Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold133
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: 2564099
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 17052 characters in sequence are not A, C, G, or T
File 4 of 17
Found at i:366999 original size:15 final size:15
Alignment explanation
Indices: 366979--367009 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
366969 GAAAAAAATG
366979 CCTTTTCTACTACAT
1 CCTTTTCTACTACAT
*
366994 CCTTTTCTACTTCAT
1 CCTTTTCTACTACAT
367009 C
1 C
367010 ATAAGGTTTA
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:0.16, C:0.35, G:0.00, T:0.48
Consensus pattern (15 bp):
CCTTTTCTACTACAT
Found at i:374984 original size:32 final size:30
Alignment explanation
Indices: 374926--374986 Score: 77
Period size: 32 Copynumber: 2.0 Consensus size: 30
374916 ATTATGAGTT
*
374926 AAATATAATTATTTTTATTTAAAAAATAAA
1 AAATATAATTATTTTAATTTAAAAAATAAA
**
374956 AAATATAAATATATTTTAATTTTTAAAATAA
1 AAATAT-AAT-TATTTTAATTTAAAAAATAA
374987 TTTATTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 6 0.23
31 3 0.12
32 17 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
AAATATAATTATTTTAATTTAAAAAATAAA
Found at i:375894 original size:27 final size:25
Alignment explanation
Indices: 375857--375911 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
375847 AAAAATTAAA
375857 TAATTTGTTTAATCTAAATTTAAATAT
1 TAATTTGTTT-ATCTAAA-TTAAATAT
* * *
375884 TAATTTTTTTATTTGAATTAAATAT
1 TAATTTGTTTATCTAAATTAAATAT
375909 TAA
1 TAA
375912 AATAATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 11 0.44
26 5 0.20
27 9 0.36
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (25 bp):
TAATTTGTTTATCTAAATTAAATAT
Found at i:375925 original size:30 final size:31
Alignment explanation
Indices: 375871--375946 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
375861 TTGTTTAATC
* *
375871 TAAAT-TTAAATATTAATTTTTTTATTTGAA-T
1 TAAATATTAAA-A-TAATATTTTTATTTAAATT
375902 TAAATATTAAAATAATATTTTTATTTAAATT
1 TAAATATTAAAATAATATTTTTATTTAAATT
* *
375933 TAATTATAAAAATA
1 TAAATATTAAAATA
375947 TGTAAATGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 15 0.38
31 19 0.49
32 5 0.13
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (31 bp):
TAAATATTAAAATAATATTTTTATTTAAATT
Found at i:375945 original size:31 final size:30
Alignment explanation
Indices: 375884--375946 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
375874 ATTTAAATAT
* * *
375884 TAATTTTTTTATTTGAATTAAATATTAAAA
1 TAATATTTTTATTTAAATTAAATATAAAAA
*
375914 TAATATTTTTATTTAAATTTAATTATAAAAA
1 TAATATTTTTATTTAAA-TTAAATATAAAAA
375945 TA
1 TA
375947 TGTAAATGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 15 0.54
31 13 0.46
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (30 bp):
TAATATTTTTATTTAAATTAAATATAAAAA
Found at i:376462 original size:16 final size:15
Alignment explanation
Indices: 376432--376478 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
376422 ATTTATATGT
*
376432 AAATATAAA-TTTTA
1 AAATTTAAATTTTTA
*
376446 AAATTATAATTTTTTA
1 AAATT-TAAATTTTTA
*
376462 ATATTTAAATTTTTA
1 AAATTTAAATTTTTA
376477 AA
1 AA
376479 TATCATATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
14 4 0.15
15 13 0.50
16 9 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AAATTTAAATTTTTA
Found at i:376480 original size:16 final size:16
Alignment explanation
Indices: 376437--376481 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
376427 TATGTAAATA
376437 TAAA-TTTTAAA-A-T
1 TAAATTTTTAAATATT
*
376450 TATAATTTTTTAATATT
1 TA-AATTTTTAAATATT
376467 TAAATTTTTAAATAT
1 TAAATTTTTAAATAT
376482 CATATGAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 2 0.08
14 2 0.08
15 6 0.23
16 13 0.50
17 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAAATTTTTAAATATT
Found at i:376631 original size:12 final size:12
Alignment explanation
Indices: 376606--376663 Score: 57
Period size: 12 Copynumber: 4.8 Consensus size: 12
376596 GATAAAAAAA
376606 TTAAAAATTAATT
1 TTAAAAATT-ATT
376619 TTAAAAATTATT
1 TTAAAAATTATT
*
376631 TAAATAAATT-TT
1 TTAA-AAATTATT
376643 TTAAAAA-TATAT
1 TTAAAAATTAT-T
*
376655 ATAAAAATT
1 TTAAAAATT
376664 TAAAATCTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 1 0.03
11 4 0.11
12 18 0.47
13 15 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TTAAAAATTATT
Found at i:377598 original size:32 final size:30
Alignment explanation
Indices: 377533--377598 Score: 71
Period size: 32 Copynumber: 2.1 Consensus size: 30
377523 AAATATATAT
* **
377533 TTTATTAAAAAATTTAAAAATTATTATCTA
1 TTTATAAAAAAATTTAAAAATTATTATAAA
377563 TTTATAAAAAATATTTTAAAAA-TATTAATAAA
1 TTTATAAAAAA-A-TTTAAAAATTATT-ATAAA
377595 TTTA
1 TTTA
377599 AAATGATACA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
30 10 0.33
31 5 0.17
32 15 0.50
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (30 bp):
TTTATAAAAAAATTTAAAAATTATTATAAA
Found at i:377638 original size:16 final size:16
Alignment explanation
Indices: 377612--377650 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
377602 TGATACATTA
*
377612 AAAATATATTAATATT
1 AAAACATATTAATATT
*
377628 AACACATATTAATATT
1 AAAACATATTAATATT
377644 AAAACAT
1 AAAACAT
377651 TAACTATGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAACATATTAATATT
Found at i:381559 original size:15 final size:16
Alignment explanation
Indices: 381529--381560 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
381519 TCAAGTAATC
381529 ATTTTTTGATTAAAAA
1 ATTTTTTGATTAAAAA
*
381545 ATTTTTTGTTTAAAAA
1 ATTTTTTGATTAAAAA
381561 CGGTCAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (16 bp):
ATTTTTTGATTAAAAA
Found at i:382183 original size:12 final size:12
Alignment explanation
Indices: 382166--382194 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
382156 ATAATTATAA
382166 TTTTATTTTTAT
1 TTTTATTTTTAT
382178 TTTTATTTTTAT
1 TTTTATTTTTAT
382190 TTTTA
1 TTTTA
382195 ATTAAGTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTATTTTTAT
Found at i:382361 original size:16 final size:16
Alignment explanation
Indices: 382310--382361 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
382300 CTGGGCAGTT
*
382310 TTTAT-ATTTATAAAA
1 TTTATAATTAATAAAA
*
382325 TTTTTAATTAA-ATAAA
1 TTTATAATTAATA-AAA
*
382341 GTTATAATTAATAAAA
1 TTTATAATTAATAAAA
382357 TTTAT
1 TTTAT
382362 TTAAAAATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
15 5 0.17
16 23 0.79
17 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
TTTATAATTAATAAAA
Found at i:383324 original size:11 final size:12
Alignment explanation
Indices: 383303--383336 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
383293 AAAATATGAC
383303 ATAAAAAATAAT
1 ATAAAAAATAAT
*
383315 -TAAAATATAAT
1 ATAAAAAATAAT
383326 ATAAAAAATAA
1 ATAAAAAATAA
383337 ATATGACACG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
ATAAAAAATAAT
Found at i:383329 original size:23 final size:23
Alignment explanation
Indices: 383278--383336 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
383268 TACTACTTTA
*
383278 AATATATAAAA-AATAAAAATAT
1 AATATAAAAAATAATAAAAATAT
* * *
383300 GACATAAAAAATAATTAAAATAT
1 AATATAAAAAATAATAAAAATAT
383323 AATATAAAAAATAA
1 AATATAAAAAATAA
383337 ATATGACACG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 8 0.27
23 22 0.73
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (23 bp):
AATATAAAAAATAATAAAAATAT
Found at i:384153 original size:31 final size:32
Alignment explanation
Indices: 384099--384163 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 32
384089 TAAACATGGT
*
