Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002460.1 Hibiscus syriacus cultivar Beakdansim tig00005036_pilon, 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: 63360
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:8074 original size:192 final size:192
Alignment explanation
Indices: 7742--8276 Score: 944
Period size: 192 Copynumber: 2.8 Consensus size: 192
7732 TGATTTTCGG
* * * * * * * * *
7742 TTGGCTCATGCCTCTTAACTATATGGCTTCAATCTTGTACTACTATTGAAACAGATTTCAACATC
1 TTGGATCATGCCACTTAAGTATATAGCTTCAATCTTCTTCTACTATTGATACAGATTTTAACAAC
*
7807 TTTGTCATTCAATTTACACAAACATGAATCATAAAAGAAAGACATAGAAACGCCAAAATCTGTAG
66 TTTTTCATTCAATTTACACAAACATGAATCATAAAAGAAAGACATAGAAACGCCAAAATCTGTAG
7872 CAGAAATGTTGGGAAAGTTCTAAGGCAACAAAAGGAAATTGAAAGACAAGGTGAATTTTCTA
131 CAGAAATGTTGGGAAAGTTCTAAGGCAACAAAAGGAAATTGAAAGACAAGGTGAATTTTCTA
7934 TTGGATCATGCCACTTAAGTATATAGCTTCAATCTTCTTCTACTATTGATACAGATTTTAACAAC
1 TTGGATCATGCCACTTAAGTATATAGCTTCAATCTTCTTCTACTATTGATACAGATTTTAACAAC
7999 TTTTTCATTCAATTTACACAAACATGAATCATAAAAGAAAGACATAGAAACGCCAAAATCTGTAG
66 TTTTTCATTCAATTTACACAAACATGAATCATAAAAGAAAGACATAGAAACGCCAAAATCTGTAG
8064 CAGAAATGTTGGGAAAGTTCTAAGGCAACAAAAGGAAATTGAAAGACAAGGTGAATTTTCTA
131 CAGAAATGTTGGGAAAGTTCTAAGGCAACAAAAGGAAATTGAAAGACAAGGTGAATTTTCTA
8126 TTGGATCATGCCACTTAAGTATATAGCTTCAATCTTCTTCTACTATTGATACAGATTTTAACAAC
1 TTGGATCATGCCACTTAAGTATATAGCTTCAATCTTCTTCTACTATTGATACAGATTTTAACAAC
* * *
8191 TTTTTCATTCAATTTACACAAACATGAATCATAAAAGAAAGGCATAGAAACACCAAAACCTGTAG
66 TTTTTCATTCAATTTACACAAACATGAATCATAAAAGAAAGACATAGAAACGCCAAAATCTGTAG
*
8256 CAGAAATGTTGGGAAACTTCT
131 CAGAAATGTTGGGAAAGTTCT
8277 GGGAAAGTTA
Statistics
Matches: 329, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
192 329 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (192 bp):
TTGGATCATGCCACTTAAGTATATAGCTTCAATCTTCTTCTACTATTGATACAGATTTTAACAAC
TTTTTCATTCAATTTACACAAACATGAATCATAAAAGAAAGACATAGAAACGCCAAAATCTGTAG
CAGAAATGTTGGGAAAGTTCTAAGGCAACAAAAGGAAATTGAAAGACAAGGTGAATTTTCTA
Found at i:14170 original size:50 final size:50
Alignment explanation
Indices: 14095--14196 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
14085 ATATAGCTTA
*
14095 TTTATGATTTATGTATGTTTTTGTCGTATTCAAACAAATTAACTCTAAAG
1 TTTATGATTTATATATGTTTTTGTCGTATTCAAACAAATTAACTCTAAAG
*
14145 TTTATGATTTATATATGTTTTTGTCGTATTGAAACAAATTAACTCTAAAG
1 TTTATGATTTATATATGTTTTTGTCGTATTCAAACAAATTAACTCTAAAG
14195 TT
1 TT
14197 GCAGGTTATA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (50 bp):
TTTATGATTTATATATGTTTTTGTCGTATTCAAACAAATTAACTCTAAAG
Found at i:15457 original size:18 final size:21
Alignment explanation
Indices: 15419--15458 Score: 59
Period size: 18 Copynumber: 2.0 Consensus size: 21
15409 AAAATAAATA
15419 AATATACAAATAAATGATTAT
1 AATATACAAATAAATGATTAT
15440 AATATA-AAA-AAA-GATTAT
1 AATATACAAATAAATGATTAT
15458 A
1 A
15459 TGAATTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
19 3 0.16
20 3 0.16
21 6 0.32
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (21 bp):
AATATACAAATAAATGATTAT
Found at i:17107 original size:19 final size:18
Alignment explanation
