Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold84
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: 4163231
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 246351 characters in sequence are not A, C, G, or T
File 8 of 11
Found at i:3066751 original size:14 final size:14
Alignment explanation
Indices: 3066711--3066752 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
3066701 AAAATATAAT
3066711 TAAAATTAAAAAAA
1 TAAAATTAAAAAAA
* *
3066725 TAAAACTACAAAAA
1 TAAAATTAAAAAAA
3066739 -AAAATTGAAAAAAA
1 TAAAATT-AAAAAAA
3066753 CTGAAATCTG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 5 0.22
14 18 0.78
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.17
Consensus pattern (14 bp):
TAAAATTAAAAAAA
Found at i:3067699 original size:11 final size:11
Alignment explanation
Indices: 3067683--3067707 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3067673 CAATAACTTT
3067683 ATTTAAACATA
1 ATTTAAACATA
3067694 ATTTAAACATA
1 ATTTAAACATA
3067705 ATT
1 ATT
3067708 AATTATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (11 bp):
ATTTAAACATA
Found at i:3068871 original size:40 final size:39
Alignment explanation
Indices: 3068822--3068900 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 39
3068812 CCCTCTAGTC
*
3068822 AAAAATGACCAAATTAGTCAAATACGTGAGATCAAAGAT
1 AAAAATGACCAAATTAGCCAAATACGTGAGATCAAAGAT
3068861 AAAACATGACCAAATTAGCCAAATACGTGAGATCAAAGAT
1 AAAA-ATGACCAAATTAGCCAAATACGTGAGATCAAAGAT
3068901 CAAATTGGTC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 4 0.11
40 34 0.89
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.19
Consensus pattern (39 bp):
AAAAATGACCAAATTAGCCAAATACGTGAGATCAAAGAT
Found at i:3068904 original size:21 final size:21
Alignment explanation
Indices: 3068839--3068905 Score: 52
Period size: 21 Copynumber: 3.3 Consensus size: 21
3068829 ACCAAATTAG
3068839 TCAAATACGTGAGATCAAAGA
1 TCAAATACGTGAGATCAAAGA
* * *
3068860 T-AAA-ACAT--GACCAAATTA
1 TCAAATACGTGAGATCAAA-GA
*
3068878 GCCAAATACGTGAGATCAAAGA
1 -TCAAATACGTGAGATCAAAGA
3068900 TCAAAT
1 TCAAAT
3068906 TGGTCTTTCT
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
17 6 0.19
18 1 0.03
19 3 0.09
20 6 0.19
21 9 0.28
22 1 0.03
23 6 0.19
ACGTcount: A:0.49, C:0.16, G:0.15, T:0.19
Consensus pattern (21 bp):
TCAAATACGTGAGATCAAAGA
Found at i:3070462 original size:2 final size:2
Alignment explanation
Indices: 3070450--3070512 Score: 51
Period size: 2 Copynumber: 33.0 Consensus size: 2
3070440 ATCTGTATTT
* * * * *
3070450 TA TA TA T- TA TA TA T- TA TA GA TA GA T- TT TT TA TA TA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3070489 TA CA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
3070513 CTTATTATAA
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
1 3 0.06
2 46 0.94
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3071773 original size:21 final size:22
Alignment explanation
Indices: 3071724--3071776 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
3071714 GTATAAATGT
3071724 AATTTTAAAATGTTTAAGATAA
1 AATTTTAAAATGTTTAAGATAA
* *
3071746 AA-ATTAAAA-G-TTAAGTTTAA
1 AATTTTAAAATGTTTAAG-ATAA
3071766 AATTTTAAAAT
1 AATTTTAAAAT
3071777 TTTGTATCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
19 5 0.20
20 6 0.24
21 12 0.48
22 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.40
Consensus pattern (22 bp):
AATTTTAAAATGTTTAAGATAA
Found at i:3072321 original size:22 final size:22
Alignment explanation
Indices: 3072274--3072318 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
3072264 ATGCAATCTT
*
3072274 AGATATGATATGCAATCTTAGA
1 AGATATGATATGCAATATTAGA
* *
3072296 AGATATGATTTTGTAATATTAGA
1 AGATATGA-TATGCAATATTAGA
3072319 GATTTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38
Consensus pattern (22 bp):
AGATATGATATGCAATATTAGA
Found at i:3072566 original size:23 final size:23
Alignment explanation
Indices: 3072522--3072566 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
3072512 TCTTATTTTG
* *
3072522 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
3072545 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
3072567 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:3077341 original size:6 final size:6
Alignment explanation
Indices: 3077329--3077390 Score: 54
Period size: 6 Copynumber: 10.2 Consensus size: 6
3077319 TGATGATGGA
* * *
3077329 AAAAAG GAAAAG GAAAA- TAAAAG AAAAAAG AAAAAG AAAAAG AAAGAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG -AAAAAG AAAAAG AAAAAG AAA-AAG
* *
3077378 AAGAGG AAAAAG A
1 AAAAAG AAAAAG A
3077391 GAGGTCAAGG
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
5 4 0.09
6 32 0.70
7 10 0.22
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:3077354 original size:24 final size:24
Alignment explanation
Indices: 3077327--3077390 Score: 78
Period size: 23 Copynumber: 2.7 Consensus size: 24
3077317 AATGATGATG
*
3077327 GAAAAAAGGAAAAGGAAAATA-AAA
1 GAAAAAAGGAAAAAGAAAA-AGAAA
3077351 GAAAAAA-GAAAAAGAAAAAGAAA
1 GAAAAAAGGAAAAAGAAAAAGAAA
*
3077374 GAAGAAGAGGAAAAAGA
1 GAA-AAAAGGAAAAAGA
3077391 GAGGTCAAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 1 0.03
23 16 0.46
24 10 0.29
25 8 0.23
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (24 bp):
GAAAAAAGGAAAAAGAAAAAGAAA
Found at i:3077369 original size:19 final size:19
Alignment explanation
Indices: 3077347--3077390 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
3077337 AAAGGAAAAT
3077347 AAAAGAAAAAAGAAAAAGA
1 AAAAGAAAAAAGAAAAAGA
* * *
3077366 AAAAGAAAGAAGAAGAGGA
1 AAAAGAAAAAAGAAAAAGA
3077385 AAAAGA
1 AAAAGA
3077391 GAGGTCAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAAAGAAAAAGA
Found at i:3079314 original size:260 final size:260
Alignment explanation
Indices: 3078844--3079365 Score: 803
Period size: 260 Copynumber: 2.0 Consensus size: 260
3078834 TGCAATGGAA
* * * * *
3078844 AAGATTGAAGCCACGACGGTGAATCTTACTTCCGTGGCGTTGTAGCGGAGCAGATTGAAACCACG
1 AAGATTGAAGCCACAACAGTGAATCTTACTTCCCTGGCATTGTAGCGGAGCAAATTGAAACCACG
*
3078909 ACGGTGAATCTTATCTCCCTACTGTTAAGGCTTGGATTAGCTGAAGTGGAGCAGATTGAAGCTGT
66 ACGGTGAATCTTATCTCCCTACTGTTAAGGCTTGGATTAGCTGAAGTGGAGCAGATTGAAGCTGA
* * *
3078974 GGGCAGCGAATCCTATTTCTTTGGCATTACAGTGAAAAAGATTGAAGCTGCAACGCCAAATCTTA
131 GGGCAGCAAATCCTATCTCTTTGGCATTACAGTGAAAAAGATTGAAGCCGCAACGCCAAATCTTA
* * * * * **
3079039 CTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGATGGTGAATCTTGTTTCCTTAACATTGC
196 CTTCCCTGACGGTGTAGTGGAACAAATCGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGC
* * * * *
3079104 AAGATTGAAGCCGCAACAGTGAATTTTACTTCCCTGGCATTGTAGCGGAGCAAATTGAAGCTATG
1 AAGATTGAAGCCACAACAGTGAATCTTACTTCCCTGGCATTGTAGCGGAGCAAATTGAAACCACG
* *
3079169 ACGGTGAATCTTATCTCCCTGGC-GTTAAGGCTTGGATTAGCTGAAGTGGAGCGGATTGAAGCTG
66 ACGGTGAATCTTATCTCCCT-ACTGTTAAGGCTTGGATTAGCTGAAGTGGAGCAGATTGAAGCTG
*
3079233 AGGGCAGCAAATCCTATCTCTTTGGCATTACAGTGAAAAAGATTGAAGCCGCAACGGCAAATCTT
130 AGGGCAGCAAATCCTATCTCTTTGGCATTACAGTGAAAAAGATTGAAGCCGCAACGCCAAATCTT
*
3079298 ACTTCCTTGACGGTGTAGTGGAACAAATCGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTG
195 ACTTCCCTGACGGTGTAGTGGAACAAATCGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTG
3079363 C
260 C
3079364 AA
1 AA
3079366 TTAAAAAGAC
Statistics
Matches: 236, Mismatches: 25, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
260 235 1.00
261 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.27
Consensus pattern (260 bp):
AAGATTGAAGCCACAACAGTGAATCTTACTTCCCTGGCATTGTAGCGGAGCAAATTGAAACCACG
ACGGTGAATCTTATCTCCCTACTGTTAAGGCTTGGATTAGCTGAAGTGGAGCAGATTGAAGCTGA
GGGCAGCAAATCCTATCTCTTTGGCATTACAGTGAAAAAGATTGAAGCCGCAACGCCAAATCTTA
CTTCCCTGACGGTGTAGTGGAACAAATCGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGC
Found at i:3079468 original size:44 final size:44
Alignment explanation
Indices: 3079387--3079713 Score: 199
Period size: 44 Copynumber: 7.5 Consensus size: 44
3079377 GAAGATGGCG
* *
3079387 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGGTTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* * **
3079431 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-AT
* * * * * *
3079475 GATCTTATCTCTCTGAAGTTACAG-AGAGCAGA-T--CG-CATCT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-AT
* * * * *
3079515 AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACT-AAG-TAAGC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA-T
* * * *****
3079558 AAGTCTTATC-CTCCTGAAGTTTCAGT-GAGGCAGACTGAAGGTGGCG
1 AA-TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAAGCCAAT
* *
3079604 AATATTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* *** *
3079648 AATCCTATCTCCCTGAAGTTGCAGTGGAATGGATTAAATCCACA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-AT
* *
3079692 GATCTTATCTCTCTGAAGTTGC
1 AATCTTATCTCCCTGAAGTTGC
3079714 TGTAGAGTAG
Statistics
Matches: 213, Mismatches: 55, Indels: 30
0.71 0.18 0.10
Matches are distributed among these distances:
39 2 0.01
40 20 0.09
41 6 0.03
42 2 0.01
43 12 0.06
44 138 0.65
45 26 0.12
46 7 0.03
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
Found at i:3079636 original size:45 final size:44
Alignment explanation
Indices: 3079519--3079636 Score: 118
Period size: 45 Copynumber: 2.7 Consensus size: 44
3079509 GCATCTAGTC
* * *
3079519 TTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGTAAGCAAGTC
1 TTATCTCCCTGAAGTTACAGTGGAGCAGACTAAGTAAGCAAGTA
* *
3079563 TTATC-CTCCTGAAGTTTCAGT-GAGGCAGACTGAAGGT-GGCGAA-TA
1 TTATCTC-CCTGAAGTTACAGTGGA-GCAGACT-AA-GTAAGC-AAGTA
3079608 TTATCTCCCTGAAGTTACAGTGGAGCAGA
1 TTATCTCCCTGAAGTTACAGTGGAGCAGA
3079637 TTAAAGCCAA
Statistics
Matches: 62, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
43 3 0.05
44 24 0.39
45 28 0.45
46 7 0.11
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTACAGTGGAGCAGACTAAGTAAGCAAGTA
Found at i:3080007 original size:44 final size:44
Alignment explanation
Indices: 3079944--3080169 Score: 346
Period size: 44 Copynumber: 5.1 Consensus size: 44
3079934 AGCAGATCAA
* * *
3079944 GTTGAAGATTGT-AAGTCCTATCTCCCTGGTTAGTAGTGAAATAG
1 GTTGAAGATTGTGAA-TCCTATCTCCCTGGTCAGCAGTGGAATAG
* *
3079988 GTTGAAGATTGTGAGTCCTATCTCCTTGGTCAGCAGTGGAATAG
1 GTTGAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAG
3080032 GTTGAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAG
1 GTTGAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAG
* *
3080076 GTTGAAGATTGTGAATCCTATCTCACTGGTCAGCAGTGGAATAT
1 GTTGAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAG
* * *
3080120 GTTGAAGATGGTGAATCTTATCTCCCTGGTCAGCAGTGGAATAA
1 GTTGAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAG
3080164 GTTGAA
1 GTTGAA
3080170 AATTACATAT
Statistics
Matches: 168, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
44 167 0.99
45 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.31
Consensus pattern (44 bp):
GTTGAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAG
