Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold275
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: 1025155
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 2 of 7
Found at i:154559 original size:14 final size:14
Alignment explanation
Indices: 154360--154590 Score: 106
Period size: 15 Copynumber: 16.0 Consensus size: 14
154350 GTGAATAAAT
154360 TTAAATTTGCAAGAAA
1 TTAAA-TTGCAA-AAA
* * *
154376 ATAAATTACATAAA
1 TTAAATTGCAAAAA
154390 TTAAAATT--AAAAA
1 TT-AAATTGCAAAAA
* * *
154403 ATAAATAGCATAAA
1 TTAAATTGCAAAAA
154417 TTAAATTGACAAAAA
1 TTAAATTG-CAAAAA
* * **
154432 ATAATTTGCTTAAA
1 TTAAATTGCAAAAA
*
154446 TTAAATTGTAAGAAA
1 TTAAATTGCAA-AAA
** *
154461 ACAAATTGCTAGAAA
1 TTAAATTGC-AAAAA
* * **
154476 CTAGATTGCTTAAA
1 TTAAATTGCAAAAA
*
154490 TTAAATTGAAAGAAA
1 TTAAATTGCAA-AAA
* * *
154505 GTAAATTGTATAAA
1 TTAAATTGCAAAAA
154519 TTAAATTGCAAGAAA
1 TTAAATTGCAA-AAA
* *
154534 ATAAATTACAAAAA
1 TTAAATTGCAAAAA
*
154548 TTAAAATGCAAAAAA
1 TTAAATTGC-AAAAA
* * *
154563 GTAAATTACATAAA
1 TTAAATTGCAAAAA
*
154577 TTAAATTGTAAAAA
1 TTAAATTGCAAAAA
154591 AATAAGTTAA
Statistics
Matches: 153, Mismatches: 53, Indels: 20
0.68 0.23 0.09
Matches are distributed among these distances:
12 4 0.03
13 5 0.03
14 67 0.44
15 72 0.47
16 5 0.03
ACGTcount: A:0.57, C:0.06, G:0.09, T:0.29
Consensus pattern (14 bp):
TTAAATTGCAAAAA
Found at i:154589 original size:29 final size:29
Alignment explanation
Indices: 154486--154591 Score: 135
Period size: 29 Copynumber: 3.7 Consensus size: 29
154476 CTAGATTGCT
**
154486 TAAATTAAATTG-AAAGAAAGTAAATTGTA
1 TAAATTAAATTGCAAA-AAAGTAAATTACA
154515 TAAATTAAATTGCAAGAAAA-TAAATTACA
1 TAAATTAAATTGCAA-AAAAGTAAATTACA
* *
154544 AAAATTAAAATGCAAAAAAGTAAATTACA
1 TAAATTAAATTGCAAAAAAGTAAATTACA
*
154573 TAAATTAAATTGTAAAAAA
1 TAAATTAAATTGCAAAAAA
154592 ATAAGTTAAC
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
28 4 0.06
29 57 0.85
30 5 0.07
31 1 0.01
ACGTcount: A:0.60, C:0.04, G:0.08, T:0.27
Consensus pattern (29 bp):
TAAATTAAATTGCAAAAAAGTAAATTACA
Found at i:154720 original size:16 final size:16
Alignment explanation
Indices: 154696--154727 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
154686 AAGATTAAAC
154696 TTAAGATTATTAAGCT
1 TTAAGATTATTAAGCT
*
154712 TTAATATTATTAAGCT
1 TTAAGATTATTAAGCT
154728 AAATAAATCA
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:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (16 bp):
TTAAGATTATTAAGCT
Found at i:155454 original size:51 final size:51
Alignment explanation
Indices: 155376--155518 Score: 250
Period size: 51 Copynumber: 2.8 Consensus size: 51
155366 TATGGAAAAG
155376 TACCCAGATGTATCGATACATTTTTCAATGTATCGATACATTCTGTCTTTT
1 TACCCAGATGTATCGATACATTTTTCAATGTATCGATACATTCTGTCTTTT
* *
155427 TACCCAGATGTATTGATACATTCTTCAATGTATCGATACATTCTGTCTTTT
1 TACCCAGATGTATCGATACATTTTTCAATGTATCGATACATTCTGTCTTTT
* *
155478 TATCCGGATGTATCGATACATTTTTCAATGTATCGATACAT
1 TACCCAGATGTATCGATACATTTTTCAATGTATCGATACAT
155519 CTAGTTAAAA
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 86 1.00
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.42
Consensus pattern (51 bp):
TACCCAGATGTATCGATACATTTTTCAATGTATCGATACATTCTGTCTTTT
Found at i:156960 original size:12 final size:11
Alignment explanation
Indices: 156934--156961 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
156924 TTGCGCATTG
156934 AAAAATTATTT
1 AAAAATTATTT
156945 AAAAATTATTT
1 AAAAATTATTT
156956 AAAAAT
1 AAAAAT
156962 CCAAAAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AAAAATTATTT
Found at i:158859 original size:15 final size:15
Alignment explanation
Indices: 158839--158867 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
158829 TTGTAATAAT
158839 AATAATAAATAAATA
1 AATAATAAATAAATA
158854 AATAATAAATAAAT
1 AATAATAAATAAAT
158868 TACAATGAAT
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AATAATAAATAAATA
Found at i:159802 original size:5 final size:5
Alignment explanation
Indices: 159794--159819 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
159784 GATATAAAAT
159794 AATTA AATTA AATTA AATTA AATTA A
1 AATTA AATTA AATTA AATTA AATTA A
159820 TTGAAATGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATTA
Found at i:159810 original size:19 final size:18
Alignment explanation
Indices: 159768--159810 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
159758 CCTTAATGGC
*
159768 TTAAAAGAATTAAATAGA
1 TTAAAAGAATTAAATAAA
*
159786 TATAAAATAATTAAATTAAA
1 T-TAAAAGAATTAAA-TAAA
159806 TTAAA
1 TTAAA
159811 TTAAATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 16 0.76
20 4 0.19
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
TTAAAAGAATTAAATAAA
Found at i:163832 original size:9 final size:9
Alignment explanation
Indices: 163807--163844 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
163797 CTTTCTTTGA
163807 TTTATTATCT
1 TTTATTAT-T
163817 TTT-TTATT
1 TTTATTATT
163825 TTTATTATT
1 TTTATTATT
163834 TTTA-TATT
1 TTTATTATT
163842 TTT
1 TTT
163845 TTTTCTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 11 0.41
9 13 0.48
10 3 0.11
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTATTATT
Found at i:163853 original size:17 final size:18
Alignment explanation
Indices: 163807--163853 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
163797 CTTTCTTTGA
*
163807 TTTATTATCTTTTTTATT
1 TTTATTATCTTTTATATT
163825 TTTATTAT-TTTTATATT
1 TTTATTATCTTTTATATT
*
163842 TTT-TTTTCTTTT
1 TTTATTATCTTTT
163854 CTCTTTACTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 3 0.12
17 15 0.58
18 8 0.31
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTATTATCTTTTATATT
Found at i:164013 original size:23 final size:23
Alignment explanation
Indices: 163978--164024 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
163968 CTCCCTTCAC
163978 TTTTCTTTATCTCTCTAAATGTT
1 TTTTCTTTATCTCTCTAAATGTT
* * *
164001 TTTTTTTTCTCTCTCTATATGTT
1 TTTTCTTTATCTCTCTAAATGTT
164024 T
1 T
164025 ATCTTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.13, C:0.17, G:0.04, T:0.66
Consensus pattern (23 bp):
TTTTCTTTATCTCTCTAAATGTT
Found at i:166032 original size:2 final size:2
Alignment explanation
Indices: 166025--166063 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
166015 GTTTTCATTT
166025 TA TA TA TA TA TA T- 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 TA
166064 AAAGAGAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:173141 original size:34 final size:33
Alignment explanation
Indices: 173102--173170 Score: 120
Period size: 34 Copynumber: 2.1 Consensus size: 33
173092 AGCTAGGTTG
173102 GAAGAAGCAAGAGAAGAAAAAAAAAAGAAGATAT
1 GAAGAAGCAAGAGAAGAAAAAAAAAA-AAGATAT
*
173136 GAAGAAGCAAGAGAAGAAGAAAAAAAAAGATAT
1 GAAGAAGCAAGAGAAGAAAAAAAAAAAAGATAT
173169 GA
1 GA
173171 GGCTTTCTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 9 0.26
34 25 0.74
ACGTcount: A:0.67, C:0.03, G:0.25, T:0.06
Consensus pattern (33 bp):
GAAGAAGCAAGAGAAGAAAAAAAAAAAAGATAT
Found at i:176400 original size:15 final size:17
Alignment explanation
Indices: 176382--176418 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
176372 TTTAAAAATA
176382 AAATATAT-C-TATATT
1 AAATATATACATATATT
176397 AAATATATACATATATT
1 AAATATATACATATATT
*
176414 TAATA
1 AAATA
176419 CTTGCTTTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 1 0.05
17 10 0.53
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATATATACATATATT
Found at i:177361 original size:17 final size:16
Alignment explanation
Indices: 177320--177373 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
177310 GTTGCTTGTA
177320 TTATTTATTTTA-ATTT
1 TTATTT-TTTTATATTT
*
177336 TTAGATTTTTTATTATTT
1 TTA-TTTTTTTA-TATTT
177354 TTATTTTTTTATAATTT
1 TTATTTTTTTAT-ATTT
177371 TTA
1 TTA
177374 AAAATTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
16 9 0.28
17 16 0.50
18 7 0.22
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (16 bp):
TTATTTTTTTATATTT
Found at i:177957 original size:16 final size:16
Alignment explanation
Indices: 177938--177968 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
177928 CGGGTTCGAA
177938 TTATTTCGAGTTCGGG
1 TTATTTCGAGTTCGGG
*
177954 TTATTTTGAGTTCGG
1 TTATTTCGAGTTCGG
177969 ACAATTTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.29, T:0.48
Consensus pattern (16 bp):
TTATTTCGAGTTCGGG
Found at i:178719 original size:19 final size:17
Alignment explanation
Indices: 178695--178733 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
178685 ATAAAATAAA
*
178695 TTATTAATTTATATTATTT
1 TTATTAACTTA-ATT-TTT
178714 TTATTAACTTAATTTTT
1 TTATTAACTTAATTTTT
178731 TTA
1 TTA
178734 AATAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 3 0.16
19 10 0.53
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTAACTTAATTTTT
Found at i:181340 original size:13 final size:13
Alignment explanation
Indices: 181318--181349 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
181308 GCAGCCATGT
*
181318 TCCAAAAATTTTG
1 TCCAAGAATTTTG
181331 TCCAAGAATTTTG
1 TCCAAGAATTTTG
181344 TCCAAG
1 TCCAAG
181350 TAGAACCGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (13 bp):
TCCAAGAATTTTG
Found at i:185996 original size:19 final size:20
Alignment explanation
Indices: 185971--186015 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
185961 GTAATAGTAC
*
185971 TTTTTTTAAGAGAT-TGATAA
1 TTTTTTTAAGA-ATATGAAAA
185991 TTTTTTTAA-AATATGAAAA
1 TTTTTTTAAGAATATGAAAA
186010 TTTTTT
1 TTTTTT
186016 AAGTGGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 12 0.52
20 9 0.39
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (20 bp):
TTTTTTTAAGAATATGAAAA
Found at i:186154 original size:64 final size:64
Alignment explanation
Indices: 186086--186217 Score: 167
Period size: 64 Copynumber: 2.1 Consensus size: 64
186076 ATAAATTTTT
* * * * * *
186086 TAAAATATATTACAT-AAAATAATTGAAAGATATAAATATTTTTATAATATTATTATTTAATTTA
1 TAAAAGATATTACATAAAAAT-ATTAAAAAATAAAAATATTCTTATAATATTATTACTTAATTTA
* * *
186150 TAAAAGATATTATATAAAAATATTAAAAAATAAAAATATTCTTATAATATTGTTGCTTAATTTA
1 TAAAAGATATTACATAAAAATATTAAAAAATAAAAATATTCTTATAATATTATTACTTAATTTA
186214 TAAA
1 TAAA
186218 GACTTTGATT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
64 53 0.91
65 5 0.09
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (64 bp):
TAAAAGATATTACATAAAAATATTAAAAAATAAAAATATTCTTATAATATTATTACTTAATTTA
Found at i:186732 original size:19 final size:19
Alignment explanation
Indices: 186708--186746 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
186698 ATACTATTGG
186708 TATATAAGAGATATGCTTA
1 TATATAAGAGATATGCTTA
*
