Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold105
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: 2918491
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 41655 characters in sequence are not A, C, G, or T
File 15 of 16
Found at i:2524774 original size:19 final size:19
Alignment explanation
Indices: 2524750--2524794 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2524740 TTAATAAAAA
* *
2524750 ATATTTTTAATATTTTAAT
1 ATATTTTTAATAGTATAAT
*
2524769 ATATTTTAAATAGTATAAT
1 ATATTTTTAATAGTATAAT
2524788 A-ATTTTT
1 ATATTTTT
2524795 TTATTTAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
ATATTTTTAATAGTATAAT
Found at i:2524809 original size:26 final size:25
Alignment explanation
Indices: 2524773--2524830 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
2524763 TTTAATATAT
2524773 TTTAAATAGTATAATAATT-TTTTT-A
1 TTTAAATAGTA-AA-AATTCTTTTTCA
*
2524798 TTTAAATAAGTAAAATTTCTTTTTCA
1 TTTAAAT-AGTAAAAATTCTTTTTCA
2524824 TTTAAAT
1 TTTAAAT
2524831 TCTGACGTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 3 0.10
25 14 0.48
26 12 0.41
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (25 bp):
TTTAAATAGTAAAAATTCTTTTTCA
Found at i:2525318 original size:22 final size:21
Alignment explanation
Indices: 2525288--2525355 Score: 65
Period size: 20 Copynumber: 3.4 Consensus size: 21
2525278 ATAATTTTAA
*
2525288 ATAACATAAAAATAATTAAAAT
1 ATAATATAAAAAT-ATTAAAAT
2525310 ATAATAT-AAAATA--AAAA-
1 ATAATATAAAAATATTAAAAT
*
2525327 ATAATATAAATATATTAAAAT
1 ATAATATAAAAATATTAAAAT
*
2525348 -TTATATAA
1 ATAATATAA
2525356 TTCAAATTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
17 7 0.18
18 9 0.23
20 12 0.31
21 5 0.13
22 6 0.15
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (21 bp):
ATAATATAAAAATATTAAAAT
Found at i:2525324 original size:17 final size:17
Alignment explanation
Indices: 2525304--2525336 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2525294 TAAAAATAAT
*
2525304 TAAAATATAATATAAAA
1 TAAAAAATAATATAAAA
2525321 TAAAAAATAATATAAA
1 TAAAAAATAATATAAA
2525337 TATATTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAAAAATAATATAAAA
Found at i:2525337 original size:28 final size:26
Alignment explanation
Indices: 2525295--2525347 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 26
2525285 TAAATAACAT
2525295 AAAAATAATTAAAATATAATATAAAATA
1 AAAAATAATTAAAATAT-AT-TAAAATA
2525323 AAAAATAA-TATAAATATATTAAAAT
1 AAAAATAATTA-AAATATATTAAAAT
2525348 TTATATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 6 0.25
27 4 0.17
28 14 0.58
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (26 bp):
AAAAATAATTAAAATATATTAAAATA
Found at i:2525986 original size:24 final size:23
Alignment explanation
Indices: 2525951--2526001 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
2525941 TATATTTGAT
2525951 AATAAAA-ATTTTTAATTAATTTA
1 AATAAAATATTTTTAATTAA-TTA
* *
2525974 AATATAAATTTTTTTTATTAATTA
1 AATA-AAATATTTTTAATTAATTA
2525998 AATA
1 AATA
2526002 CTAATCAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.17
24 10 0.42
25 10 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AATAAAATATTTTTAATTAATTA
Found at i:2526284 original size:2 final size:2
Alignment explanation
Indices: 2526277--2526313 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2526267 CCCACTCACA
2526277 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2526314 TAATATAATT
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):
AT
Found at i:2526317 original size:6 final size:7
Alignment explanation
Indices: 2526276--2526320 Score: 53
Period size: 6 Copynumber: 6.9 Consensus size: 7
2526266 CCCCACTCAC
2526276 AATATAT
1 AATATAT
2526283 -ATATAT
1 AATATAT
2526289 -ATATAT
1 AATATAT
2526295 -ATATAT
1 AATATAT
2526301 ATATATAT
1 A-ATATAT
2526309 AATAT-T
1 AATATAT
2526315 AATATA
1 AATATA
2526321 ATTTTATCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 24 0.69
7 4 0.11
8 7 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
AATATAT
Found at i:2526551 original size:16 final size:16
Alignment explanation
Indices: 2526531--2526572 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
2526521 TAGCATGACT
2526531 AATTATTAAAAAA-AA
1 AATTATTAAAAAAGAA
2526546 ACATTATTAAAAAAGAA
1 A-ATTATTAAAAAAGAA
*
2526563 AAATATTAAA
1 AATTATTAAA
2526573 TGATTGCTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 1 0.04
16 20 0.83
17 3 0.12
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (16 bp):
AATTATTAAAAAAGAA
Found at i:2526717 original size:13 final size:12
Alignment explanation
Indices: 2526699--2526740 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
2526689 GTTAATCGAA
2526699 ATTTAAAAATATT
1 ATTTAAAAAT-TT
2526712 ATTT-AAAATTT
1 ATTTAAAAATTT
*
2526723 ATTTAATATATTT
1 ATTTAA-AAATTT
2526736 ATTTA
1 ATTTA
2526741 TTATTAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 6 0.23
12 6 0.23
13 14 0.54
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTTAAAAATTT
Found at i:2527464 original size:13 final size:12
Alignment explanation
Indices: 2527446--2527475 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
2527436 TTTTTTAAAA
2527446 AATATTTATATTT
1 AATATTTATA-TT
2527459 AATATTTATATT
1 AATATTTATATT
2527471 AATAT
1 AATAT
2527476 ATAATTAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
AATATTTATATT
Found at i:2527954 original size:36 final size:33
Alignment explanation
Indices: 2527907--2528018 Score: 115
Period size: 32 Copynumber: 3.4 Consensus size: 33
2527897 TATATATATA
*
2527907 TATATAATATAAAATGTGATATAATATTTTAAAATT
1 TATATAATATAAAAT-T-AT-TAATATATTAAAATT
2527943 TATATAATAT-AAATTATTAATATATTAAAATT
1 TATATAATATAAAATTATTAATATATTAAAATT
* *
2527975 TATATAA-ATAAAAATATTTAAAATA-TAATAA-T
1 TATATAATATAAAATTA-TTAATATATTAA-AATT
*
2528007 AATATAATATAA
1 TATATAATATAA
2528019 TTATATGAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
31 2 0.03
32 36 0.53
33 15 0.22
34 1 0.01
35 4 0.06
36 10 0.15
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (33 bp):
TATATAATATAAAATTATTAATATATTAAAATT
Found at i:2527986 original size:15 final size:15
Alignment explanation
Indices: 2527936--2527987 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
2527926 TATAATATTT
2527936 TAAAATTTATATAATA
1 TAAAATTTATATAA-A
* *
2527952 TAAATTATTA-ATATAT
1 TAAAAT-TTATATA-AA
2527968 TAAAATTTATATAAA
1 TAAAATTTATATAAA
2527983 TAAAA
1 TAAAA
2527988 ATATTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
15 9 0.31
16 16 0.55
17 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAAATTTATATAAA
Found at i:2528659 original size:17 final size:17
Alignment explanation
Indices: 2528639--2528686 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
2528629 ATATTTAATC
*
2528639 TAAAAAATAAATTTAGG
1 TAAAAAATAAATTAAGG
* **
2528656 TAAAAAATTAGATTAATT
1 TAAAAAA-TAAATTAAGG
2528674 TAAAAAATAAATT
1 TAAAAAATAAATT
2528687 GAACCTTAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.33
Consensus pattern (17 bp):
TAAAAAATAAATTAAGG
Found at i:2529307 original size:20 final size:19
Alignment explanation
Indices: 2529288--2529332 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
2529278 TACATCAATA
2529288 AAAATAACAA-TAAACAAAT
1 AAAATAACAACTAAA-AAAT
*
2529307 AAACTAACAACTAAAAAATT
1 AAAATAACAACTAAAAAA-T
2529327 AAAATA
1 AAAATA
2529333 TAATACGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.71, C:0.11, G:0.00, T:0.18
Consensus pattern (19 bp):
AAAATAACAACTAAAAAAT
Found at i:2529546 original size:16 final size:17
Alignment explanation
Indices: 2529497--2529549 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
2529487 AAAAGTGTTA
*
2529497 TATAAATTTTAACATAT
1 TATAAATTTTAATATAT
*
2529514 TATTAATTTGT-AT-TAT
1 TATAAATTT-TAATATAT
2529530 T-TAAATTTTAATATAT
1 TATAAATTTTAATATAT
2529546 TATA
1 TATA
2529550 TATTCATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
14 1 0.03
15 8 0.28
16 8 0.28
17 11 0.38