384099 ATAAATACATAAATATGTTAAAATATAGATAA
1 ATAAATACATAAATATGTAAAAATATAGATAA
* * *
384131 ATAAATA-ATTAATATGTAAAAATTTATATAA
1 ATAAATACATAAATATGTAAAAATATAGATAA
384162 AT
1 AT
384164 TTATTTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 22 0.76
32 7 0.24
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (32 bp):
ATAAATACATAAATATGTAAAAATATAGATAA
Found at i:384367 original size:32 final size:33
Alignment explanation
Indices: 384305--384367 Score: 76
Period size: 32 Copynumber: 1.9 Consensus size: 33
384295 ATTAATATGT
* *
384305 AAAAAATATATAAAAATATAATATTTTAAATAC
1 AAAAAATATATAAAAATACAATATTATAAATAC
*
384338 AAAAAATA-ATATAAATACCAATA-TATAAAT
1 AAAAAATATATAAAAATA-CAATATTATAAAT
384368 TTTTTTCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
32 14 0.54
33 12 0.46
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (33 bp):
AAAAAATATATAAAAATACAATATTATAAATAC
Found at i:384781 original size:34 final size:32
Alignment explanation
Indices: 384742--384818 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 32
384732 TTTATTATTA
* *
384742 AATATTAATATTTAATTTAAATAATTCAAATAGT
1 AATATTAATATTTAATTTAAAT-ACTAAAATA-T
* *
384776 AATATTAATA-ATAATTTTAATACTAAAATAT
1 AATATTAATATTTAATTTAAATACTAAAATAT
*
384807 TATATTAATATT
1 AATATTAATATT
384819 AAATATTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
31 10 0.28
32 7 0.19
33 9 0.25
34 10 0.28
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (32 bp):
AATATTAATATTTAATTTAAATACTAAAATAT
Found at i:384823 original size:26 final size:27
Alignment explanation
Indices: 384776--384845 Score: 65
Period size: 26 Copynumber: 2.7 Consensus size: 27
384766 TTCAAATAGT
* *
384776 AATATTAATAATAAT-TTTAATA-CTAA
1 AATATT-ATATTAATATTAAATATCTAA
*
384802 AATATTATATTAATATTAAATATTTAA
1 AATATTATATTAATATTAAATATCTAA
* *
384829 AATAATAT-TTATTATTA
1 AATATTATATTAATATTA
384846 TAATTAATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 7 0.19
26 20 0.54
27 10 0.27
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (27 bp):
AATATTATATTAATATTAAATATCTAA
Found at i:384862 original size:28 final size:29
Alignment explanation
Indices: 384802--384867 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
384792 TTAATACTAA
*
384802 AATATTATATTAATATTAAATATTTAAAAT
1 AATATT-TATTAATATTAAATAATTAAAAT
* * *
384832 AATATTTATTATTA-TAATTAATTAAATT
1 AATATTTATTAATATTAAATAATTAAAAT
384860 AATATTTA
1 AATATTTA
384868 AAATACTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 19 0.59
29 7 0.22
30 6 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
AATATTTATTAATATTAAATAATTAAAAT
Found at i:384870 original size:40 final size:42
Alignment explanation
Indices: 384805--384885 Score: 114
Period size: 40 Copynumber: 2.0 Consensus size: 42
384795 ATACTAAAAT
*
384805 ATTATATTAATATTAAATATTTAAAATAATATTTATTATTATA
1 ATTATATTAATATTAAATATTTAAAATAATA-TAATTATTATA
*
384848 ATTA-ATTAA-ATT-AATATTTAAAATACTATAATTATTAT
1 ATTATATTAATATTAAATATTTAAAATAATATAATTATTAT
384886 CAAAATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
39 9 0.25
40 15 0.42
41 3 0.08
42 5 0.14
43 4 0.11
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (42 bp):
ATTATATTAATATTAAATATTTAAAATAATATAATTATTATA
Found at i:384906 original size:29 final size:30
Alignment explanation
Indices: 384874--384930 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
384864 TTTAAAATAC
*
384874 TATAATTATTATCAAAATA-TATTTTTAAA
1 TATAATAATTATCAAAATATTATTTTTAAA
*
384903 TATAATAATTATTAAAATATTATTTTTA
1 TATAATAATTATCAAAATATTATTTTTA
384931 CATTTTTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (30 bp):
TATAATAATTATCAAAATATTATTTTTAAA
Found at i:385404 original size:17 final size:18
Alignment explanation
Indices: 385352--385427 Score: 67
Period size: 17 Copynumber: 4.5 Consensus size: 18
385342 ATGCTACAAT
385352 ATATTATTAAGA-T-AATA
1 ATATTATT-AGATTAAATA
385369 ATATTATTAGATTAAATA
1 ATATTATTAGATTAAATA
385387 ATATT-TTA-ATTAAAATA
1 ATATTATTAGATT-AAATA
* *
385404 ATA-AATTATATT-AATA
1 ATATTATTAGATTAAATA
385420 AT-TTATTA
1 ATATTATTA
385428 ACTGTTATTA
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
16 16 0.31
17 23 0.45
18 12 0.24
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
ATATTATTAGATTAAATA
Found at i:386070 original size:12 final size:12
Alignment explanation
Indices: 386053--386080 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
386043 TTAATTATTT
386053 TTTGATATTGTG
1 TTTGATATTGTG
386065 TTTGATATTGTG
1 TTTGATATTGTG
386077 TTTG
1 TTTG
386081 TGTTATGTAT
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:0.14, C:0.00, G:0.25, T:0.61
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:386909 original size:10 final size:10
Alignment explanation
Indices: 386896--386934 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
386886 TTAAAATATA
386896 TAAAAAAATT
1 TAAAAAAATT
*
386906 TAAAAAAAAT
1 TAAAAAAATT
* *
386916 TAAAAATATA
1 TAAAAAAATT
386926 TAAAAAAAT
1 TAAAAAAAT
386935 ACATACTTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
TAAAAAAATT
Found at i:386919 original size:20 final size:20
Alignment explanation
Indices: 386896--386933 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
386886 TTAAAATATA
*
386896 TAAAAAAATTTAAAAAAAAT
1 TAAAAAAATATAAAAAAAAT
*
386916 TAAAAATATATAAAAAAA
1 TAAAAAAATATAAAAAAA
386934 TACATACTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (20 bp):
TAAAAAAATATAAAAAAAAT
Found at i:388235 original size:22 final size:23
Alignment explanation
Indices: 388196--388239 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
388186 CTAAAATGAC
*
388196 TTAAACCCGATTTAACCCGAATG
1 TTAAACCCGAATTAACCCGAATG
388219 TTAAACCC-AATTAACCCGAAT
1 TTAAACCCGAATTAACCCGAAT
388240 TCAGAATGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.25
Consensus pattern (23 bp):
TTAAACCCGAATTAACCCGAATG
Found at i:388315 original size:16 final size:17
Alignment explanation
Indices: 388296--388341 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
388286 CCCGAACTCG
*
388296 AAATGATCCGAAT-TCA
1 AAATGATCCAAATCTCA
*
388312 AAATGATCCAAATCTGA
1 AAATGATCCAAATCTCA
388329 AAATGATCCAAAT
1 AAATGATCCAAAT
388342 ATTTTAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.48, C:0.17, G:0.11, T:0.24
Consensus pattern (17 bp):
AAATGATCCAAATCTCA
Found at i:388609 original size:9 final size:9
Alignment explanation
Indices: 388595--388620 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
388585 TCATACCCAA
388595 AAAAAAAAG
1 AAAAAAAAG
388604 AAAAAAAAG
1 AAAAAAAAG
388613 AAAAAAAA
1 AAAAAAAA
388621 CAACGTCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:403232 original size:2 final size:2
Alignment explanation
Indices: 403225--403256 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
403215 TTTATAATAC
403225 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
403257 GAGATTGCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:405082 original size:2 final size:2
Alignment explanation
Indices: 405044--405074 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
405034 TAAGAATAGA
405044 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
405075 AAAGAGAGGG
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:405163 original size:17 final size:18
Alignment explanation
Indices: 405143--405176 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
405133 TTGACATTAT
405143 ATATTATTTTT-TATTTC
1 ATATTATTTTTGTATTTC
405160 ATATTATTTTTGTATTT
1 ATATTATTTTTGTATTT
405177 TTTTTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (18 bp):
ATATTATTTTTGTATTTC
