Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 5 of 91
Found at i:1431405 original size:23 final size:24
Alignment explanation
Indices: 1431358--1431406 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
1431348 AGCATAACTT
*
1431358 TTAATCTCTATATAAAGATTTAAA
1 TTAATCACTATATAAAGATTTAAA
1431382 TTAATCACTAT-TAATA-ATTTAAA
1 TTAATCACTATATAA-AGATTTAAA
1431405 TT
1 TT
1431407 TAAAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (24 bp):
TTAATCACTATATAAAGATTTAAA
Found at i:1431409 original size:24 final size:25
Alignment explanation
Indices: 1431357--1431409 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
1431347 AAGCATAACT
*
1431357 TTTAATCTCTATATAAAGATTTAAA
1 TTTAATCACTATATAAAGATTTAAA
1431382 -TTAATCACTAT-TAATA-ATTTAAA
1 TTTAATCACTATATAA-AGATTTAAA
1431405 TTTAA
1 TTTAA
1431410 AATTTTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 10 0.40
24 15 0.60
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (25 bp):
TTTAATCACTATATAAAGATTTAAA
Found at i:1440060 original size:21 final size:21
Alignment explanation
Indices: 1440036--1440087 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
1440026 TAGAGTTTTC
*
1440036 TGCTTCTTTTAAATAGAAATA
1 TGCTTCTTTTAAATAAAAATA
*
1440057 TGCTTCTTTTAAATAAAAATG
1 TGCTTCTTTTAAATAAAAATA
*
1440078 TGCTTATTTT
1 TGCTTCTTTT
1440088 GTGGCTTAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.48
Consensus pattern (21 bp):
TGCTTCTTTTAAATAAAAATA
Found at i:1442687 original size:52 final size:52
Alignment explanation
Indices: 1442602--1442700 Score: 135
Period size: 52 Copynumber: 1.9 Consensus size: 52
1442592 TAACTTCTTC
* * * *
1442602 TTAACTTTTTAAAGTCAACTTACAACATCTCTACTTTTTCAATGTTAAAGTG
1 TTAACTTTTCAAAATCAACTTACAACATCTCTACATTTTCAAGGTTAAAGTG
* * *
1442654 TTAACTTTTCAAAATCAAGTTAGAACCTCTCTACATTTTCAAGGTTA
1 TTAACTTTTCAAAATCAACTTACAACATCTCTACATTTTCAAGGTTA
1442701 GGGTAGAACT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 40 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.40
Consensus pattern (52 bp):
TTAACTTTTCAAAATCAACTTACAACATCTCTACATTTTCAAGGTTAAAGTG
Found at i:1444777 original size:296 final size:296
Alignment explanation
Indices: 1444237--1444814 Score: 757
Period size: 296 Copynumber: 2.0 Consensus size: 296
1444227 CCAATTTTGA
* ** * * * * *
1444237 AAAAGAATTGAATGATTATATTTCAATTGGTTAATGCTTTATAAATCGCGTGAAGTCATTTACTT
1 AAAAGAATTGAATGATTATAATTCAATTGGTTAACACTTTATAAATCACGTGAAATCATTCAATA
* * * * * *
1444302 AACATAAAACTATTTCGTTAAAAGATGAAATGTTTAAATAGATATAAAATATTATTGCACTTATT
66 AACATAAAACAATTTCATTAAAAGATAAAATGTCTAAATAGATATAAAATATTATTACACCTATT
*
1444367 AATTTTGCCAACTCATACATATTTTCTCAACGAAAAAAAAAAACATCTTCCTGAAGAAATTCTTT
131 AATTTTACCAACTCATACATATTTTCTCAACGAAAAAAAAAAACATCTTCCTGAAGAAATTCTTT
** * * *
1444432 CACTATTAGCTAAAATATTAAAATTGACATTAAATTTTAGGAAACTTGTTCTGGTAACACTGCCA
196 CACTAAGAGCTAAAATATTAAAATTGACATTAAATTTTAAGAAACTTGTTCCGGCAACACTGCCA
*
1444497 GTTTTGAAAAAGAATTTAATGAATTTTTTTGAAGAG
261 ATTTTGAAAAAGAATTTAATGAATTTTTTTGAAGAG
* *
1444533 AAAAGAATTTAATGATTATAATTCAATTGGTTAACACTTTATAAATCATGTGAAAAT-ATTCAAT
1 AAAAGAATTGAATGATTATAATTCAATTGGTTAACACTTTATAAATCACGTG-AAATCATTCAAT
* *
1444597 AAACATGAAACAATTTTATTAAAAGATAAAATGTCTAAATAGATATAAAATATTATTACACCTAT
65 AAACATAAAACAATTTCATTAAAAGATAAAATGTCTAAATAGATATAAAATATTATTACACCTAT
* * * * * * * *
1444662 TAATTTTATCAATTCATACGTGTTTTCTGATC-AAGAAAAAAAACATCTTCCT-AAGGAAATTGT
130 TAATTTTACCAACTCATACATATTTTCTCAACGAAAAAAAAAAACATCTTCCTGAA-GAAATTCT
* * * *
1444725 TTTACTAAGAGCTAAAATATTTAAATTTGACATTAAATTTTAAGATACTTGTTCCGGCAACATTG
194 TTCACTAAGAGCTAAAATA-TTAAAATTGACATTAAATTTTAAGAAACTTGTTCCGGCAACACTG
* *
1444790 TCAATTTTGAAAATGAATTTAATGA
258 CCAATTTTGAAAAAGAATTTAATGA
1444815 TTATAATTCA
Statistics
Matches: 240, Mismatches: 39, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
294 2 0.01
295 42 0.17
296 193 0.80
297 3 0.01
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (296 bp):
AAAAGAATTGAATGATTATAATTCAATTGGTTAACACTTTATAAATCACGTGAAATCATTCAATA
AACATAAAACAATTTCATTAAAAGATAAAATGTCTAAATAGATATAAAATATTATTACACCTATT
AATTTTACCAACTCATACATATTTTCTCAACGAAAAAAAAAAACATCTTCCTGAAGAAATTCTTT
CACTAAGAGCTAAAATATTAAAATTGACATTAAATTTTAAGAAACTTGTTCCGGCAACACTGCCA
ATTTTGAAAAAGAATTTAATGAATTTTTTTGAAGAG
Found at i:1445067 original size:264 final size:265
Alignment explanation
Indices: 1444532--1445120 Score: 776
Period size: 264 Copynumber: 2.2 Consensus size: 265
1444522 TTTTTGAAGA
* *
1444532 GAAAA-GAATTTAATGATTATAATTCAATTGGTTAACACTTTATAAATCATGTGAAAATATTCAA
1 GAAAATGAATTTAATGATTATAATTCAATTGGTTAACGCTTT-TAAATCATGTGAAGATATTCAA
* * *
1444596 TAAACATGAAACAATTTTATTAAAAGATAAAATGTCTAAATAGATATAAAATATTATTACACCTA
65 TAAACATGAAACAATTTCATTAAAAGATAAAATGTCTAAATAGAAATAAAATATCATTACACCTA
* * * *
1444661 TTAATTTTATCAATTCATACGTGTTTTCTGATCAAGAAAAAAAACATCTTCCTAAGGAAATTGTT
130 TTAA-TTTACCAACTCATACGCGTTTTCTAATCAAGAAAAAAAACATCTTCCTAAGGAAATTGTT
* * * * *
1444726 TTACTAAGAGCTAAAATATTTAAATTTGACATTAAATTTTAAGATACTTGTTCCGGCAACATTGT
194 TCACTAAGAGCCAAAATATTTAAATGTGACATTAAATGTTAAGATACTTGTTCCGGCAACATTGC
1444791 CAATTTT
259 CAATTTT
* * * *
1444798 GAAAATGAATTTAATGATTATAATTCAATTGGTTAATGCTTTGTAAATCACGTGAAGATATTTAC
1 GAAAATGAATTTAATGATTATAATTCAATTGGTTAACGCTTT-TAAATCATGTGAAGATATTCAA
* * ** * *
1444863 TCAATATGAAACCGTTTCGTTAAAAGATGAAATGTCTAAATAGAAATAAAATATCATTACATCC-
65 TAAACATGAAACAATTTCATTAAAAGATAAAATGTCTAAATAGAAATAAAATATCATTACA-CCT
* ** *
1444927 ATTAA-TTGCCAACTCATACGCGTTTTCTCAAT-AA-AAAAAAAACATCTTTTTGAGGAAATTGT
129 ATTAATTTACCAACTCATACGCGTTTTCT-AATCAAGAAAAAAAACATCTTCCTAAGGAAATTGT
* * *
1444989 TTCACTAAGAGCCAAAATATTTGAATGTGACATTAAATGTT-AGAATACTTGTTTCGGTAACATT
193 TTCACTAAGAGCCAAAATATTTAAATGTGACATTAAATGTTAAG-ATACTTGTTCCGGCAACATT
1445053 GCCAATTTT
257 GCCAATTTT
* *
1445062 GAAAATGAATTTAATAATTATAATTCAATTGGTTAGCGCTTTTATAATCATGTGAAGAT
1 GAAAATGAATTTAATGATTATAATTCAATTGGTTAACGCTTTTA-AATCATGTGAAGAT
1445121 GTCTACTCTT
Statistics
Matches: 282, Mismatches: 36, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
263 4 0.01
264 139 0.49
265 21 0.07
266 7 0.02
267 109 0.39
268 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (265 bp):
GAAAATGAATTTAATGATTATAATTCAATTGGTTAACGCTTTTAAATCATGTGAAGATATTCAAT
AAACATGAAACAATTTCATTAAAAGATAAAATGTCTAAATAGAAATAAAATATCATTACACCTAT
TAATTTACCAACTCATACGCGTTTTCTAATCAAGAAAAAAAACATCTTCCTAAGGAAATTGTTTC
ACTAAGAGCCAAAATATTTAAATGTGACATTAAATGTTAAGATACTTGTTCCGGCAACATTGCCA
ATTTT
Found at i:1448094 original size:265 final size:265
Alignment explanation
Indices: 1447451--1448620 Score: 1745
Period size: 265 Copynumber: 4.4 Consensus size: 265
1447441 CTATTTTGAT
*
1447451 AAAGAATTTAATGATTATAATTCAATTGGTTAATGTTTTGTAAATCACGTGAAGATATTTACTCA
1 AAAGAATTTAATGATTATAATTCAATTGGTTAATGCTTTGTAAATCACGTGAAGATATTTACTCA
* * * *
1447516 ACATGAAATCATTTCGTTAAACGATGAAACGTCAAAATAAATATAAAATATTATTACACTTATTA
66 ACATGAAACCGTTTCGTTAAAAGATGAAACGTCTAAATAAATATAAAATATTATTACACTTATTA
* * * * * * *
1447581 ATTTTGTCAACTTATACGTGTTTTCTCAATAGAAAAAAACATCTTCATAAGAAAATTGTTTCACT
131 ATTTTGCCAACTCATACGCGTTTTCTCAACAGAAAAAAACATCTTCCTGAGGAAATTGTTTCACT
* *
1447646 AAGAATTAAAATTATTTAAATGTGACATTAAATATTAAGATACATGTTCC-GATAACATTGCCAA
196 AAGAATTAAAA-TATTTAAATGTGACATTAAATATTAAGATACCTGTTCCAG-TAACATTGCAAA
*
1447710 TTTTGAAA
259 TTTCG-AA
* * *
1447718 AAAAAAATTAATGATTATAATTCAATTGGTTAATACTTTGTAAATCACGTGAAGATATTTACTCA
1 AAAGAATTTAATGATTATAATTCAATTGGTTAATGCTTTGTAAATCACGTGAAGATATTTACTCA
* * *
1447783 ATATGAAACCGTTTCGTTAAAAGAT-AAACTGTGTAAATAGATATAAAATATTATTACACTTATT
66 ACATGAAACCGTTTCGTTAAAAGATGAAAC-GTCTAAATAAATATAAAATATTATTACACTTATT
* *
1447847 AATTTTGCCAACTCATACGCGTTTTCTCAATAGAAAAAAACATCTTCTTGA-GAAAGTTGTTTCA
130 AATTTTGCCAACTCATACGCGTTTTCTCAACAGAAAAAAACATCTTCCTGAGGAAA-TTGTTTCA
* *
1447911 CTAAGAATTAAAATATTTAAATGTGACATTAAATATTAAGATACCTGTTTCAGTAAAATTGCAAA
194 CTAAGAATTAAAATATTTAAATGTGACATTAAATATTAAGATACCTGTTCCAGTAACATTGCAAA
1447976 TTTCGAA
259 TTTCGAA
**
1447983 AAAGAATTTAATGATTATAATTCAATTGGTTAATGCTTTGTAAATCACGTGAAGATATTTACTTT
1 AAAGAATTTAATGATTATAATTCAATTGGTTAATGCTTTGTAAATCACGTGAAGATATTTACTCA
* * *
1448048 ACATGAAACCGTTTCATTAAAAGATGAAACGTCCAAATAAATATAAAATATTATTACACCTATTA
66 ACATGAAACCGTTTCGTTAAAAGATGAAACGTCTAAATAAATATAAAATATTATTACACTTATTA
* * *
1448113 ATTTTGTCAACTCATACGCGTTTTCTAAACAGAAAAAAACATCTTCCTGAGGAAATTGTTTAACT
131 ATTTTGCCAACTCATACGCGTTTTCTCAACAGAAAAAAACATCTTCCTGAGGAAATTGTTTCACT
* * *
1448178 AAGAATTAAAATATTTGAATGTGACATTAAATATTAAGATACCTGTTCCAATAATATTGCAAATT
196 AAGAATTAAAATATTTAAATGTGACATTAAATATTAAGATACCTGTTCCAGTAACATTGCAAATT
*
1448243 TCAAA
261 TCGAA
* * * * *
1448248 AAAGAATTTAATGATTATCATTCAATTGGTTAATGCTTTGTAAATGAGGTGAAAATATTTACTCT
1 AAAGAATTTAATGATTATAATTCAATTGGTTAATGCTTTGTAAATCACGTGAAGATATTTACTCA
* * * *
1448313 ACATGAAACCGTTTCATTGAAAGATGAAACGTATAAATAGATATAAAATATTATT-CACTTATTA
66 ACATGAAACCGTTTCGTTAAAAGATGAAACGTCTAAATAAATATAAAATATTATTACACTTATTA
** *
1448377 ATTTTGCCAACTCATACATGTTTTCTCAACAGAAAAAAACATCTTCCTGAGGAAATTCTTTCACT
131 ATTTTGCCAACTCATACGCGTTTTCTCAACAGAAAAAAACATCTTCCTGAGGAAATTGTTTCACT
* * *
1448442 AAGTATTAAAATATTTAAATGTGACATTAAATATTAAGATACCTGTTCCGGTAACATTGCCAATT
196 AAGAATTAAAATATTTAAATGTGACATTAAATATTAAGATACCTGTTCCAGTAACATTGCAAATT
*
1448507 TCGCA
261 TCGAA
* * *
1448512 AAAGAATTTAATGATTATAATCCAATTGGTTAATACTTTGTAAATCACGTGAAGATATTTACTCG
1 AAAGAATTTAATGATTATAATTCAATTGGTTAATGCTTTGTAAATCACGTGAAGATATTTACTCA
* *
1448577 ACATGAAACTGTTTCGTTAAAAGATGAAATGTCTAAATAAATAT
66 ACATGAAACCGTTTCGTTAAAAGATGAAACGTCTAAATAAATAT
1448621 TTAAATGTGA
Statistics
Matches: 818, Mismatches: 80, Indels: 13
0.90 0.09 0.01
Matches are distributed among these distances:
264 225 0.28
265 347 0.42
266 65 0.08
267 181 0.22
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.35
Consensus pattern (265 bp):
AAAGAATTTAATGATTATAATTCAATTGGTTAATGCTTTGTAAATCACGTGAAGATATTTACTCA
ACATGAAACCGTTTCGTTAAAAGATGAAACGTCTAAATAAATATAAAATATTATTACACTTATTA
ATTTTGCCAACTCATACGCGTTTTCTCAACAGAAAAAAACATCTTCCTGAGGAAATTGTTTCACT
AAGAATTAAAATATTTAAATGTGACATTAAATATTAAGATACCTGTTCCAGTAACATTGCAAATT
TCGAA
Found at i:1448553 original size:529 final size:532
Alignment explanation
Indices: 1447451--1448620 Score: 1819
Period size: 529 Copynumber: 2.2 Consensus size: 532
1447441 CTATTTTGAT
*
1447451 AAAGAATTTAATGATTATAATTCAATTGGTTAATGTTTTGTAAATCACGTGAAGATATTTACTCA
1 AAAGAATTTAATGATTATAATTCAATTGGTTAATGCTTTGTAAATCACGTGAAGATATTTACTCA
* * * *
1447516 ACATGAAATCATTTCGTTAAACGATGAAACGTCAAAATAAATATAAAATATTATTACACTTATTA
66 ACATGAAACCGTTTCGTTAAAAGATGAAACGTCAAAATAAATATAAAATATTATTACACCTATTA
* * * * *
1447581 ATTTTGTCAACTTATACGTGTTTTCTCAATAGAAAAAAACATCTTCATAAGAAAATTGTTTCACT
131 ATTTTGTCAACTCATACGCGTTTTCTAAACAGAAAAAAACATCTTCATAAGAAAATTGTTTAACT
* *
1447646 AAGAATTAAAATTATTTAAATGTGACATTAAATATTAAGATACATGTTCCGATAACATTGCCAAT
196 AAGAATTAAAATTATTTAAATGTGACATTAAATATTAAGATACATGTTCCAATAACATTGCCAAA
* *
1447711 TTTGAAAAAAAAAATTAATGATTATAATTCAATTGGTTAATACTTTGTAAATCACGTGAAGATAT
261 TTTCAAAAAAAAAATTAATGATTATAATTCAATTGGTTAATACTTTGTAAATCACGTGAAAATAT
* * *
1447776 TTACTCAATATGAAACCGTTTCGTTAAAAGATAAACTGTGTAAATAGATATAAAATATTATTACA
326 TTACTCAACATGAAACCGTTTCATTAAAAGATAAACTGTATAAATAGATATAAAATATTATTACA
* * * *
1447841 CTTATTAATTTTGCCAACTCATACGCGTTTTCTCAATAGAAAAAAACATCTTCTTGAGAAAGTTG
391 CTTATTAATTTTGCCAACTCATACACGTTTTCTCAACAGAAAAAAACATCTTCCTGAGAAAGTTC
*
1447906 TTTCACTAAGAATTAAAATATTTAAATGTGACATTAAATATTAAGATACCTGTTTCAGTAAAATT
456 TTTCACTAAGAATTAAAATATTTAAATGTGACATTAAATATTAAGATACCTGTTCCAGTAAAATT
1447971 GCAAATTTCGAA
521 GCAAATTTCGAA
**
1447983 AAAGAATTTAATGATTATAATTCAATTGGTTAATGCTTTGTAAATCACGTGAAGATATTTACTTT
1 AAAGAATTTAATGATTATAATTCAATTGGTTAATGCTTTGTAAATCACGTGAAGATATTTACTCA
* *
1448048 ACATGAAACCGTTTCATTAAAAGATGAAACGTCCAAATAAATATAAAATATTATTACACCTATTA
66 ACATGAAACCGTTTCGTTAAAAGATGAAACGTCAAAATAAATATAAAATATTATTACACCTATTA
* * *
1448113 ATTTTGTCAACTCATACGCGTTTTCTAAACAGAAAAAAACATCTTCCTGAGGAAATTGTTTAACT
131 ATTTTGTCAACTCATACGCGTTTTCTAAACAGAAAAAAACATCTTCATAAGAAAATTGTTTAACT
* * *
1448178 AAGAATTAAAA-TATTTGAATGTGACATTAAATATTAAGATACCTGTTCCAATAATATTG-CAAA
196 AAGAATTAAAATTATTTAAATGTGACATTAAATATTAAGATACATGTTCCAATAACATTGCCAAA
* * * * * *
1448241 TTTCAAAAAAGAATTTAATGATTATCATTCAATTGGTTAATGCTTTGTAAATGAGGTGAAAATAT
261 TTTCAAAAAAAAAATTAATGATTATAATTCAATTGGTTAATACTTTGTAAATCACGTGAAAATAT
* *
1448306 TTACTCTACATGAAACCGTTTCATTGAAAGATGAAAC-GTATAAATAGATATAAAATATTATT-C
326 TTACTCAACATGAAACCGTTTCATTAAAAGAT-AAACTGTATAAATAGATATAAAATATTATTAC
*
1448369 ACTTATTAATTTTGCCAACTCATACATGTTTTCTCAACAGAAAAAAACATCTTCCTGAGGAAA-T
390 ACTTATTAATTTTGCCAACTCATACACGTTTTCTCAACAGAAAAAAACATCTTCCTGA-GAAAGT
* * *
1448433 TCTTTCACTAAGTATTAAAATATTTAAATGTGACATTAAATATTAAGATACCTGTTCCGGTAACA
454 TCTTTCACTAAGAATTAAAATATTTAAATGTGACATTAAATATTAAGATACCTGTTCCAGTAAAA
* *
1448498 TTGCCAATTTCGCA
519 TTGCAAATTTCGAA
* * *
1448512 AAAGAATTTAATGATTATAATCCAATTGGTTAATACTTTGTAAATCACGTGAAGATATTTACTCG
1 AAAGAATTTAATGATTATAATTCAATTGGTTAATGCTTTGTAAATCACGTGAAGATATTTACTCA
* * *
1448577 ACATGAAACTGTTTCGTTAAAAGATGAAATGTCTAAATAAATAT
66 ACATGAAACCGTTTCGTTAAAAGATGAAACGTCAAAATAAATAT
1448621 TTAAATGTGA
Statistics
Matches: 582, Mismatches: 54, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
529 229 0.39
530 116 0.20
531 48 0.08
532 189 0.32
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.35
