGTTTCAAGCCACCTTAATGATCATGGGAGTTGCAAATTTTTG
2688 AATGAATTCTGGAATTT
131 AATGAATTCTGGAATTT
2705 G
1 G
2706 TTGGCTGATA
Statistics
Matches: 142, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
147 142 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (147 bp):
GATGATTCTGTCTGTAAGACCTAGGCCCAAAGAAGTGAAAAGCCAACTGGGTATTGTCTTTATGG
AAGTGAAAAGGTTCTCAATTTAGGTTTCAAGCCACCTTAATGATCATGGGAGTTGCAAATTTTTG
AATGAATTCTGGAATTT
Found at i:10077 original size:3 final size:3
Alignment explanation
Indices: 10069--10181 Score: 226
Period size: 3 Copynumber: 37.7 Consensus size: 3
10059 TATAGTATAG
10069 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
10117 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
10165 ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT AT
10182 ATAAAACATA
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 110 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:16317 original size:12 final size:12
Alignment explanation
Indices: 16300--16325 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16290 CAGAGAGTTG
16300 GAGAGAAAATGA
1 GAGAGAAAATGA
16312 GAGAGAAAATGA
1 GAGAGAAAATGA
16324 GA
1 GA
16326 ATTTTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.35, T:0.08
Consensus pattern (12 bp):
GAGAGAAAATGA
Found at i:17085 original size:15 final size:14
Alignment explanation
Indices: 17060--17089 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
17050 AATAAATATA
17060 AATATTTTTATTTT
1 AATATTTTTATTTT
17074 AATATATTTTATTTT
1 AATAT-TTTTATTTT
17089 A
1 A
17090 TTGAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
AATATTTTTATTTT
Found at i:18066 original size:15 final size:14
Alignment explanation
Indices: 18048--18077 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
18038 TAATTTTCAA
18048 TAAAATAAAATATAT
1 TAAAATAAAA-ATAT
18063 TAAAATAAAAATAT
1 TAAAATAAAAATAT
18077 T
1 T
18078 TATTTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAAATAAAAATAT
Found at i:21816 original size:1 final size:1
Alignment explanation
Indices: 21777--21801 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
21767 GTTTGTTTGG
21777 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
21802 CCTCTTTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:25280 original size:2 final size:2
Alignment explanation
Indices: 25273--25300 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25263 TTATTAAGTC
25273 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
25301 AAAGGTACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25911 original size:14 final size:14
Alignment explanation
Indices: 25892--25942 Score: 70
Period size: 14 Copynumber: 3.7 Consensus size: 14
25882 GTTTGGTATC
25892 GTTTTTGTTTTTTT
1 GTTTTTGTTTTTTT
25906 GTTTTTGTTTTTTAT
1 GTTTTTGTTTTTT-T
*
25921 -TTTCTG-TTTTTT
1 GTTTTTGTTTTTTT
25933 GTTTTTGTTT
1 GTTTTTGTTT
25943 CGTTTTCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 1 0.03
13 10 0.31
14 20 0.62
15 1 0.03
ACGTcount: A:0.02, C:0.02, G:0.14, T:0.82
Consensus pattern (14 bp):
GTTTTTGTTTTTTT
Found at i:25971 original size:22 final size:22
Alignment explanation
Indices: 25929--25971 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
25919 ATTTTCTGTT
* * *
25929 TTTTGTTTTTGTTTCGTTTTCG
1 TTTTGTTCTTGTTGCGCTTTCG
25951 TTTTGTTCTTGTTGCGCTTTC
1 TTTTGTTCTTGTTGCGCTTTC
25972 AATTTTTGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.00, C:0.14, G:0.19, T:0.67
Consensus pattern (22 bp):
TTTTGTTCTTGTTGCGCTTTCG
Found at i:26509 original size:11 final size:11
Alignment explanation
Indices: 26489--26523 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
26479 TTGACAGCGC
26489 AACAAAAACAA
1 AACAAAAACAA
*
26500 AACGAAAACAA
1 AACAAAAACAA
26511 AACAAAAACAA
1 AACAAAAACAA
26522 AA
1 AA
26524 AACAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:28477 original size:25 final size:25
Alignment explanation
Indices: 28449--28496 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
28439 TTTTAACTCA
28449 TTATTTA-TTATTTAAAATATATTTG
1 TTATTTATTTA-TTAAAATATATTTG
*
28474 TTATTTATTTATTAATATATATT
1 TTATTTATTTATTAAAATATATT
28497 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
TTATTTATTTATTAAAATATATTTG
Found at i:33024 original size:30 final size:30
Alignment explanation
Indices: 32990--33050 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
32980 TCTCACGAAA
*
32990 TGTGAGTTTTCTTTATAATTTATTTGTTTG
1 TGTGAGTTTTCTTTATAATGTATTTGTTTG
33020 TGTGAGTTTTCTTTATAATGTATTTGTTTG
1 TGTGAGTTTTCTTTATAATGTATTTGTTTG
33050 T
1 T
33051 ATTTAGTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.16, C:0.03, G:0.18, T:0.62
Consensus pattern (30 bp):
TGTGAGTTTTCTTTATAATGTATTTGTTTG
Done.