Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015060.1 Corchorus olitorius cultivar O-4 contig15093, 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: 21965
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Found at i:167 original size:91 final size:91
Alignment explanation
Indices: 1--226 Score: 364
Period size: 91 Copynumber: 2.5 Consensus size: 91
* *
1 AATCAAGAAGTTTTCAATTACAACATCAGACTCAGAGTTATTTTTCAAGTTGTTTGTCAAATTGA
1 AATCAAGAAGTTTTCAGTTACAACATCAGACTCAGAGTTATTTTTCAAGTTGTTTGTCAAATTCA
*
66 CTGCAAATTGGT-CCTCTTTCATCATC
66 CCGCAAATTGGTCCCT-TTTCATCATC
* *
92 AATCAAGAAGTTTTCAGTTACAACATCAGACTCAGAGTTATTTTTCAAGTTGTTTTTCAAGTTCA
1 AATCAAGAAGTTTTCAGTTACAACATCAGACTCAGAGTTATTTTTCAAGTTGTTTGTCAAATTCA
* *
157 CCGCACATTGGTCCCTTTTTATCATC
66 CCGCAAATTGGTCCCTTTTCATCATC
*
183 AATCAAGAAGTTTTCAGTTACAACATCAGATTCAGAGTTATTTT
1 AATCAAGAAGTTTTCAGTTACAACATCAGACTCAGAGTTATTTT
227 CCAAAGGTAT
Statistics
Matches: 126, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
91 123 0.98
92 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.38
Consensus pattern (91 bp):
AATCAAGAAGTTTTCAGTTACAACATCAGACTCAGAGTTATTTTTCAAGTTGTTTGTCAAATTCA
CCGCAAATTGGTCCCTTTTCATCATC
Found at i:727 original size:50 final size:50
Alignment explanation
Indices: 308--725 Score: 683
Period size: 50 Copynumber: 8.4 Consensus size: 50
298 TCCGAATGCT
308 TAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCAACA
1 TAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCAACA
* *
358 TAGACTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTGTCAACA
1 TAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCAACA
408 TAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCAACA
1 TAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCAACA
458 TAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCAACA
1 TAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCAACA
*
508 CAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCAACA
1 TAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCAACA
** * *
558 CCGGCTTTTCCACAAGCCAAACTCATTTCCATACGAGTCAATTATCAACA
1 TAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCAACA
* * *
608 TGGGCTTTTCCACAAGCCAAAATCGTTTCCATACGAGTCAATTATCAACA
1 TAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCAACA
* * * * * *
658 CAGGGTTTTCCACAAGCCAAACCCATTTTCATACGAGTCAATTATCAACA
1 TAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCAACA
*
708 TAGGCTTTTCCATAAGCC
1 TAGGCTTTTCCACAAGCC
726 AAGTTCAATG
Statistics
Matches: 346, Mismatches: 22, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 346 1.00
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (50 bp):
TAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCAACA
Found at i:1225 original size:27 final size:29
Alignment explanation
Indices: 1167--1230 Score: 105
Period size: 27 Copynumber: 2.3 Consensus size: 29
1157 TTTACACTAA
*
1167 GGGCATTTTGGTCATTTTGGCACATTCGG
1 GGGCATTTTGGTCATTTTGGCACATTCAG
1196 GGGCATTTTGGTCA-TTT-GCACATTCAG
1 GGGCATTTTGGTCATTTTGGCACATTCAG
1223 GGGCATTT
1 GGGCATTT
1231 GAGTCAATTC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 17 0.50
28 3 0.09
29 14 0.41
ACGTcount: A:0.16, C:0.17, G:0.30, T:0.38
Consensus pattern (29 bp):
GGGCATTTTGGTCATTTTGGCACATTCAG
Found at i:3787 original size:21 final size:22
Alignment explanation
Indices: 3741--3787 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
3731 ATAATTTTGC
* * *
3741 TAAAAGTTTGGATTTTTATTGA
1 TAAAGGTTTGGATTTTGATTAA
3763 -AAAGGTTTGG-TTTTGATTAA
1 TAAAGGTTTGGATTTTGATTAA
3783 TAAAG
1 TAAAG
3788 TGTGGTAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (22 bp):
TAAAGGTTTGGATTTTGATTAA
Found at i:8233 original size:32 final size:32
Alignment explanation
Indices: 8192--8264 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
8182 CTTCAAAGAA
* * *
8192 TATTTTGTCCTAT-TTTATCAAAATTTGAGGGT
1 TATTTTGTCCT-TGTATATCAAAATTCGAGGGC
*
8224 TATTTTGTCCTTGTATATTAAAATTCGAGGGC
