Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024164.1 Corchorus olitorius cultivar O-4 contig24197, 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: 34138
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:485 original size:55 final size:55
Alignment explanation
Indices: 417--522 Score: 185
Period size: 55 Copynumber: 1.9 Consensus size: 55
407 TTTAAGATGG
* * *
417 TAGATTGGTAGTCTTTATGTTGTTTTGGATTTTTAAAAAACTGAGTTTGTCATGA
1 TAGACTGGTAGTCTTCATGTTGTTTTGGATTTTTAAAAAACTGAGATTGTCATGA
472 TAGACTGGTAGTCTTCATGTTGTTTTGGATTTTTAAAAAACTGAGATTGTC
1 TAGACTGGTAGTCTTCATGTTGTTTTGGATTTTTAAAAAACTGAGATTGTC
523 TTCGAGTCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.25, C:0.08, G:0.22, T:0.45
Consensus pattern (55 bp):
TAGACTGGTAGTCTTCATGTTGTTTTGGATTTTTAAAAAACTGAGATTGTCATGA
Found at i:946 original size:21 final size:22
Alignment explanation
Indices: 921--963 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
911 TATCTTAGAT
*
921 ATAATATATA-TTATTAAATAA
1 ATAATAAATATTTATTAAATAA
*
942 ATAATAAATATTTTTTAAATAA
1 ATAATAAATATTTATTAAATAA
964 TAAATAATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATAATAAATATTTATTAAATAA
Found at i:965 original size:21 final size:21
Alignment explanation
Indices: 921--969 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 21
911 TATCTTAGAT
*
921 ATAATATATATTATTAAATAA
1 ATAATAAATATTATTAAATAA
*
942 ATAATAAATATT-TT--TTAA
1 ATAATAAATATTATTAAATAA
960 ATAATAAATA
1 ATAATAAATA
970 ATGAGTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 13 0.50
20 2 0.08
21 11 0.42
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATAATAAATATTATTAAATAA
Found at i:11737 original size:2 final size:2
Alignment explanation
Indices: 11732--11770 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
11722 TAGGATACAT
* * *
11732 TA TA TA TA TG TG TG TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11771 TGCTAAGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13794 original size:11 final size:11
Alignment explanation
Indices: 13780--13817 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
13770 ATTCATAACA
13780 AATTTATAATT
1 AATTTATAATT
13791 AATTTATAATT
1 AATTTATAATT
13802 -ATTTGATAATT
1 AATTT-ATAATT
*
13813 TATTT
1 AATTT
13818 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:21284 original size:24 final size:25
Alignment explanation
Indices: 21250--21298 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
21240 TAGAACAATT
21250 ATAAAGAAAAGCAATTAAA-CTAAA
1 ATAAAGAAAAGCAATTAAATCTAAA
* *
21274 ATAAAGCAAAGTAATTAAATCTAAA
1 ATAAAGAAAAGCAATTAAATCTAAA
21299 CTTTGGCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.63, C:0.08, G:0.08, T:0.20
Consensus pattern (25 bp):
ATAAAGAAAAGCAATTAAATCTAAA
Found at i:22003 original size:11 final size:11
Alignment explanation
Indices: 21987--22011 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
21977 CCCTCTTCTT
21987 AAACTAGAGAA
1 AAACTAGAGAA
21998 AAACTAGAGAA
1 AAACTAGAGAA
22009 AAA
1 AAA
22012 TAAAAGATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.08, G:0.16, T:0.08
Consensus pattern (11 bp):
AAACTAGAGAA
Found at i:22661 original size:30 final size:30
Alignment explanation
Indices: 22606--22664 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
22596 GTTCTTGCTC
**
22606 CTTGAAATAATTCTTCAATGGTCTTCAATT
1 CTTGAAATAATTCTTCAATAATCTTCAATT
22636 CTTGAAATAA-TCTTCAATAAATCTTCAAT
1 CTTGAAATAATTCTTCAAT-AATCTTCAAT
22665 CACGAACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.41
Consensus pattern (30 bp):
CTTGAAATAATTCTTCAATAATCTTCAATT
Found at i:23219 original size:17 final size:17
Alignment explanation
Indices: 23199--23263 Score: 85
Period size: 17 Copynumber: 3.8 Consensus size: 17
23189 GTAATCTTTG
* *
23199 ATCACCAGTGATCTCGC
1 ATCACTAGTGATCTTGC
*
23216 ATCACTGGTGATCTTGC
1 ATCACTAGTGATCTTGC
* *
23233 ATCACTGGTGATCTTGG
1 ATCACTAGTGATCTTGC
23250 ATCACTAGTGATCT
1 ATCACTAGTGATCT
23264 GGGGGGTGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 43 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.32
Consensus pattern (17 bp):
ATCACTAGTGATCTTGC
Found at i:25961 original size:2 final size:2
Alignment explanation
Indices: 25954--25984 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
25944 CAACTTCTTA
25954 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25985 AAAAATTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26561 original size:18 final size:18
Alignment explanation
Indices: 26521--26561 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
26511 GATGAAATCC
26521 TAAAACGAAAAAGAAAAA
1 TAAAACGAAAAAGAAAAA
* * *
26539 CAAAACTAAAAAGAAAAT
1 TAAAACGAAAAAGAAAAA
26557 TAAAA
1 TAAAA
26562 TGTTAGTAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.76, C:0.07, G:0.07, T:0.10
Consensus pattern (18 bp):
TAAAACGAAAAAGAAAAA
Found at i:30172 original size:30 final size:30
Alignment explanation
Indices: 30117--30175 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
30107 ATTCTTGCTC
**
30117 CTTGAAATAATTCTTCAATGGTCTTCAATT
1 CTTGAAATAATTCTTCAATAATCTTCAATT
30147 CTTGAAATAA-TCTTCAATAAATCTTCAAT
1 CTTGAAATAATTCTTCAAT-AATCTTCAAT
30176 CACAAACTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.41
Consensus pattern (30 bp):
CTTGAAATAATTCTTCAATAATCTTCAATT
Found at i:33445 original size:27 final size:27
Alignment explanation
Indices: 33410--33487 Score: 147
Period size: 27 Copynumber: 2.9 Consensus size: 27
33400 GCACATCGGT
*
33410 CATTTAGGGGCATTTTGGTCATTTTTA
1 CATTCAGGGGCATTTTGGTCATTTTTA
33437 CATTCAGGGGCATTTTGGTCATTTTTA
1 CATTCAGGGGCATTTTGGTCATTTTTA
33464 CATTCAGGGGCATTTTGGTCATTT
1 CATTCAGGGGCATTTTGGTCATTT
33488 CAAGTTCACT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.18, C:0.14, G:0.23, T:0.45
Consensus pattern (27 bp):
CATTCAGGGGCATTTTGGTCATTTTTA
Found at i:33774 original size:13 final size:13
Alignment explanation
Indices: 33756--33785 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
33746 CAAAAAATCC
33756 AAAAAAATACAAA
1 AAAAAAATACAAA
*
33769 AAAAAAATCCAAA
1 AAAAAAATACAAA
33782 AAAA
1 AAAA
33786 TGTGATTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.83, C:0.10, G:0.00, T:0.07
Consensus pattern (13 bp):
AAAAAAATACAAA
Done.