Consensus pattern (532 bp):
AAAGAATTTAATGATTATAATTCAATTGGTTAATGCTTTGTAAATCACGTGAAGATATTTACTCA
ACATGAAACCGTTTCGTTAAAAGATGAAACGTCAAAATAAATATAAAATATTATTACACCTATTA
ATTTTGTCAACTCATACGCGTTTTCTAAACAGAAAAAAACATCTTCATAAGAAAATTGTTTAACT
AAGAATTAAAATTATTTAAATGTGACATTAAATATTAAGATACATGTTCCAATAACATTGCCAAA
TTTCAAAAAAAAAATTAATGATTATAATTCAATTGGTTAATACTTTGTAAATCACGTGAAAATAT
TTACTCAACATGAAACCGTTTCATTAAAAGATAAACTGTATAAATAGATATAAAATATTATTACA
CTTATTAATTTTGCCAACTCATACACGTTTTCTCAACAGAAAAAAACATCTTCCTGAGAAAGTTC
TTTCACTAAGAATTAAAATATTTAAATGTGACATTAAATATTAAGATACCTGTTCCAGTAAAATT
GCAAATTTCGAA
Found at i:1448724 original size:165 final size:165
Alignment explanation
Indices: 1448450--1448785 Score: 514
Period size: 165 Copynumber: 2.0 Consensus size: 165
1448440 CTAAGTATTA
* * *
1448450 AAATATTTAAATGTGACATTAAATATTAAGATACCTGTTCCGGTAACATTGCCAATTTCGCAAAA
1 AAATATTTAAATGTGACATTAAATATTAAGATACATGTTCCGATAACATTGCCAATTTCGAAAAA
* * ** *
1448515 GAATTTAATGATTATAATCCAATTGGTTAATACTTTGTAAATCACGTGAAGATATTTACTCGACA
66 GAATTTAATGATTATAATCCAATCGATTAATACTTTACAAATCACATGAAGATATTTACTCGACA
*
1448580 TGAAACTGTTTCGTTAAAAGATGAAA-TGTCTAAAT
131 TGAAACCGTTTCGTTAAAAGAT-AAACTGTCTAAAT
*
1448615 AAATATTTAAATGTGACATTAAATATTAAGATACATGTTCCGATAACATTGCCAATTTTGAAAAA
1 AAATATTTAAATGTGACATTAAATATTAAGATACATGTTCCGATAACATTGCCAATTTCG-AAAA
* *
1448680 AGAATTTAATGATTATAATTCAATCGATT-ATACTTTACAAATCACATGAAGTTATTTACTCGAC
65 AGAATTTAATGATTATAATCCAATCGATTAATACTTTACAAATCACATGAAGATATTTACTCGAC
*
1448744 ATGAAACCGTTTCGTTAAAAGATAAACTGTGTAAAT
130 ATGAAACCGTTTCGTTAAAAGATAAACTGTCTAAAT
*
1448780 AGATAT
1 AAATAT
1448786 AAAATATTAT
Statistics
Matches: 155, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
164 3 0.02
165 123 0.79
166 29 0.19
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (165 bp):
AAATATTTAAATGTGACATTAAATATTAAGATACATGTTCCGATAACATTGCCAATTTCGAAAAA
GAATTTAATGATTATAATCCAATCGATTAATACTTTACAAATCACATGAAGATATTTACTCGACA
TGAAACCGTTTCGTTAAAAGATAAACTGTCTAAAT
Found at i:1449099 original size:267 final size:265
Alignment explanation
Indices: 1448615--1449766 Score: 1580
Period size: 267 Copynumber: 4.3 Consensus size: 265
1448605 ATGTCTAAAT
1448615 AAATATTTAAATGTGACATTAAATATTAAGATACATGTTCCGATAACATTGCCAATTTTGAAAAA
1 AAATATTTAAATGTGACATTAAATATTAAGATACATGTTCCGATAACATTGCCAATTTTG-AAAA
* *
1448680 AGAATTTAATGATTATAATTCAATCGATT-ATACTTTACAAATCACATGAAGTTATTTACTCGAC
65 AGAATTTAATGATTATAATTCAATCGATTAATACTTTACAAATCACATGAAGATATTTACTCAAC
1448744 ATGAAACCGTTTCGTTAAAAGAT-AAACTGTGTAAATAGATATAAAATATTATTACACTTATTAA
130 ATGAAACCGTTTCGTTAAAAGATGAAAC-GTGTAAATAGATATAAAATATTATTACACTTATTAA
*
1448808 TTTTGCCAACTCATACGCGTTTTCTCAACAGAAAAAAACATCTTCCTGAGGAAGTTGTTTCACTA
194 TTTTGCCAACTCATACGCGTTTTCTCAACAGAAAAAAACATCTTCCTGAGGAAATTGTTTCACTA
*
1448873 AGAATTA
259 AGAACTA
1448880 AAATTATTTAAATGTGACATTAAATATTAAGATACATGTTCCGATAACATTGCCAATTTTGAAAA
1 AAA-TATTTAAATGTGACATTAAATATTAAGATACATGTTCCGATAACATTGCCAATTTTG-AAA
*
1448945 AAGAATTTAATGATTATAATTCAATCGATTAATACTTTACAAATCACATGAAGATATTTACTCGA
64 AAGAATTTAATGATTATAATTCAATCGATTAATACTTTACAAATCACATGAAGATATTTACTCAA
1449010 CATGAAACCGTTTCGTTAAAAGATGAAACGTGTAAATAGATATAAAATATTATTACACTTATTAA
129 CATGAAACCGTTTCGTTAAAAGATGAAACGTGTAAATAGATATAAAATATTATTACACTTATTAA
* *
1449075 TTTTGCCAACTCATACGTGTTTTCTCAACAGAAAAAAACATCTTCCTGAGGAAATTGTTTAACTA
194 TTTTGCCAACTCATACGCGTTTTCTCAACAGAAAAAAACATCTTCCTGAGGAAATTGTTTCACTA
*
1449140 AGAATTA
259 AGAACTA
* * * * * *
1449147 AAATATTTGAATGTGACATTAAATATTAAGATACCTGTTTC-AGTAAAATTGCAAATTTCGAAAA
1 AAATATTTAAATGTGACATTAAATATTAAGATACATGTTCCGA-TAACATTGCCAATTTTGAAAA
* * * ** *
1449211 AGAATTTAATGATTATAATTCAATTGGTTAATGCTTTGTAAATCACGTGAAGATATTTACTCAAC
65 AGAATTTAATGATTATAATTCAATCGATTAATACTTTACAAATCACATGAAGATATTTACTCAAC
* * *
1449276 ATGAAACCGTTTCATTAAAAGATAAAACGTGTAAATAGATATAAAATATTATTACACCTATTAAT
130 ATGAAACCGTTTCGTTAAAAGATGAAACGTGTAAATAGATATAAAATATTATTACACTTATTAAT
** * * * * * *
1449341 TTTATCAATTCATACGTGTTTTCTGATCAAGAAAAAAAACATCTTCCTAAGGAAATTGTTACACT
195 TTTGCCAACTCATACGCGTTTTCTCAAC-AG-AAAAAAACATCTTCCTGAGGAAATTGTTTCACT
*
1449406 AAGAGCTA
258 AAGAACTA
* * * ** * *
1449414 AAATATTTAAATTTGACATTAAATTTTAAGATACTTGTTCCGGCAACATTGTCAATTTTGAAAAT
1 AAATATTTAAATGTGACATTAAATATTAAGATACATGTTCCGATAACATTGCCAATTTTGAAAAA
* * * ** * *
1449479 GAATTTAATGATTATAATTCAATTGGTTAATGCTTTGTAAATCACGTGAAGATATTTACTCAATA
66 GAATTTAATGATTATAATTCAATCGATTAATACTTTACAAATCACATGAAGATATTTACTCAACA
* * * * *
1449544 TGAAACCGTTTCGTTAAAAGATGAAATGTCTAAATAGAAATAAAATATCATTACA-TCCATTAA-
131 TGAAACCGTTTCGTTAAAAGATGAAACGTGTAAATAGATATAAAATATTATTACACT-TATTAAT
* * **
1449607 -TTGCCAACTCATACGCGTTTTCTCAATAAAAAAAAAAACATCTTTTTGAGGAAATTGTTTCACT
195 TTTGCCAACTCATACGCGTTTTCTC-A-ACAGAAAAAAACATCTTCCTGAGGAAATTGTTTCACT
* *
1449671 AAGAGCCA
258 AAGAACTA
* * * * *
1449679 AAATATTTGAATGTGACATTAAATGTT-AGAATACTTGTTTCGGTAACATTGCCAATTTTGAAAA
1 AAATATTTAAATGTGACATTAAATATTAAG-ATACATGTTCCGATAACATTGCCAATTTTGAAAA
* *
1449743 TGAATTTAATAATTATAATTCAAT
65 AGAATTTAATGATTATAATTCAAT
1449767 TGGTTNCGTA
Statistics
Matches: 805, Mismatches: 71, Indels: 22
0.90 0.08 0.02
Matches are distributed among these distances:
264 2 0.00
265 284 0.35
266 144 0.18
267 371 0.46
268 4 0.00
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.35
Consensus pattern (265 bp):
AAATATTTAAATGTGACATTAAATATTAAGATACATGTTCCGATAACATTGCCAATTTTGAAAAA
GAATTTAATGATTATAATTCAATCGATTAATACTTTACAAATCACATGAAGATATTTACTCAACA
TGAAACCGTTTCGTTAAAAGATGAAACGTGTAAATAGATATAAAATATTATTACACTTATTAATT
TTGCCAACTCATACGCGTTTTCTCAACAGAAAAAAACATCTTCCTGAGGAAATTGTTTCACTAAG
AACTA
Found at i:1449259 original size:697 final size:694
Alignment explanation
Indices: 1447921--1449317 Score: 2161
Period size: 697 Copynumber: 2.0 Consensus size: 694
1447911 CTAAGAATTA
* *
1447921 AAATATTTAAATGTGACATTAAATATTAAGATACCTGTTTCAGTAAAATTGCAAATTTCGAAAAA
1 AAATATTTAAATGTGACATTAAATATTAAGATACATGTTCCAGTAAAATTGCAAATTTCGAAAAA
* * * ** * **
1447986 GAATTTAATGATTATAATTCAATTGGTTAATGCTTTGTAAATCACGTGAAGATATTTACTTTACA
66 GAATTTAATGATTATAATTCAATCGATTAATACTTTACAAATCACATGAAGATATTTACTCGACA
1448051 TGAAACCGTTTCATTAAAAGATGAAACGTCCAAATAAATATAAAATATTATTACACCTATTAATT
131 TGAAACCGTTTCATTAAAAGATGAAACGTCCAAATAAATATAAAATATTATTACACCTATTAATT
*
1448116 TTGTCAACTCATACGCGTTTTCTAAACAGAAAAAAACATCTTCCTGAGGAAATTGTTTAACTAAG
196 TTGCCAACTCATACGCGTTTTCTAAACAGAAAAAAACATCTTCCTGAGGAAATTGTTTAACTAAG
* * *
1448181 AATTAAAATATTTGAATGTGACATTAAATATTAAGATACCTGTTCCAATAATATTGCAAATTTCA
261 AATTAAAATATTTAAATGTGACATTAAATATTAAGATACATGTTCCAATAACATTGCAAATTTCA
* * * * ** * **
1448246 AAAAAGAATTTAATGATTATCATTCAATTGGTTAATGCTTTGTAAATGAGGTGAAAATATTTACT
326 AAAAAGAATTTAATGATTATAATTCAATCGATTAATACTTTACAAATCACATGAAAATATTTACT
* *
1448311 CTACATGAAACCGTTTCATTGAAAGATGAAACGTATAAATAGATATAAAATATTATTCACTTATT
391 CGACATGAAACCGTTTCATTAAAAGATGAAACGTATAAATAGATATAAAATATTATTCACTTATT
*
1448376 AATTTTGCCAACTCATACATGTTTTCTCAACAGAAAAAAACATCTTCCTGAGGAAATTCTTTCAC
456 AATTTTGCCAACTCATACATGTTTTCTCAACAGAAAAAAACATCTTCCTGAGGAAATTCTTTAAC
* * * *
1448441 TAAGTATTAAAATATTTAAATGTGACATTAAATATTAAGATACCTGTTCCGGTAACATTGCCAAT
521 TAAGAATTAAAATATTTAAATGTGACATTAAATATTAAGATACCTGTTCCAGTAAAATTGCAAAT
*
1448506 TTCGCAAAAGAATTTAATGATTATAATCCAATTGGTTAATACTTTGTAAATCACGTGAAGATATT
586 TTCGAAAAAGAATTTAATGATTATAATCCAATTGGTTAATACTTTGTAAATCACGTGAAGATATT
* * * * *
1448571 TACTCGACATGAAACTGTTTCGTTAAAAGATGAAATGTCTAAAT
651 TACTCAACATGAAACCGTTTCATTAAAAGATAAAACGTCTAAAT
* * *
1448615 AAATATTTAAATGTGACATTAAATATTAAGATACATGTTCC-GATAACATTGCCAATTTTGAAAA
1 AAATATTTAAATGTGACATTAAATATTAAGATACATGTTCCAG-TAAAATTGCAAATTTCG-AAA
*
1448679 AAGAATTTAATGATTATAATTCAATCGATT-ATACTTTACAAATCACATGAAGTTATTTACTCGA
64 AAGAATTTAATGATTATAATTCAATCGATTAATACTTTACAAATCACATGAAGATATTTACTCGA
* ** * *
1448743 CATGAAACCGTTTCGTTAAAAGAT-AAACTGTGTAAATAGATATAAAATATTATTACACTTATTA
129 CATGAAACCGTTTCATTAAAAGATGAAAC-GTCCAAATAAATATAAAATATTATTACACCTATTA
* * *
1448807 ATTTTGCCAACTCATACGCGTTTTCTCAACAGAAAAAAACATCTTCCTGAGGAAGTTGTTTCACT
193 ATTTTGCCAACTCATACGCGTTTTCTAAACAGAAAAAAACATCTTCCTGAGGAAATTGTTTAACT
* *
1448872 AAGAATTAAAATTATTTAAATGTGACATTAAATATTAAGATACATGTTCCGATAACATTGCCAAT
258 AAGAATTAAAA-TATTTAAATGTGACATTAAATATTAAGATACATGTTCCAATAACATTG-CAAA
* *
1448937 TTTGAAAAAAGAATTTAATGATTATAATTCAATCGATTAATACTTTACAAATCACATGAAGATAT
321 TTTCAAAAAAGAATTTAATGATTATAATTCAATCGATTAATACTTTACAAATCACATGAAAATAT
* *
1449002 TTACTCGACATGAAACCGTTTCGTTAAAAGATGAAACGTGTAAATAGATATAAAATATTATTACA
386 TTACTCGACATGAAACCGTTTCATTAAAAGATGAAACGTATAAATAGATATAAAATATTATT-CA
* *
1449067 CTTATTAATTTTGCCAACTCATACGTGTTTTCTCAACAGAAAAAAACATCTTCCTGAGGAAATTG
450 CTTATTAATTTTGCCAACTCATACATGTTTTCTCAACAGAAAAAAACATCTTCCTGAGGAAATTC
* *
1449132 TTTAACTAAGAATTAAAATATTTGAATGTGACATTAAATATTAAGATACCTGTTTCAGTAAAATT
515 TTTAACTAAGAATTAAAATATTTAAATGTGACATTAAATATTAAGATACCTGTTCCAGTAAAATT
* *
1449197 GCAAATTTCGAAAAAGAATTTAATGATTATAATTCAATTGGTTAATGCTTTGTAAATCACGTGAA
580 GCAAATTTCGAAAAAGAATTTAATGATTATAATCCAATTGGTTAATACTTTGTAAATCACGTGAA
*
1449262 GATATTTACTCAACATGAAACCGTTTCATTAAAAGATAAAACGTGTAAAT
645 GATATTTACTCAACATGAAACCGTTTCATTAAAAGATAAAACGTCTAAAT
*
1449312 AGATAT
1 AAATAT
1449318 AAAATATTAT
Statistics
Matches: 635, Mismatches: 62, Indels: 9
0.90 0.09 0.01
Matches are distributed among these distances:
693 5 0.01
694 206 0.32
695 75 0.12
696 115 0.18
697 234 0.37
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.35
Consensus pattern (694 bp):
AAATATTTAAATGTGACATTAAATATTAAGATACATGTTCCAGTAAAATTGCAAATTTCGAAAAA
GAATTTAATGATTATAATTCAATCGATTAATACTTTACAAATCACATGAAGATATTTACTCGACA
TGAAACCGTTTCATTAAAAGATGAAACGTCCAAATAAATATAAAATATTATTACACCTATTAATT
TTGCCAACTCATACGCGTTTTCTAAACAGAAAAAAACATCTTCCTGAGGAAATTGTTTAACTAAG
AATTAAAATATTTAAATGTGACATTAAATATTAAGATACATGTTCCAATAACATTGCAAATTTCA
AAAAAGAATTTAATGATTATAATTCAATCGATTAATACTTTACAAATCACATGAAAATATTTACT
CGACATGAAACCGTTTCATTAAAAGATGAAACGTATAAATAGATATAAAATATTATTCACTTATT
AATTTTGCCAACTCATACATGTTTTCTCAACAGAAAAAAACATCTTCCTGAGGAAATTCTTTAAC
TAAGAATTAAAATATTTAAATGTGACATTAAATATTAAGATACCTGTTCCAGTAAAATTGCAAAT
TTCGAAAAAGAATTTAATGATTATAATCCAATTGGTTAATACTTTGTAAATCACGTGAAGATATT
TACTCAACATGAAACCGTTTCATTAAAAGATAAAACGTCTAAAT
Found at i:1449644 original size:532 final size:530
Alignment explanation
Indices: 1448615--1449771 Score: 1617
Period size: 532 Copynumber: 2.2 Consensus size: 530
1448605 ATGTCTAAAT
* *
1448615 AAATATTTAAATGTGACATTAAATATTAAGATACATG-TTCCGATAACATTGCCAATTTTGAAAA
1 AAATATTTGAATGTGACATTAAATATTAAGATACATGTTTCAG-TAACATTGCCAATTTTG-AAA
* * * *
1448679 AAGAATTTAATGATTATAATTCAATCGATTATACTTTACAAATCACATGAAGTTATTTACTCGAC
64 AAGAATTTAATGATTATAATTCAATTGGTTATACTTTACAAATCACATGAAGATATTTACTCAAC
* *
1448744 ATGAAACCGTTTCGTTAAAAGATAAACTGTGTAAATAGATATAAAATATTATTACACTTATTAAT
129 ATGAAACCGTTTCATTAAAAGATAAACTGTGTAAATAGATATAAAATATTATTACACCTATTAAT
* * * *
1448809 TTTGCCAACTCATACGCGTTTTCTCAACAGAAAAAAACATCTTCCTGAGGAAGTTGTTTCACTAA
194 TTTACCAACTCATACGCGTTTTCTCAACAGAAAAAAACATCTTCCTAAGGAAATTGTTACACTAA
* *
1448874 GAATTAAAATTATTTAAATGTGACATTAAATATTAAGATACATGTTCCGATAACATTGCCAATTT
259 GAACTAAAATTATTTAAATGTGACATTAAATATTAAGATACATGTTCCGACAACATTGCCAATTT
1448939 TGAAAAAAGAATTTAATGATTATAATTCAATCGATTAATACTTTACAAATCACATGAAGATATTT
324 TGAAAAAAGAATTTAATGATTATAATTCAATCGATTAATACTTTACAAATCACATGAAGATATTT
* * * *
1449004 ACTCGACATGAAACCGTTTCGTTAAAAGATGAAACGTGTAAATAGATATAAAATATTATTACACT
389 ACTCAACATGAAACCGTTTCGTTAAAAGATGAAACGTCTAAATAGAAATAAAATATCATTACACT
* * * *
1449069 TATTAATTTTGCCAACTCATACGTGTTTTCTCAACAGAAAAAAACATCTTCCTGAGGAAATTGTT
454 CATTAA-TTTGCCAACTCATACGCGTTTTCTCAAAAAAAAAAAACATCTTCCTGAGGAAATTGTT
**
1449134 TAACTAAGAATTA
518 TAACTAAGAACCA
* * * *
1449147 AAATATTTGAATGTGACATTAAATATTAAGATACCTGTTTCAGTAAAATTGCAAATTTCGAAAAA
1 AAATATTTGAATGTGACATTAAATATTAAGATACATGTTTCAGTAACATTGCCAATTTTGAAAAA
* ** *
1449212 GAATTTAATGATTATAATTCAATTGGTTAATGCTTTGTAAATCACGTGAAGATATTTACTCAACA
66 GAATTTAATGATTATAATTCAATTGGTT-ATACTTTACAAATCACATGAAGATATTTACTCAACA
1449277 TGAAACCGTTTCATTAAAAGATAAAAC-GTGTAAATAGATATAAAATATTATTACACCTATTAAT
130 TGAAACCGTTTCATTAAAAGAT-AAACTGTGTAAATAGATATAAAATATTATTACACCTATTAAT
* * * * *
1449341 TTTATCAATTCATACGTGTTTTCTGATCAAGAAAAAAAACATCTTCCTAAGGAAATTGTTACACT
194 TTTACCAACTCATACGCGTTTTCTCAAC-AG-AAAAAAACATCTTCCTAAGGAAATTGTTACACT
* * * * * *
1449406 AAGAGCTAAAA-TATTTAAATTTGACATTAAATTTTAAGATACTTGTTCCGGCAACATTGTCAAT
257 AAGAACTAAAATTATTTAAATGTGACATTAAATATTAAGATACATGTTCCGACAACATTGCCAAT
* * * * ** *
1449470 TTTG-AAAATGAATTTAATGATTATAATTCAATTGGTTAATGCTTTGTAAATCACGTGAAGATAT
322 TTTGAAAAAAGAATTTAATGATTATAATTCAATCGATTAATACTTTACAAATCACATGAAGATAT
* *
1449534 TTACTCAATATGAAACCGTTTCGTTAAAAGATGAAATGTCTAAATAGAAATAAAATATCATTACA
387 TTACTCAACATGAAACCGTTTCGTTAAAAGATGAAACGTCTAAATAGAAATAAAATATCATTACA
**
1449599 -TCCATTAA-TTGCCAACTCATACGCGTTTTCTCAATAAAAAAAAAAACATCTTTTTGAGGAAAT
452 CT-CATTAATTTGCCAACTCATACGCGTTTTCTC-A-AAAAAAAAAAACATCTTCCTGAGGAAAT
* *
1449662 TGTTTCACTAAGAGCCA
514 TGTTTAACTAAGAACCA
* * *
1449679 AAATATTTGAATGTGACATTAAATGTT-AGAATACTTGTTTCGGTAACATTGCCAATTTTGAAAA
1 AAATATTTGAATGTGACATTAAATATTAAG-ATACATGTTTCAGTAACATTGCCAATTTTGAAAA
* *
1449743 TGAATTTAATAATTATAATTCAATTGGTT
65 AGAATTTAATGATTATAATTCAATTGGTT
1449772 NCGTAATATA
Statistics
Matches: 552, Mismatches: 64, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
530 23 0.04
531 35 0.06
532 394 0.71