18 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
TATAAATTTTAATATAT
Found at i:2532350 original size:2 final size:2
Alignment explanation
Indices: 2532311--2532339 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2532301 CCAAAAATCT
2532311 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
2532340 CATGAATATA
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:2538587 original size:21 final size:21
Alignment explanation
Indices: 2538544--2538596 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2538534 AACTATTATA
* * *
2538544 ATTATATAAATTATTTTATTT
1 ATTATATAAATAATTATAATT
*
2538565 ATTACATAAATAATTATAATT
1 ATTATATAAATAATTATAATT
*
2538586 ATAATATAAAT
1 ATTATATAAAT
2538597 CAATCTATCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTATATAAATAATTATAATT
Found at i:2539083 original size:228 final size:230
Alignment explanation
Indices: 2538643--2539111 Score: 583
Period size: 228 Copynumber: 2.0 Consensus size: 230
2538633 CTTTTTTTAT
* * ** *
2538643 TTACATAAATTATGATAAAATATAATAAAAATTATAATTCATAAATTTATTATATTTATATAAAA
1 TTACATAAATAATGATAAAAGATAATAAAAATTATAAAACATAAATTTATTATATTTACATAAAA
* * * *
2538708 TTTTTGTAAATTACAAAAATATATTACCACTAAATAATAGAAAGTAGTATTACATAAAAATATTA
66 ATTTTATAAATTACAAAAATATATTACCAC-AAATAATAGAAAGTAATATTACATAAAAATATAA
* * *
2538773 TAGTTACATGAATTATATTATCTAATTATATAAGTTTACATTATAGATAATAGAAATAAGTATTA
130 AAGTTACATAAATTATATTATCTAATTATATAAGTTTACATTATAGATAATAAAAATAAGTATTA
** *
2538838 CACATTTTTCTTATAATTATACGTATATATTATATA
195 CACATTTTAATTATAATTATACATATATATTATATA
*
2538874 TTACATAAATAATGATAAAAGATAAT-AAAATTGTAAAACATAAATTTATTATATTTACATAAAA
1 TTACATAAATAATGATAAAAGATAATAAAAATTATAAAACATAAATTTATTATATTTACATAAAA
* * * ** *
2538938 ATTTTATAAGTTATATAAATATATTAGTA-AAAGTAATA-AGAAGTAATATTACAT-AAACTATA
66 ATTTTATAAATTACAAAAATATATTACCACAAA-TAATAGA-AAGTAATATTACATAAAAATATA
* * * *
2539000 AAAGTTACATAAATTATATTAT-TTATTATATAA-TTT-TATTATCGTACGTAATAAAAATATGT
129 AAAGTTACATAAATTATATTATCTAATTATATAAGTTTACATTATAG-A--TAATAAAAATAAGT
* *
2539062 ATTACACGTTTTAATTATAATTATTCATATATATTATATA
191 ATTACACATTTTAATTATAATTATACATATATATTATATA
2539102 TTACATAAAT
1 TTACATAAAT
2539112 CATTATGGTA
Statistics
Matches: 205, Mismatches: 28, Indels: 13
0.83 0.11 0.05
Matches are distributed among these distances:
225 6 0.03
226 4 0.02
227 10 0.05
228 87 0.42
229 18 0.09
230 56 0.27
231 24 0.12
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (230 bp):
TTACATAAATAATGATAAAAGATAATAAAAATTATAAAACATAAATTTATTATATTTACATAAAA
ATTTTATAAATTACAAAAATATATTACCACAAATAATAGAAAGTAATATTACATAAAAATATAAA
AGTTACATAAATTATATTATCTAATTATATAAGTTTACATTATAGATAATAAAAATAAGTATTAC
ACATTTTAATTATAATTATACATATATATTATATA
Found at i:2539997 original size:390 final size:394
Alignment explanation
Indices: 2539207--2540000 Score: 871
Period size: 387 Copynumber: 2.0 Consensus size: 394
2539197 CATTATAAAG
* * * * * * *
2539207 TTATAT-AAAATATTACCTGAAAATTTAATTTATTTGTGTAGAATATTTTTTCAAAAAAATTAAA
1 TTATATAAAAACATTACCTGAAAATGTAATGTATTTATGTAAAACATTTTATCAAAAAAATTAAA
* * *
2539271 TATATTTTTTACAAAATAATTTTTGAATTTTTATTGAATATATAATATATGTTGGAAATTAATTT
66 TATAATTTTTACAAAATAATTTTTGAATTTTTATTAAATATATAATATATGTAGGAAATTAA-TT
* * **** *
2539336 TTTTAGTAATTTTTGAAGTAAATTTTTTTATATATTTTTATTATATCAATATATTTTTAATATTA
130 TTTTAATAATTATTGAAGTAAAAAAATTTATATATTTTTATTATATCAATATATTTTTAAGATTA
* *** **
2539401 GTAATAAATATATTATATTAATAAAAATAAAAATTTTATTTTTTATTAGTTAAAAAATTGTTACT
195 GTAATAAATATATTATACTAATAAAAATAAAAATTTTA-TCAATATTAGTTAAAAAATTACTACT
* * * *
2539466 AAAGATTATCAAAATTACATAAATATATTATAATTTACATAAATCATTAAAATATAGGTAATATT
259 AAAGATTACCAAAATTACATAAATATATCACAATTTACATAAATCATTAAAATATAGATAATATT
* * * * * *
2539531 TATAAATAATATGTGTTATTAATAATATATTTGAGAAAAGAATCTTGAAGGTAATGTTTCTGTGT
324 TATAAATAATATGTGTTATGAACAATATATTTGAGAAAAAAATCTTGAAGATAATATTTCTATGT
*
2539596 AATAAA
389 AACAAA
* *
2539602 TTATATAAAAACATTA-CTGAAACTGTAATGTA-TTATGTAAAACATTTTATC-AAAAATTTAAA
1 TTATATAAAAACATTACCTGAAAATGTAATGTATTTATGTAAAACATTTTATCAAAAAAATTAAA
* * *
2539664 TATAATTTTTATAAAATAATTTTT-TATTTTTATTAAATATATTATATATGTAGGAAATTTAA-T
66 TATAATTTTTACAAAATAATTTTTGAATTTTTATTAAATATATAATATATGTAGGAAA-TTAATT
* *
2539727 TTTTAATAATTATTGAAGTAAAAAAATTT-TA-ATTTTTATTTTATTAATATATATTTTAAGATT
130 TTTTAATAATTATTGAAGTAAAAAAATTTATATATTTTTATTATATCAATATAT-TTTTAAGATT
* ** *
2539790 AGTACTAAATATATTATACTAATAAAAA-ATTAATTTTA-CAATATT-GTTAAAAAAATTACTAT
194 AGTAATAAATATATTATACTAATAAAAATAAAAATTTTATCAATATTAGTT-AAAAAATTACTAC
* * * * * * * *
2539852 TAAATATTACCAAAATTATATATAA-GTATCACAATTTATATAAATCATTAGAGTGTATATAATA
258 TAAAGATTACCAAAATTACATA-AATATATCACAATTTACATAAATCATTAAAATATAGATAAT-
* * *
2539916 ATTT-TAGATAATATGTTTTATGGACAATGCAT-TTATGTA-AAAAAAATCTTTGAAGATAATAT
321 ATTTATAAATAATATGTGTTATGAACAAT--ATATT-TG-AGAAAAAAATC-TTGAAGATAATAT
2539978 TTCTATGTAACAAA
381 TTCTATGTAACAAA
2539992 TTATATAAA
1 TTATATAAA
2540001 TTATTATCGA
Statistics
Matches: 332, Mismatches: 56, Indels: 27
0.80 0.13 0.07
Matches are distributed among these distances:
386 3 0.01
387 81 0.24
388 8 0.02
389 39 0.12
390 70 0.21
391 24 0.07
392 29 0.09
393 36 0.11
394 15 0.05
395 19 0.06
396 8 0.02
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (394 bp):
TTATATAAAAACATTACCTGAAAATGTAATGTATTTATGTAAAACATTTTATCAAAAAAATTAAA
TATAATTTTTACAAAATAATTTTTGAATTTTTATTAAATATATAATATATGTAGGAAATTAATTT
TTTAATAATTATTGAAGTAAAAAAATTTATATATTTTTATTATATCAATATATTTTTAAGATTAG
TAATAAATATATTATACTAATAAAAATAAAAATTTTATCAATATTAGTTAAAAAATTACTACTAA
AGATTACCAAAATTACATAAATATATCACAATTTACATAAATCATTAAAATATAGATAATATTTA
TAAATAATATGTGTTATGAACAATATATTTGAGAAAAAAATCTTGAAGATAATATTTCTATGTAA
CAAA
Found at i:2540517 original size:26 final size:26
Alignment explanation
Indices: 2540488--2540540 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
2540478 ATAATAATAA
* *
2540488 TTAATAATACTAAATTTTAAAATATT
1 TTAATAAAAATAAATTTTAAAATATT
* *
2540514 TTAATAAAAATTAGTTTTAAAATATT
1 TTAATAAAAATAAATTTTAAAATATT
2540540 T
1 T
2540541 AAAATATACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (26 bp):
TTAATAAAAATAAATTTTAAAATATT
Found at i:2540817 original size:32 final size:31
Alignment explanation
Indices: 2540777--2540854 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 31
2540767 AATAATTAAA
2540777 ATATAATTTAATATAAACATATT-TTAAAATTT
1 ATATAATTTAA-ATAAACA-ATTATTAAAATTT
* **
2540809 ATATAATTTAAATTATTAATTATTAAAATTT
1 ATATAATTTAAATAAACAATTATTAAAATTT
*
2540840 ATATAAATATAAATA
1 ATAT-AATTTAAATA
2540855 TAATTATAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
30 3 0.08
31 17 0.44
32 19 0.49
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (31 bp):
ATATAATTTAAATAAACAATTATTAAAATTT
Found at i:2540818 original size:16 final size:17
Alignment explanation
Indices: 2540797--2540845 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 17
2540787 ATATAAACAT
2540797 ATTTTAAAATTTATATA
1 ATTTTAAAATTTATATA
2540814 A-TTT-AAA-TTAT-TA
1 ATTTTAAAATTTATATA
2540827 ATTATTAAAATTTATATA
1 ATT-TTAAAATTTATATA
2540845 A
1 A
2540846 ATATAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
13 3 0.11
14 5 0.19
15 5 0.19
16 6 0.22
17 5 0.19
18 3 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTTAAAATTTATATA
Found at i:2540838 original size:31 final size:30
Alignment explanation
Indices: 2540752--2540861 Score: 104
Period size: 30 Copynumber: 3.7 Consensus size: 30
2540742 AATTACACAA
* * *
2540752 ATAT-AATATAAATAAAATAATTAAAATAT
1 ATATAAATATAAATATAATTATTAAAATTT
* *
2540781 A-ATTTAATATAAACAT-ATT-TTAAAATTT
1 ATA-TAAATATAAATATAATTATTAAAATTT
*
2540809 ATAT-AATTTAAATTATTAATTATTAAAATTT
1 ATATAAATATAAA-TA-TAATTATTAAAATTT
2540840 ATATAAATATAAATATAATTAT
1 ATATAAATATAAATATAATTAT
2540862 AATATTATAA
Statistics
Matches: 66, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
27 7 0.11
28 12 0.18
29 6 0.09
30 19 0.29
31 15 0.23
32 7 0.11
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (30 bp):
ATATAAATATAAATATAATTATTAAAATTT
Found at i:2540873 original size:37 final size:32