Found at i:405623 original size:21 final size:19
Alignment explanation
Indices: 405564--405623 Score: 54
Period size: 21 Copynumber: 3.1 Consensus size: 19
405554 TTTAAAATAA
405564 TTTA-TTTTATTAATAATT
1 TTTATTTTTATTAATAATT
405582 TTT-TTTTTAGTTTTAA-AATT
1 TTTATTTTTA---TTAATAATT
405602 TTTATTTTTATATAATATATT
1 TTTATTTTTAT-TAATA-ATT
405623 T
1 T
405624 AAAGAGATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
18 9 0.26
19 3 0.09
20 8 0.24
21 14 0.41
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTATTTTTATTAATAATT
Found at i:407727 original size:14 final size:13
Alignment explanation
Indices: 407664--407731 Score: 56
Period size: 12 Copynumber: 5.4 Consensus size: 13
407654 GATCTCAATA
407664 ATTTATA-ATTTAT
1 ATTTATATA-TTAT
*
407677 ATTTA-ACATGTAT
1 ATTTATATAT-TAT
407690 A-TT-TATATTAT
1 ATTTATATATTAT
407701 A-TTATATATTAT
1 ATTTATATATTAT
*
407713 ATTTATGTAATTAT
1 ATTTATAT-ATTAT
407727 ATTTA
1 ATTTA
407732 AAATATAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
11 6 0.13
12 16 0.34
13 15 0.32
14 10 0.21
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.57
Consensus pattern (13 bp):
ATTTATATATTAT
Found at i:407767 original size:25 final size:25
Alignment explanation
Indices: 407739--407794 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
407729 TTAAAATATA
* *
407739 ATTATTTTATACGTCAACACAAGAT
1 ATTATTTTACAAGTCAACACAAGAT
*
407764 ATTATTTTACAAGTCAACACAATAT
1 ATTATTTTACAAGTCAACACAAGAT
407789 ATTATT
1 ATTATT
407795 ATTTTCCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.39
Consensus pattern (25 bp):
ATTATTTTACAAGTCAACACAAGAT
Found at i:408282 original size:20 final size:22
Alignment explanation
Indices: 408254--408301 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
408244 ATTAATTCAA
*
408254 TTTAAAAAAAAATTGAAGAATT
1 TTTAAAAAAATATTGAAGAATT
408276 TTTAAAAAAATATTGAAGAATT
1 TTTAAAAAAATATTGAAGAATT
408298 TTTA
1 TTTA
408302 TGTTTGGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (22 bp):
TTTAAAAAAATATTGAAGAATT
Found at i:409553 original size:6 final size:6
Alignment explanation
Indices: 409542--409567 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
409532 TTCAACACCT
409542 TTGCCA TTGCCA TTGCCA TTGCCA TT
1 TTGCCA TTGCCA TTGCCA TTGCCA TT
409568 CCTAGCCTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.31, G:0.15, T:0.38
Consensus pattern (6 bp):
TTGCCA
Found at i:410521 original size:42 final size:43
Alignment explanation
Indices: 410473--410559 Score: 115
Period size: 43 Copynumber: 2.0 Consensus size: 43
410463 ATAATAATTA
* *
410473 TTTTATTTTATAAATA-AAAAAAAT-TATTATATATTTTTTTAT
1 TTTTATTTTATAAATATAAAAAAATATATAATA-ATTTTTTAAT
* *
410515 TTTTATTTTTTAAATATATAAAAATATATAATAATTTTTTAAT
1 TTTTATTTTATAAATATAAAAAAATATATAATAATTTTTTAAT
410558 TT
1 TT
410560 ATTTATAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
42 15 0.38
43 18 0.46
44 6 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (43 bp):
TTTTATTTTATAAATATAAAAAAATATATAATAATTTTTTAAT
Found at i:417087 original size:34 final size:34
Alignment explanation
Indices: 417044--417111 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
417034 CCTTGGTGCG
*
417044 GTTTACTGGTTTTAACTAAGGTAATTAAAATTAT
1 GTTTACTGGTTTTAAATAAGGTAATTAAAATTAT
417078 GTTTACTGGTTTTAAATAAGGTAATTAAAATTAT
1 GTTTACTGGTTTTAAATAAGGTAATTAAAATTAT
417112 CTGATTGCGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.44
Consensus pattern (34 bp):
GTTTACTGGTTTTAAATAAGGTAATTAAAATTAT
Found at i:418669 original size:14 final size:15
Alignment explanation
Indices: 418649--418682 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
418639 AAATAATAAT
*
418649 TATAATATTTAAATC
1 TATAATATTCAAATC
418664 -ATAATATTCAAATC
1 TATAATATTCAAATC
418678 TATAA
1 TATAA
418683 AAAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (15 bp):
TATAATATTCAAATC
Found at i:419567 original size:17 final size:17
Alignment explanation
Indices: 419523--419588 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 17
419513 TCAATAATTG
419523 ATTTTTTATGGACA-AATA
1 ATTTTTTAT-GA-ATAATA
*
419541 TTTATTTTATGAATAATA
1 ATT-TTTTATGAATAATA
*
419559 ATTTTTTATCAATAATTA
1 ATTTTTTATGAATAA-TA
*
419577 ACTTTTTATGAA
1 ATTTTTTATGAA
419589 AAATTATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
17 12 0.30
18 22 0.55
19 6 0.15
ACGTcount: A:0.38, C:0.05, G:0.06, T:0.52
Consensus pattern (17 bp):
ATTTTTTATGAATAATA
Found at i:419584 original size:18 final size:17
Alignment explanation
Indices: 419545--419585 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
419535 CAAATATTTA
* *
419545 TTTTATGAATAATAATT
1 TTTTATCAATAATAACT
419562 TTTTATCAATAATTAACT
1 TTTTATCAATAA-TAACT
419580 TTTTAT
1 TTTTAT
419586 GAAAAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTTATCAATAATAACT
Found at i:419593 original size:18 final size:18
Alignment explanation
Indices: 419545--419594 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
419535 CAAATATTTA
*
419545 TTTTATGAATAA-TAATT
1 TTTTATGAATAATTAACT
*
419562 TTTTATCAATAATTAACT
1 TTTTATGAATAATTAACT
*
419580 TTTTATGAAAAATTA
1 TTTTATGAATAATTA
419595 TTTATTCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 11 0.39
18 17 0.61
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (18 bp):
TTTTATGAATAATTAACT
Found at i:420415 original size:8 final size:8
Alignment explanation
Indices: 420402--420435 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
420392 ACTACTTATG
420402 TAATTTTT
1 TAATTTTT
420410 TAATTTTT
1 TAATTTTT
*
420418 TTATTCTTT
1 TAATT-TTT
420427 TAATTTTT
1 TAATTTTT
420435 T
1 T
420436 TAAATCTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (8 bp):
TAATTTTT
Found at i:420419 original size:9 final size:9
Alignment explanation
Indices: 420405--420438 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
420395 ACTTATGTAA
420405 TTTTTTAAT
1 TTTTTTAAT
420414 TTTTTT-AT
1 TTTTTTAAT
*
420422 TCTTTTAAT
1 TTTTTTAAT
420431 TTTTTTAA
1 TTTTTTAA
420439 ATCTTATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTTTAAT
Found at i:420443 original size:18 final size:17
Alignment explanation
Indices: 420402--420443 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
420392 ACTACTTATG
*
420402 TAATTTTTTAATTTTTT
1 TAATCTTTTAATTTTTT
*
420419 TATTCTTTTAATTTTTT
1 TAATCTTTTAATTTTTT
420436 TAAATCTT
1 T-AATCTT
420444 ATATTTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (17 bp):
TAATCTTTTAATTTTTT
Found at i:425557 original size:15 final size:15
Alignment explanation
Indices: 425537--425566 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
425527 ATTGTATTTA
*
425537 AATAAAATAACACAT
1 AATAAAATAAAACAT
425552 AATAAAATAAAACAT
1 AATAAAATAAAACAT
425567 GTAGATAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.10, G:0.00, T:0.20
Consensus pattern (15 bp):
AATAAAATAAAACAT
Found at i:426092 original size:26 final size:26
Alignment explanation
Indices: 426046--426095 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
426036 TAATTATTTA
426046 TTATTTACTTTTATAATATTTTAATT
1 TTATTTACTTTTATAATATTTTAATT
426072 TTATTTAACATTTTA-AA-ATTTTAA
1 TTATTT-AC-TTTTATAATATTTTAA
426096 AAAATCTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 13 0.59
27 4 0.18
28 5 0.23
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (26 bp):
TTATTTACTTTTATAATATTTTAATT
Found at i:428890 original size:20 final size:19
Alignment explanation
Indices: 428867--428910 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
428857 GATTAATATG
428867 TAAAAAAGAT-GATTATTTTT
1 TAAAAAAGATAG-TTA-TTTT
*