533 61 0.11
534 39 0.07
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.35
Consensus pattern (530 bp):
AAATATTTGAATGTGACATTAAATATTAAGATACATGTTTCAGTAACATTGCCAATTTTGAAAAA
GAATTTAATGATTATAATTCAATTGGTTATACTTTACAAATCACATGAAGATATTTACTCAACAT
GAAACCGTTTCATTAAAAGATAAACTGTGTAAATAGATATAAAATATTATTACACCTATTAATTT
TACCAACTCATACGCGTTTTCTCAACAGAAAAAAACATCTTCCTAAGGAAATTGTTACACTAAGA
ACTAAAATTATTTAAATGTGACATTAAATATTAAGATACATGTTCCGACAACATTGCCAATTTTG
AAAAAAGAATTTAATGATTATAATTCAATCGATTAATACTTTACAAATCACATGAAGATATTTAC
TCAACATGAAACCGTTTCGTTAAAAGATGAAACGTCTAAATAGAAATAAAATATCATTACACTCA
TTAATTTGCCAACTCATACGCGTTTTCTCAAAAAAAAAAAACATCTTCCTGAGGAAATTGTTTAA
CTAAGAACCA
Found at i:1452061 original size:27 final size:27
Alignment explanation
Indices: 1452008--1452061 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
1451998 AAATGTCCTG
*
1452008 ATGGTGGAAAATTACAATTTTGCCCCT
1 ATGGTGGAAAATTACAATTTTGACCCT
1452035 ATGGTGGCAAAATTATC-ATTTT-ACCCT
1 ATGGTGG-AAAATTA-CAATTTTGACCCT
1452062 TTTACTCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 11 0.46
28 12 0.50
29 1 0.04
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (27 bp):
ATGGTGGAAAATTACAATTTTGACCCT
Found at i:1452951 original size:263 final size:263
Alignment explanation
Indices: 1452535--1453439 Score: 1519
Period size: 263 Copynumber: 3.4 Consensus size: 263
1452525 GAAAAAAAGG
* * *
1452535 AAATTGTTTCACTAAGAATTAAAATATTTGAATGTGACATTAAATATTAAGATACATGTT-TCGA
1 AAATTGTTTCACTAAGAATTAAAATATTTAAATGTGACATTAAATATTAAGATACCTGTTCTAG-
* * *
1452599 TAACATTGCCAATTTTGAAAAA-AATTTAATGATTATAATTCAATTGGTTAATGCTTTGTAAATT
65 TAACATTGCAAATTTCGAAAAAGAATTTAATGATTATAATTCAATTGGTTAATGCTTTGTAAATC
* *
1452663 TCGTGAAGATATTTACTCAACATGAAACCGTTTCATTAAAAGATAAAACGTGTAAATAGATATAA
130 ACGTGAAGATATTTACTCTACATGAAACCGTTTCATTAAAAGATAAAACGTGTAAATAGATATAA
1452728 AATATTATTACACCAATTAATTTTGCCAACCCATACGCGTTTTCTCAATAAAAAAACTTCTTCAT
195 AATATTATTACACCAATTAATTTTGCCAACCCATACGCGTTTTCTCAATAAAAAAACTTCTTCAT
1452793 GAGA
260 GAGA
*
1452797 AAATTGTTTCACTAAGAATTAAAATATTTAAATGTGATATTAAATATTAAGATACCTGTTCTAGT
1 AAATTGTTTCACTAAGAATTAAAATATTTAAATGTGACATTAAATATTAAGATACCTGTTCTAGT
1452862 AACATTGCAAATTTCGAAAAAGAATTTAATGATTATAATTCAATTGGTTAATGCTTTGTAAATCA
66 AACATTGCAAATTTCGAAAAAGAATTTAATGATTATAATTCAATTGGTTAATGCTTTGTAAATCA
*
1452927 CGTGAAGATATTTACTTTACATGAAACCGTTTCATTAAAAGATAAAACGTGTAAATAGATATAAA
131 CGTGAAGATATTTACTCTACATGAAACCGTTTCATTAAAAGATAAAACGTGTAAATAGATATAAA
1452992 ATATTATTACACCAATTAATTTTGCCAACCCATACGCGTTTTCTCAATAAAAAAACTTCTTCATG
196 ATATTATTACACCAATTAATTTTGCCAACCCATACGCGTTTTCTCAATAAAAAAACTTCTTCATG
1453057 AGA
261 AGA
*
1453060 AAATTGTTTCACTAAGAATTAAAATATTTAAATGTGATATTAAATATTAAGATACCTGTTCTAGT
1 AAATTGTTTCACTAAGAATTAAAATATTTAAATGTGACATTAAATATTAAGATACCTGTTCTAGT
1453125 AACATTGCAAATTTCGAAAAAGAATTTAATGATTATAATTCAATTGGTTAATGCTTTGTAAATCA
66 AACATTGCAAATTTCGAAAAAGAATTTAATGATTATAATTCAATTGGTTAATGCTTTGTAAATCA
* * *
1453190 CGTGAAAATATTTACTCTACATGAAACCGTTTCGTTAAAAGATGAAACGTGTAAATAGATATAAA
131 CGTGAAGATATTTACTCTACATGAAACCGTTTCATTAAAAGATAAAACGTGTAAATAGATATAAA
** * * * * * *
1453255 ATATTATTACACTTATTAATTTTGCTAACTCATACGCGTTTTCTCAACAGAAAAAAACATATTCT
196 ATATTATTACACCAATTAATTTTGCCAACCCATACGCGTTTTCTC-A-ATAAAAAAACTTCTTCA
*
1453320 TGAGG
259 TGAGA
* *
1453325 AAATTGTTTCACTAAGAATTAAAATATTTAAATGCGACATTAAATATTAAGATACCTGTTC-GGT
1 AAATTGTTTCACTAAGAATTAAAATATTTAAATGTGACATTAAATATTAAGATACCTGTTCTAGT
* *
1453389 AACATTGCCAATTTTGAAAAAGAATTTAATGATTATAATTCAATTGGTTAA
66 AACATTGCAAATTTCGAAAAAGAATTTAATGATTATAATTCAATTGGTTAA
1453440 CCCCTTATAT
Statistics
Matches: 611, Mismatches: 28, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
262 77 0.13
263 406 0.66
264 52 0.09
265 76 0.12
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (263 bp):
AAATTGTTTCACTAAGAATTAAAATATTTAAATGTGACATTAAATATTAAGATACCTGTTCTAGT
AACATTGCAAATTTCGAAAAAGAATTTAATGATTATAATTCAATTGGTTAATGCTTTGTAAATCA
CGTGAAGATATTTACTCTACATGAAACCGTTTCATTAAAAGATAAAACGTGTAAATAGATATAAA
ATATTATTACACCAATTAATTTTGCCAACCCATACGCGTTTTCTCAATAAAAAAACTTCTTCATG
AGA
Found at i:1456854 original size:266 final size:267
Alignment explanation
Indices: 1455598--1457404 Score: 2088
Period size: 266 Copynumber: 6.7 Consensus size: 267
1455588 TATTGAATTA
*
1455598 GCCAACTCATACGCGTTTTCTCAACAGAAAAAAAAAAAAAAACATCATT-TTGA-GAAACTTGTT
1 GCCAACTCATACGCGTTTTCTCAACAG-------AAAAAAAACATC-TTCCTGAGGAAA-TTGTT
* * * * * *
1455661 TCATTAAGAACTCAAATATTTAAATGTGACATTAAATATTAAGATATTTGTTTTGGTAACATTGC
57 TCACTAAGAACTAAAATATTTAAATGTGACATTAAATGTTAGGATACTTGTTCTGGTAACATTGC
**
1455726 CAATTTTGAAAAAAGAATTTAATGATTATAATTCAATTGGTTAATACTTTGTAAATCACGTGAAG
122 CAATTTTGAAAAAAGAATTTAATGATTATAATTCAATTGGTTAACGCTTTGTAAATCACGTGAAG
* * * * *
1455791 ATATTTACTCAATATCAAATCATTTTATTAAAAGATGAAATGTCTAAATAAATATAAAATATTAT
187 ATATTTACTCAACATGAAACCATTTTGTTAAAAGATGAAATGTCTAAATAGATATAAAATATTAT
*
1455856 TACACTTATTAATTTT
252 TACACCTATTAATTTT
* * * * *
1455872 -CCTAACTCATAAGTATCACATGATATGCGTTTACTCAA-AAAAAAAAAAAAACTTCTTGAGGAA
1 GCC-AACTC------AT-AC-------GCGTTTTCTCAACAGAAAAAAAACATCTTCCTGAGGAA
* * *
1455935 ATTGTTTCACTAAG-AGTCAAAATATTTAAATTTGACATTTAATGTTAGGATACTTGTT-TCGG-
51 ATTGTTTCACTAAGAACT-AAAATATTTAAATGTGACATTAAATGTTAGGATACTTGTTCT-GGT
* * * * * **
1455997 AAAAAT-CTCAATTTT-AAGAAAGAATTAAATGATTATAATTTAATTGGTTAACATTTTGTAAAT
114 AACATTGC-CAATTTTGAAAAAAGAATTTAATGATTATAATTCAATTGGTTAACGCTTTGTAAAT
* ** * * *
1456060 CAAGTGAAGATGCTTACTCAACATAAAACCATTTAT-CTAAAAGATGAAATGTCTAGATAGATAT
178 CACGTGAAGATATTTACTCAACATGAAACCATTT-TGTTAAAAGATGAAATGTCTAAATAGATAT
*
1456124 AAAATATTATTACACTTATTAATTTT
242 AAAATATTATTACACCTATTAATTTT
* ** * * **
1456150 GCCAACTCTTACATGTTTTCTCAAC-TAAAAAAAA-ATCTTCCTAAGGAAATTGTTTCGTTAAGA
1 GCCAACTCATACGCGTTTTCTCAACAGAAAAAAAACATCTTCCTGAGGAAATTGTTTCACTAAGA
* * * *
1456213 GCTAAAATATTTAAATGTGACATTAAATGTTAGGATACTTGTTCTAGTAACACTGTCAATTTTG-
66 ACTAAAATATTTAAATGTGACATTAAATGTTAGGATACTTGTTCTGGTAACATTGCCAATTTTGA
* * **
1456277 AAAAAGAATTTAATGATTATAATTCAATTAGTTAACACTTTGTAAATCACGTGAAGATATTTTTT
131 AAAAAGAATTTAATGATTATAATTCAATTGGTTAACGCTTTGTAAATCACGTGAAGATATTTACT
* * * * *
1456342 CAAAATGAAATCGTTTTGTTAAAAGATAAAATGTTTAAATAGATATAAAATATTATTACACCTAT
196 CAACATGAAACCATTTTGTTAAAAGATGAAATGTCTAAATAGATATAAAATATTATTACACCTAT
*
1456407 TGATTTT
261 TAATTTT
* * * *
1456414 GCCAACTCATACGCGTTTTCTCAACAGAAAAAAAATCATCATCTTGAGAAAATTGTTTCATTAAG
1 GCCAACTCATACGCGTTTTCTCAACAGAAAAAAAA-CATCTTCCTGAGGAAATTGTTTCACTAAG
* * * * *
1456479 AGCTCAAATATTTAAACGTGACATTAAATATTAGGATATTTGTTCTGGTAACATTGCCAATTTTG
65 AACTAAAATATTTAAATGTGACATTAAATGTTAGGATACTTGTTCTGGTAACATTGCCAATTTTG
1456544 -AAAAAGAAATTTAATGATTATAATTCAATTGGTTAACGC-TTGTTAAATCACGTGAAGATATTT
130 AAAAAAG-AATTTAATGATTATAATTCAATTGGTTAACGCTTTG-TAAATCACGTGAAGATATTT
* * *
1456607 ATTCAACATGAAACCATTTTGTTAAAAGATAAAATGTTTAAATAGATATAAAATATTATTACACC
193 ACTCAACATGAAACCATTTTGTTAAAAGATGAAATGTCTAAATAGATATAAAATATTATTACACC
*
1456672 TATTGATTTT
258 TATTAATTTT
1456682 GCCAACTCATACGCGTTTTCTCAACAG-AAAAAAACATCTTCCTGAGGAAATTGTTTCACTAAGA
1 GCCAACTCATACGCGTTTTCTCAACAGAAAAAAAACATCTTCCTGAGGAAATTGTTTCACTAAGA
* * *
1456746 ATTAAAATATTTAAATGTGACATTAAATATTAGGATATTTGTTCTGGTAACATTGCCAATTTTGA
66 ACTAAAATATTTAAATGTGACATTAAATGTTAGGATACTTGTTCTGGTAACATTGCCAATTTTGA
*
1456811 AAAAAGAATTTAATGATTATAATTCAATTGGTTAACGC-TTGTTAAATCACGTGAAGATATTTAT
131 AAAAAGAATTTAATGATTATAATTCAATTGGTTAACGCTTTG-TAAATCACGTGAAGATATTTAC
** ** ** * * *
1456875 TCAACATGAAACTGTTTCATTAAAAGATGAAACATATAAATGGATATAAAATATTATTACATCTA
195 TCAACATGAAACCATTTTGTTAAAAGATGAAATGTCTAAATAGATATAAAATATTATTACACCTA
1456940 TTAATTTT
260 TTAATTTT
* * *
1456948 GCCAACTCATACGCGTTTTCTCAATAGAAAAAATAAACATCTTCCTAAGGAAATTGTTACACTAA
1 GCCAACTCATACGCGTTTTCTCAACAG-AAAAA-AAACATCTTCCTGAGGAAATTGTTTCACTAA
* * *
1457013 -AAGCTAAAATATTTAAATGTGACATTAATTGTTAGGATACTTGTTCCGGTAATATTGCCAATTT
64 GAA-CTAAAATATTTAAATGTGACATTAAATGTTAGGATACTTGTTCTGGTAACATTGCCAATTT
* * * * *** *
1457077 TG-AAAGAGAATTTACTTATTATAATTCAATTGATTAACGCTTCACAAACCACGTGAAGATATTT
128 TGAAAAAAGAATTTAATGATTATAATTCAATTGGTTAACGCTTTGTAAATCACGTGAAGATATTT
* * * ** *
1457141 ACCCAATATGAAACCGTTACGTTAAAAGATGAAATGTCCAAATAGATATAAAATATTATTACACC
193 ACTCAACATGAAACCATTTTGTTAAAAGATGAAATGTCTAAATAGATATAAAATATTATTACACC
1457206 TATTAATTTT
258 TATTAATTTT
* * * *
1457216 GCCAACACATACGCGTTTTCTCAACAGAAAAAAAACATCTTCCTGAGAAAATTATTTCACTAAAA
1 GCCAACTCATACGCGTTTTCTCAACAGAAAAAAAACATCTTCCTGAGGAAATTGTTTCACTAAGA
* * * *
1457281 ATTAAAATATTTAAATGTGACATTAAATGTTAAGATACCTGTTCCGGTAACATTGCCAATTTTGA
66 ACTAAAATATTTAAATGTGACATTAAATGTTAGGATACTTGTTCTGGTAACATTGCCAATTTTGA
* * * * *
1457346 AAAAAAAAATTAATGATTATAATTCAATTAGTTAAC-CTTTTATATAATCATGTGAAGAT
131 AAAAAGAATTTAATGATTATAATTCAATTGGTTAACGC-TTTGTA-AATCACGTGAAGAT
1457405 GCATATTCTT
Statistics
Matches: 1331, Mismatches: 158, Indels: 94
0.84 0.10 0.06
Matches are distributed among these distances:
263 63 0.05
264 167 0.13
265 8 0.01
266 318 0.24
267 143 0.11
268 306 0.23
269 87 0.07
271 2 0.00
272 1 0.00
273 2 0.00
274 5 0.00
278 128 0.10
279 19 0.01
280 64 0.05
281 6 0.00
287 1 0.00
288 11 0.01
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (267 bp):
GCCAACTCATACGCGTTTTCTCAACAGAAAAAAAACATCTTCCTGAGGAAATTGTTTCACTAAGA
ACTAAAATATTTAAATGTGACATTAAATGTTAGGATACTTGTTCTGGTAACATTGCCAATTTTGA
AAAAAGAATTTAATGATTATAATTCAATTGGTTAACGCTTTGTAAATCACGTGAAGATATTTACT
CAACATGAAACCATTTTGTTAAAAGATGAAATGTCTAAATAGATATAAAATATTATTACACCTAT
TAATTTT
Found at i:1456980 original size:534 final size:531
Alignment explanation
Indices: 1455598--1457404 Score: 2158
Period size: 534 Copynumber: 3.4 Consensus size: 531
1455588 TATTGAATTA
*
1455598 GCCAACTCATACGCGTTTTCTCAACAGAAAAAAAAAAAAAAACATCATT-TTGA-GAAACTTGTT
1 GCCAACTCATACGCGTTTTCTCAACAG-------AAAAAAAACATC-TTCCTGAGGAAA-TTGTT
* * * *
1455661 TCATTAAGAACTCAAATATTTAAATGTGACATTAAATATTAAGATATTTGTTTTGGTAACATTGC
57 TCACTAAGAACTAAAATATTTAAATGTGACATTAAATATTAAGATACTTGTTCTGGTAACATTGC
* *
1455726 CAATTTTGAAAAAAGAATTTAATGATTATAATTCAATTGGTTAATACTTTGTAAATCACGTGAAG
122 CAATTTTGAAAAAAGAATTTAATGATTATAATTCAATTAGTTAACACTTTGTAAATCACGTGAAG
* * * * *
1455791 ATATTTACTCAATATCAAATCAT-TTTATTAAAAGATGAAATGTCTAAATAAATATAAAATATTA
187 ATATTTATTCAAAATGAAA-C-TGTTTATTAAAAGATGAAATGTATAAATAGATATAAAATATTA
*
1455855 TTACACTTATTAATTTT-CCTAACTCATAAGTATCACATGATATGCGTTTACTCAAA-AAAAAAA
250 TTACAC-TATTAATTTTGCC-AACTC------AT-AC-------GCGTTTTCTCAAAGAAAAAAA
* * * *
1455918 AAAAACTTCTTGAGGAAATTGTTTCACTAAGAG-TCAAAATATTTAAATTTGACATTTAATGTTA
299 AACATCTTCTTGAGGAAATTGTTTCACTAAGAGCTC-AAATATTTAAATGTGACATTAAATGTTA
* * *
1455982 GGATACTTGTT-TCGG-AAAAAT-CTCAATTTT-AAGAAAGAATTAAATGATTATAATTTAATTG
363 GGATACTTGTTCT-GGTAAAATTGC-CAATTTTGAA-AAAGAATTTAATGATTATAATTCAATTG
* * * ** * *
1456043 GTTAAC-ATTTTGTAAATCAAGTGAAGATGCTTACTCAACATAAAACCATTTAT-CTAAAAGATG
425 GTTAACGCTTCT-TAAATCACGTGAAGATATTTACTCAACATGAAACCATTT-TGTTAAAAGATG
* *
1456106 AAATGTCTAGATAGATATAAAATATTATTACACTTATTAATTTT
488 AAATGTCTAAATAGATATAAAATATTATTACACCTATTAATTTT
* ** * * **
1456150 GCCAACTCTTACATGTTTTCTCAAC-TAAAAAAAA-ATCTTCCTAAGGAAATTGTTTCGTTAAGA
1 GCCAACTCATACGCGTTTTCTCAACAGAAAAAAAACATCTTCCTGAGGAAATTGTTTCACTAAGA
* * * * * *
1456213 GCTAAAATATTTAAATGTGACATTAAATGTTAGGATACTTGTTCTAGTAACACTGTCAATTTTG-
66 ACTAAAATATTTAAATGTGACATTAAATATTAAGATACTTGTTCTGGTAACATTGCCAATTTTGA
*
1456277 AAAAAGAATTTAATGATTATAATTCAATTAGTTAACACTTTGTAAATCACGTGAAGATATTTTTT
131 AAAAAGAATTTAATGATTATAATTCAATTAGTTAACACTTTGTAAATCACGTGAAGATATTTATT
* * *
1456342 CAAAATGAAA-TCGTTTTGTTAAAAGATAAAATGTTTAAATAGATATAAAATATTATTACACCTA
196 CAAAATGAAACT-G-TTTATTAAAAGATGAAATGTATAAATAGATATAAAATATTATTACA-CTA
* * * *
1456406 TTGATTTTGCCAACTCATACGCGTTTTCTCAACAGAAAAAAAATCATCATCTTGAGAAAATTGTT
258 TTAATTTTGCCAACTCATACGCGTTTTCTCAA-AGAAAAAAAAACATCTTCTTGAGGAAATTGTT
* * * * *
1456471 TCATTAAGAGCTCAAATATTTAAACGTGACATTAAATATTAGGATATTTGTTCTGGTAACATTGC
322 TCACTAAGAGCTCAAATATTTAAATGTGACATTAAATGTTAGGATACTTGTTCTGGTAAAATTGC
*
1456536 CAATTTTGAAAAAGAAATTTAATGATTATAATTCAATTGGTTAACGCTTGTTAAATCACGTGAAG
387 CAATTTTGAAAAAG-AATTTAATGATTATAATTCAATTGGTTAACGCTTCTTAAATCACGTGAAG
* * *
1456601 ATATTTATTCAACATGAAACCATTTTGTTAAAAGATAAAATGTTTAAATAGATATAAAATATTAT
451 ATATTTACTCAACATGAAACCATTTTGTTAAAAGATGAAATGTCTAAATAGATATAAAATATTAT
*
1456666 TACACCTATTGATTTT
516 TACACCTATTAATTTT
1456682 GCCAACTCATACGCGTTTTCTCAACAG-AAAAAAACATCTTCCTGAGGAAATTGTTTCACTAAGA
1 GCCAACTCATACGCGTTTTCTCAACAGAAAAAAAACATCTTCCTGAGGAAATTGTTTCACTAAGA
* * *
1456746 ATTAAAATATTTAAATGTGACATTAAATATTAGGATATTTGTTCTGGTAACATTGCCAATTTTGA
66 ACTAAAATATTTAAATGTGACATTAAATATTAAGATACTTGTTCTGGTAACATTGCCAATTTTGA
* *
1456811 AAAAAGAATTTAATGATTATAATTCAATTGGTTAACGC-TTGTTAAATCACGTGAAGATATTTAT
131 AAAAAGAATTTAATGATTATAATTCAATTAGTTAACACTTTG-TAAATCACGTGAAGATATTTAT
* ** *
1456875 TCAACATGAAACTGTTTCATTAAAAGATGAAACATATAAATGGATATAAAATATTATTACATCTA
195 TCAAAATGAAACTGTTT-ATTAAAAGATGAAATGTATAAATAGATATAAAATATTATTACA-CTA
* *
1456940 TTAATTTTGCCAACTCATACGCGTTTTCTCAATAGAAAAAATAAACATCTTCCTAAGGAAATTGT
258 TTAATTTTGCCAACTCATACGCGTTTTCTCAA-AGAAAAAA-AAACATCTTCTTGAGGAAATTGT
* * * * * *
1457005 TACACTAAAAGCTAAAATATTTAAATGTGACATTAATTGTTAGGATACTTGTTCCGGTAATATTG
321 TTCACTAAGAGCTCAAATATTTAAATGTGACATTAAATGTTAGGATACTTGTTCTGGTAAAATTG
* * * * ** *
1457070 CCAATTTTGAAAGAGAATTTACTTATTATAATTCAATTGATTAACGCTTCACAAACCACGTGAAG
