Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021100.1 Corchorus olitorius cultivar O-4 contig21133, 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: 69639
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Found at i:9850 original size:8 final size:8
Alignment explanation
Indices: 9839--9879 Score: 82
Period size: 8 Copynumber: 5.1 Consensus size: 8
9829 CTATCTATCT
9839 ATCTATAC
1 ATCTATAC
9847 ATCTATAC
1 ATCTATAC
9855 ATCTATAC
1 ATCTATAC
9863 ATCTATAC
1 ATCTATAC
9871 ATCTATAC
1 ATCTATAC
9879 A
1 A
9880 ATATATAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (8 bp):
ATCTATAC
Found at i:9858 original size:24 final size:24
Alignment explanation
Indices: 9831--9879 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 24
9821 CAATATATCT
9831 ATCTAT-CTATCTATACATCTATAC
1 ATCTATAC-ATCTATACATCTATAC
9855 ATCTATACATCTATACATCTATAC
1 ATCTATACATCTATACATCTATAC
9879 A
1 A
9880 ATATATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.37, C:0.24, G:0.00, T:0.39
Consensus pattern (24 bp):
ATCTATACATCTATACATCTATAC
Found at i:11020 original size:25 final size:24
Alignment explanation
Indices: 10968--11024 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
10958 GTCAGCCTTG
*
10968 AATTT-TTTAATGTTTAATTCTTA
1 AATTTATTTAATGTTTAATTATTA
*
10991 AATTTATTTAATGTCTTAATTATTC
1 AATTTATTTAATGT-TTAATTATTA
*
11016 GATTTATTT
1 AATTTATTT
11025 TACAATCCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.28
25 16 0.55
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (24 bp):
AATTTATTTAATGTTTAATTATTA
Found at i:13095 original size:31 final size:31
Alignment explanation
Indices: 13057--13116 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
13047 GAGTTTTGTA
*
13057 AAACTTTTAAATCACCTATTATATCCTTATC
1 AAACTTTTAAATCACCTATTATACCCTTATC
* *
13088 AAACTTTTGAATCGCCTATTATACCCTTA
1 AAACTTTTAAATCACCTATTATACCCTTA
13117 ATTTAAGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.40
Consensus pattern (31 bp):
AAACTTTTAAATCACCTATTATACCCTTATC
Found at i:13261 original size:85 final size:85
Alignment explanation
Indices: 13154--13314 Score: 295
Period size: 85 Copynumber: 1.9 Consensus size: 85
13144 TTGTTTAAAT
**
13154 TTTTATAGTTTTTGTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
13219 TTTTATTTTTACCATTTTAC
66 TTTTATTTTTACCATTTTAC
*
13239 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
13304 TTTTATTTTTA
66 TTTTATTTTTA
13315 TGATATTACT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 73 1.00
ACGTcount: A:0.32, C:0.13, G:0.02, T:0.53
Consensus pattern (85 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
TTTTATTTTTACCATTTTAC
Found at i:14556 original size:26 final size:26
Alignment explanation
Indices: 14523--14610 Score: 85
Period size: 26 Copynumber: 3.4 Consensus size: 26
14513 ATAAAATTAT
*
14523 AATAATAATATAGATTTTATTGAATA
1 AATAATAATTTAGATTTTATTGAATA
* *
14549 AATGATAATTTAGA-ATTATT-AA-A
1 AATAATAATTTAGATTTTATTGAATA
*
14572 ATTATAATAATTTGGATTTTATTGAATA
1 A--ATAATAATTTAGATTTTATTGAATA
14600 AA-ATATAATTT
1 AATA-ATAATTT
14611 TAGTTTATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
23 2 0.04
24 2 0.04
25 17 0.34
26 25 0.50
27 2 0.04
28 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (26 bp):
AATAATAATTTAGATTTTATTGAATA
Found at i:23151 original size:64 final size:62
Alignment explanation
Indices: 23077--23206 Score: 233