Found at i:3080224 original size:132 final size:132
Alignment explanation
Indices: 3079959--3080230 Score: 278
Period size: 132 Copynumber: 2.1 Consensus size: 132
3079949 AGATTGTAAG
* * * * * *
3079959 TCCTATCTCCCTGGTTAGTAGTGAAATAGGTTGAAGATTGTGAGTCCTATCTCCTTGGTCAGCAG
1 TCCTATCTCACTGGTCAGCAGTGAAATAGGTTGAAGATGGTGAATCCTATCTCCCTGGTCAGCAG
* * ** * * * * ** * ** *
3080024 TGGAATAGGTTGAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTG
66 TGGAATAAGTTGAAAATTGACAATCCTATCTACCTAGTCAGCAGTGGAACAGATCAAAAACGGCG
3080089 AA
131 AA
* * *
3080091 TCCTATCTCACTGGTCAGCAGTGGAATATGTTGAAGATGGTGAATCTTATCTCCCTGGTCAGCAG
1 TCCTATCTCACTGGTCAGCAGTGAAATAGGTTGAAGATGGTGAATCCTATCTCCCTGGTCAGCAG
* *
3080156 TGGAATAAGTTGAAAATT-ACATATCCTATCTACCTAAG-CAGTAGTGGAGCAGATCAAAAACGG
66 TGGAATAAGTTGAAAATTGACA-ATCCTATCTACCT-AGTCAGCAGTGGAACAGATCAAAAACGG
3080219 CGAA
129 CGAA
*
3080223 TCTTATCT
1 TCCTATCT
3080231 TCCCAAGGTA
Statistics
Matches: 112, Mismatches: 26, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
131 1 0.01
132 110 0.98
133 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (132 bp):
TCCTATCTCACTGGTCAGCAGTGAAATAGGTTGAAGATGGTGAATCCTATCTCCCTGGTCAGCAG
TGGAATAAGTTGAAAATTGACAATCCTATCTACCTAGTCAGCAGTGGAACAGATCAAAAACGGCG
AA
Found at i:3080320 original size:44 final size:44
Alignment explanation
Indices: 3080256--3080356 Score: 157
Period size: 44 Copynumber: 2.3 Consensus size: 44
3080246 GAAGTCCCTG
* *
3080256 AGCAGTAGTGGAGTAAGTTGAAGATTGTAGACCTTATCTCCCAA
1 AGCAGTAGTGGAGTAAGTTGAAAATTATAGACCTTATCTCCCAA
* * *
3080300 AGCAGTAGTGGAGTAGGTTGAAAATTATAGATCTTATCTCCCTA
1 AGCAGTAGTGGAGTAAGTTGAAAATTATAGACCTTATCTCCCAA
3080344 AGCAGTAGTGGAG
1 AGCAGTAGTGGAG
3080357 CAGATCGAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.28
Consensus pattern (44 bp):
AGCAGTAGTGGAGTAAGTTGAAAATTATAGACCTTATCTCCCAA
Found at i:3081178 original size:19 final size:19
Alignment explanation
Indices: 3081132--3081187 Score: 94
Period size: 21 Copynumber: 2.8 Consensus size: 19
3081122 AATCTTCAAG
3081132 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3081151 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
3081172 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
3081188 AGATATGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 16 0.46
21 19 0.54
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:3081213 original size:22 final size:22
Alignment explanation
Indices: 3081166--3081210 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
3081156 ATGCAATCTT
*
3081166 AGATATGATATGCAATCTTAGA
1 AGATATGATATGCAATATTAGA
* *
3081188 AGATATGATTTTGTAATATTAGA
1 AGATATGA-TATGCAATATTAGA
3081211 GATTTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38
Consensus pattern (22 bp):
AGATATGATATGCAATATTAGA
Found at i:3081454 original size:23 final size:23
Alignment explanation
Indices: 3081410--3081454 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
3081400 TCTTATTTTG
* *
3081410 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
3081433 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
3081455 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:3083285 original size:35 final size:35
Alignment explanation
Indices: 3083246--3083415 Score: 250
Period size: 35 Copynumber: 4.9 Consensus size: 35
3083236 AAATGCGACT
*
3083246 TTAAAAAGGTTGGGATAGACCCGTCTAAGGCAACC
1 TTAAAAAGGTTGGGATAGACACGTCTAAGGCAACC
** * *
3083281 TTAAAAACATTGGGATAGACCCGTCTAAGGCAAAC
1 TTAAAAAGGTTGGGATAGACACGTCTAAGGCAACC
* * * *
3083316 TTTAAAAGGTTGAGATAGACACGTTTAAGGCAACT
1 TTAAAAAGGTTGGGATAGACACGTCTAAGGCAACC
3083351 TTAAAAAGGTTGGGATAGACACGTCTAAGGCAACC
1 TTAAAAAGGTTGGGATAGACACGTCTAAGGCAACC
*
3083386 TTAAAAAAGTTGGGATAGACACGTCTAAGG
1 TTAAAAAGGTTGGGATAGACACGTCTAAGG
3083416 TAATTTTTTT
Statistics
Matches: 119, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 119 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (35 bp):
TTAAAAAGGTTGGGATAGACACGTCTAAGGCAACC
Found at i:3087123 original size:4 final size:4
Alignment explanation
Indices: 3087103--3087141 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
3087093 TTTTACTTTA
* *
3087103 TATT TACT TAGTT TATT TATT TATT TATT TACT TATT TA
1 TATT TATT TA-TT TATT TATT TATT TATT TATT TATT TA
3087142 ACCTTTTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 27 0.90
5 3 0.10
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.67
Consensus pattern (4 bp):
TATT
Found at i:3087131 original size:12 final size:12
Alignment explanation
Indices: 3087094--3087141 Score: 62
Period size: 12 Copynumber: 4.0 Consensus size: 12
3087084 GACAACTTGT
*
3087094 TTTACTT-TATA
1 TTTACTTATTTA
3087105 TTTACTTAGTTTA
1 TTTACTTA-TTTA
*
3087118 TTTATTTATTTA
1 TTTACTTATTTA
3087130 TTTACTTATTTA
1 TTTACTTATTTA
3087142 ACCTTTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
11 7 0.22
12 15 0.47
13 10 0.31
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (12 bp):
TTTACTTATTTA
Found at i:3098086 original size:35 final size:36
Alignment explanation
Indices: 3098028--3098106 Score: 117
Period size: 35 Copynumber: 2.2 Consensus size: 36
3098018 TAAAGACAAC
3098028 AAAAAAAGGTTGGGCTAGACCAAATATTTTT-TGACA
1 AAAAAAAGGTTGGGCTAGACCAAATATTTTTCT-ACA
* *
3098064 AAAAAAATGTTGGG-TAGGCCAAATATTTTTCTACA
1 AAAAAAAGGTTGGGCTAGACCAAATATTTTTCTACA
3098099 AAAAAAAG
1 AAAAAAAG
3098107 AGGTTGGGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
35 25 0.64
36 14 0.36
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.27
Consensus pattern (36 bp):
AAAAAAAGGTTGGGCTAGACCAAATATTTTTCTACA
Found at i:3101633 original size:13 final size:13
Alignment explanation
Indices: 3101617--3101716 Score: 62
Period size: 13 Copynumber: 7.6 Consensus size: 13
3101607 TTGGAATGGC
*
3101617 TATACGAAATGAT
1 TATATGAAATGAT
* *
3101630 TATATGAATTGTT
1 TATATGAAATGAT
**
3101643 TATATGAAATGGG
1 TATATGAAATGAT
*
3101656 TATGTGAAATGAT
1 TATATGAAATGAT
* *
3101669 TATAAG-AATTAGT
1 TATATGAAATGA-T
3101682 TATATAGAAATAGA-
1 TATAT-GAAAT-GAT
*
3101696 TATATGGAATGGA-
1 TATATGAAAT-GAT
3101709 TATATGAA
1 TATATGAA
3101717 TCAGTTACAG
Statistics
Matches: 66, Mismatches: 17, Indels: 8
0.73 0.19 0.09
Matches are distributed among these distances:
12 4 0.06
13 52 0.79
14 6 0.09
15 3 0.05
16 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.20, T:0.36
Consensus pattern (13 bp):
TATATGAAATGAT
Found at i:3109882 original size:39 final size:40
Alignment explanation
Indices: 3109770--3109883 Score: 144
Period size: 40 Copynumber: 2.9 Consensus size: 40
3109760 GTTTGGACAA
* *
3109770 AAAAT-GCCGGTAAAAATCGAGCATTAGCGGCGTTTTATG
1 AAAATCGCCGCTAAAAGTCGAGCATTAGCGGCGTTTTATG
* * * *
3109809 GAAATCGCCACT-AAAGATGGAGCATTAGCGGCGTTTTTTG
1 AAAATCGCCGCTAAAAG-TCGAGCATTAGCGGCGTTTTATG
3109849 AAAATCGCCGCTAAAAGT-GAGCATTAGCGGCGTTT
1 AAAATCGCCGCTAAAAGTCGAGCATTAGCGGCGTTT
3109884 CTGGAAAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 24 0.38
40 36 0.56
41 4 0.06
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (40 bp):
AAAATCGCCGCTAAAAGTCGAGCATTAGCGGCGTTTTATG
Found at i:3109891 original size:39 final size:40
Alignment explanation
Indices: 3109770--3109891 Score: 135
Period size: 39 Copynumber: 3.1 Consensus size: 40
3109760 GTTTGGACAA
* *
3109770 AAAAT-GCCGGTAAAAATCGAGCATTAGCGGCGTTTTATGG
1 AAAATCGCCGCTAAAAGTCGAGCATTAGCGGCG-TTTATGG
* * * *
3109810 -AAATCGCCACT-AAAGATGGAGCATTAGCGGCGTTTTTTG
1 AAAATCGCCGCTAAAAG-TCGAGCATTAGCGGCGTTTATGG
*
3109849 AAAATCGCCGCTAAAAGT-GAGCATTAGCGGCGTTTCTGG
1 AAAATCGCCGCTAAAAGTCGAGCATTAGCGGCGTTTATGG
3109888 AAAA
1 AAAA
3109892 AACGCCACAA
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
39 35 0.51
40 30 0.43
41 4 0.06
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (40 bp):
AAAATCGCCGCTAAAAGTCGAGCATTAGCGGCGTTTATGG
Found at i:3109997 original size:41 final size:41
Alignment explanation
Indices: 3109940--3110213 Score: 372
Period size: 41 Copynumber: 6.7 Consensus size: 41
3109930 TTACCTTTCA
*
3109940 GGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGTTGG
1 GGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTGG
* * *
3109981 GGGCTTTAGCGGCGTTTTTGGATAAGAGCCGCTAATGCGGG
1 GGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTGG
* * **
3110022 GGGCTTTAGCGGCGTTTTTGGATAAGCGCCACTAATGCTAA
1 GGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTGG
* * *
3110063 GGGCTTTAAG-GGCGTTTTTGGATAAGCACCGCTAATGCTTG
1 GGGCTTT-AGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTGG
* * *
3110104 GGGATTTAGCGGCGTTTTT-TAGAAAGCGCCGCTAATGCTGA
1 GGGCTTTAGCGGCGTTTTTGGA-AAAGCGCCGCTAATGCTGG
* *
3110145 GGGATTTAGCGGCTTTTTTGGAAAAGCGCCGCTAATGCTGG
1 GGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTGG
3110186 GGGCTTTAGCGGCGTTTTTGGAAAAGCG
1 GGGCTTTAGCGGCGTTTTTGGAAAAGCG
3110214 GCACTAAAAA
Statistics
Matches: 205, Mismatches: 24, Indels: 8
0.86 0.10 0.03
Matches are distributed among these distances:
40 3 0.01
41 199 0.97
42 3 0.01
ACGTcount: A:0.19, C:0.17, G:0.34, T:0.29
Consensus pattern (41 bp):
GGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTGG
Found at i:3120395 original size:14 final size:14
Alignment explanation
Indices: 3120375--3120408 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
3120365 TAAAGTTTAT
3120375 AGGTTAGGGGCTAG
1 AGGTTAGGGGCTAG
*
3120389 GGGTTAGGGGCTAG
1 AGGTTAGGGGCTAG
3120403 AGGTTA
1 AGGTTA
3120409 AGATCAGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.06, G:0.50, T:0.24
Consensus pattern (14 bp):
AGGTTAGGGGCTAG
Found at i:3120557 original size:33 final size:33
Alignment explanation
Indices: 3120506--3120569 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
3120496 ATTAAATAAT
* *
3120506 GTTTAGGGGTTATGGATTCTGGGTTGGGTTAGG
1 GTTTAGGGATTATGGATTCAGGGTTGGGTTAGG
3120539 GTTTAGGGATTA-GAGATTCAGGGTTGGGTTA
1 GTTTAGGGATTATG-GATTCAGGGTTGGGTTA
3120570 AGATTTAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.17, C:0.03, G:0.42, T:0.38
Consensus pattern (33 bp):
GTTTAGGGATTATGGATTCAGGGTTGGGTTAGG
Found at i:3120590 original size:21 final size:22
Alignment explanation
Indices: 3120564--3120606 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
3120554 ATTCAGGGTT
*
3120564 GGGTTAAGATTTAAGG-TTTAG
1 GGGTTAAGAGTTAAGGATTTAG
*
3120585 GGGTTAATAGTTAAGGATTTAG
1 GGGTTAAGAGTTAAGGATTTAG
3120607 AGTTTAGGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.37
Consensus pattern (22 bp):
GGGTTAAGAGTTAAGGATTTAG
Found at i:3120886 original size:14 final size:15
Alignment explanation
Indices: 3120856--3120910 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 15
3120846 GGGGATTAGA
*
3120856 TATGGATTTAGGGAT
1 TATGGATTTAAGGAT
3120871 TATGGA-TTAAGGAT
1 TATGGATTTAAGGAT
*
3120885 TAT-GATTTAAGGGT
1 TATGGATTTAAGGAT
*
3120899 TGT-GATTTAAGG
1 TATGGATTTAAGG
3120911 TTTAGGGGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
13 2 0.06
14 28 0.78
15 6 0.17
ACGTcount: A:0.29, C:0.00, G:0.31, T:0.40