186727 TATATAAGAGATATGTTTA
1 TATATAAGAGATATGCTTA
186746 T
1 T
186747 GGGTCGGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (19 bp):
TATATAAGAGATATGCTTA
Found at i:188843 original size:15 final size:15
Alignment explanation
Indices: 188819--188848 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
188809 TATGTTGTAT
188819 ATATTATTTAAAAAA
1 ATATTATTTAAAAAA
*
188834 ATATTTTTTAAAAAA
1 ATATTATTTAAAAAA
188849 GTATAATCTA
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATTATTTAAAAAA
Found at i:189630 original size:29 final size:28
Alignment explanation
Indices: 189585--189646 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
189575 TTTTTACTAA
*
189585 AAATATTATCATTTTTATATTTATTTTT
1 AAATATTATCATTTTTATATTTATATTT
* * *
189613 AAATATTGTTATTATTTATTTTTATATTT
1 AAATATTATCATT-TTTATATTTATATTT
*
189642 CAATA
1 AAATA
189647 AAATTTTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 11 0.39
29 17 0.61
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (28 bp):
AAATATTATCATTTTTATATTTATATTT
Found at i:189881 original size:16 final size:16
Alignment explanation
Indices: 189855--189897 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
189845 CAATTGATCT
* * *
189855 GAACTCGAAATGACTT
1 GAACTCAAAATAACTC
*
189871 GAACTTAAAATAACTC
1 GAACTCAAAATAACTC
189887 GAACTCAAAAT
1 GAACTCAAAAT
189898 CACCCAAAAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.23
Consensus pattern (16 bp):
GAACTCAAAATAACTC
Found at i:190501 original size:29 final size:29
Alignment explanation
Indices: 190460--190519 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
190450 TTATTATAAA
190460 TATTATTAGGCTATTAGAAAGGATCCACT
1 TATTATTAGGCTATTAGAAAGGATCCACT
*
190489 TATTATTAGGCTATTAGAAGGGATCCACT
1 TATTATTAGGCTATTAGAAAGGATCCACT
190518 TA
1 TA
190520 GACGTATGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.35
Consensus pattern (29 bp):
TATTATTAGGCTATTAGAAAGGATCCACT
Found at i:191424 original size:22 final size:22
Alignment explanation
Indices: 191390--191441 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
191380 AATAAGTCAT
* * *
191390 TAATTCATGAATTGTATTATAA
1 TAATTTATAAATTATATTATAA
* *
191412 TGATTTATAAATTATGTTATAA
1 TAATTTATAAATTATATTATAA
191434 TAATTTAT
1 TAATTTAT
191442 TTATAATAAG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (22 bp):
TAATTTATAAATTATATTATAA
Found at i:191445 original size:14 final size:15
Alignment explanation
Indices: 191418--191450 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
191408 ATAATGATTT
191418 ATAAATTATGTTATA
1 ATAAATTATGTTATA
*
191433 ATAATTTAT-TTATA
1 ATAAATTATGTTATA
191447 ATAA
1 ATAA
191451 GTAGGTGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
ATAAATTATGTTATA
Found at i:193237 original size:14 final size:14
Alignment explanation
Indices: 193206--193249 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
193196 CTTTAATAAT
*
193206 TAATTATAT-TAAA
1 TAATTATATATATA
193219 TAATTATATATATA
1 TAATTATATATATA
193233 TAATTA-ATTATATA
1 TAATTATA-TATATA
193247 TAA
1 TAA
193250 AAATAAATAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 10 0.36
14 18 0.64
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TAATTATATATATA
Found at i:193303 original size:27 final size:27
Alignment explanation
Indices: 193231--193304 Score: 64
Period size: 27 Copynumber: 2.7 Consensus size: 27
193221 ATTATATATA
*
193231 TATAATTAATTATATATAAAAATAAATAG
1 TATAA-TAA-TATAAATAAAAATAAATAG
*
193260 -A-AAAAATATGAATATAAAAATAAA-ATG
1 TATAATAATAT-AA-ATAAAAATAAATA-G
193287 TATAATAATATAAATAAA
1 TATAATAATATAAATAAA
193305 TTAATATACA
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
25 3 0.08
26 4 0.11
27 19 0.51
28 4 0.11
29 7 0.19
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (27 bp):
TATAATAATATAAATAAAAATAAATAG
Found at i:193319 original size:15 final size:14
Alignment explanation
Indices: 193292--193322 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
193282 AAATGTATAA
193292 TAATATAAATAAAT
1 TAATATAAATAAAT
193306 TAATATACAATAAAT
1 TAATATA-AATAAAT
193321 TA
1 TA
193323 TCATTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (14 bp):
TAATATAAATAAAT
Found at i:193332 original size:15 final size:16
Alignment explanation
Indices: 193294--193339 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 16
193284 ATGTATAATA
193294 ATATAAATAAATTA--
1 ATATAAATAAATTATC
193308 ATATACAATAAATTATC
1 ATATA-AATAAATTATC
193325 AT-TAAAT-AATTATC
1 ATATAAATAAATTATC
193339 A
1 A
193340 ATTTTAGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 13 0.45
15 12 0.41
16 2 0.07
17 2 0.07
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (16 bp):
ATATAAATAAATTATC
Found at i:193465 original size:2 final size:2
Alignment explanation
Indices: 193458--193482 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
193448 ATTTGTATGC
193458 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
193483 CACATCTAAT
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:200823 original size:42 final size:39
Alignment explanation
Indices: 200769--200853 Score: 100
Period size: 44 Copynumber: 2.1 Consensus size: 39
200759 AACCGCATCC
*
200769 TTTTATTAAAA-TTTTAAAATAAATGAAAAGTAAGTTTTACT
1 TTTTATTAAAATTTTTAAAATAAAT-AAAAATAA-TTTTA-T
*
200810 TTTTAATTTAAATTTTTTAAAATAAATAAAAATAATTTTAT
1 TTTT-A-TTAAAATTTTTAAAATAAATAAAAATAATTTTAT
200851 TTT
1 TTT
200854 ATAAGGAGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
41 8 0.21
42 6 0.15
43 12 0.31
44 13 0.33
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (39 bp):
TTTTATTAAAATTTTTAAAATAAATAAAAATAATTTTAT
Found at i:204001 original size:42 final size:38
Alignment explanation
Indices: 203935--204016 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 38
203925 ACCGTCATCC
*
203935 TTTATTAAAAATTTTAAATAAATAAAATTAAGTTTTACTT
1 TTTATTAAAAATTTTAAATAAATAAAAATAA-TTTTA-TT
*
203975 TTTATTAAAATTTTTTAAAATAAATAAAAATAATTTTATT
1 TTTATTAAAA-ATTTT-AAATAAATAAAAATAATTTTATT
204015 TT
1 TT
204017 AATGAATAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
40 14 0.37
41 9 0.24
42 15 0.39
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (38 bp):
TTTATTAAAAATTTTAAATAAATAAAAATAATTTTATT
Found at i:204219 original size:33 final size:34
Alignment explanation
Indices: 204182--204245 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
204172 TATTAATATA
* *
204182 AAAAT-AATTTTAATTTTTAAAT-TTTTAAATAAT
1 AAAATAAATTTTAA-ATTTAAATAATTTAAATAAT
204215 AAAATAAATTTTAAATTTAAATAATTTAAAT
1 AAAATAAATTTTAAATTTAAATAATTTAAAT
204246 TAAATTAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 12 0.44
34 15 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (34 bp):
AAAATAAATTTTAAATTTAAATAATTTAAATAAT
Found at i:204249 original size:27 final size:26
Alignment explanation
Indices: 204191--204251 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
204181 AAAAATAATT
*
204191 TTAATTTTTAAATTTTTAAATAATAAA
1 TTAAATTTTAAA-TTTTAAATAATAAA
*
204218 ATAAATTTTAAA-TTTAAATAATTTAAA
1 TTAAATTTTAAATTTTAAATAA--TAAA
204245 TTAAATT
1 TTAAATT
204252 AACTCAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 9 0.31
27 20 0.69
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TTAAATTTTAAATTTTAAATAATAAA
Found at i:204364 original size:14 final size:13
Alignment explanation
Indices: 204347--204452 Score: 58
Period size: 14 Copynumber: 7.6 Consensus size: 13
204337 TAAATTTTTA
204347 ATATTAAATATATT
1 ATATTAAATATA-T
204361 ATATTAAA-ATA-
1 ATATTAAATATAT
*
204372 ATA-TAAATAAAT
1 ATATTAAATATAT
204384 A-ATTAAAATATAAT
1 ATATT-AAATAT-AT
204398 ATAATATAAATATAT
1 AT-AT-TAAATATAT
*
204413 ATTTTAAAATTTATAT
1 ATATT-AAA--TATAT
*
204429 AATATTAATTATTAAT
1 -ATATTAAATA-T-AT
204445 ATATTAAA
1 ATATTAAA
204453 ATTTATAAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 27
0.69 0.06 0.26
Matches are distributed among these distances:
10 4 0.06
11 6 0.08
12 2 0.03
13 9 0.12
14 17 0.24
15 12 0.17
16 17 0.24
17 5 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTAAATATAT
Found at i:204383 original size:13 final size:13
Alignment explanation
Indices: 204367--204413 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
204357 TATTATATTA
204367 AAATAATATAAAT
1 AAATAATATAAAT
204380 AAATAAT-TAAA-
1 AAATAATATAAAT
*
204391 ATATAATATAATAT
1 AAATAATATAA-AT
204405 AAAT-ATATA
1 AAATAATATA
204414 TTTTAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 6 0.21
12 7 0.24
13 13 0.45
14 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AAATAATATAAAT
Found at i:204388 original size:22 final size:25
Alignment explanation
Indices: 204345--204412 Score: 79
Period size: 24 Copynumber: 2.7 Consensus size: 25
204335 TATAAATTTT
*
204345 TAATATTAAATATATTATATT-AAA-A
1 TAATA-TAAATA-AATATATTAAAATA
204370 TAATATAAATAAATA-ATTAAAATA
1 TAATATAAATAAATATATTAAAATA
204394 TAATATAATATAAATATAT
1 TAATATAA-ATAAATATAT
204413 ATTTTAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
22 3 0.08
23 6 0.16
24 15 0.39
25 12 0.32
26 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
TAATATAAATAAATATATTAAAATA
Found at i:204405 original size:29 final size:29
Alignment explanation
Indices: 204351--204507 Score: 109
Period size: 29 Copynumber: 5.5 Consensus size: 29
204341 TTTTTAATAT
* *
204351 TAAATATATT-ATATTAAAATAATATAAA
1 TAAATATATTAAAATTAATATAATATAAA
204379 TAAATA-ATTAAAATATAATATAATATAAA
1 TAAATATATTAAAAT-TAATATAATATAAA
* * *
204408 TATATATTTTAAAATTTATATAATATTAATTA
1 TAAATATATTAAAATTAATATAATA-TAA--A
* *
204440 TTAATATATTAAAATT--TATAA-A-AATT
1 TAAATATATTAAAATTAATATAATATAA-A
*
204466 TAAAAAT-TTAAAATATAATTATAATAT-AA
1 TAAATATATTAAAAT-TAA-TATAATATAAA
204495 TAAA-ATA-TAAAAT
1 TAAATATATTAAAAT
204508 ACGATAAAAA
Statistics
Matches: 104, Mismatches: 12, Indels: 26
0.73 0.08 0.18
Matches are distributed among these distances:
25 7 0.07
26 7 0.07
27 5 0.05
28 17 0.16
29 37 0.36
30 17 0.16
32 14 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
TAAATATATTAAAATTAATATAATATAAA
Found at i:204428 original size:18 final size:18
Alignment explanation
Indices: 204407--204459 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
204397 TATAATATAA
*
204407 ATATATATTTTAAAATTT
1 ATATATATATTAAAATTT
204425 ATATA-ATATT--AA-TT
1 ATATATATATTAAAATTT
204439 AT-TAATATATTAAAATTT
1 ATAT-ATATATTAAAATTT
204457 ATA
1 ATA
204460 AAAATTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 11
0.70 0.03 0.28
Matches are distributed among these distances:
13 1 0.04
14 5 0.18
15 7 0.25
17 6 0.21
18 9 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATATATATTAAAATTT
Found at i:204432 original size:34 final size:32
