Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008880.1 Corchorus capsularis cultivar CVL-1 contig08901, 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: 66642
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:328 original size:23 final size:23
Alignment explanation
Indices: 279--333 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
269 CTCGGGTATT
* * *
279 TTCGGGTTCGGGCTCAGATCGGG
1 TTCGGGTTCGGGCCCAGATCAGA
* *
302 TTCGGGTTCGGGCCCGGGTCAGA
1 TTCGGGTTCGGGCCCAGATCAGA
325 TTCGGGTTC
1 TTCGGGTTC
334 ACTTTCGATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.07, C:0.24, G:0.42, T:0.27
Consensus pattern (23 bp):
TTCGGGTTCGGGCCCAGATCAGA
Found at i:1651 original size:17 final size:18
Alignment explanation
Indices: 1614--1651 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1604 AGCTTTAAAG
1614 TTTAAACATAAAATTAATT
1 TTTAAACATAAAA-TAATT
*
1633 TTTAAATATAAAA-AATT
1 TTTAAACATAAAATAATT
1650 TT
1 TT
1652 AGAAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (18 bp):
TTTAAACATAAAATAATT
Found at i:1926 original size:1 final size:1
Alignment explanation
Indices: 1920--1954 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
1910 TTCAGACCTG
1920 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1955 TCAGTGTGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4415 original size:360 final size:360
Alignment explanation
Indices: 3797--4483 Score: 829
Period size: 360 Copynumber: 1.9 Consensus size: 360
3787 CAAGGATCAC
* * **
3797 AAGGTTTGAACAATTTCCAATCTCCATAGGTATTTGCCCTCTAAGGACATTATGACCTAACAACA
1 AAGGTTTGAACAATTCCCAATCTCCATAGGTATTTGCCCACTAAGGACATTATGAAATAACAACA
* *
3862 AATATGTCAAGCTTCGATGCATCCCAATTTCCTTGGGAATTTCCCCTCCAATTTGGTTGGCAGAA
66 AATATGTCAAGCTTCGAAGCATCCCAATTTCCTTGGGAATTTCCCCTCCAAGTTGGTTGGCAGAA
* * * * *
3927 AGTCCCAAAAGTTCCAGCTTTTGACATCTAGATATTTCTGAAGGAATGTTGCCAAAAATCGCATT
131 AGTCCCAAAAATTCAAGCTTCTGACATCTACATATTTCTGAAGGAATGTTACCAAAAATCGCATT
* * *
3992 GCCTCCGACTCGAAATGCCATCAAAGCTTGGAGATTGCCAATTCCACGAGGTAGTGTACCAGTCA
196 GCCTCCGACTCGAAATGCCATCAAAGCTTGGAGATTGCCAATACCACGAGGCAGTGCACCAGTCA
*
4057 AACTGTTATCGA-CTGCCACAAACTCTTCAAGCAAAGACAAATTTCCAAGTC-TCTCCGGAATCG
261 AACTGTTATC-ATCTGCCACAAACTCTTCAAGCAAAGACAAATCTCCAA-TCTTCTCCGGAATCG
4120 GACCACTAAGCCGATTGGCACTTAAATCAAAACTCAA
324 GACCACTAAGCCGATTGGCACTTAAATCAAAACTCAA
* * *
4157 AAGGTTTGAACAATTCCCGATCTCCATTGGTATTTGCCCAACTAA-G-CTATTATGAAATAACCA
1 AAGGTTTGAACAATTCCCAATCTCCATAGGTATTTGCCC-ACTAAGGAC-ATTATGAAATAACAA
* * * * *
4220 CAAATCTGTTAAG-TTCCGAAGCATCCCAATTTCCTTTGGAATTTCGCCTCCAAGTTGGTT-GTA
64 CAAATATGTCAAGCTT-CGAAGCATCCCAATTTCCTTGGGAATTTCCCCTCCAAGTTGGTTGGCA
* * * ** *
4283 GGCAAG-CCCAAGAAATTGCAATC-TCTGACATCTACATATTTCTGCAGGAATGTTACCGGATAT
128 -GAAAGTCCCAA-AAATT-CAAGCTTCTGACATCTACATATTTCTGAAGGAATGTTACCAAAAAT
* * *** *
4346 TGCATTGTCC-CC-AGCTCGAAATATCC-TCAACTTTTGGAGATTGCCAATACTACGAGGCAGTG
190 CGCATTG-CCTCCGA-CTCGAAAT-GCCATCAAAGCTTGGAGATTGCCAATACCACGAGGCAGTG
* * * * **
4408 CACCAGTCAATCTGTTGTCATGTGCCACAAACTCTTCAAGCAAAGACAAGTCTCCAATCTTCTTT
252 CACCAGTCAAACTGTTATCATCTGCCACAAACTCTTCAAGCAAAGACAAATCTCCAATCTTCTCC
4473 GGAATCGGACC
317 GGAATCGGACC
4484 GCTCAGCTGA
Statistics
Matches: 275, Mismatches: 41, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
