Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold257
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1615106
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 208026 characters in sequence are not A, C, G, or T
File 3 of 5
Found at i:300087 original size:21 final size:21
Alignment explanation
Indices: 299993--300195 Score: 158
Period size: 21 Copynumber: 9.7 Consensus size: 21
299983 CATACAACTT
*
299993 ATAAGTTGCATGTCAACATAT
1 ATAAGTTGCATGTCAACATAA
* ** * *
300014 TTATCTCGCATGTAAACATAA
1 ATAAGTTGCATGTCAACATAA
* *
300035 CTAAGTTGCATGTCAAC-TCA
1 ATAAGTTGCATGTCAACATAA
* *
300055 TTTA-TCTCGCATGTCAACATAA
1 ATAAGT-T-GCATGTCAACATAA
* *
300077 CTAAGTTGCATGTCAACTTAA
1 ATAAGTTGCATGTCAACATAA
**
300098 ATAAGTTGCATGTTGACATAA
1 ATAAGTTGCATGTCAACATAA
** **
300119 ATAAGTTGCATGTTGACATTT
1 ATAAGTTGCATGTCAACATAA
* *
300140 ATAAGTTGCATGTCAGCATAT
1 ATAAGTTGCATGTCAACATAA
* ** *
300161 TTATCTTGCATGTTAACATAA
1 ATAAGTTGCATGTCAACATAA
300182 ATAAGTTGCATGTC
1 ATAAGTTGCATGTC
300196 GACAAAAAAA
Statistics
Matches: 140, Mismatches: 38, Indels: 8
0.75 0.20 0.04
Matches are distributed among these distances:
19 1 0.01
20 5 0.04
21 128 0.91
22 5 0.04
23 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (21 bp):
ATAAGTTGCATGTCAACATAA
Found at i:300321 original size:21 final size:21
Alignment explanation
Indices: 300289--300375 Score: 131
Period size: 21 Copynumber: 4.2 Consensus size: 21
300279 TCTGATTGTA
300289 ATTT-TCTTGCATGTCAACAT
1 ATTTATCTTGCATGTCAACAT
* * *
300309 AGTTATGTTGCATGTTAACAT
1 ATTTATCTTGCATGTCAACAT
300330 ATTTATCTTGCATGTCAACAT
1 ATTTATCTTGCATGTCAACAT
*
300351 ATTTATCTTGCATGTCGACAT
1 ATTTATCTTGCATGTCAACAT
300372 ATTT
1 ATTT
300376 GATAGAAAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
20 3 0.05
21 56 0.95
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (21 bp):
ATTTATCTTGCATGTCAACAT
Found at i:305757 original size:17 final size:17
Alignment explanation
Indices: 305735--305778 Score: 65
Period size: 15 Copynumber: 2.7 Consensus size: 17
305725 TCAGTTTGTG
305735 TATATCCGTAAATTCGT
1 TATATCCGTAAATTCGT
305752 TATATCCG--AATTCGT
1 TATATCCGTAAATTCGT
*
305767 TATAACCGTAAA
1 TATATCCGTAAA
305779 ATTTTGCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 14 0.58
17 10 0.42
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.36
Consensus pattern (17 bp):
TATATCCGTAAATTCGT
Found at i:314919 original size:12 final size:12
Alignment explanation
Indices: 314884--314925 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
314874 TTATTTTATT
*
314884 ATTAATTGATTT
1 ATTAATTGATTA
*
314896 ATTAATCGATTA
1 ATTAATTGATTA
*
314908 ATTATTTGATTA
1 ATTAATTGATTA
314920 A-TAATT
1 ATTAATT
314926 AATAGAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 4 0.16
12 21 0.84
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.52
Consensus pattern (12 bp):
ATTAATTGATTA
Found at i:325521 original size:11 final size:11
Alignment explanation
Indices: 325505--325549 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
325495 AGCTATTTCC
325505 AAGTAAACCCA
1 AAGTAAACCCA
*
325516 AAGTAAACCGA
1 AAGTAAACCCA
325527 AAGTAAACCCA
1 AAGTAAACCCA
* *
325538 GAGTGAACCCA
1 AAGTAAACCCA
325549 A
1 A
325550 TTTTCAAAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.51, C:0.24, G:0.16, T:0.09
Consensus pattern (11 bp):
AAGTAAACCCA
Found at i:327422 original size:21 final size:21
Alignment explanation
Indices: 327368--327443 Score: 100
Period size: 21 Copynumber: 3.6 Consensus size: 21
327358 TACACCATAG
327368 CATAGCATAGCATTGAAATCT
1 CATAGCATAGCATTGAAATCT
*
327389 CATAGTA-ATGCATTGAAATCT
1 CATAGCATA-GCATTGAAATCT
* * *
327410 CACACCATAGCATTGGAATCT
1 CATAGCATAGCATTGAAATCT
327431 CATAGCATAGCAT
1 CATAGCATAGCAT
327444 ACAATCTCAT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 1 0.02
21 44 0.96
22 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (21 bp):
CATAGCATAGCATTGAAATCT
Found at i:327760 original size:21 final size:21
Alignment explanation
Indices: 327696--327746 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
327686 CATTTCAATT
* **
327696 TCTCATAGCATAACATACAAA
1 TCTCATAACATAGTATACAAA
327717 TCTCATAACATAGTATACAAA
1 TCTCATAACATAGTATACAAA
327738 TCTCATAAC
1 TCTCATAAC
327747 GTATCATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.45, C:0.24, G:0.04, T:0.27
Consensus pattern (21 bp):
TCTCATAACATAGTATACAAA
Found at i:332187 original size:7 final size:7
Alignment explanation
Indices: 332175--332232 Score: 62
Period size: 7 Copynumber: 8.3 Consensus size: 7
332165 GAGAAGGATC
332175 ATTCGAG
1 ATTCGAG
332182 ATTCGAG
1 ATTCGAG
* *
332189 ATTCAAA
1 ATTCGAG
*
332196 ATACGAG
1 ATTCGAG
*
332203 ATTCGAA
1 ATTCGAG
*
332210 ATACGAG
1 ATTCGAG
*
332217 ATTCGAA
1 ATTCGAG
332224 ATTCGAG
1 ATTCGAG
332231 AT
1 AT
332233 CCAATATCTA
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.26
Consensus pattern (7 bp):
ATTCGAG
Found at i:332192 original size:14 final size:14
Alignment explanation
Indices: 332175--332232 Score: 80
Period size: 14 Copynumber: 4.1 Consensus size: 14
332165 GAGAAGGATC
* *
332175 ATTCGAGATTCGAG
1 ATTCGAAATACGAG
*
332189 ATTCAAAATACGAG
1 ATTCGAAATACGAG
332203 ATTCGAAATACGAG
1 ATTCGAAATACGAG
*
332217 ATTCGAAATTCGAG
1 ATTCGAAATACGAG
332231 AT
1 AT
332233 CCAATATCTA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 39 1.00
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.26
Consensus pattern (14 bp):
ATTCGAAATACGAG
Found at i:349556 original size:169 final size:167
Alignment explanation
Indices: 349148--349816 Score: 840
Period size: 168 Copynumber: 4.0 Consensus size: 167
349138 CATAGGCCAG
* * * * *
349148 GCATTTAGTTTTTAACAAATATATATGGGAGTAAAGAGGAAGATTTTTTAAGATTTAAAACATTA
1 GCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTT
* ***
349213 TTACTATATGGCCATATTAGTCCCACCCTAGAGCCTGAACCCCTGTTAAAGGGGTCATGAATTTC
66 TTACTATATGGCCATA-TAGACCCACCCTAGAGCCTGAACCCCTGACCAAGGGGTCATGAATTTC
* * * ** *
349278 ACAATTTTGGTAGGGGGCTTCATGGATATTGTAA-CAAG
130 ACAATTTTGGTAGAGGGCCTCATGGACATCATAATC-AT
* * *
349316 GCATTTAGTTTTTAACAAATATACAT-AGAGTAGAGAAGAAAATTTTCTAAGATTTAATACATTT
1 GCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTT
* * **
349380 TTACTATAGGGCCATAATAGACCCACCCTAGAGCCTGAACCCCTGACCAAGGGGTTCAGGCTTTT
66 TTACTATATGGCCAT-ATAGACCCACCCTAGAGCCTGAACCCCTGACCAAGGGG-TCATGAATTT
*
349445 CACAATTTTGGTAGAAGGCCTCATGGACATCATAATCAT
129 CACAATTTTGGTAGAGGGCCTCATGGACATCATAATCAT
* * *
349484 GAATTTAGTTTTTAACAAATAAATATGGGAGTAGAGAAGAAGATTTTCTAGGATTTAATACATTT
1 GCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTT
* * * * *
349549 TTACTATATGACCATATTGGCCCTACCCTAGAGCCTGAAACCCTGACCAAGAGGTCATGAATTTC
66 TTACTATATGGCCATATAGACCC-ACCCTAGAGCCTGAACCCCTGACCAAGGGGTCATGAATTTC
* * * *
349614 ACAATTTTTGAATAGGGCCTCATTGACATCATAATCAT
130 ACAATTTTGGTAGAGGGCCTCATGGACATCATAATCAT
* * * *
349652 GCATTCAGTTTTTAACAAATATATGTGGCAGTAGAGAAGAAGATTTTCTAGGATTTAATACATTT
1 GCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTT
* * * * *
349717 TAACTATATGGCCATATTGACCCCACCCTAGAGCGTAGAACCCCTAATCC-AGGGGCCATGAATT
66 TTACTATATGGCCATATAGA-CCCACCCTAGAGCCT-GAACCCCTGA-CCAAGGGGTCATGAATT
*
349781 TCACAATTTTGGTAGAGGGTCTCATGGACATCATAA
128 TCACAATTTTGGTAGAGGGCCTCATGGACATCATAA
349817 CTATACAACC
Statistics
Matches: 432, Mismatches: 61, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
167 78 0.18
168 221 0.51
169 131 0.30
170 2 0.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Consensus pattern (167 bp):
GCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTT
TTACTATATGGCCATATAGACCCACCCTAGAGCCTGAACCCCTGACCAAGGGGTCATGAATTTCA
CAATTTTGGTAGAGGGCCTCATGGACATCATAATCAT
Found at i:350757 original size:2 final size:2
Alignment explanation
Indices: 350752--350794 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
350742 TTTTTACCAC
350752 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
350794 A
1 A
350795 TTGTTAATCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:350935 original size:2 final size:2
Alignment explanation
Indices: 350928--350971 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
350918 CTTGCACTTN
350928 AG AG AG AG AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
350969 AG A
1 AG A
350972 TTGTTAATCA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:351059 original size:177 final size:175
Alignment explanation
Indices: 350752--351103 Score: 686
Period size: 177 Copynumber: 2.0 Consensus size: 175
350742 TTTTTACCAC
350752 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATTGTTAATCATATAATCATACT
1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATTGTTAATCATATAATCATACT
350817 TGTCAAGTATTGTTTGTCAAAAGCAATGCATTAAATAAGCAATCCTTTGTTAGTATACACAACTA
66 TGTCAAGTATTGTTTGTCAAAAGCAATGCATTAAATAAGCAATCCTTTGTTAGTATACACAACTA
350882 GGTCACACCAGCGAGCACCACATATTCCTAGTTGACCTTGCACTT
131 GGTCACACCAGCGAGCACCACATATTCCTAGTTGACCTTGCACTT
350927 NAGAGAGAGAGAGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATTGTTAATCATATAATCATA
1 -AGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATTGTTAATCATATAATCATA
350992 CTTGTCAAGTATTGTTTGTCAAAAGCAATGCATTAAATAAGCAATCCTTTGTTAGTATACACAAC
64 CTTGTCAAGTATTGTTTGTCAAAAGCAATGCATTAAATAAGCAATCCTTTGTTAGTATACACAAC
351057 TAGGTCACACCAGCGAGCACCACATATTCCTAGTTGACCTTGCACTT
129 TAGGTCACACCAGCGAGCACCACATATTCCTAGTTGACCTTGCACTT
351104 GGCTGTAGTA
Statistics
Matches: 175, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
176 11 0.06
177 164 0.94
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.24
Consensus pattern (175 bp):
AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATTGTTAATCATATAATCATACT
TGTCAAGTATTGTTTGTCAAAAGCAATGCATTAAATAAGCAATCCTTTGTTAGTATACACAACTA
GGTCACACCAGCGAGCACCACATATTCCTAGTTGACCTTGCACTT
Found at i:351569 original size:10 final size:11
Alignment explanation
Indices: 351551--351578 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
351541 TATCTGATAA
351551 ACTTTTTTTGT
1 ACTTTTTTTGT
351562 ACTTTTTTTGT
1 ACTTTTTTTGT
351573 ACTTTT
1 ACTTTT
351579 CTCGGTTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.11, C:0.11, G:0.07, T:0.71
Consensus pattern (11 bp):
ACTTTTTTTGT
Found at i:367535 original size:15 final size:16
Alignment explanation
Indices: 367515--367546 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
367505 TAGAATTTTC
367515 TGGGTTTA-TTTCCTT
1 TGGGTTTATTTTCCTT
367530 TGGGTTTATTTTCCTT
1 TGGGTTTATTTTCCTT
367546 T
1 T
367547 CTCAATAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.06, C:0.12, G:0.19, T:0.62
Consensus pattern (16 bp):
TGGGTTTATTTTCCTT
Found at i:368278 original size:20 final size:20
Alignment explanation
Indices: 368253--368290 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
368243 ACCCGGGTTC
368253 TCCACCACTATATCATAATG
1 TCCACCACTATATCATAATG
368273 TCCACCACTATATCATAA
1 TCCACCACTATATCATAA
368291 CACCTCCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.32, G:0.03, T:0.29
Consensus pattern (20 bp):
TCCACCACTATATCATAATG
Found at i:378310 original size:35 final size:32
Alignment explanation
Indices: 378231--378315 Score: 125
Period size: 36 Copynumber: 2.5 Consensus size: 32
378221 GTTTTCCCCC
378231 ATAGTAGCTTTTCCCCCCGGAAAACCTACTAT
1 ATAGTAGCTTTTCCCCCCGGAAAACCTACTAT
*
378263 ATAGTAGCCTTTTCCCCCGGGGGAAAAACCTACTAT
1 ATAGTAG-CTTTTCCCCC--CGG-AAAACCTACTAT
378299 ATAGTAGCTTTTCCCCC
1 ATAGTAGCTTTTCCCCC
378316 ATAGTAGGGT
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
32 7 0.15
33 10 0.21
35 12 0.25
36 19 0.40
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (32 bp):
ATAGTAGCTTTTCCCCCCGGAAAACCTACTAT
Found at i:379433 original size:111 final size:108
Alignment explanation
Indices: 379179--379405 Score: 283
Period size: 108 Copynumber: 2.0 Consensus size: 108
379169 AAACATCATT
* ** * *
379179 TAAAAATACACAATCACTTATATATTTCTTTATCAAAATGATTGAAAATTACGTTTAATTCTGCT
1 TAAAAATACACAATCACTTATAAACATCTTAATCAAAATGATTGAAAACTACGTTTAATTCTGCT
* ***
379244 GCTTTTTTTTATTTTCGAACAAATGTGTTTAAAAAAGATCTTT
66 GCTTTTTTTTATTTTCGAACAAATGTGTTTAAAAAAGAGCGGG
* ** *
379287 TAAAAATACACAATCACTTATATATTTCTTCATCAAAATGATTGAAAACTACGTTTAATTCTGCT
1 TAAAAATACACAATCACTTATAAACATCTTAATCAAAATGATTGAAAACTACGTTTAATTCTGCT
379352 GCTTTTTTTTTTTATTTTCGAACAAATGTGTTTAAAAAAGGTACGCGGG
66 GC---TTTTTTTTATTTTCGAACAAATGTGTTTAAAAAA-G-A-GCGGG
379401 TAAAA
1 TAAAA
379406 TTCATTATTC
Statistics
Matches: 107, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
108 65 0.61
111 34 0.32
112 1 0.01
113 1 0.01
114 6 0.06
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (108 bp):
TAAAAATACACAATCACTTATAAACATCTTAATCAAAATGATTGAAAACTACGTTTAATTCTGCT