Alignment explanation
Indices: 204391--204459 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 32
204381 AATAATTAAA
*
204391 ATATAATA-TAATATAAATATATATTTTAAAATTT
1 ATATAATATTAAT-T-AATA-ATATATTAAAATTT
*
204425 ATATAATATTAATTATTAATATATTAAAATTT
1 ATATAATATTAATTAATAATATATTAAAATTT
204457 ATA
1 ATA
204460 AAAATTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 16 0.50
33 3 0.09
34 9 0.28
35 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
ATATAATATTAATTAATAATATATTAAAATTT
Found at i:205473 original size:2 final size:2
Alignment explanation
Indices: 205462--205508 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
205452 AAATTAAAAA
* *
205462 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT CT 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
205504 AT AT A
1 AT AT A
205509 GTTGCATGGA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:208119 original size:2 final size:2
Alignment explanation
Indices: 208112--208147 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
208102 CAATGCAATG
208112 TA TA 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 TA TA
208148 ATACCTTTTC
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):
TA
Found at i:211236 original size:13 final size:14
Alignment explanation
Indices: 211208--211237 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
211198 CCTAGAGGAC
211208 AAAAAGAAAGACAAA
1 AAAAAGAAAGA-AAA
211223 AAAAAGAAAGAAAA
1 AAAAAGAAAGAAAA
211237 A
1 A
211238 TAAGAAAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAGAAAA
Found at i:215379 original size:21 final size:21
Alignment explanation
Indices: 215350--215406 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
215340 ATTTTTATCC
215350 AAATGTATCGATACATTTATA
1 AAATGTATCGATACATTTATA
* * *
215371 AAATATATCGATATATTTGTA
1 AAATGTATCGATACATTTATA
*
215392 GAATGTATCGATACA
1 AAATGTATCGATACA
215407 AGGTCCCAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (21 bp):
AAATGTATCGATACATTTATA
Found at i:215460 original size:19 final size:19
Alignment explanation
Indices: 215436--215497 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
215426 TTTTGAACTT
215436 CAAACAGTTTGTATCGATA
1 CAAACAGTTTGTATCGATA
**
215455 CAAACAGAAAATGTATCGATA
1 CAAACAG--TTTGTATCGATA
*
215476 CATA-AGTGTTGTATCGATA
1 CAAACAGT-TTGTATCGATA
215495 CAA
1 CAA
215498 TGTATCGATA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 19 0.56
20 2 0.06
21 13 0.38
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (19 bp):
CAAACAGTTTGTATCGATA
Found at i:215503 original size:13 final size:13
Alignment explanation
Indices: 215485--215509 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
215475 ACATAAGTGT
215485 TGTATCGATACAA
1 TGTATCGATACAA
215498 TGTATCGATACA
1 TGTATCGATACA
215510 TAAGTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:215505 original size:32 final size:32
Alignment explanation
Indices: 215464--215536 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
215454 ACAAACAGAA
215464 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
*
215496 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
215528 AATGTATCG
1 AATGTATCG
215537 CTACGAAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTGTATCGATAC
Found at i:215522 original size:19 final size:18
Alignment explanation
Indices: 215466--215528 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
215456 AAACAGAAAA
215466 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
215485 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
215498 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
215517 TGTATCGATACA
1 TGTATCGATACA
215529 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:218016 original size:52 final size:51
Alignment explanation
Indices: 217944--218339 Score: 182
Period size: 52 Copynumber: 7.6 Consensus size: 51
217934 TTAAGTTTCT
*
217944 CAATTGTT-CATAATTGGGGATACTCCAACCCTGGTTTTATTTTCAAAACAC
1 CAATT-TTCCATAATCGGGGATACTCCAACCCTGGTTTTATTTTCAAAACAC
* **
217995 CAATTTTCCTTTAATCGGGGATACTCCAACTCC-CATTTTATTTTCAAAAACAC
1 CAATTTTCC-ATAATCGGGGATACTCCAAC-CCTGGTTTTATTTTC-AAAACAC
* * * * ** * ***** * *
218048 CAATTTTTCACAATCGAGGATACTTCAACCTCATTATTTCATCGGGGATACTC
1 CAATTTTCCATAATCGGGGATACTCCAACC-C-TGGTTTTATTTTCAAAACAC
** * * * * * * * *
218101 CAA--CCCCGTTACCTCCGAGGGGATACTCCCA-CCTCAGCTTTATTTCCAAAATAT
1 CAATTTTCC-ATA-AT-C--GGGGATACTCCAACCCT-GGTTTTATTTTCAAAACAC
** *
218155 TGA-TTTCTCATAATCGGGGATAC-CTCAACCCCGGTTTTA-TTTCTAAAACAC
1 CAATTTTC-CATAATCGGGGATACTC-CAACCCTGGTTTTATTTTC-AAAACAC
* * * * *
218206 TAATTTTCCACAATCGAGGATACTCCAACCCCGGTTTTATCTTCAAAACAC
1 CAATTTTCCATAATCGGGGATACTCCAACCCTGGTTTTATTTTCAAAACAC
* * *
218257 CAATTTTCCTTTAATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAAACAC
1 CAATTTTCC-ATAATCGGGGATACTCCAAC-CCTGGTTTTATTTTC-AAAACAC
* *
218310 CAAATTTT-CACAATCGAGGATACTCCAACC
1 C-AATTTTCCATAATCGGGGATACTCCAACC
218340 TCGTTATTTC
Statistics
Matches: 253, Mismatches: 67, Indels: 50
0.68 0.18 0.14
Matches are distributed among these distances:
50 6 0.02
51 73 0.29
52 99 0.39
53 38 0.15
54 22 0.09
55 4 0.02
56 11 0.04
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (51 bp):
CAATTTTCCATAATCGGGGATACTCCAACCCTGGTTTTATTTTCAAAACAC
Found at i:218194 original size:51 final size:51
Alignment explanation
Indices: 218119--218339 Score: 207
Period size: 51 Copynumber: 4.3 Consensus size: 51
218109 TTACCTCCGA
* * * * * * *
218119 GGGGATACTCCCACCTCAGCTTTATTTCCAAAATATTGA-TTTCTCATAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTC-CATAATC
* *
218170 GGGGATAC-CTCAACCCCGGTTTTATTTCTAAAACACTAATTTTCCACAATC
1 GGGGATACTC-CAACCCCGGTTTTATTTCCAAAACACTAATTTTCCATAATC
* * *
218221 GAGGATACTCCAACCCCGGTTTTATCTT-CAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCGGTTTTAT-TTCCAAAACACTAATTTTCC-ATAATC
* * * *
218273 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAATTTT-CACAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCC-AAAACA-CTAATTTTCCATAATC
*
218325 GAGGATACTCCAACC
1 GGGGATACTCCAACC
218340 TCGTTATTTC
Statistics
Matches: 140, Mismatches: 22, Indels: 15
0.79 0.12 0.08
Matches are distributed among these distances:
50 1 0.01
51 74 0.53
52 51 0.36
53 7 0.05
54 7 0.05
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTCCATAATC
Found at i:218448 original size:262 final size:262
Alignment explanation
Indices: 217961--218448 Score: 809
Period size: 262 Copynumber: 1.9 Consensus size: 262
217951 TCATAATTGG
* *
217961 GGATACTCCAACCCTGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACTCCAACT
1 GGATACTCCAACCCCGGTTTTATCTTCAAAACACCAATTTTCCTTTAATCGGGGATACTCCAACT
* * *
218026 CCCATTTTATTTTCAAAAACACCAATTTTTCACAATCGAGGATACTTCAACCTCATTATTTCATC
66 CCCATTTTATTTCCAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCTCATTATTTCATC
* *
218091 GGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCCACCTCAGCTTTATTTCCAAAATATT
131 GGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCAGCTTTATTTCCAAAATATT
* **
218156 GATTTCTCATAATCGGGGATACCTCAACCCCGGTTTTATTTCTAAAACACTAATTTTCCACAATC
196 CATTTCTCATAATCGACGATACCTCAACCCCGGTTTTATTTCTAAAACACTAATTTTCCACAATC
218221 GA
261 GA
218223 GGATACTCCAACCCCGGTTTTATCTTCAAAACACCAATTTTCCTTTAATCGGGGATACTCCAACT
1 GGATACTCCAACCCCGGTTTTATCTTCAAAACACCAATTTTCCTTTAATCGGGGATACTCCAACT
* *
218288 CCGATTTTATTTCCAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCTCGTTATTTCATC
66 CCCATTTTATTTCCAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCTCATTATTTCATC
* *
218353 GGGGATACTCTAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTA-TTCTCAAAATAT
131 GGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCAGCTTTATTTC-CAAAATAT
*
218417 TCATTTCTCATAATTGACGATA-CTCCAACCCC
195 TCATTTCTCATAATCGACGATACCT-CAACCCC
218449 TTTATTTTCG
Statistics
Matches: 209, Mismatches: 15, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
261 5 0.02
262 204 0.98
ACGTcount: A:0.28, C:0.29, G:0.12, T:0.31
Consensus pattern (262 bp):
GGATACTCCAACCCCGGTTTTATCTTCAAAACACCAATTTTCCTTTAATCGGGGATACTCCAACT
CCCATTTTATTTCCAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCTCATTATTTCATC
GGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCAGCTTTATTTCCAAAATATT
CATTTCTCATAATCGACGATACCTCAACCCCGGTTTTATTTCTAAAACACTAATTTTCCACAATC
GA
Found at i:230212 original size:11 final size:11
Alignment explanation
Indices: 230193--230263 Score: 72
Period size: 11 Copynumber: 6.3 Consensus size: 11
230183 CTTCTCTTCT
230193 AAAAA-AAAAC
1 AAAAACAAAAC
230203 AAAAACAAAAGC
1 AAAAACAAAA-C
*
230215 AAAAAAAAAAAC
1 -AAAAACAAAAC
* *
230227 AAAAAATAAAAA
1 -AAAAACAAAAC
*
230239 AAAAACAAAAA
1 AAAAACAAAAC
230250 AAAAACAAAAC
1 AAAAACAAAAC
230261 AAA
1 AAA
230264 GAAAAAGAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
10 5 0.09
11 27 0.51
12 12 0.23
13 9 0.17
ACGTcount: A:0.87, C:0.10, G:0.01, T:0.01
Consensus pattern (11 bp):
AAAAACAAAAC
Found at i:230224 original size:18 final size:16
Alignment explanation
Indices: 230193--230269 Score: 91
Period size: 18 Copynumber: 4.5 Consensus size: 16
230183 CTTCTCTTCT
*
230193 AAAAAAAAACAAAAAC
1 AAAAAAAAAAAAAAAC
230209 AAAAGCAAAAAAAAAAAC
1 AAAA--AAAAAAAAAAAC
230227 AAAAAATAAAAAAAAAAC
1 -AAAAA-AAAAAAAAAAC
*
230245 AAAAAAAAAACAAAAC
1 AAAAAAAAAAAAAAAC
230261 AAAGAAAAA
1 AAA-AAAAA
230270 GAGAGAAAAG
Statistics
Matches: 54, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
16 17 0.31
17 11 0.20
18 22 0.41
19 4 0.07
ACGTcount: A:0.87, C:0.09, G:0.03, T:0.01
Consensus pattern (16 bp):
AAAAAAAAAAAAAAAC
Found at i:230284 original size:1 final size:1
Alignment explanation
Indices: 230193--230269 Score: 64
Period size: 1 Copynumber: 77.0 Consensus size: 1
230183 CTTCTCTTCT
* * ** * * * *
230193 AAAAAAAAACAAAAACAAAAGCAAAAAAAAAAACAAAAAATAAAAAAAAAACAAAAAAAAAACAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
230258 AACAAAGAAAAA
1 AAAAAAAAAAAA
230270 GAGAGAAAAG
Statistics
Matches: 57, Mismatches: 19, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 57 1.00
ACGTcount: A:0.87, C:0.09, G:0.03, T:0.01
Consensus pattern (1 bp):
A
Found at i:231352 original size:55 final size:55
Alignment explanation
Indices: 231287--231487 Score: 269
Period size: 55 Copynumber: 3.5 Consensus size: 55
231277 TTTCTCCTTT
*
231287 CGCCCTTTAGTCCTCAAAGAGCAGGACGCTTTTCAAAGCCCACACAAGTTGGTGG
1 CGCCTTTTAGTCCTCAAAGAGCAGGACGCTTTTCAAAGCCCACACAAGTTGGTGG
* *
231342 CGCCTTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCTGGTGG
1 CGCCTTTTAGTCCTCAAAGAGCAGGACGCTTTTCAAAGCCCACACAAGTTGGTGG
* *
231397 CACCTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