Indices: 17083--17134 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
17073 CCCTTGCATG
*
17083 CCCCATGCAACTGCTGCCA
1 CCCCATGC-ACTACTGCCA
*
17102 CCCCATGCGCTACTGCCA
1 CCCCATGCACTACTGCCA
*
17120 CCCCATGCGCTACTG
1 CCCCATGCACTACTG
17135 TCATGTTGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 23 0.74
19 8 0.26
ACGTcount: A:0.17, C:0.48, G:0.17, T:0.17
Consensus pattern (18 bp):
CCCCATGCACTACTGCCA
Found at i:17119 original size:18 final size:18
Alignment explanation
Indices: 17096--17134 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
17086 CATGCAACTG
17096 CTGCCACCCCATGCGCTA
1 CTGCCACCCCATGCGCTA
17114 CTGCCACCCCATGCGCTA
1 CTGCCACCCCATGCGCTA
17132 CTG
1 CTG
17135 TCATGTTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.49, G:0.18, T:0.18
Consensus pattern (18 bp):
CTGCCACCCCATGCGCTA
Found at i:17343 original size:2 final size:2
Alignment explanation
Indices: 17336--17364 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17326 GTTTTAAATC
17336 TA TA 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 T
17365 GGGGTGTAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17421 original size:19 final size:19
Alignment explanation
Indices: 17397--17458 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
17387 CACCGGGAGT
*
17397 GAAAGAAAGAAGGAGAGAA
1 GAAAGAAAGAAGAAGAGAA
17416 GAAAGAAGAGAA-AAGAGAAA
1 GAAAGAA-AGAAGAAGAG-AA
*
17436 GAAA-CAAGAAGAAGAGAA
1 GAAAGAAAGAAGAAGAGAA
*
17454 TAAAG
1 GAAAG
17459 TTAAAGTCGG
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 9 0.25
19 17 0.47
20 10 0.28
ACGTcount: A:0.66, C:0.02, G:0.31, T:0.02
Consensus pattern (19 bp):
GAAAGAAAGAAGAAGAGAA
Found at i:19178 original size:14 final size:14
Alignment explanation
Indices: 19154--19204 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
19144 ATATAATAAT
19154 ATTTAATTTAATTTA
1 ATTT-ATTTAATTTA
*
19169 ATTTATTTAAATTA
1 ATTTATTTAATTTA
*
19183 AGTTATTT-ATTTA
1 ATTTATTTAATTTA
19196 TATTTATTT
1 -ATTTATTT
19205 CTTTTTTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 4 0.13
14 23 0.74
15 4 0.13
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (14 bp):
ATTTATTTAATTTA
Found at i:19202 original size:10 final size:9
Alignment explanation
Indices: 19153--19204 Score: 52
Period size: 10 Copynumber: 5.6 Consensus size: 9
19143 AATATAATAA
19153 TATTTAATT
1 TATTTAATT
19162 TAATTTAATT
1 T-ATTTAATT
19172 TATTTAAATT
1 TATTT-AATT
* *
19182 AAGTT-ATT
1 TATTTAATT
19190 TATTTATATT
1 TATTTA-ATT
19200 TATTT
1 TATTT
19205 CTTTTTTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
8 6 0.17
9 5 0.14
10 24 0.69
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:20317 original size:21 final size:23
Alignment explanation
Indices: 20269--20314 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
20259 TTGACAAACT
*
20269 TAAAAAAACATAAATTATTATAC
1 TAAAAAAACATAAATGATTATAC
20292 TAAAAAATACATAAATGATTATA
1 TAAAAAA-ACATAAATGATTATA
20315 AAATAAAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (23 bp):
TAAAAAAACATAAATGATTATAC
Found at i:20336 original size:34 final size:34