GCTTTTTTTTATTTTCGAACAAATGTGTTTAAAAAAGAGCGGG
Found at i:382307 original size:25 final size:25
Alignment explanation
Indices: 382277--382324 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
382267 TCAAATCAAG
*
382277 GAGTGAATGTTGA-AAAAAAAGAAAC
1 GAGTG-ATGATGACAAAAAAAGAAAC
*
382302 GAGTGATGATGACGAAAAAAGAA
1 GAGTGATGATGACAAAAAAAGAA
382325 TCACTACTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.54, C:0.04, G:0.27, T:0.15
Consensus pattern (25 bp):
GAGTGATGATGACAAAAAAAGAAAC
Found at i:385197 original size:12 final size:12
Alignment explanation
Indices: 385182--385208 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
385172 ATGTTTTGAT
385182 TAATTGTTTACA
1 TAATTGTTTACA
385194 TAATTGTTTACA
1 TAATTGTTTACA
385206 TAA
1 TAA
385209 ATCGATGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (12 bp):
TAATTGTTTACA
Found at i:387050 original size:2 final size:2
Alignment explanation
Indices: 387043--387097 Score: 85
Period size: 2 Copynumber: 27.5 Consensus size: 2
387033 TATCAACGGT
387043 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A-
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
387084 ATG AG TG AG AG AG A
1 A-G AG AG AG AG AG A
387098 TCTTAATGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 1 0.02
2 47 0.96
3 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.47, T:0.04
Consensus pattern (2 bp):
AG
Found at i:389579 original size:20 final size:21
Alignment explanation
Indices: 389554--389608 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
389544 ATTTAACTTG
389554 TATAGATAGATACAT-GTAGA
1 TATAGATAGATACATAGTAGA
*
389574 TATAGAAAGATAC-TAGTAGA
1 TATAGATAGATACATAGTAGA
389594 TCAT-GATAGA-ACATA
1 T-ATAGATAGATACATA
389609 CCGATGAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 3 0.10
20 25 0.83
21 2 0.07
ACGTcount: A:0.47, C:0.07, G:0.18, T:0.27
Consensus pattern (21 bp):
TATAGATAGATACATAGTAGA
Found at i:392573 original size:17 final size:17
Alignment explanation
Indices: 392549--392670 Score: 208
Period size: 17 Copynumber: 7.2 Consensus size: 17
392539 GCACTGTGCT
392549 ACAGGTAAAGTAATGTA
1 ACAGGTAAAGTAATGTA
*
392566 AAAGGTAAAGTAATGTA
1 ACAGGTAAAGTAATGTA
392583 ACAGGTAAAGTAATGTA
1 ACAGGTAAAGTAATGTA
*
392600 AAAGGTAAAGTAATGTA
1 ACAGGTAAAGTAATGTA
*
392617 ACAGGTAAAATAATGTA
1 ACAGGTAAAGTAATGTA
392634 ACAGGTAAAGTAATGTA
1 ACAGGTAAAGTAATGTA
*
392651 ACAGGTAAAGTAGTGTA
1 ACAGGTAAAGTAATGTA
392668 ACA
1 ACA
392671 TGCAACATAT
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 98 1.00
ACGTcount: A:0.49, C:0.05, G:0.23, T:0.23
Consensus pattern (17 bp):
ACAGGTAAAGTAATGTA
Found at i:393744 original size:3 final size:3
Alignment explanation
Indices: 393736--393766 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
393726 TTTTATTAGT
*
393736 TGA TGA TGA TGA TGA TAA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
393767 TGAATTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:403641 original size:136 final size:134
Alignment explanation
Indices: 403296--403793 Score: 619
Period size: 135 Copynumber: 3.7 Consensus size: 134
403286 CTTGTTCCAT
* * *
403296 GGGTGGTCCTGACCCCCTTCAAACAGGAAGTGCACAAATAACTTGAAAATGGTTAAGATCCCCAC
1 GGGTGGTCCTGACCCCCCTCAAACAGGAAGTGCACAAATATCTTGAAAACGGTTAAGATCCCCAC
* * **
403361 CCCTAAACCACATATATTCTTGTTTCTTGTGCCAAGGGGCATCAAATGGTATGTAGGTCATGGGC
66 CCCTAAACCATATATATTCTTGTTCCTTGTGTTAAGGGGCATCAAATGGTATGTAGGTCATGGGC
403426 TCTGG
131 T-TGG
* * * * * *
403431 GGGTGGTTCTGACCCCTCTCAAACAGGAAGTGCCCGAATATCTTGAAAACGGTTAAGAACCCCAA
1 GGGTGGTCCTGACCCCCCTCAAACAGGAAGTGCACAAATATCTTGAAAACGGTTAAGATCCCCAC
*
403496 CCCTAAACCATATATATTCTTGTTCCATT-TGTTAAGGGGCATCAAATGGTATATAGGTCATGGG
66 CCCTAAACCATATATATTCTTGTTCC-TTGTGTTAAGGGGCATCAAATGGTATGTAGGTCATGGG
403560 TCTTGGG
130 -CTT-GG
* * * ** *
403567 GGGTGGTCCTGACCCCCCTCAAACAGGAAGTGCCCGAAA-ATCTTGAAAGCAGTCGAGATCCTCA
1 GGGTGGTCCTGACCCCCCTCAAACAGGAAGTGCAC-AAATATCTTGAAAACGGTTAAGATCCCCA
* * * * *
403631 CCCC-ATAACCATATAT-TTCTTGTTCCTTGCGTTAAGGGGAATCACATGGTCTGTAGGTCATTT
65 CCCCTA-AACCATATATATTCTTGTTCCTTGTGTTAAGGGGCATCAAATGGTATGTAGGTCA-TG
* *
403694 GCCCTGG
128 GGCTTGG
* * *
403701 GGGTGGTCCTGACCCCCTTCAAACAGGAAGTGCACAAATATCTTGAAAACGGTTAAGATTCCTAC
1 GGGTGGTCCTGACCCCCCTCAAACAGGAAGTGCACAAATATCTTGAAAACGGTTAAGATCCCCA-
403766 CCCCT-AACCATATATATTCTTGTTCCTT
65 CCCCTAAACCATATATATTCTTGTTCCTT
403794 CGGTCATGTT
Statistics
Matches: 311, Mismatches: 41, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
133 3 0.01
134 65 0.21
135 168 0.54
136 73 0.23
137 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (134 bp):
GGGTGGTCCTGACCCCCCTCAAACAGGAAGTGCACAAATATCTTGAAAACGGTTAAGATCCCCAC
CCCTAAACCATATATATTCTTGTTCCTTGTGTTAAGGGGCATCAAATGGTATGTAGGTCATGGGC
TTGG
Found at i:404186 original size:48 final size:48
Alignment explanation
Indices: 404129--404227 Score: 153
Period size: 48 Copynumber: 2.1 Consensus size: 48
404119 TTTCTCTGCA
* * * **
404129 GTGCTTATAACAAAATTCTACGCAACAAGAGTATTGGATTGTGTGTCT
1 GTGCATATAACAAAATTCTAAGCAACAAGAGAATTGGATTGTACGTCT
404177 GTGCATATAACAAAATTCTAAGCAACAAGAGAATTGGATTGTACGTCT
1 GTGCATATAACAAAATTCTAAGCAACAAGAGAATTGGATTGTACGTCT
404225 GTG
1 GTG
404228 TGTTAAGAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.30
Consensus pattern (48 bp):
GTGCATATAACAAAATTCTAAGCAACAAGAGAATTGGATTGTACGTCT
Found at i:404564 original size:40 final size:40
Alignment explanation
Indices: 404505--404705 Score: 348
Period size: 40 Copynumber: 5.0 Consensus size: 40
404495 AGAAATCCAT
**
404505 TATAGTTAAGATATCTGATCATTTGAAATATGATAAACTA
1 TATAGTTAAGATATCTGATCAAATGAAATATGATAAACTA
* *
404545 TATGGTTAAGATATCTGATCAAATGAAATATGCTAAACTA
1 TATAGTTAAGATATCTGATCAAATGAAATATGATAAACTA
*
404585 TAGAGTTAAGATATCTGATCAAATGAAATATGATAAACTA
1 TATAGTTAAGATATCTGATCAAATGAAATATGATAAACTA
*
404625 TATAGTTAAGATATCTGATCAAATGAAATATGATCAACTA
1 TATAGTTAAGATATCTGATCAAATGAAATATGATAAACTA
404665 TATAGTTAAGATATCTGATCAAATGAAATATGATAAACTA
1 TATAGTTAAGATATCTGATCAAATGAAATATGATAAACTA
404705 T
1 T
404706 TAAAATGATC
Statistics
Matches: 151, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 151 1.00
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.33
Consensus pattern (40 bp):
TATAGTTAAGATATCTGATCAAATGAAATATGATAAACTA
Found at i:408225 original size:77 final size:74
Alignment explanation
Indices: 407999--408226 Score: 278
Period size: 75 Copynumber: 3.0 Consensus size: 74
407989 CACAGAGTTA
*
407999 AATACACTTCATACAAACACAATAGTCAGAGAGCATACAAATTCATCAGT-TGTACAGCACAAAT
1 AATACACTTCATACAAACACATTAGTCAGAGAGCATACAAATTCATCAGTCT-TACAGCAC-AAT
408063 CTTACCTGGGC
64 CTTACCTGGGC
* * * * * * *
408074 AAAACACTTCATACAAACTCGTAAGTCAGATAGCACACAAATTCATCAGTCGTACAGCACAATTC
1 AATACACTTCATACAAACACATTAGTCAGAGAGCATACAAATTCATCAGTCTTACAGCACAA-TC
408139 TTACCTGGGC
65 TTACCTGGGC
* * * * *
408149 AATACACTTCATAAAAACACATTGGTCAGAGGGCATATACAAGTCCATCAGTCTTACAGCACTAA
1 AATACACTTCATACAAACACATTAGTCAGAGAGC--ATACAAATTCATCAGTCTTACAGCAC-AA
408214 TCTTACCTGGGC
63 TCTTACCTGGGC
408226 A
1 A
408227 TTGTTCTTTT
Statistics
Matches: 128, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
74 2 0.02
75 89 0.70
77 35 0.27
78 2 0.02
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.23
Consensus pattern (74 bp):
AATACACTTCATACAAACACATTAGTCAGAGAGCATACAAATTCATCAGTCTTACAGCACAATCT
TACCTGGGC
Found at i:408347 original size:43 final size:42
Alignment explanation
Indices: 408299--408384 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 42
408289 AGAGAATGCT
408299 AGTCCCCAGCCCTGCATTTCTGCTTTCACTTTTTCATTCCTA
1 AGTCCCCAGCCCTGCATTTCTGCTTTCACTTTTTCATTCCTA
408341 NAGTCCCCAGCCCTGCATTTCTGCTTTCACTTTTTCATTCCTA
1 -AGTCCCCAGCCCTGCATTTCTGCTTTCACTTTTTCATTCCTA
408384 A
1 A
408385 ATAAAAAGAG
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 1 0.02
43 42 0.98
ACGTcount: A:0.15, C:0.35, G:0.09, T:0.40
Consensus pattern (42 bp):
AGTCCCCAGCCCTGCATTTCTGCTTTCACTTTTTCATTCCTA
Found at i:418110 original size:24 final size:24
Alignment explanation
Indices: 418070--418128 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
418060 CCTATAACCA
* *
418070 TAAAAAATGTATTAAAAGA-TGGC
1 TAAAAAATGTATAAAAAAAGTGGC
418093 TTAAAAAATGCTA-AAAAAAAGTGGC
1 -TAAAAAATG-TATAAAAAAAGTGGC
*
418118 TAAAAACTGTA
1 TAAAAAATGTA
418129 CTAAGCATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 2 0.07
24 22 0.73
25 6 0.20
ACGTcount: A:0.54, C:0.07, G:0.15, T:0.24
Consensus pattern (24 bp):
TAAAAAATGTATAAAAAAAGTGGC
Found at i:418870 original size:4 final size:4
Alignment explanation
Indices: 418827--418888 Score: 81
Period size: 4 Copynumber: 15.8 Consensus size: 4
418817 AAAGTTTACA
* * * *
418827 GACG GACA GACA GACG GACA GACG GACG GACG GACA GACG GACG GACG
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG
418875 GACG GAC- GACG GAC
1 GACG GACG GACG GAC
418889 AAAAAGTGAT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
3 3 0.06
4 48 0.94
ACGTcount: A:0.32, C:0.26, G:0.42, T:0.00
Consensus pattern (4 bp):
GACG
Found at i:431380 original size:14 final size:13
Alignment explanation
Indices: 431354--431388 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
431344 TAGCAGTACC
431354 AATTTTAAAAAAAA
1 AATTTT-AAAAAAA
431368 AATCTTTAAAAAAA
1 AAT-TTTAAAAAAA
431382 AATTTTA
1 AATTTTA
431389 CCGTCTGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 13 0.65
15 3 0.15
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (13 bp):
AATTTTAAAAAAA
Found at i:432390 original size:16 final size:16
Alignment explanation
Indices: 432371--432401 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
432361 ATTTTTTTAT
432371 CAAAGTTAGCAGTTTG
1 CAAAGTTAGCAGTTTG
*
432387 CAAAGTTAGGAGTTT
1 CAAAGTTAGCAGTTT
432402 TTATACAACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.32
Consensus pattern (16 bp):
CAAAGTTAGCAGTTTG
Found at i:441761 original size:20 final size:20
Alignment explanation
Indices: 441736--441796 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
441726 TCTGTACATC
* *
441736 AAAACACTGGCTCTGATGTA
1 AAAACAATGGCTCTGATGAA
*
441756 AAAACAATAGCTCTGATGAA
1 AAAACAATGGCTCTGATGAA
*
441776 AAAACAATGGCTATGATGAA
1 AAAACAATGGCTCTGATGAA
441796 A
1 A
441797 CACATGTAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.21
Consensus pattern (20 bp):
AAAACAATGGCTCTGATGAA
Found at i:442270 original size:52 final size:52
Alignment explanation
Indices: 442110--442278 Score: 185
Period size: 52 Copynumber: 3.2 Consensus size: 52
442100 TGTATTAAAT
* * * *
442110 GTTTTACACTTTTGAGACTAACCCTGATGTAATTACACTACTTAAAACTCAA
1 GTTTTACACTTTTGACACTAACTCTAATGTGATTACACTACTTAAAACTCAA
* * ** * * * *
442162 GTTTAAAACTACTGACACTAATTCTAATGTGATTACACTAGTTAACACCCAA
1 GTTTTACACTTTTGACACTAACTCTAATGTGATTACACTACTTAAAACTCAA
* * * *
442214 GTTTTACACTTTTCACATTAACTCTAATGTGATAACACTACTTAAAACTCAT
1 GTTTTACACTTTTGACACTAACTCTAATGTGATTACACTACTTAAAACTCAA
*
442266 GTTTTATACTTTT
1 GTTTTACACTTTT
442279 TTACTCATGT
Statistics
Matches: 92, Mismatches: 25, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
52 92 1.00
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.37
Consensus pattern (52 bp):
GTTTTACACTTTTGACACTAACTCTAATGTGATTACACTACTTAAAACTCAA
Found at i:442285 original size:21 final size:21
Alignment explanation
Indices: 442260--442300 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
442250 ACTACTTAAA
442260 ACTCATGTTTTA-TACTTTTTT
1 ACTCATGTTTTACT-CTTTTTT
442281 ACTCATGTTTTACTCTTTTT
1 ACTCATGTTTTACTCTTTTT
442301 AGTTTAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.17, C:0.17, G:0.05, T:0.61
Consensus pattern (21 bp):
ACTCATGTTTTACTCTTTTTT
Found at i:442411 original size:52 final size:52
Alignment explanation
Indices: 442351--442518 Score: 300
Period size: 52 Copynumber: 3.2 Consensus size: 52
442341 TAAGCTATAC
* *
442351 ACTAACCCTGATGTGATTACACTGTTTAACACTCAAGCTCTACACTTTTGAG
1 ACTAACCCTGATGCGATTACACTGTTTTACACTCAAGCTCTACACTTTTGAG
442403 ACTAACCCTGATGCGATTACACTGTTTTACACTCAAGCTCTACACTTTTGAG
1 ACTAACCCTGATGCGATTACACTGTTTTACACTCAAGCTCTACACTTTTGAG
* *
442455 ACTAACCCTGATGCGATTACATTGTTTTACACTCAAGCTCTACACTTTTGAC
1 ACTAACCCTGATGCGATTACACTGTTTTACACTCAAGCTCTACACTTTTGAG
442507 ACTAACCCTGAT
1 ACTAACCCTGAT
442519 TTCCTGCTCT
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 112 1.00
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.33
Consensus pattern (52 bp):
ACTAACCCTGATGCGATTACACTGTTTTACACTCAAGCTCTACACTTTTGAG
Found at i:444113 original size:42 final size:40
Alignment explanation
Indices: 444059--444189 Score: 136
Period size: 42 Copynumber: 3.1 Consensus size: 40
444049 TCAGTTGTTG
*
444059 CATTGAATTTTGTGATGATGAAGGAAATAAGACACTGACTAA