1 CGCCTTTTAGTCCTCAAAGAGCAGGACG-CTTTT-C----AAAGCCCACACAAGTTGGTGG
* *
231458 C-ACTTCTCAGTCCTCAAAGAGCAGGACGCT
1 CGCCTT-TTAGTCCTCAAAGAGCAGGACGCT
231488 CCCTCCTTTC
Statistics
Matches: 129, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
55 78 0.60
56 4 0.03
57 1 0.01
60 5 0.04
61 41 0.32
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.23
Consensus pattern (55 bp):
CGCCTTTTAGTCCTCAAAGAGCAGGACGCTTTTCAAAGCCCACACAAGTTGGTGG
Found at i:231528 original size:155 final size:155
Alignment explanation
Indices: 231342--231751 Score: 543
Period size: 155 Copynumber: 2.5 Consensus size: 155
231332 AAGTTGGTGG
231342 CGCCTTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTAG
1 CGCCTTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTAG
* *
231407 TCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTT-CTCAGTCC
66 TCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCT-AGTCC
231471 TCAAAGAGCAGGACGCTCCCTCCTTT
130 TCAAAGAGCAGGACGCTCCCTCCTTT
* * *
231497 CGCCTTTTTGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTTAG
1 CGCCTTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTAG
*
231562 TCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCGCACAAGTTGGTGGCACTTCCTAGTCCT
66 TCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCT
*
231627 CAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGT
131 CAAAGAGCAGGACG-C--T-----CCCTC-C---TT--T
* * * * *
231666 GGCACATTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCT
1 CGC-C-TTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTT
*
231731 AGTCCTCAAAGAGCAAGACGC
64 AGTCCTCAAAGAGCAGGACGC
231752 TCTCTTTTTT
Statistics
Matches: 224, Mismatches: 14, Indels: 18
0.88 0.05 0.07
Matches are distributed among these distances:
155 135 0.60
156 3 0.01
158 1 0.00
163 4 0.02
164 1 0.00
167 2 0.01
169 3 0.01
170 1 0.00
171 74 0.33
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24
Consensus pattern (155 bp):
CGCCTTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTAG
TCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCT
CAAAGAGCAGGACGCTCCCTCCTTT
Found at i:231560 original size:210 final size:212
Alignment explanation
Indices: 231188--231696 Score: 754
Period size: 210 Copynumber: 2.4 Consensus size: 212
231178 CTTCTCCTTC
231188 CACTTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACT
1 CACTTTT-AGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACT
**
231253 TC-CAGTCCTCAAAGAGCAGGACGCTTTCTCCTTTCGCCCTTTAGTCCTCAAAGAGCAGGACGCT
65 TCTCAGTCCTCAAAGAGCAGGACGCTCCCTCCTTTCGCCCTTTAGTCCTCAAAGAGCAGGACGCT
* *
231317 TTTCAAAGCCCACACAAGTTGGTGGCGCCTTTTAGTCCTCAAAGAGCAGGACGCCTT-T-C-AAA
130 TTTCAAAGCCCACACAAGCTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGCCTTCTCCTAAA
231379 GCCCACACAAGCTGGTGG
195 GCCCACACAAGCTGGTGG
231397 CACCTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACT
1 CA-CTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACT
* * *
231462 TCTCAGTCCTCAAAGAGCAGGACGCTCCCTCCTTTCGCCTTTTTGTCCTCAAAGAGCAGGATGCC
65 TCTCAGTCCTCAAAGAGCAGGACGCTCCCTCCTTTCGCCCTTTAGTCCTCAAAGAGCAGGACG-C
231527 TTTT-AAAGCCCACACAAGCTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTT
129 TTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGCCTTCTCC---
* *
231591 TAAAGCCCGCACAAGTTGGTGG
191 TAAAGCCCACACAAGCTGGTGG
* * *
231613 CACTTCCTAGTCCTCAAAGAGCAGGACGCC-TTT-C----AAAGCCCACACGAGTTGGTGGCACA
1 CACTT-TTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC-
231672 TT-TCAGTCCTCAAAGAGCAGGACGC
64 TTCTCAGTCCTCAAAGAGCAGGACGC
231697 CTTTTAAAGC
Statistics
Matches: 277, Mismatches: 12, Indels: 21
0.89 0.04 0.07
Matches are distributed among these distances:
209 61 0.22
210 157 0.57
211 8 0.03
212 1 0.00
214 1 0.00
215 6 0.02
216 43 0.16
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.25
Consensus pattern (212 bp):
CACTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTT
CTCAGTCCTCAAAGAGCAGGACGCTCCCTCCTTTCGCCCTTTAGTCCTCAAAGAGCAGGACGCTT
TTCAAAGCCCACACAAGCTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGCCTTCTCCTAAAG
CCCACACAAGCTGGTGG
Found at i:231583 original size:55 final size:55
Alignment explanation
Indices: 231499--231751 Score: 337
Period size: 55 Copynumber: 4.5 Consensus size: 55
231489 CCTCCTTTCG
* * *
231499 CCTTTTTGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
*
231554 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCGCACAAGTTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACG------CCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
231615 -CTTCCTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCA
1 CCTT-TTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
231670 CATTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
231725 CCTTCTAGTCCTCAAAGAGCAAGACGC
1 CCTTTTAGTCCTCAAAGAGCAGGACGC
231752 TCTCTTTTTT
Statistics
Matches: 173, Mismatches: 17, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
55 120 0.69
56 2 0.01
60 3 0.02
61 48 0.28
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (55 bp):
CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:231590 original size:94 final size:95
Alignment explanation
Indices: 231399--231580 Score: 269
Period size: 94 Copynumber: 1.9 Consensus size: 95
231389 GCTGGTGGCA
*
231399 CCTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTC
1 CCTTTTAGTCCTCAAAGAGCAGGATG-----TCCTTTTAAAGCCCACACAAGCTGGTGGCACTTC
231464 TCAGTCCTCAAAGAGCAGGACGCTCCCTCCTTTCG
61 TCAGTCCTCAAAGAGCAGGACGCTCCCTCCTTTCG
* *
231499 CCTTTTTGTCCTCAAAGAGCAGGATG-CCTTTTAAAGCCCACACAAGCTGGTGGCACCTT-TTAG
1 CCTTTTAGTCCTCAAAGAGCAGGATGTCCTTTTAAAGCCCACACAAGCTGGTGGCA-CTTCTCAG
231562 TCCTCAAAGAGCAGGACGC
65 TCCTCAAAGAGCAGGACGC
231581 CTTCTCCTTT
Statistics
Matches: 78, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
94 50 0.64
95 3 0.04
100 25 0.32
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (95 bp):
CCTTTTAGTCCTCAAAGAGCAGGATGTCCTTTTAAAGCCCACACAAGCTGGTGGCACTTCTCAGT
CCTCAAAGAGCAGGACGCTCCCTCCTTTCG
Found at i:231763 original size:116 final size:112
Alignment explanation
Indices: 231506--231751 Score: 338
Period size: 116 Copynumber: 2.2 Consensus size: 112
231496 TCGCCTTTTT
* * * *
231506 GTCCTCAAAGAGCAGGATGCCTTTT-AAAGCCCACACAAGCTGGTGGCACCTTTTAGTCCTCAAA
1 GTCCTCAAAGAGCAAGACGCCTTTTCAAAGCCCACACAAGCTGGTGGCACATTTCAGTCCTCAAA
*
231570 GAGCAGGACGCCTTCTCCTTTTAAAGCCCGCACAAGTTGGTGGCACTTCCTA
66 GAGCAGGACG----C-CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTA
* * *
231622 GTCCTCAAAGAGCAGGACGCC-TTTCAAAGCCCACACGAGTTGGTGGCACATTTCAGTCCTCAAA
1 GTCCTCAAAGAGCAAGACGCCTTTTCAAAGCCCACACAAGCTGGTGGCACATTTCAGTCCTCAAA
231686 GAGCAGGACG-CCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CTA
66 GAGCAGGACGCCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTA
231732 GTCCTCAAAGAGCAAGACGC
1 GTCCTCAAAGAGCAAGACGC
231752 TCTCTTTTTT
Statistics
Matches: 121, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
110 50 0.41
111 3 0.02
115 3 0.02
116 65 0.54
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (112 bp):
GTCCTCAAAGAGCAAGACGCCTTTTCAAAGCCCACACAAGCTGGTGGCACATTTCAGTCCTCAAA
GAGCAGGACGCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTA
Found at i:231777 original size:265 final size:265
Alignment explanation
Indices: 231291--231905 Score: 834
Period size: 265 Copynumber: 2.3 Consensus size: 265
231281 TCCTTTCGCC
* * *
231291 CTTTAGTCCTCAAAGAGCAGGACG----CT-TTTCAAAGCCCACACAAGTTGGTGGCGCCTTTTA
1 CTTTAGTCCTCAAAGAGCAGGACGCCTTCTCTTTTAAAGCCCACACAAGTTGGTGGC-ACTTCTA
* *
231351 GTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTAGTCCTCAAAG
65 GTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCTGGTGGCACATTTCAGTCCTCAAAG
*
231416 AGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCA
130 AGCAGGA--CC--TGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCA
* * * * * * *
231481 GGACGCTCCCTCCTTTCGCCTTTTTGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGC
191 AGACGCTCCCTCCTTTCACCCTTTAGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGC
231546 TGGTGGCACCT
256 TGGTGGC-CCT
*
231557 -TTTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCGCACAAGTTGGTGGCACTTCCT
1 CTTTAGTCCTCAAAGAGCAGGACGCCTTCT-CTTTTAAAGCCCACACAAGTTGGTGGCACTT-CT
* *
231621 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACATTTCAGTCCTCAAA
64 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCTGGTGGCACATTTCAGTCCTCAAA
231686 GAGCAGGA-C-GCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCT-AGTCCTCAAAGAGCAAG
129 GAGCAGGACCTGCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCTCAGTCCTCAAAGAGCAAG
* ** ** *
231748 ACGCTCTCTTTTTTCACCCTTTAGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACATGAGTTG
193 ACGCTCCCTCCTTTCACCCTTTAGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGCTG
231813 GTGGCCCT
258 GTGGCCCT
* * *
231821 CTCTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTG
1 CTTTAGTCCTCAAAGAGCAGGACGCC-TTCTCTTTT-AAAGCCCACACAAGTTGGTGGCAC-TTC
231886 TAGTCCTCAAAGAGCAGGAC
63 TAGTCCTCAAAGAGCAGGAC
231906 TCACTTTATT
Statistics
Matches: 311, Mismatches: 26, Indels: 24
0.86 0.07 0.07
Matches are distributed among these distances:
264 3 0.01
265 155 0.50
266 51 0.16
267 2 0.01
268 1 0.00
269 2 0.01
270 3 0.01
271 94 0.30
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (265 bp):
CTTTAGTCCTCAAAGAGCAGGACGCCTTCTCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTAG
TCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCTGGTGGCACATTTCAGTCCTCAAAGA
GCAGGACCTGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCAAGACG
CTCCCTCCTTTCACCCTTTAGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGCTGGTG
GCCCT
Found at i:232028 original size:46 final size:43
Alignment explanation
Indices: 231888--232054 Score: 171
Period size: 42 Copynumber: 3.8 Consensus size: 43
231878 GCACTTTGTA
* * *
231888 GTCCTCAAAGAGCAGGACTCACTTTATTTTCCGCTTTCT--TTT
1 GTCCTCAAAGAGCAGGACGCATTTTATTTTCC-TTTTCTCCTTT
* *
231930 GTCCTCAAAAAGCAGGACGCATTTTGTTTTCCTTTTCTCCTTT
1 GTCCTCAAAGAGCAGGACGCATTTTATTTTCCTTTTCTCCTTT
*
231973 GTCCTCAAAGAGCAGGACGC-TCTTTA-TTTCCTTCTTTTCCCTTCT
1 GTCCTCAAAGAGCAGGACGCAT-TTTATTTTCCTT-TTCT-CCTT-T
* * *
232018 AGTCCTCAAAGAGCAGGACACATTTCATTTTCTTTTT
1 -GTCCTCAAAGAGCAGGACGCATTTTATTTTCCTTTT
232055 TTTCTTTTTC
Statistics
Matches: 105, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
41 5 0.05
42 36 0.34
43 28 0.27
44 4 0.04
45 1 0.01
46 24 0.23
47 7 0.07
ACGTcount: A:0.20, C:0.26, G:0.14, T:0.40
Consensus pattern (43 bp):
GTCCTCAAAGAGCAGGACGCATTTTATTTTCCTTTTCTCCTTT
Found at i:232067 original size:43 final size:43