Period size: 64 Copynumber: 2.1 Consensus size: 62
23067 CAAAACATTA
23077 GAATCCATCTTTTATAAATCTTTAGATAGATTTGATCACTTATTCTTGTTCTTTTTTTTTCTTT
1 GAATCCATCTTTTATAAATCTTTAGATAGATTTGATCACTTATTCTTG-T-TTTTTTTTTCTTT
*
23141 GAATCCATCTTTTATAAATCTTTGGATAGATTTGATCACTTATTCTTGTTTTTTTTTTCTTT
1 GAATCCATCTTTTATAAATCTTTAGATAGATTTGATCACTTATTCTTGTTTTTTTTTTCTTT
23203 GAAT
1 GAAT
23207 TTTGGAATTA
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
62 17 0.26
63 1 0.02
64 47 0.72
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.55
Consensus pattern (62 bp):
GAATCCATCTTTTATAAATCTTTAGATAGATTTGATCACTTATTCTTGTTTTTTTTTTCTTT
Found at i:45221 original size:22 final size:22
Alignment explanation
Indices: 45191--45233 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
45181 TATTTCTAGG
45191 TACACTATTCTTGTACACTACA
1 TACACTATTCTTGTACACTACA
*
45213 TACATTATTCTTGTACACTAC
1 TACACTATTCTTGTACACTAC
45234 CATCTATAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.26, G:0.05, T:0.40
Consensus pattern (22 bp):
TACACTATTCTTGTACACTACA
Found at i:46605 original size:32 final size:32
Alignment explanation
Indices: 46569--46635 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
46559 CATTACCATG
*
46569 TCATCGATTTGGTTTGACGTGGCAATGCCACA
1 TCATCAATTTGGTTTGACGTGGCAATGCCACA
* * *
46601 TCATCAATTTGGTTTGATGTGGTATTGCCACA
1 TCATCAATTTGGTTTGACGTGGCAATGCCACA
46633 TCA
1 TCA
46636 CCGACATGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (32 bp):
TCATCAATTTGGTTTGACGTGGCAATGCCACA
Found at i:59505 original size:6 final size:6
Alignment explanation
Indices: 59490--59531 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
59480 AGCAACCCAT
* *
59490 TCCCCG TCCCCA TCCCCG TCCCTG TCCCCG TCCCCG TCCCCG
1 TCCCCG TCCCCG TCCCCG TCCCCG TCCCCG TCCCCG TCCCCG
59532 GCGGGGAGCG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.02, C:0.64, G:0.14, T:0.19
Consensus pattern (6 bp):
TCCCCG
Found at i:59507 original size:12 final size:12
Alignment explanation
Indices: 59485--59531 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
59475 GAATTAGCAA
59485 CCCATTCCCCGTC
1 CCCA-TCCCCGTC
59498 CCCATCCCCGTC
1 CCCATCCCCGTC
**
59510 CCTGTCCCCGTC
1 CCCATCCCCGTC
*
59522 CCCGTCCCCG
1 CCCATCCCCG
59532 GCGGGGAGCG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
12 27 0.87
13 4 0.13
ACGTcount: A:0.04, C:0.64, G:0.13, T:0.19
Consensus pattern (12 bp):
CCCATCCCCGTC
Found at i:59655 original size:22 final size:22
Alignment explanation
Indices: 59621--59664 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
59611 ATAATAAAAT
59621 AATATATTATTATATTATTAAA
1 AATATATTATTATATTATTAAA
* * *
59643 AATATTTTTTTATCTTATTAAA
1 AATATATTATTATATTATTAAA
59665 TAAAAAGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
AATATATTATTATATTATTAAA
Found at i:62824 original size:3 final size:3
Alignment explanation
Indices: 62816--62863 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
62806 TACTGAATTA
62816 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
62864 CTTTACTTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:68613 original size:19 final size:19
Alignment explanation
Indices: 68593--68629 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
68583 AATTAATTAT
68593 TTTA-ATATTAAATTTTTA
1 TTTATATATTAAATTTTTA
*
68611 TTTATATATTATATTTTTA
1 TTTATATATTAAATTTTTA
68630 CTTAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTAAATTTTTA
Done.