Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014384.1 Corchorus olitorius cultivar O-4 contig14417, 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: 40528
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:697 original size:30 final size:30
Alignment explanation
Indices: 663--755 Score: 141
Period size: 30 Copynumber: 3.1 Consensus size: 30
653 CTGGCTTTGG
*
663 TAAAGGTTTTGGTTTTGATAAGGATTCTGA
1 TAAAGGTTTTGGTTTGGATAAGGATTCTGA
* *
693 TAAAGGTTTTCGCTTGGATAAGGATTCTGA
1 TAAAGGTTTTGGTTTGGATAAGGATTCTGA
* *
723 TAAAGGTTTTGGTTTGGATAAGGGTTTTGA
1 TAAAGGTTTTGGTTTGGATAAGGATTCTGA
753 TAA
1 TAA
756 GCTAGATACG
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.27, C:0.04, G:0.28, T:0.41
Consensus pattern (30 bp):
TAAAGGTTTTGGTTTGGATAAGGATTCTGA
Found at i:7390 original size:15 final size:16
Alignment explanation
Indices: 7372--7404 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
7362 GAAAGAAATA
7372 AATTAAAC-AGAAAAC
1 AATTAAACTAGAAAAC
*
7387 AATTATACTAGAAAAC
1 AATTAAACTAGAAAAC
7403 AA
1 AA
7405 AACAAAGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.64, C:0.12, G:0.06, T:0.18
Consensus pattern (16 bp):
AATTAAACTAGAAAAC
Found at i:8868 original size:12 final size:12
Alignment explanation
Indices: 8851--8881 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
8841 AGTCTTCAAA
8851 TCTTCAAATAAG
1 TCTTCAAATAAG
8863 TCTTC-AATAAG
1 TCTTCAAATAAG
8874 TCTTCAAA
1 TCTTCAAA
8882 CACGATCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.35
Consensus pattern (12 bp):
TCTTCAAATAAG
Found at i:8873 original size:11 final size:11
Alignment explanation
Indices: 8840--8880 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
8830 AATATGTCAG
8840 AAGTCTTC-A-
1 AAGTCTTCAAT
8849 AA-TCTTCAAAT
1 AAGTCTTC-AAT
8860 AAGTCTTCAAT
1 AAGTCTTCAAT
8871 AAGTCTTCAA
1 AAGTCTTCAA
8881 ACACGATCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 5 0.18
9 2 0.07
10 1 0.04
11 15 0.54
12 5 0.18
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (11 bp):
AAGTCTTCAAT
Found at i:13600 original size:31 final size:31
Alignment explanation
Indices: 13565--13643 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
13555 GATAAGTCTA
13565 TTTTCCTTCCCCGGCAAAAACCAGGAGAAAG
1 TTTTCCTTCCCCGGCAAAAACCAGGAGAAAG
*
13596 TTTTCCTTCGCCGGCAAAAACCAGGAGAAAG
1 TTTTCCTTCCCCGGCAAAAACCAGGAGAAAG
* *
13627 TTTCCCTTTCCCGGCAA
1 TTTTCCTTCCCCGGCAA
13644 CGGCGCCAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (31 bp):
TTTTCCTTCCCCGGCAAAAACCAGGAGAAAG
Found at i:13854 original size:16 final size:16
Alignment explanation
Indices: 13817--13857 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
13807 CAGAGGTTGA
*
13817 TAGAAAGCAATTAAAC
1 TAGAAAACAATTAAAC
*
13833 -AGAAAACAATTATAC
1 TAGAAAACAATTAAAC
13848 TAGAAAACAA
1 TAGAAAACAA
13858 AACAAAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.61, C:0.12, G:0.10, T:0.17
Consensus pattern (16 bp):
TAGAAAACAATTAAAC
Found at i:15276 original size:29 final size:30
Alignment explanation
Indices: 15239--15298 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
15229 AATTCTTTCC
* *
15239 TCTTGAAATAATTCTTCAAT-GTCTTCAAA
1 TCTTCAAATAAGTCTTCAATAGTCTTCAAA
15268 TCTTCAAATAAGTCTTCAATGAGTCTTCAAA
1 TCTTCAAATAAGTCTTCAAT-AGTCTTCAAA
15299 CACGATCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 18 0.67
31 9 0.33
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.38
Consensus pattern (30 bp):
TCTTCAAATAAGTCTTCAATAGTCTTCAAA
Found at i:34721 original size:16 final size:16
Alignment explanation
Indices: 34700--34730 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34690 ACATATTCAA
34700 TTCATCAAGTAAAGAT
1 TTCATCAAGTAAAGAT
*
34716 TTCATCAATTAAAGA
1 TTCATCAAGTAAAGA
34731 ACAACTAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (16 bp):
TTCATCAAGTAAAGAT
Found at i:35443 original size:16 final size:16
Alignment explanation
Indices: 35398--35443 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
35388 AGTAGATATG
35398 ATGAGAT-AGGAAGAAT
1 ATGAGATAAGGAA-AAT
*
35414 ATGAGCACAA-GAAAAT
1 ATGAG-ATAAGGAAAAT
35430 ATGAGATAAGGAAA
1 ATGAGATAAGGAAA
35444 GAATTCACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 3 0.12
16 17 0.68
17 4 0.16
18 1 0.04
ACGTcount: A:0.54, C:0.04, G:0.26, T:0.15
Consensus pattern (16 bp):
ATGAGATAAGGAAAAT
Done.