Alignment explanation
Indices: 231888--232067 Score: 166
Period size: 43 Copynumber: 4.1 Consensus size: 43
231878 GCACTTTGTA
* * *** *
231888 GTCCTCAAAGAGCAGGACTCACTTTATTTTC-CGCTTTCTTTT
1 GTCCTCAAAGAGCAGGACGCATTTTATTTTCTTTTTTTCCTTT
* * * *
231930 GTCCTCAAAAAGCAGGACGCATTTTGTTTTCCTTTTCTCCTTT
1 GTCCTCAAAGAGCAGGACGCATTTTATTTTCTTTTTTTCCTTT
* *
231973 GTCCTCAAAGAGCAGGACGC-TCTTTATTTCCTTCTTTTCCCTTCT
1 GTCCTCAAAGAGCAGGACGCAT-TTTATTTTCTT-TTTTTCCTT-T
* * *
232018 AGTCCTCAAAGAGCAGGACACATTTCATTTTCTTTTTTTTCTTT
1 -GTCCTCAAAGAGCAGGACGCATTTTATTTTCTTTTTTTCCTTT
*
232062 TTCCTC
1 GTCCTC
232068 GAAAAACGGG
Statistics
Matches: 111, Mismatches: 21, Indels: 11
0.78 0.15 0.08
Matches are distributed among these distances:
42 28 0.25
43 38 0.34
44 8 0.07
45 8 0.07
46 28 0.25
47 1 0.01
ACGTcount: A:0.18, C:0.27, G:0.13, T:0.42
Consensus pattern (43 bp):
GTCCTCAAAGAGCAGGACGCATTTTATTTTCTTTTTTTCCTTT
Found at i:232183 original size:40 final size:42
Alignment explanation
Indices: 232087--232186 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 42
232077 GACATACTCT
* *
232087 TTTTCACTTTGTCCTCAAGAAGCATGACACTTTCCTTTCCTTC
1 TTTTC-CTTTGTCCTCAAGAAGCAAGACACTTTCCATTCCTTC
* * * *
232130 TCTTCCTTCGTCCTCAAGGAGCAAGAC-CTATTTCATT-C-TC
1 TTTTCCTTTGTCCTCAAGAAGCAAGACACT-TTCCATTCCTTC
232170 TTTTCCTTTGTCCTCAA
1 TTTTCCTTTGTCCTCAA
232187 AAAGTGGGAC
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
40 17 0.35
41 3 0.06
42 24 0.50
43 4 0.08
ACGTcount: A:0.18, C:0.31, G:0.10, T:0.41
Consensus pattern (42 bp):
TTTTCCTTTGTCCTCAAGAAGCAAGACACTTTCCATTCCTTC
Found at i:232843 original size:19 final size:20
Alignment explanation
Indices: 232819--232880 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 20
232809 TTTTGAACTT
232819 CAAACAG-TTTGTATCGATA
1 CAAACAGATTTGTATCGATA
**
232838 CAAACAGAAAATGTATCGATA
1 CAAACAG-ATTTGTATCGATA
* *
232859 CATA-AGTTTTGTATCGATA
1 CAAACAGATTTGTATCGATA
232878 CAA
1 CAA
232881 TGTATCGCTA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
19 19 0.56
20 2 0.06
21 13 0.38
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (20 bp):
CAAACAGATTTGTATCGATA
Found at i:232929 original size:13 final size:13
Alignment explanation
Indices: 232911--232936 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
232901 ACCAAGGAAA
232911 TGTATCGATACAT
1 TGTATCGATACAT
232924 TGTATCGATACAT
1 TGTATCGATACAT
232937 CGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:235366 original size:52 final size:51
Alignment explanation
Indices: 235298--235693 Score: 195
Period size: 52 Copynumber: 7.6 Consensus size: 51
235288 TTAAGTTTCT
* *
235298 CAATTGTT-CATAATCGGGGATACTCCAACCCTAGTTTTATTTTC-AAAACAC
1 CAATT-TTCCATAATCGGGGATACTCCAACCCGA-TTTTATTTCCAAAAACAC
*
235349 CAATTTTCCGTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACAC
1 CAATTTTCC-ATAATCGGGGATACTCCAAC-CCGATTTTATTTCCAAAAACAC
* * * * ** * *
235402 TAATTTTTCACAATCGAGGATACTCCAACCTC-A--TTATTTCATCGGGGATACTC
1 CAATTTTCCATAATCGGGGATACTCCAACC-CGATTTTATTTC--C--AAAAACAC
** * * * * * *
235455 CAA--CCCCATTACTTCCGAGGGGATACTCCCACCCCAGCTTTATTTCC-AAAATAT
1 CAATTTTCCA-TA-AT-C--GGGGATACTCCAACCCGA-TTTTATTTCCAAAAACAC
** * * * * *
235509 TGA-TTTCTCATAATCAGGGATACCCCAATCTCGGTTTTATTT-CTAAAACAC
1 CAATTTTC-CATAATCGGGGATACTCCAA-CCCGATTTTATTTCCAAAAACAC
* * * * *
235560 TAATTTTTCACAATCGAGGATACTCCAACCCCGGTTTTATCTT-C-AAAACAC
1 CAATTTTCCATAATCGGGGATACTCCAA-CCCGATTTTAT-TTCCAAAAACAC
* *
235611 CAATTTTCCTTTAATCGGGGATACTCCAACTCTGATTTTATTTCCAAAAACAC
1 CAATTTTCC-ATAATCGGGGATACTCCAAC-CCGATTTTATTTCCAAAAACAC
* * *
235664 CAATTTTTCACAATCGAGGATACTCCAACC
1 CAATTTTCCATAATCGGGGATACTCCAACC
235694 TCGTTATTTC
Statistics
Matches: 259, Mismatches: 58, Indels: 56
0.69 0.16 0.15
Matches are distributed among these distances:
49 7 0.03
50 3 0.01
51 79 0.31
52 97 0.37
53 40 0.15
54 5 0.02
55 4 0.02
56 16 0.06
57 1 0.00
59 7 0.03
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (51 bp):
CAATTTTCCATAATCGGGGATACTCCAACCCGATTTTATTTCCAAAAACAC
Found at i:235450 original size:28 final size:28
Alignment explanation
Indices: 235414--235490 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
235404 ATTTTTCACA
* * *
235414 ATCGAGGATACTCCAACCTCATTATTTC
1 ATCGGGGATACTCCAACCCCATTACTTC
235442 ATCGGGGATACTCCAACCCCATTACTTC
1 ATCGGGGATACTCCAACCCCATTACTTC
*** *
235470 CGAGGGGATACTCCCACCCCA
1 ATCGGGGATACTCCAACCCCA
235491 GCTTTATTTC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.26, C:0.35, G:0.16, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCATTACTTC
Found at i:235581 original size:51 final size:50
Alignment explanation
Indices: 235526--235696 Score: 200
Period size: 52 Copynumber: 3.3 Consensus size: 50
235516 TCATAATCAG
* * *
235526 GGATACCCCAATCTCGGTTTTATTTCTAAAACACTAATTTTTCACAATCGA
1 GGATACTCCAACCTCGGTTTTATTTC-AAAACACCAATTTTTCACAATCGA
* * ** *
235577 GGATACTCCAACCCCGGTTTTATCTTCAAAACACCAATTTTCCTTTAATCGG
1 GGATACTCCAACCTCGGTTTTAT-TTCAAAACACCAATTTTTC-ACAATCGA
*
235629 GGATACTCCAA-CTCTGATTTTATTTCCAAAAACACCAATTTTTCACAATCGA
1 GGATACTCCAACCTC-GGTTTTATTT-C-AAAACACCAATTTTTCACAATCGA
235681 GGATACTCCAACCTCG
1 GGATACTCCAACCTCG
235697 TTATTTCATC
Statistics
Matches: 100, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
51 38 0.38
52 44 0.44
53 18 0.18
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (50 bp):
GGATACTCCAACCTCGGTTTTATTTCAAAACACCAATTTTTCACAATCGA
Found at i:235780 original size:262 final size:262
Alignment explanation
Indices: 235299--235798 Score: 829
Period size: 262 Copynumber: 1.9 Consensus size: 262
235289 TAAGTTTCTC
* * * *
235299 AATTGTTCATAATCGGGGATACTCCAACCCTAGTTTTATTTTCAAAACACCAATTTTCCGTTAAT
1 AATTGTTCACAATCGAGGATACTCCAACCCCAGTTTTATCTTCAAAACACCAATTTTCCGTTAAT
*
235364 CGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACTAATTTTTCACAATCGAGGATACTCCA
66 CGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCA
* * *
235429 ACCTCATTATTTCATCGGGGATACTCCAACCCCATTACTTCCGAGGGGATACTCCCACCCCAGCT
131 ACCTCATTATTTCATCGGGAATACTCCAACCCCATTACCTCCGAGGGGATACTCCAACCCCAGCT
*
235494 TTATTTCCAAAATATTGATTTCTCATAATCAGGGATACCCCAATCTCGGTTTTATTTCTAAAACA
196 TTATTCCCAAAATATTGATTTCTCATAATCAGGGATACCCCAATCTCGGTTTTATTTCTAAAACA
235559 CT
261 CT
* * *
235561 AATTTTTCACAATCGAGGATACTCCAACCCCGGTTTTATCTTCAAAACACCAATTTTCCTTTAAT
1 AATTGTTCACAATCGAGGATACTCCAACCCCAGTTTTATCTTCAAAACACCAATTTTCCGTTAAT
*
235626 CGGGGATACTCCAACTCTGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCA
66 CGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCA
* * *
235691 ACCTCGTTATTTCATCGGGAATACTCCAACCTCATTACCTCCGAGGGGATACTCCAACCCCGGCT
131 ACCTCATTATTTCATCGGGAATACTCCAACCCCATTACCTCCGAGGGGATACTCCAACCCCAGCT
** *
235756 TTATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAA
196 TTATTCCCAAAATATTGATTTCTCATAATCAGGGATACCCCAA
235799 CCCCGTTATT
Statistics
Matches: 219, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
262 219 1.00
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (262 bp):
AATTGTTCACAATCGAGGATACTCCAACCCCAGTTTTATCTTCAAAACACCAATTTTCCGTTAAT
CGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCA
ACCTCATTATTTCATCGGGAATACTCCAACCCCATTACCTCCGAGGGGATACTCCAACCCCAGCT
TTATTCCCAAAATATTGATTTCTCATAATCAGGGATACCCCAATCTCGGTTTTATTTCTAAAACA
CT
Found at i:235855 original size:79 final size:79
Alignment explanation
Indices: 235738--235963 Score: 285
Period size: 79 Copynumber: 2.9 Consensus size: 79
235728 CCTCCGAGGG
* * * * *
235738 GATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCC
1 GATACTCCAACCCCGACTTTATTTCCAAAATATCGATTTCTCACAATCGGGGATACTCCAACCCC
*
235803 GTTA-TTTCTGAGGA
66 GTTATTTTC-AAGGA
* * * * * *
235817 GATACTCCAATCCTGATTTTATTTCC-TAATCATCGATTTTTCACAACCGGGGATACTCCAACCC
1 GATACTCCAACCCCGACTTTATTTCCAAAAT-ATCGATTTCTCACAATCGGGGATACTCCAACCC
*
235881 CGTTATTTTCAAGGG
65 CGTTATTTTCAAGGA
* *
235896 GATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTCTCACAATCGGGGATACTCCAACCCC
1 GATACTCCAACCCCGACTTTATTTCCAAAATATCGATTTCTCACAATCGGGGATACTCCAACCCC
235961 GTT
66 GTT
235964 GTTATCTCCA
Statistics
Matches: 123, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
78 3 0.02
79 113 0.92
80 7 0.06
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.32
Consensus pattern (79 bp):
GATACTCCAACCCCGACTTTATTTCCAAAATATCGATTTCTCACAATCGGGGATACTCCAACCCC
GTTATTTTCAAGGA
Found at i:238325 original size:2 final size:2
Alignment explanation
Indices: 238318--238352 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
238308 CCAACTTAAC
238318 TA TA TA TA TA TA TA TA TA TA TA TA TA -A GTA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA T
238353 TACCCTCCGC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.94
3 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:246429 original size:20 final size:20
Alignment explanation
Indices: 246391--246429 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
246381 TCAATATTTT
* *
246391 CAATTGAATATAAATGTTTC
1 CAATTGAATAAAAAGGTTTC
*
246411 CAATTGAGTAAAAAGGTTT
1 CAATTGAATAAAAAGGTTT
246430 TCATTGTTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (20 bp):
CAATTGAATAAAAAGGTTTC
Found at i:248986 original size:3 final size:3
Alignment explanation
Indices: 248980--249009 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
248970 TTTAAGCAGC
248980 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
249010 TACAAAGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:249757 original size:16 final size:17
Alignment explanation
Indices: 249726--249760 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
249716 TTAGTGTATC
*
249726 AAAATTTTTATAAATAT
1 AAAATATTTATAAATAT
249743 AAAATATTT-TAAATAT
1 AAAATATTTATAAATAT
249759 AA
1 AA
249761 TTATGGTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAATATTTATAAATAT
Found at i:251762 original size:13 final size:13
Alignment explanation
Indices: 251744--251771 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
251734 TAAAAGTTAG
251744 GATTAGAGATTTA
1 GATTAGAGATTTA
251757 GATTAGAGATTTA
1 GATTAGAGATTTA
251770 GA
1 GA
251772 ACTAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (13 bp):
GATTAGAGATTTA
Found at i:252065 original size:29 final size:29
Alignment explanation
Indices: 251969--252068 Score: 94
Period size: 30 Copynumber: 3.4 Consensus size: 29
251959 ATTTGTAACC
* * * * *
251969 AAAGTAAAATGCATAAATTTAACTTGCAAG
1 AAAGTAAATTGTATAAA-TTAAATTACAAA
* * *
251999 AAACTAAAGTGTATAAATTAAAATTATAAGA
1 AAAGTAAATTGTATAAATT-AAATTACAA-A
252030 AAA-TAAATTGTATAAATTAAATTACAAA
1 AAAGTAAATTGTATAAATTAAATTACAAA
252058 AAAGTAAATTG
1 AAAGTAAATTG