386 CCAATTTTGAAAAAGAATTTAATGATTATAATTCAATTGGTTAACGCTTCTTAAATCACGTGAAG
* * * ** *
1457135 ATATTTACCCAATATGAAACCGTTACGTTAAAAGATGAAATGTCCAAATAGATATAAAATATTAT
451 ATATTTACTCAACATGAAACCATTTTGTTAAAAGATGAAATGTCTAAATAGATATAAAATATTAT
1457200 TACACCTATTAATTTT
516 TACACCTATTAATTTT
* * * *
1457216 GCCAACACATACGCGTTTTCTCAACAGAAAAAAAACATCTTCCTGAGAAAATTATTTCACTAAAA
1 GCCAACTCATACGCGTTTTCTCAACAGAAAAAAAACATCTTCCTGAGGAAATTGTTTCACTAAGA
* * * *
1457281 ATTAAAATATTTAAATGTGACATTAAATGTTAAGATACCTGTTCCGGTAACATTGCCAATTTTGA
66 ACTAAAATATTTAAATGTGACATTAAATATTAAGATACTTGTTCTGGTAACATTGCCAATTTTGA
* * * *
1457346 AAAAAAAAATTAATGATTATAATTCAATTAGTTAAC-CTTTTATATAATCATGTGAAGAT
131 AAAAAGAATTTAATGATTATAATTCAATTAGTTAACAC-TTTGTA-AATCACGTGAAGAT
1457405 GCATATTCTT
Statistics
Matches: 1097, Mismatches: 130, Indels: 72
0.84 0.10 0.06
Matches are distributed among these distances:
528 11 0.01
529 1 0.00
530 70 0.06
531 19 0.02
532 142 0.13
533 92 0.08
534 288 0.26
535 219 0.20
536 17 0.02
539 1 0.00
542 127 0.12
543 76 0.07
544 12 0.01
552 22 0.02
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (531 bp):
GCCAACTCATACGCGTTTTCTCAACAGAAAAAAAACATCTTCCTGAGGAAATTGTTTCACTAAGA
ACTAAAATATTTAAATGTGACATTAAATATTAAGATACTTGTTCTGGTAACATTGCCAATTTTGA
AAAAAGAATTTAATGATTATAATTCAATTAGTTAACACTTTGTAAATCACGTGAAGATATTTATT
CAAAATGAAACTGTTTATTAAAAGATGAAATGTATAAATAGATATAAAATATTATTACACTATTA
ATTTTGCCAACTCATACGCGTTTTCTCAAAGAAAAAAAAACATCTTCTTGAGGAAATTGTTTCAC
TAAGAGCTCAAATATTTAAATGTGACATTAAATGTTAGGATACTTGTTCTGGTAAAATTGCCAAT
TTTGAAAAAGAATTTAATGATTATAATTCAATTGGTTAACGCTTCTTAAATCACGTGAAGATATT
TACTCAACATGAAACCATTTTGTTAAAAGATGAAATGTCTAAATAGATATAAAATATTATTACAC
CTATTAATTTT
Found at i:1462697 original size:30 final size:30
Alignment explanation
Indices: 1462661--1462721 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1462651 AAAATCATTA
* * *
1462661 CACGTATTAATTTTGTCAGCTCATAAGCAT
1 CACGTATTAATATTGCCAACTCATAAGCAT
1462691 CACGTATTAATATTGCCAACTCATAAGCAT
1 CACGTATTAATATTGCCAACTCATAAGCAT
1462721 C
1 C
1462722 TTTCAATGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (30 bp):
CACGTATTAATATTGCCAACTCATAAGCAT
Found at i:1463667 original size:2 final size:2
Alignment explanation
Indices: 1463660--1463698 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
1463650 GTTATAATGT
1463660 TA TA TA TA -A TA TA TA -A TA TA TA TA T- TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1463698 T
1 T
1463699 NAACTAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
1 4 0.12
2 29 0.88
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1463671 original size:7 final size:7
Alignment explanation
Indices: 1463661--1463698 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
1463651 TTATAATGTT
1463661 ATATATA
1 ATATATA
1463668 ATATATA
1 ATATATA
1463675 ATATAT-
1 ATATATA
1463681 ATAT-TA
1 ATATATA
1463687 TATATATA
1 -ATATATA
1463695 ATAT
1 ATAT
1463699 NAACTAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
5 1 0.04
6 4 0.14
7 21 0.75
8 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
ATATATA
Found at i:1463674 original size:9 final size:9
Alignment explanation
Indices: 1463660--1463698 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
1463650 GTTATAATGT
1463660 TATATATAA
1 TATATATAA
1463669 TATATA-ATA
1 TATATATA-A
*
1463678 TATATATTA
1 TATATATAA
1463687 TATATATAA
1 TATATATAA
1463696 TAT
1 TAT
1463699 NAACTAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
8 1 0.04
9 25 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
TATATATAA
Found at i:1464581 original size:11 final size:12
Alignment explanation
Indices: 1464565--1464593 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1464555 TGCACCAAAA
1464565 AAATTTCCAAC-
1 AAATTTCCAACG
1464576 AAATTTCCAACG
1 AAATTTCCAACG
1464588 AAATTT
1 AAATTT
1464594 GTCTATTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.31
Consensus pattern (12 bp):
AAATTTCCAACG
Found at i:1466635 original size:133 final size:133
Alignment explanation
Indices: 1466450--1466711 Score: 353
Period size: 133 Copynumber: 2.0 Consensus size: 133
1466440 AAAATCTTTG
* * * *
1466450 ACTCAACATGAAACATTACAAATTGTCATTGGTTATTATTTTAAATATATATACGCTAAATATGT
1 ACTCAACATGAAACATTACAAATTGTCATTGGGTATTATTTTAAAGATATATACACCAAATATGT
* * * *
1466515 TACTCTCTACGTAATTTAACTTATTGAAACATTTTCATATGAAATTATTTTTCATTTGAGAATCA
66 TACTCTCAACGTAATTTAACTTATTCAAACATTTTCACATGAAATTATTTTTAATTTGAGAATCA
1466580 ATA
131 ATA
* * * * * * *
1466583 ACTCAACGTGAGACGTTACAATTTGTGATTGGGTATTATTTTAAAGATATATATACCGAATATGT
1 ACTCAACATGAAACATTACAAATTGTCATTGGGTATTATTTTAAAGATATATACACCAAATATGT
* ** *
1466648 TACTTTCAATTTAATTTAACTTATTCAAACATTTTCACATGAAATTGTTTTTAATTTGAGAATC
66 TACTCTCAACGTAATTTAACTTATTCAAACATTTTCACATGAAATTATTTTTAATTTGAGAATC
1466712 GCTAATTTGA
Statistics
Matches: 110, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
133 110 1.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (133 bp):
ACTCAACATGAAACATTACAAATTGTCATTGGGTATTATTTTAAAGATATATACACCAAATATGT
TACTCTCAACGTAATTTAACTTATTCAAACATTTTCACATGAAATTATTTTTAATTTGAGAATCA
ATA
Found at i:1467181 original size:271 final size:271
Alignment explanation
Indices: 1466593--1467443 Score: 1034
Period size: 272 Copynumber: 3.1 Consensus size: 271
1466583 ACTCAACGTG
* * * * *
1466593 AGACGTTACAATTTGTGATTGGGTATTATTTT-AAAGATATATATACCGAATATGTTACTTTC-A
1 AGACATTACAAATTGTAATTGGTTATTATTTTAAAAGATATATATACAG-ATATGTTACTTTCTA
* *
1466656 ATTTAATTTAACTTATTCAAACATTTTCACATGAAATTGTTTTTAATTTGAGAATCGCTAATTTG
65 CTTT-ATTTAACTTATTCAAACATTTTCACATGAAATTGTTTTTAATTTGAGAATCACTAATTTG
* * * * ** *
1466721 AGACGTTATGCATTATGACCAATTATTTTCTTCAAAATCACATGATGATGTTTTACTTTTTACTT
129 AGACGTTATGAATTGTGACCAATTATTTTCTTAAAAATCAC-TCAAAATGTTCTACTTTTTACTT
* ** *
1466786 AATTAATATATCTTTTGTTGTATTCAAACATATTTACGTGAAATTGTTCCTCTAATTTGAAAATC
193 AATTAATATATCTTTTGTCGTATTCAAACATATTTACGTGAAATTGTTTTTTTAATTTGAAAATC
* *
1466851 TCTCACTTAACACG
258 TCTAACTTAACACT
* *
1466865 AGA-AGTTATAATTTGTAATTGGTTATTATTTT-AAAGATATATATATCAGATATGTTACTTTCT
1 AGACA-TTACAAATTGTAATTGGTTATTATTTTAAAAGATATATATA-CAGATATGTTACTTTCT
* * * *
1466928 ACTTTATTTAACTTATTCAAACATTCTCACATAAAATTGTTTTTATTTTGAGAATCACTGATTTG
64 ACTTTATTTAACTTATTCAAACATTTTCACATGAAATTGTTTTTAATTTGAGAATCACTAATTTG
* *
1466993 AGACGTTATGAATTGTGACCAATTA-TTTATTAAAAATCACGTCAAAATGTTCTACTTTTTGCTT
129 AGACGTTATGAATTGTGACCAATTATTTTCTTAAAAATCAC-TCAAAATGTTCTACTTTTTACTT
* * * * *
1467057 AATTAATATATCTTCTGTCGTATTCAAACATATTTATGTGAGACTGTTTTTTTAATTTGAGAATC
193 AATTAATATATCTTTTGTCGTATTCAAACATATTTACGTGAAATTGTTTTTTTAATTTGAAAATC
*
1467122 TCTAAGTTAACACT
258 TCTAACTTAACACT
* * *
1467136 AGACATTACAAATTGTAATTGGCTATTATTTTAAACAGATATATATACCAAATACGTTACTTTCT
1 AGACATTACAAATTGTAATTGGTTATTATTTTAAA-AGATATATATA-CAGATATGTTACTTTCT
* * * * * *
1467201 ACTTAATTTAACTTATTCAAATATTTTCACGTGAAGTTATTTGTAATTTGAGAATCACTAATTTG
64 ACTTTATTTAACTTATTCAAACATTTTCACATGAAATTGTTTTTAATTTGAGAATCACTAATTTG
* * * * *
1467266 AGATGTTATGAACTGTGACCAATTATTTTCTTAAAGACCACACGAAGATAT-TTC-ACTTTTTAC
129 AGACGTTATGAATTGTGACCAATTATTTTCTTAAAAATCACTC-AA-A-ATGTTCTACTTTTTAC
* * * * *
1467329 TTAATTAATATATTTTTTGTCGTATTCAAATATATTCACATGAAATTGTTTTTTTAATTTAAAAA
191 TTAATTAATATATCTTTTGTCGTATTCAAACATATTTACGTGAAATTGTTTTTTTAATTTGAAAA
1467394 TCTCTAACTTAACA-T
256 TCTCTAACTTAACACT
** *
1467409 GAGATGTTACAAATTGTAATTGATTATTATTTTAA
1 -AGACATTACAAATTGTAATTGGTTATTATTTTAA
1467444 GAATCACGTG
Statistics
Matches: 497, Mismatches: 71, Indels: 20
0.85 0.12 0.03
Matches are distributed among these distances:
271 125 0.25
272 134 0.27
273 112 0.23
274 120 0.24
275 4 0.01
276 2 0.00
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.44
Consensus pattern (271 bp):
AGACATTACAAATTGTAATTGGTTATTATTTTAAAAGATATATATACAGATATGTTACTTTCTAC
TTTATTTAACTTATTCAAACATTTTCACATGAAATTGTTTTTAATTTGAGAATCACTAATTTGAG
ACGTTATGAATTGTGACCAATTATTTTCTTAAAAATCACTCAAAATGTTCTACTTTTTACTTAAT
TAATATATCTTTTGTCGTATTCAAACATATTTACGTGAAATTGTTTTTTTAATTTGAAAATCTCT
AACTTAACACT
Found at i:1468226 original size:272 final size:271
Alignment explanation
Indices: 1467728--1468336 Score: 716
Period size: 272 Copynumber: 2.2 Consensus size: 271
1467718 TCTTGATAAT
* * * * * * * * *
1467728 TTTAGTTTGAGAATCTCTAACTCAATATGAGACATTGCAAATTGTGATTGATTATTATTTTAAAA
1 TTTAATTTGAGAATCTCTAACTTAACACGAAACGTTACAAATTGTAATTGATTATTATTTT-AAG
*** * * *
1467793 ATATATATACCAGATATGTTACTTTTTACTTACTTTAACTTACTCAAATATTTTCACATGAAATT
65 ATATATATACCAGATACAATACTTTCTACTTAATTTAACTTACTCAAACATTTTCACATGAAATT
* * * *
1467858 AATTTTAATTTGAGAATCGCTAATTTCAGACGTTATGATTTGTAACAAATTATTTTCTTAAAGAC
130 AATTTTAATATGAGAATCGCTAATTTCAGACGTTATGAATCGTAACAAATTATTTTCTTAAAAAC
* * * ** *
1467923 CATGTGAAGATGATTGACTTTTTATTTAATTAATATATTTTTTATTATATTGAAATATATTCATG
195 CATGTGAAGATGATTGACTTTTTACTTAATTAATATATCTTTTATCATATACAAACATATTCATG
*
1467988 TGAAACAATTTC
260 TCAAACAATTTC
* * *
1468000 TTTAATTTGAGTATCTCTAACTTAACACGAAATGTTACAAATTGTAATTGACTATTATTTTCAAG
1 TTTAATTTGAGAATCTCTAACTTAACACGAAACGTTACAAATTGTAATTGATTATTATTTT-AAG
* * *
1468065 ATATATATACCATATACAATACTTTCTACTTAATTTAACTTATTCAAACATTTTCACGTGAAA-T
65 ATATATATACCAGATACAATACTTTCTACTTAATTTAACTTACTCAAACATTTTCACATGAAATT
* * * * * ** *
1468129 AGTTTTTTATATGAGATTTGCTAATTTTAGTTGTTATGAATCGTAACCAATTATTTTCTTAAAAA
130 A-ATTTTAATATGAGAATCGCTAATTTCAGACGTTATGAATCGTAACAAATTATTTTCTTAAAAA
* * * * *
1468194 CCATGTGAAGATGTTTTATTTTTTACTTAATTAATATATCTTTTGTCGTATACAAACATATTCAT
194 CCATGTGAAGATGATTGACTTTTTACTTAATTAATATATCTTTTATCATATACAAACATATTCAT
* * *
1468259 TTCAAACTATTTT
259 GTCAAACAATTTC
* * * *
1468272 TTTAATTTGAGAATTTCTAACTTAACAGGAGACGTTACAAATTGTAATTGGTTATTATTTTAAGA
1 TTTAATTTGAGAATCTCTAACTTAACACGAAACGTTACAAATTGTAATTGATTATTATTTTAAGA
1468337 ATCACGTGAA
Statistics
Matches: 280, Mismatches: 56, Indels: 3
0.83 0.17 0.01
Matches are distributed among these distances:
271 6 0.02
272 274 0.98
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (271 bp):
TTTAATTTGAGAATCTCTAACTTAACACGAAACGTTACAAATTGTAATTGATTATTATTTTAAGA
TATATATACCAGATACAATACTTTCTACTTAATTTAACTTACTCAAACATTTTCACATGAAATTA
ATTTTAATATGAGAATCGCTAATTTCAGACGTTATGAATCGTAACAAATTATTTTCTTAAAAACC
ATGTGAAGATGATTGACTTTTTACTTAATTAATATATCTTTTATCATATACAAACATATTCATGT
CAAACAATTTC
Found at i:1470988 original size:13 final size:13
Alignment explanation
Indices: 1470970--1470994 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1470960 ATTTTCAAAA
1470970 ATTTTATAAAATT
1 ATTTTATAAAATT
1470983 ATTTTATAAAAT
1 ATTTTATAAAAT
1470995 CTCATTTTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTATAAAATT
Found at i:1476631 original size:268 final size:264
Alignment explanation
Indices: 1475618--1476792 Score: 1411
Period size: 268 Copynumber: 4.4 Consensus size: 264
1475608 ATATATATAT
* *
1475618 ATATCTTTTGTTC-TATTCAAACATATAT-ACATGAAACTGTTTTTTTAATTTGAGAATCTCTAA
1 ATATATTTTG-TCATATTCAAACATAT-TCACGTGAAACTG-TTTTTTAATTTGAGAATCTCT-A
* * * * * * *
1475681 ATTAACACAAAATGTTACAAATTGTAATTGATTATTATTTTAAATATATATACCAGATACGTTCT
62 ATTTACACGAGACGTTATAAAATGTAATTGATTATTATTTTAAATATATATACCAGATACATTCT
*
1475746 TTCTACTTAATTTAACTTATTCAAACATTTTCATGTGAAATTGTTTTTAATTTGAAAATTGCTAA
127 TTCTACTTAATTTAACTTATTCAAACATTTTCATGTGAAATTGTTTTTAATTTGAAAATCGCTAA
* * * *
1475811 TTTGAGACGTTATGAATTGTGACTAATTATTTTCTTCAAAATCACGTG-AGATGCTTTACTTTTT
192 TTTGAGACGTTATGAATTGTGACCAATTATTTTCTTAAAAACCACGTGAAGATGTTTTA-TTTTT
*
1475875 ATTTAATTA
256 ACTTAATTA
* * *
1475884 ATATATCTTTTGTCGTATTCAGACATATTCACGTGAAACTGTTTCTTTAGTTTGAGAATCTCTAA
1 ATATA--TTTTGTCATATTCAAACATATTCACGTGAAACTGTTT-TTTAATTTGAGAATCTCTAA
* * * * *
1475949 TTTAACATGAGACGTTACT-AATTATAATTGATTATTATTTTAAAAATATATATACCAAATATAT
63 TTT-ACACGAGACGTTA-TAAAATGTAATTGATTATTATTTT--AAATATATATACCAGATACAT
**
1476013 TACTTTCTACTTAATTTAACTTATTCAAACATTTTCATGTGAAATTGTTTTTAATTTGAAAATTA
124 T-CTTTCTACTTAATTTAACTTATTCAAACATTTTCATGTGAAATTGTTTTTAATTTGAAAATCG
* * * *
1476078 CTAATTTGAGACGTTATAAATTGTGATCAATTATTTTCTTAAAAACCACGT-AAAAAG----A-T
188 CTAATTTGAGACGTTATGAATTGTGACCAATTATTTTCTTAAAAACCACGTGAAGATGTTTTATT
1476137 TTTACTTAATTA
253 TTTACTTAATTA
* * *
1476149 ATATATCTTTTGTCATATTCAAACATATTCACATGAAACCGTTTTTTTAATTTAAGAATCTCTTA
1 ATATA--TTTTGTCATATTCAAACATATTCACGTGAAACTG-TTTTTTAATTTGAGAATCTC-TA
* * * *
1476214 ATTAACACGAGACGTTACAAATTGTAATTGATTATTATTTTAAATATATATACCAGATACGTTCT
62 ATTTACACGAGACGTTATAAAATGTAATTGATTATTATTTTAAATATATATACCAGATACATTCT
* *
1476279 TTCTACTTAATTTAACTTATTCAAGCATTTTCACGTGAAATTGTTTTTAATTTGAAAATCGCTAA
127 TTCTACTTAATTTAACTTATTCAAACATTTTCATGTGAAATTGTTTTTAATTTGAAAATCGCTAA
* *
1476344 TTTGAGACGTTATGAATTGTGACCAATTATTTTCTTCAAAACCACGTGAATATGTTTTACTTTTT
192 TTTGAGACGTTATGAATTGTGACCAATTATTTTCTTAAAAACCACGTGAAGATGTTTTA-TTTTT
1476409 ACTTAATTA
256 ACTTAATTA
* *
1476418 ATATATTTTGTCATATTCAAACATATTCACGTGAAATTATTTTTATAATTTGAGAATCTCTAACT
1 ATATATTTTGTCATATTCAAACATATTCACGTGAAACTGTTTTT-TAATTTGAGAATCTCTAA-T
* * * * * ** * *
1476483 TTATATGAGACGTTATAAAATGCAATTGGTTCTTATTTTAAAGCTATATATCAGATACATTAGTT
64 TTACACGAGACGTTATAAAATGTAATTGATTATTATTTTAAATATATATACCAGATACATT-CTT
* * * ** *
1476548 TCTACTTAATTTAACTTATTTAAACATTTTCATGTGAAATTATTTGTAATTTGAGGATCGTTAAT
128 TCTACTTAATTTAACTTATTCAAACATTTTCATGTGAAATTGTTTTTAATTTGAAAATCGCTAAT
* * * *
1476613 TTGAGACGATACGAATTGTAACCAATTATTTT-TTAAAAGATCACGTGAAGATGTTTTATTTTTA