Alignment explanation
Indices: 2540799--2540873 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 32
2540789 ATAAACATAT
* *
2540799 TTTAAAATTTATATAATTTAAATTATTAATTA
1 TTTAAAATTTATATAATATAAATTATTAAATA
2540831 -TTAAAATTTATATAAATATAAATATAATTATAATA
1 TTTAAAATTTATAT-AATATAAAT-T-ATTA-AATA
2540866 TTATAAAA
1 TT-TAAAA
2540874 AAATACAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
31 13 0.37
32 8 0.23
33 1 0.03
34 4 0.11
35 3 0.09
36 1 0.03
37 5 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (32 bp):
TTTAAAATTTATATAATATAAATTATTAAATA
Found at i:2541351 original size:13 final size:13
Alignment explanation
Indices: 2541333--2541358 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2541323 AAAATATAAC
2541333 TTTTTTAAAAATA
1 TTTTTTAAAAATA
2541346 TTTTTTAAAAATA
1 TTTTTTAAAAATA
2541359 AATTAAGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTTTTAAAAATA
Found at i:2542228 original size:22 final size:22
Alignment explanation
Indices: 2542207--2542276 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
2542197 AAAAAGTTTA
2542207 AATTTAAATTTAATTATATTTAAT
1 AATTT-AATTT-ATTATATTTAAT
*
2542231 AATTTAATTTATTATTTATTAA-
1 AATTTAATTTATTATAT-TTAAT
*
2542253 AAATTAA-TT-TTATA-TTAAT
1 AATTTAATTTATTATATTTAAT
2542272 -ATTTA
1 AATTTA
2542277 TATATTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
18 8 0.20
20 4 0.10
21 2 0.05
22 12 0.30
23 9 0.22
24 5 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AATTTAATTTATTATATTTAAT
Found at i:2542252 original size:23 final size:22
Alignment explanation
Indices: 2542206--2542276 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 22
2542196 AAAAAAGTTT
2542206 AAATTTAAATTTAATTATATTTA
1 AAATTT-AATTTAATTATATTTA
*
2542229 ATAATTTAATTT-ATTATTTATTA
1 A-AATTTAATTTAATTATAT-TTA
*
2542252 AAAATTAATTTTATATTAATATTTA
1 AAATTTAA-TTTA-ATT-ATATTTA
2542277 TATATTTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
22 12 0.31
23 13 0.33
24 5 0.13
25 6 0.15
26 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
AAATTTAATTTAATTATATTTA
Found at i:2545722 original size:2 final size:2
Alignment explanation
Indices: 2545715--2545752 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2545705 GATGATGATG
2545715 AT AT AT 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 AT AT AT
2545753 TACCAAGCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2546232 original size:15 final size:15
Alignment explanation
Indices: 2546212--2546242 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2546202 ATCAGAGTTG
2546212 ATCAAAAATCAAGAA
1 ATCAAAAATCAAGAA
2546227 ATCAAAAATCAAGAA
1 ATCAAAAATCAAGAA
2546242 A
1 A
2546243 ATGCTTACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.13, G:0.06, T:0.13
Consensus pattern (15 bp):
ATCAAAAATCAAGAA
Found at i:2546438 original size:2 final size:2
Alignment explanation
Indices: 2546431--2546472 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2546421 TCTGTGGAAA
2546431 AT AT AT AT AT 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 AT AT AT AT AT
2546473 CATCAACTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2549121 original size:2 final size:2
Alignment explanation
Indices: 2549114--2549149 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2549104 ACGGATCCTC
2549114 AT AT 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 AT AT
2549150 TTGGATTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2555027 original size:101 final size:101
Alignment explanation
Indices: 2554852--2555150 Score: 580
Period size: 101 Copynumber: 3.0 Consensus size: 101
2554842 TGGAAGCATT
* *
2554852 GTAAAATTCTATCATCCCATTTTATCAAGTACTAATTTTTTAAGGCCTTACCTGCGGCATATCTA
1 GTAAAATTCTATCATCCCATTTTATCTAGTATTAATTTTTTAAGGCCTTACCTGCGGCATATCTA
2554917 CAGCATATTTGATTTCATTAAAGCTCATAGAAGGAA
66 CAGCATATTTGATTTCATTAAAGCTCATAGAAGGAA
2554953 GTAAAATTCTATCATCCCATTTTATCTAGTATTAATTTTTTAAGGCCTTACCTGCGGCATATCTA
1 GTAAAATTCTATCATCCCATTTTATCTAGTATTAATTTTTTAAGGCCTTACCTGCGGCATATCTA
2555018 CAGCATATTTGATTTCATTAAAGCTCATAGAAGGAA
66 CAGCATATTTGATTTCATTAAAGCTCATAGAAGGAA
2555054 GTAAAATTCTATCATCCCATTTTATCTAGTATTAATTTTTTAAGGCCTTACCTGCGGCATATCTA
1 GTAAAATTCTATCATCCCATTTTATCTAGTATTAATTTTTTAAGGCCTTACCTGCGGCATATCTA
2555119 CAGCATATTTGATTTCATTAAAGCTCATAGAA
66 CAGCATATTTGATTTCATTAAAGCTCATAGAA
2555151 AGGGGTTCAA
Statistics
Matches: 196, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 196 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.37
Consensus pattern (101 bp):
GTAAAATTCTATCATCCCATTTTATCTAGTATTAATTTTTTAAGGCCTTACCTGCGGCATATCTA
CAGCATATTTGATTTCATTAAAGCTCATAGAAGGAA
Found at i:2559356 original size:2 final size:2
Alignment explanation
Indices: 2559349--2559384 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2559339 TCTATATGTC
2559349 TA TA TA 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 T
2559385 TGGAGTCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2559858 original size:7 final size:7
Alignment explanation
Indices: 2559848--2559874 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2559838 GTTTTTTTTT
2559848 TTTTGCA
1 TTTTGCA
2559855 TTTTGCA
1 TTTTGCA
2559862 TTTTGCA
1 TTTTGCA
2559869 TTTTGC
1 TTTTGC
2559875 TGGTGTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.15, G:0.15, T:0.59
Consensus pattern (7 bp):
TTTTGCA
Found at i:2560534 original size:15 final size:17
Alignment explanation
Indices: 2560492--2560534 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
2560482 TAAATTAGGT
*
2560492 TTATATTCATATTTTTTA
1 TTATATT-ATATTTATTA
2560510 TTATATTATATTTATT-
1 TTATATTATATTTATTA
2560526 TTA-ATTATA
1 TTATATTATA
2560535 AATATAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 6 0.25
16 3 0.12
17 8 0.33
18 7 0.29
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATATTATATTTATTA
Found at i:2561408 original size:28 final size:29
Alignment explanation
Indices: 2561347--2561426 Score: 85
Period size: 28 Copynumber: 2.8 Consensus size: 29
2561337 TTAATTTTAA
*
2561347 ATTTAATAATTTTTATATTTATATCATAT
1 ATTTAATAATTTTTATATTTATAACATAT
* *
2561376 TTTTAAT-ATTTTTATGTATTATAAC-TAT
1 ATTTAATAATTTTTATAT-TTATAACATAT
*
2561404 ATTTAA-AATATTATATATTTATA
1 ATTTAATAAT-TTTTATATTTATA
2561427 TAAATTTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
28 24 0.57
29 18 0.43
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (29 bp):
ATTTAATAATTTTTATATTTATAACATAT
Found at i:2561523 original size:17 final size:18
Alignment explanation
Indices: 2561501--2561535 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2561491 ATTTATATAT
*
2561501 TATTTTTTATT-TTTTTA
1 TATTTTATATTATTTTTA
2561518 TATTTTATATTATTTTTA
1 TATTTTATATTATTTTTA
2561536 GGTAGTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (18 bp):
TATTTTATATTATTTTTA
Found at i:2565093 original size:2 final size:2
Alignment explanation
Indices: 2565086--2565126 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2565076 ATATGCTTAG
2565086 TA TA TA TA TA 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 TA TA TA TA TA T
2565127 TACATTTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2565703 original size:32 final size:28
Alignment explanation
Indices: 2565638--2565700 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 28
2565628 ATTTATTAGT
* *
2565638 AAAATTTTATTTTTATTTATAATTTTAA
1 AAAATTATATTTTTATTCATAATTTTAA
2565666 AAAATTATATTTATTATTCATAAATTTTCAA
1 AAAATTATATTT-TTATTCAT-AATTTT-AA
2565697 AAAA
1 AAAA
2565701 ATTTATCATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 11 0.37
29 7 0.23
30 6 0.20
31 6 0.20
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (28 bp):
AAAATTATATTTTTATTCATAATTTTAA
Found at i:2577289 original size:2 final size:2
Alignment explanation
Indices: 2577277--2577309 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2577267 GCCCTTTGTT
*