252069 CAAAAAGAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
28 4 0.07
29 17 0.29
30 34 0.59
31 3 0.05
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.29
Consensus pattern (29 bp):
AAAGTAAATTGTATAAATTAAATTACAAA
Found at i:252768 original size:34 final size:34
Alignment explanation
Indices: 252704--252886 Score: 260
Period size: 34 Copynumber: 5.4 Consensus size: 34
252694 TGGCCGAACC
* *
252704 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
252737 TGTTGACTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
252771 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
252805 TATTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
252839 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
252873 TGTTGATTAAATGG
1 TGTTGATTAAATGG
252887 TGGTTTTTAC
Statistics
Matches: 132, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 11 0.08
34 121 0.92
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:257366 original size:34 final size:34
Alignment explanation
Indices: 257300--257484 Score: 264
Period size: 34 Copynumber: 5.5 Consensus size: 34
257290 AAGTGGGAGA
* *
257300 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
257333 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
257367 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
257401 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
257435 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
257469 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
257485 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 121 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:258512 original size:14 final size:13
Alignment explanation
Indices: 258493--258530 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
258483 GTTTACTAAA
258493 AAATTTTACATATG
1 AAATTTTACAT-TG
*
258507 AAATTTTA-ATTT
1 AAATTTTACATTG
258519 AAATTTTACATT
1 AAATTTTACATT
258531 CAAAGTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 9 0.41
13 5 0.23
14 8 0.36
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (13 bp):
AAATTTTACATTG
Found at i:258524 original size:12 final size:13
Alignment explanation
Indices: 258493--258539 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
258483 GTTTACTAAA
*
258493 AAATTTTACATATG
1 AAATTTTACAT-TC
*
258507 AAATTTTA-ATTT
1 AAATTTTACATTC
258519 AAATTTTACATTC
1 AAATTTTACATTC
*
258532 AAAGTTTA
1 AAATTTTA
258540 ATAAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 9 0.31
13 12 0.41
14 8 0.28
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (13 bp):
AAATTTTACATTC
Found at i:259853 original size:28 final size:28
Alignment explanation
Indices: 259812--259868 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
259802 GCTTTCAACA
*
259812 AACTACTATAAACTAAAACAAAGAATCG
1 AACTAATATAAACTAAAACAAAGAATCG
* *
259840 AACTAATATCAACTAAAACAAAGTATCG
1 AACTAATATAAACTAAAACAAAGAATCG
259868 A
1 A
259869 TGAAACAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.56, C:0.18, G:0.07, T:0.19
Consensus pattern (28 bp):
AACTAATATAAACTAAAACAAAGAATCG
Found at i:261544 original size:19 final size:18
Alignment explanation
Indices: 261522--261575 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
261512 TTTTTCAACT
*
261522 TTTTTTCATTTTTTTATAA
1 TTTTTTAATTTTTTTAT-A
261541 TTTTTATAATTTTTTT-TA
1 TTTTT-TAATTTTTTTATA
261559 TTTTTTAAGTTTTTTTA
1 TTTTTTAA-TTTTTTTA
261576 GTACGTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 3 0.10
18 13 0.42
19 6 0.19
20 9 0.29
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTTTTAATTTTTTTATA
Found at i:261562 original size:17 final size:17
Alignment explanation
Indices: 261542--261575 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
261532 TTTTTATAAT
*
261542 TTTTATAATTTTTTTTA
1 TTTTATAAGTTTTTTTA
*
261559 TTTTTTAAGTTTTTTTA
1 TTTTATAAGTTTTTTTA
261576 GTACGTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTATAAGTTTTTTTA
Found at i:261571 original size:9 final size:10
Alignment explanation
Indices: 261531--261596 Score: 57
Period size: 10 Copynumber: 6.6 Consensus size: 10
261521 TTTTTTTCAT
261531 TTTTTTATA-
1 TTTTTTATAG
* *
261540 ATTTTTATAA
1 TTTTTTATAG
*
261550 TTTTTTTTA-
1 TTTTTTATAG
261559 TTTTTTA-AG
1 TTTTTTATAG
261568 TTTTTTTAGTACG
1 -TTTTTTA-TA-G
261581 TTTTTTATAG
1 TTTTTTATAG
261591 TTTTTT
1 TTTTTT
261597 TTAAGTTATA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
8 1 0.02
9 14 0.30
10 21 0.45
11 2 0.04
12 8 0.17
13 1 0.02
ACGTcount: A:0.20, C:0.02, G:0.06, T:0.73
Consensus pattern (10 bp):
TTTTTTATAG
Found at i:261725 original size:21 final size:22
Alignment explanation
Indices: 261699--261751 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
261689 AATCTTGTAC
*
261699 TTTTTTTTAGTTTTACTTTAT-
1 TTTTTTTTAGTTTTACATTATA
261720 TTTTTTTTAGTTTTACATTATA
1 TTTTTTTTAGTTTTACATTATA
*
261742 TTTTTGTTAG
1 TTTTTTTTAG
261752 GTCTCTCTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 20 0.69
22 9 0.31
ACGTcount: A:0.17, C:0.04, G:0.08, T:0.72
Consensus pattern (22 bp):
TTTTTTTTAGTTTTACATTATA
Found at i:265258 original size:89 final size:89
Alignment explanation
Indices: 265058--265665 Score: 661
Period size: 89 Copynumber: 6.8 Consensus size: 89
265048 AAAAAAATTG
* * * * * * *
265058 TCATGTCAGAAGGAATCCGATACCCACATACGTCTGTCATATCTTTC-AGGTTCCAAAAAATTTA
1 TCATGTTAGAAGGAATCTGATACCCATATGCATCTGTCACATCTTTCGA-GTTCCAAGAAATTTA
265122 TTTAGTC-ATTAGTCAAATATTTTCTA
65 -TTAG-CAATTAGTCAAATATTTTCTA
* * *
265148 TCATGTTAGAAGAAATTTGATACCCATATGCATCTGTCACATCTTTCGAGTTCTAAGAAATTTAT
1 TCATGTTAGAAGGAATCTGATACCCATATGCATCTGTCACATCTTTCGAGTTCCAAGAAATTTAT
* * *
265213 TAGTAATTAGTCAAATATTTTATG
66 TAGCAATTAGTCAAATATTTTCTA
*
265237 TCATATTAGAAGGAATCTGATACCCATATGCATCTGTCACATCTTTC-AGATTCCAAGAAATTTA
1 TCATGTTAGAAGGAATCTGATACCCATATGCATCTGTCACATCTTTCGAG-TTCCAAGAAATTTA
*
265301 TTAGCAATTAGTTAAATATTTTCTA
65 TTAGCAATTAGTCAAATATTTTCTA
* * * * * * * *
265326 TCGTGTTAAAAAGAATCTGACACTCACATGCATCTGTCACATCTTTTGAGTTTCAAGAAATTTAT
1 TCATGTTAGAAGGAATCTGATACCCATATGCATCTGTCACATCTTTCGAGTTCCAAGAAATTTAT
* * * *
265391 TAACCATTAGTCAAATATTTCCTG
66 TAGCAATTAGTCAAATATTTTCTA
* * * *
265415 TCATGTTAAAAGGAATCTGATATCTACATAT--ATATGTCACATCTTTCGGGTTCCAAGAAATTT
1 TCATGTTAGAAGGAATCTGATA-C-CCATATGCATCTGTCACATCTTTCGAGTTCCAAGAAATTT
* * * *
265478 ATTAACCATTAGTTAAATATTTTTTA
64 ATTAGCAATTAGTCAAATATTTTCTA
* * * * *
265504 TCGTGTTAGAAGGAATCTGATACCTATATGCATTTATCACATCTTTCGGGTTCCAAGAAATTTAT
1 TCATGTTAGAAGGAATCTGATACCCATATGCATCTGTCACATCTTTCGAGTTCCAAGAAATTTAT
* *
265569 TAGTAATTAGTCAAATATTTTATAA
66 TAGCAATTAGTCAAATATTTTCT-A
* * * * * * *
265594 T-AGTGTCAGAATGAATCTGATACCCACATGCATTTGTCACATCTTTTGGGTTCCAAAAAATTTA
1 TCA-TGTTAGAAGGAATCTGATACCCATATGCATCTGTCACATCTTTCGAGTTCCAAGAAATTTA
265658 TTAGCAAT
65 TTAGCAAT
265666 CTGTCATCTA
Statistics
Matches: 440, Mismatches: 68, Indels: 20
0.83 0.13 0.04
Matches are distributed among these distances:
87 4 0.01
88 3 0.01
89 310 0.70
90 118 0.27
91 5 0.01
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (89 bp):
TCATGTTAGAAGGAATCTGATACCCATATGCATCTGTCACATCTTTCGAGTTCCAAGAAATTTAT
TAGCAATTAGTCAAATATTTTCTA
Found at i:265389 original size:178 final size:178
Alignment explanation
Indices: 265056--266156 Score: 937
Period size: 178 Copynumber: 6.3 Consensus size: 178
265046 GTAAAAAAAT
* * * * * *
265056 TGTCATGTCAGAAGGAATCCGATACCCACATACGTCTGTCATATCTTTCAGGTTCCAAAAAATTT
1 TGTCATGTCAGAAGGAATCTGATACCCATATGCATCTGTCACATCTTTCAGGTTCCAAGAAATTT
* * * *
265121 ATTTAGTC-ATTAGTCAAATATTTTCTATCATGTT-AGAAGAAATTTGATACCCATATGCATCTG
66 A-TTAG-CAATTAGTCAAATATTTTCTATCGTGTTAAAAAG-AATCTGATACCCACATGCATCTG
* *
265184 TCACATCTTTCGAG-TTCTAAGAAATTTATTAGTAATTAGTCAAATATTTTA
128 TCACATCTTTCGAGTTTC-AAGAAATTTATTAGCAATTAGTCAAATATTTTC
* * *
265235 TGTCATATTAGAAGGAATCTGATACCCATATGCATCTGTCACATCTTTCAGATTCCAAGAAATTT
1 TGTCATGTCAGAAGGAATCTGATACCCATATGCATCTGTCACATCTTTCAGGTTCCAAGAAATTT
* * *
265300 ATTAGCAATTAGTTAAATATTTTCTATCGTGTTAAAAAGAATCTGACACTCACATGCATCTGTCA
66 ATTAGCAATTAGTCAAATATTTTCTATCGTGTTAAAAAGAATCTGATACCCACATGCATCTGTCA
* * * *
265365 CATCTTTTGAGTTTCAAGAAATTTATTAACCATTAGTCAAATATTTCC
131 CATCTTTCGAGTTTCAAGAAATTTATTAGCAATTAGTCAAATATTTTC
* * * * *
265413 TGTCATGTTAAAAGGAATCTGATATCTACATAT--ATATGTCACATCTTTCGGGTTCCAAGAAAT
1 TGTCATGTCAGAAGGAATCTGATA-C-CCATATGCATCTGTCACATCTTTCAGGTTCCAAGAAAT
* * * * * * * * * *
265476 TTATTAACCATTAGTTAAATATTTTTTATCGTGTTAGAAGGAATCTGATACCTATATGCATTTAT
64 TTATTAGCAATTAGTCAAATATTTTCTATCGTGTTAAAAAGAATCTGATACCCACATGCATCTGT
* * * *
265541 CACATCTTTCGGGTTCCAAGAAATTTATTAGTAATTAGTCAAATATTTTA
129 CACATCTTTCGAGTTTCAAGAAATTTATTAGCAATTAGTCAAATATTTTC
* * * * ** *
265591 TAAT-AGTGTCAGAATGAATCTGATACCCACATGCATTTGTCACATCTTTTGGGTTCCAAAAAAT
1 T-GTCA-TGTCAGAAGGAATCTGATACCCATATGCATCTGTCACATCTTTCAGGTTCCAAGAAAT
* *
265655 TTATTAGC-A--A-TC------TGTC-ATC----TAAGAAGAAATCTGATACCCACATGCATCTG
64 TTATTAGCAATTAGTCAAATATTTTCTATCGTGTTAAAAAG-AATCTGATACCCACATGCATCTG
* *
265705 TCACATCTTTCGAG-TTCTAAAAAATTTATTAGCCATTAGTCAAATATTTTC
128 TCACATCTTTCGAGTTTC-AAGAAATTTATTAGCAATTAGTCAAATATTTTC
* * * * * * *
265756 TATCGTGTCAGAAAGAAT-TCGATACCCATATGCATCTATTACATCTTT-TGAGTTTCAAGAAAT
1 TGTCATGTCAGAAGGAATCT-GATACCCATATGCATCTGTCACATCTTTCAG-GTTCCAAGAAAT
* * * * ** * *
265819 TTATTAGCAATTGGTCATATATTTTTTGTCGTGTCCAAAAGAATTTGATACCCACATGTATCTGT
64 TTATTAGCAATTAGTCAAATATTTTCTATCGTGTTAAAAAGAATCTGATACCCACATGCATCTGT
* *
265884 CATATGTTTC-AGGTTTCAAGAAATTTATTAGCAATTAGTCAAATATTTTC
129 CACATCTTTCGA-GTTTCAAGAAATTTATTAGCAATTAGTCAAATATTTTC
* * *
265934 TGTCGTGTCAGAAGGAATCTGATACCC--A--C-T-TG---C-TC-TTGAGCTT-CAAGAAATTT
1 TGTCATGTCAGAAGGAATCTGATACCCATATGCATCTGTCACATCTTTCAGGTTCCAAGAAATTT
* * * * * * * * * *
265987 ACTAGCCATTAGTC-AATATTTTCTGTCGTGTCAGAAGGAATCTGATACCTAAATACATTTGTCA
66 ATTAGCAATTAGTCAAATATTTTCTATCGTGTTAAAAAGAATCTGATACCCACATGCATCTGTCA
* * * * * * *
266051 CATCTTTCGGGTTCCAAGAAATTTATTAACCATTAATTAAATATTCTC
131 CATCTTTCGAGTTTCAAGAAATTTATTAGCAATTAGTCAAATATTTTC
* * * * * * * * *
266099 TATCGTATCAGAAGGAATTTAATACCCACATGCATCTGTTATATCTTTCAAGTTCCAA
1 TGTCATGTCAGAAGGAATCTGATACCCATATGCATCTGTCACATCTTTCAGGTTCCAA
266157 AATTAATTTT
Statistics
Matches: 745, Mismatches: 131, Indels: 94
0.77 0.14 0.10
Matches are distributed among these distances:
163 2 0.00
164 62 0.08
165 163 0.22
166 21 0.03
167 5 0.01
168 8 0.01
169 4 0.01
170 1 0.00
171 2 0.00
172 1 0.00
173 1 0.00
174 3 0.00
175 5 0.01
176 7 0.01
177 9 0.01
178 322 0.43
179 124 0.17
180 5 0.01
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (178 bp):
TGTCATGTCAGAAGGAATCTGATACCCATATGCATCTGTCACATCTTTCAGGTTCCAAGAAATTT