193 TTGAGACGTTATGAATTGTGACCAATTATTTTCTTAAAA-ACCACGTGAAGATGTTTTATTTTTA
1476677 CTTAATTA
257 CTTAATTA
* * * * *
1476685 ATATATTTT-TTATTGTATTTAAATATATTCACGTAAAATTGTGTTTTTAATTTGAGAATCTCTA
1 ATATATTTTGTCA---TATTCAAACATATTCACGTGAAACTGT-TTTTTAATTTGAGAATCTCTA
* *
1476749 ATTTAACACGAGACGTTATAAATTATAATTGATTATTATTTTAA
62 ATTT-ACACGAGACGTTATAAAATGTAATTGATTATTATTTTAA
1476793 GAATCACGTA
Statistics
Matches: 790, Mismatches: 89, Indels: 57
0.84 0.10 0.06
Matches are distributed among these distances:
262 107 0.14
263 23 0.03
265 97 0.12
266 22 0.03
267 134 0.17
268 182 0.23
269 91 0.12
270 23 0.03
271 111 0.14
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (264 bp):
ATATATTTTGTCATATTCAAACATATTCACGTGAAACTGTTTTTTAATTTGAGAATCTCTAATTT
ACACGAGACGTTATAAAATGTAATTGATTATTATTTTAAATATATATACCAGATACATTCTTTCT
ACTTAATTTAACTTATTCAAACATTTTCATGTGAAATTGTTTTTAATTTGAAAATCGCTAATTTG
AGACGTTATGAATTGTGACCAATTATTTTCTTAAAAACCACGTGAAGATGTTTTATTTTTACTTA
ATTA
Found at i:1481339 original size:2 final size:2
Alignment explanation
Indices: 1481332--1481372 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1481322 TTGTTTTAGC
1481332 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1481373 CTTCTCATAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1482543 original size:2 final size:2
Alignment explanation
Indices: 1482538--1482567 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1482528 TTAAAAAATA
1482538 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1482568 CAATACATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1490520 original size:30 final size:30
Alignment explanation
Indices: 1490436--1490514 Score: 122
Period size: 30 Copynumber: 2.6 Consensus size: 30
1490426 TGGAAAATAA
*
1490436 TAAAAAGAGAATTAGAGAATAGGAGAAAAT
1 TAAAAAGAGAATTAGAGAATAGAAGAAAAT
* *
1490466 TAAGAAGAGAATTACAGAATAGAAGAAAAT
1 TAAAAAGAGAATTAGAGAATAGAAGAAAAT
1490496 TAAAAAGAGAATTTAGAGA
1 TAAAAAGAGAA-TTAGAGA
1490515 GAGAAGTTCT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 37 0.86
31 6 0.14
ACGTcount: A:0.59, C:0.01, G:0.22, T:0.18
Consensus pattern (30 bp):
TAAAAAGAGAATTAGAGAATAGAAGAAAAT
Found at i:1490878 original size:29 final size:29
Alignment explanation
Indices: 1490837--1490919 Score: 105
Period size: 29 Copynumber: 2.9 Consensus size: 29
1490827 TAAGAGAAAG
*
1490837 AGAAAAAGGTGTACGTGAACAAGTATAAA
1 AGAAAAAAGTGTACGTGAACAAGTATAAA
* *
1490866 A-AAAATAAGTGTACGTGAATAGGTATAAA
1 AGAAAA-AAGTGTACGTGAACAAGTATAAA
* *
1490895 AGAAGAAAGCGTACGTGAACAAGTA
1 AGAAAAAAGTGTACGTGAACAAGTA
1490920 CATAAAAACA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
28 4 0.09
29 38 0.84
30 3 0.07
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18
Consensus pattern (29 bp):
AGAAAAAAGTGTACGTGAACAAGTATAAA
Found at i:1520682 original size:13 final size:13
Alignment explanation
Indices: 1520664--1520697 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1520654 CATTCAATCA
1520664 TTCTTTTTTTTTT
1 TTCTTTTTTTTTT
*
1520677 TTCTTTTGTTTTT
1 TTCTTTTTTTTTT
*
1520690 GTCTTTTT
1 TTCTTTTT
1520698 GGCAGGACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (13 bp):
TTCTTTTTTTTTT
Found at i:1522323 original size:21 final size:22
Alignment explanation
Indices: 1522294--1522334 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1522284 GGGAAAAGAA
1522294 TGTTCTTGCTTTGGAAATTTTG
1 TGTTCTTGCTTTGGAAATTTTG
*
1522316 TGTT-TTGCTTTGGATATTT
1 TGTTCTTGCTTTGGAAATTT
1522335 AACTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.12, C:0.07, G:0.22, T:0.59
Consensus pattern (22 bp):
TGTTCTTGCTTTGGAAATTTTG
Found at i:1528574 original size:33 final size:33
Alignment explanation
Indices: 1528537--1528611 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 33
1528527 GCCATGTTAT
* *
1528537 TATGTCACATCATCATCAATTATGATATGTCAA
1 TATGTCACATCATCATCAAGTATGACATGTCAA
* *
1528570 TATGTCACATTATTATCAAGTATGACATGTCAA
1 TATGTCACATCATCATCAAGTATGACATGTCAA
* *
1528603 CATGCCACA
1 TATGTCACA
1528612 ATAACGCCAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (33 bp):
TATGTCACATCATCATCAAGTATGACATGTCAA
Found at i:1528707 original size:30 final size:31
Alignment explanation
Indices: 1528667--1528727 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
1528657 AAATAATGAC
1528667 AAAGACTTATTT-GATTCAAAATAAAAATATA
1 AAAGACTTATTTAGATT-AAAATAAAAATATA
*
1528698 AAAGA-TTATTTAGCTTAAAATAAAAATATA
1 AAAGACTTATTTAGATTAAAATAAAAATATA
1528728 CGAATTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 20 0.71
31 8 0.29
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.33
Consensus pattern (31 bp):
AAAGACTTATTTAGATTAAAATAAAAATATA
Found at i:1529267 original size:18 final size:19
Alignment explanation
Indices: 1529232--1529270 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
1529222 TTCAATTTTA
1529232 AATAAAAGAATTTATTATT
1 AATAAAAGAATTTATTATT
1529251 AATAAAA-AA-TTATTTATT
1 AATAAAAGAATTTA-TTATT
1529269 AA
1 AA
1529271 ATACATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.16
18 9 0.47
19 7 0.37
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
AATAAAAGAATTTATTATT
Found at i:1529757 original size:13 final size:13
Alignment explanation
Indices: 1529741--1529766 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1529731 GAGTTTACAA
1529741 AAATAAATTTAAC
1 AAATAAATTTAAC
1529754 AAATAAATTTAAC
1 AAATAAATTTAAC
1529767 TTAATTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATAAATTTAAC
Found at i:1531668 original size:7 final size:7
Alignment explanation
Indices: 1531656--1531695 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
1531646 ATTAAGGGCC
1531656 GGCAATT
1 GGCAATT
1531663 GGCAATT
1 GGCAATT
1531670 GGCAATT
1 GGCAATT
1531677 GGCAATT
1 GGCAATT
1531684 GGCAATT
1 GGCAATT
1531691 GGCAA
1 GGCAA
1531696 GTCATTAAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.25
Consensus pattern (7 bp):
GGCAATT
Found at i:1533009 original size:12 final size:12
Alignment explanation
Indices: 1532992--1533016 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1532982 TGGTTTCATG
1532992 ATAAATTGTAGT
1 ATAAATTGTAGT
1533004 ATAAATTGTAGT
1 ATAAATTGTAGT
1533016 A
1 A
1533017 ATAACATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (12 bp):
ATAAATTGTAGT
Found at i:1533858 original size:21 final size:22
Alignment explanation
Indices: 1533833--1533880 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
1533823 TTTATTTTAA
1533833 AATAAATAAATT-ATTATGATT
1 AATAAATAAATTAATTATGATT
* *
1533854 AAT-AATTAATTAATTATTATT
1 AATAAATAAATTAATTATGATT
1533875 AATAAA
1 AATAAA
1533881 AATACTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 7 0.30
21 14 0.61
22 2 0.09
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
AATAAATAAATTAATTATGATT
Found at i:1546208 original size:14 final size:14
Alignment explanation
Indices: 1546189--1546215 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1546179 TATATCATTG
1546189 CAGTTTGTTAAAAA
1 CAGTTTGTTAAAAA
1546203 CAGTTTGTTAAAA
1 CAGTTTGTTAAAA
1546216 CGCTAAGCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (14 bp):
CAGTTTGTTAAAAA
Found at i:1552500 original size:10 final size:10
Alignment explanation
Indices: 1552485--1552515 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
1552475 TGCAGCCCTT
1552485 GAAAATAAAA
1 GAAAATAAAA
1552495 GAAAATAAAA
1 GAAAATAAAA
1552505 GAAAATAAAA
1 GAAAATAAAA
1552515 G
1 G
1552516 GGGATGTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (10 bp):
GAAAATAAAA
Found at i:1555433 original size:14 final size:15
Alignment explanation
Indices: 1555407--1555440 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
1555397 TTTATATATT
1555407 ATTAATAAAATTAAA
1 ATTAATAAAATTAAA
1555422 ATTAAT-AAATTAAA
1 ATTAATAAAATTAAA
1555436 ATTAA
1 ATTAA
1555441 CTTGTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATTAATAAAATTAAA
Found at i:1557307 original size:2 final size:2
Alignment explanation
Indices: 1557300--1557364 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
1557290 TAACTTTTAC
1557300 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1557342 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
1557365 AAAAAAANNN
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1557985 original size:15 final size:15
Alignment explanation
Indices: 1557965--1558002 Score: 53
Period size: 13 Copynumber: 2.6 Consensus size: 15
1557955 TAAAATTTAT
1557965 TAATTTTTTAAATTA
1 TAATTTTTTAAATTA
1557980 TAA--TTTTAAATTA
1 TAATTTTTTAAATTA
1557993 TAATTATTTT
1 TAATT-TTTT
1558003 TATAAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
13 13 0.65
15 3 0.15
16 4 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TAATTTTTTAAATTA
Found at i:1557986 original size:13 final size:13
Alignment explanation
Indices: 1557970--1557997 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1557960 TTTATTAATT
1557970 TTTTAAATTATAA
1 TTTTAAATTATAA
1557983 TTTTAAATTATAA
1 TTTTAAATTATAA
1557996 TT
1 TT
1557998 ATTTTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTAAATTATAA
Found at i:1558003 original size:30 final size:31
Alignment explanation
Indices: 1557967--1558028 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 31
1557957 AAATTTATTA
1557967 ATTTTT-TAAATTATAATTTTAAATTA-TAATT
1 ATTTTTATAAA-T-TAATTTTAAATTATTAATT
*
1557998 ATTTTTATAAATTAATTTTAATTTATTAATT
1 ATTTTTATAAATTAATTTTAAATTATTAATT
1558029 CAATTTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 12 0.43
31 12 0.43
32 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (31 bp):
ATTTTTATAAATTAATTTTAAATTATTAATT
Found at i:1558858 original size:13 final size:12
Alignment explanation
Indices: 1558834--1558881 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
1558824 TTTCAAAGAA
*
1558834 TCTTTTTCTTTT
1 TCTTTTTATTTT
1558846 TCTTTTTAGTTTT
1 TCTTTTTA-TTTT
1558859 T-TGTTTTATTTAT
1 TCT-TTTTATTT-T
1558872 TCTTTTTATT
1 TCTTTTTATT
1558882 GAAAAGAGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 11 0.35
13 19 0.61
14 1 0.03
ACGTcount: A:0.08, C:0.08, G:0.04, T:0.79
Consensus pattern (12 bp):
TCTTTTTATTTT
Found at i:1561794 original size:21 final size:21
Alignment explanation
Indices: 1561770--1561814 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1561760 CATTGTCAGC
1561770 ATCATCATCGTCTGCATCATT
1 ATCATCATCGTCTGCATCATT
* **
1561791 ATCATCATCTTCTTTATCATT
1 ATCATCATCGTCTGCATCATT
1561812 ATC
1 ATC
1561815 GATGGTAGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.27, G:0.04, T:0.44
Consensus pattern (21 bp):
ATCATCATCGTCTGCATCATT
Found at i:1564738 original size:29 final size:29
Alignment explanation
Indices: 1564703--1564783 Score: 103
Period size: 29 Copynumber: 2.8 Consensus size: 29
1564693 AAAAAATTCA
1564703 AATAAGTTCTTATATTTTTATTATG-CTC
1 AATAAGTTCTTATATTTTTATTATGACTC
* *
1564731 AATTAAGTTTTTATATTTTTATTTTGAAC-C
1 AA-TAAGTTCTTATATTTTTATTATG-ACTC
1564761 GAATAAGTTCTTATATTTTTATT
1 -AATAAGTTCTTATATTTTTATT
1564784 TTAAATCAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
28 2 0.04
29 21 0.46
30 20 0.43
31 3 0.07
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (29 bp):
AATAAGTTCTTATATTTTTATTATGACTC
Found at i:1564775 original size:30 final size:28
Alignment explanation
Indices: 1564703--1564785 Score: 105
Period size: 30 Copynumber: 2.9 Consensus size: 28
1564693 AAAAAATTCA
*
1564703 AATAAGTTCTTATATTTTTATTATGCTC
1 AATAAGTTCTTATATTTTTATTTTGCTC
*
1564731 AATTAAGTTTTTATATTTTTATTTTGAAC-C
1 AA-TAAGTTCTTATATTTTTATTTTG--CTC
1564761 GAATAAGTTCTTATATTTTTATTTT
1 -AATAAGTTCTTATATTTTTATTTT
1564786 AAATCAAATA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
28 2 0.04
29 21 0.44
30 22 0.46
31 3 0.06
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (28 bp):
AATAAGTTCTTATATTTTTATTTTGCTC
Found at i:1564805 original size:30 final size:30
Alignment explanation
Indices: 1564701--1564805 Score: 99
Period size: 30 Copynumber: 3.5 Consensus size: 30
1564691 TAAAAAAATT
* **
1564701 CAAATAAGTTCTTATATTTTTA--TTATGC
1 CAAATAAGTTTTTATATTTTTATTTTAAAC
* *
1564729 TCAATTAAGTTTTTATATTTTTATTTTGAAC
1 -CAAATAAGTTTTTATATTTTTATTTTAAAC
* * *
1564760 CGAATAAGTTCTTATATTTTTATTTTAAAT
1 CAAATAAGTTTTTATATTTTTATTTTAAAC
1564790 CAAAT-AGATTTTTATA
1 CAAATAAG-TTTTTATA
1564806 ATTAACAATT
Statistics
Matches: 61, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
29 22 0.36
30 36 0.59
31 3 0.05
ACGTcount: A:0.33, C:0.08, G:0.07, T:0.52
Consensus pattern (30 bp):
CAAATAAGTTTTTATATTTTTATTTTAAAC
Found at i:1573912 original size:57 final size:58
Alignment explanation
Indices: 1573840--1573972 Score: 234
Period size: 58 Copynumber: 2.3 Consensus size: 58
1573830 TCAGATTTTG
*
1573840 TTATGTGTTTGATATACTTAGCAG-GGTGAGTGTTTTAGTGGATTTCA-ATTTTCTTTA
1 TTATGTGTTTGATATACTGAGCAGTGGTGAGTGTTTTAGTGGATTT-ATATTTTCTTTA
1573897 TTATGTGTTTGATATACTGAGCAGTGGTGAGTGTTTTAGTGGATTTATATTTTCTTTA
1 TTATGTGTTTGATATACTGAGCAGTGGTGAGTGTTTTAGTGGATTTATATTTTCTTTA
1573955 TTATGTGTTTGATATACT
1 TTATGTGTTTGATATACT
1573973 CGGCGTTGGA
Statistics
Matches: 73, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
57 24 0.33
58 49 0.67
ACGTcount: A:0.21, C:0.06, G:0.23, T:0.50
Consensus pattern (58 bp):
TTATGTGTTTGATATACTGAGCAGTGGTGAGTGTTTTAGTGGATTTATATTTTCTTTA
Found at i:1587413 original size:20 final size:20