428887 TAAAATAGATAGTTATTTT
1 TAAAAAAGATAGTTATTTT
428906 TAAAA
1 TAAAA
428911 GGGAAATGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 9 0.41
20 12 0.55
21 1 0.05
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (19 bp):
TAAAAAAGATAGTTATTTT
Found at i:430752 original size:928 final size:913
Alignment explanation
Indices: 429377--431254 Score: 3199
Period size: 928 Copynumber: 2.0 Consensus size: 913
429367 TATAATTGGC
* * * *
429377 ATTATTCAAATAGATCTCAATTTTGTGTCACATGTTATTGTGTTTATGTTCATAACACGTTAATA
1 ATTATTCAAATAAATATTAATTTTGTGTCACATGTTATTGTGTTCATGTTCATAACACGTTAATA
* *
429442 ATTTATTTTATATAGATTTTGATACATTATTTGTCTAATTGTATTGTGTTCAAATTATTTTTATA
66 ATTTATTTTATATAGATTTTGACACATTATTTGTCTAATTGAATTGTGTTCAAATTATTTTTATA
*
429507 TCATATCATATTTTAATTATTTTTTTCATATTATGTTTATAATGTATATATATAATATCTTGAAT
131 TCATATCATATTTTAATTATTTTTTTCATATTATGTTTATAATATATATATATAATATCTTGAAT
429572 ATGATTATATTATAAAAGATAACACAAATATAACATGTGATAATTATAAAAAATTATAATTATTT
196 ATGATTATATTATAAAAGATAACACAAATATAACATGTGATAATTATAAAAAATTATAATTATTT
429637 GTTATGTGATAAGTAAAATAAGATAACTTTTGTCTTATTTCATAAGATATATGCAATTTCGCATT
261 GTTATGTGATAAGTAAAATAAGATAACTTTTGTCTTATTTCATAAGATATATGCAATTTCGCATT
*
429702 TCATATGGGTTCTATTTTTCTAACATTGTTTAATAGCTAATTTTTAATTAAAATAACATAAAAAA
326 TCATATGAGTTCTATTTTTCTAACATTGTTTAATAGCTAATTTTTAATTAAAATAACATAAAAAA
429767 TAAAAAAGATTGAATTAAATATTTTATTGTATTGTATAACATAAAACAAAAAAATAATTAAAATT
391 TAAAAAAGATTGAATTAAATATTTTATTGTATTGTATAACATAAAACAAAAAAATAATTAAAATT
*
429832 AATATTTTATCCATATTTCACGAATAGGTTAATTTTTGCCCATCAATAATTATAAAAATAACATT
456 AATATTTTATCCATATTTCACGAATAGGTTAATTTTTGCCCATAAATAATTATAAAAATAACATT
* * *
429897 AAAGATATAATATGCTTAAATAATAATTAATTATAATAGACGTACACAATTTTAAATTTCATTAT
521 AAAAATATAATATACTTAAATAATAATTAATTATAATAGACGTACACAATTTTAAAATTCATTAT
*
429962 TGGTTAGACTTTTACTTATACTAAACCTTATTAAAATTATTTTACAAAATAATTATATTGAAAAA
586 TGGTTAGACTTTTACTTATACTAAACCTTATTAAAATTATTTTACAAAATAATTATAATGAAAAA
* * *
430027 TTACATTTATAATTATCTAATCTTATAAAGTTAATTTTTAAATTTTTACAAATTTTAATATATTC
651 TTACATTTATAATTATCTAATCTTATAAAGTTAATTTTTAAACTTTTACAAATTTTAACATACTC
430092 ATACATTTATTCATATTATTGCTATTATTTGATATTGTA-T-TTTTAGTTATTTTTATATAGTGT
716 ATACATTTATTCATATTATTGCTATTATTTGATATTGTATTATTTTAGTTATTTTTATATAGTGT
*
430155 TCAACATTATCAGGTCTAATTTGCATTATTCAAATAACTCTTAATTTTGTATTACGTTCATTTTA
781 TCAACATTATCAAGTCTAATTTGCATTATTCAAATAACTCTTAATTTTGTATTACGTTCATTTTA
* *
430220 GATAAATTTCAACAA-GTTCGTATAATTGTATTATATTCATTATAATATTTTTTTCATATTCATA
846 GATAAATTTCAACAACGTTCGTATAATTATATTATATTCA-TAT--TATTTTTTTCAAATTCATA
430284 TGTGAT
908 TGTGAT
430290 ATTATTCAAATAAATATTAATTTTGTGTCACATGTTATTGTGTTCATGTTCATAACACGTTAATA
1 ATTATTCAAATAAATATTAATTTTGTGTCACATGTTATTGTGTTCATGTTCATAACACGTTAATA
* * * *
430355 ATTTATTTTATGTAGATTTTGACATATTATTTGTCTAATTGAATTGTGTTTATATTATTTTTATA
66 ATTTATTTTATATAGATTTTGACACATTATTTGTCTAATTGAATTGTGTTCAAATTATTTTTATA
** *
430420 TCATATTGTATTTTAATTA-TTTTTTCATATTACGTTCATAACGTGTGTGTGTGTATATATATAT
131 TCATATCATATTTTAATTATTTTTTTC--A-TA---T--T-A----TGT-T-TATA-ATATATAT
*
430484 ATATAATATCTTGAATATGATTATATTATAAAAGATAACACAAATATAACATGTTATAATTATAA
180 ATATAATATCTTGAATATGATTATATTATAAAAGATAACACAAATATAACATGTGATAATTATAA
430549 AAAATTATAATTATTTGTTATGTGATAAGTAAAA-AAGGATAACTTTTGTCTTATTTCATAAGAT
245 AAAATTATAATTATTTGTTATGTGATAAGTAAAATAA-GATAACTTTTGTCTTATTTCATAAGAT
*
430613 ATATGCAATTTCGCATTTCATATGAGTTCTATTTTTCTAACATTGTTTAATATCTAATTTTTAAT
309 ATATGCAATTTCGCATTTCATATGAGTTCTATTTTTCTAACATTGTTTAATAGCTAATTTTTAAT
430678 TAAAATAACATAAAAAATAAAAAAGATTGAATTAAATATTTTATTGTATTGTATAACATAAAACA
374 TAAAATAACATAAAAAATAAAAAAGATTGAATTAAATATTTTATTGTATTGTATAACATAAAACA
430743 AAAAAATAATTAAAATTAATATTTTATCCATATTTCACGAATAGGTTAATTTTTGCCCATAAATA
439 AAAAAATAATTAAAATTAATATTTTATCCATATTTCACGAATAGGTTAATTTTTGCCCATAAATA
430808 ATTATAAAAATAACATTAAAAATATAATATACTTAAATAATAATTAATTATAATAGACGTACACA
504 ATTATAAAAATAACATTAAAAATATAATATACTTAAATAATAATTAATTATAATAGACGTACACA
*
430873 ATTTTAAAATTCATTATTGGTTAGACTTTTACTTATACTAAACTTTATTAAAATTATTTTACAAA
569 ATTTTAAAATTCATTATTGGTTAGACTTTTACTTATACTAAACCTTATTAAAATTATTTTACAAA
430938 ATAATTATAATGAAAAATTACATTTATAATTATCTAATCTTATAAAGTTAATTTTTAAACTTTTA
634 ATAATTATAATGAAAAATTACATTTATAATTATCTAATCTTATAAAGTTAATTTTTAAACTTTTA
* *
431003 CAAATTTTAACATACTCATGCATTTATTCATGTTATTGCTATTATTTGATATTGTATTGTATTTT
699 CAAATTTTAACATACTCATACATTTATTCATATTATTGCTATTATTTGATATTGTA-T-TATTTT
*
431068 AGTTATTTTTATATAGTGTTCAACATTATCAAGTCTAATTTGCATTATTCAAATAATTCTTAATT
762 AGTTATTTTTATATAGTGTTCAACATTATCAAGTCTAATTTGCATTATTCAAATAACTCTTAATT
**
431133 TTGTATTACGTTTGTTTTAGATAAATTTCAACAACGTTCGTATAATTATATTATATTCATATTAT
827 TTGTATTACGTTCATTTTAGATAAATTTCAACAACGTTCGTATAATTATATTATATTCATATTAT
*
431198 TTTTTTCAAATTCATGTGTGAT
892 TTTTTTCAAATTCATATGTGAT
*
431220 ATTATTCAAATAACTATTAATTTTGTGTCACATGT
1 ATTATTCAAATAAATATTAATTTTGTGTCACATGT
431255 CATATAATGA
Statistics
Matches: 907, Mismatches: 36, Indels: 27
0.94 0.04 0.03
Matches are distributed among these distances:
912 7 0.01
913 137 0.15
914 1 0.00
915 2 0.00
918 1 0.00
920 1 0.00
921 1 0.00
925 3 0.00
926 1 0.00
927 5 0.01
928 565 0.62
930 57 0.06
931 1 0.00
932 102 0.11
933 23 0.03
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (913 bp):
ATTATTCAAATAAATATTAATTTTGTGTCACATGTTATTGTGTTCATGTTCATAACACGTTAATA
ATTTATTTTATATAGATTTTGACACATTATTTGTCTAATTGAATTGTGTTCAAATTATTTTTATA
TCATATCATATTTTAATTATTTTTTTCATATTATGTTTATAATATATATATATAATATCTTGAAT
ATGATTATATTATAAAAGATAACACAAATATAACATGTGATAATTATAAAAAATTATAATTATTT
GTTATGTGATAAGTAAAATAAGATAACTTTTGTCTTATTTCATAAGATATATGCAATTTCGCATT
TCATATGAGTTCTATTTTTCTAACATTGTTTAATAGCTAATTTTTAATTAAAATAACATAAAAAA
TAAAAAAGATTGAATTAAATATTTTATTGTATTGTATAACATAAAACAAAAAAATAATTAAAATT
AATATTTTATCCATATTTCACGAATAGGTTAATTTTTGCCCATAAATAATTATAAAAATAACATT
AAAAATATAATATACTTAAATAATAATTAATTATAATAGACGTACACAATTTTAAAATTCATTAT
TGGTTAGACTTTTACTTATACTAAACCTTATTAAAATTATTTTACAAAATAATTATAATGAAAAA
TTACATTTATAATTATCTAATCTTATAAAGTTAATTTTTAAACTTTTACAAATTTTAACATACTC
ATACATTTATTCATATTATTGCTATTATTTGATATTGTATTATTTTAGTTATTTTTATATAGTGT
TCAACATTATCAAGTCTAATTTGCATTATTCAAATAACTCTTAATTTTGTATTACGTTCATTTTA
GATAAATTTCAACAACGTTCGTATAATTATATTATATTCATATTATTTTTTTCAAATTCATATGT
GAT
Found at i:433297 original size:3 final size:3
Alignment explanation
Indices: 433289--433319 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
433279 ATTTTGATTC
433289 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
433320 TCCTGTATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:441409 original size:40 final size:41
Alignment explanation
Indices: 441346--441434 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 41
441336 TTAAGTTTCG
* * *
441346 TTTA-ATTTA-AAATAAATATTTTAT-TTTATTTAAATTTA
1 TTTATATTTATAAATAAATAATTTATATTAACTTAAATTTA
*
441384 TTTATATTTATAAATAGATAATTTATATTAACTTAAATTTA
1 TTTATATTTATAAATAAATAATTTATATTAACTTAAATTTA
*
441425 TCTAT-TTTAT
1 TTTATATTTAT
441435 TTTTTAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
38 4 0.09
39 5 0.12
40 18 0.42
41 16 0.37
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.56
Consensus pattern (41 bp):
TTTATATTTATAAATAAATAATTTATATTAACTTAAATTTA
Found at i:441488 original size:36 final size:36
Alignment explanation
Indices: 441432--441513 Score: 91
Period size: 37 Copynumber: 2.3 Consensus size: 36
441422 TTATCTATTT
* *
441432 TATTTTTTA--AAAATTTAATTTTTAGTAA-TTTAA
1 TATTTTTTATTAAAATTTAATTTTAAATAATTTTAA
*
441465 TATTTTTTATTAAATTTTAAATTTTAAATAATTTTAA
1 TATTTTTTATTAAAATTT-AATTTTAAATAATTTTAA
441502 -ATTTTTTTATTA
1 TA-TTTTTTATTA
441514 TTTATATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