ATTAGCAATTAGTCAAATATTTTCTATCGTGTTAAAAAGAATCTGATACCCACATGCATCTGTCA
CATCTTTCGAGTTTCAAGAAATTTATTAGCAATTAGTCAAATATTTTC
Found at i:265783 original size:89 final size:90
Alignment explanation
Indices: 265678--266153 Score: 431
Period size: 89 Copynumber: 5.5 Consensus size: 90
265668 GTCATCTAAG
* *
265678 AAGAAATCTGATACCCACATGCATCTGTCACATCTTTCGAGTTCTAAAAAATTTATTAGCCATTA
1 AAGAATTCTGATACCCACATGCATCTGTCACATCTTTCGAGTTCTAAGAAATTTATTAGCCATTA
*
265743 GTCAAATATTTTCTATCGTGTCAGA
66 GTCAAATATTTTCTGTCGTGTCAGA
* * * * *
265768 AAGAATTC-GATACCCATATGCATCTATTACATCTTTTGAGTT-TCAAGAAATTTATTAGCAATT
1 AAGAATTCTGATACCCACATGCATCTGTCACATCTTTCGAGTTCT-AAGAAATTTATTAGCCATT
* * *
265831 GGTCATATATTTTTTGTCGTGTCCA-A
65 AGTCAAATATTTTCTGTCGTGT-CAGA
* * * *
265857 AAGAATT-TGATACCCACATGTATCTGTCATATGTTTC-AGGTT-TCAAGAAATTTATTAGCAAT
1 AAGAATTCTGATACCCACATGCATCTGTCACATCTTTCGA-GTTCT-AAGAAATTTATTAGCCAT
265919 TAGTCAAATATTTTCTGTCGTGTCAGA
64 TAGTCAAATATTTTCTGTCGTGTCAGA
* *
265946 AGGAA-TCTGATA-CC-CA--C-T-TG---C-TC-TT-GAGCTTC-AAGAAATTTACTAGCCATT
1 AAGAATTCTGATACCCACATGCATCTGTCACATCTTTCGAG-TTCTAAGAAATTTATTAGCCATT
265997 AGTC-AATATTTTCTGTCGTGTCAGA
65 AGTCAAATATTTTCTGTCGTGTCAGA
* * * * * * * *
266022 AGGAA-TCTGATACCTAAATACATTTGTCACATCTTTCGGGTTCCAAGAAATTTATTAACCATTA
1 AAGAATTCTGATACCCACATGCATCTGTCACATCTTTCGAGTTCTAAGAAATTTATTAGCCATTA
* * * * *
266086 ATTAAATATTCTCTATCGTATCAGA
66 GTCAAATATTTTCTGTCGTGTCAGA
* * * * *
266111 AGGAATT-TAATACCCACATGCATCTGTTATATCTTTCAAGTTC
1 AAGAATTCTGATACCCACATGCATCTGTCACATCTTTCGAGTTC
266154 CAAAATTAAT
Statistics
Matches: 316, Mismatches: 46, Indels: 49
0.77 0.11 0.12
Matches are distributed among these distances:
76 33 0.10
77 23 0.07
78 6 0.02
79 1 0.00
80 1 0.00
81 1 0.00
82 2 0.01
83 2 0.01
84 1 0.00
85 1 0.00
86 2 0.01
87 7 0.02
88 28 0.09
89 198 0.63
90 10 0.03
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (90 bp):
AAGAATTCTGATACCCACATGCATCTGTCACATCTTTCGAGTTCTAAGAAATTTATTAGCCATTA
GTCAAATATTTTCTGTCGTGTCAGA
Found at i:266031 original size:343 final size:342
Alignment explanation
Indices: 265061--266156 Score: 919
Period size: 343 Copynumber: 3.2 Consensus size: 342
265051 AAAATTGTCA
* * * * * * * *
265061 TGTCAGAAGGAATCCGATACCCACATACGTCTGTCATATCTTTC-AGGTTCCAAAAAATTTATTT
1 TGTCAGAAAGAATTCGATACCCATATGCATCTGTTACATCTTTCGA-GTTCCAAGAAATTTA-TT
* * * *
265125 AGTC-ATTAGTCAAATATTTTCTATCATGTTAG-AAGAAATTTGATACCCATATGCATCTGTCAC
64 A-ACAATTAGTCAAATATTTTTTATCGTGTCAGAAAG-AATTTGATACCCATATGCATCTGTCAC
* * *
265188 ATCTTTCGAG-TTCTAAGAAATTTATTAGTAATTAGTCAAATATTTTATGTCATATTAGAAGGAA
127 ATCTTTCG-GTTTC-AAGAAATTTATTAGTAATTAGTCAAATATTTTATGTCGTGTCAGAAGGAA
* * *
265252 TCTGATACCCATATGCATCTGTCACATCTTTCAGATTCCAAGAAATTTATTAGCAATTAGTTAAA
190 TCTGATACCC--A--C-T-TG---CATC-TTGAGCTT-CAAGAAATTTACTAGCAATTAG-T-AA
* * * * *
265317 TATTTTCTATCGTGTTAA-AAAGAATCTGACACTCACATGCATCTGTCACATCTTTTGAGTT-TC
242 TATTTTCTGTCGTG-TAAGAAGGAATCTGATACCCACATGCATCTGTCACATCTTTCGAGTTCT-
* * *
265380 AAGAAATTTATTAACCATTAGTCAAATATTTCCTGTCA
305 AAGAAATTTATTAACCATTAGTCAAATATTTTCTATCG
* * * * *
265418 TGTTA-AAAGGAA-TCTGATATCTACATAT--ATATGTCACATCTTTCGGGTTCCAAGAAATTTA
1 TGTCAGAAA-GAATTC-GATA-C-CCATATGCATCTGTTACATCTTTCGAGTTCCAAGAAATTTA
* * * * * * * *
265479 TTAACCATTAGTTAAATATTTTTTATCGTGTTAGAAGGAATCTGATACCTATATGCATTTATCAC
62 TTAACAATTAGTCAAATATTTTTTATCGTGTCAGAAAGAATTTGATACCCATATGCATCTGTCAC
* * * *
265544 ATCTTTCGGGTTCCAAGAAATTTATTAGTAATTAGTCAAATATTTTATAATAGTGTCAGAATGAA
127 ATCTTTC-GGTTTCAAGAAATTTATTAGTAATTAGTCAAATATTTTAT-GTCGTGTCAGAAGGAA
* * ******* * * ** * ***
265609 TCTGATACCCACATGCAT-TTGTCA-CATCTTTTGGGTTCCAAAAAATT--TATTAGCAATCTGT
190 TCTGATACCCACTTGCATCTTG--AGCTTCAAGAAATTTACTAGCAATTAGTAATA-TTTTCTGT
* * * *
265670 CATCTAAGAAGAAATCTGATACCCACATGCATCTGTCACATCTTTCGAGTTCTAAAAAATTTATT
252 CGTGTAAGAAGGAATCTGATACCCACATGCATCTGTCACATCTTTCGAGTTCTAAGAAATTTATT
*
265735 AGCCATTAGTCAAATATTTTCTATCG
317 AACCATTAGTCAAATATTTTCTATCG
* * * *
265761 TGTCAGAAAGAATTCGATACCCATATGCATCTATTACATCTTTTGAGTTTCAAGAAATTTATTAG
1 TGTCAGAAAGAATTCGATACCCATATGCATCTGTTACATCTTTCGAGTTCCAAGAAATTTATTAA
* * * * * * *
265826 CAATTGGTCATATATTTTTTGTCGTGTCCA-AAAGAATTTGATACCCACATGTATCTGTCATATG
66 CAATTAGTCAAATATTTTTTATCGTGT-CAGAAAGAATTTGATACCCATATGCATCTGTCACATC
* *
265890 TTTCAGGTTTCAAGAAATTTATTAGCAATTAGTCAAATATTTTCTGTCGTGTCAGAAGGAATCTG
130 TTTC-GGTTTCAAGAAATTTATTAGTAATTAGTCAAATATTTTATGTCGTGTCAGAAGGAATCTG
* *
265955 ATACCCACTTGC-TCTTGAGCTTCAAGAAATTTACTAGCCATTAGTCAATATTTTCTGTCGTGTC
194 ATACCCACTTGCATCTTGAGCTTCAAGAAATTTACTAGCAATTAGT-AATATTTTCTGTCGTGTA
* * * * * *
266019 AGAAGGAATCTGATACCTAAATACATTTGTCACATCTTTCGGGTTCCAAGAAATTTATTAACCAT
258 AGAAGGAATCTGATACCCACATGCATCTGTCACATCTTTCGAGTTCTAAGAAATTTATTAACCAT
* * *
266084 TAATTAAATATTCTCTATCG
323 TAGTCAAATATTTTCTATCG
* * ** * * *
266104 TATCAGAAGGAATTTAATACCCACATGCATCTGTTATATCTTTCAAGTTCCAA
1 TGTCAGAAAGAATTCGATACCCATATGCATCTGTTACATCTTTCGAGTTCCAA
266157 AATTAATTTT
Statistics
Matches: 581, Mismatches: 133, Indels: 64
0.75 0.17 0.08
Matches are distributed among these distances:
340 1 0.00
341 16 0.03
342 38 0.07
343 332 0.57
344 10 0.02
346 10 0.02
347 1 0.00
348 4 0.01
351 2 0.00
353 1 0.00
355 2 0.00
356 96 0.17
357 63 0.11
358 1 0.00
359 4 0.01
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (342 bp):
TGTCAGAAAGAATTCGATACCCATATGCATCTGTTACATCTTTCGAGTTCCAAGAAATTTATTAA
CAATTAGTCAAATATTTTTTATCGTGTCAGAAAGAATTTGATACCCATATGCATCTGTCACATCT
TTCGGTTTCAAGAAATTTATTAGTAATTAGTCAAATATTTTATGTCGTGTCAGAAGGAATCTGAT
ACCCACTTGCATCTTGAGCTTCAAGAAATTTACTAGCAATTAGTAATATTTTCTGTCGTGTAAGA
AGGAATCTGATACCCACATGCATCTGTCACATCTTTCGAGTTCTAAGAAATTTATTAACCATTAG
TCAAATATTTTCTATCG
Found at i:266112 original size:165 final size:166
Alignment explanation
Indices: 265803--266127 Score: 402
Period size: 165 Copynumber: 2.0 Consensus size: 166
265793 ATTACATCTT
* * * * *
265803 TTGAGTTTCAAGAAATTTATTAGCAATTGGTCATATATTTTTTGTCGTGTCCAAAAGAATTTGAT
1 TTGAGCTTCAAGAAATTTACTAGCAATTAGTCATATATTTTCTGTCGTGTCCAAAAGAATCTGAT
* ** * * * * * *
265868 ACCCACATGTATCTGTCATATGTTTCAGGTTTCAAGAAATTTATTAGCAATTAGTCAAATATTTT
66 ACCCAAATACATCTGTCACATCTTTCAGGTTCCAAGAAATTTATTAACAATTAATCAAATATTCT
* * *
265933 CTGTCGTGTCAGAAGGAATCTGATACCCACTTGCTC
131 CTATCGTATCAGAAGGAATCTAATACCCACTTGCTC
* *
265969 TTGAGCTTCAAGAAATTTACTAGCCATTAGTCA-ATATTTTCTGTCGTGT-CAGAAGGAATCTGA
1 TTGAGCTTCAAGAAATTTACTAGCAATTAGTCATATATTTTCTGTCGTGTCCA-AAAGAATCTGA
* * * * *
266032 TACCTAAATACATTTGTCACATCTTTCGGGTTCCAAGAAATTTATTAACCATTAATTAAATATTC
65 TACCCAAATACATCTGTCACATCTTTCAGGTTCCAAGAAATTTATTAACAATTAATCAAATATTC
*
266097 TCTATCGTATCAGAAGGAATTTAATACCCAC
130 TCTATCGTATCAGAAGGAATCTAATACCCAC
266128 ATGCATCTGT
Statistics
Matches: 133, Mismatches: 25, Indels: 3
0.83 0.16 0.02
Matches are distributed among these distances:
164 2 0.02
165 102 0.77
166 29 0.22
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (166 bp):
TTGAGCTTCAAGAAATTTACTAGCAATTAGTCATATATTTTCTGTCGTGTCCAAAAGAATCTGAT
ACCCAAATACATCTGTCACATCTTTCAGGTTCCAAGAAATTTATTAACAATTAATCAAATATTCT
CTATCGTATCAGAAGGAATCTAATACCCACTTGCTC
Found at i:268726 original size:23 final size:24
Alignment explanation
Indices: 268676--268726 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
268666 TAATAAGAAT
*
268676 AAAAAAAACAAAAAAAAACCTATC
1 AAAAAAAACAAAAAAAAACCTAAC
*
268700 AAAACAAA-AAAAAAAAACC-AAC
1 AAAAAAAACAAAAAAAAACCTAAC
268722 AAAAA
1 AAAAA
268727 GAGTATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 6 0.25
23 11 0.46
24 7 0.29
ACGTcount: A:0.80, C:0.16, G:0.00, T:0.04
Consensus pattern (24 bp):
AAAAAAAACAAAAAAAAACCTAAC
Found at i:269297 original size:10 final size:10
Alignment explanation
Indices: 269268--269301 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
269258 TCCACACACA
269268 TATATATATAT
1 TATATAT-TAT
269279 ATATATATTAT
1 -TATATATTAT
269290 TATATATTAT
1 TATATATTAT
269300 TA
1 TA
269302 ATGTCTTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
11 3 0.14
12 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TATATATTAT
Found at i:270561 original size:19 final size:19
Alignment explanation
Indices: 270518--270562 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
270508 AAAAAACATT
*
270518 TTAAAAATTATAAAAAATA
1 TTAAAAATGATAAAAAATA
*
270537 TAAAAAATGA-AAAAAATCA
1 TTAAAAATGATAAAAAAT-A
270556 TTAAAAA
1 TTAAAAA
270563 CTTCCCAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (19 bp):
TTAAAAATGATAAAAAATA
Found at i:275836 original size:12 final size:11
Alignment explanation
Indices: 275821--275871 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
275811 ATTTATATTT
275821 ATATATATATA
1 ATATATATATA
275832 CATATATATA-A
1 -ATATATATATA
* *
275843 AGATATATTTA
1 ATATATATATA
*
275854 CATATTTATATA
1 -ATATATATATA
275866 ATATAT
1 ATATAT
275872 CTTATTAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
10 7 0.23
11 7 0.23
12 17 0.55
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (11 bp):
ATATATATATA
Found at i:276219 original size:18 final size:18
Alignment explanation
Indices: 276193--276227 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
276183 TTCTATTGTA
* *
276193 AAATTAAATGAAGGAAAT
1 AAATGAAATGAAAGAAAT
276211 AAATGAAATGAAAGAAA
1 AAATGAAATGAAAGAAA
276228 CGAAAATGCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (18 bp):
AAATGAAATGAAAGAAAT
Found at i:277949 original size:4 final size:4
Alignment explanation
Indices: 277898--277944 Score: 85
Period size: 4 Copynumber: 11.8 Consensus size: 4
277888 TAAGTCTTGA
*
277898 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
277945 TATATGAACT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (4 bp):
ATAC
Found at i:283890 original size:15 final size:15
Alignment explanation
Indices: 283870--283901 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
283860 AAGCCTAAAC
283870 AATTATAGTTGATAA
1 AATTATAGTTGATAA
283885 AATTATAGTTGATAA
1 AATTATAGTTGATAA
283900 AA
1 AA
283902 CATAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (15 bp):
AATTATAGTTGATAA
Found at i:286464 original size:15 final size:14
Alignment explanation
Indices: 286444--286476 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
286434 GTATCGATAC
286444 ATACAAGATGTATCG
1 ATACAA-ATGTATCG
286459 ATAC-AATGTATCG
1 ATACAAATGTATCG
286472 ATACA
1 ATACA
286477 TGACCAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 12 0.71
14 1 0.06
15 4 0.24
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (14 bp):
ATACAAATGTATCG
Found at i:286469 original size:13 final size:13
Alignment explanation
Indices: 286451--286476 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
286441 TACATACAAG