359 14 0.05
360 250 0.91
361 11 0.04
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (360 bp):
AAGGTTTGAACAATTCCCAATCTCCATAGGTATTTGCCCACTAAGGACATTATGAAATAACAACA
AATATGTCAAGCTTCGAAGCATCCCAATTTCCTTGGGAATTTCCCCTCCAAGTTGGTTGGCAGAA
AGTCCCAAAAATTCAAGCTTCTGACATCTACATATTTCTGAAGGAATGTTACCAAAAATCGCATT
GCCTCCGACTCGAAATGCCATCAAAGCTTGGAGATTGCCAATACCACGAGGCAGTGCACCAGTCA
AACTGTTATCATCTGCCACAAACTCTTCAAGCAAAGACAAATCTCCAATCTTCTCCGGAATCGGA
CCACTAAGCCGATTGGCACTTAAATCAAAACTCAA
Found at i:12683 original size:22 final size:22
Alignment explanation
Indices: 12657--12703 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
12647 ATTTATTCAT
12657 TATTAATTAACTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
*
12679 TATTAATTAGCTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
12701 TAT
1 TAT
12704 AGTATAATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (22 bp):
TATTAATTAACTATTAATTAGA
Found at i:12699 original size:11 final size:11
Alignment explanation
Indices: 12657--12699 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
12647 ATTTATTCAT
*
12657 TATTAATTAAC
1 TATTAATTAGC
*
12668 TATTAATTAGA
1 TATTAATTAGC
12679 TATTAATTAGC
1 TATTAATTAGC
12690 TATTAATTAG
1 TATTAATTAG
12700 ATATAGTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (11 bp):
TATTAATTAGC
Found at i:14406 original size:3 final size:3
Alignment explanation
Indices: 14380--14423 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
14370 TTTTAGGAAT
*
14380 ATA AT- ATA TATA AT- ATA TTA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
14424 TTATTATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 4 0.11
3 29 0.81
4 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:17557 original size:167 final size:163
Alignment explanation
Indices: 17065--17557 Score: 603
Period size: 167 Copynumber: 3.0 Consensus size: 163
17055 TCATTTGTCA
* * *
17065 ATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCTCCTCAAGAATAAAAAATTAGGACATTTAA
1 ATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCACCTCAAGAATCAAAAGTTAGGACATTTAA
* * * * *
17130 GTAATCTGCCAAGTAGGTAAAGACGAAAAAAATTAGTTCTCTACCTCATCATCAATACTTGATGG
65 GTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCT-CCTCCTCATCAATCCTTGGTAG
* * * *
17195 GGATCTTTTATTAATTCCACTACTCTATTCAAGTCC
129 GGATCTTTTAGTAATTCCACTAGTTTATTAAAGT-C
* *
17231 ATTGAGAAATGACCAAAAAGATTATTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAA
1 ATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCACCTCAAGAATCAAAAGTTAGGACATTTAA
* * ** * *
17296 GTAATCTGCCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACTCCAAAAGCAAGCCTTGGTA
65 GTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCT-CCTCC-TCATCAATCCTTGGTA
*
17361 GGGATCTTTTAGTAATTCCACTGGTTTATTAAAGTC
128 GGGATCTTTTAGTAATTCCACTAGTTTATTAAAGTC
* **
17397 AGTTGAGAAATGACCAAAAAGTCTAGTTATTTAATCACCTCAAAAATCAAAAGTTAGGGTATTTA
1 A-TTGAGAAATGACCAAAAAGT-TAGTTATTTAATCACCTCAAGAATCAAAAGTTAGGACATTTA
* * * **
17462 AGTAATCGGTCAAGT-GTGAAAAGACGAAAAAAATTAGTTCTCTCGCTCCTCATTAATCCGAGGT
64 AGTAATCTGCCAAGTAG-GAAAAGACGAAAAAAATTAGTTCTCTC-CTCCTCATCAATCCTTGGT
17526 AGGGATCTTTTAGTAATTTCCA-TATGTTTATT
127 AGGGATCTTTTAGTAA-TTCCACTA-GTTTATT
17558 CAAATAATAT
Statistics