Consensus pattern (15 bp):
TATGGATTTAAGGAT
Found at i:3120936 original size:21 final size:22
Alignment explanation
Indices: 3120911--3120960 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
3120901 TGATTTAAGG
*
3120911 TTTAGGGGTTAGGAAATAGGGA
1 TTTAGGGGTTAAGAAATAGGGA
**
3120933 -TTAGGGGTTAAGAGTTAGGGA
1 TTTAGGGGTTAAGAAATAGGGA
3120954 TTTAGGG
1 TTTAGGG
3120961 TTTCAAGGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.28, C:0.00, G:0.42, T:0.30
Consensus pattern (22 bp):
TTTAGGGGTTAAGAAATAGGGA
Found at i:3124729 original size:43 final size:43
Alignment explanation
Indices: 3124613--3124956 Score: 392
Period size: 43 Copynumber: 8.3 Consensus size: 43
3124603 ATGATATATT
** * *
3124613 TTTAGCGGCGTTT-TCCGAAAAGTGCCGCTAAAGGTCTAT--TA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCT-TGGTC
* * * ** * *
3124654 TATAGCGGCGTTTGTGTGAAAAGTGCTACTAAAGGCCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* **
3124697 TTTAGCAGCGTTTGTGGGAAAAGCGTTGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
3124740 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
3124783 TTTA-C--CG---GT-----AAGCGCTGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
3124815 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
3124858 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* * *
3124901 TTTAGTGGCGTTTGTGGGAAAAGGGCCGCTAAAGGTCCTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
3124944 TTTAGTGGCGTTT
1 TTTAGCGGCGTTT
3124957 ATTTATAAAA
Statistics
Matches: 262, Mismatches: 27, Indels: 26
0.83 0.09 0.08
Matches are distributed among these distances:
32 26 0.10
33 1 0.00
35 2 0.01
37 2 0.01
38 2 0.01
40 2 0.01
41 13 0.05
42 19 0.07
43 195 0.74
ACGTcount: A:0.20, C:0.17, G:0.32, T:0.31
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:3124840 original size:75 final size:79
Alignment explanation
Indices: 3124717--3124948 Score: 310
Period size: 75 Copynumber: 2.9 Consensus size: 79
3124707 TTTGTGGGAA
*
3124717 AAGCGTTGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
1 AAGCGCTGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
3124782 CTTTA-C-CG-GT-
66 CTTTAGCGCGTGTG
*
3124792 AAGCGCTGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGGT
1 AAGCGCTGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
3124857 CTTTAGCGGCGTTTGTGGG
66 CTTTAGC-GCG--TGT--G
* * * * *
3124876 AAAAGCGCCGCTAAAGGTTTTGGTCTTTAGTGGCGTTTGTGGGAAAAGGGCCGCTAAAGGTCCTG
1 --AAGCGCTGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTG
3124941 GTCTTTAG
64 GTCTTTAG
3124949 TGGCGTTTAT
Statistics
Matches: 138, Mismatches: 8, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
75 68 0.49
76 1 0.01
78 2 0.01
81 2 0.01
86 65 0.47
ACGTcount: A:0.19, C:0.18, G:0.33, T:0.30
Consensus pattern (79 bp):
AAGCGCTGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
CTTTAGCGCGTGTG
Found at i:3124890 original size:118 final size:118
Alignment explanation
Indices: 3124682--3124904 Score: 383
Period size: 118 Copynumber: 1.9 Consensus size: 118
3124672 AAAAGTGCTA
* **
3124682 CTAAAGGCCATGGTCTTTAGCAGCGTTTGTGGGAAAAGCGTTGCTAAAGGTCTTGGTCTTTAGCG
1 CTAAAGGCCATGGTCTTTAGCAGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCG
3124747 GCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTACCGGTAAGCGCTG
66 GCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTACCGGTAAGCGCTG
* * *
3124800 CTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCG
1 CTAAAGGCCATGGTCTTTAGCAGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCG
*
3124865 GCGTTTGTGGGAAAAGCGCCGCTAAAGGTTTTGGTCTTTA
66 GCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTA
3124905 GTGGCGTTTG
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
118 98 1.00
ACGTcount: A:0.20, C:0.18, G:0.32, T:0.30
Consensus pattern (118 bp):
CTAAAGGCCATGGTCTTTAGCAGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCG
GCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTACCGGTAAGCGCTG
Found at i:3124921 original size:161 final size:161
Alignment explanation
Indices: 3124656--3124947 Score: 460
Period size: 161 Copynumber: 1.8 Consensus size: 161
3124646 GTCTATTATA
* *
3124656 TAGCGGCGTTTGTGTGAAAAGTGCTACTAAAGGCCATGGTCTTTAGCAGCGTTTGTGGGAAAAGC
1 TAGCGGCGTTTGTGTGAAAAGCGCCACTAAAGGCCATGGTCTTTAGCAGCGTTTGTGGGAAAAGC
** *
3124721 GTTGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTT
66 GCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTCTTT
3124786 ACCGGTAAGCGCTGCTAAAGGTCTTGGTCTT
131 ACCGGTAAGCGCTGCTAAAGGTCTTGGTCTT
* * * *
3124817 TAGCGGCGTTTGTG-GAAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAG
1 TAGCGGCGTTTGTGTG-AAAAGCGCCACTAAAGGCCATGGTCTTTAGCAGCGTTTGTGGGAAAAG
* * *
3124881 CGCCGCTAAAGGTTTTGGTCTTTAGTGGCGTTTGTGGGAAAAGGGCCGCTAAAGGTCCTGGTCTT
65 CGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTCTT
3124946 TA
130 TA
3124948 GTGGCGTTTA
Statistics
Matches: 118, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
160 1 0.01
161 117 0.99
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (161 bp):
TAGCGGCGTTTGTGTGAAAAGCGCCACTAAAGGCCATGGTCTTTAGCAGCGTTTGTGGGAAAAGC
GCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTCTTT
ACCGGTAAGCGCTGCTAAAGGTCTTGGTCTT
Found at i:3133694 original size:125 final size:122
Alignment explanation
Indices: 3133350--3133710 Score: 354
Period size: 122 Copynumber: 2.9 Consensus size: 122
3133340 CCATTAGTGG
* * ** *** ** *
3133350 CGTTTCCTTAAAAACGCCGCAAAAAATAAGTATTAGTGGCGTTTTTAGCAAAAACGT-CACAAAA
1 CGTTTCATTAAAATCGCCGCAAAAAATAACCATTAGTGGCGTTTTTTTTAAAAAAATGCGC-AAA
* * *
3133414 TAATAAAACCCAACGGCGTCGTTTGGTGGCCTTTCAGGGGATTTAGTGGAGCATCAGC
65 TAATAAAAGCCAACGGCGTCGTTTGGTGACCTTTCGGGGGATTTAGTGGAGCATCAGC
* * * * ** *** *
3133472 CGTGTTACACTAAAATTGCCCCAAAAAA-AATCATTAGT-GC-CATTTTTTGGGAAAACGCCGCA
1 CGT-TT-CATTAAAATCGCCGCAAAAAATAACCATTAGTGGCGTTTTTTTTAAAAAAATG-CGCA
* * *
3133534 AA-AATTAAATGCCAACGGCGTCGTTTGGTGCCCTTTCGGGGGATTTAGTGGAGCATTAGC
63 AATAA-TAAAAGCCAACGGCGTCGTTTGGTGACCTTTCGGGGGATTTAGTGGAGCATCAGC
*
3133594 ATCGTTTCTTTAAAATCGCCGCAAAAAATAACCATTAGTGGCGTTTTTTTTAAAAAAATGCTGCA
1 --CGTTTCATTAAAATCGCCGCAAAAAATAACCATTAGTGGCGTTTTTTTTAAAAAAATGC-GCA
*
3133659 AATAATAAAAGCCAACGGCGTCGTTTGGTGACCTTTCGGGGGGAATTAGTGG
63 AATAATAAAAGCCAACGGCGTCGTTTGGTGACCTTTC-GGGGGATTTAGTGG
3133711 CGTTTTTATT
Statistics
Matches: 188, Mismatches: 38, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
121 7 0.04
122 75 0.40
123 23 0.12
124 22 0.12
125 46 0.24
126 15 0.08
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Consensus pattern (122 bp):
CGTTTCATTAAAATCGCCGCAAAAAATAACCATTAGTGGCGTTTTTTTTAAAAAAATGCGCAAAT
AATAAAAGCCAACGGCGTCGTTTGGTGACCTTTCGGGGGATTTAGTGGAGCATCAGC
Found at i:3133818 original size:42 final size:41
Alignment explanation
Indices: 3133765--3133895 Score: 138
Period size: 41 Copynumber: 3.2 Consensus size: 41
3133755 TTATAAATAT
* *
3133765 GCGCTGCTAATGCTCGAGGTTTTTAGCGGCGTTTTTCATGAA
1 GCGCCGCTAATGCT-GAGGCTTTTAGCGGCGTTTTTCATGAA
* * * * *
3133807 GCGCCGTTAATGCTTAGACTTTTAGCAGCGTTTTTTATGAA
1 GCGCCGCTAATGCTGAGGCTTTTAGCGGCGTTTTTCATGAA
* * * *
3133848 TCGCCGCTAATTCT-AGGGGTTTTAGCGGCGTTTTTGATGAA
1 GCGCCGCTAATGCTGA-GGCTTTTAGCGGCGTTTTTCATGAA
3133889 GCGCCGC
1 GCGCCGC
3133896 AAAAATAATT
Statistics
Matches: 73, Mismatches: 15, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
40 1 0.01
41 60 0.82
42 12 0.16
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (41 bp):
GCGCCGCTAATGCTGAGGCTTTTAGCGGCGTTTTTCATGAA
Found at i:3134239 original size:103 final size:104
Alignment explanation
Indices: 3134112--3134320 Score: 411
Period size: 103 Copynumber: 2.0 Consensus size: 104
3134102 TTAAAAAATT
3134112 TAAAATTATTATCGTAATTAAAAGAGATAGTATTAATTTAAATTTAAAATATTAAATTAAGCATA
1 TAAAATTATTATCGTAATTAAAAGAGATAGTATTAATTTAAATTTAAAATATTAAATTAAGCATA
3134177 TCACTATAGTTAATTTAGGGTTTTAGGTTTAAGGGTATA
66 TCACTATAGTTAATTTAGGGTTTTAGGTTTAAGGGTATA
3134216 TAAAATTATT-TCGTAATTAAAAGAGATAGTATTAATTTAAATTTAAAATATTAAATTAAGCATA
1 TAAAATTATTATCGTAATTAAAAGAGATAGTATTAATTTAAATTTAAAATATTAAATTAAGCATA
3134280 TCACTATAGTTAATTTAGGGTTTTAGGTTTAAGGGTATA
66 TCACTATAGTTAATTTAGGGTTTTAGGTTTAAGGGTATA
3134319 TA
1 TA
3134321 TATGATATTA
Statistics
Matches: 105, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
103 95 0.90
104 10 0.10
ACGTcount: A:0.42, C:0.04, G:0.13, T:0.41
Consensus pattern (104 bp):
TAAAATTATTATCGTAATTAAAAGAGATAGTATTAATTTAAATTTAAAATATTAAATTAAGCATA
TCACTATAGTTAATTTAGGGTTTTAGGTTTAAGGGTATA
Found at i:3135593 original size:269 final size:270
Alignment explanation
Indices: 3135086--3135673 Score: 797
Period size: 269 Copynumber: 2.2 Consensus size: 270
3135076 AAATTTTGAG
* * * * * *
3135086 TAAACGACGCTGTTTCTCTCCATGATTTTTAACTT-ATAAAAGTTTAGAATTATTTACTTAAAAC
1 TAAACGGCGCTGTTTCTGTACACGATTTTTAACTTAAAAAAATTTTAGAATTATTTACTTAAAAC
* **
3135150 GTCACCGTTTGGCTTAAAGTACGTTAAGTATTAGTGGCGTTTTAACATAAAACGCCAGAAACAAT
66 ATCACCGTTTGGCTTAAAGTAAATTAAGTATTAGTGGCGTTTTAACATAAAACGCCAGAAACAAT
* * * *** * *
3135215 GCAATTTGAGAGTAGCAAAACGGCGCCGTTTTTGTTTACGACTTTAAATATTTATTGCATTTTTG
131 GCAATTTGAGACTAACAAAACGGCGACGTTTCCCTTTACAACTTTAAATATTTATGGCATTTTTG
* * *
3135280 GCAAAACGCCGGAACTTTGGAAGCAATAGCGGCGTTTGTACAGTAAACGCCGCAAAAGGGTATTA
196 GCAAAACGCCGGAAATGTGGAAGCAATAGCGGCATTTGTACAGTAAACGCCGCAAAAGGGTATTA
*
3135345 AAATAATGTC
261 AAATAATGGC
* *
3135355 TAAACGGCGATGTTTCTGTACACGATTTTTAACTTAAAAAAATTTTAGAATTATTTATTTAAAAC
1 TAAACGGCGCTGTTTCTGTACACGATTTTTAACTTAAAAAAATTTTAGAATTATTTACTTAAAAC
* * * *
3135420 ATCACCGTTTGGGTTAAAGTAAATTAAGTATTAGTGGCGTTTTTACATAAAATGCCAGAAATAAT
66 ATCACCGTTTGGCTTAAAGTAAATTAAGTATTAGTGGCGTTTTAACATAAAACGCCAGAAACAAT
3135485 GCAATTTGAGACTAACAAAACGGC-ACGTTTCCCTTTACAACTTT-AATATTTAGTGGCATTTTT
131 GCAATTTGAGACTAACAAAACGGCGACGTTTCCCTTTACAACTTTAAATATTTA-TGGCATTTTT
* *
3135548 AGG-AAAACGCCGGAAATGTGGAAGCAATAGCGGCATTTTTACAGTAAACGTCGCAAAAGGGTAT
195 -GGCAAAACGCCGGAAATGTGGAAGCAATAGCGGCATTTGTACAGTAAACGCCGCAAAAGGGTAT
* * *
3135612 TAGAGTAATGGG
259 TAAAATAATGGC
* * ** *
3135624 TAAACGGTGCCGTTTCTGTGTACGATTTTTAACTTAGAAAAATTTTAGAA
1 TAAACGGCGCTGTTTCTGTACACGATTTTTAACTTAAAAAAATTTTAGAA
3135674 ATCAAGTATT
Statistics
Matches: 278, Mismatches: 38, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
268 8 0.03
269 162 0.58
270 108 0.39
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (270 bp):
TAAACGGCGCTGTTTCTGTACACGATTTTTAACTTAAAAAAATTTTAGAATTATTTACTTAAAAC
ATCACCGTTTGGCTTAAAGTAAATTAAGTATTAGTGGCGTTTTAACATAAAACGCCAGAAACAAT
GCAATTTGAGACTAACAAAACGGCGACGTTTCCCTTTACAACTTTAAATATTTATGGCATTTTTG
GCAAAACGCCGGAAATGTGGAAGCAATAGCGGCATTTGTACAGTAAACGCCGCAAAAGGGTATTA
AAATAATGGC
Found at i:3135854 original size:233 final size:232
Alignment explanation
Indices: 3135440--3135906 Score: 663
Period size: 233 Copynumber: 2.0 Consensus size: 232
3135430 GGGTTAAAGT
*
3135440 AAATTAAGTATTAGTGGCGTTTTTACATAAAATGCCAGAAATAATGCAATTTGAGACTAACAAAA