Alignment explanation
Indices: 1587376--1587414 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1587366 TTTAATGGAC
*
1587376 AAAATTTTAAATTATTTTAA
1 AAAATTTAAAATTATTTTAA
1587396 AAAATTTAATAATT-TTTTA
1 AAAATTTAA-AATTATTTTA
1587415 TTTTTATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AAAATTTAAAATTATTTTAA
Found at i:1587456 original size:24 final size:26
Alignment explanation
Indices: 1587403--1587466 Score: 78
Period size: 24 Copynumber: 2.5 Consensus size: 26
1587393 TAAAAAATTT
* * *
1587403 AATAATTTTTTATTTTTATTGTATTT
1 AATAAATTTTTATATTTATTGTATTA
1587429 AATAAATTTTTATATTT-TT-TATTA
1 AATAAATTTTTATATTTATTGTATTA
*
1587453 AATAAACTTTTATA
1 AATAAATTTTTATA
1587467 ATTAACGGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 17 0.50
25 2 0.06
26 15 0.44
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (26 bp):
AATAAATTTTTATATTTATTGTATTA
Found at i:1592533 original size:27 final size:27
Alignment explanation
Indices: 1592503--1592752 Score: 191
Period size: 27 Copynumber: 9.3 Consensus size: 27
1592493 TGGACCCTTT
*
1592503 CAAGCACCACCCCCTGCAATATGTGTA
1 CAAGCACCATCCCCTGCAATATGTGTA
* * * ** *
1592530 CAAGCACCATCTCCTGCTAGACCCTCT-
1 CAAGCACCATCCCCTGCAATA-TGTGTA
*
1592557 CAAGCACCAGCCCCTGCAATATGTGTA
1 CAAGCACCATCCCCTGCAATATGTGTA
* *** ** *
1592584 CAAGCACCATCTCCTGCTGGACCCTCT-
1 CAAGCACCATCCCCTGCAATA-TGTGTA
* * *
1592611 CAAGCACCAGCCCCAGCAATATGTGTG
1 CAAGCACCATCCCCTGCAATATGTGTA
* *** * *
1592638 CAAGCACCATCTCCTGCTGGATCCTCT-
1 CAAGCACCATCCCCTGCAATAT-GTGTA
* * *
1592665 CAGGCACCAGCCCCAGCAATATGTGTA
1 CAAGCACCATCCCCTGCAATATGTGTA
*
1592692 CAAGCACCATCCCCTGCAATAAGTGTA
1 CAAGCACCATCCCCTGCAATATGTGTA
*
1592719 CAAGCACCATCCCCTGCAATAAGTGTA
1 CAAGCACCATCCCCTGCAATATGTGTA
1592746 CAAGCAC
1 CAAGCAC
1592753 AATATCAGGA
Statistics
Matches: 165, Mismatches: 52, Indels: 12
0.72 0.23 0.05
Matches are distributed among these distances:
26 6 0.04
27 153 0.93
28 6 0.04
ACGTcount: A:0.28, C:0.37, G:0.16, T:0.19
Consensus pattern (27 bp):
CAAGCACCATCCCCTGCAATATGTGTA
Found at i:1592560 original size:54 final size:54
Alignment explanation
Indices: 1592486--1592752 Score: 365
Period size: 54 Copynumber: 4.9 Consensus size: 54
1592476 TTAGAAGCAG
* *
1592486 CTCCTGCTGGACCCTTTCAAGCACCACCCCCTGCAATATGTGTACAAGCACCAT
1 CTCCTGCTGGACCCTCTCAAGCACCAGCCCCTGCAATATGTGTACAAGCACCAT
*
1592540 CTCCTGCTAGACCCTCTCAAGCACCAGCCCCTGCAATATGTGTACAAGCACCAT
1 CTCCTGCTGGACCCTCTCAAGCACCAGCCCCTGCAATATGTGTACAAGCACCAT
* *
1592594 CTCCTGCTGGACCCTCTCAAGCACCAGCCCCAGCAATATGTGTGCAAGCACCAT
1 CTCCTGCTGGACCCTCTCAAGCACCAGCCCCTGCAATATGTGTACAAGCACCAT
* * *
1592648 CTCCTGCTGGATCCTCTCAGGCACCAGCCCCAGCAATATGTGTACAAGCACCAT
1 CTCCTGCTGGACCCTCTCAAGCACCAGCCCCTGCAATATGTGTACAAGCACCAT
* *** ** * * *
1592702 CCCCTGCAATA-AGTGTACAAGCACCATCCCCTGCAATAAGTGTACAAGCAC
1 CTCCTGCTGGACCCTCT-CAAGCACCAGCCCCTGCAATATGTGTACAAGCAC
1592753 AATATCAGGA
Statistics
Matches: 192, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
53 2 0.01
54 190 0.99
ACGTcount: A:0.26, C:0.37, G:0.16, T:0.20
Consensus pattern (54 bp):
CTCCTGCTGGACCCTCTCAAGCACCAGCCCCTGCAATATGTGTACAAGCACCAT
Found at i:1602827 original size:183 final size:183
Alignment explanation
Indices: 1602539--1602873 Score: 476
Period size: 183 Copynumber: 1.8 Consensus size: 183
1602529 CTCGTAATAC
* ** * * *
1602539 TGACGTGGTGTTGATATATAAAGTGAAATGTTATATGATCATATCATCATATTACGTTATCATTT
1 TGACGTGGTGCTGATATATAAAGTGAAATACTACATGATCATATCATCATACTACATTATCATTT
* *
1602604 ATTATAATATATCAATATATTACGTCAGTATCACGTGATATAAAATAATAAGATGAAATGTTATA
66 ATTATAATATATCAATATATTACGTCAGTATCACGTGATATAAAACAATAAGATGAAATGCTATA
1602669 TGACCATGTCATTTATTATAATGTGTCATCAATCATTTTATGCTTTGTGGTAA
131 TGACCATGTCATTTATTATAATGTGTCATCAATCATTTTATGCTTTGTGGTAA
* *
1602722 TGACGTGGTGCTGATGTAT-AAGATGAAATACTACATGA-CTATATCATCATACTATATTATCAT
1 TGACGTGGTGCTGATATATAAAG-TGAAATACTACATGATC-ATATCATCATACTACATTATCAT
* * * * * *
1602785 TTATTATAATATGTTAATATGTTACGTCAGTGTCATGTGATATAAAACAATAAGGTGAAATGCTA
64 TTATTATAATATATCAATATATTACGTCAGTATCACGTGATATAAAACAATAAGATGAAATGCTA
**
1602850 TATGACTTTGTCATTTATTATAAT
129 TATGACCATGTCATTTATTATAAT
1602874 TATGAAGTTT
Statistics
Matches: 132, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
182 4 0.03
183 128 0.97
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.40
Consensus pattern (183 bp):
TGACGTGGTGCTGATATATAAAGTGAAATACTACATGATCATATCATCATACTACATTATCATTT
ATTATAATATATCAATATATTACGTCAGTATCACGTGATATAAAACAATAAGATGAAATGCTATA
TGACCATGTCATTTATTATAATGTGTCATCAATCATTTTATGCTTTGTGGTAA
Found at i:1603318 original size:22 final size:23
Alignment explanation
Indices: 1603275--1603318 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
1603265 GATAATAACG
*
1603275 TAATTGATAAACAAAATAATAAA
1 TAATTGATAAACAAAACAATAAA
1603298 TAATT-ATAAA-AAAACACATAA
1 TAATTGATAAACAAAACA-ATAA
1603319 TTCATAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 9 0.47
23 5 0.26
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.25
Consensus pattern (23 bp):
TAATTGATAAACAAAACAATAAA
Found at i:1611522 original size:15 final size:17
Alignment explanation
Indices: 1611497--1611529 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1611487 TGTGTTAACA
1611497 TTATAAAAATTA-TAAT
1 TTATAAAAATTATTAAT
1611513 TTAT-AAAATTATTAAT
1 TTATAAAAATTATTAAT
1611529 T
1 T
1611530 GTAATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTATAAAAATTATTAAT
Found at i:1612081 original size:40 final size:40
Alignment explanation
Indices: 1611998--1612136 Score: 188
Period size: 40 Copynumber: 3.5 Consensus size: 40
1611988 TATATTTTTT
* * *
1611998 GTTATTTAAATTTATGTTATTTGTTTGGATATTTGTGTTTA
1 GTTATTTAAGTTTATGTT-GTTGTTTGGATATTTATGTTTA
* *
1612039 GTTATTTAAGTTTATGTTGTTATTTGGATATTTATGTATA
1 GTTATTTAAGTTTATGTTGTTGTTTGGATATTTATGTTTA
* * * *
1612079 GTTATTTAAGTTTATATCGTTGTATGGATATTTATTTTTA
1 GTTATTTAAGTTTATGTTGTTGTTTGGATATTTATGTTTA
1612119 GTTATTTAAGTTTATGTT
1 GTTATTTAAGTTTATGTT
1612137 TAAGATTTTT
Statistics
Matches: 85, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
40 68 0.80
41 17 0.20
ACGTcount: A:0.24, C:0.01, G:0.17, T:0.59
Consensus pattern (40 bp):
GTTATTTAAGTTTATGTTGTTGTTTGGATATTTATGTTTA
Found at i:1621451 original size:12 final size:12
Alignment explanation
Indices: 1621434--1621468 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1621424 TGTATGGAAC
1621434 ATGTGAAGATGA
1 ATGTGAAGATGA
1621446 ATGTGAAGATGA
1 ATGTGAAGATGA
**
1621458 AACTGAAGATG
1 ATGTGAAGATG
1621469 GGCAGTTGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.43, C:0.03, G:0.31, T:0.23
Consensus pattern (12 bp):
ATGTGAAGATGA
Found at i:1625416 original size:12 final size:13
Alignment explanation
Indices: 1625399--1625436 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1625389 ATTTAAAATT
1625399 AATAATTATAA-A
1 AATAATTATAACA
1625411 AATAATTATAACA
1 AATAATTATAACA
*
1625424 AATAATAATAACA
1 AATAATTATAACA
1625437 TCAAATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATTATAACA
Found at i:1625441 original size:16 final size:16
Alignment explanation
Indices: 1625422--1625468 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 16
1625412 ATAATTATAA
1625422 CAAATAATAATAACAT
1 CAAATAATAATAACAT
*
1625438 CAAAT-ATAATAAAAT
1 CAAATAATAATAACAT
*
1625453 CTAA-AATAAATAACAT
1 CAAATAAT-AATAACAT
1625469 ATATAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.64, C:0.11, G:0.00, T:0.26
Consensus pattern (16 bp):
CAAATAATAATAACAT
Found at i:1625448 original size:15 final size:15
Alignment explanation
Indices: 1625422--1625468 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
1625412 ATAATTATAA
1625422 CAAATAATAATAACAT
1 CAAAT-ATAATAACAT
*
1625438 CAAATATAATAAAAT
1 CAAATATAATAACAT
1625453 CTAAA-ATAAATAACAT
1 C-AAATAT-AATAACAT
1625469 ATATAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.64, C:0.11, G:0.00, T:0.26
Consensus pattern (15 bp):
CAAATATAATAACAT
Found at i:1626459 original size:128 final size:117
Alignment explanation
Indices: 1626225--1626456 Score: 317
Period size: 117 Copynumber: 2.0 Consensus size: 117
1626215 ATATAAATAA
* * *
1626225 AAATAAAGAAAAAGTAAAAAGAAATTAAAATTAAAAAATATATTAATAATTTAATAATAATTATA
1 AAATAAAGAAAAAATAAAAAGAAATTAAAAGTAAAAAATATATTAATAATTTAAGAATAATTATA
* * *
1626290 ATTTTAAATTTTTTATGAAAATAGAAATTAAAAGATTAAAAAATGAAACTAC
66 ATTTTAAATTTATAATGAAAATAGAAATTAAAAAATTAAAAAATGAAACTAC
* * *
1626342 AAATAGAGAAAAAATAAAGAGAAATT-GAAGTAAAAAATCATATTAATAATTTAAGAATGAATTA
1 AAATAAAGAAAAAATAAAAAGAAATTAAAAGTAAAAAAT-ATATTAATAATTTAAGAAT-AATTA
1626406 TTAATATTTTAAATTTATAATGAAAATA-AAATTAAAAAATTAAAAAA-GAAA
64 -T-A-ATTTTAAATTTATAATGAAAATAGAAATTAAAAAATTAAAAAATGAAA
1626457 AAATATTATT
Statistics
Matches: 101, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
116 10 0.10
117 41 0.41
118 5 0.05
119 5 0.05
120 19 0.19
121 21 0.21
ACGTcount: A:0.61, C:0.01, G:0.07, T:0.30
Consensus pattern (117 bp):
AAATAAAGAAAAAATAAAAAGAAATTAAAAGTAAAAAATATATTAATAATTTAAGAATAATTATA
ATTTTAAATTTATAATGAAAATAGAAATTAAAAAATTAAAAAATGAAACTAC
Found at i:1639593 original size:26 final size:25
Alignment explanation
Indices: 1639564--1639618 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
1639554 ATAAATGCTT
*
1639564 ATTTGACTCAAAATAAAAATATAAGA
1 ATTTGA-TCAAAATAAAAAAATAAGA
** *
1639590 ATTTGATTGAAATAAAAAAATAATA
1 ATTTGATCAAAATAAAAAAATAAGA
1639615 ATTT
1 ATTT
1639619 ATTTTAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 19 0.76
26 6 0.24
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (25 bp):
ATTTGATCAAAATAAAAAAATAAGA
Found at i:1640726 original size:11 final size:11
Alignment explanation
Indices: 1640710--1640734 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1640700 TTTTTTAACT
1640710 TTTAAAATTTA
1 TTTAAAATTTA
1640721 TTTAAAATTTA
1 TTTAAAATTTA
1640732 TTT
1 TTT
1640735 TTAGAGTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTAAAATTTA
Found at i:1644610 original size:3 final size:3
Alignment explanation
Indices: 1644602--1644628 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1644592 TTTAAATATG
1644602 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1644629 TGCCTTAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1647191 original size:8 final size:8
Alignment explanation
Indices: 1647149--1647190 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
1647139 TCACTCACCA
1647149 TTATTATT
1 TTATTATT
* *
1647157 TTGATAATA
1 TT-ATTATT
1647166 TTATTATT
1 TTATTATT
1647174 TTATTATT
1 TTATTATT
1647182 TTATT-TT
1 TTATTATT
1647189 TT
1 TT
1647191 TCACATCTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
7 4 0.14
8 19 0.66
9 6 0.21
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (8 bp):
TTATTATT
Found at i:1649453 original size:39 final size:39
Alignment explanation
Indices: 1649401--1649594 Score: 210
Period size: 39 Copynumber: 5.0 Consensus size: 39
1649391 TCATCTCTTA
* * ** *
1649401 CTGCCAACATCAAGTGCTAGCTCCCTCAACTCTACATTG
1 CTGCCACCTTCAAGTGCTAGCTCCCAGAACTCCACATTG
* * * *
1649440 CTTCCATCTTCAAGTGCTAGCTCCCAGAATTCCATATTG
1 CTGCCACCTTCAAGTGCTAGCTCCCAGAACTCCACATTG
* * * *
1649479 TTTCCACCTTCAAGTGCTAGCCCCCAGAACTCCACAATG
1 CTGCCACCTTCAAGTGCTAGCTCCCAGAACTCCACATTG
* * *
1649518 CAGCCACCTTCAAGTGCTAGCTCCCAGAACCCCACAGTG
1 CTGCCACCTTCAAGTGCTAGCTCCCAGAACTCCACATTG
* *
1649557 CTGCCACCTTCAAGTGCTAGCACCCTA-AACTCTACATT
1 CTGCCACCTTCAAGTGCTAGCTCCC-AGAACTCCACATT
1649595 TGTATCAATC
Statistics
Matches: 129, Mismatches: 25, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
39 128 0.99
40 1 0.01
ACGTcount: A:0.25, C:0.37, G:0.13, T:0.25
Consensus pattern (39 bp):
CTGCCACCTTCAAGTGCTAGCTCCCAGAACTCCACATTG
Found at i:1653874 original size:16 final size:16
Alignment explanation
Indices: 1653853--1653907 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
1653843 GAAACTCTGG
*
1653853 TCATTTTGGGTTTGGA
1 TCATTTTAGGTTTGGA
*
1653869 TCATTTTAGATATTGG-
1 TCATTTTAGGT-TTGGA
* *
1653885 TCATTTCAGGTTCGGA
1 TCATTTTAGGTTTGGA
1653901 TCATTTT
1 TCATTTT
1653908 CGGATTCAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
15 3 0.10
16 24 0.77
17 4 0.13
ACGTcount: A:0.18, C:0.11, G:0.22, T:0.49
Consensus pattern (16 bp):
TCATTTTAGGTTTGGA
Found at i:1656543 original size:27 final size:29
Alignment explanation
Indices: 1656508--1656565 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 29
1656498 TCAAGATAGT
* *
1656508 AATTAAAAAAGAAAA-GAAAAATAA-CAG
1 AATTAAAAAAAAAAAGGAAAAAGAATCAG
*
1656535 AATTTAAAAAAAAAAGGAAAAAGAATCAG
1 AATTAAAAAAAAAAAGGAAAAAGAATCAG
1656564 AA
1 AA
1656566 AAGAACAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 13 0.50
28 8 0.31
29 5 0.19
ACGTcount: A:0.72, C:0.03, G:0.12, T:0.12
Consensus pattern (29 bp):
AATTAAAAAAAAAAAGGAAAAAGAATCAG
Found at i:1656554 original size:28 final size:29
Alignment explanation
Indices: 1656510--1656565 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
1656500 AAGATAGTAA
*
1656510 TTAAAAAAGAAAAGAAAAATAA-CAGAAT
1 TTAAAAAAGAAAAGAAAAAGAATCAGAAT
1656538 TTAAAAAA-AAAAGGAAAAAGAATCAGAA
1 TTAAAAAAGAAAA-GAAAAAGAATCAGAA
1656566 AAGAACAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 4 0.16
28 16 0.64
29 5 0.20
ACGTcount: A:0.71, C:0.04, G:0.12, T:0.12
Consensus pattern (29 bp):
TTAAAAAAGAAAAGAAAAAGAATCAGAAT