2577277 TA TA T- TA TA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2577310 ATTATAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2583103 original size:21 final size:20
Alignment explanation
Indices: 2583073--2583146 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 20
2583063 TAATAAAAAT
2583073 TTATTTTTTAAAATGAA-TCAA
1 TTATTTTTTAAAA--AAGTCAA
*
2583094 TTATTCTTTAAAAAAGGTCAA
1 TTATTTTTTAAAAAA-GTCAA
2583115 TTATTTTTTAAAAAA-T-AA
1 TTATTTTTTAAAAAAGTCAA
2583133 TTAATCTTTTTAAA
1 TT-AT-TTTTTAAA
2583147 TATAAATTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
18 4 0.09
19 5 0.11
20 8 0.17
21 30 0.64
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.47
Consensus pattern (20 bp):
TTATTTTTTAAAAAAGTCAA
Found at i:2592805 original size:2 final size:2
Alignment explanation
Indices: 2592798--2592827 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2592788 AACATACATG
2592798 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
2592828 AATCTCTCTC
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:2593135 original size:25 final size:25
Alignment explanation
Indices: 2593080--2593145 Score: 82
Period size: 24 Copynumber: 2.7 Consensus size: 25
2593070 TATAAATTTG
* *
2593080 ATAATTTATATATTTTATTTTATTT
1 ATAATTTATATAATTTATTTTATTA
*
2593105 GT-ATTTATATAAATTTA-TTTATTA
1 ATAATTTATAT-AATTTATTTTATTA
2593129 ATAATTTATATAATTTA
1 ATAATTTATATAATTTA
2593146 AATTTAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 21 0.60
25 14 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
ATAATTTATATAATTTATTTTATTA
Found at i:2593721 original size:22 final size:23
Alignment explanation
Indices: 2593641--2593723 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 23
2593631 TTTATGTTTT
* *
2593641 ATTATTTTTTAATTAAATATTTTA
1 ATTATTTTATAATTAAATA-TATA
* * *
2593665 ATTTTTTTATCAAATAAATATATGT
1 ATTATTTTAT-AATTAAATATAT-A
2593690 ATTATATTTAT-ATTAAATATATA
1 ATTAT-TTTATAATTAAATATATA
2593713 ATTATTTTATA
1 ATTATTTTATA
2593724 CTAATATCAT
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
22 5 0.11
23 5 0.11
24 20 0.43
25 12 0.26
26 5 0.11
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (23 bp):
ATTATTTTATAATTAAATATATA
Found at i:2593754 original size:31 final size:28
Alignment explanation
Indices: 2593676--2593755 Score: 74
Period size: 31 Copynumber: 2.8 Consensus size: 28
2593666 TTTTTTTATC
*
2593676 AAATAAATATATG-TATTATATTTATATT
1 AAATAAATAT-TGATATTATATATATATT
* *
2593704 AAATATATAATT-ATTTTATACTAATATCATT
1 AAATAAAT-ATTGATATTATA-T-ATAT-ATT
2593735 AAATAAATATTGATATTATAT
1 AAATAAATATTGATATTATAT
2593756 TTAATATTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
28 14 0.34
29 3 0.07
30 7 0.17
31 17 0.41
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (28 bp):
AAATAAATATTGATATTATATATATATT
Found at i:2593971 original size:14 final size:15
Alignment explanation
Indices: 2593952--2593991 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
2593942 AAATTATTTT
2593952 AAATATTTAAT-TAA
1 AAATATTTAATATAA
2593966 AAATATTATAATATAA
1 AAATATT-TAATATAA
2593982 AAATTATTTA
1 AAA-TATTTA
2593992 TGTATTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 7 0.30
15 4 0.17
16 8 0.35
17 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATATTTAATATAA
Found at i:2597113 original size:146 final size:146
Alignment explanation
Indices: 2596848--2597120 Score: 375
Period size: 146 Copynumber: 1.9 Consensus size: 146
2596838 GTTTAGTAGT
* * **** * *
2596848 AAGTTTATATGGGATTGTTACAATTTTTACCCGTTGAGAGGAATTTTATATGACTGAAAACATCT
1 AAGTTTATATAGGATTGTTACAATATTTACCAACCGAAAGGAATTTAATATGACTGAAAACATCT
* * *
2596913 AGTGTGATTTGCTAATGCTACTTGTCATATTTACATGTTATATTGCTTATCAATCATATTTTGCT
66 AGTGTGATTTGCTAATGCTACTTGTCACATTTACATGGTATATTGCTTACCAATCATATTTTGCT
2596978 AATACATTTTGTGAGG
131 AATACATTTTGTGAGG
* ** *
2596994 AAGTTTATATAGGATTGTTGCAATATTTACCAACCGAAAGGAATTTAATATGGTTGAAAACTTCT
1 AAGTTTATATAGGATTGTTACAATATTTACCAACCGAAAGGAATTTAATATGACTGAAAACATCT
* * * *
2597059 AGTTTGCTTTGCTAATGCTACTTGTCACATTTACGTGGTATATTGCTTACCAATCATTTTTT
66 AGTGTGATTTGCTAATGCTACTTGTCACATTTACATGGTATATTGCTTACCAATCATATTTT
2597121 TCTGGACACA
Statistics
Matches: 108, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
146 108 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (146 bp):
AAGTTTATATAGGATTGTTACAATATTTACCAACCGAAAGGAATTTAATATGACTGAAAACATCT
AGTGTGATTTGCTAATGCTACTTGTCACATTTACATGGTATATTGCTTACCAATCATATTTTGCT
AATACATTTTGTGAGG
Found at i:2599871 original size:32 final size:32
Alignment explanation
Indices: 2599810--2599880 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
2599800 TGATAGATAT
*
2599810 TTTTAAGATATATTTTAAAAAATAAAAATTTAC
1 TTTTAAGATATATTATAAAAAAT-AAAATTTAC
*
2599843 TTTTAA-ATATATATATAAATAAAT-AAATTTAT
1 TTTTAAGATATAT-TATAAA-AAATAAAATTTAC
2599875 TTTTAA
1 TTTTAA
2599881 TAAAATTACA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 19 0.56
33 11 0.32
34 4 0.12
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (32 bp):
TTTTAAGATATATTATAAAAAATAAAATTTAC
Found at i:2601087 original size:32 final size:33
Alignment explanation
Indices: 2601028--2601095 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 33
2601018 AATACAAGTT
2601028 TAATATAAATATACGAACGTGTCAAAAT-TCATA
1 TAATATAAATATACGAACGTGTCAAAATCT-ATA
** *
2601061 TAATATAAAT-TATTAACGTGTTAAAATCTATA
1 TAATATAAATATACGAACGTGTCAAAATCTATA
2601093 TAA
1 TAA
2601096 GTATGTAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 20 0.65
33 11 0.35
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (33 bp):
TAATATAAATATACGAACGTGTCAAAATCTATA
Found at i:2603796 original size:21 final size:21
Alignment explanation
Indices: 2603763--2603891 Score: 52
Period size: 21 Copynumber: 6.1 Consensus size: 21
2603753 TTTTTTATGA
*
2603763 TTTTGATAGTTTTTAATATAAT
1 TTTTGTTA-TTTTTAATATAAT
*
2603785 TTTTGTTA-TTTTAATA-ATT
1 TTTTGTTATTTTTAATATAAT
* * *
2603804 TTTTATATAATTTTGATA-AA-
1 TTTTGT-TATTTTTAATATAAT
* * *
2603824 TTTTGATATGATTTAA-AAAAT
1 TTTTGTTAT-TTTTAATATAAT
* *
2603845 TTTATGATGATCTTTAATATAAT
1 TTT-TG-TTATTTTTAATATAAT
* * * *
2603868 TTTTATAATCTTTGATATAAT
1 TTTTGTTATTTTTAATATAAT
2603889 TTT
1 TTT
2603892 ATTAAAATTT
Statistics
Matches: 82, Mismatches: 17, Indels: 17
0.71 0.15 0.15
Matches are distributed among these distances:
19 10 0.12
20 20 0.24
21 28 0.34
22 15 0.18
23 9 0.11
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTTGTTATTTTTAATATAAT
Found at i:2603796 original size:30 final size:30
Alignment explanation
Indices: 2603745--2603817 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 30
2603735 TTCAATATAA
* * *
2603745 TTTAATAT-TTTTTTATGATTTTGATAGTT
1 TTTAATATAATTTTTATGATTTTAATAATT
* *
2603774 TTTAATATAATTTTTGTTATTTTAATAATT
1 TTTAATATAATTTTTATGATTTTAATAATT
*
2603804 TTTTATATAATTTT
1 TTTAATATAATTTT
2603818 GATAAATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 8 0.22
30 29 0.78
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (30 bp):
TTTAATATAATTTTTATGATTTTAATAATT
Found at i:2603876 original size:9 final size:10
Alignment explanation
Indices: 2603773--2603912 Score: 65
Period size: 10 Copynumber: 13.4 Consensus size: 10
2603763 TTTTGATAGT
2603773 TTTTAATATAA
1 TTTT-ATATAA
* *
2603784 TTTT-TGTTA
1 TTTTATATAA
2603793 TTTTA-ATAA
1 TTTTATATAA
2603802 TTTTTTATATAA
1 --TTTTATATAA
2603814 TTTTGATA-AA
1 TTTT-ATATAA
*
2603824 TTTTGATATGA
1 TTTT-ATATAA
* *
2603835 -TTTAAAAAA
1 TTTTATATAA
*
2603844 TTTTATGATGA
1 TTTTAT-ATAA
2603855 TCTTTAATATAA
1 T-TTT-ATATAA
2603867 TTTT-TATAA
1 TTTTATATAA
2603876 TCTTTGATATAA
1 T-TTT-ATATAA
*
2603888 TTTTATTAAAA
1 TTTTA-TATAA
* *
2603899 TTTGATATGA
1 TTTTATATAA
2603909 TTTT
1 TTTT
2603913 GTCGTTTTGA
Statistics
Matches: 98, Mismatches: 17, Indels: 29
0.68 0.12 0.20
Matches are distributed among these distances:
9 18 0.18
10 31 0.32
11 30 0.31
12 17 0.17
13 2 0.02
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.56
Consensus pattern (10 bp):
TTTTATATAA
Found at i:2603902 original size:21 final size:21