Matches: 282, Mismatches: 38, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
166 133 0.47
167 149 0.53
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (163 bp):
ATTGAGAAATGACCAAAAAGTTAGTTATTTAATCACCTCAAGAATCAAAAGTTAGGACATTTAAG
TAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTCCTCCTCATCAATCCTTGGTAGGG
ATCTTTTAGTAATTCCACTAGTTTATTAAAGTC
Found at i:20674 original size:12 final size:12
Alignment explanation
Indices: 20657--20684 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
20647 TAATGATTAT
20657 ATCACTATTTAA
1 ATCACTATTTAA
20669 ATCACTATTTAA
1 ATCACTATTTAA
20681 ATCA
1 ATCA
20685 GTGATTATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (12 bp):
ATCACTATTTAA
Found at i:28892 original size:21 final size:21
Alignment explanation
Indices: 28868--28912 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
28858 CTTTCTTCAG
*
28868 CATTATCTTTCAGAGGAAGTT
1 CATTATCTTTCAAAGGAAGTT
28889 CATTATCTTTCAAAGGAAGTT
1 CATTATCTTTCAAAGGAAGTT
28910 CAT
1 CAT
28913 AAGTTGGGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (21 bp):
CATTATCTTTCAAAGGAAGTT
Found at i:34661 original size:21 final size:22
Alignment explanation
Indices: 34635--34680 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
34625 TTCCTCCTAA
* *
34635 TTTAACACTATAG-AATTTTTT
1 TTTAACACCATAGAAATTTGTT
*
34656 TTTAACTCCATAGAAATTTGTT
1 TTTAACACCATAGAAATTTGTT
34678 TTT
1 TTT
34681 CAAGTCCATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (22 bp):
TTTAACACCATAGAAATTTGTT
Found at i:34688 original size:23 final size:21
Alignment explanation
Indices: 34644--34691 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
34634 ATTTAACACT
*
34644 ATAGAATTTTTTTTTAACTCC
1 ATAGAATTTTTTTTCAACTCC
*
34665 ATAGAAATTTGTTTTTCAAGTCC
1 ATAG-AATTT-TTTTTCAACTCC
34688 ATAG
1 ATAG
34692 GTTTCTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
22 5 0.22
23 14 0.61
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.46
Consensus pattern (21 bp):
ATAGAATTTTTTTTCAACTCC
Found at i:38519 original size:22 final size:22
Alignment explanation
Indices: 38487--38528 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
38477 GTTTATAATA
*
38487 TTCTCGGGTCAGTCGGATTAAC
1 TTCTCGAGTCAGTCGGATTAAC
*
38509 TTCTCGAGTCATTCGGATTA
1 TTCTCGAGTCAGTCGGATTA
38529 CGGGTTTGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (22 bp):
TTCTCGAGTCAGTCGGATTAAC
Found at i:44317 original size:78 final size:78
Alignment explanation
Indices: 44229--44476 Score: 417
Period size: 78 Copynumber: 3.2 Consensus size: 78
44219 GTTTTTGAAT
*
44229 TAAAATAGTAAAATGGTAAAATATAATAGTAATAAGGATATTATATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTATATTTAATTATATAAAAATAGA
44294 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
*
44307 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAAATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTATATTTAATTATATAAAAATAGA
44372 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
* * * *
44385 TGAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTATATTTAATTATATAAAAATAGA
44450 GTTTTTTAGTTGAG
66 G-TTTTTAGTTGAG
44464 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
44477 ACTTAAACAA
Statistics
Matches: 160, Mismatches: 8, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