1 AAATCAAGTATTAGTGGCGTTTTTACATAAAATGCCAGAAATAATGCAATTTGAGACTAACAAAA
*
3135505 CGGCACGTTTCCCTTTACAACTTTAATATTTAGTGGCATTTTTAGGAAAACGCCGGAAATGTGGA
66 CGGCACGTTCCCCTTTACAACTTTAATATTTAGTGGCATTTTTAGGAAAACGCCGGAAATGTGGA
* * * * * ***
3135570 AGCAATAGCGGCATTTTTACAGTAAACGTCGCAAAAGGGTATTAGAGTAATGGGTAAACGGTGCC
131 AGCAATAGCGGCATTTGTACAGAAAACGCCGCAAAAGGGTATTAAAGTAATGGCTAAACAACGCC
** *
3135635 GTTTCTGTGTACGATTTTTAACTTAGAAAAATTTTAG
196 GTTTCTGTAAACAATTTTTAACTTAGAAAAATTTTAG
*
3135672 AAATCAAGTATTAGTGGCGTTTTTACGTAAAACT-CCAGAAA-ATATGCAATTTGAGACTAACAA
1 AAATCAAGTATTAGTGGCGTTTTTACATAAAA-TGCCAGAAATA-ATGCAATTTGAGACTAACAA
* *
3135735 AATGGCGTCG-TCCCTCTTTACAACTTTAATATTTAGTGGCATTTTTAGGAAAACGCCGGAAATG
64 AACGGC-ACGTTCCC-CTTTACAACTTTAATATTTAGTGGCATTTTTAGGAAAACGCCGGAAATG
* * *
3135799 TGTAAGCAATAGCGGCGTTTGTACCA-AAAATGCCGCAAAAGGGTATTAAAGTAATGGCTAAACA
127 TGGAAGCAATAGCGGCATTTGTA-CAGAAAACGCCGCAAAAGGGTATTAAAGTAATGGCTAAACA
** *
3135863 ACGTTGTTTCTGTAAACAATTTTTAACTTATAAAAATTTTAG
191 ACGCCGTTTCTGTAAACAATTTTTAACTTAGAAAAATTTTAG
3135905 AA
1 AA
3135907 TTATTTATTT
Statistics
Matches: 208, Mismatches: 22, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
231 1 0.00
232 65 0.31
233 140 0.67
234 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (232 bp):
AAATCAAGTATTAGTGGCGTTTTTACATAAAATGCCAGAAATAATGCAATTTGAGACTAACAAAA
CGGCACGTTCCCCTTTACAACTTTAATATTTAGTGGCATTTTTAGGAAAACGCCGGAAATGTGGA
AGCAATAGCGGCATTTGTACAGAAAACGCCGCAAAAGGGTATTAAAGTAATGGCTAAACAACGCC
GTTTCTGTAAACAATTTTTAACTTAGAAAAATTTTAG
Found at i:3136731 original size:60 final size:60
Alignment explanation
Indices: 3136638--3136757 Score: 197
Period size: 60 Copynumber: 2.0 Consensus size: 60
3136628 GTGAATTTTG
* *
3136638 TGAATTTTGGTTACAGTGCGTGAGGGATTTAGGTAT-AATTAGTTTATTTAGCAGTTGCCC
1 TGAATTTTGGTTACAGTGCATGAGGGATTTAGGTATAAATTA-TTTATTTAACAGTTGCCC
*
3136698 TGAATTTTGGTTACAGTGTATGAGGGATTTAGGTATAAATTATTTATTTAACAGTTGCCC
1 TGAATTTTGGTTACAGTGCATGAGGGATTTAGGTATAAATTATTTATTTAACAGTTGCCC
3136758 AAATGAATTT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
60 51 0.91
61 5 0.09
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (60 bp):
TGAATTTTGGTTACAGTGCATGAGGGATTTAGGTATAAATTATTTATTTAACAGTTGCCC
Found at i:3136826 original size:13 final size:13
Alignment explanation
Indices: 3136802--3136842 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
3136792 ATTTTGCGAC
*
3136802 ATTTTCTAAATGA
1 ATTTTCTTAATGA
3136815 ATTTT-TTGAATGA
1 ATTTTCTT-AATGA
3136828 ATTTTCTTAATGA
1 ATTTTCTTAATGA
3136841 AT
1 AT
3136843 ATAGTAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 1 0.04
13 22 0.88
14 2 0.08
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.51
Consensus pattern (13 bp):
ATTTTCTTAATGA
Found at i:3137195 original size:23 final size:23
Alignment explanation
Indices: 3137143--3137195 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
3137133 TCATTTTTTT
* * *
3137143 TTTGCT-TGCATTTCTTTGCTTA
1 TTTGCTCTACATTTCTTGGCTGA
3137165 TCTT-CTCTACATTTCTTGGCTGA
1 T-TTGCTCTACATTTCTTGGCTGA
3137188 TTTGCTCT
1 TTTGCTCT
3137196 TTGTTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.09, C:0.23, G:0.13, T:0.55
Consensus pattern (23 bp):
TTTGCTCTACATTTCTTGGCTGA
Found at i:3138391 original size:9 final size:9
Alignment explanation
Indices: 3138377--3138639 Score: 103
Period size: 9 Copynumber: 30.2 Consensus size: 9
3138367 NNNNNNNNNN
3138377 AACTTACAT
1 AACTTACAT
3138386 AACTTACAT
1 AACTTACAT
3138395 AA--TACAT
1 AACTTACAT
*
3138402 AACTCT-GAT
1 AACT-TACAT
*
3138411 AACTAACAGT
1 AACTTACA-T
*
3138421 -A--TACAC
1 AACTTACAT
3138427 AACTTACAT
1 AACTTACAT
*
3138436 AA--GACAT
1 AACTTACAT
*
3138443 TACTTACAT
1 AACTTACAT
3138452 AACTTACAT
1 AACTTACAT
* *
3138461 TA--TACAC
1 AACTTACAT
3138468 AACTTACAT
1 AACTTACAT
* ***
3138477 AAATTTTTT
1 AACTTACAT
*
3138486 AATATTATACAT
1 -A-ACT-TACAT
*
3138498 AACGTACAT
1 AACTTACAT
*
3138507 TA--TACAT
1 AACTTACAT
3138514 AACTTACAT
1 AACTTACAT
3138523 AAC-T-CAT
1 AACTTACAT
3138530 AACTTACAT
1 AACTTACAT
3138539 AACTTA-AT
1 AACTTACAT
*
3138547 TACATTATGCA-
1 AAC-TTA--CAT
**
3138558 CCCTTTACAT
1 AAC-TTACAT
3138568 AACTTACAT
1 AACTTACAT
*
3138577 AGCTTACAT
1 AACTTACAT
* *
3138586 -TC-TACAC
1 AACTTACAT
3138593 AACTTACAT
1 AACTTACAT
*
3138602 AACATACAT
1 AACTTACAT
* **
3138611 TACTTTGAT
1 AACTTACAT
3138620 AACTTACAT
1 AACTTACAT
3138629 AACTTACAT
1 AACTTACAT
3138638 AA
1 AA
3138640 TACACAACTT
Statistics
Matches: 183, Mismatches: 45, Indels: 52
0.65 0.16 0.19
Matches are distributed among these distances:
7 37 0.20
8 8 0.04
9 123 0.67
10 5 0.03
11 7 0.04
12 3 0.02
ACGTcount: A:0.43, C:0.21, G:0.03, T:0.34
Consensus pattern (9 bp):
AACTTACAT
Found at i:3138437 original size:25 final size:25
Alignment explanation
Indices: 3138377--3138437 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
3138367 NNNNNNNNNN
* *
3138377 AACTTACATAACTTACATAATACAT
1 AACTTACATAACTAACATAATACAC
*
3138402 AACTCT-GATAACTAACAGT-ATACAC
1 AACT-TACATAACTAACA-TAATACAC
3138427 AACTTACATAA
1 AACTTACATAA
3138438 GACATTACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
24 1 0.03
25 26 0.90
26 2 0.07
ACGTcount: A:0.48, C:0.21, G:0.03, T:0.28
Consensus pattern (25 bp):
AACTTACATAACTAACATAATACAC
Found at i:3138454 original size:41 final size:41
Alignment explanation
Indices: 3138381--3138478 Score: 126
Period size: 41 Copynumber: 2.4 Consensus size: 41
3138371 NNNNNNAACT
* * *
3138381 TACATAACTTACATAATACATAACTCTGATAACTAACAGTA
1 TACACAACTTACATAAGACATAACTCTCATAACTAACAGTA
* * *
3138422 TACACAACTTACATAAGACATTACT-TACATAACTTACATTA
1 TACACAACTTACATAAGACATAACTCT-CATAACTAACAGTA
3138463 TACACAACTTACATAA
1 TACACAACTTACATAA
3138479 ATTTTTTAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
40 1 0.02
41 49 0.98
ACGTcount: A:0.46, C:0.21, G:0.03, T:0.30
Consensus pattern (41 bp):
TACACAACTTACATAAGACATAACTCTCATAACTAACAGTA
Found at i:3138466 original size:16 final size:16
Alignment explanation
Indices: 3138447--3138680 Score: 90
Period size: 16 Copynumber: 14.4 Consensus size: 16
3138437 AGACATTACT
3138447 TACATAACTTACATTA
1 TACATAACTTACATTA
*
3138463 TACACAACTTACA-TA
1 TACATAACTTACATTA
*** *
3138478 -A-ATTTTTTAATATTA
1 TACATAACTT-ACATTA
*
3138493 TACATAACGTACATTA
1 TACATAACTTACATTA
*
3138509 TACATAACTTACATAA
1 TACATAACTTACATTA
3138525 CT-CATAACTTACA-TA
1 -TACATAACTTACATTA
*
3138540 -ACTTAA-TTACATTA
1 TACATAACTTACATTA
* ** *
3138554 TGCA-CCCTTTACATAA
1 TACATAAC-TTACATTA
* *
3138570 CTTACATAGCTTACATTC
1 --TACATAACTTACATTA
* *
3138588 TACACAACTTACATAACA
1 TACATAACTTACAT--TA
* ** *
3138606 TACATTACTTTGATAA
1 TACATAACTTACATTA
*
3138622 CTTACATAACTTACATAA
1 --TACATAACTTACATTA
*
3138640 TACACAACTTTA-ACTTA
1 TACATAAC-TTACA-TTA
*
3138657 GTACATAACTTACATAA
1 -TACATAACTTACATTA
3138674 TACATAA
1 TACATAA
3138681 AAATATATCA
Statistics
Matches: 156, Mismatches: 41, Indels: 42
0.65 0.17 0.18
Matches are distributed among these distances:
13 8 0.05
14 9 0.06
15 6 0.04
16 78 0.50
17 14 0.09
18 40 0.26
19 1 0.01
ACGTcount: A:0.42, C:0.21, G:0.02, T:0.35
Consensus pattern (16 bp):
TACATAACTTACATTA
Found at i:3138643 original size:34 final size:34
Alignment explanation
Indices: 3138588--3138680 Score: 98
Period size: 34 Copynumber: 2.7 Consensus size: 34
3138578 GCTTACATTC
* * * *
3138588 TACACAACTTACATAACATACATTACTTTGA-TAACT
1 TACATAACTTACAT-A-ATACATAACTTTAACTAA-G
* *
3138624 TACATAACTTACATAATACACAACTTTAACTTAG
1 TACATAACTTACATAATACATAACTTTAACTAAG
3138658 TACATAACTTACATAATACATAA
1 TACATAACTTACATAATACATAA
3138681 AAATATATCA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
34 33 0.67
35 3 0.06
36 13 0.27
ACGTcount: A:0.45, C:0.20, G:0.02, T:0.32
Consensus pattern (34 bp):
TACATAACTTACATAATACATAACTTTAACTAAG
Found at i:3138662 original size:52 final size:50
Alignment explanation
Indices: 3138566--3138667 Score: 116
Period size: 52 Copynumber: 2.0 Consensus size: 50
3138556 CACCCTTTAC
* ** *
3138566 ATAACTTACATAGCTTACATTCTACACAACTTACATAACATACATTACTTTG
1 ATAACTTACATAACTTACATAATACACAACTT--ATAACATACATAACTTTG
3138618 ATAACTTACATAACTTACATAATACACAACTT-TAACTTAGTACATAACTT
1 ATAACTTACATAACTTACATAATACACAACTTATAAC--A-TACATAACTT
3138668 ACATAATACA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
49 4 0.09
51 1 0.02
52 38 0.88
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.34
Consensus pattern (50 bp):
ATAACTTACATAACTTACATAATACACAACTTATAACATACATAACTTTG
Found at i:3144099 original size:21 final size:21
Alignment explanation
Indices: 3144071--3144120 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
3144061 CTACAACTTA
3144071 AAGCAGAGGCAGCAGCAAGGG
1 AAGCAGAGGCAGCAGCAAGGG
* ** *
3144092 AAGTAGAGGTTGCAGCGAGGG
1 AAGCAGAGGCAGCAGCAAGGG
3144113 AAGCAGAG
1 AAGCAGAG
3144121 CAAAGCAGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.14, G:0.44, T:0.06
Consensus pattern (21 bp):
AAGCAGAGGCAGCAGCAAGGG
Found at i:3144639 original size:42 final size:43
Alignment explanation
Indices: 3144483--3144775 Score: 251
Period size: 43 Copynumber: 6.9 Consensus size: 43
3144473 CATTTTTGGA
* *
3144483 AAAAGTGCCGCTAAAGAACATGACCTTTAGGGGCGTTTCCG-A-G
1 AAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTT--GTAGG
* * ** *
3144526 AAAAGTGCCACTAAAGAACATGACCTTTAGCAACGTTTGT-GTA
1 AAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTGTAG-G
*
3144569 AAAAGCGTCGCTAAAGAACATGACCTTTAGCGGCGTTTGT-GG
1 AAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTGTAGG
* * ** ** *
3144611 GAAAGCGCCGCTAAAGATCATGTTCTTTAGCGGATTTTCTATGG
1 AAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTGTA-GG
* * * * *
3144655 --AAGCGCCGCTAATGAACTTGACCTTTAGCGGCATTTTTCTGG
1 AAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTGT-AGG
** * *
3144697 --TTGCGCCGCTAAAGAATATGACCTTTAGCGGCGTTTGTAGA
1 AAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTGTAGG
* *
3144738 AAAAGCACAGCTAAAGAACATGACCTTTAGCGGCGTTT
1 AAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTT
3144776 ATTTCCATGA
Statistics
Matches: 200, Mismatches: 42, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
41 2 0.01
42 95 0.47
43 101 0.50
44 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTGTAGG
Found at i:3144723 original size:84 final size:84
Alignment explanation
Indices: 3144489--3144771 Score: 207
Period size: 84 Copynumber: 3.3 Consensus size: 84
3144479 TGGAAAAAGT
* * ** * * * *
3144489 GCCGCTAAAGAACATGACCTTTAGGGGCGTTTCCGAGAAAAGTGCCACTAAAGAACATGACCTTT
1 GCCGCTAAAGAACATGACCTTTAGCGGCATTTGTG-GGAAAGCGCCGCTAAAGATCATGACCTTT
* * **
3144554 AGC-AACGTTTGTGTA-AAAAGC
65 AGCGGA--TTT-TCTATGGAAGC
* * **
3144575 GTCGCTAAAGAACATGACCTTTAGCGGCGTTTGTGGGAAAGCGCCGCTAAAGATCATGTTCTTTA
1 GCCGCTAAAGAACATGACCTTTAGCGGCATTTGTGGGAAAGCGCCGCTAAAGATCATGACCTTTA
3144640 GCGGATTTTCTATGGAAGC
66 GCGGATTTTCTATGGAAGC
* * * * **
3144659 GCCGCTAATGAACTTGACCTTTAGCGGCATTTTTCTGG-TTGCGCCGCTAAAGAAT-ATGACCTT