1 CATT-AATTTTGTGATGATGAAGGAAA-AAGACACTGACTTA
* * * * *
444101 CATTAACTTTTGTCATGATGAAGGAAAGAAGATATTGCCTTG
1 CATTAA-TTTTGTGATGATGAAGGAAA-AAGACACTGACTTA
* *
444143 CATTGTATTTTGTGATGATGAAGGAAAGAGAACACTGACTTA
1 CATT-AATTTTGTGATGATGAAGGAAAAAG-ACACTGACTTA
444185 CATTA
1 CATTA
444190 TTAGTAAAAC
Statistics
Matches: 71, Mismatches: 15, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
41 4 0.06
42 66 0.93
43 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (40 bp):
CATTAATTTTGTGATGATGAAGGAAAAAGACACTGACTTA
Found at i:452418 original size:11 final size:11
Alignment explanation
Indices: 452402--452438 Score: 65
Period size: 11 Copynumber: 3.3 Consensus size: 11
452392 TCTTAAATTC
452402 TTTATTTTTTT
1 TTTATTTTTTT
452413 TTTATTTTTTTT
1 TTTA-TTTTTTT
452425 TTTATTTTTTT
1 TTTATTTTTTT
452436 TTT
1 TTT
452439 CTTTCCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTATTTTTTT
Found at i:452423 original size:12 final size:12
Alignment explanation
Indices: 452402--452438 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
452392 TCTTAAATTC
452402 TTTA-TTTTTTT
1 TTTATTTTTTTT
452413 TTTATTTTTTTT
1 TTTATTTTTTTT
452425 TTTATTTTTTTT
1 TTTATTTTTTTT
452437 TT
1 TT
452439 CTTTCCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 4 0.16
12 21 0.84
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTATTTTTTTT
Found at i:452451 original size:23 final size:23
Alignment explanation
Indices: 452402--452452 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
452392 TCTTAAATTC
*** *
452402 TTTATTTTTTTTTTATTTTTTTT
1 TTTATTTTTTTTTTATTTCCATA
*
452425 TTTATTTTTTTTTTCTTTCCATA
1 TTTATTTTTTTTTTATTTCCATA
452448 TTTAT
1 TTTAT
452453 AACACAGATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (23 bp):
TTTATTTTTTTTTTATTTCCATA
Found at i:467346 original size:19 final size:19
Alignment explanation
Indices: 467307--467346 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
467297 ATGGTACATG
*
467307 TATCATCATATTTTCTTAA
1 TATCATCATATTTTCTAAA
467326 TATCATCATTATTTT-TAAA
1 TATCATCA-TATTTTCTAAA
467345 TA
1 TA
467347 CATTGTAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (19 bp):
TATCATCATATTTTCTAAA
Found at i:468646 original size:31 final size:31
Alignment explanation
Indices: 468611--468708 Score: 142
Period size: 31 Copynumber: 3.2 Consensus size: 31
468601 AAACCAGTCC
* * *
468611 TGTATTGCTCACTGTATTAACTACATGATAT
1 TGTATTCCTTACTGTATCAACTACATGATAT
* *
468642 TGTATTCCTTACTGTATCAACTACATCATTT
1 TGTATTCCTTACTGTATCAACTACATGATAT
*
468673 TGTATTCCTTACTATATCAACTACATGATAT
1 TGTATTCCTTACTGTATCAACTACATGATAT
468704 TGTAT
1 TGTAT
468709 CGGGACCCTT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 59 1.00
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (31 bp):
TGTATTCCTTACTGTATCAACTACATGATAT
Found at i:470674 original size:2 final size:2
Alignment explanation
Indices: 470667--470694 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
470657 ATTCAAAATA
470667 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
470695 ATCTATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:477841 original size:252 final size:252
Alignment explanation
Indices: 477396--477897 Score: 923
Period size: 252 Copynumber: 2.0 Consensus size: 252
477386 ATAATTTGGC
* *
477396 TCCATTTTTGATGCCTTCATTAATTGAACATCCCGGTCTGAATCTGGCTCCCTTTTCAGTGCCTC
1 TCCATTTTTGATGCCTTCATTAATTGAACATCCCGGTCTGAATCAGGCTCCCTTTCCAGTGCCTC
*
477461 CGCTGATTGTAAATCACAGTTCATAGGATCCCTTTCCAATGAGTCATTTAATTGTAAATCCAAAA
66 CACTGATTGTAAATCACAGTTCATAGGATCCCTTTCCAATGAGTCATTTAATTGTAAATCCAAAA
* *
477526 CAGGTCCCATTTTCTGTGCTTCAGTGGATTGTATATCACAATTTGGCTCCATTTCTGGTTCCTCT
131 CAGGTCCCATTTTCTGTGCCTCAGTGGATTGAATATCACAATTTGGCTCCATTTCTGGTTCCTCT
* *
477591 GCTAACCGAACTTCCCAGTCAGGCTCCATTTTTGGTGCTTCAACTGATTGAAATTTT
196 GATAACCGAAATTCCCAGTCAGGCTCCATTTTTGGTGCTTCAACTGATTGAAATTTT
477648 TCCATTTTTGATGCCTTCATTAATTGAACATCCCGGTCTGAATCAGGCTCCCTTTCCAGTGCCTC
1 TCCATTTTTGATGCCTTCATTAATTGAACATCCCGGTCTGAATCAGGCTCCCTTTCCAGTGCCTC
477713 CACTGATTGTAAATCACAGTTCATAGGATCCCTTTCCAATGAGTCATTTAATTGTAAATCCAAAA
66 CACTGATTGTAAATCACAGTTCATAGGATCCCTTTCCAATGAGTCATTTAATTGTAAATCCAAAA
*
477778 CAGGTTCCATTTTCTGTGCCTCAGTGGATTGAATATCACAATTTGGCTCCATTTCTGGTTCCTCT
131 CAGGTCCCATTTTCTGTGCCTCAGTGGATTGAATATCACAATTTGGCTCCATTTCTGGTTCCTCT
*
477843 GATAACCGAAATTCCCAGTCAGGCTCCATTTTTGGTGCTTCAGCTGATTGAAATT
196 GATAACCGAAATTCCCAGTCAGGCTCCATTTTTGGTGCTTCAACTGATTGAAATT
477898 CCTGCACAGT
Statistics
Matches: 241, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
252 241 1.00
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (252 bp):
TCCATTTTTGATGCCTTCATTAATTGAACATCCCGGTCTGAATCAGGCTCCCTTTCCAGTGCCTC
CACTGATTGTAAATCACAGTTCATAGGATCCCTTTCCAATGAGTCATTTAATTGTAAATCCAAAA
CAGGTCCCATTTTCTGTGCCTCAGTGGATTGAATATCACAATTTGGCTCCATTTCTGGTTCCTCT
GATAACCGAAATTCCCAGTCAGGCTCCATTTTTGGTGCTTCAACTGATTGAAATTTT
Found at i:479236 original size:252 final size:252
Alignment explanation
Indices: 478791--479292 Score: 891
Period size: 252 Copynumber: 2.0 Consensus size: 252
478781 ATAATTTGGC
* *
478791 TCCATTTTTGATGCCTTCATTAATTGAACATCCCGGTCTGAATCTGGCTCCCTTTTCAGTGCCTC
1 TCCATTTTTGATGCCTTCATTAATTGAACATCCCGGTCTGAATCAGGCTCCCTTTCCAGTGCCTC
*
478856 AGCTGATTGTAAATCACAGTTCATAGGATCCCTTTCCAATGAGTCATTAAATTGTAAATCCAGAA
66 AGCTGATTGTAAATCACAGTTCATAGGATCCCTTTCCAATGAGTCATTAAATTGTAAATCCAAAA
*
478921 CAGGTCCTATTTTCTGTGCTTCAGTGGATTGAATATCACAATTTGGCTCCATTTCTGGTTCCTCT
131 CAGGTCCTATTTTCTGTGCCTCAGTGGATTGAATATCACAATTTGGCTCCATTTCTGGTTCCTCT
*
478986 GCTAACCGAACTTCCCAGTCAGGCTCCATTTTTTGTGCTTCAACTGATTGAAATTTT
196 GCTAACCGAACTTCCCAGTCAGGCTCCATTTTTGGTGCTTCAACTGATTGAAATTTT
*
479043 TCCATTTTTGATGCCTTCATTAATTGAACATCCTGGTCTGAATCAGGCTCCCTTTCCAGTGCCTC
1 TCCATTTTTGATGCCTTCATTAATTGAACATCCCGGTCTGAATCAGGCTCCCTTTCCAGTGCCT-
*
479108 CA-CTGATTGTAAATCACAGTTCATAGGATCCCTTTCCAATGAGTCATTTAATTGTAAATCCAAA
65 CAGCTGATTGTAAATCACAGTTCATAGGATCCCTTTCCAATGAGTCATTAAATTGTAAATCCAAA
479172 ACAGGTTCC-ATTTTCTGTGCCTCAGTGGATTGAATATCACAATTTGGCTCCATTTCTGGTTCCT
130 ACAGG-TCCTATTTTCTGTGCCTCAGTGGATTGAATATCACAATTTGGCTCCATTTCTGGTTCCT
* *
479236 CTGCTAACTGAACTTCCCAGTCAGGCTCCATTTTTGGTGCTTCAGCTGATTGAAATT
194 CTGCTAACCGAACTTCCCAGTCAGGCTCCATTTTTGGTGCTTCAACTGATTGAAATT
479293 CCTGCACAGT
Statistics
Matches: 239, Mismatches: 9, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
252 234 0.98
253 5 0.02
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.36
Consensus pattern (252 bp):
TCCATTTTTGATGCCTTCATTAATTGAACATCCCGGTCTGAATCAGGCTCCCTTTCCAGTGCCTC
AGCTGATTGTAAATCACAGTTCATAGGATCCCTTTCCAATGAGTCATTAAATTGTAAATCCAAAA
CAGGTCCTATTTTCTGTGCCTCAGTGGATTGAATATCACAATTTGGCTCCATTTCTGGTTCCTCT
GCTAACCGAACTTCCCAGTCAGGCTCCATTTTTGGTGCTTCAACTGATTGAAATTTT
Found at i:491334 original size:72 final size:66
Alignment explanation
Indices: 491244--491406 Score: 213
Period size: 66 Copynumber: 2.4 Consensus size: 66
491234 TATATCAATC
491244 TTTG-AATC-AAACATCACAAACAGTAAAGAATACATGCACTTCATTGTTAGGCATGCTTCCTGT
1 TTTGAAATCAAAACATCACAAACAGTAAAGAATAC-T--A---CATTGTTAGGCATGCTTCCTGT
491307 CTCTTTA
60 CTCTTTA
** *
491314 TTTGAAATCAAAACATCACAAACAGTGTAGAATACTACATTGTTAGGCATGCTTCCTTTCTCTTT
1 TTTGAAATCAAAACATCACAAACAGTAAAGAATACTACATTGTTAGGCATGCTTCCTGTCTCTTT
*
491379 C
66 A
*
491380 CTTGAAATCAAAACATCACAAACAGTA
1 TTTGAAATCAAAACATCACAAACAGTA
491407 CTAGTGTAGA
Statistics
Matches: 85, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
66 52 0.61
69 1 0.01
70 4 0.05
71 5 0.06
72 23 0.27
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (66 bp):
TTTGAAATCAAAACATCACAAACAGTAAAGAATACTACATTGTTAGGCATGCTTCCTGTCTCTTT
A
Found at i:492354 original size:6 final size:6
Alignment explanation
Indices: 492343--492406 Score: 74
Period size: 6 Copynumber: 10.7 Consensus size: 6
492333 GGCAAGGTAA
* * * * *
492343 CTCTCT CTCTCT CTGTCT CTGTCT CTGTCT CTCTCT CTGTCT CTGTCT
1 CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT
*
492391 CTATCT CTCTCT CTCT
1 CTCTCT CTCTCT CTCT
492407 NNNNNNNNNN
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.02, C:0.41, G:0.08, T:0.50
Consensus pattern (6 bp):
CTCTCT
Found at i:492367 original size:12 final size:12
Alignment explanation
Indices: 492346--492404 Score: 91
Period size: 12 Copynumber: 4.9 Consensus size: 12
492336 AAGGTAACTC
492346 TCTCTCTCTCTG
1 TCTCTCTCTCTG
*
492358 TCTCTGTCTCTG
1 TCTCTCTCTCTG
492370 TCTCTCTCTCTG
1 TCTCTCTCTCTG
* *
492382 TCTCTGTCTCTA
1 TCTCTCTCTCTG
492394 TCTCTCTCTCT
1 TCTCTCTCTCT
492405 CTNNNNNNNN
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 42 1.00
ACGTcount: A:0.02, C:0.39, G:0.08, T:0.51
Consensus pattern (12 bp):
TCTCTCTCTCTG
Found at i:492378 original size:24 final size:24
Alignment explanation
Indices: 492346--492404 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
492336 AAGGTAACTC
*
492346 TCTCTCTCTCTGTCTCTGTCTCTG
1 TCTCTCTCTCTGTCTCTGTCTCTA
492370 TCTCTCTCTCTGTCTCTGTCTCTA
1 TCTCTCTCTCTGTCTCTGTCTCTA
492394 TCTCTCTCTCT
1 TCTCTCTCTCT
492405 CTNNNNNNNN
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.02, C:0.39, G:0.08, T:0.51
Consensus pattern (24 bp):
TCTCTCTCTCTGTCTCTGTCTCTA
Found at i:507881 original size:16 final size:16
Alignment explanation
Indices: 507860--507903 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
507850 CTCCCAATAG
507860 GTGAGAGGAGAGTGGA
1 GTGAGAGGAGAGTGGA
* *
507876 GTGAGAGGAGAATGGG
1 GTGAGAGGAGAGTGGA
507892 GTGAGAGGAGAG
1 GTGAGAGGAGAG
507904 AGTGGGGCGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.57, T:0.11
Consensus pattern (16 bp):
GTGAGAGGAGAGTGGA
Found at i:507909 original size:18 final size:18
Alignment explanation
Indices: 507859--507928 Score: 94
Period size: 18 Copynumber: 4.1 Consensus size: 18
507849 CCTCCCAATA
507859 GGTGAGA-G-GAGAGTGG
1 GGTGAGAGGAGAGAGTGG
*
507875 AGTGAGAGGAGA-A-TGG
1 GGTGAGAGGAGAGAGTGG
507891 GGTGAGAGGAGAGAGTGG
1 GGTGAGAGGAGAGAGTGG
*
507909 GGCGAGAGGAGAGAGTGG
1 GGTGAGAGGAGAGAGTGG
507927 GG
1 GG
507929 CGAAAGAGAG
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
16 20 0.43
17 3 0.06
18 24 0.51
ACGTcount: A:0.29, C:0.01, G:0.60, T:0.10
Consensus pattern (18 bp):
GGTGAGAGGAGAGAGTGG
Found at i:507936 original size:20 final size:18
Alignment explanation
Indices: 507867--507942 Score: 90
Period size: 18 Copynumber: 4.5 Consensus size: 18
507857 TAGGTGAGAG
* *
507867 GAGAGTGGAGTGAGAGGA
1 GAGAGTGGGGCGAGAGGA
*
507885 GA-A-TGGGGTGAGAGGA
1 GAGAGTGGGGCGAGAGGA
507901 GAGAGTGGGGCGAGAGGA
1 GAGAGTGGGGCGAGAGGA
507919 GAGAGTGGGGCGA-A--A
1 GAGAGTGGGGCGAGAGGA
507934 GAGAGTGGG
1 GAGAGTGGG
507943 ACAGGAGAGT
Statistics
Matches: 54, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
15 10 0.19
16 14 0.26
17 3 0.06
18 27 0.50
ACGTcount: A:0.30, C:0.03, G:0.58, T:0.09
Consensus pattern (18 bp):
GAGAGTGGGGCGAGAGGA
Found at i:508081 original size:16 final size:16
Alignment explanation
Indices: 508060--508103 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
508050 CTCCCAATAG
508060 GTGAGAGGAGAGTGGA
1 GTGAGAGGAGAGTGGA
* *
508076 GTGAGAGGAGAATGGG
1 GTGAGAGGAGAGTGGA
508092 GTGAGAGGAGAG
1 GTGAGAGGAGAG
508104 AGTGGGGCGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.57, T:0.11
Consensus pattern (16 bp):
GTGAGAGGAGAGTGGA
Found at i:508115 original size:200 final size:200
Alignment explanation
Indices: 507772--508171 Score: 800
Period size: 200 Copynumber: 2.0 Consensus size: 200
507762 CCCACTCATT
507772 TGCTCATGACCCTCACTTAAACACTATTACCCATTCTTTACCTCTCAAAAGCTCTCTTAACCAAT
1 TGCTCATGACCCTCACTTAAACACTATTACCCATTCTTTACCTCTCAAAAGCTCTCTTAACCAAT
507837 TCTACTCTCTTCCCTCCCAATAGGTGAGAGGAGAGTGGAGTGAGAGGAGAATGGGGTGAGAGGAG
66 TCTACTCTCTTCCCTCCCAATAGGTGAGAGGAGAGTGGAGTGAGAGGAGAATGGGGTGAGAGGAG
507902 AGAGTGGGGCGAGAGGAGAGAGTGGGGCGAAAGAGAGTGGGACAGGAGAGTGGGGTGAGATAGTG
131 AGAGTGGGGCGAGAGGAGAGAGTGGGGCGAAAGAGAGTGGGACAGGAGAGTGGGGTGAGATAGTG
507967 TGAAA
196 TGAAA
507972 TGCTCATGACCCTCACTTAAACACTATTACCCATTCTTTACCTCTCAAAAGCTCTCTTAACCAAT
1 TGCTCATGACCCTCACTTAAACACTATTACCCATTCTTTACCTCTCAAAAGCTCTCTTAACCAAT
508037 TCTACTCTCTTCCCTCCCAATAGGTGAGAGGAGAGTGGAGTGAGAGGAGAATGGGGTGAGAGGAG
66 TCTACTCTCTTCCCTCCCAATAGGTGAGAGGAGAGTGGAGTGAGAGGAGAATGGGGTGAGAGGAG
508102 AGAGTGGGGCGAGAGGAGAGAGTGGGGCGAAAGAGAGTGGGACAGGAGAGTGGGGTGAGATAGTG
131 AGAGTGGGGCGAGAGGAGAGAGTGGGGCGAAAGAGAGTGGGACAGGAGAGTGGGGTGAGATAGTG
508167 TGAAA
196 TGAAA
508172 GTGGGGCATG
Statistics
Matches: 200, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
200 200 1.00
ACGTcount: A:0.29, C:0.17, G:0.33, T:0.21
Consensus pattern (200 bp):
TGCTCATGACCCTCACTTAAACACTATTACCCATTCTTTACCTCTCAAAAGCTCTCTTAACCAAT
TCTACTCTCTTCCCTCCCAATAGGTGAGAGGAGAGTGGAGTGAGAGGAGAATGGGGTGAGAGGAG