78 137 0.86
79 21 0.13
80 2 0.01
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.36
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTATATTTAATTATATAAAAATAGA
GTTTTTAGTTGAG
Found at i:44591 original size:126 final size:127
Alignment explanation
Indices: 44437--44690 Score: 483
Period size: 126 Copynumber: 2.0 Consensus size: 127
44427 ATATTTAATT
*
44437 AAATAAAAATAGAGTTTTTTAGTTGAGTAAAACTATAAAAACTTAAACAATGGCAATTTAGAAAT
1 AAATAAAAATAGAGTTTTTTAGTTGAGTAAAACTATAAAAACTTAAACAATGACAATTTAGAAAT
44502 ATATTTGACAAATAAGGGTATAATAGGCTATTCAAAAGTTTTACAGGTGAATGTACTTTTTA
66 ATATTTGACAAATAAGGGTATAATAGGCTATTCAAAAGTTTTACAGGTGAATGTACTTTTTA
44564 AAATAAAAATAGAG-TTTTTAGTTGAGTAAAACTATAAAAACTTAAACAATGACAATTTAGAAAT
1 AAATAAAAATAGAGTTTTTTAGTTGAGTAAAACTATAAAAACTTAAACAATGACAATTTAGAAAT
*
44628 ATATTTGACGAATAAGGGTATAATAGGCTATTCAAAAGTTTTACAGGTGAATGTACTTTTTA
66 ATATTTGACAAATAAGGGTATAATAGGCTATTCAAAAGTTTTACAGGTGAATGTACTTTTTA
44690 A
1 A
44691 TATAGTATAG
Statistics
Matches: 125, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
126 111 0.89
127 14 0.11
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.33
Consensus pattern (127 bp):
AAATAAAAATAGAGTTTTTTAGTTGAGTAAAACTATAAAAACTTAAACAATGACAATTTAGAAAT
ATATTTGACAAATAAGGGTATAATAGGCTATTCAAAAGTTTTACAGGTGAATGTACTTTTTA
Found at i:46309 original size:1 final size:1
Alignment explanation
Indices: 46303--46327 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
46293 ACAGTAGGAG
46303 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
46328 AAAGAATAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:47820 original size:21 final size:21
Alignment explanation
Indices: 47796--47841 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
47786 ACGATTGGGA
47796 AATTCATGTT-CAATCTATTGT
1 AATTCATGTTACAATC-ATTGT
* *
47817 AATTTATGTTATAATCATTGT
1 AATTCATGTTACAATCATTGT
47838 AATT
1 AATT
47842 TCATTTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.50
Consensus pattern (21 bp):
AATTCATGTTACAATCATTGT
Found at i:48057 original size:2 final size:2
Alignment explanation
Indices: 48050--48113 Score: 56
Period size: 2 Copynumber: 30.5 Consensus size: 2
48040 TTTGTGTACA
* * * * *
48050 AT AT AT AT AT AT AT AT AT AT AT AT AGT TT CT GT GT AC ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT
48094 AT AT AT AT AT ACT AT AT AT A
1 AT AT AT AT AT A-T AT AT AT A
48114 AAAGTACGGG
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 49 0.92
3 4 0.08
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Found at i:48066 original size:38 final size:38
Alignment explanation
Indices: 48019--48104 Score: 104
Period size: 38 Copynumber: 2.3 Consensus size: 38
48009 CTGTGTACAC
*
48019 TATATATATA-AAAGTACGGGTTT-TGTGTACAATATATA
1 TATATATATATAAA-TA-GAGTTTCTGTGTACAATATATA
* * *
48057 TATATATATATATATATAGTTTCTGTGTACACTATATA
1 TATATATATATAAATAGAGTTTCTGTGTACAATATATA
48095 TATATATATA
1 TATATATATA
48105 CTATATATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
37 4 0.10
38 36 0.86
39 2 0.05
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (38 bp):
TATATATATATAAATAGAGTTTCTGTGTACAATATATA
Found at i:53451 original size:107 final size:109
Alignment explanation
Indices: 53274--53501 Score: 352