1 GCCGCTAAAGAACATGACCTTTAGCGGCATTTGT-GGGAAAGCGCCGCTAAAG-ATCATGACCTT
** * *
3144722 TAGCGGCGTTTGTA-GAAAAAGC
64 TAGCGGATTTTCTATG--GAAGC
* *
3144744 ACAGCTAAAGAACATGACCTTTAGCGGC
1 GCCGCTAAAGAACATGACCTTTAGCGGC
3144772 GTTTATTTCC
Statistics
Matches: 159, Mismatches: 32, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
83 4 0.03
84 65 0.41
85 58 0.36
86 32 0.20
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.26
Consensus pattern (84 bp):
GCCGCTAAAGAACATGACCTTTAGCGGCATTTGTGGGAAAGCGCCGCTAAAGATCATGACCTTTA
GCGGATTTTCTATGGAAGC
Found at i:3152962 original size:75 final size:75
Alignment explanation
Indices: 3152876--3153019 Score: 218
Period size: 75 Copynumber: 1.9 Consensus size: 75
3152866 ACACCATCCT
* *
3152876 GTCGAGCGAAGAATAGAAAGATGAATGAA-TAGTTTAAAGCGAGAAAACCAGCTAGAGCCTATGC
1 GTCGAGCGAAGAATAGAAAGATGAATGAACTA-TCTAAAGAGAGAAAACCAGCTAGAGCCTATGC
3152940 AATCAGACCCA
65 AATCAGACCCA
* ** *
3152951 GTCGAGGGAAGAATAGTGAGATGAATGAACTATCTGAAGAGAGAAAACCAGCTAGAGCCTATGCA
1 GTCGAGCGAAGAATAGAAAGATGAATGAACTATCTAAAGAGAGAAAACCAGCTAGAGCCTATGCA
3153016 ATCA
66 ATCA
3153020 AAGCTTGTGA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
75 60 0.97
76 2 0.03
ACGTcount: A:0.42, C:0.16, G:0.26, T:0.17
Consensus pattern (75 bp):
GTCGAGCGAAGAATAGAAAGATGAATGAACTATCTAAAGAGAGAAAACCAGCTAGAGCCTATGCA
ATCAGACCCA
Found at i:3155764 original size:43 final size:42
Alignment explanation
Indices: 3155693--3155774 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 42
3155683 NGTGAACCGA
* *
3155693 GTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACC
1 GTATCATTGAATATAAGGGGGTTGCTAAGTGCTGATTCCACC
*
3155735 GTATCTTTGAATATAAAGGGGGTTGCTAAGTGCTGATTCC
1 GTATCATTGAATAT-AAGGGGGTTGCTAAGTGCTGATTCC
3155775 CCCAAGGGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 12 0.33
43 24 0.67
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (42 bp):
GTATCATTGAATATAAGGGGGTTGCTAAGTGCTGATTCCACC
Found at i:3161881 original size:20 final size:21
Alignment explanation
Indices: 3161824--3161884 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 21
3161814 TGTGCCCTTG
3161824 TTTGTACTTCGGTACCCCTGA
1 TTTGTACTTCGGTACCCCTGA
* * ** *
3161845 -TTGCACATATGTGCCCCT-A
1 TTTGTACTTCGGTACCCCTGA
3161864 TTTGTACTTCGGTACCCCTGA
1 TTTGTACTTCGGTACCCCTGA
3161885 ACATATTTTT
Statistics
Matches: 28, Mismatches: 10, Indels: 4
0.67 0.24 0.10
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.16, C:0.30, G:0.18, T:0.36
Consensus pattern (21 bp):
TTTGTACTTCGGTACCCCTGA
Found at i:3161883 original size:40 final size:40
Alignment explanation
Indices: 3161762--3161884 Score: 183
Period size: 40 Copynumber: 3.1 Consensus size: 40
3161752 AATTACTGAA
* * *
3161762 TGATTGCACATACGTGCCCCTGTTCGTACTTCGGTATCCC
1 TGATTGCACATATGTGCCCCTGTTTGTACTTCGGTACCCC
* * *
3161802 TAATTGCTCATATGTGCCCTTGTTTGTACTTCGGTACCCC
1 TGATTGCACATATGTGCCCCTGTTTGTACTTCGGTACCCC
*
3161842 TGATTGCACATATGTGCCCCTATTTGTACTTCGGTACCCC
1 TGATTGCACATATGTGCCCCTGTTTGTACTTCGGTACCCC
3161882 TGA
1 TGA
3161885 ACATATTTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 73 1.00
ACGTcount: A:0.16, C:0.29, G:0.19, T:0.36
Consensus pattern (40 bp):
TGATTGCACATATGTGCCCCTGTTTGTACTTCGGTACCCC
Found at i:3161903 original size:80 final size:80
Alignment explanation
Indices: 3161762--3161917 Score: 181
Period size: 80 Copynumber: 1.9 Consensus size: 80
3161752 AATTACTGAA
* * * * *
3161762 TGATTGCACATACGTGCCCCTGTTCGTACTTCGGTATCCCTAATTGCTCATATGTGCCCTTGTTT
1 TGATTGCACATACGTGCCCCTATTCGTACTTCGGTACCCCTAAATGATCATATGTGCCCTTGATT
3161827 GTACTTCGGTACCCC
66 GTACTTCGGTACCCC
* * ** *
3161842 TGATTGCACATATGTGCCCCTATTTGTACTTCGGTACCCCTGAACAT-ATTTTTTGTG-CCTTGA
1 TGATTGCACATACGTGCCCCTATTCGTACTTCGGTACCCCT-AA-ATGATCATATGTGCCCTTGA
*
3161905 TTGTACTTTGGTA
64 TTGTACTTCGGTA
3161918 AACCTGAAAC
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
80 54 0.86
81 8 0.13
82 1 0.02
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.39
Consensus pattern (80 bp):
TGATTGCACATACGTGCCCCTATTCGTACTTCGGTACCCCTAAATGATCATATGTGCCCTTGATT
GTACTTCGGTACCCC
Found at i:3168312 original size:16 final size:16
Alignment explanation
Indices: 3168291--3168327 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
3168281 CTAGTAAAAT
3168291 AGAGAATAACTCTCGA
1 AGAGAATAACTCTCGA
3168307 AGAGAATAACTCTCGA
1 AGAGAATAACTCTCGA
3168323 AGAGA
1 AGAGA
3168328 GGGAAAGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.16
Consensus pattern (16 bp):
AGAGAATAACTCTCGA
Found at i:3179370 original size:84 final size:84
Alignment explanation
Indices: 3179206--3179498 Score: 338
Period size: 84 Copynumber: 3.5 Consensus size: 84
3179196 ATTAAACGGT
* * * * * * * ** *
3179206 GGCGGGAATAAATCCCAAAATAGA-ATTATTTGATTTCA-TCTTTATTTGGAAACAAACCAATAT
1 GGCGGGAATAAATCCCAAAACAGATTTTATTTAATTTAATTC-TAATCTGAAAACAAAATAAAAT
* *
3179269 CGAATAAAATCTAGTTAAAC
65 CAAATAAAATCTTGTTAAAC
* * * *
3179289 GACGGGAATAAATCCCAAAACAGATTTTATTTTATTTAATTCTAATCTGAAAATAAAATATAATC
1 GGCGGGAATAAATCCCAAAACAGATTTTATTTAATTTAATTCTAATCTGAAAACAAAATAAAATC
*
3179354 AAATAAAACCTTGTTAAAC
66 AAATAAAATCTTGTTAAAC
* * *
3179373 GGCGGGAATAAATCCCAAAATAGATTTTATTTAATTTAATTCTAATTTGGAAACAAAATAAAATC
1 GGCGGGAATAAATCCCAAAACAGATTTTATTTAATTTAATTCTAATCTGAAAACAAAATAAAATC
*
3179438 AAATAAAATCTTGTTAAAT
66 AAATAAAATCTTGTTAAAC
* * *
3179457 GGTGGGAATAAATCTCAAAACAGATTTTATTTGATTTTAATT
1 GGCGGGAATAAATCCCAAAACAGATTTTATTT-AATTTAATT
3179499 TCTTGTTTTT
Statistics
Matches: 178, Mismatches: 29, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
83 22 0.12
84 146 0.82
85 10 0.06
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (84 bp):
GGCGGGAATAAATCCCAAAACAGATTTTATTTAATTTAATTCTAATCTGAAAACAAAATAAAATC
AAATAAAATCTTGTTAAAC
Found at i:3179629 original size:88 final size:87
Alignment explanation
Indices: 3179549--3179944 Score: 274
Period size: 88 Copynumber: 4.7 Consensus size: 87
3179539 TTGATAAACG
* *
3179549 GGAATAAATC-CTGAAACAGATTTTAATTTAGTTTTAATACTCATTTTGGAAATAACATCAAAAT
1 GGAATAAATCTC-GAAACAGATTTTAATTTAATTTTAATACTCATTTTGGAAATAAAATCAAAAT
3179613 TGAAATAAAATCCGTTGAACGGTA
65 TGAAATAAAATCCGTTGAACGG-A
* **
3179637 GGAATAAATCTCGAAACAGATTTTATTTTAATTTTAATACTTGTTTTGGAAATAAAATCAAAATT
1 GGAATAAATCTCGAAACAGATTTTAATTTAATTTTAATACTCATTTTGGAAATAAAATCAAAA-T
** * *
3179702 TGGTATAAAAT-TGTTGAACGGCG
65 TGAAATAAAATCCGTTGAACGG-A
* * * * *
3179725 GGAATTAATCCCGAAAC-G----GAATTT-A-TTT--TACTCATTTTTGGAAATAAAATAAAAAA
1 GGAATAAATCTCGAAACAGATTTTAATTTAATTTTAATACTCA-TTTTGGAAATAAAATCAAAAT
*
3179781 TGAAATAAAA-CCGTTGAACGACA
65 TGAAATAAAATCCGTTGAACG-GA
* * * * * * *
3179804 GGAATCAATCCCGAAA-AAATTTT-ATTTACA-TTTAAT-TTCCTGTTTAGAAAT-AAATAAAAA
1 GGAATAAATCTCGAAACAGATTTTAATTTA-ATTTTAATACTCAT-TTTGGAAATAAAATCAAAA
* * * * *
3179864 TAATGGAATTAAATCCATTAAACGAA
64 T--TGAAATAAAATCCGTTGAACGGA
* * * *
3179890 GGGAATAAATCCCGAAATAGATTTT-A-TTAGTTTTAATATTCA-TTTGGAAATAAAA
1 -GGAATAAATCTCGAAACAGATTTTAATTTAATTTTAATACTCATTTTGGAAATAAAA
3179945 AACAAGATAG
Statistics
Matches: 245, Mismatches: 40, Indels: 47
0.74 0.12 0.14
Matches are distributed among these distances:
79 35 0.14
80 19 0.08
81 3 0.01
82 5 0.02
83 4 0.02
84 14 0.06
85 10 0.04
86 18 0.07
87 36 0.15
88 90 0.37
89 11 0.04
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.33
Consensus pattern (87 bp):
GGAATAAATCTCGAAACAGATTTTAATTTAATTTTAATACTCATTTTGGAAATAAAATCAAAATT
GAAATAAAATCCGTTGAACGGA
Found at i:3179729 original size:176 final size:170
Alignment explanation
Indices: 3179364--3180006 Score: 475
Period size: 176 Copynumber: 3.7 Consensus size: 170
3179354 AAATAAAACC
* * * * * * *
3179364 TTGTTAAACGGCGGGAATAAATCCCAAAATAGATTTTATTTAATTTAATTCT-AATTTGGAAACA
1 TTGTTAAACGACGGGAATAAATCCCGAAACAGATTTTATTTATTTTAATACTCATTTTGGAAATA
* * * * * * *
3179428 AAATAAAATCAAATAAAATCTTGTTAAATGGTGGGAATAAATCTCAAAACAGATTTTATTTGATT
66 AAATAAAATGAAATAAAATC-CGTTGAACGGTAGGAATAAATCTCGAAACAGATTTTATTTAATT
* * *
3179493 TTAATTTCTTGTTTTTTTGGCAACAAAATC-AAATGT-GATAAA
130 TTAATTTCTTG---TTTTGGAAATAAAATCAAAATATGGATAAA
*
3179535 TTCGTTGATAA--ACGGGAATAAATCCTGAAACAGATTTTAATTTAGTTTTAATACTCATTTTGG
1 TT-GTT-A-AACGACGGGAATAAATCCCGAAACAGATTTT-ATTTA-TTTTAATACTCATTTTGG
*
3179598 AAATAACATCAAAATTGAAATAAAATCCGTTGAACGGTAGGAATAAATCTCGAAACAGATTTTAT
61 AAATAAAAT-AAAA-TGAAATAAAATCCGTTGAACGGTAGGAATAAATCTCGAAACAGATTTTA-
* *
3179663 TTTAATTTTAA-TACTTGTTTTGGAAATAAAATCAAAATTTGGTATAAAA
123 TTTAATTTTAATTTCTTGTTTTGGAAATAAAATCAAAATATGG-AT-AAA
* * * *
3179712 TTGTTGAACGGCGGGAATTAATCCCGAAACGGA----ATTTA-TTT--TACTCATTTTTGGAAAT
1 TTGTTAAACGACGGGAATAAATCCCGAAACAGATTTTATTTATTTTAATACTCA-TTTTGGAAAT
** * * *
3179770 AAAATAAAAAATGAAATAAAA-CCGTTGAACGACAGGAATCAATCCCGAAA-AAATTTTATTTAC
65 AAAAT--AAAATGAAATAAAATCCGTTGAACGGTAGGAATAAATCTCGAAACAGATTTTATTTA-
* * *
3179833 A-TTTAATTTCCTG-TTTAGAAAT-AAATAAAAATAATGGAATTAAA
127 ATTTTAATTTCTTGTTTTGGAAATAAAATCAAAAT-ATGG-A-TAAA
** * * *
3179877 TCCATTAAACGAAGGGAATAAATCCCGAAATAGATTTTA-TTAGTTTTAATATTCA-TTTGGAAA
1 T-TGTTAAACGACGGGAATAAATCCCGAAACAGATTTTATTTA-TTTTAATACTCATTTTGGAAA
* * * * * * *
3179940 TAAAAAACAAGATAGAGAAAAAAAATCTGTTGAATGGCAGGAA-AACTCCCGAAACAGA-TTTAT
64 TAAAATA-AA-AT---GAAATAAAATCCGTTGAACGGTAGGAATAAATCTCGAAACAGATTTTAT
3180003 TTAA
124 TTAA
3180007 AAAATTTTTA
Statistics
Matches: 380, Mismatches: 55, Indels: 72
0.75 0.11 0.14
Matches are distributed among these distances:
164 9 0.02
165 25 0.07
166 37 0.10
167 31 0.08
168 24 0.06
169 11 0.03
170 3 0.01
171 25 0.07
172 26 0.07
173 26 0.07
174 42 0.11
175 30 0.08
176 65 0.17
177 26 0.07
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (170 bp):
TTGTTAAACGACGGGAATAAATCCCGAAACAGATTTTATTTATTTTAATACTCATTTTGGAAATA
AAATAAAATGAAATAAAATCCGTTGAACGGTAGGAATAAATCTCGAAACAGATTTTATTTAATTT
TAATTTCTTGTTTTGGAAATAAAATCAAAATATGGATAAA
Found at i:3180028 original size:17 final size:17
Alignment explanation
Indices: 3180006--3180038 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3179996 GATTTATTTA
3180006 AAAAAT-TTTTATTTTTG
1 AAAAATATTTT-TTTTTG
3180023 AAAAATATTTTTTTTT
1 AAAAATATTTTTTTTT
3180039 CTTTTCGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
AAAAATATTTTTTTTTG
Found at i:3181001 original size:9 final size:9
Alignment explanation
Indices: 3180972--3181008 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
3180962 TGAGTTTTCG
3180972 AATTCGAAT
1 AATTCGAAT
*
3180981 AACTCGAAT
1 AATTCGAAT
3180990 AATTCGAAT
1 AATTCGAAT
*
3180999 AATTCAAAT
1 AATTCGAAT
3181008 A
1 A
3181009 TTAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:3181255 original size:30 final size:31
Alignment explanation
Indices: 3181221--3181280 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
3181211 AAACCTTTTA
*
3181221 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
3181251 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
3181281 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:3186256 original size:14 final size:14
