Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017406.1 Corchorus olitorius cultivar O-4 contig17439, 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: 22423
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:1270 original size:18 final size:18
Alignment explanation
Indices: 1257--1292 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1247 TCTTATTATT
1257 ATAATAATTATTATTAGTG
1 ATAA-AATTATTATTAGTG
*
1276 GTAAAATTATTATTAGT
1 ATAAAATTATTATTAGT
1293 TTATATGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (18 bp):
ATAAAATTATTATTAGTG
Found at i:9277 original size:22 final size:22
Alignment explanation
Indices: 9252--9382 Score: 81
Period size: 22 Copynumber: 6.0 Consensus size: 22
9242 TTTTAATAAT
*
9252 TAACTACCCTATTAAATTTTGA
1 TAACTACCCTATGAAATTTTGA
* *
9274 TAACCACCATATGAAATTTTGA
1 TAACTACCCTATGAAATTTTGA
* **
9296 TAATTA-CCTATGAAATTGGGA
1 TAACTACCCTATGAAATTTTGA
* * *
9317 TAAACT-CCATATGACACTTTGA
1 T-AACTACCCTATGAAATTTTGA
** *
9339 TAACCTA-ATTATGAAATTTTAA
1 TAA-CTACCCTATGAAATTTTGA
*
9361 TAAATCT-TCCTATGAAATTTTG
1 T-AA-CTACCCTATGAAATTTTG
9383 CAATCTTCCT
Statistics
Matches: 80, Mismatches: 23, Indels: 11
0.70 0.20 0.10
Matches are distributed among these distances:
21 15 0.19
22 50 0.62
23 15 0.19
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.37
Consensus pattern (22 bp):
TAACTACCCTATGAAATTTTGA
Found at i:15769 original size:20 final size:21
Alignment explanation
Indices: 15729--15769 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
15719 GCCACTGCTA
* *
15729 AAAAGTAAAAATCCCCCAAAC
1 AAAAGTAAAAATACCCAAAAC
15750 AAAAGTAAAAA-ACCCAAAAC
1 AAAAGTAAAAATACCCAAAAC
15770 CATAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.63, C:0.24, G:0.05, T:0.07
Consensus pattern (21 bp):
AAAAGTAAAAATACCCAAAAC
Found at i:18023 original size:15 final size:15
Alignment explanation
Indices: 18005--18035 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17995 ATTTAACTAT
18005 AAAATCTTTAGGTGC
1 AAAATCTTTAGGTGC
*
18020 AAAATCTTTAGTTGC
1 AAAATCTTTAGGTGC
18035 A
1 A
18036 GTTTCACTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (15 bp):
AAAATCTTTAGGTGC
Found at i:20854 original size:2 final size:2
Alignment explanation
Indices: 20847--20884 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
20837 GAGTATAGAG
*
20847 TA TA TA TA TA CA 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 TA TA
20885 CTAGTAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:21092 original size:38 final size:38
Alignment explanation
Indices: 21050--21163 Score: 112
Period size: 38 Copynumber: 3.1 Consensus size: 38
21040 TATTTTTTAT
21050 TATTATTCATAATTGAACTAAAAGTTTATTTATGAGAA
1 TATTATTCATAATTGAACTAAAAGTTTATTTATGAGAA
* * * * * ** *
21088 TATTAATCTTAA-AGAACT-ACA-TATATTT-T-TTAT
1 TATTATTCATAATTGAACTAAAAGTTTATTTATGAGAA
*
21121 TATTATTCATAATTAAACTAAAAGTTTATTTATGAGAA
1 TATTATTCATAATTGAACTAAAAGTTTATTTATGAGAA
21159 TATTA
1 TATTA
21164 ATCTTAAAGA
Statistics
Matches: 54, Mismatches: 17, Indels: 10
0.67 0.21 0.12
Matches are distributed among these distances:
33 11 0.20
34 5 0.09
35 8 0.15
36 8 0.15
37 6 0.11
38 16 0.30
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (38 bp):
TATTATTCATAATTGAACTAAAAGTTTATTTATGAGAA
Found at i:21117 original size:71 final size:71
Alignment explanation
Indices: 21032--21177 Score: 274
Period size: 71 Copynumber: 2.1 Consensus size: 71
21022 TGTAATAATT
* *
21032 ACTACTTATATTTTTTATTATTATTCATAATTGAACTAAAAGTTTATTTATGAGAATATTAATCT
1 ACTACATATATTTTTTATTATTATTCATAATTAAACTAAAAGTTTATTTATGAGAATATTAATCT
21097 TAAAGA
66 TAAAGA
21103 ACTACATATATTTTTTATTATTATTCATAATTAAACTAAAAGTTTATTTATGAGAATATTAATCT