Alignment explanation
Indices: 20298--20363 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
20288 ATACTAAAAA
20298 ATACATAAATGATTATAAAATAAAGTTAATTATT
1 ATACATAAATGATTATAAAATAAAGTTAATTATT
* *
20332 ATACATAAATTATTATAAAATCAAGTTAATTA
1 ATACATAAATGATTATAAAATAAAGTTAATTA
20364 AGTTAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (34 bp):
ATACATAAATGATTATAAAATAAAGTTAATTATT
Found at i:21237 original size:21 final size:20
Alignment explanation
Indices: 21206--21273 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 20
21196 TATGATAATA
*
21206 AATAGTAAAAATGATATTATAC
1 AATA-TAAAAATAATATTA-AC
21228 AATATAAAAATAATATTAAC
1 AATATAAAAATAATATTAAC
21248 ATATATTTATAAAAATAATATTAAC
1 --A-A--TATAAAAATAATATTAAC
21273 A
1 A
21274 TAATAATTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
20 2 0.05
21 13 0.32
22 5 0.12
23 2 0.05
25 18 0.45
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.34
Consensus pattern (20 bp):
AATATAAAAATAATATTAAC
Found at i:21878 original size:142 final size:142
Alignment explanation
Indices: 21614--21879 Score: 410
Period size: 142 Copynumber: 1.9 Consensus size: 142
21604 GGATAGAGGT
21614 ATGGGTTAAACTTTTATCATTCGAATGCCAGCTACCAACTGTACCTACGTGAATGGCATGCCATG
1 ATGGGTTAAACTTTTATCATTCGAATGCCAGCTACCAACTGTACCTACGTGAATGGCATGCCATG
* * *
21679 CGACTTTTCCAGCCATGCGAGAGGACCCCGAGGAGACGCATGCGGCCGCTTGCAACCCAGCCCGC
66 CGACTTTTCCAGCCACGCGAGAGGACCCCGAGGAGACGCATGCGACCACTTGCAACCCAGCCCGC
21744 CTTAGGAGACGC
131 CTTAGGAGACGC
* * *
21756 ATGGGTTTAACTTTTATCATTTGAATGCCAGCTA-CATACTGTACCTACGTGAGTGGCATGCCAT
1 ATGGGTTAAACTTTTATCATTCGAATGCCAGCTACCA-ACTGTACCTACGTGAATGGCATGCCAT
* * * *
21820 GCGA-TTTTGCCGGCCACGCGAGGGGACCCTGAGGAGACGCATGCGACCACTTGTAACCCA
65 GCGACTTTT-CCAGCCACGCGAGAGGACCCCGAGGAGACGCATGCGACCACTTGCAACCCA
21880 ACCCAGGAGA
Statistics
Matches: 112, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
141 6 0.05
142 106 0.95
ACGTcount: A:0.24, C:0.28, G:0.26, T:0.23
Consensus pattern (142 bp):
ATGGGTTAAACTTTTATCATTCGAATGCCAGCTACCAACTGTACCTACGTGAATGGCATGCCATG
CGACTTTTCCAGCCACGCGAGAGGACCCCGAGGAGACGCATGCGACCACTTGCAACCCAGCCCGC
CTTAGGAGACGC
Found at i:22721 original size:32 final size:32
Alignment explanation
Indices: 22680--22758 Score: 149
Period size: 32 Copynumber: 2.5 Consensus size: 32
22670 GTGTCGCATG
22680 GTTCTATGCGACTTAGGTGGGTATTGCATTGT
1 GTTCTATGCGACTTAGGTGGGTATTGCATTGT
22712 GTTCTATGCGACTTAGGTGGGTATTGCATTGT
1 GTTCTATGCGACTTAGGTGGGTATTGCATTGT
*
22744 GTTCCATGCGACTTA
1 GTTCTATGCGACTTA
22759 AGGTTCACAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.16, C:0.15, G:0.29, T:0.39
Consensus pattern (32 bp):
GTTCTATGCGACTTAGGTGGGTATTGCATTGT
Found at i:44365 original size:22 final size:22
Alignment explanation
Indices: 44320--44377 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
44310 AGGGTATCGA
*
44320 TTCCCCTAC-AGGGGGAATCAG
1 TTCCCCTTCAAGGGGGAATCAG
*
44341 TTCCCCTTCAAAGGGGG-ATCGG
1 TTCCCCTTC-AAGGGGGAATCAG
44363 TTCCCCTTCAAGGGG
1 TTCCCCTTCAAGGGG
44378 ATATCGATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.42
22 13 0.39
23 6 0.18
ACGTcount: A:0.19, C:0.29, G:0.29, T:0.22