AGAGTGGGGCGAGAGGAGAGAGTGGGGCGAAAGAGAGTGGGACAGGAGAGTGGGGTGAGATAGTG
TGAAA
Found at i:508259 original size:55 final size:51
Alignment explanation
Indices: 508200--508326 Score: 164
Period size: 55 Copynumber: 2.4 Consensus size: 51
508190 GAGTGGGAAT
508200 TGGGGCGAGAGGGAGTGGGGCGAGAGGAGAGAGAGAGGGGCGAGAGGAGAGAGAG
1 TGGGGCGAGAGGGAGTGGGGCGAGA-G-GAGAGAGAGGGGCGAGA-G-GAGAGAG
* *
508255 TGGGGGTGAGAGGAGAGTGGGGCGAGAGGAGAGAGTGGGGCGAGAGGAGAGAG
1 T-GGGGCGAGAGG-GAGTGGGGCGAGAGGAGAGAGAGGGGCGAGAGGAGAGAG
* *
508308 TGGGGCGAAAGAGAGTGGG
1 TGGGGCGAGAGGGAGTGGG
508327 ACAGGAGAGT
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
51 7 0.11
52 8 0.12
53 8 0.12
54 1 0.02
55 17 0.26
56 11 0.17
57 13 0.20
ACGTcount: A:0.28, C:0.05, G:0.61, T:0.06
Consensus pattern (51 bp):
TGGGGCGAGAGGGAGTGGGGCGAGAGGAGAGAGAGGGGCGAGAGGAGAGAG
Found at i:508268 original size:184 final size:177
Alignment explanation
Indices: 508062--508488 Score: 653
Period size: 184 Copynumber: 2.4 Consensus size: 177
508052 CCCAATAGGT
*
508062 GAGAGGAGAGT-GGAGTGAGAGGAGAATGGGGTGAGAGGAGAGAGTGGGGCGAGAGGAGAGAGTG
1 GAGA-GAGAGTGGGGGTGAGAGGAGAATGGGGTGAGAGGAGAGAGTGGGGCGAGAGGAGAGAGTG
508126 GGGCGAAAGAGAGTGGGACAGGAGAGTGGGGTGAGATAGTGTGAAAGTGGGGCATGAGGAGAGAG
65 GGGCGAAAGAGAGTGGGACAGGAGAGTGGGGTGAGATAGTGTGAAAGTGGGGCATGAGGAGAGAG
508191 AGTGGGAATTGGGGCGAGAGGGAGTGGGGCGAGAGGAGAGAGAGAGGGGCGAGAG
130 AGTGGGAATTGGGGCGAGAGGGAGTGGGGC------A-AGAGAGAGGGGCGAGAG
* *
508246 GAGAGAGAGTGGGGGTGAGAGGAGAGTGGGGCGAGAGGAGAGAGTGGGGCGAGAGGAGAGAGTGG
1 GAGAGAGAGTGGGGGTGAGAGGAGAATGGGGTGAGAGGAGAGAGTGGGGCGAGAGGAGAGAGTGG
508311 GGCGAAAGAGAGTGGGACAGGAGAGTGGGGTGAGATAGTGTGAAAGTGGGGCATGAGGAGAGAGA
66 GGCGAAAGAGAGTGGGACAGGAGAGTGGGGTGAGATAGTGTGAAAGTGGGGCATGAGGAGAGAGA
*
508376 GTGGGAATTGGGGCGAGAGGGAGTGGGGCAAGAGAGTGGGGCGAGAG
131 GTGGGAATTGGGGCGAGAGGGAGTGGGGCAAGAGAGAGGGGCGAGAG
* *
508423 GAGAGAGAGAGAGGGGCGAGAGGAGAGAGAGTGGGGGTGAGA-G-GAGAGTGGGGCGAGAGGAGA
1 GAGAGAGAGTG-GGGGTGAGA-G-GAGA-A-T-GGGGTGAGAGGAGAGAGTGGGGCGAGAGGAGA
508486 GAG
60 GAG
508489 AGAGTGGGGC
Statistics
Matches: 228, Mismatches: 8, Indels: 17
0.90 0.03 0.07
Matches are distributed among these distances:
177 26 0.11
178 9 0.04
179 1 0.00
180 4 0.02
181 23 0.10
182 2 0.01
183 14 0.06
184 149 0.65
ACGTcount: A:0.30, C:0.04, G:0.57, T:0.09
Consensus pattern (177 bp):
GAGAGAGAGTGGGGGTGAGAGGAGAATGGGGTGAGAGGAGAGAGTGGGGCGAGAGGAGAGAGTGG
GGCGAAAGAGAGTGGGACAGGAGAGTGGGGTGAGATAGTGTGAAAGTGGGGCATGAGGAGAGAGA
GTGGGAATTGGGGCGAGAGGGAGTGGGGCAAGAGAGAGGGGCGAGAG
Found at i:508404 original size:15 final size:15
Alignment explanation
Indices: 508384--508423 Score: 57
Period size: 13 Copynumber: 2.8 Consensus size: 15
508374 GAGTGGGAAT
508384 TGGGGCGAGAGGGAG
1 TGGGGCGAGAGGGAG
*
508399 TGGGGC-A-AGAGAG
1 TGGGGCGAGAGGGAG
508412 TGGGGCGAGAGG
1 TGGGGCGAGAGG
508424 AGAGAGAGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
13 11 0.52
14 2 0.10
15 8 0.38
ACGTcount: A:0.23, C:0.07, G:0.62, T:0.07
Consensus pattern (15 bp):
TGGGGCGAGAGGGAG
Found at i:508438 original size:22 final size:21
Alignment explanation
Indices: 508406--509326 Score: 351
Period size: 20 Copynumber: 47.1 Consensus size: 21
508396 GAGTGGGGCA
508406 AGAGAGTGGGGCGAGAGGAGAG
1 AGAGAGTGGGGCGAGA-GAGAG
*
508428 AGAGAGAGGGGCGAGAG-GAG
1 AGAGAGTGGGGCGAGAGAGAG
*
508448 AGAGAGT-GGG-G-GTGAGAG
1 AGAGAGTGGGGCGAGAGAGAG
508466 -GAGAGTGGGGCGAGAGGAGAG
1 AGAGAGTGGGGCGAGA-GAGAG
*
508487 AGAGAGTGGGGCGATAGAGAG
1 AGAGAGTGGGGCGAGAGAGAG
* *
508508 -G-GACG-AGAG-GAGAGCA-AG
1 AGAGA-GTGGGGCGAGAG-AGAG
*
508526 A-A-AGTGGGGCGAGAG-GAT
1 AGAGAGTGGGGCGAGAGAGAG
508544 AGAGAGT--GG-G-GAGAGAG
1 AGAGAGTGGGGCGAGAGAGAG
* *
508561 -GAGAGTGGGGTGAGAGAGGAA
1 AGAGAGTGGGGCGAGAGA-GAG
508582 AGAGAGTGGGGC-A-AGAG-G
1 AGAGAGTGGGGCGAGAGAGAG
508600 AGAGAGTGGGG-GCA-AGAG-G
1 AGAGAGTGGGGCG-AGAGAGAG
* *
508619 GGAGAGTGGGGCGAAAGAGAG
1 AGAGAGTGGGGCGAGAGAGAG
* *
508640 TG-GAGT-GGG-GAGAGAGTG
1 AGAGAGTGGGGCGAGAGAGAG
* * *
508658 -G-G-GCGAGAG-GAGAGAGTG
1 AGAGAGTG-GGGCGAGAGAGAG
* *
508676 -GTA-ATTTGGGCGAGAG-GAG
1 AG-AGAGTGGGGCGAGAGAGAG
*
508695 AGAGCG-GGGGCGAGAG-GAG
1 AGAGAGTGGGGCGAGAGAGAG
*
508714 AGAGAGT-GGG-G-GTGAGAG
1 AGAGAGTGGGGCGAGAGAGAG
*
508732 -GAGAGTGGGGC----TAGA-
1 AGAGAGTGGGGCGAGAGAGAG
* * *
508747 TGAGAGTGGGGTGAGAGAGGAA
1 AGAGAGTGGGGCGAGAGA-GAG
508769 AGAGAGTGGGGC--GAGAG-G
1 AGAGAGTGGGGCGAGAGAGAG
508787 AGAGAGTGGGGC--GAGAGA-
1 AGAGAGTGGGGCGAGAGAGAG
508805 AG-GAGTGGGGCGAGAG-GAG
1 AGAGAGTGGGGCGAGAGAGAG
*
508824 AGAGTGTGGGGC--GAGAG-G
1 AGAGAGTGGGGCGAGAGAGAG
*
508842 AGAGAGTGGGGCGATAGAGAG
1 AGAGAGTGGGGCGAGAGAGAG
* * * * * * *
508863 TGGGAATGAGGAGAGAGTGTTGTG
1 AGAGAGTG-GG-GCGAGAG-AGAG
508887 AGAGAGTGGGGC-A-AGAG-G
1 AGAGAGTGGGGCGAGAGAGAG
* * * *
508905 -G-GTGTGGGAGTG-GGGCGAG
1 AGAGAGTGGG-GCGAGAGAGAG
* *
508924 AGAGTG-CGGGCGAGAGAAGAG
1 AGAGAGTGGGGCGAGAG-AGAG
508945 -G-GAGTGGGGC--GAGAG-G
1 AGAGAGTGGGGCGAGAGAGAG
* *
508961 AGAGAGTGGGGTGATAGAGAG
1 AGAGAGTGGGGCGAGAGAGAG
* *
508982 TGGGAGTGGGGCGAGGAGAGAG
1 AGAGAGTGGGGCGA-GAGAGAG
*
509004 AGGCGATAGTGAGTGG-G-GAGAGAG
1 A---GAGAGTG-G-GGCGAGAGAGAG
* *
509028 -GAGAGTGGGGTGAGAGAGGAA
1 AGAGAGTGGGGCGAGAGA-GAG
509049 AGAGAGTGGGGC--GAGAG-G
1 AGAGAGTGGGGCGAGAGAGAG
509067 AGAGAGTGGGGCGAGAG-GAG
1 AGAGAGTGGGGCGAGAGAGAG
*
509087 AGAGAGTGGGCCGAGAG-GAG
1 AGAGAGTGGGGCGAGAGAGAG
509107 A-AGGAGTGGGGCGAGAG-GAG
1 AGA-GAGTGGGGCGAGAGAGAG
*
509127 AGAGTGTGGGGCGAGAG-GAG
1 AGAGAGTGGGGCGAGAGAGAG
*
509147 A-AGGAGTGGGGCGATAGAGAG
1 AGA-GAGTGGGGCGAGAGAGAG
* * * * * *
509168 TGGGAATGGGGAGAGAGTGTTGTG
1 AGAGAGTGGGGCGAGA--G-AGAG
509192 AGAGAGTGGGGC-A-AGAG-G
1 AGAGAGTGGGGCGAGAGAGAG
* * * *
509210 -G-GTGTGGGAGTG-GGGCGAG
1 AGAGAGTGGG-GCGAGAGAGAG
* *
509229 AGAGTG-CGGGCGAGAGAAGAG
1 AGAGAGTGGGGCGAGAG-AGAG
509250 -G-GAGTGGGGC--GAGAG-G
1 AGAGAGTGGGGCGAGAGAGAG
509266 AGAGAGTGGGGC--GAGAG-G
1 AGAGAGTGGGGCGAGAGAGAG
*
509284 AGAGAGTGGGGCGATAGAGAG
1 AGAGAGTGGGGCGAGAGAGAG
* *
509305 TGGGAGTGGGGCGAG-GAGAG
1 AGAGAGTGGGGCGAGAGAGAG
509325 AG
1 AG
509327 TGTTGTGAGG
Statistics
Matches: 683, Mismatches: 109, Indels: 216
0.68 0.11 0.21
Matches are distributed among these distances:
16 37 0.05
17 41 0.06
18 156 0.23
19 87 0.13
20 174 0.25
21 78 0.11
22 69 0.10
23 8 0.01
24 24 0.04
25 5 0.01
26 2 0.00
27 2 0.00
ACGTcount: A:0.29, C:0.05, G:0.58, T:0.09
Consensus pattern (21 bp):
AGAGAGTGGGGCGAGAGAGAG
Found at i:508471 original size:17 final size:16
Alignment explanation
Indices: 508445--508486 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
508435 GGGGCGAGAG
*
508445 GAGA-GAGAGTGGGGGT
1 GAGAGGAGAGT-GGGGC
508461 GAGAGGAGAGTGGGGC
1 GAGAGGAGAGTGGGGC
508477 GAGAGGAGAG
1 GAGAGGAGAG
508487 AGAGAGTGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.29, C:0.02, G:0.62, T:0.07
Consensus pattern (16 bp):
GAGAGGAGAGTGGGGC
Found at i:508719 original size:154 final size:150
Alignment explanation
Indices: 508406--509123 Score: 376
Period size: 154 Copynumber: 4.6 Consensus size: 150
508396 GAGTGGGGCA
* * * *
508406 AGAGAGTGGGGCGAGAG-GAGAGAGAGAGAGGGGCGAGAGGAGAGAGAGTGGGGG-TGAGAGGAG
1 AGAGAGTGGGG-GAGAGAG-GA-AGAGAGTGGGGCAAGA-G-GAGAGAGTGGGGGAAGAGGGGAG
* * * * * *
508469 AGTGGGGCGAGAGGAGAGAGAGAGTGGGGCGATAGAGAGGGACGAGAGGAGAGCA--AGAAAGTG
61 AGTGGGGCGAGAAGAGAGTG-GAGT-GGG-GAGAGAGTGGGGCGAGAGGAGAG-AGTGGAAAGTG
* *
508532 GGGCGAGAGGATAGAGAGTGGGGAGAGAG
122 GGGCGAGAGGAGAGAGAGGGGGGAGAGAG
508561 -GAGAGTGGGGTGAGAGAGGAAAGAGAGTGGGGCAAGAGGAGAGAGTGGGGGCAAGAGGGGAGAG
1 AGAGAGTGGGG-GAGAGAGG-AAGAGAGTGGGGCAAGAGGAGAGAGTGGGGG-AAGAGGGGAGAG
* * *
508625 TGGGGCGA-AAGAGAGTGGAGTGGGGAGAGAGTGGGGCGAGAGGAGAGAGTGGTAATTTGGGCGA
63 TGGGGCGAGAAGAGAGTGGAGTGGGGAGAGAGTGGGGCGAGAGGAGAGAGTGGAAAGTGGGGCGA
*
508689 GAGGAGAGAGCGGGGGCGAGAGGAG
128 GAGGAGAGAGAGGGGG-GAGA-GAG
* * * *
508714 AGAGAGTGGGGGTGAGA-G--GAGAGTGGGGCTAGA--TGAGAGTGGGGTGAGAGAGGAAAGAGA
1 AGAGAGTGGGGGAGAGAGGAAGAGAGTGGGGCAAGAGGAGAGAGTGGGG-GA-AGAGG--GGAGA
*
508774 GTGGGGCGAGAGGAGAGAGTGG-G-GCGAGAGAAGGAGTGGGGCGAGAGGAGAGAGT-----GTG
62 GTGGGGCGAGA--AGAGAGTGGAGTG-GGGAG-A-GAGTGGGGCGAGAGGAGAGAGTGGAAAGTG
* *
508832 GGGCGAGAGGAGAGAGTGGGGCGATAGAGAG
122 GGGCGAGAGGAGAGAGAGGGG-G-GAGAGAG
* * * * * * * * * *
508863 TGGGAATGAGGAGAGAGTGTTGTGAGAGAGTGGGGCAAGAGG-G-GTGTGGGAG-TGGGGCGAGA
1 AGAGAGTG-GGGGAGAGAG--G-AAGAGAGTGGGGCAAGAGGAGAGAGTGGGGGAAGAGG-G-GA
* * * * *
508925 GAGTGCGGGCGAG-AGAAGAG-GGAGTGGGGCGAGAGGAGAGAGTGGGGTGA-TAGAGAGTGG-G
60 GAGTG-GGGCGAGAAG-AGAGTGGAGT-GGG-GAGA-GAGTG-G-GGCGAGAGGAGAGAGTGGAA
*
508986 AGTGGGGCGAGGAGAGAGAGGCGATAGTGAGTGGG-GAGAG
118 AGTGGGGCGA-GAG-GAGA---GAGAG-G-G-GGGAGAGAG
*
509026 AGGAGAGTGGGGTGAGAGAGGAAAGAGAGTGGGGCGAGAGGAGAGAGTGGGGCG-AGAGGAGAGA
1 A-GAGAGTGGGG-GAGAGAGG-AAGAGAGTGGGGCAAGAGGAGAGAGTGGGG-GAAGAGG-G-GA
* * * *
509090 GAGTGGGCCGAGAGGAGA-AGGAGTGGGGCGAGAG
60 GAGTGGGGCGAGAAGAGAGTGGAGTGGGGAGAGAG
509124 GAGAGAGTGT
Statistics
Matches: 442, Mismatches: 64, Indels: 108
0.72 0.10 0.18
Matches are distributed among these distances:
147 11 0.02
148 6 0.01
149 44 0.10
150 43 0.10
151 32 0.07
152 32 0.07
153 44 0.10
154 98 0.22
155 8 0.02
156 20 0.05
157 1 0.00
158 9 0.02
159 3 0.01
160 4 0.01
161 3 0.01
162 21 0.05
163 14 0.03
164 32 0.07
165 16 0.04
166 1 0.00
ACGTcount: A:0.29, C:0.04, G:0.58, T:0.09
Consensus pattern (150 bp):
AGAGAGTGGGGGAGAGAGGAAGAGAGTGGGGCAAGAGGAGAGAGTGGGGGAAGAGGGGAGAGTGG
GGCGAGAAGAGAGTGGAGTGGGGAGAGAGTGGGGCGAGAGGAGAGAGTGGAAAGTGGGGCGAGAG
GAGAGAGAGGGGGGAGAGAG
Found at i:508928 original size:13 final size:14
Alignment explanation
Indices: 508912--508940 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
508902 AGGGGTGTGG
508912 GAGTG-GGGCGAGA
1 GAGTGCGGGCGAGA
508925 GAGTGCGGGCGAGA
1 GAGTGCGGGCGAGA
508939 GA
1 GA
508941 AGAGGGAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.24, C:0.10, G:0.59, T:0.07
Consensus pattern (14 bp):
GAGTGCGGGCGAGA
Found at i:509012 original size:35 final size:35
Alignment explanation
Indices: 508908--509020 Score: 113
Period size: 35 Copynumber: 3.1 Consensus size: 35
508898 CAAGAGGGGT
* *
508908 GTGGGAGTGGGGCGA-GAGAGTGCGGGCGAGAGA-A
1 GTGGGAGTGGGGCGAGGAGAGAG-GGGCGATAGAGA
* *
508942 GAGGGAGTGGGGCGAGAGGAGAGAGTGGGGTGATAGAGA
1 GTGGGAGTGGGGC--GAGGAGAGA--GGGGCGATAGAGA
* *
508981 GTGGGAGTGGGGCGAGGAGAGAGAGGCGATAGTGA
1 GTGGGAGTGGGGCGAGGAGAGAGGGGCGATAGAGA
509016 GTGGG
1 GTGGG
509021 GAGAGAGGAG
Statistics
Matches: 65, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
34 12 0.18
35 15 0.23
36 2 0.03
37 14 0.22
38 8 0.12
39 14 0.22
ACGTcount: A:0.25, C:0.05, G:0.59, T:0.11
Consensus pattern (35 bp):
GTGGGAGTGGGGCGAGGAGAGAGGGGCGATAGAGA
Found at i:509056 original size:38 final size:37
Alignment explanation
Indices: 509014--509147 Score: 144
Period size: 38 Copynumber: 3.5 Consensus size: 37
509004 AGGCGATAGT
* *
509014 GAGTGGGGAGAGAGGAGAGTGGGGTGAGAGAGGAAAGA
1 GAGTGGGGAGAGAGGAGAGTGGGG-GCGAGAGGAGAGA
* *
509052 GAGTGGGGCGAGAGGAGAGAGTGGGGCGAGAGGAGAGA
1 GAGTGGGGAGAGAGGAGAGTG-GGGGCGAGAGGAGAGA
*
509090 GAGTGGGCCGAGAGGAGAAGGAGT-GGGGCGAGAGGAGAGA
1 GAGTGGG--GAGA-GAGGA-GAGTGGGGGCGAGAGGAGAGA
* *
509130 GTGTGGGGCGAGAGGAGA
1 GAGTGGGGAGAGAGGAGA
509148 AGGAGTGGGG
Statistics
Matches: 81, Mismatches: 10, Indels: 12
0.79 0.10 0.12
Matches are distributed among these distances:
36 2 0.02
37 4 0.05
38 40 0.49
39 3 0.04
40 25 0.31
41 4 0.05
42 3 0.04
ACGTcount: A:0.30, C:0.04, G:0.59, T:0.07
Consensus pattern (37 bp):
GAGTGGGGAGAGAGGAGAGTGGGGGCGAGAGGAGAGA
Found at i:509233 original size:13 final size:14
Alignment explanation
Indices: 509217--509245 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
509207 AGGGGTGTGG
509217 GAGTG-GGGCGAGA
1 GAGTGCGGGCGAGA
509230 GAGTGCGGGCGAGA
1 GAGTGCGGGCGAGA
509244 GA
1 GA
509246 AGAGGGAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.24, C:0.10, G:0.59, T:0.07
Consensus pattern (14 bp):
GAGTGCGGGCGAGA
Found at i:509324 original size:35 final size:35
Alignment explanation
Indices: 509285--509397 Score: 90
Period size: 35 Copynumber: 3.3 Consensus size: 35
509275 GGCGAGAGGA
*
509285 GAGAGTGGGGCGATAGAGAGTGGGAGTGGGGCGAG
1 GAGAGTGGGGCGATAGGGAGTGGGAGTGGGGCGAG
* * ** * * *
509320 GAGAGAGTGTTG-TGAGGGAGTGGG-GCGAGGAGAG
1 GAGAGTGGGGCGAT-AGGGAGTGGGAGTGGGGCGAG
* *
509354 G-GAGTGGGGCGAGAGGGGTGTGGGAGTGGGGCGA-
1 GAGAGTGGGGCGATA-GGGAGTGGGAGTGGGGCGAG
509388 GAGAGTGGGG
1 GAGAGTGGGG
509398 GAGTGTGGTG
Statistics
Matches: 56, Mismatches: 17, Indels: 10
0.67 0.20 0.12
Matches are distributed among these distances:
33 7 0.12
34 18 0.32
35 31 0.55
ACGTcount: A:0.20, C:0.04, G:0.63, T:0.12
Consensus pattern (35 bp):
GAGAGTGGGGCGATAGGGAGTGGGAGTGGGGCGAG
Found at i:509401 original size:21 final size:21
Alignment explanation