1 ACTACATATATTTTTTATTATTATTCATAATTAAACTAAAAGTTTATTTATGAGAATATTAATCT
21168 TAAAGA
66 TAAAGA
21174 ACTA
1 ACTA
21178 AAGGAAAATT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (71 bp):
ACTACATATATTTTTTATTATTATTCATAATTAAACTAAAAGTTTATTTATGAGAATATTAATCT
TAAAGA
Found at i:21153 original size:33 final size:33
Alignment explanation
Indices: 21045--21153 Score: 82
Period size: 33 Copynumber: 3.2 Consensus size: 33
21035 ACTTATATTT
*
21045 TTTATTATTATTCATAATTGAACTAAAAGTTTA
1 TTTATTATTATTCATAATTAAACTAAAAGTTTA
* *
21078 TTTATGAGAATATTAATCTTAA--AGAACTACATATA-TTT-
1 TTTAT-----TATTATTCATAATTA-AACTA-A-A-AGTTTA
21116 TTTATTATTATTCATAATTAAACTAAAAGTTTA
1 TTTATTATTATTCATAATTAAACTAAAAGTTTA
21149 TTTAT
1 TTTAT
21154 GAGAATATTA
Statistics
Matches: 58, Mismatches: 5, Indels: 26
0.65 0.06 0.29
Matches are distributed among these distances:
31 1 0.02
32 4 0.07
33 21 0.36
34 5 0.09
35 1 0.02
37 5 0.09
38 16 0.28
39 4 0.07
40 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (33 bp):
TTTATTATTATTCATAATTAAACTAAAAGTTTA
Found at i:21194 original size:71 final size:71
Alignment explanation
Indices: 21048--21195 Score: 226
Period size: 71 Copynumber: 2.1 Consensus size: 71
21038 TATATTTTTT
* * *
21048 ATTATTATTCATAATTGAACTAAAAGTTTATTTATGAGAATATTAATCTTAAAGAACTACATATA
1 ATTATTATTCATAATTAAACTAAAAGTTTATTTATGAGAATATTAATCTTAAAGAACTAAAGATA
** *
21113 TTTTTT
66 AATTTA
21119 ATTATTATTCATAATTAAACTAAAAGTTTATTTATGAGAATATTAATCTTAAAGAACTAAAGGA-
1 ATTATTATTCATAATTAAACTAAAAGTTTATTTATGAGAATATTAATCTTAAAGAACTAAA-GAT
21183 AAATTTA
65 AAATTTA
21190 ATTATT
1 ATTATT
21196 TAAAATTTAC
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
71 69 0.99
72 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (71 bp):
ATTATTATTCATAATTAAACTAAAAGTTTATTTATGAGAATATTAATCTTAAAGAACTAAAGATA
AATTTA
Found at i:21515 original size:39 final size:40
Alignment explanation
Indices: 21459--21539 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
21449 TTTAATTCCT
21459 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
21499 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
21538 AT
1 AT
21540 TCTTAGGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:22013 original size:203 final size:202
Alignment explanation
Indices: 21648--22057 Score: 725
Period size: 203 Copynumber: 2.0 Consensus size: 202
21638 TTCCTTAATA
*
21648 ATAAATAAATCGGGTCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
1 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
*
21713 ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTGGTATAGTTCTATATATATAATAGTA
66 ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTGGTATAGTTCTATATATATAATAATA
*
21778 ATGTGTTGTATCTGATTCATTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
131 ATGTGTTGTATCTGATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
21843 ACCATTG
196 ACCATTG
*
21850 ATAAATAAATCGGATCTTTAATATCTTTTATGATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
*
21915 AATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTTTGGTATAGTT-T-TATATATAATA
65 AATTTAATAAATCAACCACTAATGTTCAACTA--ATTTTTTTGGTATAGTTCTATATATATAATA
*
21978 ATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACA
128 ATAATGTGTTGTATCTGATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACA
22043 TTCACCATTG
193 TTCACCATTG
22053 ATAAA
1 ATAAA
22058 GTTATTAAGC
Statistics
Matches: 199, Mismatches: 6, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
202 15 0.08
203 167 0.84
204 1 0.01
205 16 0.08
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (202 bp):
ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTGGTATAGTTCTATATATATAATAATA
ATGTGTTGTATCTGATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
ACCATTG
Done.