Consensus pattern (22 bp):
TTCCCCTTCAAGGGGGAATCAG
Found at i:44390 original size:21 final size:22
Alignment explanation
Indices: 44314--44389 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
44304 CCCCAGAGGG
* *
44314 TATCGATTCCCCTACAGGGGGA
1 TATCGATTCCCCTTCAAGGGGA
44336 -ATC-AGTTCCCCTTCAAAGGGG-
1 TATCGA-TTCCCCTTC-AAGGGGA
* *
44357 GATCGGTTCCCCTTCAAGGGGA
1 TATCGATTCCCCTTCAAGGGGA
44379 TATCGATTCCC
1 TATCGATTCCC
44390 TCTGCCCTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 17 0.39
22 26 0.59
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.25
Consensus pattern (22 bp):
TATCGATTCCCCTTCAAGGGGA
Found at i:51641 original size:89 final size:91
Alignment explanation
Indices: 51478--51731 Score: 223
Period size: 91 Copynumber: 2.8 Consensus size: 91
51468 ACATACAGGC
* * * * * * * * *
51478 ATAGTTAAGCTAGAGGGGTGTGTAAGTTTC-GAGATGTAACCTTCAGCCA-CATCATGATGCTTA
1 ATAGGTAACCTAGATGGGTGTGTAAG-CTCAGAGATGTACCCCTCA-ACAGCACCATGATGCCTA
*
51541 GCTCAGCTTGTGTGT-CT-CAAAGTAGT
64 CCTCAGCTTGTGTGTGCTGCAAAGTAGT
* *
51567 GTAGGTAACCTAGA-GGGTGTGTGAGCTCCA-AGATGTAACCCCTCAACAGCACCATGATGCCTA
1 ATAGGTAACCTAGATGGGTGTGTAAGCT-CAGAGATGT-ACCCCTCAACAGCACCATGATGCCTA
* * *
51630 CCTCAGTTTGTGTGTGTTGCATAGTAGT
64 CCTCAGCTTGTGTGTGCTGCAAAGTAGT
* ** * * * **
51658 ATGGGTAGGCTAGATGGGTGTGTAAGCTCAGAGATGTAGCCCTCAGCCGTGCCATGATGCCTACC
1 ATAGGTAACCTAGATGGGTGTGTAAGCTCAGAGATGTACCCCTCAACAGCACCATGATGCCTACC
51723 TCAGCTTGT
66 TCAGCTTGT
51732 ATGTTACATA
Statistics
Matches: 132, Mismatches: 25, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
87 1 0.01
88 19 0.14
89 42 0.32
90 1 0.01
91 51 0.39
92 18 0.14
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (91 bp):
ATAGGTAACCTAGATGGGTGTGTAAGCTCAGAGATGTACCCCTCAACAGCACCATGATGCCTACC
TCAGCTTGTGTGTGCTGCAAAGTAGT
Found at i:51793 original size:32 final size:32
Alignment explanation
Indices: 51757--51835 Score: 158
Period size: 32 Copynumber: 2.5 Consensus size: 32
51747 ATCAATATTG
51757 CATTTAGATAATGCATAGTAGAGTTAGTGTTA
1 CATTTAGATAATGCATAGTAGAGTTAGTGTTA
51789 CATTTAGATAATGCATAGTAGAGTTAGTGTTA
1 CATTTAGATAATGCATAGTAGAGTTAGTGTTA
51821 CATTTAGATAATGCA
1 CATTTAGATAATGCA
51836 CAAGAACGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (32 bp):
CATTTAGATAATGCATAGTAGAGTTAGTGTTA
Found at i:55638 original size:29 final size:29
Alignment explanation
Indices: 55573--55638 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
55563 TTTGTTTTAG
*
55573 TCTCTAAAATTTTATAAATTTAAATTCGTT
1 TCTCTAAAATTTTATAAATTTAAATTCG-A
*
55603 TCCCTAAAATTTTAT-AATTTAAAATTC-A
1 TCTCTAAAATTTTATAAATTT-AAATTCGA
55631 TCATCTAA
1 TC-TCTAA
55639 TATAAAATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 2 0.06
29 9 0.29
30 20 0.65
ACGTcount: A:0.39, C:0.14, G:0.02, T:0.45
Consensus pattern (29 bp):
TCTCTAAAATTTTATAAATTTAAATTCGA
Found at i:59445 original size:2 final size:2
Alignment explanation
Indices: 59438--59468 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
59428 ACAATCTACT
59438 TA TA TA 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 T