Indices: 509335--509417 Score: 82
Period size: 21 Copynumber: 4.0 Consensus size: 21
509325 AGTGTTGTGA
*
509335 GGGAGTGGGGCGAG-GA--GA
1 GGGAGTGGGGCGAGAGAGTGG
* *
509353 GGGAGTGGGGCGAGAGGGGTGT
1 GGGAGTGGGGCGAGA-GAGTGG
509375 GGGAGTGGGGCGAGAGAGTGG
1 GGGAGTGGGGCGAGAGAGTGG
* * *
509396 GGGAGTGTGGTGAGATAGTGG
1 GGGAGTGGGGCGAGAGAGTGG
509417 G
1 G
509418 CGAGAGAGTG
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
18 14 0.26
20 1 0.02
21 23 0.43
22 16 0.30
ACGTcount: A:0.18, C:0.04, G:0.65, T:0.13
Consensus pattern (21 bp):
GGGAGTGGGGCGAGAGAGTGG
Found at i:509415 original size:13 final size:13
Alignment explanation
Indices: 509398--509436 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
509388 GAGAGTGGGG
509398 GAGTGTGGTGAGA
1 GAGTGTGGTGAGA
* *
509411 TAGTG-GGCGAGA
1 GAGTGTGGTGAGA
509423 GAGTGTGGTGAGA
1 GAGTGTGGTGAGA
509436 G
1 G
509437 TGGGTCGAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.23, C:0.03, G:0.54, T:0.21
Consensus pattern (13 bp):
GAGTGTGGTGAGA
Found at i:509426 original size:25 final size:24
Alignment explanation
Indices: 509398--509449 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 24
509388 GAGAGTGGGG
509398 GAGTGTGGTGAGATAGTGGG-CGAGA
1 GAGTGTGGTGAG--AGTGGGTCGAGA
509423 GAGTGTGGTGAGAGTGGGTCGAGA
1 GAGTGTGGTGAGAGTGGGTCGAGA
509447 GAG
1 GAG
509450 AGAGTGTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 6 0.23
24 8 0.31
25 12 0.46
ACGTcount: A:0.23, C:0.04, G:0.54, T:0.19
Consensus pattern (24 bp):
GAGTGTGGTGAGAGTGGGTCGAGA
Found at i:509448 original size:13 final size:12
Alignment explanation
Indices: 509355--509527 Score: 52
Period size: 11 Copynumber: 15.2 Consensus size: 12
509345 CGAGGAGAGG
*
509355 GAGTGGG-GCGA
1 GAGTGGGTGAGA
* *
509366 GAG-GGGTGTGG
1 GAGTGGGTGAGA
*
509377 GAGTGGGGCGAGA
1 GAGT-GGGTGAGA
509390 GAGTGGG-G-GA
1 GAGTGGGTGAGA
*
509400 GTGT-GGTGAGA
1 GAGTGGGTGAGA
* *
509411 TAGTGGGCGAGA
1 GAGTGGGTGAGA
509423 GAGTGTGGT--GA
1 GAGTG-GGTGAGA
509434 GAGTGGGTCGAGA
1 GAGTGGGT-GAGA
* * *
509447 GAGAGAGTGTTG-
1 GAGTGGGTG-AGA
*
509459 GAGTGGG-GCGA
1 GAGTGGGTGAGA
*
509470 GA---GGAGAGA
1 GAGTGGGTGAGA
*
509479 GAGTGGG-GCGA
1 GAGTGGGTGAGA
* *
509490 GAG-GAGAGAGA
1 GAGTGGGTGAGA
*
509501 CAG-GGGTGAGA
1 GAGTGGGTGAGA
509512 GAGTGGGGTGAGA
1 GAGT-GGGTGAGA
509525 GAG
1 GAG
509528 GAGAGAGTGG
Statistics
Matches: 118, Mismatches: 25, Indels: 36
0.66 0.14 0.20
Matches are distributed among these distances:
8 2 0.02
9 7 0.06
10 15 0.13
11 42 0.36
12 21 0.18
13 31 0.26
ACGTcount: A:0.24, C:0.04, G:0.59, T:0.13
Consensus pattern (12 bp):
GAGTGGGTGAGA
Found at i:509476 original size:26 final size:27
Alignment explanation
Indices: 509419--509479 Score: 81
Period size: 25 Copynumber: 2.3 Consensus size: 27
509409 GATAGTGGGC
*
509419 GAGAGAGTGTGGTGAGAGTGGGTCGAGA
1 GAGAGAGTGT-GTGAGAGTGGGGCGAGA
509447 GAGAGAGTGT-TG-GAGTGGGGCGAGA
1 GAGAGAGTGTGTGAGAGTGGGGCGAGA
509472 GGAGAGAG
1 -GAGAGAG
509480 AGTGGGGCGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 12 0.39
26 9 0.29
28 10 0.32
ACGTcount: A:0.26, C:0.03, G:0.56, T:0.15
Consensus pattern (27 bp):
GAGAGAGTGTGTGAGAGTGGGGCGAGA
Found at i:509513 original size:35 final size:34
Alignment explanation
Indices: 509473--509655 Score: 110
Period size: 33 Copynumber: 5.3 Consensus size: 34
509463 GGGGCGAGAG
509473 GAGAGAGAGTGGGGCGAGAGGAGAGAGACAGGGGT
1 GAGAGAGAGTGGGGCGAGA-GAGAGAGACAGGGGT
* *
509508 --GAGAGAGTGGGGTGAGAGAG-GAGAGAGTGGGAT
1 GAGAGAGAGTGGGGCGAGAGAGAGAGACAG-GGG-T
** * * * *
509541 GAGAGGAGAGT-GGTTGAGAGAGTGGGGC--GAGT
1 GAGA-GAGAGTGGGGCGAGAGAGAGAGACAGGGGT
* **
509573 GGAGAGAGAGTAGGGCGAGAGAGAGTATGGGAGTGGGT
1 -GAGAGAGAGTGGGGCGAGAGAGAG-A-GACAG-GGGT
* *
509611 GAGAGAGAGTGGGGCGAGAG-GAGAGAGAGTAGGGC
1 GAGAGAGAGTGGGGCGAGAGAGAGAGACAG--GGGT
509646 GAGAGAGAGT
1 GAGAGAGAGT
509656 ATGGGAGTGG
Statistics
Matches: 117, Mismatches: 17, Indels: 28
0.72 0.10 0.17
Matches are distributed among these distances:
31 6 0.05
32 13 0.11
33 33 0.28
34 4 0.03
35 28 0.24
36 11 0.09
37 19 0.16
38 3 0.03
ACGTcount: A:0.30, C:0.03, G:0.56, T:0.10
Consensus pattern (34 bp):
GAGAGAGAGTGGGGCGAGAGAGAGAGACAGGGGT
Found at i:509652 original size:37 final size:36
Alignment explanation
Indices: 509574--509898 Score: 156
Period size: 37 Copynumber: 8.8 Consensus size: 36
509564 GGGGCGAGTG
* * *
509574 GAGAGAGAGTAGGGCGAGAGAGAGTATGGGAGT-GG-GT
1 GAGAGAGAGTGGGGCGAGAG-GAG-A-GAGAGTGGGCGA
509611 GAGAGAGAGTGGGGCGAGAGGAGAGAGAGTAGGGCGA
1 GAGAGAGAGTGGGGCGAGAGGAGAGAGAGT-GGGCGA
*
509648 GAGAGAGTA-TGGGAGTG-G-GCGAGAGAGAGTGGG-G-
1 GAGAGAG-AGTGGG-GCGAGAG-GAGAGAGAGTGGGCGA
* * *
509682 CA-AGAGAGTGGGG-GAGTGTGGTGAGAGAGTGGGCGA
1 GAGAGAGAGTGGGGCGA--GAGGAGAGAGAGTGGGCGA
* * ** *
509718 GAGAGTGTGGGAGTGGGGCAAGAGGAGAGAGACAGGGTGA
1 GAGA----GAGAGTGGGGCGAGAGGAGAGAGAGTGGGCGA
* *
509758 GAGAGTGCGGGAGTGGGGCGAGA-G-GAGAGAGTGGGATGA
1 GAGA----GAGAGTGGGGCGAGAGGAGAGAGAGTGGG-CGA
* * *
509797 GAG-GAGAGTGGTTGAGAGAGAAGAGAGAGTGGGGCGA
1 GAGAGAGAGTGG-GGCGAGAGGAGAGAGAGT-GGGCGA
* *
509834 GAGGAGAGAGTAGGGCGAGAGAGAGTATGGGAGTGGGC--
1 GA-GAGAGAGTGGGGCGAGAG-GAG-A-GAGAGTGGGCGA
*
509872 GAGAGAGAGTTGGGCGAGAGGAGAGAG
1 GAGAGAGAGTGGGGCGAGAGGAGAGAG
509899 TGGGGTAAGA
Statistics
Matches: 229, Mismatches: 30, Indels: 61
0.72 0.09 0.19
Matches are distributed among these distances:
31 1 0.00
32 2 0.01
33 8 0.03
34 28 0.12
35 10 0.04
36 13 0.06
37 72 0.31
38 24 0.10
39 16 0.07
40 40 0.17
41 14 0.06
42 1 0.00
ACGTcount: A:0.29, C:0.04, G:0.56, T:0.10
Consensus pattern (36 bp):
GAGAGAGAGTGGGGCGAGAGGAGAGAGAGTGGGCGA
Found at i:509655 original size:57 final size:57
Alignment explanation
Indices: 509556--509687 Score: 237
Period size: 57 Copynumber: 2.3 Consensus size: 57
509546 GAGAGTGGTT
* *
509556 GAGAGAGTGGGGCGAGTGGAGAGAGAGTAGGGCGAGAGAGAGTATGGGAGTGGGTGA
1 GAGAGAGTGGGGCGAGAGGAGAGAGAGTAGGGCGAGAGAGAGTATGGGAGTGGGCGA
509613 GAGAGAGTGGGGCGAGAGGAGAGAGAGTAGGGCGAGAGAGAGTATGGGAGTGGGCGA
1 GAGAGAGTGGGGCGAGAGGAGAGAGAGTAGGGCGAGAGAGAGTATGGGAGTGGGCGA
*
509670 GAGAGAGTGGGGCAAGAG
1 GAGAGAGTGGGGCGAGAG
509688 AGTGGGGGAG
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 72 1.00
ACGTcount: A:0.30, C:0.05, G:0.56, T:0.10
Consensus pattern (57 bp):
GAGAGAGTGGGGCGAGAGGAGAGAGAGTAGGGCGAGAGAGAGTATGGGAGTGGGCGA
Found at i:509672 original size:35 final size:35
Alignment explanation
Indices: 509611--509734 Score: 107
Period size: 35 Copynumber: 3.6 Consensus size: 35
509601 GGGAGTGGGT
* * *
509611 GAGAGAGAGTGGGGCGAG-AGGAGAGAGAGTAGGGC
1 GAGAGAGAGTGTGG-GAGTGGGCGAGAGAGTAGGGC
* *
509646 GAGAGAGAGTATGGGAGTGGGCGAGAGAG-AGTGGG
1 GAGAGAGAGTGTGGGAGTGGGCGAGAGAGTAG-GGC
* *
509681 GCA-AGAGAGTGGGGGAGTGTGGTGAGAGAGT-GGGC
1 G-AGAGAGAGTGTGGGAGTG-GGCGAGAGAGTAGGGC
509716 --GAGAGAGTGTGGGAGTGGG
1 GAGAGAGAGTGTGGGAGTGGG
509735 GCAAGAGGAG
Statistics
Matches: 73, Mismatches: 10, Indels: 15
0.74 0.10 0.15
Matches are distributed among these distances:
32 2 0.03
33 15 0.21
34 5 0.07
35 40 0.55
36 11 0.15
ACGTcount: A:0.27, C:0.04, G:0.58, T:0.11
Consensus pattern (35 bp):
GAGAGAGAGTGTGGGAGTGGGCGAGAGAGTAGGGC
Found at i:509835 original size:22 final size:20
Alignment explanation
Indices: 508406--509880 Score: 249
Period size: 20 Copynumber: 74.0 Consensus size: 20
508396 GAGTGGGGCA
508406 AGAGAGTGGGGCGAGAGGAGAG
1 AGAGAGT-GGGCGAGA-GAGAG
*
508428 AGAGAGAGGGGCGAGAG-GAG
1 AGAGAG-TGGGCGAGAGAGAG
*
508448 AGAGAGTGGG-G-GTGAGAG
1 AGAGAGTGGGCGAGAGAGAG
508466 -GAGAGTGGGGCGAGAGGAGAG
1 AGAGAGT-GGGCGAGA-GAGAG
*
508487 AGAGAGTGGGGCGATAGAGAG
1 AGAGAGT-GGGCGAGAGAGAG
* *
508508 -G-GACGAGAG-GAGAGCA-AG
1 AGAGA-GTGGGCGAGAG-AGAG
*
508526 A-A-AGTGGGGCGAGAG-GAT
1 AGAGAGT-GGGCGAGAGAGAG
508544 AGAGAGTGGG-GAGAGAG-G
1 AGAGAGTGGGCGAGAGAGAG
* * *
508562 AGAGTG-GGGTGAGAGAGGAA
1 AGAGAGTGGGCGAGAGA-GAG
508582 AGAGAGTGGG-GCA-AGAG-G
1 AGAGAGTGGGCG-AGAGAGAG
*
508600 AGAGAGTGGGGGCA-AGAG-G
1 AGAGAGTGGGCG-AGAGAGAG
* *
508619 GGAGAGTGGGGCGAAAGAGAG
1 AGAGAGT-GGGCGAGAGAGAG
* *
508640 TG-GAGTGGG-GAGAGAGTG
1 AGAGAGTGGGCGAGAGAGAG
* * * * *
508658 -GGGCGAGAG-GAGAGAGTG
1 AGAGAGTGGGCGAGAGAGAG
*
508676 -GTA-ATTTGGGCGAGAG-GAG
1 AG-AGA-GTGGGCGAGAGAGAG
* *
508695 AGAGCGGGGGCGAGAG-GAG
1 AGAGAGTGGGCGAGAGAGAG
*
508714 AGAGAGTGGG-G-GTGAGAG
1 AGAGAGTGGGCGAGAGAGAG
** *
508732 -GAGAGTGGG-GCTAGA-TG
1 AGAGAGTGGGCGAGAGAGAG
* * *
508749 AGAGTG-GGGTGAGAGAGGAA
1 AGAGAGTGGGCGAGAGA-GAG
*
508769 AGAGAGTGGG-GCGAGAG-G
1 AGAGAGTGGGCGAGAGAGAG
*
508787 AGAGAGTGGG-GCGAGAGA-
1 AGAGAGTGGGCGAGAGAGAG
508805 AG-GAGTGGGGCGAGAG-GAG
1 AGAGAGT-GGGCGAGAGAGAG
* *
508824 AGAGTGTGGG-GCGAGAG-G
1 AGAGAGTGGGCGAGAGAGAG
*
508842 AGAGAGTGGGGCGATAGAGAG
1 AGAGAGT-GGGCGAGAGAGAG
* * * * * *
508863 TGGGAATGAGGAGAGAGTGTTGTG
1 AGAGAGTG-GGCGAGA--G-AGAG
508887 AGAGAGTGGG-GCA-AGAG-G
1 AGAGAGTGGGCG-AGAGAGAG
* * * * *
508905 -G-GTGTGGGAGTG-GGGCG
1 AGAGAGTGGGCGAGAGAGAG
508922 AGAGAGTGCGGGCGAGAGA-AG
1 AGAGAGT--GGGCGAGAGAGAG
* *
508943 AGGGAGTGGG-GCGAGAG-G
1 AGAGAGTGGGCGAGAGAGAG
* *
508961 AGAGAGTGGGGTGATAGAGAG
1 AGAGAGT-GGGCGAGAGAGAG
* *
508982 TGGGAGTGGGGCGAGGAGAGAG
1 AGAGAGT-GGGCGA-GAGAGAG
* *
509004 AGGCGATAGTGAGTG-GGGAGAGAG
1 A---GAGAGTG-G-GCGAGAGAGAG
* *
509028 -GAGAGTGGGGTGAGAGAGGAA
1 AGAGAGT-GGGCGAGAGA-GAG
*
509049 AGAGAGTGGG-GCGAGAG-G
1 AGAGAGTGGGCGAGAGAGAG
509067 AGAGAGTGGGGCGAGAG-GAG
1 AGAGAGT-GGGCGAGAGAGAG
509087 AGAGAGTGGGCCGAGAG-GAG
1 AGAGAGTGGG-CGAGAGAGAG
509107 A-AGGAGTGGGGCGAGAG-GAG
1 AGA-GAGT-GGGCGAGAGAGAG
*
509127 AGAGTGTGGGGCGAGAG-GAG
1 AGAGAGT-GGGCGAGAGAGAG
*
509147 A-AGGAGTGGGGCGATAGAGAG
1 AGA-GAGT-GGGCGAGAGAGAG
* * * *
509168 TGGGAATGGG-GAGAGAGTGTTGTG
1 AGAGAGTGGGCGAGAGA-----GAG
509192 AGAGAGTGGG-GCA-AGAG-G
1 AGAGAGTGGGCG-AGAGAGAG
* * * * *
509210 -G-GTGTGGGAGTG-GGGCG
1 AGAGAGTGGGCGAGAGAGAG
509227 AGAGAGTGCGGGCGAGAGA-AG
1 AGAGAGT--GGGCGAGAGAGAG
* *
509248 AGGGAGTGGG-GCGAGAG-G
1 AGAGAGTGGGCGAGAGAGAG
*
509266 AGAGAGTGGG-GCGAGAG-G
1 AGAGAGTGGGCGAGAGAGAG
*
509284 AGAGAGTGGGGCGATAGAGAG
1 AGAGAGT-GGGCGAGAGAGAG
* *
509305 TGGGAGTGGGGCGAGGAGAGAGTGTTGTG
1 AGAGAGT-GGGCGA-GAGAGA-------G
*
509334 AGGGAGTGGGGCGAG-GAGAG
1 AGAGAGT-GGGCGAGAGAGAG
*
509354 -G-GAGTGGG-GCGAGAG-G
1 AGAGAGTGGGCGAGAGAGAG
* * * * *
509370 -G-GTGTGGGAGTG-GGGCG
1 AGAGAGTGGGCGAGAGAGAG
* * * *
509387 AGAGAGTGGGGGAGTGTGGTG
1 AGAGAGTGGGCGAGAG-AGAG
* *
509408 AGATAGTGGGCGAGAGAGTGTGG
1 AGAGAGTGGGCGAGAGA--G-AG
*
509431 TGAGAGTGGGTCGAGAGAGAG
1 AGAGAGTGGG-CGAGAGAGAG
*
509452 AGTGTTGGAGTGGGGCGAGAG-GAG
1 A--G--AGAGT-GGGCGAGAGAGAG
509476 AGAGAGTGGGGCGAGAGGAGAG
1 AGAGAGT-GGGCGAGA-GAGAG
* * *
509498 AGACAG-GGGTGAGAGAGTG
1 AGAGAGTGGGCGAGAGAGAG
* *
509517 -G-G-GTGAGAGAG-GAGAG
1 AGAGAGTGGGCGAGAGAGAG
* * * *
509533 AGTGGGATGAGAG-GAGAGTGGTTG
1 AGAGAG-TG-G-GCGAGAG-AG-AG
*
509557 AGAGAGTGGGGCGAGTG-GAG
1 AGAGAGT-GGGCGAGAGAGAG
509577 AGAGAGTAGGGCGAGAGAGAG
1 AGAGAGT-GGGCGAGAGAGAG
* *
509598 TATGGGAGT--G-G-GTGAGAG
1 -A-GAGAGTGGGCGAGAGAGAG
*
509616 AGAGTG-GGGCGAGAG-GAG
1 AGAGAGTGGGCGAGAGAGAG
509634 AGAGAGTAGGGCGAGAGAGAG
1 AGAGAGT-GGGCGAGAGAGAG
*
509655 TATGGGAGTGGGCGAGAGAGAGTGGGG
1 -A-GAGAGTGGGCGAGAGAGA-----G
* * * *
509682 CAAGAGAGTGGGGGAGTGTGGTG
1 --AGAGAGTGGGCGAGAG-AGAG
*
509705 AGAGAGTGGGCGAGAGAGTG
1 AGAGAGTGGGCGAGAGAGAG
* * *
509725 TGGGAGTGGGGCAAGAG-GAG
1 AGAGAGT-GGGCGAGAGAGAG
** * *
509745 AGAGACAGGGTGAGAGAGTG
1 AGAGAGTGGGCGAGAGAGAG
* * *
509765 CGGGAGTGGG-GCGAGAG-G
1 AGAGAGTGGGCGAGAGAGAG
*
509783 AGAGAGT-GG-GA-TGAGAG
1 AGAGAGTGGGCGAGAGAGAG
**
509800 -GAGAGTGGTTGAGAGAGAAG
1 AGAGAGTGGGCGAGAGAG-AG
*
509820 AGAGAGTGGG-GCGAGAG-G
1 AGAGAGTGGGCGAGAGAGAG
509838 AGAGAGTAGGGCGAGAGAGAG
1 AGAGAGT-GGGCGAGAGAGAG
*
509859 TATGGGAGTGGGCGAGAGAGAG
1 -A-GAGAGTGGGCGAGAGAGAG
509881 TTGGGCGAGA
Statistics
Matches: 1084, Mismatches: 196, Indels: 346
0.67 0.12 0.21
Matches are distributed among these distances:
16 45 0.04
17 61 0.06
18 205 0.19
19 150 0.14
20 241 0.22
21 154 0.14
22 91 0.08
23 37 0.03
24 45 0.04
25 17 0.02
26 4 0.00
27 17 0.02
28 3 0.00
29 14 0.01
ACGTcount: A:0.28, C:0.04, G:0.58, T:0.10
Consensus pattern (20 bp):
AGAGAGTGGGCGAGAGAGAG
Found at i:509838 original size:55 final size:53
Alignment explanation
Indices: 509768--509902 Score: 157
Period size: 55 Copynumber: 2.5 Consensus size: 53
509758 GAGAGTGCGG
*
509768 GAGTGGGGCGAGAGGAGAGAGTGGGATGAGAG-GAGAGTGGTTGAGAGAG-AAGAGA
1 GAGTGGGGCGAGAGGAGAGAGTGGG-CGAGAGAGAGA-TGG--GAGAGAGCAAGAGA
* * *
509823 GAGTGGGGCGAGAGGAGAGAGTAGGGCGAGAGAGAGTATGGGAGTGGGCGAGAGA
1 GAGTGGGGCGAGAGGAGAGAGT-GGGCGAGAGAGAG-ATGGGAGAGAGCAAGAGA
*
509878 GAGTTGGGCGAGAGGAGAGAGTGGG
1 GAGTGGGGCGAGAGGAGAGAGTGGG
509903 GTAAGAGAAG
Statistics
Matches: 71, Mismatches: 5, Indels: 9
0.84 0.06 0.11
Matches are distributed among these distances:
54 8 0.11