1 TATTTTGTCCTTGTATATCAAAATTCGAGGGC
8256 TATTTTGTC
1 TATTTTGTC
8265 TATCAATTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
31 1 0.03
32 35 0.97
ACGTcount: A:0.23, C:0.11, G:0.16, T:0.49
Consensus pattern (32 bp):
TATTTTGTCCTTGTATATCAAAATTCGAGGGC
Found at i:8784 original size:3 final size:3
Alignment explanation
Indices: 8776--8825 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
8766 CATGATTAAA
*
8776 ATT ATT ATT AAT 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
8824 AT
1 AT
8826 AATAAAGTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:8791 original size:12 final size:12
Alignment explanation
Indices: 8770--8821 Score: 77
Period size: 12 Copynumber: 4.3 Consensus size: 12
8760 ATGGGGCATG
*
8770 ATTAAAATTATT
1 ATTAATATTATT
8782 ATTAATATTATT
1 ATTAATATTATT
*
8794 ATTATTATTATT
1 ATTAATATTATT
*
8806 ATTATTATTATT
1 ATTAATATTATT
8818 ATTA
1 ATTA
8822 TTATAATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
ATTAATATTATT
Found at i:9264 original size:30 final size:30
Alignment explanation
Indices: 9230--9291 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
9220 TTCAATATCT
* *
9230 TTTTATAATT-ATGAAATAGAATTTTAATGA
1 TTTTATAATTAAT-AAATAAAAGTTTAATGA
9260 TTTTATAATTAATAAATAAAAGTTTAATGA
1 TTTTATAATTAATAAATAAAAGTTTAATGA
9290 TT
1 TT
9292 AAAAATTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 27 0.93
31 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (30 bp):
TTTTATAATTAATAAATAAAAGTTTAATGA
Found at i:9480 original size:35 final size:35
Alignment explanation
Indices: 9441--9559 Score: 229
Period size: 35 Copynumber: 3.4 Consensus size: 35
9431 TACTATAATA
9441 TTAAGGGTATTTTAGTAATTGACTAATTAAGATTT
1 TTAAGGGTATTTTAGTAATTGACTAATTAAGATTT
9476 TTAAGGGTATTTTAGTAATTGACTAATTAAGATTT
1 TTAAGGGTATTTTAGTAATTGACTAATTAAGATTT
9511 TTAAGGGTATTTTAGTAATTGACTAATTAAGATTT
1 TTAAGGGTATTTTAGTAATTGACTAATTAAGATTT
9546 TTAAGGGGTATTTT
1 TTAA-GGGTATTTT
9560 TGAGTTCGTG
Statistics
Matches: 83, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
35 74 0.89
36 9 0.11
ACGTcount: A:0.33, C:0.03, G:0.18, T:0.46
Consensus pattern (35 bp):
TTAAGGGTATTTTAGTAATTGACTAATTAAGATTT
Found at i:15632 original size:6 final size:6
Alignment explanation
Indices: 15617--15653 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
15607 ATGTGAAAGG
*
15617 AAAA-A AAAACA AAAACA AAAAC- AAAACA AAAAGA AAA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAA
15654 GAAATAAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
5 9 0.31
6 20 0.69
ACGTcount: A:0.86, C:0.11, G:0.03, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:15642 original size:17 final size:16
Alignment explanation
Indices: 15617--15653 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
15607 ATGTGAAAGG
15617 AAAAAAAAACAAAAAC
1 AAAAAAAAACAAAAAC
*
15633 AAAAACAAAACAAAAAG
1 AAAAA-AAAACAAAAAC
15650 AAAA
1 AAAA
15654 GAAATAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.86, C:0.11, G:0.03, T:0.00
Consensus pattern (16 bp):
AAAAAAAAACAAAAAC
Found at i:15664 original size:8 final size:8
Alignment explanation
Indices: 15651--15680 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
15641 AACAAAAAGA
15651 AAAGAAAT
1 AAAGAAAT
15659 AAAGAAAT
1 AAAGAAAT
15667 AAAGAAAT
1 AAAGAAAT
15675 AAAGAA
1 AAAGAA
15681 TTGGACTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (8 bp):
AAAGAAAT
Found at i:16803 original size:24 final size:24
Alignment explanation
Indices: 16746--16803 Score: 57
Period size: 24 Copynumber: 2.4 Consensus size: 24
16736 CCCGTTGAGG
* *
16746 AAATGTTTTATAACTGCTTTATAT
1 AAATGTTTTGTAAATGCTTTATAT
*
16770 AAAT-TCTTTGTAAAATGTTTTA-AT
1 AAATGT-TTTGT-AAATGCTTTATAT
16794 AAATGTTTTG
1 AAATGTTTTG
16804 GGTGCATAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
23 1 0.04
24 18 0.64
25 9 0.32
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.50
Consensus pattern (24 bp):
AAATGTTTTGTAAATGCTTTATAT
Done.