33 9 0.22
35 6 0.15
36 11 0.27
37 15 0.37
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (36 bp):
TATTTTTTATTAAAATTTAATTTTAAATAATTTTAA
Found at i:441529 original size:17 final size:17
Alignment explanation
Indices: 441509--441565 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 17
441499 TAAATTTTTT
441509 TATTATTTATATTATAA
1 TATTATTTATATTATAA
441526 TATTA--TATATT-T-A
1 TATTATTTATATTATAA
* *
441539 TATTTTTTATATGATCAA
1 TATTATTTATATTAT-AA
*
441557 AATTATTTA
1 TATTATTTA
441566 ATATATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
13 5 0.16
14 1 0.03
15 11 0.35
16 1 0.03
17 5 0.16
18 8 0.26
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (17 bp):
TATTATTTATATTATAA
Found at i:442176 original size:11 final size:12
Alignment explanation
Indices: 442157--442203 Score: 53
Period size: 11 Copynumber: 4.0 Consensus size: 12
442147 TTATAACATA
*
442157 AAAAAATAAT-T
1 AAAATATAATAT
442168 AAAATATAATAT
1 AAAATATAATAT
*
442180 AAAAATAAAATAT
1 -AAAATATAATAT
442193 AAAA-ATAATAT
1 AAAATATAATAT
442204 TATTACAGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
11 15 0.48
12 5 0.16
13 11 0.35
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
AAAATATAATAT
Found at i:442184 original size:13 final size:13
Alignment explanation
Indices: 442148--442199 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
442138 TAGATCTCCT
*
442148 TATAACATAAAAA
1 TATAATATAAAAA
*
442161 AATAAT-T-AAAA
1 TATAATATAAAAA
442172 TATAATATAAAAA
1 TATAATATAAAAA
*
442185 TAAAATATAAAAA
1 TATAATATAAAAA
442198 TA
1 TA
442200 ATATTATTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 9 0.27
12 2 0.06
13 22 0.67
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (13 bp):
TATAATATAAAAA
Found at i:442201 original size:24 final size:24
Alignment explanation
Indices: 442148--442203 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
442138 TAGATCTCCT
*
442148 TATAACATAAAAAAATAATTAAAA
1 TATAATATAAAAAAATAATTAAAA
442172 TATAATATAAAAATAA-AATATAAAA
1 TATAATATAAAAA-AATAAT-TAAAA
442197 -ATAATAT
1 TATAATAT
442204 TATTACAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 22 0.76
25 7 0.24
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (24 bp):
TATAATATAAAAAAATAATTAAAA
Found at i:442234 original size:19 final size:19
Alignment explanation
Indices: 442158--442248 Score: 57
Period size: 19 Copynumber: 4.9 Consensus size: 19
442148 TATAACATAA
* *
442158 AAAAATAATTAAAATATAAT
1 AAAAATAA-TATAATATATT
*
442178 ATAAA-AATA-AA-ATA-T
1 AAAAATAATATAATATATT
* * *
442193 AAAAATAATATTATTACAGT
1 AAAAATAATA-TAATATATT
442213 AAAAAT-ATATAAATATATT
1 AAAAATAATAT-AATATATT
*
442232 AAAATTAATATAATATA
1 AAAAATAATATAATATA
442249 AATTATTATT
Statistics
Matches: 56, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
15 5 0.09
16 7 0.12
17 2 0.04
18 4 0.07
19 23 0.41
20 15 0.27
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (19 bp):
AAAAATAATATAATATATT
Found at i:442273 original size:16 final size:16
Alignment explanation
Indices: 442240--442300 Score: 54
Period size: 16 Copynumber: 3.7 Consensus size: 16
442230 TTAAAATTAA
442240 TATAA-TAT-AAATTAT
1 TATAATTATAAAATT-T
* *
442255 TATTATTTTAAAATTT
1 TATAATTATAAAATTT
442271 TATAATTATAAATATTT
1 TATAATTATAAA-ATTT
442288 TAATATATTATAA
1 T-ATA-ATTATAA
442301 TATAAAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
15 4 0.11
16 13 0.35
17 10 0.27
18 3 0.08
19 7 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATAATTATAAAATTT
Found at i:442286 original size:25 final size:25
Alignment explanation
Indices: 442249--442306 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
442239 ATATAATATA
* * *
442249 AATTATTATTATTTTAAAATTTTAT
1 AATTATAAATATTTTAAAATATTAT
*
442274 AATTATAAATATTTTAATATATTAT
1 AATTATAAATATTTTAAAATATTAT
442299 AA-TATAAA
1 AATTATAAA
442307 AAATATAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 6 0.21
25 23 0.79
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
AATTATAAATATTTTAAAATATTAT
Found at i:442327 original size:2 final size:2
Alignment explanation
Indices: 442322--442360 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
442312 TAACAAACAC
442322 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
442361 CGTCAGGTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:442746 original size:2 final size:2
Alignment explanation
Indices: 442739--442766 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
442729 TCGTATTCTG
442739 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
442767 TGTTTCTCCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:444036 original size:16 final size:16
Alignment explanation
Indices: 444015--444046 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
444005 GGTTTTTGAT
444015 TATATCATATTTATTA
1 TATATCATATTTATTA
444031 TATATCATATTTATTA
1 TATATCATATTTATTA
444047 CGGTTGTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (16 bp):
TATATCATATTTATTA
Found at i:445812 original size:14 final size:16
Alignment explanation
Indices: 445793--445830 Score: 62
Period size: 14 Copynumber: 2.5 Consensus size: 16
445783 TAAAATGTCA
445793 TTAAAATTAA-AA-TT
1 TTAAAATTAATAATTT
445807 TTAAAATTAATAATTT
1 TTAAAATTAATAATTT
445823 TTAAAATT
1 TTAAAATT
445831 CAATGTGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 10 0.45
15 2 0.09
16 10 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAATTAATAATTT
Found at i:446454 original size:24 final size:24
Alignment explanation
Indices: 446427--446479 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
446417 ATGATTAAAA
*
446427 AAATTAAGGTTTAAATT-TTAATTT
1 AAATT-AGATTTAAATTATTAATTT
* *
446451 AAATTTGATTTAATTTATTAATTT
1 AAATTAGATTTAAATTATTAATTT
446475 AAATT
1 AAATT
446480 TATTGGTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (24 bp):
AAATTAGATTTAAATTATTAATTT
Found at i:446463 original size:11 final size:12
Alignment explanation
Indices: 446436--446480 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 12
446426 AAAATTAAGG
446436 TTTAAATTTTAA
1 TTTAAATTTTAA
*
446448 TTTAAA-TTTGA
1 TTTAAATTTTAA
*
446459 TTTAATTTATTAA
1 TTTAAATT-TTAA
446472 TTTAAATTT
1 TTTAAATTT
446481 ATTGGTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
11 9 0.33
12 8 0.30
13 10 0.37
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (12 bp):
TTTAAATTTTAA
Found at i:446480 original size:24 final size:23
Alignment explanation
Indices: 446436--446480 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
446426 AAAATTAAGG
446436 TTTAAATTTTAATTTAAATTTGA
1 TTTAAATTTTAATTTAAATTTGA
*
446459 TTTAATTTATTAATTTAAATTT
1 TTTAAATT-TTAATTTAAATTT
446481 ATTGGTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
TTTAAATTTTAATTTAAATTTGA
Found at i:446594 original size:17 final size:18
Alignment explanation
Indices: 446540--446596 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 18
446530 ATATATTTTT
446540 ATAATTAAATTTAAA-TAA
1 ATAATT-AATTTAAATTAA
* *
446558 AAAATTATTTTAATATTTAA
1 ATAATTAATTTAA-A-TTAA
446578 ATAA-TAATTTAAATTAA
1 ATAATTAATTTAAATTAA
446595 AT
1 AT
446597 TAAATTAACT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
17 12 0.38
18 7 0.22
19 7 0.22
20 6 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAATTAATTTAAATTAA
Found at i:446594 original size:24 final size:24
Alignment explanation
Indices: 446499--446601 Score: 72
Period size: 24 Copynumber: 4.5 Consensus size: 24
446489 AATATATTAA
* * * *
446499 AATATTAAAAAAATATTTTATATT
1 AATATTTAAATAATAATTTAAATT
* *
446523 AATATTTATAT-AT-TTTTATAATT