55 53 0.75
56 9 0.13
57 1 0.01
ACGTcount: A:0.30, C:0.04, G:0.56, T:0.10
Consensus pattern (53 bp):
GAGTGGGGCGAGAGGAGAGAGTGGGCGAGAGAGAGATGGGAGAGAGCAAGAGA
Found at i:509881 original size:22 final size:22
Alignment explanation
Indices: 509841--509885 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
509831 CGAGAGGAGA
509841 GAGTAGGGCGAGAGAGAGTATGG
1 GAGTAGGGCGAGAGAGAGT-TGG
509864 GAGT-GGGCGAGAGAGAGTTGG
1 GAGTAGGGCGAGAGAGAGTTGG
509885 G
1 G
509886 CGAGAGGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 4 0.18
22 14 0.64
23 4 0.18
ACGTcount: A:0.27, C:0.04, G:0.56, T:0.13
Consensus pattern (22 bp):
GAGTAGGGCGAGAGAGAGTTGG
Found at i:509887 original size:15 final size:16
Alignment explanation
Indices: 509867--509896 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
509857 AGTATGGGAG
509867 TGGGCGAGA-GAGAGT
1 TGGGCGAGAGGAGAGT
509882 TGGGCGAGAGGAGAG
1 TGGGCGAGAGGAGAG
509897 AGTGGGGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.07, G:0.57, T:0.10
Consensus pattern (16 bp):
TGGGCGAGAGGAGAGT
Found at i:509897 original size:22 final size:22
Alignment explanation
Indices: 509845--509898 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
509835 AGGAGAGAGT
*
509845 AGGGCGAGAGAGAGTATGGGAG
1 AGGGAGAGAGAGAGTATGGGAG
* * *
509867 TGGGCGAGAGAGAGT-TGGGCG
1 AGGGAGAGAGAGAGTATGGGAG
509888 AGAGGAGAGAG
1 AG-GGAGAGAG
509899 TGGGGTAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 6 0.22
22 21 0.78
ACGTcount: A:0.30, C:0.06, G:0.56, T:0.09
Consensus pattern (22 bp):
AGGGAGAGAGAGAGTATGGGAG
Found at i:509909 original size:18 final size:18
Alignment explanation
Indices: 508067--509903 Score: 533
Period size: 18 Copynumber: 99.6 Consensus size: 18
508057 TAGGTGAGAG
* *
508067 GAGAGTGGAGTGAGAGGA
1 GAGAGTGGGGCGAGAGGA
*
508085 GA-A-TGGGGTGAGAGGA
1 GAGAGTGGGGCGAGAGGA
508101 GAGAGTGGGGCGAGAGGA
1 GAGAGTGGGGCGAGAGGA
508119 GAGAGTGGGGCGA-A--A
1 GAGAGTGGGGCGAGAGGA
*
508134 GAGAGT--GG-GACA-G-
1 GAGAGTGGGGCGAGAGGA
* *
508147 GAGAGTGGGGTGAGATAGTGT
1 GAGAGTGGGGCGAG--AG-GA
*
508168 GAAAGTGGGGCATGAGGAGAGA
1 GAGAGTGGGGC--GA-GAG-GA
*
508190 GAGTGGGAATTGGGGCGAGA-G-
1 GA----G-AGTGGGGCGAGAGGA
508211 G-GAGTGGGGCGAGAGGAGA
1 GAGAGTGGGGCGAGA-G-GA
*
508230 GAGAGAGGGGCGAGAGGAGA
1 GAGAGTGGGGCGAGA-G-GA
*
508250 GAGAGTGGGG-GTGA-GA
1 GAGAGTGGGGCGAGAGGA
508266 GGAGAGTGGGGCGAGAGGA
1 -GAGAGTGGGGCGAGAGGA
508285 GAGAGTGGGGCGAGAGGA
1 GAGAGTGGGGCGAGAGGA
508303 GAGAGTGGGGCGA-A--A
1 GAGAGTGGGGCGAGAGGA
*
508318 GAGAGT--GG-GACA-G-
1 GAGAGTGGGGCGAGAGGA
* *
508331 GAGAGTGGGGTGAGATAGTGT
1 GAGAGTGGGGCGAG--AG-GA
*
508352 GAAAGTGGGGC-ATGAGGA
1 GAGAGTGGGGCGA-GAGGA
* * * *
508370 GAGAGAGTGGG-AATTGGGGC
1 GAGAGTG-GGGCGA--GAGGA
* *
508390 GAGAG-GGAGTG-G-GGCAA
1 GAGAGTGGGGCGAGAGG--A
508407 GAGAGTGGGGCGAGAGGAGAGA
1 GAGAGTGGGGC--GA-GAG-GA
*
508429 GAGAGAGGGGCGAGAGGAGA
1 GAGAGTGGGGCGAGA-G-GA
*
508449 GAGAGTGGGG-GTGA-GA
1 GAGAGTGGGGCGAGAGGA
508465 GGAGAGTGGGGCGAGAGGAGAGA
1 -GAGAGTGGGGC--GA-GAG-GA
*
508488 GAGAGTGGGGCGATAGAGA
1 GAGAGTGGGGCGAGAG-GA
* * * *
508507 GGGACG-AGAG-GAGAGCAA
1 GAGA-GTGGGGCGAGAG-GA
*
508525 GAAAGTGGGGCGAGAGGATA
1 GAGAGTGGGGCGAGAGG--A
*
508545 GAGAGTGGGGAGAGAGGA
1 GAGAGTGGGGCGAGAGGA
* *
508563 GAGTG-GGGTGAGAGAGGAAA
1 GAGAGTGGG-GCGAGAGG--A
*
508583 GAGAGTGGGGCAAGAGGA
1 GAGAGTGGGGCGAGAGGA
* *
508601 GAGAGTGGGGGCAAGAGGG
1 GAGAGT-GGGGCGAGAGGA
508620 GAGAGTGGGGCGA-A--A
1 GAGAGTGGGGCGAGAGGA
* *
508635 GAGAGTGGAGTG-G-GGA
1 GAGAGTGGGGCGAGAGGA
508651 GAGAGTGGGGCGAGAGGA
1 GAGAGTGGGGCGAGAGGA
508669 GAGAGTGGTAATTTGGGCGAGAGGA
1 GAGAGT-G------GGGCGAGAGGA
*
508694 GAGAGCGGGGGCGAGAGGAGA
1 GAGAG-TGGGGCGAGA-G-GA
*
508715 GAGAGTGGGG-GTGA-GA
1 GAGAGTGGGGCGAGAGGA
* *
508731 GGAGAGTGGGGCTAGATGA
1 -GAGAGTGGGGCGAGAGGA
* *
508750 GAGTG-GGGTGAGAGAGGAAA
1 GAGAGTGGG-GCGAGAGG--A
508770 GAGAGTGGGGCGAGAGGA
1 GAGAGTGGGGCGAGAGGA
*
508788 GAGAGTGGGGCGAGAGAA
1 GAGAGTGGGGCGAGAGGA
508806 G-GAGTGGGGCGAGAGGA
1 GAGAGTGGGGCGAGAGGA
508823 GAGAGTGTGGGGCGAGAGGA
1 GAGA--GTGGGGCGAGAGGA
*
508843 GAGAGTGGGGC--GA-TA
1 GAGAGTGGGGCGAGAGGA
*
508858 GAGAGT-GGG-AATGAGGA
1 GAGAGTGGGGCGA-GAGGA
** *
508875 GAGAGT---G-TTG-TGA
1 GAGAGTGGGGCGAGAGGA
*
508888 GAGAGTGGGGCAAGAGG-
1 GAGAGTGGGGCGAGAGGA
* * *
508905 G-GTGTGGGAGTG-GGGCGA
1 GAGAGTGGG-GCGAGAG-GA
508923 GAGAGTGCGGGCGAGAGAAGA
1 GAGAGTG-GGGCGAGAG--GA
*
508944 GGGAGTGGGGCGAGAGGA
1 GAGAGTGGGGCGAGAGGA
* *
508962 GAGAGTGGGGTGATAGAGAGT
1 GAGAGTGGGGCG--AGAG-GA
*
508983 GGGAGTGGGGC--GAGGA
1 GAGAGTGGGGCGAGAGGA
* *
508999 GAGA--GAGGC--GA-TA
1 GAGAGTGGGGCGAGAGGA
* *
509012 GTGAGTGGGGAGAGAGGA
1 GAGAGTGGGGCGAGAGGA
* *
509030 GAGTG-GGGTGAGAGAGGAAA
1 GAGAGTGGG-GCGAGAGG--A
509050 GAGAGTGGGGCGAGAGGA
1 GAGAGTGGGGCGAGAGGA
509068 GAGAGTGGGGCGAGAGGAGA
1 GAGAGTGGGGCGAGA-G-GA
*
509088 GAGAGTGGGCCGAGAGGA
1 GAGAGTGGGGCGAGAGGA
509106 GAAGGAGTGGGGCGAGAGGA
1 G-A-GAGTGGGGCGAGAGGA
509126 GAGAGTGTGGGGCGAGAGGA
1 GAGA--GTGGGGCGAGAGGA
*
509146 GAAGGAGTGGGGCGATAGAGAGT
1 G-A-GAGTGGGGCG--AGAG-GA
* * *
509169 GGGAATGGGGAGAGAGTGTTGTGA
1 GAGAGTGGGGCGAGA-----G-GA
*
509193 GAGAGTGGGGCAAGAGG-
1 GAGAGTGGGGCGAGAGGA
* * *
509210 G-GTGTGGGAGTG-GGGCGA
1 GAGAGTGGG-GCGAGAG-GA
509228 GAGAGTGCGGGCGAGAGAAGA
1 GAGAGTG-GGGCGAGAG--GA
*
509249 GGGAGTGGGGCGAGAGGA
1 GAGAGTGGGGCGAGAGGA
509267 GAGAGTGGGGCGAGAGGA
1 GAGAGTGGGGCGAGAGGA
*
509285 GAGAGTGGGGCGATAGAGAGT
1 GAGAGTGGGGCG--AGAG-GA
*
509306 GGGAGTGGGGC--GAGGA
1 GAGAGTGGGGCGAGAGGA
** *
509322 GAGAGT--GTTGTGA-G-
1 GAGAGTGGGGCGAGAGGA
509336 G-GAGTGGGGCGAG-GAGA
1 GAGAGTGGGGCGAGAG-GA
*
509353 GGGAGTGGGGCGAGAGG-
1 GAGAGTGGGGCGAGAGGA
* * *
509370 G-GTGTGGGAGTG-GGGCGA
1 GAGAGTGGG-GCGAGAG-GA
*
509388 GAGAGTGGGG-GAGTGTGGTGA
1 GAGAGTGGGGCGA--G-AG-GA
* * *
509409 GATAGTGGGCGAGAGAGTGTGGT
1 GAGAGTGGG-GCGAGA----GGA
*
509432 GAGAGTGGGTCGAGAGAGA
1 GAGAGTGGGGCGAGAG-GA
509451 GAGTGTTGGAGTGGGGCGAGAGGAGA
1 GA------GAGTGGGGCGAGA-G-GA
509477 GAGAGTGGGGCGAGAGGA
1 GAGAGTGGGGCGAGAGGA
* *
509495 GAGAGACAGGGGTGAGA-GA
1 GAGAG--TGGGGCGAGAGGA
* * *
509514 GTG-G-GGTGAGAGAGGA
1 GAGAGTGGGGCGAGAGGA
**
509530 GAGAGTGGGATGAGA-G-
1 GAGAGTGGGGCGAGAGGA
**
509546 GAGAGT-----G-GTTGA
1 GAGAGTGGGGCGAGAGGA
*
509558 GAGAGTGGGGCGAGTGGAGA
1 GAGAGTGGGGCGAG-AG-GA
*
509578 GAGAGTAGGGCGAGA-GA
1 GAGAGTGGGGCGAGAGGA
* * *
509595 GAGTA-TGGGAGTGGGTGAGA
1 GAG-AGTGGG-GCGAGAG-GA
509615 GAGAGTGGGGCGAGAGGAGA
1 GAGAGTGGGGCGAGA-G-GA
*
509635 GAGAGTAGGGCGAGA-GA
1 GAGAGTGGGGCGAGAGGA
* * *
509652 GAGTA-TGGGAGTGGGCGAGA
1 GAG-AGTGGG-GCGAGAG-GA
509672 GAGAGTGGGGC-A-A-GA
1 GAGAGTGGGGCGAGAGGA
* * * *
509687 GAGTG-GGGGAGTGTGGTGA
1 GAGAGTGGGGCGAG-AG-GA
* *
509706 GAGAGTGGGCGAGAGAGTGT
1 GAGAGTGGG-GCGAGAG-GA
* *
509726 GGGAGTGGGGCAAGAGGA
1 GAGAGTGGGGCGAGAGGA
* * *
509744 GAGAGACAGGGTGAGAGAGTGC
1 GAGAG--TGGG-GCGAGAG-GA
*
509766 GGGAGTGGGGCGAGAGGA
1 GAGAGTGGGGCGAGAGGA
**
509784 GAGAGTGGGATGAGAGGA
1 GAGAGTGGGGCGAGAGGA
* * * * *
509802 GAGTGGTTGAGAGAGAAGA
1 GAG-AGTGGGGCGAGAGGA
509821 GAGAGTGGGGCGAGAGGA
1 GAGAGTGGGGCGAGAGGA
*
509839 GAGAGTAGGGCGAGA-GA
1 GAGAGTGGGGCGAGAGGA
* * *
509856 GAGTA-TGGGAGTGGGCGAGA
1 GAG-AGTGGG-GCGAGAG-GA
*
509876 GAGAGTTGGGCGAGAGGA
1 GAGAGTGGGGCGAGAGGA
509894 GAGAGTGGGG
1 GAGAGTGGGG
509904 TAAGAGAAGG
Statistics
Matches: 1375, Mismatches: 221, Indels: 446
0.67 0.11 0.22
Matches are distributed among these distances:
10 1 0.00
11 2 0.00
12 10 0.01
13 34 0.02
14 16 0.01
15 69 0.05
16 89 0.06
17 122 0.09
18 340 0.25
19 139 0.10
20 322 0.23
21 106 0.08
22 45 0.03
23 18 0.01
24 18 0.01
25 31 0.02
26 6 0.00
27 7 0.01
ACGTcount: A:0.28, C:0.04, G:0.57, T:0.10
Consensus pattern (18 bp):
GAGAGTGGGGCGAGAGGA
Found at i:510082 original size:18 final size:18
Alignment explanation
Indices: 510057--510124 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
510047 GCGAGAGATA
* *
510057 GAGAGAGTGGGGTGAGA-
1 GAGAGAGTGAGGCGAGAG
510074 GATGAGAGTGAGGCGAGAG
1 GA-GAGAGTGAGGCGAGAG
*
510093 GAGAGAGTGTGGCGAGAG
1 GAGAGAGTGAGGCGAGAG
* *
510111 GAGAAAGTGGGGCG
1 GAGAGAGTGAGGCG
510125 TATATACATG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
17 2 0.05
18 40 0.91
19 2 0.05
ACGTcount: A:0.29, C:0.04, G:0.56, T:0.10
Consensus pattern (18 bp):
GAGAGAGTGAGGCGAGAG
Found at i:510120 original size:16 final size:18
Alignment explanation
Indices: 510046--510114 Score: 59
Period size: 18 Copynumber: 3.7 Consensus size: 18
510036 CACAGCGAGG
*
510046 GGCGAGAGATAGAGAGAGT
1 GGCGAGAG-GAGAGAGAGT
* *
510065 GGGGTGA-GAGATGAGAGT
1 GGCGAGAGGAGA-GAGAGT
*
510083 GAGGCGAGAGGAGAGAGTGT
1 --GGCGAGAGGAGAGAGAGT
510103 GGCGAGAGGAGA
1 GGCGAGAGGAGA
510115 AAGTGGGGCG
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
17 3 0.08
18 18 0.45
19 5 0.12
20 10 0.25
21 4 0.10
ACGTcount: A:0.32, C:0.04, G:0.54, T:0.10
Consensus pattern (18 bp):
GGCGAGAGGAGAGAGAGT
Found at i:518618 original size:16 final size:16
Alignment explanation
Indices: 518599--518630 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
518589 AACGAATGCT
518599 GGAGAAAACGTACCCA
1 GGAGAAAACGTACCCA
518615 GGAGAAAACGTACCCA
1 GGAGAAAACGTACCCA
518631 ATTTATAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.25, G:0.25, T:0.06
Consensus pattern (16 bp):
GGAGAAAACGTACCCA
Found at i:518676 original size:31 final size:31
Alignment explanation
Indices: 518638--518699 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
518628 CCAATTTATA
*
518638 GGGTACGTTTTCTCCAGGAGAAAACGTACCC
1 GGGTACGTTTTCTCCAAGAGAAAACGTACCC
**
518669 GGGTACGTTTTCTTTAAGAGAAAACGTACCC
1 GGGTACGTTTTCTCCAAGAGAAAACGTACCC
518700 TATGGAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (31 bp):
GGGTACGTTTTCTCCAAGAGAAAACGTACCC
Found at i:519268 original size:16 final size:16
Alignment explanation
Indices: 519247--519295 Score: 98
Period size: 16 Copynumber: 3.1 Consensus size: 16
519237 GATTTTCATA
519247 GGGTACGTTTTCTCCT
1 GGGTACGTTTTCTCCT
519263 GGGTACGTTTTCTCCT
1 GGGTACGTTTTCTCCT
519279 GGGTACGTTTTCTCCT
1 GGGTACGTTTTCTCCT
519295 G
1 G
519296 ACTCCTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.06, C:0.24, G:0.27, T:0.43
Consensus pattern (16 bp):
GGGTACGTTTTCTCCT
Found at i:522332 original size:15 final size:16
Alignment explanation
Indices: 522297--522336 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
522287 TCAAAATCAG
*
522297 TTCGCTATATCCGTAAA
1 TTCGTTATATCCG-AAA
522314 TTCGTTATATCCG-AA
1 TTCGTTATATCCGAAA
522329 TTCGTTAT
1 TTCGTTAT
522337 TACCGTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.45
17 12 0.55
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.42
Consensus pattern (16 bp):
TTCGTTATATCCGAAA
Found at i:529451 original size:19 final size:19
Alignment explanation
Indices: 529429--529491 Score: 99
Period size: 19 Copynumber: 3.3 Consensus size: 19
529419 AAGGAAAGCT
*
529429 ATGAACCGAGTATAAAGGA
1 ATGAACCGAGTATAACGGA
*
529448 ATGATCCGAGTATAACGGA
1 ATGAACCGAGTATAACGGA
*
529467 ATGAACCGAGTATAACGAA
1 ATGAACCGAGTATAACGGA
529486 ATGAAC
1 ATGAAC
529492 TGGTTATAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.44, C:0.14, G:0.24, T:0.17
Consensus pattern (19 bp):
ATGAACCGAGTATAACGGA
Found at i:532083 original size:41 final size:42
Alignment explanation
Indices: 532038--532119 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 42
532028 TCTTTTTGTT
532038 TACATTGTTAAAATGTAATTTTCTTTT-TATACTTAATAATA
1 TACATTGTTAAAATGTAATTTTCTTTTCTATACTTAATAATA
* * *
532079 TACATTGTTAAAATGTATTTTTCTTTTCTTTTCTTAATAAT
1 TACATTGTTAAAATGTAATTTTCTTTTCTATACTTAATAAT
532120 TAAAAATTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
41 26 0.70
42 11 0.30
ACGTcount: A:0.32, C:0.09, G:0.05, T:0.55
Consensus pattern (42 bp):
TACATTGTTAAAATGTAATTTTCTTTTCTATACTTAATAATA
Found at i:534930 original size:12 final size:12
Alignment explanation
Indices: 534905--534942 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
534895 GTTGTCAGTC
534905 GTCCGTCCGTCT
1 GTCCGTCCGTCT
* *
534917 GTCTGTCTGTCT
1 GTCCGTCCGTCT
534929 GTCCGTCCGTCT
1 GTCCGTCCGTCT
534941 GT
1 GT
534943 AAACTTTTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.34, G:0.26, T:0.39
Consensus pattern (12 bp):
GTCCGTCCGTCT
Found at i:541611 original size:9 final size:9
Alignment explanation
Indices: 541589--541628 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
541579 ACAATTTGTC
541589 CGTTGTCTGT
1 CGTTGTC-GT
541599 CGTTGTCGT
1 CGTTGTCGT
*
541608 CGTTGGCGT
1 CGTTGTCGT
541617 CGTTGTCGT
1 CGTTGTCGT
541626 CGT
1 CGT
541629 CGTTTTAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
9 21 0.75
10 7 0.25
ACGTcount: A:0.00, C:0.23, G:0.35, T:0.42
Consensus pattern (9 bp):
CGTTGTCGT
Found at i:542233 original size:166 final size:163
Alignment explanation