Alignment explanation
Indices: 3186237--3186263 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3186227 TATAATTAAT
3186237 AAATATTTTTTTTC
1 AAATATTTTTTTTC
3186251 AAATATTTTTTTT
1 AAATATTTTTTTT
3186264 ATTTTTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (14 bp):
AAATATTTTTTTTC
Found at i:3186265 original size:91 final size:91
Alignment explanation
Indices: 3186166--3186544 Score: 758
Period size: 91 Copynumber: 4.2 Consensus size: 91
3186156 CTTAATTGTA
3186166 TTTTTTTATTTTTTATTTATTTTATGTTGTTTCAAGCTTTTTATTATTTTTAGTTAATGTTTATA
1 TTTTTTTATTTTTTATTTATTTTATGTTGTTTCAAGCTTTTTATTATTTTTAGTTAATGTTTATA
3186231 ATTAATAAATATTTTTTTTCAAATAT
66 ATTAATAAATATTTTTTTTCAAATAT
3186257 TTTTTTTATTTTTTATTTATTTTATGTTGTTTCAAGCTTTTTATTATTTTTAGTTAATGTTTATA
1 TTTTTTTATTTTTTATTTATTTTATGTTGTTTCAAGCTTTTTATTATTTTTAGTTAATGTTTATA
3186322 ATTAATAAATATTTTTTTTCAAATAT
66 ATTAATAAATATTTTTTTTCAAATAT
3186348 TTTTTTTATTTTTTATTTATTTTATGTTGTTTCAAGCTTTTTATTATTTTTAGTTAATGTTTATA
1 TTTTTTTATTTTTTATTTATTTTATGTTGTTTCAAGCTTTTTATTATTTTTAGTTAATGTTTATA
3186413 ATTAATAAATATTTTTTTTCAAATAT
66 ATTAATAAATATTTTTTTTCAAATAT
3186439 TTTTTTTATTTTTTATTTATTTTATGTTGTTTCAAGCTTTTTATTATTTTTAGTTAATGTTTATA
1 TTTTTTTATTTTTTATTTATTTTATGTTGTTTCAAGCTTTTTATTATTTTTAGTTAATGTTTATA
3186504 ATTAATAAATATTTTTTTTCAAATAT
66 ATTAATAAATATTTTTTTTCAAATAT
3186530 TTTTTTTATTTTTTA
1 TTTTTTTATTTTTTA
3186545 ATTCATCTCT
Statistics
Matches: 288, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 288 1.00
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (91 bp):
TTTTTTTATTTTTTATTTATTTTATGTTGTTTCAAGCTTTTTATTATTTTTAGTTAATGTTTATA
ATTAATAAATATTTTTTTTCAAATAT
Found at i:3186347 original size:14 final size:14
Alignment explanation
Indices: 3186328--3186354 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3186318 TATAATTAAT
3186328 AAATATTTTTTTTC
1 AAATATTTTTTTTC
3186342 AAATATTTTTTTT
1 AAATATTTTTTTT
3186355 ATTTTTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (14 bp):
AAATATTTTTTTTC
Found at i:3186438 original size:14 final size:14
Alignment explanation
Indices: 3186419--3186445 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3186409 TATAATTAAT
3186419 AAATATTTTTTTTC
1 AAATATTTTTTTTC
3186433 AAATATTTTTTTT
1 AAATATTTTTTTT
3186446 ATTTTTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (14 bp):
AAATATTTTTTTTC
Found at i:3186529 original size:14 final size:14
Alignment explanation
Indices: 3186510--3186536 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3186500 TATAATTAAT
3186510 AAATATTTTTTTTC
1 AAATATTTTTTTTC
3186524 AAATATTTTTTTT
1 AAATATTTTTTTT
3186537 ATTTTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (14 bp):
AAATATTTTTTTTC
Found at i:3186613 original size:20 final size:21
Alignment explanation
Indices: 3186579--3186619 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3186569 ATTAAATAAT
* *
3186579 AAATATGTAATTAATTTTTTA
1 AAATATGTAACTAATTCTTTA
3186600 AAATAT-TAACTAATTCTTTA
1 AAATATGTAACTAATTCTTTA
3186620 GATATATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (21 bp):
AAATATGTAACTAATTCTTTA
Found at i:3192934 original size:239 final size:239
Alignment explanation
Indices: 3192515--3192981 Score: 679
Period size: 239 Copynumber: 2.0 Consensus size: 239
3192505 CTGAGTAAAA
* *
3192515 TGGTACATCTAGTTCGTACTTAGGATAACAGGGAAAATACTAGCGACAACTAACTGTAACTGCAA
1 TGGTACATCTAGTTCGGACTTAGGATAACAGGGAAAATACTAACGACAACTAACTGTAACTGCAA
* * * * *
3192580 TGAAATCCAAGCACATAGAATAAATATGATGTGACATACAAGTTACAGATCATTTAATACATAAT
66 TGAAATCCAAGCACACAAAATAAATATGATGTGACATACAAGTTACAGATAAATAAATACATAAT
* * * *
3192645 CCAATTAGAAGTAGCACGATACTTGTGTCTATGTTTAACCCCCTCAGCATTTGCTGCTTAAGTAG
131 CCAATTAGAAGTAGCACAATACTTATATCTATGTTTAACCCCCTCAGCATTTGCTACTTAAGTAG
* *
3192710 AAATCGCATGCCAGTACACATCTTCAAATAAAATTTTAGTCAAC
196 AAATAGCATGCCAGTACACATCTTAAAATAAAATTTTAGTCAAC
* * * * *
3192754 TGGTACATCTAGTTTGGACTTAGGATATCA-GGAAAATTACTAATGACAACTAACTGTAAGTGCG
1 TGGTACATCTAGTTCGGACTTAGGATAACAGGGAAAA-TACTAACGACAACTAACTGTAACTGCA
* *
3192818 ATGAAATCCAAGCACACAAAATAAGTATGATGTGACATACAAGTTACGGATAAATAAATACATAA
65 ATGAAATCCAAGCACACAAAATAAATATGATGTGACATACAAGTTACAGATAAATAAATACATAA
*
3192883 TCCAATTAGACA-TAGTACAATACTTATATCTATGTTT-ACCCCCGTCAGCATTTGCTACTTAAG
130 TCCAATTAGA-AGTAGCACAATACTTATATCTATGTTTAACCCCC-TCAGCATTTGCTACTTAAG
**
3192946 TAGAAATAGCATGCCAGTATGCATCTTAAAATAAAA
193 TAGAAATAGCATGCCAGTACACATCTTAAAATAAAA
3192982 CTGTAGCCAA
Statistics
Matches: 202, Mismatches: 23, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
238 12 0.06
239 189 0.94
240 1 0.00
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (239 bp):
TGGTACATCTAGTTCGGACTTAGGATAACAGGGAAAATACTAACGACAACTAACTGTAACTGCAA
TGAAATCCAAGCACACAAAATAAATATGATGTGACATACAAGTTACAGATAAATAAATACATAAT
CCAATTAGAAGTAGCACAATACTTATATCTATGTTTAACCCCCTCAGCATTTGCTACTTAAGTAG
AAATAGCATGCCAGTACACATCTTAAAATAAAATTTTAGTCAAC
Found at i:3197732 original size:16 final size:18
Alignment explanation
Indices: 3197711--3197748 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
3197701 CGCAACGGAA
3197711 ATTTTGTT-AAAATC-AT
1 ATTTTGTTAAAAATCAAT
3197727 ATTTTGTTAAAAATCAAT
1 ATTTTGTTAAAAATCAAT
3197745 ATTT
1 ATTT
3197749 CATACAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 6 0.30
18 6 0.30
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (18 bp):
ATTTTGTTAAAAATCAAT
Found at i:3208479 original size:20 final size:20
Alignment explanation
Indices: 3208450--3208492 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3208440 TTATGCTAAA
*
3208450 TAAATGGAAAGAAAAGTAAG
1 TAAATCGAAAGAAAAGTAAG
* *
3208470 TAAATCGAAAGATAAGTATG
1 TAAATCGAAAGAAAAGTAAG
3208490 TAA
1 TAA
3208493 GTGAAGTGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.56, C:0.02, G:0.21, T:0.21
Consensus pattern (20 bp):
TAAATCGAAAGAAAAGTAAG
Found at i:3220249 original size:21 final size:21
Alignment explanation
Indices: 3220225--3220265 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3220215 TCTTTCTTGC
*
3220225 TTTCCTTTTCGCCTTTTTCAT
1 TTTCATTTTCGCCTTTTTCAT
**
3220246 TTTCATTTTCTTCTTTTTCA
1 TTTCATTTTCGCCTTTTTCA
3220266 CTTGTATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.24, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTCATTTTCGCCTTTTTCAT
Found at i:3221071 original size:36 final size:37
Alignment explanation
Indices: 3221031--3221103 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
3221021 TCAAAAACCT
3221031 GCAAAACAAA-CACTCAA-CACTCAAAAAGAAAAATTA
1 GCAAAACAAACCA-TCAATCACTCAAAAAGAAAAATTA
* ** *
3221067 GCAAACCTCACCATTAATCACTCAAAAAGAAAAATTA
1 GCAAAACAAACCATCAATCACTCAAAAAGAAAAATTA
3221104 AATTCTCAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
36 10 0.32
37 21 0.68
ACGTcount: A:0.56, C:0.23, G:0.05, T:0.15
Consensus pattern (37 bp):
GCAAAACAAACCATCAATCACTCAAAAAGAAAAATTA
Found at i:3229741 original size:17 final size:17
Alignment explanation
Indices: 3229729--3229827 Score: 60
Period size: 17 Copynumber: 5.8 Consensus size: 17
3229719 ATTATTTTAA
3229729 TAAATTTAATATTAAAT
1 TAAATTTAATATTAAAT
*
3229746 TAAATTTAATACTTAACT
1 TAAATTTAATA-TTAAAT
* * **
3229764 T-GA--TAGTATTTTAT
1 TAAATTTAATATTAAAT
*
3229778 TAATTTTAATATTAAAGT
1 TAAATTTAATATTAAA-T
* *
3229796 GATTATCTTAATATTAAAT
1 TA-AAT-TTAATATTAAAT
*
3229815 TTAATTTAATATT
1 TAAATTTAATATT
3229828 TATCTTGTAG
Statistics
Matches: 58, Mismatches: 17, Indels: 14
0.65 0.19 0.16
Matches are distributed among these distances:
14 4 0.07
15 4 0.07
17 27 0.47
18 10 0.17
19 2 0.03
20 11 0.19
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (17 bp):
TAAATTTAATATTAAAT
Found at i:3247853 original size:3 final size:3
Alignment explanation
Indices: 3247841--3247883 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
3247831 GTGGCCAGCA
3247841 ATG A-G ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
3247884 TCCTTCATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:3250141 original size:16 final size:16
Alignment explanation
Indices: 3250120--3250151 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3250110 ATTTTGTTGC
*
3250120 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
3250136 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
3250152 CTTTCAATCA
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:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:3256233 original size:16 final size:16
Alignment explanation
Indices: 3256214--3256245 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3256204 ATTTTTTTGT
*
3256214 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
3256230 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
3256246 CTTTCAATCA
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:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:3256531 original size:51 final size:52
Alignment explanation
Indices: 3256473--3256663 Score: 241
Period size: 51 Copynumber: 3.8 Consensus size: 52
3256463 TCAGTTCACA
* *
3256473 TAGTAGCCTGCACATAGTACTACACATGTGA-CCATCACTATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGATCCATCACTATCCGGTACACG
* * *
3256524 TAGTAGCCTGCACATAGTACTATACACGTGATCGA--AGCTATCCGGTACGCG
1 TAGTAGCCTGCACATAGTACTACACACGTGATCCATCA-CTATCCGGTACACG
* * * * *
3256575 TAGTAGCCTGTACATAGTACTACACATGCGATCTATCA-T-TCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGATCCATCACTATCCGGTACACG
3256625 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCACT
1 TAGTAGCCTGCACATAGTACTACACACGTGATCCATCACT
3256664 TTCACTTTCG
Statistics
Matches: 119, Mismatches: 16, Indels: 11
0.82 0.11 0.08
Matches are distributed among these distances:
49 5 0.04
50 39 0.33
51 72 0.61
52 2 0.02
53 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.25
Consensus pattern (52 bp):
TAGTAGCCTGCACATAGTACTACACACGTGATCCATCACTATCCGGTACACG
Found at i:3256637 original size:101 final size:102
Alignment explanation
Indices: 3256473--3256655 Score: 289
Period size: 101 Copynumber: 1.8 Consensus size: 102
3256463 TCAGTTCACA
*
3256473 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGCCTGCACA
1 TAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTGCACA
*
3256538 TAGTACTATACACGTGATCGAAGCTATCCGGTACGCG
66 TAGTACTACACACGTGATCGAAGCTATCCGGTACGCG
* * * *
3256575 TAGTAGCCTGTACATAGTACTACACATGCGATCTATCA-T-TCTGGTACACGTAGTAGCCTGCAC
1 TAGTAGCCTGCACATAGTACTACACATGCGA-CCATCACTATCCGATACACGTAGTAGCCTGCAC
3256638 ATAGTACTACACACGTGA
65 ATAGTACTACACACGTGA
3256656 CCATCACTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
101 39 0.53
102 30 0.41
103 5 0.07
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (102 bp):
TAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTGCACA
TAGTACTACACACGTGATCGAAGCTATCCGGTACGCG
Found at i:3259653 original size:22 final size:22
Alignment explanation
Indices: 3259625--3259669 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
3259615 TAAGGTAACC
3259625 ATTCATCTTTCTATTAGTTTTT
1 ATTCATCTTTCTATTAGTTTTT