286451 ATGTATCGATACA
1 ATGTATCGATACA
286464 ATGTATCGATACA
1 ATGTATCGATACA
286477 TGACCAAATT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:286495 original size:34 final size:32
Alignment explanation
Indices: 286433--286497 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 32
286423 CTTAACTGTT
286433 TGTATCGATACATACAAGATGTATCGATACAA
1 TGTATCGATACATACAAGATGTATCGATACAA
286465 TGTATCGATACATGACCAA-ATTGTATCGATACA
1 TGTATCGATACAT-A-CAAGA-TGTATCGATACA
286498 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 13 0.43
33 2 0.07
34 15 0.50
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (32 bp):
TGTATCGATACATACAAGATGTATCGATACAA
Found at i:292649 original size:13 final size:13
Alignment explanation
Indices: 292631--292655 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
292621 CAGCATTCTC
292631 TGTATCGATACAG
1 TGTATCGATACAG
292644 TGTATCGATACA
1 TGTATCGATACA
292656 AAGGGTTTAT
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:293131 original size:20 final size:22
Alignment explanation
Indices: 293102--293142 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
293092 CACTCACCAA
*
293102 GTCGCGACC-GGCA-CCCCCAG
1 GTCGCAACCGGGCAGCCCCCAG
293122 GTCGCAACCGGGCAGCCCCCA
1 GTCGCAACCGGGCAGCCCCCA
293143 CACTCATAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 4 0.22
22 6 0.33
ACGTcount: A:0.17, C:0.49, G:0.29, T:0.05
Consensus pattern (22 bp):
GTCGCAACCGGGCAGCCCCCAG
Found at i:294516 original size:15 final size:16
Alignment explanation
Indices: 294484--294516 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
294474 AGAGAGATAC
294484 ATGTGATTAAAGGGAA
1 ATGTGATTAAAGGGAA
294500 ATGTGATTAAA-GGAA
1 ATGTGATTAAAGGGAA
294515 AT
1 AT
294517 TGTTTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.45, C:0.00, G:0.27, T:0.27
Consensus pattern (16 bp):
ATGTGATTAAAGGGAA
Found at i:294558 original size:17 final size:16
Alignment explanation
Indices: 294524--294557 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
294514 AATTGTTTTA
294524 TTAAGGGGGAGAAATT
1 TTAAGGGGGAGAAATT
294540 TTAAGGGGGAGAAATT
1 TTAAGGGGGAGAAATT
294556 TT
1 TT
294558 TTATTTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (16 bp):
TTAAGGGGGAGAAATT
Found at i:295149 original size:13 final size:13
Alignment explanation
Indices: 295131--295155 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
295121 ATAATGCATA
295131 GTATCGATACATT
1 GTATCGATACATT
295144 GTATCGATACAT
1 GTATCGATACAT
295156 GACGAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:295168 original size:20 final size:21
Alignment explanation
Indices: 295143--295195 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
295133 ATCGATACAT
*
295143 TGTATCGATACATG--ACGAAA
1 TGTATCGATACATGCAAAG-AA
*
295163 TGTATCGATACTTGCAAAGAA
1 TGTATCGATACATGCAAAGAA
295184 TGTATCGATACA
1 TGTATCGATACA
295196 AGTGATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 13 0.46
21 13 0.46
22 2 0.07
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGCAAAGAA
Found at i:295268 original size:15 final size:14
Alignment explanation
Indices: 295248--295280 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
295238 GTATCGATAC
295248 ATACAAGATGTATCG
1 ATACAA-ATGTATCG
295263 ATAC-AATGTATCG
1 ATACAAATGTATCG
295276 ATACA
1 ATACA
295281 TGACCAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 12 0.71
14 1 0.06
15 4 0.24
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (14 bp):
ATACAAATGTATCG
Found at i:295273 original size:13 final size:13
Alignment explanation
Indices: 295255--295280 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
295245 TACATACAAG
295255 ATGTATCGATACA
1 ATGTATCGATACA
295268 ATGTATCGATACA
1 ATGTATCGATACA
295281 TGACCAAATT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:300000 original size:307 final size:307
Alignment explanation
Indices: 299446--300059 Score: 1219
Period size: 307 Copynumber: 2.0 Consensus size: 307
299436 GAATGACCCT
299446 CATTGAGCCTCAAATTCATCAGCTTTCGCATCAAGAAAATTTTTTCTTGTGCATTCTTGATCTCG
1 CATTGAGCCTCAAATTCATCAGCTTTCGCATCAAGAAAATTTTTTCTTGTGCATTCTTGATCTCG
299511 TACATGTTCTCCAATTTCTTCCAAACAATATAAGGATCTGTTTTTTTGGCAACATGGTTATAGAG
66 TACATGTTCTCCAATTTCTTCCAAACAATATAAGGATCTGTTTTTTTGGCAACATGGTTATAGAG
299576 ACTGATATCCACCCATTAGCGAATAGCACCCAATATTTTCTTCTTTAATTTCTTCCATTTAGCAT
131 ACTGATATCCACCCATTAGCGAATAGCACCCAATATTTTCTTCTTTAATTTCTTCCATTTAGCAT
299641 CTGACATGTCACTTGGTTTGGCATTATCTCCCTCAAGAGGATCATATAAATCCTTGCAATCCTTA
196 CTGACATGTCACTTGGTTTGGCATTATCTCCCTCAAGAGGATCATATAAATCCTTGCAATCCTTA
299706 TAATTTTATCTCTCAATACTCTCTCTGTGAAGTATTATATTTCTCAC
261 TAATTTTATCTCTCAATACTCTCTCTGTGAAGTATTATATTTCTCAC
299753 CATTGAGCCTCAAATTCATCAGCTTTCGCATCAAGAAAATTTTTTCTTGTGCATTCTTGATCTCG
1 CATTGAGCCTCAAATTCATCAGCTTTCGCATCAAGAAAATTTTTTCTTGTGCATTCTTGATCTCG
*
299818 TACATGTTCTCCAATTTCTTCCAAACAGTATAAGGATCTGTTTTTTTGGCAACATGGTTATAGAG
66 TACATGTTCTCCAATTTCTTCCAAACAATATAAGGATCTGTTTTTTTGGCAACATGGTTATAGAG
299883 ACTGATATCCACCCATTAGCGAATAGCACCCAATATTTTCTTCTTTAATTTCTTCCATTTAGCAT
131 ACTGATATCCACCCATTAGCGAATAGCACCCAATATTTTCTTCTTTAATTTCTTCCATTTAGCAT
299948 CTGACATGTCACTTGGTTTGGCATTATCTCCCTCAAGAGGATCATATAAATCCTTGCAATCCTTA
196 CTGACATGTCACTTGGTTTGGCATTATCTCCCTCAAGAGGATCATATAAATCCTTGCAATCCTTA
300013 TAATTTTATCTCTCAATACTCTCTCTGTGAAGTATTATATTTCTCAC
261 TAATTTTATCTCTCAATACTCTCTCTGTGAAGTATTATATTTCTCAC
300060 TATTCTCTCT
Statistics
Matches: 306, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
307 306 1.00
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (307 bp):
CATTGAGCCTCAAATTCATCAGCTTTCGCATCAAGAAAATTTTTTCTTGTGCATTCTTGATCTCG
TACATGTTCTCCAATTTCTTCCAAACAATATAAGGATCTGTTTTTTTGGCAACATGGTTATAGAG
ACTGATATCCACCCATTAGCGAATAGCACCCAATATTTTCTTCTTTAATTTCTTCCATTTAGCAT
CTGACATGTCACTTGGTTTGGCATTATCTCCCTCAAGAGGATCATATAAATCCTTGCAATCCTTA
TAATTTTATCTCTCAATACTCTCTCTGTGAAGTATTATATTTCTCAC
Found at i:302524 original size:61 final size:62
Alignment explanation
Indices: 302445--302561 Score: 193
Period size: 61 Copynumber: 1.9 Consensus size: 62
302435 TAATCAAAGT
*
302445 TTTTTTAATAATTATTTATTATAATGACTATATTTATAAATATCTT-TTA-AATGATTACTTA
1 TTTTATAATAATTATTTATTATAATGACTATATTTATAAATAT-TTATTATAATGATTACTTA
*
302506 TTTTATAATAATTATTTATTATAATGATTATATTTATAAATATTTATTATAATGAT
1 TTTTATAATAATTATTTATTATAATGACTATATTTATAAATATTTATTATAATGAT
302562 CATTTATCAT
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
60 2 0.04
61 44 0.85
62 6 0.12
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (62 bp):
TTTTATAATAATTATTTATTATAATGACTATATTTATAAATATTTATTATAATGATTACTTA
Found at i:302529 original size:13 final size:13
Alignment explanation
Indices: 302507--302558 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
302497 GATTACTTAT
*
302507 TTTATAATAATTA
1 TTTATTATAATTA
*
302520 TTTATTATAATGA
1 TTTATTATAATTA
*
302533 TTATATTTATAAATA
1 TT-TA-TTATAATTA
302548 TTTATTATAAT
1 TTTATTATAAT
302559 GATCATTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 19 0.59
14 4 0.12
15 9 0.28
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (13 bp):
TTTATTATAATTA
Found at i:302529 original size:16 final size:16
Alignment explanation
Indices: 302450--302573 Score: 61
Period size: 16 Copynumber: 8.2 Consensus size: 16
302440 AAAGTTTTTT
302450 TAATAATTATTTATTA
1 TAATAATTATTTATTA
* *
302466 TAATGACTA--TATT-
1 TAATAATTATTTATTA
*
302479 T-ATAAATATCTT-TTA
1 TAATAATTAT-TTATTA
* *
302494 -AATGATTACTTATTTTA
1 TAATAATTA-TT-TATTA
302511 TAATAATTATTTATTA
1 TAATAATTATTTATTA
*
302527 TAATGATTA--TATT-
1 TAATAATTATTTATTA
*
302540 T-ATAAATATTTATTA
1 TAATAATTATTTATTA
* * *
302555 TAATGATCATTTATCA
1 TAATAATTATTTATTA
302571 TAA
1 TAA
302574 GTTTAGCTGA
Statistics
Matches: 80, Mismatches: 15, Indels: 26
0.66 0.12 0.21
Matches are distributed among these distances:
12 10 0.12
13 2 0.03
14 14 0.17
15 8 0.10
16 34 0.43
17 5 0.06
18 7 0.09
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (16 bp):
TAATAATTATTTATTA
Found at i:302550 original size:28 final size:28
Alignment explanation
Indices: 302452--302561 Score: 125
Period size: 28 Copynumber: 3.8 Consensus size: 28
302442 AGTTTTTTTA
* *
302452 ATAATTATTTATTATAATGACTATATTT
1 ATAAATATTTATTATAATGATTATATTT
302480 ATAAATATCTT-TTA-AATGATTACTTATTTT
1 ATAAATAT-TTATTATAATGATTA--TA-TTT
302510 ATAATAATTATTTATTATAATGATTATATTT
1 AT-A-AA-TATTTATTATAATGATTATATTT
302541 ATAAATATTTATTATAATGAT
1 ATAAATATTTATTATAATGAT
302562 CATTTATCAT
Statistics
Matches: 71, Mismatches: 2, Indels: 18
0.78 0.02 0.20
Matches are distributed among these distances:
27 7 0.10
28 26 0.37
29 6 0.08
30 6 0.08
31 6 0.08
32 6 0.08
33 6 0.08
34 8 0.11
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.53
Consensus pattern (28 bp):
ATAAATATTTATTATAATGATTATATTT
Found at i:303542 original size:6 final size:5
Alignment explanation
Indices: 303509--303541 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
303499 AAGAAGCACT
*
303509 TTTTC TTCT- TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
303542 TTTCCTTTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 22 0.88
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:310572 original size:11 final size:11
Alignment explanation
Indices: 310531--310576 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
310521 GATATGAAAA
310531 AAATA-ATTA-
1 AAATATATTAT
*
310540 AAATATAATAT
1 AAATATATTAT
*
310551 AAAAATATTAT
1 AAATATATTAT
*
310562 AAATATTTTAT
1 AAATATATTAT
310573 AAAT
1 AAAT
310577 TTATAAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
9 5 0.17
10 3 0.10
11 22 0.73
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATATATTAT
Found at i:310582 original size:19 final size:18
Alignment explanation
Indices: 310552--310606 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
310542 ATATAATATA
*
310552 AAAATATTATAAATATTTT
1 AAAAT-TTATAAATATTTC
*
310571 ATAAATTTATAAATATGTC
1 A-AAATTTATAAATATTTC
310590 AAAATTTATATAATATT
1 AAAATTTATA-AATATT
310607 AATAATTAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 9 0.29
19 18 0.58
20 4 0.13
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
AAAATTTATAAATATTTC
Found at i:310828 original size:14 final size:14
Alignment explanation
Indices: 310790--310830 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
310780 TGATGGTGAG
*
310790 GAAA-GAAAGAAAA
1 GAAAGGAAAGAGAA
*
310803 GAAGGGAAAGAGAA
1 GAAAGGAAAGAGAA
310817 GAAAGGAAAGAGAA
1 GAAAGGAAAGAGAA
310831 AAAAATAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
13 3 0.12
14 21 0.88
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (14 bp):
GAAAGGAAAGAGAA
Done.