1 AATATTTAAATAATAATTTA-AATT
* * **
446546 AA-ATTTAAATAAAAAATTATTTT
1 AATATTTAAATAATAATTTAAATT
446569 AATATTTAAATAATAATTTAAATT
1 AATATTTAAATAATAATTTAAATT
446593 AA-A-TTAAAT
1 AATATTTAAAT
446602 TAACTAAATC
Statistics
Matches: 61, Mismatches: 14, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
22 18 0.30
23 13 0.21
24 30 0.49
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AATATTTAAATAATAATTTAAATT
Found at i:448218 original size:11 final size:11
Alignment explanation
Indices: 448204--448255 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
448194 TACATTATTC
448204 TTTATATTATA
1 TTTATATTATA
*
448215 TTTATTTTATAA
1 TTTATATTAT-A
*
448227 TATTTTATATATA
1 T-TTATAT-TATA
*
448240 TTTTTATTATA
1 TTTATATTATA
448251 TTTAT
1 TTTAT
448256 CGTATAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
11 17 0.50
12 8 0.24
13 6 0.18
14 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTATATTATA
Found at i:448254 original size:21 final size:20
Alignment explanation
Indices: 448205--448255 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
448195 ACATTATTCT
*
448205 TTATA-TTATATTTATTTTA
1 TTATATTTATATATATTTTA
*
448224 TAATATTTTATATATATTTTTA
1 TTATA-TTTATATATA-TTTTA
448246 TTATATTTAT
1 TTATATTTAT
448256 CGTATAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 4 0.15
21 13 0.50
22 9 0.35
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATATTTATATATATTTTA
Found at i:448261 original size:22 final size:22
Alignment explanation
Indices: 448210--448253 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
448200 ATTCTTTATA
*
448210 TTATATTTA-TTTTATAATATT
1 TTATATATATTTTTATAATATT
*
448231 TTATATATATTTTTATTATATT
1 TTATATATATTTTTATAATATT
448253 T
1 T
448254 ATCGTATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTATATATATTTTTATAATATT
Found at i:449374 original size:2 final size:2
Alignment explanation
Indices: 449369--449395 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
449359 GATATATGTT
449369 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 T
449396 CAAAATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:452436 original size:25 final size:26
Alignment explanation
Indices: 452408--452480 Score: 73
Period size: 25 Copynumber: 2.9 Consensus size: 26
452398 AATTATATTT
452408 TTTTAAT-TTTATTATATTTAAAATA
1 TTTTAATATTTATTATATTTAAAATA
* *
452433 TTTT-ATATTTA-TATAAATTATAATA
1 TTTTAATATTTATTAT-ATTTAAAATA
* *
452458 TATTAATAATT-TTATATTTAAAA
1 TTTTAATATTTATTATATTTAAAA
452481 AAATAAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
24 5 0.13
25 25 0.66
26 8 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
TTTTAATATTTATTATATTTAAAATA
Found at i:452438 original size:16 final size:15
Alignment explanation
Indices: 452419--452481 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 15
452409 TTTAATTTTA
452419 TTATATTTAAAATATT
1 TTATATTTAAAA-ATT
452435 TTATATTTATATAAATT
1 TTATATTTA-A-AAATT
* *
452452 ATAATATATTAATAATT
1 -TTATAT-TTAAAAATT
452469 TTATATTTAAAAA
1 TTATATTTAAAAA
452482 AATAAAAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
15 6 0.15
16 14 0.36
17 8 0.21
18 8 0.21
19 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTATATTTAAAAATT
Found at i:452526 original size:28 final size:28
Alignment explanation
Indices: 452461--452526 Score: 64
Period size: 29 Copynumber: 2.3 Consensus size: 28
452451 TATAATATAT
*
452461 TAATAATTTTATATTTAAAAAAATAAAA
1 TAATAATTTAATATTTAAAAAAATAAAA
* *
452489 -ATTTAGATTTAA-ATTTTTAAAAAATAAAA
1 TA-ATA-ATTTAATA-TTTAAAAAAATAAAA
452518 TAATAATTT
1 TAATAATTT
452527 TGACGAAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
27 1 0.03
28 7 0.23
29 21 0.70
30 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (28 bp):
TAATAATTTAATATTTAAAAAAATAAAA
Found at i:453988 original size:18 final size:18
Alignment explanation
Indices: 453937--453998 Score: 76
Period size: 18 Copynumber: 3.4 Consensus size: 18
453927 AATATATTTG
453937 ATTAA-TTATT-TATTAAA
1 ATTAATTTATTATA-TAAA
453954 ATCTATATTTA-TATATAAA
1 AT-TA-ATTTATTATATAAA
453973 ATTAATTTATTATATAAA
1 ATTAATTTATTATATAAA
453991 ATTAATTT
1 ATTAATTT
453999 TTTAAATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
17 7 0.17
18 20 0.50
19 8 0.20
20 5 0.12
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTAATTTATTATATAAA
Found at i:454007 original size:18 final size:18
Alignment explanation
Indices: 453937--454007 Score: 65
Period size: 18 Copynumber: 3.9 Consensus size: 18
453927 AATATATTTG
* *
453937 ATTAA-TTATTTATTAAA
1 ATTAATTTATTAAATAAA
*
453954 ATCTATATTTA-TATATAAA
1 AT-TA-ATTTATTAAATAAA
*
453973 ATTAATTTATTATATAAA
1 ATTAATTTATTAAATAAA
*
453991 ATTAATTTTTTAAATAA
1 ATTAATTTATTAAATAA
454008 TTTATTATTA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
17 7 0.16
18 27 0.60
19 8 0.18
20 3 0.07
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTAATTTATTAAATAAA
Found at i:456820 original size:15 final size:15
Alignment explanation
Indices: 456800--456828 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
456790 TCTTTCATTC
456800 TTTTCTTATTTTTTT
1 TTTTCTTATTTTTTT
456815 TTTTCTTATTTTTT
1 TTTTCTTATTTTTT
456829 GTATTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTCTTATTTTTTT
Found at i:457627 original size:16 final size:16
Alignment explanation
Indices: 457569--457628 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
457559 GTTTGAGTTT
457569 TTTCGAGTTCGAGCT-
1 TTTCGAGTTCGAGCTA
457584 TTCTC-AGGTTCGAGCTA
1 TT-TCGA-GTTCGAGCTA
* *
457601 TCTCTGA-TTCGGGCTA
1 TTTC-GAGTTCGAGCTA
457617 TTTCGAGTTCGA
1 TTTCGAGTTCGA
457629 ATAATTTTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 11
0.70 0.08 0.22
Matches are distributed among these distances:
15 5 0.14
16 28 0.80
17 1 0.03
18 1 0.03
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (16 bp):
TTTCGAGTTCGAGCTA
Found at i:457975 original size:2 final size:2
Alignment explanation
Indices: 457968--458053 Score: 53
Period size: 2 Copynumber: 46.0 Consensus size: 2
457958 TATCATATGC
* *
457968 AT AT AT AT AT AT AT AT A- AA AG AGT AT AT AT AT A- AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
* * *
458008 A- AT CT -T AT AT GAT -T TT AT -T AT AT AT AT AT AT AT AT CT A-
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
458046 AT AT AT AT
1 AT AT AT AT
458054 TAAAAATATG
Statistics
Matches: 68, Mismatches: 6, Indels: 20
0.72 0.06 0.21
Matches are distributed among these distances:
1 8 0.12
2 57 0.84
3 3 0.04
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:458468 original size:20 final size:19
Alignment explanation
Indices: 458443--458485 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
458433 TAATTTGTAT
458443 ATTTTTAT-TTAATATATTTA
1 ATTTTTATATTAAT-TA-TTA
458463 ATTTTTTATATTAATTATTA
1 A-TTTTTATATTAATTATTA
458483 ATT
1 ATT
458486 GATTCAAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
19 2 0.10
20 5 0.24
21 9 0.43
22 5 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTTTTATATTAATTATTA
Found at i:459479 original size:17 final size:17
Alignment explanation
Indices: 459454--459496 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
459444 TTTTAAAATT
*
459454 TTAATATAATTTTATTA
1 TTAATATAACTTTATTA
* *
459471 TTAAAATAACTTTATTT
1 TTAATATAACTTTATTA
459488 TTAATATAA
1 TTAATATAA
459497 AATTAAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAATATAACTTTATTA
Found at i:460147 original size:19 final size:19
Alignment explanation
Indices: 460115--460151 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