59469 GATGTATGTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59581 original size:27 final size:27
Alignment explanation
Indices: 59541--59607 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
59531 ATGCATGTAC
* *
59541 ATATATATATATATATATTGAT-TAATG
1 ATATATGTACATATATATTGATGT-ATG
* *
59568 ATATATGTACATATGTATTTATGTATG
1 ATATATGTACATATATATTGATGTATG
*
59595 ATGTATGTACATA
1 ATATATGTACATA
59608 AGTATGAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 33 0.97
28 1 0.03
ACGTcount: A:0.39, C:0.03, G:0.12, T:0.46
Consensus pattern (27 bp):
ATATATGTACATATATATTGATGTATG
Found at i:59601 original size:125 final size:125
Alignment explanation
Indices: 59443--59682 Score: 426
Period size: 125 Copynumber: 1.9 Consensus size: 125
59433 CTACTTATAT
*
59443 ATATATATATATATATATATATATATGATGTATGTACATAAGTATGAATATAAATTTAATATATA
1 ATATATATACATATATATATATATATGATGTATGTACATAAGTATGAATATAAATTTAATATATA
*
59508 TAAGCACTTATCATTAATCAATGATGCATGTACATATATATATATATATATTGATTAATG
66 TAAGCACTTATCATTAATCAATGATGCATGTACATACATATATATATATATTGATTAATG
* * * *
59568 ATATATGTACATATGTATTTATGTATGATGTATGTACATAAGTATGAATATAAATTTAATATATA
1 ATATATATACATATATATATATATATGATGTATGTACATAAGTATGAATATAAATTTAATATATA
59633 TAAGCACTTATCATTAATCAATGATGCATGTACATACATATATATATATA
66 TAAGCACTTATCATTAATCAATGATGCATGTACATACATATATATATATA
59683 CTTATATGTT
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
125 109 1.00
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.41
Consensus pattern (125 bp):
ATATATATACATATATATATATATATGATGTATGTACATAAGTATGAATATAAATTTAATATATA
TAAGCACTTATCATTAATCAATGATGCATGTACATACATATATATATATATTGATTAATG
Found at i:59680 original size:61 final size:61
Alignment explanation
Indices: 59467--59668 Score: 237
Period size: 61 Copynumber: 3.3 Consensus size: 61
59457 ATATATATAT
*
59467 ATGATGTATGTACATAAGTATGAATATAAATTTAATATATATAAGCACTTATCATTAATCA
1 ATGATGCATGTACATAAGTATGAATATAAATTTAATATATATAAGCACTTATCATTAATCA
* * * * * * * * *
59528 ATGATGCATGTACATATA-TAT-ATATATATATTGATTAATGATATATGTACATATGTATTTATG
1 ATGATGCATGTACATA-AGTATGA-ATATAAATTTAAT-AT-ATATAAGCACTTAT-CATTAATC
*
59591 T
61 A
*
59592 ATGATGTATGTACATAAGTATGAATATAAATTTAATATATATAAGCACTTATCATTAATCA
1 ATGATGCATGTACATAAGTATGAATATAAATTTAATATATATAAGCACTTATCATTAATCA
59653 ATGATGCATGTACATA
1 ATGATGCATGTACATA
59669 CATATATATA
Statistics
Matches: 111, Mismatches: 23, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
60 1 0.01
61 48 0.43
62 14 0.13
63 14 0.13
64 33 0.30
65 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (61 bp):
ATGATGCATGTACATAAGTATGAATATAAATTTAATATATATAAGCACTTATCATTAATCA
Found at i:61097 original size:12 final size:12
Alignment explanation
Indices: 61079--61122 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
61069 CATATGTACT
61079 TATATATATAAG
1 TATATATATAAG
*
61091 --TACATATAAG
1 TATATATATAAG
*
61101 TATATACATAAG
1 TATATATATAAG
61113 TATATATATA
1 TATATATATA
61123 TATATATGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 9 0.35
12 17 0.65
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.39
Consensus pattern (12 bp):
TATATATATAAG
Found at i:61106 original size:22 final size:20