Indices: 541798--542689 Score: 864
Period size: 166 Copynumber: 5.5 Consensus size: 163
541788 TTTGTATTTT
* * * * * * * *
541798 TCTTCAAAAATCTTCTTC-CCAAAACTATTCGGCC-TGAAAAGCTTAAACTTGTGTGGAAGCATC
1 TCTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAAG-AAAGCTCAAATTTGAGTGAAAGCATC
* * * *
541861 CTCAGGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGAGGGACCACAAGA
65 CTCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAA-T
* * * *
541926 GGGGGATCAAGTTTTACAGAGGAATATATAGAG----
129 GGGGGAT-AAATTTTA-ACATGTATATATAGAGAAAA
* * * * * *
541959 ------AAAATCTTCTTCTCAAAAACTATAAGGCCAAGAAAGCTCAAAATGGCGTGTAACCATCC
1 TCTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAAGAAAGCTCAAATTTGAGTGAAAGCATCC
* * * * * *
542018 TCAGATAATGTAGATTAAAGTTTGTTCTAATCATGGTCCCCGGGGGTAGGGAGGGACCACAAGAG
66 TCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAA-TG
** * * * *
542083 GGGGACCAAGTTTAACATAGGAATATATTGAAAAAA
130 GGGGATAAATTTTAACAT--GTATATATAGAGAAAA
*
542119 TCTTTAAAAATCTTCTTCTCAAATACTATTAGGCCAAGAAAGCTCAAATTTGAGTGAAAGCATCC
1 TCTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAAGAAAGCTCAAATTTGAGTGAAAGCATCC
*
542184 TCAGATAGTGTAGATTCAAGTTTGTTCAAATCGTGGTCCCCGGGGGTAGGGTGGGGCCACAATTG
66 TCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAA-TG
542249 GGGGATAAATTTTCATACATGTATATATAGAGAAAA
130 GGGGATAAATTTT-A-ACATGTATATATAGAGAAAA
* * * *
542285 TCTTTAAAAATCGTCTTCTCAAAAACTATTAGGCCAAGAAAGCTCAAATTGGCGTGTAA-CTATC
1 TCTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAAGAAAGCTCAAATTTGAGTGAAAGC-ATC
* * * *
542349 ATCAGATAGTGTAGATTCAGGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGCGGGGCCACAATG
65 CTCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATG
542414 GGGGATAAA-TTT----T-TATATATAGAGAAAA
130 GGGGATAAATTTTAACATGTATATATAGAGAAAA
* * * *
542442 TCTTTAAAAATCTTCTTCTC-AAAACTATTAGGTCAGGAAAGCCCAAATTTGAGTGGAAGCATCC
1 TCTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAAGAAAGCTCAAATTTGAGTGAAAGCATCC
* * * * * * *
542506 -CAGATCGTATAGATTCAAGTTTGTTTAAATAATAGT--CCAGGGGTAGGGTGAGGCCACAATGG
66 TCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATGG
* *
542568 GGGATGAATTTTTACATAG-ATATATAGAGAAAA
131 GGGATAAATTTTAACAT-GTATATATAGAGAAAA
* * * * * * * *
542601 TCTTTAAAAATCTTCTTTTTAAAGACTATTTGGCC-AGAAAAGCTTAAACTTGTGT-AGAGGCAT
1 TCTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAAG-AAAGCTCAAATTTGAGTGA-AAGCAT
* * *
542664 CCTCGGGTAGTGTAAATTCAAGTTTG
64 CCTCAGATAGTGTAGATTCAAGTTTG
542690 CAAAATCACA
Statistics
Matches: 613, Mismatches: 89, Indels: 58
0.81 0.12 0.08
Matches are distributed among these distances:
153 29 0.05
154 5 0.01
155 47 0.08
156 145 0.24
157 36 0.06
158 2 0.00
159 33 0.05
160 31 0.05
161 18 0.03
164 3 0.00
165 12 0.02
166 247 0.40
167 1 0.00
168 4 0.01
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (163 bp):
TCTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAAGAAAGCTCAAATTTGAGTGAAAGCATCC
TCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATGG
GGGATAAATTTTAACATGTATATATAGAGAAAA
Found at i:542254 original size:322 final size:308
Alignment explanation
Indices: 541798--542604 Score: 911
Period size: 322 Copynumber: 2.5 Consensus size: 308
541788 TTTGTATTTT
* * * * * * *
541798 TCTTCAAAAATCTTCTTCCCAAAACTATTCGGCC-TGAAAAGCTTAAACTTGTGTGGAAGCATCC
1 TCTTTAAAAATCTTCTTCTCAAAACTATTAGGCCAAG-AAAGCTCAAATTTGAGTGGAAGCATCC
* * * *
541862 TCAGGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGAGGGACCACAAGAG
65 TCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAA-TG
* *
541927 GGGGATCAAGTTTTACAGAGGAATATATAGAGAAAATCTTCTTCTCAAAAACTATAAGGCCAAGA
129 GGGGAT-AAATTTTACACA-G-ATATATAGAGAAAATCTTCTTCTCAAAAACTATAAGGCCAAGA
* *
541992 AAGCTCAAAATGGCGTGTAACCATCCTCAGATAATGTAGATTAAAGTTTGTTCTAATCATGGTCC
191 AAGCTCAAAATGGCGTGTAACCATCATCAGATAATGTAGATTAAAGTTTGTTCAAATCATGGTCC
* *
542057 CCGGGGGTAGGGAGGGACCACAAGAGGGGGACCAAGTTTAACATAGGAATATATTGAAAAAA
256 CCGGGGGTAGGGAGGGACCACAA-AGGGGGA-CAAATTT----T---AATATATAGAAAAAA
*
542119 TCTTTAAAAATCTTCTTCTCAAATACTATTAGGCCAAGAAAGCTCAAATTTGAGTGAAAGCATCC
1 TCTTTAAAAATCTTCTTCTCAAA-ACTATTAGGCCAAGAAAGCTCAAATTTGAGTGGAAGCATCC
*
542184 TCAGATAGTGTAGATTCAAGTTTGTTCAAATCGTGGTCCCCGGGGGTAGGGTGGGGCCACAATTG
65 TCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAA-TG
*
542249 GGGGATAAATTTTCATACATGTATATATAGAGAAAATCTTTAAAAATCGTCTTCTCAAAAACTAT
129 GGGGATAAATTTT-ACACA-G-ATATATAGAGAAAATC--------T--TCTTCTCAAAAACTAT
* * * * * *
542314 TAGGCCAAGAAAGCTCAAATTGGCGTGTAACTATCATCAGATAGTGTAGATTCAGGTTTGTTCAA
181 AAGGCCAAGAAAGCTCAAAATGGCGTGTAACCATCATCAGATAATGTAGATTAAAGTTTGTTCAA
* * * * * * *
542379 ATCATGGTCCCTGGGGGTAGGGCGGGGCCACAATGGGGGATAAATTTTTATATATAGAGAAAA
246 ATCATGGTCCCCGGGGGTAGGGAGGGACCACAAAGGGGGACAAATTTTAATATATAGAAAAAA
* * *
542442 TCTTTAAAAATCTTCTTCTCAAAACTATTAGGTCAGGAAAGCCCAAATTTGAGTGGAAGCATCC-
1 TCTTTAAAAATCTTCTTCTCAAAACTATTAGGCCAAGAAAGCTCAAATTTGAGTGGAAGCATCCT
* * * * * * *
542506 CAGATCGTATAGATTCAAGTTTGTTTAAATAATAGT--CCAGGGGTAGGGTGAGGCCACAATGGG
66 CAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATGGG
* *
542569 GGATGAATTTTTACATAGATATATAGAGAAAATCTT
131 GGAT-AAATTTTACACAGATATATAGAGAAAATCTT
542605 TAAAAATCTT
Statistics
Matches: 421, Mismatches: 51, Indels: 43
0.82 0.10 0.08
Matches are distributed among these distances:
306 1 0.00
308 1 0.00
316 16 0.04
317 1 0.00
318 11 0.03
319 27 0.06
321 57 0.14
322 155 0.37
323 36 0.09
326 1 0.00
330 6 0.01
331 6 0.01
332 103 0.24
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (308 bp):
TCTTTAAAAATCTTCTTCTCAAAACTATTAGGCCAAGAAAGCTCAAATTTGAGTGGAAGCATCCT
CAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATGGG
GGATAAATTTTACACAGATATATAGAGAAAATCTTCTTCTCAAAAACTATAAGGCCAAGAAAGCT
CAAAATGGCGTGTAACCATCATCAGATAATGTAGATTAAAGTTTGTTCAAATCATGGTCCCCGGG
GGTAGGGAGGGACCACAAAGGGGGACAAATTTTAATATATAGAAAAAA
Found at i:542744 original size:316 final size:318
Alignment explanation
Indices: 541798--542721 Score: 805
Period size: 322 Copynumber: 2.9 Consensus size: 318
541788 TTTGTATTTT
* * * * ** * * *
541798 TCTTCAAAAATCTTCTTCCCAAA-ACTATTCGGCC-TGAAAAGCTTAAACTTGTGTGGAAGCATC
1 TCTTTAAAAATCTTCTTCTCAAATACTATTAGGCCAAG-AAAGCCCAAATTTGAGTGAAAGCATC
* * * * * * *
541861 CTCAGGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGAG-GGACCACAAG
65 CTCAGATAGTATAGATTCAAGTTTGTTCAAATAATAGT-CCCAGGGGTAGGGTGAGG-CCACAAT
* * * * * *
541925 AGGGGGATCAAGTTTTACAGAGGAATATATAGAGAAAATC--------T--TCTTCTCAAAAACT
128 TGGGGGAT-AAATTTTATACATGTATATATAGAGAAAATCTTTAAAAATCGTCTTCTCAAAAACT
* * * * * * *
541980 ATAAGGCCAAGAAAGCTCAAAATGGCGTGTAACCATCCTCAGATAATGTAGATTAAAGTTTGTTC
192 ATTAGGCCAAGAAAGCTC-AAATTG-GTGTAACTATCATCAGATAGTGTAAATTCAAGTTTG-TC
* ** ** * * * * * *
542045 TAATCATGGTCCCCGGGGGTAGGGAGGGACCACAAGAGGGGGACCAAGTTTAACATAGGAATATA
254 AAATCACAGTCCCTAGGGGTAGGGCGGGGCCACAA-TGGGGGA-TAAATTT----T---TATATA
*
542110 TTGAAAAAA
310 TAGAAAAAA
*
542119 TCTTTAAAAATCTTCTTCTCAAATACTATTAGGCCAAGAAAGCTCAAATTTGAGTGAAAGCATCC
1 TCTTTAAAAATCTTCTTCTCAAATACTATTAGGCCAAGAAAGCCCAAATTTGAGTGAAAGCATCC
* ** * * *
542184 TCAGATAGTGTAGATTCAAGTTTGTTCAAATCGTGGTCCCCGGGGGTAGGGTGGGGCCACAATTG
66 TCAGATAGTATAGATTCAAGTTTGTTCAAATAATAGT-CCCAGGGGTAGGGTGAGGCCACAATTG
542249 GGGGATAAATTTTCATACATGTATATATAGAGAAAATCTTTAAAAATCGTCTTCTCAAAAACTAT
130 GGGGATAAATTTT-ATACATGTATATATAGAGAAAATCTTTAAAAATCGTCTTCTCAAAAACTAT
* *
542314 TAGGCCAAGAAAGCTCAAATTGGCGTGTAACTATCATCAGATAGTGTAGATTCAGGTTTGTTCAA
194 TAGGCCAAGAAAGCTCAAATT-G-GTGTAACTATCATCAGATAGTGTAAATTCAAGTTTG-TCAA
** * *
542379 ATCATGGTCCCTGGGGGTAGGGCGGGGCCACAATGGGGGATAAATTTTTATATATAGAGAAAA
256 ATCACAGTCCCTAGGGGTAGGGCGGGGCCACAATGGGGGATAAATTTTTATATATAGAAAAAA
* * *
542442 TCTTTAAAAATCTTCTTCTCAAA-ACTATTAGGTCAGGAAAGCCCAAATTTGAGTGGAAGCATCC
1 TCTTTAAAAATCTTCTTCTCAAATACTATTAGGCCAAGAAAGCCCAAATTTGAGTGAAAGCATCC
* *
542506 -CAGATCGTATAGATTCAAGTTTGTTTAAATAATAGT-CCAGGGGTAGGGTGAGGCCACAA-TGG
66 TCAGATAGTATAGATTCAAGTTTGTTCAAATAATAGTCCCAGGGGTAGGGTGAGGCCACAATTGG
* * * * *
542568 GGGATGAATTTT-TACATAG-ATATATAGAGAAAATCTTTAAAAATCTTCTTTTTAAAGACTATT
131 GGGATAAATTTTATACAT-GTATATATAGAGAAAATCTTTAAAAATCGTCTTCTCAAAAACTATT
* * * * *
542631 TGGCC-AGAAAAGCTTAAACTT-GTGTAGAGGC-ATCCTCGGGTAGTGTAAATTCAAGTTTG-CA
195 AGGCCAAG-AAAGCTCAAA-TTGGTGTA-A--CTATCATCAGATAGTGTAAATTCAAGTTTGTC-
*
542692 AAATCACAGTCCCTAGTGGTAGGGCGGGGC
254 AAATCACAGTCCCTAGGGGTAGGGCGGGGC
542722 TGTGATGGCG
Statistics
Matches: 518, Mismatches: 63, Indels: 50
0.82 0.10 0.08
Matches are distributed among these distances:
314 6 0.01
315 29 0.06
316 81 0.16
317 4 0.01
318 14 0.03
319 21 0.04
321 57 0.11
322 153 0.30
323 38 0.07
326 1 0.00
330 6 0.01
331 10 0.02
332 98 0.19
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (318 bp):
TCTTTAAAAATCTTCTTCTCAAATACTATTAGGCCAAGAAAGCCCAAATTTGAGTGAAAGCATCC
TCAGATAGTATAGATTCAAGTTTGTTCAAATAATAGTCCCAGGGGTAGGGTGAGGCCACAATTGG
GGGATAAATTTTATACATGTATATATAGAGAAAATCTTTAAAAATCGTCTTCTCAAAAACTATTA
GGCCAAGAAAGCTCAAATTGGTGTAACTATCATCAGATAGTGTAAATTCAAGTTTGTCAAATCAC
AGTCCCTAGGGGTAGGGCGGGGCCACAATGGGGGATAAATTTTTATATATAGAAAAAA
Found at i:551607 original size:2 final size:2
Alignment explanation
Indices: 551600--551638 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
551590 TGAGTATGAC
*
551600 GA GA GA GA GA GA GA GA GA GG GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
551639 CACCTTTCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
GA
Found at i:552126 original size:2 final size:2
Alignment explanation
Indices: 552119--552170 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
552109 CAAAAACAAA
552119 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
552161 TC TC TC TC TC
1 TC TC TC TC TC
552171 ATAGGGAGCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:554036 original size:23 final size:24
Alignment explanation
Indices: 553991--554037 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
553981 GGCATCTACA
* *
553991 GGGTAATTGTTTTCTTAAAACTAT
1 GGGTAATTGTCTTCGTAAAACTAT
554015 GGGTAATT-TCTTCGTAAAACTAT
1 GGGTAATTGTCTTCGTAAAACTAT
554038 ATTTCCCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.43
Consensus pattern (24 bp):
GGGTAATTGTCTTCGTAAAACTAT
Found at i:556106 original size:8 final size:8
Alignment explanation
Indices: 556093--556121 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
556083 TTTTAGAAGC
556093 AAAAAAAT
1 AAAAAAAT
556101 AAAAAAAT
1 AAAAAAAT
556109 AAAAAAAT
1 AAAAAAAT
556117 AAAAA
1 AAAAA
556122 TAAAATCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:556132 original size:14 final size:14
Alignment explanation
Indices: 556093--556126 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 14
556083 TTTTAGAAGC
556093 AAAAAAATAAAAAAAT
1 AAAAAAAT--AAAAAT
556109 AAAAAAATAAAAAT
1 AAAAAAATAAAAAT
556123 AAAA
1 AAAA
556127 TCATAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
16 8 0.44
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (14 bp):
AAAAAAATAAAAAT
Found at i:558563 original size:20 final size:19
Alignment explanation
Indices: 558508--558564 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
558498 TTACCTTTCA
558508 AAAATAA-ATTCCTATAGG
1 AAAATAATATTCCTATAGG
* *
558526 AAAATAATTTTCCCATAGG
1 AAAATAATATTCCTATAGG
558545 AAAATCAATATTCCTATAGG
1 AAAAT-AATATTCCTATAGG
558565 TAATTTGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.21
19 14 0.42
20 12 0.36
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (19 bp):
AAAATAATATTCCTATAGG
Found at i:558727 original size:20 final size:20
Alignment explanation
Indices: 558688--558727 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
558678 TGAATCAAAT
* *
558688 TCCTAGAGGAATTATCATTC
1 TCCTAGAGGAAATATAATTC
*
558708 TCCTATAGGAAATATAATTC
1 TCCTAGAGGAAATATAATTC
558728 CTACAGGACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (20 bp):
TCCTAGAGGAAATATAATTC
Found at i:558735 original size:18 final size:19
Alignment explanation
Indices: 558685--558735 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 19
558675 GTCTGAATCA
* *
558685 AATTCCTAGAGGAATTATC
1 AATTCCTACAGGAAATATC
* *
558704 ATTCTCCTATAGGAAATAT-
1 AAT-TCCTACAGGAAATATC
558723 AATTCCTACAGGA
1 AATTCCTACAGGA
558736 CTTTTAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 9 0.35
19 4 0.15
20 13 0.50
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (19 bp):
AATTCCTACAGGAAATATC
Found at i:560420 original size:2 final size:2
Alignment explanation
Indices: 560413--560461 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
560403 CATGGAAGTC
560413 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
560455 AG AG AG A
1 AG AG AG A
560462 TTAATCTATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:560964 original size:2 final size:2