Found at i:1658435 original size:6 final size:6
Alignment explanation
Indices: 1658426--1658467 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
1658416 TTGTGCTCTA
* *
1658426 GAGAGG GAGAGA GAGAGG GAGAGG GAGA-G GAG-GG GAAAGG GA
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GA
1658468 TCAAAAAGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
5 7 0.23
6 24 0.77
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:1661400 original size:29 final size:28
Alignment explanation
Indices: 1661334--1661405 Score: 65
Period size: 29 Copynumber: 2.5 Consensus size: 28
1661324 TTCAGATATA
*
1661334 TAAAATAAATAAATTTTTTATTTTTTCAT
1 TAAAATTAATAAATTTTTTATTTTTT-AT
* * *
1661363 TATATTTAATCAATATTTTTATTTTATT-T
1 TAAAATTAATAAAT-TTTTTATTTT-TTAT
*
1661392 TAAAATTAAAAAAT
1 TAAAATTAATAAAT
1661406 AAAATTTTTT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
29 21 0.64
30 10 0.30
31 2 0.06
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (28 bp):
TAAAATTAATAAATTTTTTATTTTTTAT
Found at i:1663765 original size:20 final size:20
Alignment explanation
Indices: 1663740--1663779 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1663730 AAGTTCAAAT
1663740 CGTCTAACAAAGTGAAGAAG
1 CGTCTAACAAAGTGAAGAAG
1663760 CGTCTAACAAAGTGAAGAAG
1 CGTCTAACAAAGTGAAGAAG
1663780 AAGAACCCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.15, G:0.25, T:0.15
Consensus pattern (20 bp):
CGTCTAACAAAGTGAAGAAG
Found at i:1678654 original size:14 final size:15
Alignment explanation
Indices: 1678635--1678677 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
1678625 TTAATTAATC
*
1678635 AATTAAATTTTTA-T
1 AATTAAATTATTATT
1678649 AATT-AATTATTATT
1 AATTAAATTATTATT
*
1678663 AATTAAAATATTATT
1 AATTAAATTATTATT
1678678 TTATATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 7 0.28
14 9 0.36
15 9 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AATTAAATTATTATT
Found at i:1678849 original size:29 final size:28
Alignment explanation
Indices: 1678797--1678884 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 28
1678787 TTTAATTACA
* *
1678797 ATAAAAATATTAATATTATATTAAATATT
1 ATAAAAATATAAAAATTAT-TTAAATATT
*
1678826 ATAAAAATATAAAAAATTATTTAAATTTTT
1 ATAAAAATAT-AAAAATTATTTAAA-TATT
* *
1678856 ATAAATAATTTATAAATT-TTTAAATATT
1 ATAAA-AATATAAAAATTATTTAAATATT
1678884 A
1 A
1678885 CGTCTAAACA
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
28 4 0.08
29 21 0.42
30 21 0.42
31 4 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
ATAAAAATATAAAAATTATTTAAATATT
Found at i:1678866 original size:19 final size:19
Alignment explanation
Indices: 1678839--1678881 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1678829 AAAATATAAA
* *
1678839 AAATTATTTA-AATTTTTAT
1 AAATAATTTATAAATTTT-T
1678858 AAATAATTTATAAATTTTT
1 AAATAATTTATAAATTTTT
1678877 AAATA
1 AAATA
1678882 TTACGTCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATAATTTATAAATTTTT
Found at i:1678873 original size:21 final size:22
Alignment explanation
Indices: 1678833--1678877 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
1678823 ATTATAAAAA
*
1678833 TATAAAAAATTATTTAAATTTT
1 TATAAAAAATTATATAAATTTT
*
1678855 TATAAATAATT-TATAAATTTT
1 TATAAAAAATTATATAAATTTT
1678876 TA
1 TA
1678878 AATATTACGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TATAAAAAATTATATAAATTTT
Found at i:1679290 original size:17 final size:17
Alignment explanation
Indices: 1679266--1679329 Score: 62
Period size: 16 Copynumber: 3.9 Consensus size: 17
1679256 AAATAAAATA
1679266 TTTA-AATATTAATATT
1 TTTATAATATTAATATT
* *
1679282 TTTATAATAAATAAAATT
1 TTTATAAT-ATTAATATT
*
1679300 TAT-TAATATTAA-ATT
1 TTTATAATATTAATATT
*
1679315 TTTATTATATTAATA
1 TTTATAATATTAATA
1679330 AATATTATGA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
15 5 0.13
16 16 0.42
17 8 0.21
18 9 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTATAATATTAATATT
Found at i:1679330 original size:39 final size:37
Alignment explanation
Indices: 1679245--1679333 Score: 98
Period size: 34 Copynumber: 2.5 Consensus size: 37
1679235 AAAGATCGTA
1679245 TATTA-ATTAATAAATAAAATATTTAAATATTAATAT
1 TATTATATTAATAAATAAAATATTTAAATATTAATAT
* *
1679281 T-TT-TA-TAATAAATAAAAT-TTATTAATATTAAATTTT
1 TATTATATTAATAAATAAAATATT-TAAATATT-AA-TAT
1679317 TATTATATTAATAAATA
1 TATTATATTAATAAATA
1679334 TTATGATATT
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
33 2 0.05
34 20 0.45
35 5 0.11
36 4 0.09
37 2 0.05
38 2 0.05
39 9 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (37 bp):
TATTATATTAATAAATAAAATATTTAAATATTAATAT
Found at i:1679343 original size:34 final size:34
Alignment explanation
Indices: 1679252--1679319 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 34
1679242 GTATATTAAT
*
1679252 TAATAAATAAAATATT-TAAATATTAATATTTTTA
1 TAATAAATAAAAT-TTATTAATATTAATATTTTTA
1679286 TAATAAATAAAATTTATTAATATTAA-ATTTTTA
1 TAATAAATAAAATTTATTAATATTAATATTTTTA
1679319 T
1 T
1679320 TATATTAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 10 0.31
34 22 0.69
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (34 bp):
TAATAAATAAAATTTATTAATATTAATATTTTTA
Found at i:1680353 original size:2 final size:2
Alignment explanation
Indices: 1680348--1680381 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1680338 AAAAAAATGN
1680348 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1680382 ATTATTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1680463 original size:26 final size:26
Alignment explanation
Indices: 1680409--1680463 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
1680399 AAATAAGTTT
* **
1680409 TTTTTTTACTTTCAATCAAATTATTA
1 TTTTTTTACTTTCAATCAAATAAGCA
* *
1680435 TTTTTTTATTTTGAATCAAATAAGCA
1 TTTTTTTACTTTCAATCAAATAAGCA
1680461 TTT
1 TTT
1680464 ATAACTAATG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.09, G:0.04, T:0.56
Consensus pattern (26 bp):
TTTTTTTACTTTCAATCAAATAAGCA
Found at i:1685966 original size:15 final size:14
Alignment explanation
Indices: 1685946--1685979 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1685936 TGATTAACTA
1685946 TAATTAATTAATTTT
1 TAATTAATTAA-TTT
*
1685961 TAATTAATTTATTT
1 TAATTAATTAATTT
1685975 TAATT
1 TAATT
1685980 TAAAACAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TAATTAATTAATTT
Found at i:1688179 original size:18 final size:18
Alignment explanation
Indices: 1688149--1688194 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1688139 ATTAAAATTA
1688149 AAATTTT-AATATTATATT
1 AAATTTTAAATATT-TATT
*
1688167 -AATTTTAAATATTTTTT
1 AAATTTTAAATATTTATT
1688184 AAATTTTAAAT
1 AAATTTTAAAT
1688195 TAATAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AAATTTTAAATATTTATT
Found at i:1692472 original size:2 final size:2
Alignment explanation
Indices: 1692465--1692505 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1692455 ACATTTCTTT
1692465 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1692506 GTACTATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1695193 original size:16 final size:16
Alignment explanation
Indices: 1695172--1695223 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
1695162 ATCATGTCAT
*
1695172 TATCAATTATGATATC
1 TATCAATTATGATATA
*
1695188 TATCAATATATCATATTA
1 TATCAAT-TATGATA-TA
1695206 TCATCAATTATGATATA
1 T-ATCAATTATGATATA
1695223 T
1 T
1695224 TAATATGTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 7 0.23
17 9 0.30
18 8 0.27
19 6 0.20
ACGTcount: A:0.40, C:0.12, G:0.04, T:0.44
Consensus pattern (16 bp):
TATCAATTATGATATA
Found at i:1696120 original size:29 final size:28
Alignment explanation
Indices: 1696087--1696243 Score: 86
Period size: 28 Copynumber: 5.6 Consensus size: 28
1696077 GATGTATAAC
* *
1696087 AATTTTTTCATCATGACGTATAACAATTA
1 AATTTTTT-AACATGACGTATAACAACTA
* *
1696116 AATTTTTTAACATGATGTGTAACAACTA
1 AATTTTTTAACATGACGTATAACAACTA
* * * ** *
1696144 AA-TTTTCAATATAATATATAATAACTA
1 AATTTTTTAACATGACGTATAACAACTA
* * * *
1696171 TATTTTTAAACATGACATGTAAC-ACTTA
1 AATTTTTTAACATGACGTATAACAAC-TA
* * * ** *
1696199 CATTTTTCAACATAACACATAATAAC-A
1 AATTTTTTAACATGACGTATAACAACTA
*
1696226 AATTTTTTAACATAACGT
1 AATTTTTTAACATGACGT
1696244 GTAATAATTA
Statistics
Matches: 98, Mismatches: 27, Indels: 8
0.74 0.20 0.06
Matches are distributed among these distances:
27 37 0.38
28 51 0.52
29 10 0.10
ACGTcount: A:0.43, C:0.13, G:0.05, T:0.39
Consensus pattern (28 bp):
AATTTTTTAACATGACGTATAACAACTA
Found at i:1696176 original size:55 final size:54
Alignment explanation
Indices: 1696115--1696263 Score: 156
Period size: 55 Copynumber: 2.7 Consensus size: 54
1696105 TATAACAATT
* * * *
1696115 AAATTTTTTAACATGATGTGTAACAACTAAATTTTCAATATAATATATAATAAC
1 AAATTTTTTAACATGACGTGTAACAACTAAATTTTCAACATAACACATAATAAC
* * * *
1696169 TATATTTTTAAACATGACATGTAAC-ACTTACATTTTTCAACATAACACATAATAAC
1 -AAATTTTTTAACATGACGTGTAACAAC-TA-AATTTTCAACATAACACATAATAAC
* * * *
1696225 AAATTTTTTAACATAACGTGTAATAATTATATTTTCAAC
1 AAATTTTTTAACATGACGTGTAACAACTAAATTTTCAAC
1696264 GTGAATTTTT
Statistics
Matches: 75, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
54 10 0.13
55 43 0.57
56 22 0.29
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.39
Consensus pattern (54 bp):
AAATTTTTTAACATGACGTGTAACAACTAAATTTTCAACATAACACATAATAAC
Found at i:1696259 original size:27 final size:28
Alignment explanation
Indices: 1696162--1696259 Score: 81
Period size: 28 Copynumber: 3.5 Consensus size: 28
1696152 ATATAATATA
* *
1696162 TAATAACTATATTTTTAAACATGACATG
1 TAATAATTATATTTTTAAACATAACATG
* * * * **
1696190 TAACACTTACATTTTTCAACATAACACA
1 TAATAATTATATTTTTAAACATAACATG
* * * *
1696218 TAATAA-CAAATTTTTTAACATAACGTG
1 TAATAATTATATTTTTAAACATAACATG
1696245 TAATAATTATATTTT
1 TAATAATTATATTTT
1696260 CAACGTGAAT
Statistics
Matches: 51, Mismatches: 18, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
27 21 0.41
28 30 0.59
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.40
Consensus pattern (28 bp):
TAATAATTATATTTTTAAACATAACATG
Found at i:1703911 original size:135 final size:135
Alignment explanation
Indices: 1703756--1704025 Score: 540
Period size: 135 Copynumber: 2.0 Consensus size: 135
1703746 ATGAACTGCA
1703756 ATGCATGCCATTCTTCATTATTATATCTTTGATAACATAACCATTTCTGAAGCTTTTGTTGTCCT
1 ATGCATGCCATTCTTCATTATTATATCTTTGATAACATAACCATTTCTGAAGCTTTTGTTGTCCT
1703821 TTGTGCTGTTGTTGACAAGTATGTTTTTGACTTAACAGACAATAGACACTTGCATCAAACTTGCT
66 TTGTGCTGTTGTTGACAAGTATGTTTTTGACTTAACAGACAATAGACACTTGCATCAAACTTGCT
1703886 TTTGC
131 TTTGC
1703891 ATGCATGCCATTCTTCATTATTATATCTTTGATAACATAACCATTTCTGAAGCTTTTGTTGTCCT
1 ATGCATGCCATTCTTCATTATTATATCTTTGATAACATAACCATTTCTGAAGCTTTTGTTGTCCT
1703956 TTGTGCTGTTGTTGACAAGTATGTTTTTGACTTAACAGACAATAGACACTTGCATCAAACTTGCT
66 TTGTGCTGTTGTTGACAAGTATGTTTTTGACTTAACAGACAATAGACACTTGCATCAAACTTGCT
1704021 TTTGC
131 TTTGC
1704026 CCTTGCAAGA
Statistics
Matches: 135, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
135 135 1.00
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (135 bp):
ATGCATGCCATTCTTCATTATTATATCTTTGATAACATAACCATTTCTGAAGCTTTTGTTGTCCT
TTGTGCTGTTGTTGACAAGTATGTTTTTGACTTAACAGACAATAGACACTTGCATCAAACTTGCT
TTTGC
Found at i:1704375 original size:2 final size:2
Alignment explanation
Indices: 1704363--1704415 Score: 63
Period size: 2 Copynumber: 27.0 Consensus size: 2
1704353 AGGCATGTAC
* * *
1704363 AT AT A- AT AT AT AT AT AA AT AT CT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1704404 AT AT AT GT AT AT
1 AT AT AT AT AT AT
1704416 TTACTATGTC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1705779 original size:63 final size:63
Alignment explanation
Indices: 1705675--1705863 Score: 249
Period size: 63 Copynumber: 3.0 Consensus size: 63
1705665 GTGGCAAAAA
* * * * *
1705675 TAACAATTAAATGTGTTTCAAGTGGGAGATAGAGATGACCAACGGATCACAAAATTGTTGTCT
1 TAACAATCAAATGTGTTTCAAGTGGGAGTTAGAGACGACCAAGGGAACACAAAATTGTTGTCT
* *
1705738 TAACAATCAAATGTGTTTTAAGTGGGAGTTAGAGACAACCAAGGGAACACAAAATTGGTT-T-T
1 TAACAATCAAATGTGTTTCAAGTGGGAGTTAGAGACGACCAAGGGAACACAAAATT-GTTGTCT
* * *
1705800 GTAACAATCAAATG-ATTTCAAGTGGGAGTCAGAGACGACCAAGGGAACTCAAAATTGTTGTCT
1 -TAACAATCAAATGTGTTTCAAGTGGGAGTTAGAGACGACCAAGGGAACACAAAATTGTTGTCT
1705863 T
1 T
1705864 TTGTTACTTC
Statistics
Matches: 110, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
61 3 0.03
62 40 0.36
63 64 0.58
64 3 0.03
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (63 bp):
TAACAATCAAATGTGTTTCAAGTGGGAGTTAGAGACGACCAAGGGAACACAAAATTGTTGTCT
Found at i:1714442 original size:79 final size:79
Alignment explanation
Indices: 1714348--1714508 Score: 313
Period size: 79 Copynumber: 2.0 Consensus size: 79
1714338 ATGTAACAAA
1714348 TTAGAGCCTATCTTGTTATGTGTGGGTTTCTTCCTCCTGCTTGGTTTCTGAATTAGGGAAATCTC
1 TTAGAGCCTATCTTGTTATGTGTGGGTTTCTTCCTCCTGCTTGGTTTCTGAATTAGGGAAATCTC
*
1714413 AAATCTGTTGCAAT
66 AAATCTGCTGCAAT
1714427 TTAGAGCCTATCTTGTTATGTGTGGGTTTCTTCCTCCTGCTTGGTTTCTGAATTAGGGAAATCTC
1 TTAGAGCCTATCTTGTTATGTGTGGGTTTCTTCCTCCTGCTTGGTTTCTGAATTAGGGAAATCTC
1714492 AAATCTGCTGCAAT
66 AAATCTGCTGCAAT
1714506 TTA
1 TTA
1714509 TGACCACCAC
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 81 1.00
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (79 bp):
TTAGAGCCTATCTTGTTATGTGTGGGTTTCTTCCTCCTGCTTGGTTTCTGAATTAGGGAAATCTC