Alignment explanation
Indices: 2603861--2603912 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2603851 ATGATCTTTA
**
2603861 ATATAATTTTTATAATCTTTG
1 ATATAATTTTTATAAAATTTG
2603882 ATATAA-TTTTATTAAAATTTG
1 ATATAATTTTTA-TAAAATTTG
*
2603903 ATATGATTTT
1 ATATAATTTT
2603913 GTCGTTTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 5 0.19
21 18 0.69
22 3 0.12
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (21 bp):
ATATAATTTTTATAAAATTTG
Found at i:2604033 original size:21 final size:20
Alignment explanation
Indices: 2604005--2604048 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
2603995 ATTATATACT
2604005 TTTAGTAAC-TTTGGATATAA
1 TTTAGTAACATTT-GATATAA
*
2604025 TTTACGTAACATTTTATATAA
1 TTTA-GTAACATTTGATATAA
2604046 TTT
1 TTT
2604049 TAAAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 14 0.67
22 3 0.14
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.50
Consensus pattern (20 bp):
TTTAGTAACATTTGATATAA
Found at i:2604077 original size:10 final size:11
Alignment explanation
Indices: 2604035--2604071 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
2604025 TTTACGTAAC
2604035 ATTTT-ATATA
1 ATTTTAATATA
*
2604045 ATTTTAA-AAA
1 ATTTTAATATA
2604055 ATTTTAATATA
1 ATTTTAATATA
2604066 ATTTTA
1 ATTTTA
2604072 CTTAATCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATTTTAATATA
Found at i:2604255 original size:21 final size:21
Alignment explanation
Indices: 2604207--2604266 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
2604197 TAGTTTTAGC
* *
2604207 AACATTTAATACAATTTTGAT
1 AACATTTTATATAATTTTGAT
2604228 AACA-TTTATAATAATTTTGAT
1 AACATTTTAT-ATAATTTTGAT
**
2604249 ATTATTTTATATAATTTT
1 AACATTTTATATAATTTT
2604267 ATACAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 4 0.12
21 24 0.73
22 5 0.15
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (21 bp):
AACATTTTATATAATTTTGAT
Found at i:2604650 original size:2 final size:2
Alignment explanation
Indices: 2604643--2604667 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2604633 TCTAGGTGAT
2604643 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 T
2604668 GAGACAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2605182 original size:3 final size:3
Alignment explanation
Indices: 2605174--2605219 Score: 74
Period size: 3 Copynumber: 15.0 Consensus size: 3
2605164 ATCGAACAAT
*
2605174 TAA TAA TAA TAA TAGT TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2605220 CGTATCATGT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 38 0.95
4 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2607221 original size:17 final size:17
Alignment explanation
Indices: 2607195--2607234 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
2607185 TAAGATATAA
*
2607195 ATATTGAATACAAATAT
1 ATATTTAATACAAATAT
*
2607212 ATATTTAATATAAATAT
1 ATATTTAATACAAATAT
2607229 ATATTT
1 ATATTT
2607235 TTTGAGGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (17 bp):
ATATTTAATACAAATAT
Found at i:2608902 original size:4 final size:4
Alignment explanation
Indices: 2608888--2608925 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
2608878 CGTCAAGAAC
*
2608888 CATA AATA CATA CATA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CA
2608926 ACTCATTCGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:2612228 original size:3 final size:3
Alignment explanation
Indices: 2612220--2612275 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
2612210 TTTAACTGGT
* *
2612220 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -ATA GAG GAT GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA-A GAA GAA GAA
*
2612265 GCA GAA GAA GA
1 GAA GAA GAA GA
2612276 TGAAATTGGG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
2 1 0.02
3 44 0.96
4 1 0.02
ACGTcount: A:0.61, C:0.02, G:0.34, T:0.04
Consensus pattern (3 bp):
GAA
Found at i:2618183 original size:2 final size:2
Alignment explanation
Indices: 2618176--2618200 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2618166 GTTTCTTTTA
2618176 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2618201 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2618205 original size:2 final size:2
Alignment explanation
Indices: 2618200--2618226 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2618190 ATATATATAT
2618200 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 A
2618227 TCTATGTATC
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2625827 original size:25 final size:25
Alignment explanation
Indices: 2625793--2625843 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2625783 TGAAACAAAG
2625793 ATAGTCTGCCCAAAAGAGACTGAAA
1 ATAGTCTGCCCAAAAGAGACTGAAA
2625818 ATAGTCTGCCCAAAAGAGACTGAAA
1 ATAGTCTGCCCAAAAGAGACTGAAA
2625843 A
1 A
2625844 AAAGTGCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.16
Consensus pattern (25 bp):
ATAGTCTGCCCAAAAGAGACTGAAA
Found at i:2628664 original size:2 final size:2
Alignment explanation
Indices: 2628657--2628687 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2628647 GGAAAGCAAG
*
2628657 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2628688 TGATGATACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2630205 original size:24 final size:21
Alignment explanation
Indices: 2630163--2630211 Score: 53
Period size: 24 Copynumber: 2.2 Consensus size: 21
2630153 TTTAAATAAT
* *
2630163 TTAATTTTTTTATTATTAAAC
1 TTAATTTTTTTATCATTAAAA
2630184 TTAATATTTTTTATACATTTAAAA
1 TTAAT-TTTTTTAT-CA-TTAAAA
2630208 TTAA
1 TTAA
2630212 AACAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 5 0.22
22 8 0.35
23 1 0.04
24 9 0.39
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAATTTTTTTATCATTAAAA
Found at i:2637252 original size:13 final size:14
Alignment explanation
Indices: 2637234--2637288 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 14
2637224 CTTAATTTTG
2637234 AAATAA-ATTATTA
1 AAATAATATTATTA
2637247 AAATAATATTATTTTA
1 AAATAATATTA--TTA
*
2637263 AAATTAT-TTATTA
1 AAATAATATTATTA
* *
2637276 AACTATTATTATT
1 AAATAATATTATT
2637289 TTACTTATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
13 13 0.38
14 9 0.26
15 3 0.09
16 9 0.26
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (14 bp):
AAATAATATTATTA
Found at i:2637261 original size:29 final size:29
Alignment explanation
Indices: 2637228--2637291 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
2637218 AGTAATCTTA
*
2637228 ATTTTGAAATAAATTATTAAAATAATATT
1 ATTTTAAAATAAATTATTAAAATAATATT
* * * *
2637257 ATTTTAAAATTATTTATTAAACTATTATT
1 ATTTTAAAATAAATTATTAAAATAATATT
2637286 ATTTTA
1 ATTTTA
2637292 CTTATGTGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (29 bp):
ATTTTAAAATAAATTATTAAAATAATATT
Found at i:2649275 original size:1 final size:1
Alignment explanation
Indices: 2649265--2649355 Score: 74
Period size: 1 Copynumber: 91.0 Consensus size: 1
2649255 TGGCAATTGG
* * * ** * * * **
2649265 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAAAAAAAAACAAAACAAAAAAAAGGAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
2649330 AAGAAAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
2649356 GTGAAGATTT
Statistics
Matches: 70, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:2649313 original size:33 final size:34
Alignment explanation
Indices: 2649264--2649355 Score: 161
Period size: 33 Copynumber: 2.7 Consensus size: 34
2649254 ATGGCAATTG
2649264 GAAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAA
1 GAAAAA-AAAAAAACAAAACAAAAAAAAGGAAAAA
2649299 G-AAAAAAAAAAACAAAACAAAAAAAAGGAAAAA
1 GAAAAAAAAAAAACAAAACAAAAAAAAGGAAAAA
2649332 GAAAAAAAAAAAACAAAA-AAAAAA
1 GAAAAAAAAAAAACAAAACAAAAAA
2649356 GTGAAGATTT
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
33 35 0.62
34 20 0.36
35 1 0.02
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (34 bp):
GAAAAAAAAAAAACAAAACAAAAAAAAGGAAAAA
Found at i:2649362 original size:29 final size:28