Alignment explanation
Indices: 560957--561018 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
560947 GAATAAACAC
*
560957 GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
560999 GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA
561019 ATATTATTAC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:562682 original size:10 final size:10
Alignment explanation
Indices: 562669--562695 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
562659 CCCCCCCCAA
562669 AAAAAAAAAT
1 AAAAAAAAAT
562679 AAAAAAAAAT
1 AAAAAAAAAT
562689 AAAAAAA
1 AAAAAAA
562696 TATCTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (10 bp):
AAAAAAAAAT
Found at i:564694 original size:16 final size:16
Alignment explanation
Indices: 564673--564707 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
564663 GTTTCAGACA
564673 AAAATGAGGAATTCTC
1 AAAATGAGGAATTCTC
564689 AAAATGAGGAATTCTC
1 AAAATGAGGAATTCTC
564705 AAA
1 AAA
564708 TATGTGTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.11, G:0.17, T:0.23
Consensus pattern (16 bp):
AAAATGAGGAATTCTC
Found at i:566721 original size:2 final size:2
Alignment explanation
Indices: 566714--566765 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
566704 TGCATAAATG
566714 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
566756 GA GA GA GA GA
1 GA GA GA GA GA
566766 ATTACATAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:571529 original size:21 final size:21
Alignment explanation
Indices: 571505--571575 Score: 115
Period size: 21 Copynumber: 3.4 Consensus size: 21
571495 GTGCTTGTTT
* *
571505 TGGGGTGGGGTGGTCGGACGG
1 TGGGGTGGGGTAGTCGGACCG
*
571526 TGGGGTGGGGTAGTCGGACCA
1 TGGGGTGGGGTAGTCGGACCG
571547 TGGGGTGGGGTAGTCGGACCG
1 TGGGGTGGGGTAGTCGGACCG
571568 TGGGGTGG
1 TGGGGTGG
571576 CCGTCCTAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.08, C:0.11, G:0.61, T:0.20
Consensus pattern (21 bp):
TGGGGTGGGGTAGTCGGACCG
Found at i:572828 original size:18 final size:18
Alignment explanation
Indices: 572801--572835 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
572791 AGCTGCCTTA
*
572801 TGTGGCTATTTCTTATGC
1 TGTGGCTATTTCATATGC
*
572819 TGTGGTTATTTCATATG
1 TGTGGCTATTTCATATG
572836 AAGATGGTGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.11, G:0.23, T:0.51
Consensus pattern (18 bp):
TGTGGCTATTTCATATGC
Found at i:572857 original size:21 final size:21
Alignment explanation
Indices: 572831--573062 Score: 225
Period size: 21 Copynumber: 11.3 Consensus size: 21
572821 TGGTTATTTC
572831 ATATGAAGATGGTGCTTTATT
1 ATATGAAGATGGTGCTTTATT
*
572852 GTATGAAGATGGTGCTTTATT
1 ATATGAAGATGGTGCTTTATT
*
572873 ATATGAAGATGGTG-TTTTTT
1 ATATGAAGATGGTGCTTTATT
572893 ATATGAAGATGGTGC-TTATTT
1 ATATGAAGATGGTGCTTTA-TT
572914 ATATGAAGATGGTGCTTTAATT
1 ATATGAAGATGGTGCTTT-ATT
572936 ATATGAAGATGGTGC-TT-TT
1 ATATGAAGATGGTGCTTTATT
*
572955 -TATG-TGATGGTGCTTT-TT
1 ATATGAAGATGGTGCTTTATT
* *
572973 -TATG-CGATTGTGCTTT-TT
1 ATATGAAGATGGTGCTTTATT
* * ** *
572991 CATGTTAAAAGGGGGTGCTTTTTT
1 -AT-AT-GAAGATGGTGCTTTATT
*
573015 ACATGAAGATGGTGCTTTATT
1 ATATGAAGATGGTGCTTTATT
*
573036 ATATGAAAATGGTGCTATT-TT
1 ATATGAAGATGGTGCT-TTATT
573057 ATATGA
1 ATATGA
573063 TGGTGCTTTT
Statistics
Matches: 178, Mismatches: 21, Indels: 24
0.80 0.09 0.11
Matches are distributed among these distances:
17 8 0.04
18 24 0.13
19 2 0.01
20 22 0.12
21 88 0.49
22 22 0.12
23 10 0.06
24 2 0.01
ACGTcount: A:0.25, C:0.06, G:0.25, T:0.44
Consensus pattern (21 bp):
ATATGAAGATGGTGCTTTATT
Found at i:572907 original size:41 final size:42
Alignment explanation
Indices: 572831--573062 Score: 232
Period size: 41 Copynumber: 5.6 Consensus size: 42
572821 TGGTTATTTC
* *
572831 ATATGAAGATGGTGCTTTATTGTATGAAGATGGTGCTTTATT
1 ATATGAAGATGGTGCTTTTTTATATGAAGATGGTGCTTTATT
572873 ATATGAAGATGGTG-TTTTTTATATGAAGATGGTGC-TTATTT
1 ATATGAAGATGGTGCTTTTTTATATGAAGATGGTGCTTTA-TT
*
572914 ATATGAAGATGGTGCTTTAATTATATGAAGATGGTGC-TT-TT
1 ATATGAAGATGGTGCTTT-TTTATATGAAGATGGTGCTTTATT
* * *
572955 -TATG-TGATGGTGC-TTTTT-TATG-CGATTGTGCTTT-TT
1 ATATGAAGATGGTGCTTTTTTATATGAAGATGGTGCTTTATT
* * ** *
572991 CATGTTAAAAGGGGGTGCTTTTTTACATGAAGATGGTGCTTTATT
1 -AT-AT-GAAGATGGTGCTTTTTTATATGAAGATGGTGCTTTATT
* *
573036 ATATGAAAATGGTGCTATTTTATATGA
1 ATATGAAGATGGTGCTTTTTTATATGA
573063 TGGTGCTTTT
Statistics
Matches: 155, Mismatches: 22, Indels: 26
0.76 0.11 0.13
Matches are distributed among these distances:
35 7 0.05
36 8 0.05
37 2 0.01
38 3 0.02
39 9 0.06
40 7 0.05
41 43 0.28
42 39 0.25
43 23 0.15
44 12 0.08
45 2 0.01
ACGTcount: A:0.25, C:0.06, G:0.25, T:0.44
Consensus pattern (42 bp):
ATATGAAGATGGTGCTTTTTTATATGAAGATGGTGCTTTATT
Found at i:572965 original size:17 final size:17
Alignment explanation
Indices: 572943--572995 Score: 70
Period size: 18 Copynumber: 3.0 Consensus size: 17
572933 ATTATATGAA
572943 GATGGTGCTTTTTATGT
1 GATGGTGCTTTTTATGT
*
572960 GATGGTGCTTTTTTATGC
1 GATGGTGC-TTTTTATGT
*
572978 GATTGTGCTTTTTCATGT
1 GATGGTGCTTTTT-ATGT
572996 TAAAAGGGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 13 0.42
18 18 0.58
ACGTcount: A:0.11, C:0.09, G:0.26, T:0.53
Consensus pattern (17 bp):
GATGGTGCTTTTTATGT
Found at i:573530 original size:21 final size:18
Alignment explanation
Indices: 573486--573677 Score: 79
Period size: 21 Copynumber: 9.7 Consensus size: 18
573476 CCTTCACAGT
573486 AAAAAGCACCATCATATA
1 AAAAAGCACCATCATATA
*
573504 AAAAAGCACCATCTTCATA
1 AAAAAGCACCATCAT-ATA
* *
573523 AAATA--A--AGCATATA
1 AAAAAGCACCATCATATA
*
573537 ATAAAGCACCATCTTCATATA
1 AAAAAGCACCA---TCATATA
*
573558 ATAAAGCACCACCTTCATATA
1 AAAAAGCACCA---TCATATA
573579 ATAAAA-CACCATCTTCATATA
1 A-AAAAGCACCA---TCATATA
*
573600 ATAAAGCACCATCTTCATATA
1 AAAAAGCACCA---TCATATA
573621 TAATAAAGCACCACCCTCATATA
1 -AA-AAAGCACCA---TCATATA
*
573644 ACAAAGCACCACCCTCATATA
1 AAAAAGCACCA---TCATATA
*
573665 ATAAAGCACCATC
1 AAAAAGCACCATC
573678 TTCACATGAA
Statistics
Matches: 146, Mismatches: 16, Indels: 24
0.78 0.09 0.13
Matches are distributed among these distances:
14 6 0.04
15 3 0.02
16 1 0.01
17 1 0.01
18 17 0.12
19 7 0.05
20 3 0.02
21 86 0.59
22 5 0.03
23 17 0.12
ACGTcount: A:0.47, C:0.26, G:0.05, T:0.22
Consensus pattern (18 bp):
AAAAAGCACCATCATATA
Found at i:573535 original size:33 final size:33
Alignment explanation
Indices: 573498--573565 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
573488 AAAGCACCAT
573498 CATATAAAAAAGCACCATCTTCATAAAATAAAG
1 CATATAAAAAAGCACCATCTTCATAAAATAAAG
* *
573531 CATATAATAAAGCACCATCTTCATATAATAAAG
1 CATATAAAAAAGCACCATCTTCATAAAATAAAG
573564 CA
1 CA
573566 CCACCTTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.51, C:0.19, G:0.06, T:0.24
Consensus pattern (33 bp):
CATATAAAAAAGCACCATCTTCATAAAATAAAG
Found at i:573578 original size:42 final size:42
Alignment explanation
Indices: 573531--573681 Score: 230
Period size: 42 Copynumber: 3.5 Consensus size: 42
573521 TAAAATAAAG
573531 CATATAATAAAGCACCATCTTCATATAATAAAGCACCACCTT
1 CATATAATAAAGCACCATCTTCATATAATAAAGCACCACCTT
* *
573573 CATATAATAAAACACCATCTTCATATAATAAAGCACCATCTT
1 CATATAATAAAGCACCATCTTCATATAATAAAGCACCACCTT
* * * *
573615 CATATATAATAAAGCACCACCCTCATATAACAAAGCACCACCCT
1 C--ATATAATAAAGCACCATCTTCATATAATAAAGCACCACCTT
573659 CATATAATAAAGCACCATCTTCA
1 CATATAATAAAGCACCATCTTCA
573682 CATGAAATAA
Statistics
Matches: 97, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
42 61 0.63
44 36 0.37
ACGTcount: A:0.44, C:0.28, G:0.04, T:0.25
Consensus pattern (42 bp):
CATATAATAAAGCACCATCTTCATATAATAAAGCACCACCTT
Found at i:573691 original size:65 final size:64
Alignment explanation
Indices: 573531--573691 Score: 243
Period size: 65 Copynumber: 2.5 Consensus size: 64
573521 TAAAATAAAG
* * * *
573531 CATATAATAAAGCACCATCTTCATAT-AATAAAGCACCACCTTCATATAATAAAACACCATCTT
1 CATATAATAAAGCACCATCTTCATATAAATAAAGCACCACCCTCATATAACAAAACACCACCCT
*
573594 CATATAATAAAGCACCATCTTCATATATAATAAAGCACCACCCTCATATAACAAAGCACCACCCT
1 CATATAATAAAGCACCATCTTCATATA-AATAAAGCACCACCCTCATATAACAAAACACCACCCT
*
573659 CATATAATAAAGCACCATCTTCACATGAAATAA
1 CATATAATAAAGCACCATCTTCATAT-AAATAA
573692 CCACAGCATA
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
63 26 0.29
65 62 0.70
66 1 0.01
ACGTcount: A:0.45, C:0.27, G:0.04, T:0.24
Consensus pattern (64 bp):
CATATAATAAAGCACCATCTTCATATAAATAAAGCACCACCCTCATATAACAAAACACCACCCT
Found at i:581724 original size:2 final size:2
Alignment explanation
Indices: 581717--581756 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
581707 TATAGTTAGT
581717 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
581757 ATCCATTACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:582097 original size:16 final size:15
Alignment explanation
Indices: 582080--582387 Score: 351
Period size: 16 Copynumber: 19.7 Consensus size: 15
582070 CGTATTTTTG
*
582080 TACTATATCATTTATG
1 TACTA-ATCATTTATA
*
582096 TACTAAATCACTTATA
1 TACT-AATCATTTATA
582112 TACTGAATCATTTATA
1 TACT-AATCATTTATA
582128 TACTGAATCATTTATA
1 TACT-AATCATTTATA
582144 TACTGAATCATTTATA
1 TACT-AATCATTTATA
*
582160 TACTAAATCATTTGTA
1 TACT-AATCATTTATA
582176 TACTATATCATTTATA
1 TACTA-ATCATTTATA
582192 TACTGAATCATTTATA
1 TACT-AATCATTTATA
582208 TACTAAATCATTTATA
1 TACT-AATCATTTATA
582224 TACTGAATCATTTATA
1 TACT-AATCATTTATA
582240 TACTGAATCATTTATA
1 TACT-AATCATTTATA
*
582256 TACTAAATCATTTGTA
1 TACT-AATCATTTATA
582272 TACTAAATCATTTATA
1 TACT-AATCATTTATA
*
582288 TACTGAATCATTAATA
1 TACT-AATCATTTATA
582304 TACTAAATCATTTATA
1 TACT-AATCATTTATA
582320 TACT-A--A---AT-
1 TACTAATCATTTATA
582328 TACTGAATCATTTATA
1 TACT-AATCATTTATA
582344 TACTAAATCATTTATA
1 TACT-AATCATTTATA
582360 TACTAAATCATTTATA
1 TACT-AATCATTTATA
582376 TACTAAATCATT
1 TACT-AATCATT
582388 GATGGTCGGC
Statistics
Matches: 264, Mismatches: 17, Indels: 22
0.87 0.06 0.07
Matches are distributed among these distances:
8 4 0.02
9 2 0.01
10 1 0.00
12 2 0.01
14 1 0.00
15 3 0.01
16 249 0.94
17 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.44
Consensus pattern (15 bp):
TACTAATCATTTATA
Found at i:582137 original size:32 final size:32
Alignment explanation
Indices: 582080--582387 Score: 425
Period size: 32 Copynumber: 9.9 Consensus size: 32
582070 CGTATTTTTG
* * *
582080 TACTATATCATTTATGTACTAAATCACTTATA
1 TACTAAATCATTTATATACTAAATCATTTATA
* *
582112 TACTGAATCATTTATATACTGAATCATTTATA
1 TACTAAATCATTTATATACTAAATCATTTATA
* *
582144 TACTGAATCATTTATATACTAAATCATTTGTA
1 TACTAAATCATTTATATACTAAATCATTTATA
* *
582176 TACTATATCATTTATATACTGAATCATTTATA
1 TACTAAATCATTTATATACTAAATCATTTATA
*
582208 TACTAAATCATTTATATACTGAATCATTTATA
1 TACTAAATCATTTATATACTAAATCATTTATA
* *
582240 TACTGAATCATTTATATACTAAATCATTTGTA
1 TACTAAATCATTTATATACTAAATCATTTATA
* *
582272 TACTAAATCATTTATATACTGAATCATTAATA
1 TACTAAATCATTTATATACTAAATCATTTATA
582304 TACTAAATCATTTATATACT--A--A---AT-
1 TACTAAATCATTTATATACTAAATCATTTATA
*
582328 TACTGAATCATTTATATACTAAATCATTTATA
1 TACTAAATCATTTATATACTAAATCATTTATA
582360 TACTAAATCATTTATATACTAAATCATT
1 TACTAAATCATTTATATACTAAATCATT
582388 GATGGTCGGC
Statistics
Matches: 247, Mismatches: 21, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
24 19 0.08
25 2 0.01
26 1 0.00
28 2 0.01
30 1 0.00
31 2 0.01
32 220 0.89
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.44
Consensus pattern (32 bp):
TACTAAATCATTTATATACTAAATCATTTATA
Found at i:582159 original size:48 final size:47
Alignment explanation
Indices: 582080--582387 Score: 441
Period size: 48 Copynumber: 6.6 Consensus size: 47
582070 CGTATTTTTG
* * * *
582080 TACTATATCATTTATGTACTAAATCACTTATATACTGAATCATTTATA
1 TACTA-ATCATTTATATACTGAATCATTTATATACTAAATCATTTATA
*
582128 TACTGAATCATTTATATACTGAATCATTTATATACTAAATCATTTGTA
1 TACT-AATCATTTATATACTGAATCATTTATATACTAAATCATTTATA
582176 TACTATATCATTTATATACTGAATCATTTATATACTAAATCATTTATA
1 TACTA-ATCATTTATATACTGAATCATTTATATACTAAATCATTTATA
*
582224 TACTGAATCATTTATATACTGAATCATTTATATACTAAATCATTTGTA
1 TACT-AATCATTTATATACTGAATCATTTATATACTAAATCATTTATA
*
582272 TACTAAATCATTTATATACTGAATCATTAATATACTAAATCATTTATA
1 TACT-AATCATTTATATACTGAATCATTTATATACTAAATCATTTATA
582320 TACT-A--A---AT-TACTGAATCATTTATATACTAAATCATTTATA
1 TACTAATCATTTATATACTGAATCATTTATATACTAAATCATTTATA
*
582360 TACTAAATCATTTATATACTAAATCATT
1 TACT-AATCATTTATATACTGAATCATT
582388 GATGGTCGGC
Statistics
Matches: 237, Mismatches: 12, Indels: 22
0.87 0.04 0.08
Matches are distributed among these distances:
40 35 0.15
41 2 0.01
42 1 0.00
44 2 0.01
46 1 0.00
47 3 0.01
48 191 0.81
49 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.44
Consensus pattern (47 bp):
TACTAATCATTTATATACTGAATCATTTATATACTAAATCATTTATA
Done.