3259647 ATTCATCTTTCTATTAGTTTTT
1 ATTCATCTTTCTATTAGTTTTT
3259669 A
1 A
3259670 ATGTTATCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.13, G:0.04, T:0.62
Consensus pattern (22 bp):
ATTCATCTTTCTATTAGTTTTT
Found at i:3264975 original size:39 final size:39
Alignment explanation
Indices: 3264877--3264975 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
3264867 CACATGTTTT
* * *
3264877 TGAGTATTGTGATATATGCTCGAACGTTATGCAATTATA
1 TGAGTAATGTGATATATGCTTGAACATTATGCAATTATA
* * * * * *
3264916 TGAGTATTGCGATGTGTGCTTGAATATTATGTAATTATA
1 TGAGTAATGTGATATATGCTTGAACATTATGCAATTATA
*
3264955 TGTGTAATGTGATATATGCTT
1 TGAGTAATGTGATATATGCTT
3264976 AAAAGTGAAT
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.42
Consensus pattern (39 bp):
TGAGTAATGTGATATATGCTTGAACATTATGCAATTATA
Found at i:3276736 original size:84 final size:84
Alignment explanation
Indices: 3276645--3276804 Score: 248
Period size: 84 Copynumber: 1.9 Consensus size: 84
3276635 ACGTCTTTGC
* * *
3276645 TTGGAAACAAAACAATATCGAATAAAATCTTGTTAAACGGCGGGAATAAATCCAGAAACAAATTT
1 TTGGAAACAAAACAAAATCAAATAAAATCTTGTTAAACAGCGGGAATAAATCCAGAAACAAATTT
3276710 TATTTAATTTAGTTCGAAT
66 TATTTAATTTAGTTCGAAT
* * * * *
3276729 TTGGAAACAAAATAAAATCAAATAAAATCTTGTTAAATAGCGGGAATAAATTCTGAAACAGATTT
1 TTGGAAACAAAACAAAATCAAATAAAATCTTGTTAAACAGCGGGAATAAATCCAGAAACAAATTT
3276794 TATTTAATTTA
66 TATTTAATTTA
3276805 ATTTCTCATT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
84 68 1.00
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (84 bp):
TTGGAAACAAAACAAAATCAAATAAAATCTTGTTAAACAGCGGGAATAAATCCAGAAACAAATTT
TATTTAATTTAGTTCGAAT
Found at i:3276942 original size:77 final size:78
Alignment explanation
Indices: 3276848--3277124 Score: 283
Period size: 77 Copynumber: 3.4 Consensus size: 78
3276838 AATAAATTCA
*
3276848 TTGAACGGTGGGAATCAATCCCGAAACGGA-TTTTATGTTACTCGTTTTT-GAAATAAAACAAAT
1 TTGAACGGCGGGAATCAATCCCGAAACGGATTTTTAT-TTACTCGTTTTTGGAAATAAAACAAAT
3276911 TTGGAATAAAATTG
65 TTGGAATAAAATTG
** * *
3276925 TTGAACGGCGGGAATCAATCCTAAAAC-GATTTTTATTTACTCGTTTTTGGAAATAAGACAATTT
1 TTGAACGGCGGGAATCAATCCCGAAACGGATTTTTATTTACTCGTTTTTGGAAATAAAACAAATT
3276989 TGGAATAAAATTG
66 TGGAATAAAATTG
*** * **
3277002 TTGAACGGAAAGAATCAATCCCGAAA-TGATTTTTATTTTACCTTTAATTTCCCGTTTGGAAATA
1 TTGAACGGCGGGAATCAATCCCGAAACGGATTTTTA-TTTA-C--T-CGTT----TTTGGAAATA
** *
3277066 AAGTAAATTAATGAAATAAAATATG
57 AAACAAATT--TGGAATAAAAT-TG
3277091 TTGAACGGCGGGAATCAATCCCGAAACGGATTTT
1 TTGAACGGCGGGAATCAATCCCGAAACGGATTTT
3277125 ACCTATTCTT
Statistics
Matches: 163, Mismatches: 21, Indels: 19
0.80 0.10 0.09
Matches are distributed among these distances:
76 14 0.09
77 85 0.52
78 4 0.02
79 1 0.01
81 1 0.01
82 2 0.01
86 15 0.09
88 10 0.06
89 25 0.15
90 6 0.04
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (78 bp):
TTGAACGGCGGGAATCAATCCCGAAACGGATTTTTATTTACTCGTTTTTGGAAATAAAACAAATT
TGGAATAAAATTG
Found at i:3279184 original size:31 final size:31
Alignment explanation
Indices: 3279119--3279189 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
3279109 AAGGTTCGGA
3279119 TTTAGTCCATATACTTTAATTTGATTATTAAT
1 TTTAGTCCATATACTTT-ATTTGATTATTAAT
*
3279151 TTTAGTCCATATAC-TT-TTTGAATTCGTTAAT
1 TTTAGTCCATATACTTTATTTG-ATT-ATTAAT
3279182 TTTAGTCC
1 TTTAGTCC
3279190 TTTTACCTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 4 0.11
30 3 0.08
31 15 0.42
32 14 0.39
ACGTcount: A:0.27, C:0.13, G:0.08, T:0.52
Consensus pattern (31 bp):
TTTAGTCCATATACTTTATTTGATTATTAAT
Found at i:3280002 original size:18 final size:17
Alignment explanation
Indices: 3279959--3279996 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
3279949 TTTAGAAGAA
* *
3279959 AAAAAATGA-ATGTTGT
1 AAAAAATTAGATGTTCT
3279975 AAAAAATTAGATGTTCT
1 AAAAAATTAGATGTTCT
3279992 AAAAA
1 AAAAA
3279997 TCTTAGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.55, C:0.03, G:0.13, T:0.29
Consensus pattern (17 bp):
AAAAAATTAGATGTTCT
Found at i:3291938 original size:17 final size:18
Alignment explanation
Indices: 3291918--3291964 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
3291908 AAAAACTCGT
3291918 AAAAACCTTAAACC-AGA
1 AAAAACCTTAAACCTAGA
* *
3291935 AAAATCCCTT-AACCTATA
1 AAAA-ACCTTAAACCTAGA
3291953 AAAAACCTTAAA
1 AAAAACCTTAAA
3291965 AACTAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.55, C:0.23, G:0.02, T:0.19
Consensus pattern (18 bp):
AAAAACCTTAAACCTAGA
Found at i:3292078 original size:26 final size:25
Alignment explanation
Indices: 3292045--3292096 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
3292035 CCTAAACTTT
*
3292045 AAACCTTAGAA-CTAACCAAACCCTAA
1 AAACCTTA-AACCTAA-AAAACCCTAA
3292071 AAACCTTAAACCTAAAAAACCCTAA
1 AAACCTTAAACCTAAAAAACCCTAA
3292096 A
1 A
3292097 CAAAAAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.54, C:0.29, G:0.02, T:0.15
Consensus pattern (25 bp):
AAACCTTAAACCTAAAAAACCCTAA
Found at i:3296550 original size:25 final size:25
Alignment explanation
Indices: 3296521--3296580 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
3296511 CTCGAGCTTT
3296521 GAACCCAATACTTTATAATTTGAGC
1 GAACCCAATACTTTATAATTTGAGC
*
3296546 GAACCAAATACTTTATAATTTGAGC
1 GAACCCAATACTTTATAATTTGAGC
*
3296571 AAACCCAATA
1 GAACCCAATA
3296581 TTTGGTTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (25 bp):
GAACCCAATACTTTATAATTTGAGC
Found at i:3297700 original size:50 final size:50
Alignment explanation
Indices: 3297625--3297724 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
3297615 CCATAAACAG
3297625 ATTCAAGATCTATTCTTCTCAGGTCCAGTCAGTCACATCTATGTATCTAT
1 ATTCAAGATCTATTCTTCTCAGGTCCAGTCAGTCACATCTATGTATCTAT
3297675 ATTCAAGATCTATTCTTCTCAGGTCCAGTCAGTCACATCTATGTATCTAT
1 ATTCAAGATCTATTCTTCTCAGGTCCAGTCAGTCACATCTATGTATCTAT
3297725 CTTATATGAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (50 bp):
ATTCAAGATCTATTCTTCTCAGGTCCAGTCAGTCACATCTATGTATCTAT
Found at i:3298936 original size:27 final size:27
Alignment explanation
Indices: 3298906--3298973 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
3298896 TAGTCCGCCG
*
3298906 GGACATTAAACACGGGGTAGTCCATCA
1 GGACACTAAACACGGGGTAGTCCATCA
* *
3298933 GGACACTGAACATGGGGTAGTCCATCA
1 GGACACTAAACACGGGGTAGTCCATCA
* *
3298960 GGATAGTAAACACG
1 GGACACTAAACACG
3298974 AGAATTTTGT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.34, C:0.21, G:0.28, T:0.18
Consensus pattern (27 bp):
GGACACTAAACACGGGGTAGTCCATCA
Found at i:3300327 original size:24 final size:21
Alignment explanation
Indices: 3300298--3300349 Score: 54
Period size: 24 Copynumber: 2.4 Consensus size: 21
3300288 ATTTATCTTT
3300298 TTAAATATTAGGTTAAATTTAATA
1 TTAAATATTA--TTAAA-TTAATA
*
3300322 TTAAATCTTATTAAATTAATA
1 TTAAATATTATTAAATTAATA
3300343 --AAATATT
1 TTAAATATT
3300350 TATACACAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 6 0.23
21 6 0.23
22 5 0.19
24 9 0.35
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (21 bp):
TTAAATATTATTAAATTAATA
Found at i:3300413 original size:20 final size:18
Alignment explanation
Indices: 3300363--3300414 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
3300353 ACACAAGATA
*
3300363 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTC
3300380 AATATTAAGA-TAATCACTTC
1 AATATTAA-ATTAAT-A-TTC
3300400 AATATTAAATTAATA
1 AATATTAAATTAATA
3300415 AAATACTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
17 11 0.38
18 1 0.03
19 3 0.10
20 14 0.48
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (18 bp):
AATATTAAATTAATATTC
Found at i:3303777 original size:21 final size:21
Alignment explanation
Indices: 3303735--3303777 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3303725 CTTTTTCTGA
* *
3303735 AATAAAATTGTGTCTTGTATC
1 AATAAAATTGTGTCATGCATC
3303756 AATAAAATTGTGTCATGCATC
1 AATAAAATTGTGTCATGCATC
3303777 A
1 A
3303778 TCCAATCAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (21 bp):
AATAAAATTGTGTCATGCATC
Found at i:3305764 original size:31 final size:31
Alignment explanation
Indices: 3305721--3305784 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
3305711 CCATCATTCT
3305721 TTATTAAACCAAATCCTCATTCTTTATTTTA
1 TTATTAAACCAAATCCTCATTCTTTATTTTA
*
3305752 TTATTAATCCAAATCCTCATTCTTTATTTTA
1 TTATTAAACCAAATCCTCATTCTTTATTTTA
3305783 TT
1 TT
3305785 TGTTTTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.52
Consensus pattern (31 bp):
TTATTAAACCAAATCCTCATTCTTTATTTTA
Found at i:3305834 original size:19 final size:19
Alignment explanation
Indices: 3305810--3305858 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
3305800 AAACCTTAAT
3305810 TAAACTAATCATAAATAAA
1 TAAACTAATCATAAATAAA
3305829 TAAACTAATCATAAATAAA
1 TAAACTAATCATAAATAAA
3305848 TAAACTAATCA
1 TAAACTAATCA
3305859 ATGTTCAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (19 bp):
TAAACTAATCATAAATAAA
Found at i:3309747 original size:16 final size:16
Alignment explanation
Indices: 3309723--3309755 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3309713 ACAATTGATT
*
3309723 ATTATGCCTCTATTCC
1 ATTACGCCTCTATTCC
3309739 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
3309755 A
1 A
3309756 ATACAGCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.33, G:0.06, T:0.39
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:3318172 original size:9 final size:9
Alignment explanation
Indices: 3318158--3318187 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
3318148 AAAATATCAT
3318158 ATTAATTTA
1 ATTAATTTA
*
3318167 ATTAATTTG
1 ATTAATTTA
3318176 ATTAATTTA
1 ATTAATTTA
3318185 ATT
1 ATT
3318188 TTACTTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (9 bp):
ATTAATTTA
Found at i:3321329 original size:27 final size:27
Alignment explanation
Indices: 3321278--3321329 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
3321268 AACCAGTATA
* *
3321278 GTCTACCAGGAAAGTAAAGATGGGGTG
1 GTCTACCAGGAAAGTAAACACGGGGTG
*
3321305 GTCTATCAGGAAAGTAAACACGGGG
1 GTCTACCAGGAAAGTAAACACGGGG
3321330 ATTAAGGGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.35, C:0.13, G:0.35, T:0.17
Consensus pattern (27 bp):
GTCTACCAGGAAAGTAAACACGGGGTG
Found at i:3327876 original size:50 final size:50
Alignment explanation
Indices: 3327801--3327954 Score: 227
Period size: 50 Copynumber: 3.1 Consensus size: 50
3327791 AAAGGGTCCA
* *
3327801 TGAATTGTCTATACAAAGTATGTGCGTGCTGCTTATTTAAGTTCTATGTG
1 TGAATTGTCTATACAAAGTATGTGCGTGCTGATTATATAAGTTCTATGTG
* * *
3327851 TGAATTGTCTATACAAAGTATGTGCGTGTTGATTATATAATTTCTCTGTG
1 TGAATTGTCTATACAAAGTATGTGCGTGCTGATTATATAAGTTCTATGTG
* * * *
3327901 TGAACTGTCTATACAAAGTATGTGTGTGCTAATTATATAAGTTATATGTG
1 TGAATTGTCTATACAAAGTATGTGCGTGCTGATTATATAAGTTCTATGTG
3327951 TGAA
1 TGAA
3327955 CTAGTATTGT
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 92 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.42
Consensus pattern (50 bp):
TGAATTGTCTATACAAAGTATGTGCGTGCTGATTATATAAGTTCTATGTG
Found at i:3334789 original size:33 final size:33