Alignment explanation
Indices: 2649268--2649362 Score: 84
Period size: 29 Copynumber: 3.1 Consensus size: 28
2649258 CAATTGGAAA
* *
2649268 AAGAAAAAAACAAAACAAAAAAAAGGAA-A
1 AAGAAAAAAAAAAAACAAAAAAAA--AAGG
*
2649297 AAGAAAAAAAAAAACAAAACAAAAAAAAGG
1 AAGAAAAAAAAAAA-ACAA-AAAAAAAAGG
2649327 AAAAAGAAAAAAAAAAAACAAAAAAAAAAGTG
1 ---AAGAAAAAAAAAAAACAAAAAAAAAAG-G
2649359 AAGA
1 AAGA
2649363 TTTGTTCCTT
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
29 19 0.35
30 3 0.05
31 15 0.27
32 4 0.07
33 14 0.25
ACGTcount: A:0.83, C:0.05, G:0.11, T:0.01
Consensus pattern (28 bp):
AAGAAAAAAAAAAAACAAAAAAAAAAGG
Found at i:2655598 original size:16 final size:17
Alignment explanation
Indices: 2655567--2655600 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2655557 TTATTATTCA
*
2655567 TAATTCAAATTTGTTGC
1 TAATTCAAATTCGTTGC
2655584 TAATTC-AATTCGTTGC
1 TAATTCAAATTCGTTGC
2655600 T
1 T
2655601 TACATTGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.26, C:0.15, G:0.12, T:0.47
Consensus pattern (17 bp):
TAATTCAAATTCGTTGC
Found at i:2659935 original size:2 final size:2
Alignment explanation
Indices: 2659928--2659959 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2659918 CCTCAAAAGC
2659928 TA 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
2659960 ATAGGGTTTG
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):
TA
Found at i:2661297 original size:2 final size:2
Alignment explanation
Indices: 2661292--2661317 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2661282 TGCTCTCTGA
2661292 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
2661318 TAAAAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2664992 original size:10 final size:10
Alignment explanation
Indices: 2664967--2665000 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
2664957 TTCCTGTAAG
2664967 TAAAATTAAA
1 TAAAATTAAA
2664977 -AAAATTAAA
1 TAAAATTAAA
2664986 TAAAATTAAA
1 TAAAATTAAA
2664996 TAAAA
1 TAAAA
2665001 CTCAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
TAAAATTAAA
Found at i:2667245 original size:12 final size:12
Alignment explanation
Indices: 2667228--2667258 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2667218 ACATGTAAAA
2667228 AAGGATTAACCC
1 AAGGATTAACCC
2667240 AAGGATTAACCC
1 AAGGATTAACCC
*
2667252 AAAGATT
1 AAGGATT
2667259 TGAGATTGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.19
Consensus pattern (12 bp):
AAGGATTAACCC
Found at i:2674277 original size:32 final size:33
Alignment explanation
Indices: 2674236--2674329 Score: 106
Period size: 32 Copynumber: 2.9 Consensus size: 33
2674226 TAATATAAAA
*
2674236 AATATATTAAATTTTATAT-AATATAA-ATTATT
1 AATATATTAAATTCTATATAAATATAATATT-TT
*
2674268 AATATATTAAAATCTATATAAATATAATATTTT
1 AATATATTAAATTCTATATAAATATAATATTTT
**
2674301 AA-ATA-TAAATAAATATATAAATATAATAT
1 AATATATTAAAT-TCTATATAAATATAATAT
2674330 AAATAAAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
31 4 0.07
32 36 0.67
33 11 0.20
34 3 0.06
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (33 bp):
AATATATTAAATTCTATATAAATATAATATTTT
Found at i:2674294 original size:6 final size:6
Alignment explanation
Indices: 2674283--2674334 Score: 54
Period size: 6 Copynumber: 8.5 Consensus size: 6
2674273 ATTAAAATCT
*
2674283 ATATAA ATATAA TATTTTAA ATATAA ATA-AA TATATAA ATAT-A ATATAA
1 ATATAA ATATAA -A-TATAA ATATAA ATATAA -ATATAA ATATAA ATATAA
2674332 ATA
1 ATA
2674335 AAAAAATTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
5 7 0.18
6 24 0.62
7 4 0.10
8 4 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
ATATAA
Found at i:2676390 original size:83 final size:82
Alignment explanation
Indices: 2676252--2676421 Score: 277
Period size: 83 Copynumber: 2.1 Consensus size: 82
2676242 AAAATAAAGG
*
2676252 CATTTAAAGATTTGTGCAAAAATGCTCTAGTTTAACATTCCAGTTAGATATAATATCAAACAATG
1 CATTTAAAGATTTGTGCAAAAATGCTCTAGTTCAACATTCCAGTTAGATATAATATCAAACAATG
2676317 CAAGCCCAGTGTCATGA
66 CAAGCCCAGTGTCATGA
* * *
2676334 CATTTAAAGATTTGGTGCAAAAATGCTCTAGTTCAATATTCCAGTTGGATATAATATCCAACAAT
1 CATTTAAAGATTT-GTGCAAAAATGCTCTAGTTCAACATTCCAGTTAGATATAATATCAAACAAT
* *
2676399 GTAAGCCCAGTGTCATGG
65 GCAAGCCCAGTGTCATGA
2676417 CATTT
1 CATTT
2676422 GAAGCTTCCA
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
82 13 0.16
83 68 0.84
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (82 bp):
CATTTAAAGATTTGTGCAAAAATGCTCTAGTTCAACATTCCAGTTAGATATAATATCAAACAATG
CAAGCCCAGTGTCATGA
Found at i:2678281 original size:64 final size:64
Alignment explanation
Indices: 2678180--2678308 Score: 222
Period size: 64 Copynumber: 2.0 Consensus size: 64
2678170 ATTCTAAAAC
* *
2678180 TCTCTATTCTTAGAAAGAAAGATATTTAACGAAAAAAATCACCAGACGGATACCTTATCAGGAT
1 TCTCTATTCTCAGAAAGAAAGAAATTTAACGAAAAAAATCACCAGACGGATACCTTATCAGGAT
* *
2678244 TCTCTATTCTCAGAAAGAAAGAAATTTAACGAAAAAAATCACCAGAGGGATACCTTATTAGGAT
1 TCTCTATTCTCAGAAAGAAAGAAATTTAACGAAAAAAATCACCAGACGGATACCTTATCAGGAT
2678308 T
1 T
2678309 GTTTTTAGCA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.26
Consensus pattern (64 bp):
TCTCTATTCTCAGAAAGAAAGAAATTTAACGAAAAAAATCACCAGACGGATACCTTATCAGGAT
Found at i:2680653 original size:17 final size:18
Alignment explanation
Indices: 2680631--2680664 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2680621 ATTTGTGATA
2680631 TAAA-TTTAAATAAATTT
1 TAAATTTTAAATAAATTT
*
2680648 TAAATTTTATATAAATT
1 TAAATTTTAAATAAATT
2680665 AAAAAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAAATTTTAAATAAATTT
Found at i:2681417 original size:24 final size:24
Alignment explanation
Indices: 2681376--2681432 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
2681366 TAATTCGATT
*
2681376 AATAAAAT-TTATTAATTTAATAA
1 AATAAAATATAATTAATTTAATAA
*
2681399 AATAAAATATAATTAATTTTATAA
1 AATAAAATATAATTAATTTAATAA
* *
2681423 TATAACATAT
1 AATAAAATAT
2681433 TTTGAGAGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 8 0.28
24 21 0.72
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
AATAAAATATAATTAATTTAATAA
Found at i:2686414 original size:2 final size:2
Alignment explanation
Indices: 2686407--2686437 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2686397 ACACTCTTCC
2686407 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2686438 CCTATCTTTG
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2687877 original size:20 final size:21
Alignment explanation
Indices: 2687854--2687896 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
2687844 TTTATCTCAA
2687854 ATTTTAAAATTTAAATTT-AT
1 ATTTTAAAATTTAAATTTGAT
*
2687874 ATTTTAAATTTTAAATTTGAT
1 ATTTTAAAATTTAAATTTGAT
2687895 AT
1 AT
2687897 GATCTTAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTTTAAAATTTAAATTTGAT
Found at i:2687889 original size:7 final size:7
Alignment explanation
Indices: 2687852--2687891 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
2687842 ATTTTATCTC
2687852 AAATTTT
1 AAATTTT
*
2687859 AAAATTT
1 AAATTTT
2687866 AAA-TTT
1 AAATTTT
*
2687872 ATATTTT
1 AAATTTT
2687879 AAATTTT
1 AAATTTT
2687886 AAATTT
1 AAATTT
2687892 GATATGATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 5 0.17
7 24 0.83
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
AAATTTT
Found at i:2689177 original size:6 final size:6
Alignment explanation
Indices: 2689158--2689193 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
2689148 TTATAAAAAT
*
2689158 TATAAA TA-AAA TATAAA TATAAA TATAAG TATAAA T
1 TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA T
2689194 TTTAAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (6 bp):
TATAAA
Found at i:2689507 original size:27 final size:27
Alignment explanation
Indices: 2689477--2689532 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
2689467 TTTGTATATT
2689477 TTTTAT-TTTATA-ATAATATTTAAAATA
1 TTTTATATTTATATA-AAT-TTTAAAATA
*
2689504 TTTTATATTTATATAAATTTTAATATA
1 TTTTATATTTATATAAATTTTAAAATA
2689531 TT
1 TT