Period size: 107 Copynumber: 2.1 Consensus size: 109
53264 AGGTTTTTTA
* * **
53274 TTATAGACTTTTAGAAATAAAATATATAAAACTAATTTCACTAAGTTTAGCGTCAAATTAAAATT
1 TTATAGAGTTTTAGAAATAAAATATACAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATT
* *
53339 TTATTTTTATTTTAAGGGTAAATTTAAAAATTAATAATTTATTG
66 TTATTTATATTTTAAGGGTAAATTCAAAAATTAATAATTTATTG
*
53383 TTATAGGGTTTTAGAAAT-AAA-ATACAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATT
1 TTATAGAGTTTTAGAAATAAAATATACAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATT
* **
53446 TTATTTATATTTTAAGGGTAAATTCCATGATTAATAATTTATTG
66 TTATTTATATTTTAAGGGTAAATTCAAAAATTAATAATTTATTG
53490 TTATAGAGTTTT
1 TTATAGAGTTTT
53502 GGACTAAGTT
Statistics
Matches: 108, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
107 89 0.82
108 3 0.03
109 16 0.15
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.43
Consensus pattern (109 bp):
TTATAGAGTTTTAGAAATAAAATATACAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATT
TTATTTATATTTTAAGGGTAAATTCAAAAATTAATAATTTATTG
Found at i:58309 original size:10 final size:10
Alignment explanation
Indices: 58282--58321 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
58272 CTCAGGTGCA
*
58282 TATCTATGTC
1 TATCTATATC
*
58292 TATTTATATC
1 TATCTATATC
58302 TATCTATATC
1 TATCTATATC
58312 TATACTATAT
1 TAT-CTATAT
58322 ATATAAAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 20 0.77
11 6 0.23
ACGTcount: A:0.30, C:0.15, G:0.03, T:0.53
Consensus pattern (10 bp):
TATCTATATC
Found at i:58584 original size:26 final size:26
Alignment explanation
Indices: 58555--58606 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
58545 TATTAAAATG
* *
58555 TTTTATTTAGAACAATTCAATTTCTA
1 TTTTATATAGAAAAATTCAATTTCTA
*
58581 TTTTATATAGAAAAATTTAATTTCTA
1 TTTTATATAGAAAAATTCAATTTCTA
58607 CATTATCATC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (26 bp):
TTTTATATAGAAAAATTCAATTTCTA
Found at i:58612 original size:26 final size:26
Alignment explanation
Indices: 58557--58612 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
58547 TTAAAATGTT
* * **
58557 TTATTTAGAACAATTCAATTTCTATT
1 TTATATAGAAAAATTCAATTTCTACA
*
58583 TTATATAGAAAAATTTAATTTCTACA
1 TTATATAGAAAAATTCAATTTCTACA
58609 TTAT
1 TTAT
58613 CATCTAGATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (26 bp):
TTATATAGAAAAATTCAATTTCTACA
Found at i:58937 original size:12 final size:14
Alignment explanation
Indices: 58909--58940 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
58899 ACATAAATTT
58909 AATGTTATAACATA
1 AATGTTATAACATA
58923 AATGTTAT-A-ATA
1 AATGTTATAACATA
58935 AATGTT
1 AATGTT
58941 CTAGAATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.50
13 1 0.06
14 8 0.44
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (14 bp):
AATGTTATAACATA
Found at i:62711 original size:30 final size:29
Alignment explanation
Indices: 62649--62711 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
62639 ACCTAACCGT
****
62649 CAAATAAGCCCCTGAACTTTTATTTTGGC
1 CAAATAAGCCCCTGAACTTTTAAAAAGGC
62678 CAAATAAGCCCCTGAACTCTTTAAAAAGGC
1 CAAATAAGCCCCTGAACT-TTTAAAAAGGC
62708 CAAA
1 CAAA
62712 CAATCCCTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 18 0.62
30 11 0.38
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTTTTAAAAAGGC
Done.