460105 CGAATCCATC
*
460115 ATTTGTATAAATAAAAAAG
1 ATTTGAATAAATAAAAAAG
*
460134 ATTTGAATATATAAAAAA
1 ATTTGAATAAATAAAAAA
460152 TCTTAATATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.32
Consensus pattern (19 bp):
ATTTGAATAAATAAAAAAG
Found at i:462544 original size:2 final size:2
Alignment explanation
Indices: 462537--462572 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
462527 GGCTACTGGG
*
462537 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
462573 GACCCTTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:467957 original size:15 final size:14
Alignment explanation
Indices: 467937--467973 Score: 58
Period size: 13 Copynumber: 2.6 Consensus size: 14
467927 GCATATAAAG
467937 TATATATTATTTTAA
1 TATATATTA-TTTAA
467952 TATATA-TATTTAA
1 TATATATTATTTAA
467965 TATATATTA
1 TATATATTA
467974 AAAATATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 11 0.52
14 4 0.19
15 6 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATATATTATTTAA
Found at i:467992 original size:22 final size:22
Alignment explanation
Indices: 467967--468008 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
467957 ATATTTAATA
467967 TATATTAAAA-ATATAAAAAAAT
1 TATA-TAAAATATATAAAAAAAT
*
467989 TATATAAAATATTTAAAAAA
1 TATATAAAATATATAAAAAA
468009 TAAATTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
TATATAAAATATATAAAAAAAT
Found at i:468330 original size:15 final size:15
Alignment explanation
Indices: 468298--468327 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
468288 TAATTTTTAA
468298 ATATTAATTTAAATT
1 ATATTAATTTAAATT
468313 ATATTAAATTTAAAT
1 ATATT-AATTTAAAT
468328 ATAAATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATTAATTTAAATT
Found at i:469275 original size:18 final size:18
Alignment explanation
Indices: 469252--469291 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
469242 AACCTACCAT
*
469252 AACCAGCCATCCACCAAC
1 AACCAGCCATCCAACAAC
469270 AACCAGCCATCCAACAAC
1 AACCAGCCATCCAACAAC
469288 AACC
1 AACC
469292 CAAAGCTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.42, C:0.47, G:0.05, T:0.05
Consensus pattern (18 bp):
AACCAGCCATCCAACAAC
Found at i:470893 original size:17 final size:16
Alignment explanation
Indices: 470872--470918 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
470862 ATATTAATAT
470872 AAATTTAAATATATTA
1 AAATTTAAATATATTA
*
470888 ATAATTTATATCATA-TA
1 A-AATTTAAAT-ATATTA
470905 AAATTTAAA-ATATT
1 AAATTTAAATATATT
470919 TATATTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
14 3 0.12
15 1 0.04
16 8 0.31
17 11 0.42
18 3 0.12
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATTTAAATATATTA
Found at i:470906 original size:32 final size:33
Alignment explanation
Indices: 470854--470928 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
470844 TTATATTTAA
470854 AATATTTTATATTAATAT-AAATTTAAATATATT
1 AATATTTTATATTAATATAAAATTTAAA-ATATT
* *
470887 AATAATTTATA-TCATATAAAATTTAAAATATT
1 AATATTTTATATTAATATAAAATTTAAAATATT
*
470919 TATATTTTAT
1 AATATTTTAT
470929 TTTATAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 18 0.49
33 19 0.51
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (33 bp):
AATATTTTATATTAATATAAAATTTAAAATATT
Found at i:470930 original size:20 final size:20
Alignment explanation
Indices: 470908--470947 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
470898 TCATATAAAA
470908 TTTAAAATATTTATATTTTAT
1 TTTAAAATA-TTATATTTTAT
*
470929 TTTATAATATTATATTTTA
1 TTTAAAATATTATATTTTA
470948 ATTATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTAAAATATTATATTTTAT
Found at i:470938 original size:15 final size:14
Alignment explanation
Indices: 470920--470958 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
470910 TAAAATATTT
470920 ATATTTTATTTTATA
1 ATATTTTATTTTA-A
*
470935 ATATTATATTTTAA
1 ATATTTTATTTTAA
*
470949 TTATTTTATT
1 ATATTTTATT
470959 AAATAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
ATATTTTATTTTAA
Found at i:471399 original size:33 final size:34
Alignment explanation
Indices: 471324--471402 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 34
471314 TGTATTTATT
* * * *
471324 TTATTTTTATTTTTATAATATAATTATATTTTAA
1 TTATTTATATTTATATAATATAATAATATGTTAA
* *
471358 ATATTTTATATTTATATAA-ATTATAATATGTTAA
1 TTA-TTTATATTTATATAATATAATAATATGTTAA
471392 TTATTTATATT
1 TTATTTATATT
471403 AAATAAAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
33 8 0.22
34 16 0.43
35 13 0.35
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TTATTTATATTTATATAATATAATAATATGTTAA
Found at i:473550 original size:17 final size:17
Alignment explanation
Indices: 473528--473566 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
473518 TTATTTTAAT
**
473528 ATTTATTTTTTAAAATA
1 ATTTATTTAATAAAATA
473545 ATTTATTTAATAAAATA
1 ATTTATTTAATAAAATA
473562 ATTTA
1 ATTTA
473567 ATAATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTATTTAATAAAATA
Found at i:475951 original size:13 final size:13
Alignment explanation
Indices: 475933--475957 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
475923 ATCTGCATCC
475933 TTTTTTTCTAATT
1 TTTTTTTCTAATT
475946 TTTTTTTCTAAT
1 TTTTTTTCTAAT
475958 AAAGGAGTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTTTCTAATT
Found at i:476280 original size:19 final size:19
Alignment explanation
Indices: 476256--476295 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
476246 TTCAACAGTC
476256 ATCCAATACTTAATTACAA
1 ATCCAATACTTAATTACAA
*
476275 ATCCAATACTTCATTACAA
1 ATCCAATACTTAATTACAA
476294 AT
1 AT
476296 GGGTTAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.33
Consensus pattern (19 bp):
ATCCAATACTTAATTACAA
Found at i:478568 original size:1 final size:1
Alignment explanation
Indices: 478562--478594 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
478552 CTTGACCTCG
*
478562 TTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
478595 CCTTACCTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:479227 original size:2 final size:2
Alignment explanation
Indices: 479216--479252 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
479206 TATTCAAACT
479216 TA TA TA -A TA TA 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
479253 CACACTTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:489022 original size:22 final size:21
Alignment explanation
Indices: 488990--489031 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
488980 TTTCTGCACA
*
488990 TTGTGCATTCTTTGGAGTACTC
1 TTGTGCATTC-TCGGAGTACTC
*
489012 TTGTGCGTTCTCGGAGTACT
1 TTGTGCATTCTCGGAGTACT
489032 TTAATTTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.12, C:0.19, G:0.26, T:0.43
Consensus pattern (21 bp):
TTGTGCATTCTCGGAGTACTC
Found at i:492495 original size:2 final size:2
Alignment explanation
Indices: 492488--492532 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
492478 TTCACAGCAC
* *
492488 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
492530 TA T
1 TA T
492533 GTAAGTTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:495986 original size:3 final size:3
Alignment explanation
Indices: 495978--496005 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
495968 AGAGAGAGAG
495978 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
496006 AAGGAAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:501597 original size:2 final size:2
Alignment explanation
Indices: 501580--501613 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
501570 TAATTATGAA
* *
501580 AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