2689533 AATAATATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 16 0.62
28 9 0.35
29 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTTATATTTATATAAATTTTAAAATA
Found at i:2689537 original size:18 final size:18
Alignment explanation
Indices: 2689490--2689540 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
2689480 TATTTTATAA
2689490 TAATATTTAA-AATATTT
1 TAATATTTAATAATATTT
2689507 T-ATATTTATATAA-ATTT
1 TAATATTTA-ATAATATTT
2689524 TAATATATTAATAATAT
1 TAATAT-TTAATAATAT
2689541 CAAAATATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 7 0.24
17 7 0.24
18 10 0.34
19 5 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATATTTAATAATATTT
Found at i:2693128 original size:15 final size:15
Alignment explanation
Indices: 2693108--2693138 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2693098 ACCGCCCAAA
2693108 CAAAATAACCGGCTG
1 CAAAATAACCGGCTG
*
2693123 CAAAATAATCGGCTG
1 CAAAATAACCGGCTG
2693138 C
1 C
2693139 CACAAGTCCA
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:0.39, C:0.26, G:0.19, T:0.16
Consensus pattern (15 bp):
CAAAATAACCGGCTG
Found at i:2696126 original size:3 final size:3
Alignment explanation
Indices: 2696118--2696146 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2696108 AATAATTGAC
2696118 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2696147 ATTCAGTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2715898 original size:21 final size:24
Alignment explanation
Indices: 2715863--2715905 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
2715853 GGCTCTATGC
2715863 AATTGATATAAATGA-CTTATTTT
1 AATTGATATAAATGATCTTATTTT
2715886 AATT-ATA-AAATGATCTTATT
1 AATTGATATAAATGATCTTATT
2715906 AACTAAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 9 0.47
23 4 0.21
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (24 bp):
AATTGATATAAATGATCTTATTTT
Found at i:2716844 original size:27 final size:28
Alignment explanation
Indices: 2716788--2716861 Score: 73
Period size: 27 Copynumber: 2.6 Consensus size: 28
2716778 AATTTAAAAA
*
2716788 TAATTAAAAAAATTATTTATTTGTTAATATT
1 TAATTAAAAAAA-TA-TTAATTGTTAATA-T
2716819 TAATTAAAAAAATATTAATT-TT-ATAT
1 TAATTAAAAAAATATTAATTGTTAATAT
2716845 T-ATTATATAAAAATATT
1 TAATTA-A-AAAAATATT
2716862 TTTTATTGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
25 4 0.10
26 3 0.08
27 12 0.30
28 2 0.05
29 5 0.12
30 2 0.05
31 12 0.30
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (28 bp):
TAATTAAAAAAATATTAATTGTTAATAT
Found at i:2720670 original size:16 final size:16
Alignment explanation
Indices: 2720630--2720683 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
2720620 GTTTGTGAAG
*
2720630 ATTTAAAATGTAAAAAAA
1 ATTTAAAA--TAATAAAA
2720648 CATTTAAAATAATAAAA
1 -ATTTAAAATAATAAAA
2720665 ATTTAAAA-ATATAAAA
1 ATTTAAAATA-ATAAAA
2720681 ATT
1 ATT
2720684 ATTTTATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
15 1 0.03
16 17 0.52
17 7 0.21
19 8 0.24
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (16 bp):
ATTTAAAATAATAAAA
Found at i:2720722 original size:13 final size:13
Alignment explanation
Indices: 2720679--2720727 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 13
2720669 AAAAATATAA
2720679 AAATTATTTTATTT
1 AAATTA-TTTATTT
*
2720693 AAAAATTAATT-TTT
1 --AAATTATTTATTT
2720707 AAATTATTTATTT
1 AAATTATTTATTT
2720720 AAATTATT
1 AAATTATT
2720728 AAATTATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 8 0.27
13 11 0.37
14 3 0.10
15 2 0.07
16 6 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
AAATTATTTATTT
Found at i:2720738 original size:27 final size:28
Alignment explanation
Indices: 2720679--2720736 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
2720669 AAAAATATAA
* *
2720679 AAATTATTTTATTTAAAAATTAATTTTT
1 AAATTATTTTATTTAAAAATTAAATTAT
*
2720707 AAATTA-TTTATTTAAATTATTAAATTAT
1 AAATTATTTTATTTAAA-AATTAAATTAT
2720735 AA
1 AA
2720737 TTTTAAACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
AAATTATTTTATTTAAAAATTAAATTAT
Found at i:2720743 original size:21 final size:21
Alignment explanation
Indices: 2720700--2720739 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2720690 TTTAAAAATT
* *
2720700 AATTTTTAAATTATTTATTTA
1 AATTATTAAATTATATATTTA
2720721 AATTATTAAATTATA-ATTT
1 AATTATTAAATTATATATTT
2720740 TAAACATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
AATTATTAAATTATATATTTA
Found at i:2725542 original size:3 final size:3
Alignment explanation
Indices: 2725534--2725558 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2725524 GCAGTCAAGG
2725534 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
2725559 GCTCAAGGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:2730345 original size:14 final size:14
Alignment explanation
Indices: 2730322--2730349 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2730312 ATTTTAAAAA
2730322 TTATATTTTTATAT
1 TTATATTTTTATAT
2730336 TTATATTTTTATAT
1 TTATATTTTTATAT
2730350 AAATCAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTATATTTTTATAT
Found at i:2731458 original size:2 final size:2
Alignment explanation
Indices: 2731451--2731493 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2731441 ATATCCACAT
2731451 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2731493 A
1 A
2731494 TTAGCCAAGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2731788 original size:18 final size:18
Alignment explanation
Indices: 2731765--2731801 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2731755 ATATTTTCCT
2731765 ATGAATTATGTAATTAAA
1 ATGAATTATGTAATTAAA
2731783 ATGAATTATGTAATTAAA
1 ATGAATTATGTAATTAAA
2731801 A
1 A
2731802 GACTTCAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (18 bp):
ATGAATTATGTAATTAAA
Found at i:2734161 original size:6 final size:6
Alignment explanation
Indices: 2734152--2734177 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2734142 TCTCATCAAC
2734152 ATCATG ATCATG ATCATG ATCATG AT
1 ATCATG ATCATG ATCATG ATCATG AT
2734178 TATGGGGTAA
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:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (6 bp):
ATCATG
Found at i:2734924 original size:39 final size:42
Alignment explanation
Indices: 2734871--2734951 Score: 105
Period size: 39 Copynumber: 2.0 Consensus size: 42
2734861 TTCTAAAATG
* * *
2734871 TTAAATTATTAATAAAAATTAA-TA-TTAAA-TTAAATTTTA
1 TTAAAATAATAATAAAAATTAATTATTTAAATTTAAAATTTA
*
2734910 TTAAAATAATAATAATAATTAATTATTTAAATTTAAAATTTA
1 TTAAAATAATAATAAAAATTAATTATTTAAATTTAAAATTTA
2734952 AAACTATAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
39 19 0.54
40 2 0.06
41 5 0.14
42 9 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (42 bp):
TTAAAATAATAATAAAAATTAATTATTTAAATTTAAAATTTA
Found at i:2735181 original size:20 final size:19
Alignment explanation
Indices: 2735144--2735183 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
2735134 TAAATATTTT
2735144 ATTTAAAAATAAAATAAAA
1 ATTTAAAAATAAAATAAAA
2735163 ATTT-AAAATAATTAATAAAA
1 ATTTAAAAATAA--AATAAAA
2735183 A
1 A
2735184 AATATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
19 4 0.21
20 8 0.42
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
ATTTAAAAATAAAATAAAA
Found at i:2735208 original size:36 final size:37
Alignment explanation
Indices: 2735161--2735230 Score: 115
Period size: 36 Copynumber: 1.9 Consensus size: 37
2735151 AATAAAATAA
*
2735161 AAATTTAAAATAATTAATAAAAAAATATT-TTTATCC
1 AAATCTAAAATAATTAATAAAAAAATATTCTTTATCC
*
2735197 AAATCTAAAATAATTAATAAAATAATATTCTTTA
1 AAATCTAAAATAATTAATAAAAAAATATTCTTTA
2735231 AACATATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 27 0.87
37 4 0.13
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (37 bp):
AAATCTAAAATAATTAATAAAAAAATATTCTTTATCC
Found at i:2736085 original size:3 final size:3
Alignment explanation
Indices: 2736077--2736106 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2736067 AATTAATGAA
*