Alignment explanation
Indices: 3334751--3334818 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
3334741 TATTATTTAT
3334751 TTTTCGACAAGAATTTTACCGAAACTGTATATA
1 TTTTCGACAAGAATTTTACCGAAACTGTATATA
3334784 TTTTCGACAAGAATTTTACCGAAACTGTATATA
1 TTTTCGACAAGAATTTTACCGAAACTGTATATA
3334817 TT
1 TT
3334819 AATTAAAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (33 bp):
TTTTCGACAAGAATTTTACCGAAACTGTATATA
Found at i:3335420 original size:7 final size:7
Alignment explanation
Indices: 3335408--3335439 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
3335398 AAGATAGGAG
3335408 AAAATTA
1 AAAATTA
3335415 AAAATTA
1 AAAATTA
3335422 AAAATTA
1 AAAATTA
3335429 AAAATTA
1 AAAATTA
3335436 AAAA
1 AAAA
3335440 AAAAACAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (7 bp):
AAAATTA
Found at i:3336663 original size:36 final size:36
Alignment explanation
Indices: 3336595--3336671 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 36
3336585 TTTACACGCG
*
3336595 AACCATTGTCGATTCATTCGACCAGCGTTGGGCGCA
1 AACCATTGTCGATTCATTCGACCAGCGCTGGGCGCA
* * * *
3336631 AACCTTTGTCGATTTATTCGACTAGTGCT-GG-GCA
1 AACCATTGTCGATTCATTCGACCAGCGCTGGGCGCA
3336665 AACCATT
1 AACCATT
3336672 ATATTTGTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
34 9 0.26
35 2 0.06
36 24 0.69
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (36 bp):
AACCATTGTCGATTCATTCGACCAGCGCTGGGCGCA
Found at i:3336770 original size:40 final size:39
Alignment explanation
Indices: 3336715--3336845 Score: 101
Period size: 40 Copynumber: 3.4 Consensus size: 39
3336705 TGACTTTCGC
**
3336715 CAGTTTATTTGACTAGTGTTGGGCACACCATTATATTTTT
1 CAGTTTATCCGACTAGTGTTGGGCACA-CATTATATTTTT
* * * *
3336755 CAGTTTATCCGACTAGCGTTGGGCGCA-A--CT-TTCTT
1 CAGTTTATCCGACTAGTGTTGGGCACACATTATATTTTT
** ** *
3336790 CAGTTTATCAAACTAGTGAAGGGCACAACATTGTATTTTT
1 CAGTTTATCCGACTAGTGTTGGGCAC-ACATTATATTTTT
3336830 C-GATTTATCCGACTAG
1 CAG-TTTATCCGACTAG
3336846 CGCTGGGCGC
Statistics
Matches: 69, Mismatches: 16, Indels: 12
0.71 0.16 0.12
Matches are distributed among these distances:
35 24 0.35
36 2 0.03
37 1 0.01
38 1 0.01
39 2 0.03
40 39 0.57
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.37
Consensus pattern (39 bp):
CAGTTTATCCGACTAGTGTTGGGCACACATTATATTTTT
Found at i:3336873 original size:75 final size:75
Alignment explanation
Indices: 3336651--3336932 Score: 282
Period size: 75 Copynumber: 3.8 Consensus size: 75
3336641 GATTTATTCG
* * * ** **
3336651 ACTAGTGCTGGGCA-AACCATTATATTTGTT-GGTGTATCCGACTAGCATTGGGCGTGACTTTCG
1 ACTAGTGTTGGGCACAA-CATTATATTT-TTCGATTTATCCGACTAGCGCTGGGCGCAACTTTCG
* * *
3336714 CCAGTTTATTTG
64 TCAGTTTATCTA
* * *
3336726 ACTAGTGTTGGGCACACCATTATATTTTTC-AGTTTATCCGACTAGCGTTGGGCGCAACTTTCTT
1 ACTAGTGTTGGGCACAACATTATATTTTTCGA-TTTATCCGACTAGCGCTGGGCGCAACTTTCGT
*
3336790 CAGTTTATCAA
65 CAGTTTATCTA
** * *
3336801 ACTAGTGAAGGGCACAACATTGTATTTTTCGATTTATCCGACTAGCGCTGGGCGCAACCTTCGTC
1 ACTAGTGTTGGGCACAACATTATATTTTTCGATTTATCCGACTAGCGCTGGGCGCAACTTTCGTC
3336866 AGTTTATCTA
66 AGTTTATCTA
* * * * * * * *
3336876 ACTGGTGTTGGGCACATCATTATATCTATCGGTTTATCCAACTAGTGCGGGGCGCAA
1 ACTAGTGTTGGGCACAACATTATATTTTTCGATTTATCCGACTAGCGCTGGGCGCAA
3336933 AACTTGGTTA
Statistics
Matches: 172, Mismatches: 31, Indels: 8
0.82 0.15 0.04
Matches are distributed among these distances:
74 2 0.01
75 168 0.98
76 2 0.01
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (75 bp):
ACTAGTGTTGGGCACAACATTATATTTTTCGATTTATCCGACTAGCGCTGGGCGCAACTTTCGTC
AGTTTATCTA
Found at i:3346033 original size:54 final size:54
Alignment explanation
Indices: 3345964--3346112 Score: 176
Period size: 54 Copynumber: 2.8 Consensus size: 54
3345954 ACATAGCCTG
* *
3345964 GACACGGGCGTATGGCCCAAGTTAGTGAGTTACACGGTTTGACACACGGGTTGA
1 GACACGGGCGTATGGCCCAAGTTAGTGAGTTACACGGTCTGACACAAGGGTTGA
* ** * *
3346018 GACATGGGTC-TATGGCTAAAGTCAGTGAGTTACATGGTCTGACACAAGGGTTGA
1 GACACGGG-CGTATGGCCCAAGTTAGTGAGTTACACGGTCTGACACAAGGGTTGA
* * *
3346072 GACACGGGCGTGTGGCCCAA-ATATGTGAGTTACATGGTCTG
1 GACACGGGCGTATGGCCCAAGTTA-GTGAGTTACACGGTCTG
3346113 GCAGACATTT
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
53 2 0.03
54 76 0.96
55 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (54 bp):
GACACGGGCGTATGGCCCAAGTTAGTGAGTTACACGGTCTGACACAAGGGTTGA
Found at i:3346681 original size:20 final size:20
Alignment explanation
Indices: 3346632--3346683 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
3346622 GTTCTATTTG
**
3346632 ATTTAGTCCAATTTATTACA
1 ATTTAGTCCTTTTTATTACA
3346652 ATTTAGTCCTTTTTATTACA
1 ATTTAGTCCTTTTTATTACA
3346672 ATTTAGTCCTTT
1 ATTTAGTCCTTT
3346684 GTCCAAAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.27, C:0.15, G:0.06, T:0.52
Consensus pattern (20 bp):
ATTTAGTCCTTTTTATTACA
Found at i:3349299 original size:21 final size:21
Alignment explanation
Indices: 3349274--3349317 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
3349264 CCATTTTGAC
3349274 AATTTGGCCTGATTTTCAACT
1 AATTTGGCCTGATTTTCAACT
3349295 AATTTGGCCTGATTTTCAACT
1 AATTTGGCCTGATTTTCAACT
3349316 AA
1 AA
3349318 GTATGATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (21 bp):
AATTTGGCCTGATTTTCAACT
Found at i:3349816 original size:20 final size:19
Alignment explanation
Indices: 3349789--3349841 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 19
3349779 GTTGGAGCTG
*
3349789 AAATATCGATACCTTATGA
1 AAATATCGATACCTTAAGA
3349808 AATATATCGATACCTTAAGA
1 AA-ATATCGATACCTTAAGA
3349828 AAAGTATCGATACC
1 AAA-TATCGATACC
3349842 GGATCGATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 3 0.10
20 28 0.90
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.28
Consensus pattern (19 bp):
AAATATCGATACCTTAAGA
Found at i:3350226 original size:31 final size:32
Alignment explanation
Indices: 3350190--3350250 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
3350180 AGATTACTCC
*
3350190 CCCTTA-ATAAAATTCATTTTCAATTTAAGCT
1 CCCTTATATAAAAATCATTTTCAATTTAAGCT
3350221 CCCTTATATAAAAATCATTTTCAATTTAAG
1 CCCTTATATAAAAATCATTTTCAATTTAAG
3350251 GCATAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 6 0.21
32 22 0.79
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.41
Consensus pattern (32 bp):
CCCTTATATAAAAATCATTTTCAATTTAAGCT
Found at i:3359328 original size:212 final size:212
Alignment explanation
Indices: 3358961--3359390 Score: 815
Period size: 212 Copynumber: 2.0 Consensus size: 212
3358951 AAGAGAAAAA
*
3358961 AGATGAAACAGAAGGAAAATACAAGACATAAGCAATTCATTTTTTCAGTTTCTTAATTTTCTGTC
1 AGATGAAACAGAAGAAAAATACAAGACATAAGCAATTCATTTTTTCAGTTTCTTAATTTTCTGTC
*
3359026 TTCTGTTGTGTTTCTACATAGAGCGCACTAGTCATTGCAAGTCACATTTGATCCAAAACCTGAAA
66 TTCTGTTATGTTTCTACATAGAGCGCACTAGTCATTGCAAGTCACATTTGATCCAAAACCTGAAA
*
3359091 GCTAGCAAGGTCTCTCCCTAATCAATGGTGTTGTGTATACAAACTAAACTAAACCTGTCCTTTAA
131 GCTAGCAAGGTCTCTCCCTAATCAATGGTGTTGTGTATACAAACTAAACTAAACCTGACCTTTAA
3359156 GATGCAAAGTAAAATGT
196 GATGCAAAGTAAAATGT
*
3359173 AGATGAAACAGAAGAAAAATACAAGACATACGCAATTCATTTTTTCAGTTTCTTAATTTTCTGTC
1 AGATGAAACAGAAGAAAAATACAAGACATAAGCAATTCATTTTTTCAGTTTCTTAATTTTCTGTC
*
3359238 TTCTGTTATGTTTCTACATAGAGCGCACTAGTCATTGCAAGTCACATTTGATCCAAAAGCTGAAA
66 TTCTGTTATGTTTCTACATAGAGCGCACTAGTCATTGCAAGTCACATTTGATCCAAAACCTGAAA
3359303 GCTAGCAAGGTCTCTCCCTAATCAATGGTGTTGTGTATACAAACTAAACTAAACCTGACCTTTAA
131 GCTAGCAAGGTCTCTCCCTAATCAATGGTGTTGTGTATACAAACTAAACTAAACCTGACCTTTAA
3359368 GATGCAAAGTAAAATGT
196 GATGCAAAGTAAAATGT
3359385 AGATGA
1 AGATGA
3359391 GACATCTATA
Statistics
Matches: 213, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
212 213 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (212 bp):
AGATGAAACAGAAGAAAAATACAAGACATAAGCAATTCATTTTTTCAGTTTCTTAATTTTCTGTC
TTCTGTTATGTTTCTACATAGAGCGCACTAGTCATTGCAAGTCACATTTGATCCAAAACCTGAAA
GCTAGCAAGGTCTCTCCCTAATCAATGGTGTTGTGTATACAAACTAAACTAAACCTGACCTTTAA
GATGCAAAGTAAAATGT
Found at i:3361309 original size:12 final size:12
Alignment explanation
Indices: 3361292--3361316 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3361282 AATATTAATA
3361292 TTAAAATAAGAT
1 TTAAAATAAGAT
3361304 TTAAAATAAGAT
1 TTAAAATAAGAT
3361316 T
1 T
3361317 ATCTTGGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (12 bp):
TTAAAATAAGAT
Found at i:3367989 original size:15 final size:14
Alignment explanation
Indices: 3367965--3368002 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
3367955 GTTTGCCACT
3367965 AAAATG-TTTTTCGG
1 AAAATGATTTTT-GG
3367979 AAAATGATTTTTGG
1 AAAATGATTTTTGG
3367993 AAAATGATTT
1 AAAATGATTT
3368003 AATTTTCTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.37, C:0.03, G:0.18, T:0.42
Consensus pattern (14 bp):
AAAATGATTTTTGG
Found at i:3368015 original size:20 final size:19
Alignment explanation
Indices: 3367985--3368023 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
3367975 TCGGAAAATG
3367985 ATTTTTGGAAAATGATTTA
1 ATTTTTGGAAAATGATTTA
3368004 ATTTTCTGGAAAATGATTTA
1 ATTTT-TGGAAAATGATTTA
3368024 CTAAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.46
Consensus pattern (19 bp):
ATTTTTGGAAAATGATTTA
Found at i:3368031 original size:34 final size:32
Alignment explanation
Indices: 3367972--3368035 Score: 76
Period size: 34 Copynumber: 1.9 Consensus size: 32
3367962 ACTAAAATGT
* *
3367972 TTTTCGGAAAATGATTTTTGGAAAATGATTTAA
1 TTTTCGGAAAATGATTTCTGAAAAAT-ATTTAA
3368005 TTTTCTGGAAAATGATTTACT-AAAAATATTT
1 TTTTC-GGAAAATGATTT-CTGAAAAATATTT
3368036 TCTAGTGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 9 0.33
34 17 0.63
35 1 0.04
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.44
Consensus pattern (32 bp):
TTTTCGGAAAATGATTTCTGAAAAATATTTAA
Found at i:3368101 original size:32 final size:34
Alignment explanation
Indices: 3368025--3368101 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 34
3368015 AATGATTTAC
* *
3368025 TAAAAATATTTTCTAGTGTTTGGATAAATCTGTG
1 TAAAAATATTTTCTAGTGTTTGGACAAATCTCTG
*
3368059 T-AAAATATTTTCT-GTTGTTTGG-CAAATTTCT-
1 TAAAAATATTTTCTAG-TGTTTGGACAAATCTCTG
3368090 TAAAAATATTTT
1 TAAAAATATTTT
3368102 GCAAAAAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
31 1 0.03
32 17 0.45
33 19 0.50
34 1 0.03
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.48
Consensus pattern (34 bp):
TAAAAATATTTTCTAGTGTTTGGACAAATCTCTG
Found at i:3374127 original size:21 final size:21
Alignment explanation
Indices: 3374081--3374173 Score: 109
Period size: 21 Copynumber: 4.5 Consensus size: 21
3374071 CGAATACGCC
* *
3374081 AACAGAAGCTC-GAA-AGCTG
1 AACAGAAGCTCATAAGAGCTT
3374100 AACAGAAGCTCATAAGAGCTT
1 AACAGAAGCTCATAAGAGCTT
* * *
3374121 AATAGAAGCTCGTAAGAGCTA
1 AACAGAAGCTCATAAGAGCTT
* *
3374142 AACAAAAGCTCATAAGAACTT
1 AACAGAAGCTCATAAGAGCTT
3374163 AACAGAAGCTC
1 AACAGAAGCTC
3374174 GTAAAAAGCT
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
19 11 0.18
20 2 0.03
21 48 0.79
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.16
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTT
Done.