501614 GCACACACAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:501937 original size:16 final size:17
Alignment explanation
Indices: 501880--501937 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
501870 ATCGATTAAT
501880 TTAATATTAA-AAATAA
1 TTAATATTAATAAATAA
501896 TTTTAATATTAAATAAAT-A
1 --TTAATATT-AATAAATAA
501915 TTAA-ATATAATAAATAA
1 TTAATAT-TAATAAATAA
501932 TTAATA
1 TTAATA
501938 AAAATTTGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
16 9 0.26
17 10 0.29
18 9 0.26
19 3 0.09
20 4 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAATATTAATAAATAA
Found at i:503379 original size:23 final size:23
Alignment explanation
Indices: 503346--503391 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
503336 ATACCAATTG
503346 AAAAATCTAAATATACATATAAA
1 AAAAATCTAAATATACATATAAA
*
503369 AAAAATTTAAATATACATATAAA
1 AAAAATCTAAATATACATATAAA
503392 TATTAATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (23 bp):
AAAAATCTAAATATACATATAAA
Found at i:503400 original size:12 final size:12
Alignment explanation
Indices: 503353--503394 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
503343 TTGAAAAATC
503353 TAAATATACATA
1 TAAATATACATA
* * *
503365 TAAA-AAAAATT
1 TAAATATACATA
503376 TAAATATACATA
1 TAAATATACATA
503388 TAAATAT
1 TAAATAT
503395 TAATATCCAA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
11 8 0.35
12 15 0.65
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (12 bp):
TAAATATACATA
Found at i:503743 original size:29 final size:30
Alignment explanation
Indices: 503686--503752 Score: 68
Period size: 29 Copynumber: 2.2 Consensus size: 30
503676 TTAAAGTGAA
*
503686 AAAAAGTAAAAAAGATATAAAATAAAGGAC
1 AAAAAGTAAAAAAGATATAAAAAAAAGGAC
*
503716 AAAAA-TAAAAGAA-AT-TAAAAAAAGAGGAA
1 AAAAAGTAAAA-AAGATATAAAAAAA-AGGAC
503745 ATAAAAGT
1 A-AAAAGT
503753 TTACAAATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
28 7 0.23
29 12 0.39
30 11 0.35
31 1 0.03
ACGTcount: A:0.72, C:0.01, G:0.13, T:0.13
Consensus pattern (30 bp):
AAAAAGTAAAAAAGATATAAAAAAAAGGAC
Found at i:505364 original size:13 final size:13
Alignment explanation
Indices: 505346--505372 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
505336 ATGATGTTAT
505346 TATTTTTATTTTA
1 TATTTTTATTTTA
505359 TATTTTTATTTTA
1 TATTTTTATTTTA
505372 T
1 T
505373 TTTAAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TATTTTTATTTTA
Found at i:508627 original size:15 final size:15
Alignment explanation
Indices: 508607--508639 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
508597 ACAGGTTTGA
508607 ATAAAA-TTAATTTCG
1 ATAAAATTTAA-TTCG
508622 ATAAAATTTAATTCG
1 ATAAAATTTAATTCG
508637 ATA
1 ATA
508640 GTAATGATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (15 bp):
ATAAAATTTAATTCG
Found at i:510453 original size:2 final size:2
Alignment explanation
Indices: 510446--510473 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
510436 TCTATCTATC
510446 TA 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
510474 ATCAAGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:510783 original size:17 final size:16
Alignment explanation
Indices: 510759--510798 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
510749 CATAACAAAT
510759 ATAAATATTAAAAAAA
1 ATAAATATTAAAAAAA
* *
510775 ATCAAATATTATAAATA
1 AT-AAATATTAAAAAAA
510792 ATAAATA
1 ATAAATA
510799 CCCATTAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAAATATTAAAAAAA
Found at i:511941 original size:2 final size:2
Alignment explanation
Indices: 511934--511963 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
511924 GTGTTAAGAC
511934 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
511964 TGATAGTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:512708 original size:2 final size:2
Alignment explanation
Indices: 512701--512735 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
512691 TGGAGAATAC
*
512701 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
512736 AAAAGGAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:513141 original size:30 final size:28
Alignment explanation
Indices: 513115--513189 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 28
513105 GGTAAAAATT
513115 TATTTATAA-TTTTATATTATAATAAAAA
1 TATTT-TAATTTTTATATTATAATAAAAA
513143 TATTTTAATTTTTATATTAT--TAAATTTAA
1 TATTTTAATTTTTATATTATAATAAA---AA
*
513172 TATTTTAATTTATATATT
1 TATTTTAATTTTTATATT
513190 TTTAAAATTA
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
26 4 0.10
27 3 0.07
28 16 0.38
29 19 0.45
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
TATTTTAATTTTTATATTATAATAAAAA
Found at i:513159 original size:14 final size:14
Alignment explanation
Indices: 513142--513191 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
513132 TATAATAAAA
513142 ATATTTTAATTTTT
1 ATATTTTAATTTTT
* *
513156 ATATTATTAAATTTA
1 ATATT-TTAATTTTT
*
513171 ATATTTTAATTTAT
1 ATATTTTAATTTTT
513185 ATATTTT
1 ATATTTT
513192 TAAAATTATA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATATTTTAATTTTT
Found at i:513174 original size:29 final size:31
Alignment explanation
Indices: 513141--513204 Score: 96
Period size: 29 Copynumber: 2.1 Consensus size: 31
513131 TTATAATAAA
*
513141 AATATTTTAATTTTTATATTATT-AAATT-T
1 AATATTTTAATTTATATATTATTAAAATTAT
*
513170 AATATTTTAATTTATATATTTTTAAAATTAT
1 AATATTTTAATTTATATATTATTAAAATTAT
513201 AATA
1 AATA
513205 AATAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 21 0.68
30 5 0.16
31 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (31 bp):
AATATTTTAATTTATATATTATTAAAATTAT
Found at i:513221 original size:21 final size:20
Alignment explanation
Indices: 513197--513243 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
513187 ATTTTTAAAA
513197 TTATAATAAATAAAAAATAAT
1 TTATAATAAATAAAAAAT-AT
*
513218 TTATAAT-ATTAAAAAATAT
1 TTATAATAAATAAAAAATAT
513237 TTA-AATA
1 TTATAATA
513244 TCAATAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 3 0.12
19 5 0.21
20 9 0.38
21 7 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TTATAATAAATAAAAAATAT
Found at i:513238 original size:19 final size:19
Alignment explanation
Indices: 513197--513256 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
513187 ATTTTTAAAA
*
513197 TTATAATAAATAAAAAATAAT
1 TTATAAT-ATTAAAAAAT-AT
513218 TTATAATATTAAAAAATAT
1 TTATAATATTAAAAAATAT
*
513237 TTA-AATATCAATAAAATAT
1 TTATAATATTAA-AAAATAT
513256 T
1 T
513257 GATATTTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.19
19 13 0.36
20 9 0.25
21 7 0.19
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
TTATAATATTAAAAAATAT
Found at i:513688 original size:14 final size:13
Alignment explanation
Indices: 513647--513688 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
513637 AGTATACGTA
513647 AAATAAAAAAT-T
1 AAATAAAAAATAT
*
513659 TAA-AAAAAATAT
1 AAATAAAAAATAT
513671 AAATAAAAAATAT
1 AAATAAAAAATAT
513684 CAAAT
1 -AAAT
513689 TTATTATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 7 0.28
12 5 0.20
13 9 0.36
14 4 0.16
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAAAAAATAT
Found at i:515137 original size:23 final size:22
Alignment explanation
Indices: 515110--515161 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
515100 TGTTAACCTA
*
515110 ATAAAAAAT-TATTTTATTTAAT
1 ATAAAAAATATATATTA-TTAAT
*
515132 -TATAAATATATATATTATTAAT
1 ATA-AAAAATATATATTATTAAT
515154 ATAAAAAA
1 ATAAAAAA
515162 AATAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
21 2 0.08
22 14 0.58
23 8 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATAAAAAATATATATTATTAAT
Done.