Alignment explanation
Indices: 61079--61129 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
61069 CATATGTACT
61079 TATATATATAAGTACATATAA
1 TATATATATAAGTACATAT-A
* *
61100 GTATATACATAAGTATATATA
1 -TATATATATAAGTACATATA
61121 TATATATAT
1 TATATATAT
61130 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 8 0.31
21 1 0.04
22 17 0.65
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (20 bp):
TATATATATAAGTACATATA
Found at i:62243 original size:21 final size:22
Alignment explanation
Indices: 62219--62263 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
62209 GATTTTTTTT
62219 TATT-TTTATATTATT-AAAATA
1 TATTCTTTA-ATTATTAAAAATA
62240 TATTCTTTAATTATTAAAAATA
1 TATTCTTTAATTATTAAAAATA
62262 TA
1 TA
62264 AAAATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTCTTTAATTATTAAAAATA
Found at i:62291 original size:42 final size:43
Alignment explanation
Indices: 62227--62330 Score: 131
Period size: 42 Copynumber: 2.4 Consensus size: 43
62217 TTTATTTTTA
* *
62227 TATTATTAAAATATATT-CTTTAATTATTAAAAATATAA-AAAT
1 TATTA-TAAAATATATTATTTTAATAATTAAAAATATAATAAAT
*
62269 TATTATAAAATATATTATTTTAATAATTTAAAATATAATAAAT
1 TATTATAAAATATATTATTTTAATAATTAAAAATATAATAAAT
* *
62312 AATTATAATATATTATTAT
1 TATTATAAAATA-TATTAT
62331 AAAATATTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
41 11 0.20
42 23 0.43
43 14 0.26
44 6 0.11
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (43 bp):
TATTATAAAATATATTATTTTAATAATTAAAAATATAATAAAT
Found at i:62336 original size:28 final size:27
Alignment explanation
Indices: 62260--62336 Score: 73
Period size: 28 Copynumber: 2.8 Consensus size: 27
62250 TTATTAAAAA
* * *
62260 TATAAAAATTATTATAAAATATATTAT
1 TATAATAATTATTATAAAATAAATAAT
* ** *
62287 TTTAATAATTTAAAATATAATAAATAAT
1 TATAATAA-TTATTATAAAATAAATAAT
62315 TATAATATATTATTATAAAATA
1 TATAATA-ATTATTATAAAATA
62337 TTATTTTAAT
Statistics
Matches: 37, Mismatches: 11, Indels: 3
0.73 0.22 0.06
Matches are distributed among these distances:
27 6 0.16
28 30 0.81
29 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
TATAATAATTATTATAAAATAAATAAT
Found at i:63154 original size:7 final size:7
Alignment explanation
Indices: 63139--63180 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
63129 TTAATATTCC
63139 TTATTTT
1 TTATTTT
63146 TT-TTATT
1 TTATT-TT
63153 TTATTTCT
1 TTATTT-T
*
63161 TAATTTT
1 TTATTTT
63168 TTATTTT
1 TTATTTT
63175 TTATTT
1 TTATTT
63181 ATTTCACATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
6 2 0.07
7 20 0.67
8 8 0.27
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (7 bp):
TTATTTT
Found at i:63166 original size:22 final size:21
Alignment explanation
Indices: 63133--63180 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
63123 CAACTATTAA
*
63133 TATTCCTTATTTTTT-TTATTT
1 TATTTCTTATTTTTTATT-TTT
63154 TATTTCTTAATTTTTTATTTTT
1 TATTTCTT-ATTTTTTATTTTT
63176 TATTT
1 TATTT
63181 ATTTCACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 7 0.29
22 15 0.62
23 2 0.08
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (21 bp):
TATTTCTTATTTTTTATTTTT
Done.