2736077 ATT ATT ATT ATT ATT ATT ATT CTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2736107 GTTAGTTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2761852 original size:229 final size:232
Alignment explanation
Indices: 2761401--2761937 Score: 875
Period size: 229 Copynumber: 2.3 Consensus size: 232
2761391 GCAAAATCCA
* *
2761401 TTGCTTCATTGTCTACCACTTGGCCTATTTAACAAACTACAAGAAGGCAAGCAGAATGCATTATA
1 TTGCTTCATTGTCTTCCACTTGGCCTA--TAACAAACTACAAGAAGGCAAGCAGAATACATTATA
*
2761466 AAAAAGAAACCTTTTAAAATTAAACTGAAAAAGAAATCCGGAACACCAAGGCCAAATCCAGCACC
64 AAAAAGAAACCTTTTAAAATTAAAATGAAAAAGAAATCCGGAACACCAAGGCCAAATCCAGCACC
* * * *
2761531 TTGCCTACTTACTCTGAATCAATTGGGTTCATAAAAGGAATTGCTTGAAAATGGACGAATCATTC
129 TTGCCTACTTACTCTAAATCAATTGAGTTCATAAAAAGAATAGCTTGAAAATGGACGAATCATTC
*
2761596 AAAAAAAACTCTTTCACCAGTATCCTTTCTAGAACCGGT
194 AAAAAAAACTCTTTCACCAGCATCCTTTCTAGAACCGGT
* *
2761635 TTGCTTCATTGTCTTCCACTTGGCCTAT-A-TAACTACAAGAAGGCAAGCAGAATACATTACAAA
1 TTGCTTCATTGTCTTCCACTTGGCCTATAACAAACTACAAGAAGGCAAGCAGAATACATTATAAA
2761698 AAAGAAACCTTTTAAAATTAAAAT-AAAAACGAAATCCGGAACACCAAGGCC-AATCCAGCACCT
66 AAAGAAACCTTTTAAAATTAAAATGAAAAA-GAAATCCGGAACACCAAGGCCAAATCCAGCACCT
*
2761761 TGCCTACTTACTCTAAATCAATTGAGTTCATAAAAAGAATAGCTTGGAAATGGACGAATCATTCA
130 TGCCTACTTACTCTAAATCAATTGAGTTCATAAAAAGAATAGCTTGAAAATGGACGAATCATTCA
* *
2761826 AAAAAAACTCTTTCGCCAGCATCCTTTCTAGAACTGGT
195 AAAAAAACTCTTTCACCAGCATCCTTTCTAGAACCGGT
*
2761864 TTGCTTCATTGTCTTCCGCTTGGCCTATCGAACAAACTACAAGAAGGCAAGCAGAATACATTATA
1 TTGCTTCATTGTCTTCCACTTGGCCTAT--AACAAACTACAAGAAGGCAAGCAGAATACATTATA
2761929 AAAAAGAAA
64 AAAAAGAAA
2761938 TCCAGAACAC
Statistics
Matches: 282, Mismatches: 16, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
229 139 0.49
230 75 0.27
231 1 0.00
232 2 0.01
233 39 0.14
234 26 0.09
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.25
Consensus pattern (232 bp):
TTGCTTCATTGTCTTCCACTTGGCCTATAACAAACTACAAGAAGGCAAGCAGAATACATTATAAA
AAAGAAACCTTTTAAAATTAAAATGAAAAAGAAATCCGGAACACCAAGGCCAAATCCAGCACCTT
GCCTACTTACTCTAAATCAATTGAGTTCATAAAAAGAATAGCTTGAAAATGGACGAATCATTCAA
AAAAAACTCTTTCACCAGCATCCTTTCTAGAACCGGT
Found at i:2762625 original size:58 final size:58
Alignment explanation
Indices: 2762534--2762650 Score: 216
Period size: 58 Copynumber: 2.0 Consensus size: 58
2762524 ATAATTTTGA
* *
2762534 AAATTCTCCATCCTAGTACAAAGCATAATGACCCTAGCCTAATATAGAAAAGATTCCT
1 AAATTCTCCATCCTAGTACAAAGCATAACGACCCTAGCCTAATATAGAAAAGAATCCT
2762592 AAATTCTCCATCCTAGTACAAAGCATAACGACCCTAGCCTAATATAGAAAAGAATCCT
1 AAATTCTCCATCCTAGTACAAAGCATAACGACCCTAGCCTAATATAGAAAAGAATCCT
2762650 A
1 A
2762651 GCCTTCCCTG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.41, C:0.25, G:0.10, T:0.24
Consensus pattern (58 bp):
AAATTCTCCATCCTAGTACAAAGCATAACGACCCTAGCCTAATATAGAAAAGAATCCT
Found at i:2771226 original size:21 final size:20
Alignment explanation
Indices: 2771202--2771249 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2771192 GGAGTCGGAG
2771202 AAAATTTTAACAAAAGATGTC
1 AAAATTTT-ACAAAAGATGTC
**
2771223 AAAATTTTAGTAAAGATGTC
1 AAAATTTTACAAAAGATGTC
*
2771243 AGAATTT
1 AAAATTT
2771250 AGAAGAACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (20 bp):
AAAATTTTACAAAAGATGTC
Found at i:2771365 original size:12 final size:12
Alignment explanation
Indices: 2771348--2771372 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2771338 TCATATAAAC
2771348 ATCTTTGACTAA
1 ATCTTTGACTAA
2771360 ATCTTTGACTAA
1 ATCTTTGACTAA
2771372 A
1 A
2771373 GTACAAGGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (12 bp):
ATCTTTGACTAA
Found at i:2772040 original size:2 final size:2
Alignment explanation
Indices: 2772033--2772069 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2772023 CTGTAGGTAA
*
2772033 AG AG AG AG AG AG AG AC 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 AG AG AG A
2772070 AACGTTGGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2772507 original size:18 final size:19
Alignment explanation
Indices: 2772486--2772523 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2772476 TATATGATTT
*
2772486 TATTT-AAATAAATTTTTA
1 TATTTAAAATAAAATTTTA
2772504 TATTTAAAATAAAATTTTA
1 TATTTAAAATAAAATTTTA
2772523 T
1 T
2772524 TTAAATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTTAAAATAAAATTTTA
Found at i:2772515 original size:19 final size:18
Alignment explanation
Indices: 2772482--2772536 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
2772472 TAATTATATG
2772482 ATTTTATTT-AAATAAAT
1 ATTTTATTTAAAATAAAT
*
2772499 TTTTATATTTAAAATAAA-
1 ATTT-TATTTAAAATAAAT
2772517 ATTTTATTTAAATATAAAT
1 ATTTTATTTAAA-ATAAAT
2772536 A
1 A
2772537 AAAATAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 11 0.34
18 13 0.41
19 8 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTTATTTAAAATAAAT
Found at i:2772535 original size:17 final size:17
Alignment explanation
Indices: 2772482--2772535 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
2772472 TAATTATATG
2772482 ATTTTATTTAAATA-AA
1 ATTTTATTTAAATATAA
*
2772498 TTTTTATATTTAAA-ATAAA
1 -ATTT-TATTTAAATAT-AA
2772517 ATTTTATTTAAATATAA
1 ATTTTATTTAAATATAA
2772534 AT
1 AT
2772536 AAAAATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
17 16 0.52
18 13 0.42
19 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTTTATTTAAATATAA
Found at i:2772564 original size:29 final size:28
Alignment explanation
Indices: 2772509--2772564 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
2772499 TTTTATATTT
* *
2772509 AAAATAAAATTTTATTTAAATATAAATA
1 AAAATAAAAATTTATTTAAATAAAAATA
**
2772537 AAAATAAAAAATTTATTTTGATAAAAAT
1 AAAAT-AAAAATTTATTTAAATAAAAAT
2772565 TAAATATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (28 bp):
AAAATAAAAATTTATTTAAATAAAAATA
Found at i:2772763 original size:22 final size:22
Alignment explanation
Indices: 2772737--2772790 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
2772727 TTAAAGCTCA
**
2772737 AAAAATATATTTTCAAATTTTTT
1 AAAAATAT-TTTAAAAATTTTTT
*
2772760 AAAAATTTTTTAAAAATTTTTT
1 AAAAATATTTTAAAAATTTTTT
2772782 AAAAA-ATTT
1 AAAAATATTT
2772791 GAGCTCTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 3 0.11
22 17 0.63
23 7 0.26
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
AAAAATATTTTAAAAATTTTTT
Found at i:2772768 original size:10 final size:11
Alignment explanation
Indices: 2772751--2772786 Score: 72
Period size: 11 Copynumber: 3.3 Consensus size: 11
2772741 ATATATTTTC
2772751 AAATTTTTTAA
1 AAATTTTTTAA
2772762 AAATTTTTTAA
1 AAATTTTTTAA
2772773 AAATTTTTTAA
1 AAATTTTTTAA
2772784 AAA
1 AAA
2772787 ATTTGAGCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AAATTTTTTAA
Found at i:2772769 original size:12 final size:12
Alignment explanation
Indices: 2772754--2772790 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
2772744 TATTTTCAAA
2772754 TTTTTTAAAAA-
1 TTTTTTAAAAAT
2772765 TTTTTTAAAAAT
1 TTTTTTAAAAAT
*
2772777 TTTTTAAAAAAT
1 TTTTTTAAAAAT
2772789 TT
1 TT
2772791 GAGCTCTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 11 0.46
12 13 0.54
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TTTTTTAAAAAT
Found at i:2773052 original size:14 final size:14
Alignment explanation
Indices: 2773035--2773063 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2773025 TATTTTAATA
2773035 TTATTATTATTTTT
1 TTATTATTATTTTT
2773049 TTATTATTATTTTT
1 TTATTATTATTTTT
2773063 T
1 T
2773064 GAATTCGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTATTATTATTTTT
Found at i:2773543 original size:23 final size:23
Alignment explanation
Indices: 2773512--2773555 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
2773502 TTATAAGAGA
*
2773512 ATGATAAATTATAAACTTTTTTTC
1 ATGATAAATT-TAAAATTTTTTTC
2773536 ATGA-AAATTTAAAATTTTTT
1 ATGATAAATTTAAAATTTTTT
2773556 ATTTAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 5 0.26
24 4 0.21
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (23 bp):
ATGATAAATTTAAAATTTTTTTC
Done.