AAATCTGCTGCAAT
Found at i:1719435 original size:15 final size:15
Alignment explanation
Indices: 1719415--1719450 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
1719405 ATTAAGGAGA
1719415 GTAGCTGGTAGCCTT
1 GTAGCTGGTAGCCTT
1719430 GTAGCTGGTAGCCTT
1 GTAGCTGGTAGCCTT
1719445 GTAGCT
1 GTAGCT
1719451 CGCTACTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.14, C:0.19, G:0.33, T:0.33
Consensus pattern (15 bp):
GTAGCTGGTAGCCTT
Found at i:1727771 original size:102 final size:103
Alignment explanation
Indices: 1727595--1727797 Score: 372
Period size: 102 Copynumber: 2.0 Consensus size: 103
1727585 AACCTAAGCT
* *
1727595 AATAAAACTAATACTCTAAGATTTGTTGTTTCTAGATGCTACCAAAGGAATCATTGTACTTTCAA
1 AATAAAACTAATACTCTAAGATTAGTTGTTTCCAGATGCTACCAAAGGAATCATTGTACTTTCAA
1727660 CTTTAAATTGTAACA-TCAAATTCATTTATATGTATGC
66 CTTTAAATTGTAACATTCAAATTCATTTATATGTATGC
*
1727697 AATAAAACTGATACTCTAAGATTAGTTGTTTCCAGATGCTACCAAAGGAATCATTGTACTTTCAA
1 AATAAAACTAATACTCTAAGATTAGTTGTTTCCAGATGCTACCAAAGGAATCATTGTACTTTCAA
1727762 CTTTAAATTGTAACATTCAAATTCATTTATATGTAT
66 CTTTAAATTGTAACATTCAAATTCATTTATATGTAT
1727798 ATATGTATAG
Statistics
Matches: 97, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
102 77 0.79
103 20 0.21
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (103 bp):
AATAAAACTAATACTCTAAGATTAGTTGTTTCCAGATGCTACCAAAGGAATCATTGTACTTTCAA
CTTTAAATTGTAACATTCAAATTCATTTATATGTATGC
Found at i:1728019 original size:2 final size:2
Alignment explanation
Indices: 1728012--1728040 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1728002 AATGAGGGCA
1728012 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1728041 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1731471 original size:2 final size:2
Alignment explanation
Indices: 1731458--1731513 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
1731448 GTATTTATGC
*
1731458 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1731500 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1731514 CTTTCTGAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1733459 original size:21 final size:22
Alignment explanation
Indices: 1733420--1733460 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1733410 GAGAAGGTAG
1733420 AACAATTAATTGAAATTTTTAT
1 AACAATTAATTGAAATTTTTAT
*
1733442 AACATTTAATTG-AATTTTT
1 AACAATTAATTGAAATTTTT
1733461 GTAATATACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (22 bp):
AACAATTAATTGAAATTTTTAT
Found at i:1754834 original size:93 final size:93
Alignment explanation
Indices: 1754675--1754861 Score: 356
Period size: 93 Copynumber: 2.0 Consensus size: 93
1754665 TCAAATGATA
*
1754675 ACTACAAACTGAAATTAGTGATGATGATATTTTTGTTAAACAGGACAAATACAGCTGATGCAATG
1 ACTACAAACTGAAATTAGTGATCATGATATTTTTGTTAAACAGGACAAATACAGCTGATGCAATG
1754740 ATTCAGAAGATTAAAAATCAAATCAGAT
66 ATTCAGAAGATTAAAAATCAAATCAGAT
1754768 ACTACAAACTGAAATTAGTGATCATGATATTTTTGTTAAACAGGACAAATACAGCTGATGCAATG
1 ACTACAAACTGAAATTAGTGATCATGATATTTTTGTTAAACAGGACAAATACAGCTGATGCAATG
*
1754833 ATTCGGAAGATTAAAAATCAAATCAGAT
66 ATTCAGAAGATTAAAAATCAAATCAGAT
1754861 A
1 A
1754862 ATATGTTGAT
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (93 bp):
ACTACAAACTGAAATTAGTGATCATGATATTTTTGTTAAACAGGACAAATACAGCTGATGCAATG
ATTCAGAAGATTAAAAATCAAATCAGAT
Found at i:1756243 original size:45 final size:45
Alignment explanation
Indices: 1756179--1756306 Score: 139
Period size: 45 Copynumber: 2.8 Consensus size: 45
1756169 CACTCTATGA
* *
1756179 TGTTACACGTCATGTACAAAAACCTGTGACAAGCCATGGTTAACG
1 TGTTACACGTCATGCACAAAAACATGTGACAAGCCATGGTTAACG
* * * * * *
1756224 TGTTATACGTTATGCACAAAAATATGTGACAAGTCATGGTTAGCT
1 TGTTACACGTCATGCACAAAAACATGTGACAAGCCATGGTTAACG
** * * *
1756269 TGTTACACACCATGTACAAAAATATGTGACAAGTCATG
1 TGTTACACGTCATGCACAAAAACATGTGACAAGCCATG
1756307 TATAAAAACC
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 70 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (45 bp):
TGTTACACGTCATGCACAAAAACATGTGACAAGCCATGGTTAACG
Found at i:1756313 original size:24 final size:24
Alignment explanation
Indices: 1756279--1756326 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1756269 TGTTACACAC
*
1756279 CATGTACAAAAATATGTGACAAGT
1 CATGTACAAAAACATGTGACAAGT
* *
1756303 CATGTATAAAAACCTGTGACAAGT
1 CATGTACAAAAACATGTGACAAGT
1756327 TATAATTAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.25
Consensus pattern (24 bp):
CATGTACAAAAACATGTGACAAGT
Found at i:1756350 original size:45 final size:45
Alignment explanation
Indices: 1756301--1756397 Score: 113
Period size: 45 Copynumber: 2.2 Consensus size: 45
1756291 TATGTGACAA
* * *
1756301 GTCATGTATAAAAACCTGTGACAAGTTATAATTAGCTTGTTATAC
1 GTCATGTACAAAAACCTATGACAAGTTATAATTAGCTTGTTACAC
* * ** *
1756346 GTCATATACAAAAACCTATTACAAGTTATGGTTAGGTTGTTACAC
1 GTCATGTACAAAAACCTATGACAAGTTATAATTAGCTTGTTACAC
*
1756391 GCCATGT
1 GTCATGT
1756398 TGAAAAAAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Consensus pattern (45 bp):
GTCATGTACAAAAACCTATGACAAGTTATAATTAGCTTGTTACAC
Found at i:1756404 original size:114 final size:114
Alignment explanation
Indices: 1756178--1756397 Score: 273
Period size: 114 Copynumber: 1.9 Consensus size: 114
1756168 ACACTCTATG
* * ** * *
1756178 ATGTTACACGTCATGTACAAAAACCTGTGACAAGCCATGGTTAACGTGTTATACGTTATGCACAA
1 ATGTGACAAGTCATGTACAAAAACCTGTGACAAGCCATAATTAACGTGTTATACGTCATACACAA
1756243 AAATATGTGACAAGTCATGGTTAGCTTGTTACACACCATGTACAAAAAT
66 AAATATGTGACAAGTCATGGTTAGCTTGTTACACACCATGTACAAAAAT
* ** * * *
1756292 ATGTGACAAGTCATGTATAAAAACCTGTGACAAGTTATAATTAGCTTGTTATACGTCATATACAA
1 ATGTGACAAGTCATGTACAAAAACCTGTGACAAGCCATAATTAACGTGTTATACGTCATACACAA
* * *
1756357 AAACCTAT-T-ACAAGTTATGGTTAGGTTGTTACACGCCATGT
66 AAA--TATGTGACAAGTCATGGTTAGCTTGTTACACACCATGT
1756398 TGAAAAAAAT
Statistics
Matches: 89, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
114 85 0.96
115 1 0.01
116 3 0.03
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (114 bp):
ATGTGACAAGTCATGTACAAAAACCTGTGACAAGCCATAATTAACGTGTTATACGTCATACACAA
AAATATGTGACAAGTCATGGTTAGCTTGTTACACACCATGTACAAAAAT
Found at i:1756427 original size:30 final size:30
Alignment explanation
Indices: 1756382--1756441 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1756372 TATGGTTAGG
**
1756382 TTGTTACACGCCATGTTGAAAAAAATATTA
1 TTGTTACACGCCATGTACAAAAAAATATTA
* * *
1756412 TTGTTTCACGGCATGTACAAAAATATATTA
1 TTGTTACACGCCATGTACAAAAAAATATTA
1756442 CACGTCATGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (30 bp):
TTGTTACACGCCATGTACAAAAAAATATTA
Found at i:1756525 original size:29 final size:29
Alignment explanation
Indices: 1756462--1756558 Score: 108
Period size: 29 Copynumber: 3.3 Consensus size: 29
1756452 TTAAAAAAGG
* *
1756462 TTGTTACACCTCATGTTGAAAAAAATATATTA
1 TTGTTACACCACATATTG--AAAAA-ATATTA
*
1756494 TTGTTACACCCCATATTGAAAAAATATTA
1 TTGTTACACCACATATTGAAAAAATATTA
* *
1756523 TTGTTACACGACATATT-AAAAAACATT-
1 TTGTTACACCACATATTGAAAAAATATTA
1756550 TTGTTACAC
1 TTGTTACAC
1756559 TTTAATGCCA
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 9 0.15
28 9 0.15
29 21 0.35
30 5 0.08
32 16 0.27
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.36
Consensus pattern (29 bp):
TTGTTACACCACATATTGAAAAAATATTA
Found at i:1757293 original size:29 final size:29
Alignment explanation
Indices: 1757260--1757315 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
1757250 AGGAAAAAAA
1757260 ATTTAAATAAAATTTTAT-TTTTATATTAT
1 ATTTAAATAAAATTTTATATTTT-TATTAT
* *
1757289 ATTTAATTAAATTTTTATATTTTTATT
1 ATTTAAATAAAATTTTATATTTTTATT
1757316 TTCAATTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
ATTTAAATAAAATTTTATATTTTTATTAT
Found at i:1758665 original size:2 final size:2
Alignment explanation
Indices: 1758658--1758695 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1758648 CCAAAACGTA
* *
1758658 AG AG AG AG AG AG AG AG AG AA AA 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
1758696 GAAAAGAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1758685 original size:20 final size:20
Alignment explanation
Indices: 1758660--1758702 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1758650 AAAACGTAAG
1758660 AGAGAGAGAGAGAGAGAAAA
1 AGAGAGAGAGAGAGAGAAAA
*
1758680 AGAGAGAGAGAGAGAGGAAA
1 AGAGAGAGAGAGAGAGAAAA
1758700 AGA
1 AGA
1758703 AAAGGAAGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (20 bp):
AGAGAGAGAGAGAGAGAAAA
Found at i:1768788 original size:2 final size:2
Alignment explanation
Indices: 1768783--1768818 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1768773 TATATATATA
1768783 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1768819 NTTCTCTCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1768861 original size:2 final size:2
Alignment explanation
Indices: 1768856--1768894 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1768846 TATATATATA
1768856 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1768895 TAAAGATGCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1776117 original size:30 final size:31
Alignment explanation
Indices: 1776052--1776118 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
1776042 GCATACATAC
*
1776052 ATACACATATATATATACATATATAAATAAT
1 ATACACATATACATATACATATATAAATAAT
*
1776083 -TACACATTATACAT-TACATATATATA-AAT
1 ATACACA-TATACATATACATATATAAATAAT
1776112 ATACACA
1 ATACACA
1776119 AATAATTACA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 3 0.09
30 23 0.72
31 6 0.19
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.34
Consensus pattern (31 bp):
ATACACATATACATATACATATATAAATAAT
Found at i:1776126 original size:28 final size:32
Alignment explanation
Indices: 1776070--1776128 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
1776060 ATATATATAC
*
1776070 ATATATAAATAATTACACATTATACATTACAT
1 ATATATAAATAATTACACATAATACATTACAT
1776102 ATATATAAAT-A-TACACA-AATA-ATTACA
1 ATATATAAATAATTACACATAATACATTACA
1776129 CATTAGAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 6 0.23
29 3 0.12
30 6 0.23
31 1 0.04
32 10 0.38
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (32 bp):
ATATATAAATAATTACACATAATACATTACAT
Found at i:1787603 original size:17 final size:19
Alignment explanation
Indices: 1787561--1787605 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 19
1787551 CCTTTCTTTC
1787561 TCTCTTCTCTTTCACCGAG
1 TCTCTTCTCTTTCACCGAG
*
1787580 -CTC-TCTCTTTC-TC-AG
1 TCTCTTCTCTTTCACCGAG
1787595 TCTCTTCTCTT
1 TCTCTTCTCTT
1787606 CCCGTCGTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
15 2 0.09
16 4 0.17
17 14 0.61
18 3 0.13
ACGTcount: A:0.07, C:0.38, G:0.07, T:0.49
Consensus pattern (19 bp):
TCTCTTCTCTTTCACCGAG
Found at i:1788727 original size:42 final size:42
Alignment explanation
Indices: 1788636--1788727 Score: 98
Period size: 42 Copynumber: 2.2 Consensus size: 42
1788626 ACTGTTTAGT
* * * * * *
1788636 ATATTCAAGTAACAATTTAAAATTTAATGGATATTATTTAAG
1 ATATTTAAATAACAATTTAAAATTGAATAGATATTATATAAA
1788678 ATATTTAAATAACAATTTTAAAATTGAATCAGATATT-TATAAA
1 ATATTTAAATAACAA-TTTAAAATTGAAT-AGATATTATATAAA
1788721 AT-TTTAA
1 ATATTTAA
1788728 TACCTTATCA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
42 18 0.43
43 18 0.43
44 6 0.14
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (42 bp):
ATATTTAAATAACAATTTAAAATTGAATAGATATTATATAAA
Found at i:1794150 original size:112 final size:113
Alignment explanation
Indices: 1794028--1794231 Score: 356
Period size: 112 Copynumber: 1.8 Consensus size: 113
1794018 GATTTAATCA
*
1794028 ATTTTTATTTAATTAAATGCATGAAATTGTTAATAAATCTCAAATAAATGTTTATAAGACAAAAC
1 ATTTTTATTTAATTAAATGCATGAAATTGTTAATAAATCTCAAATAAATGTTTATAAAACAAAAC
1794093 AAATTTAATTTT-TATTTAATCAATTTTAATGAAAAAACTTTTAATTG
66 AAATTTAATTTTATATTTAATCAATTTTAATGAAAAAACTTTTAATTG
* * *
1794140 ATTTTTATTTAATTCAATGCATGCAATTGTTAATAAATCTCAAATAAATGTTTATAAAACAAAAT
1 ATTTTTATTTAATTAAATGCATGAAATTGTTAATAAATCTCAAATAAATGTTTATAAAACAAAAC
*
1794205 AAATTTAATTTTATATTTAATCGATTT
66 AAATTTAATTTTATATTTAATCAATTT
1794232 AAAAAAAATT
Statistics
Matches: 86, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
112 73 0.85
113 13 0.15
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.44
Consensus pattern (113 bp):
ATTTTTATTTAATTAAATGCATGAAATTGTTAATAAATCTCAAATAAATGTTTATAAAACAAAAC
AAATTTAATTTTATATTTAATCAATTTTAATGAAAAAACTTTTAATTG
Found at i:1794191 original size:21 final size:20
Alignment explanation
Indices: 1794167--1794213 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
1794157 TGCATGCAAT
* *
1794167 TGTTAATAAATCTCAAATAAA
1 TGTTAATAAAAC-AAAATAAA
*
1794188 TGTTTATAAAACAAAATAAA
1 TGTTAATAAAACAAAATAAA
1794208 T-TTAAT
1 TGTTAAT
1794214 TTTATATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 4 0.18
20 8 0.36
21 10 0.45
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.36
Consensus pattern (20 bp):
TGTTAATAAAACAAAATAAA
Found at i:1794910 original size:26 final size:25
Alignment explanation
Indices: 1794881--1794929 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1794871 TTTATTCATA
*
1794881 AAGGTATTGCGGTCCCTTTTTTAAGG
1 AAGG-ATTACGGTCCCTTTTTTAAGG
* *
1794907 AAGGATTATGGTCCTTTTTTTAA
1 AAGGATTACGGTCCCTTTTTTAA
1794930 CTCATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.43
Consensus pattern (25 bp):
AAGGATTACGGTCCCTTTTTTAAGG
Done.