Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008668.1 Hibiscus syriacus cultivar Beakdansim tig00111671_pilon, whole genome shotgun sequence
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: 2122653
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 9
Found at i:416993 original size:489 final size:487
Alignment explanation
Indices: 416079--417148 Score: 1995
Period size: 489 Copynumber: 2.2 Consensus size: 487
416069 AGGTATATAC
416079 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTACG
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTACG
*
416144 TTACG--GTATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCT
66 TTACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCT
416207 TTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAATATCAAAACAATCAAATAAT
131 TTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAATATCAAAACAATCAAATAAT
416272 TTTTGTGTAAATGAAATTATTAAATTAATATGTAGGTGGAAAACATGAAACACTATTAAAAAAAA
196 TTTTGTGTAAATGAAATTATTAAATTAATATGTAGGTGGAAAACATGAAACACTATTAAAAAAAA
* *
416337 ATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCTTTTTTATAAAAAGTATGGACACT
261 ATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAATATGGACACT
416402 TTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTAGCGTTT
326 TTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTAGCGTTT
*
416467 ATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACT
391 ATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCCATACT
416532 TTTTTCACTGTGGAAAACATTAATTTAAGGTT
456 TTTTTCACTGTGGAAAACATTAATTTAAGGTT
416564 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTACG
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTACG
416629 TTACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCT
66 TTACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCT
416694 TTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAA
131 TTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTAT-AAATATCAAAACAATCAAATAA
416759 TTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAA
195 -TTTTTGTGTAAATGAAATTATTAAATTAATA-TGTAGGTGGAAAACATGAAACACTATTAAAAA
416823 AAAATTGAAACATAAATTACATAACTTTAAACA-AAGTATCGATCCTTTTTATAAAAAATATGGA
258 AAAATTGAAACATAAATTACATAACTTTAAA-AGAAGTATCGATCCTTTTTATAAAAAATATGGA
*
416887 CACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTATC
322 CACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTAGC
* *
416952 GTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCTA
387 GTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCCA
417017 TACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
452 TACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
*
417053 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTCAT
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTT-AC
417118 GTTACGATATATATTATTATTAAATTAAAAA
65 GTTACGATATATATTATTATTAAATTAAAAA
417149 TTCTAAATAT
Statistics
Matches: 570, Mismatches: 8, Indels: 9
0.97 0.01 0.02
Matches are distributed among these distances:
485 70 0.12
487 99 0.17
488 22 0.04
489 319 0.56
490 60 0.11
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.41
Consensus pattern (487 bp):
ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTACG
TTACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCT
TTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAATATCAAAACAATCAAATAAT
TTTTGTGTAAATGAAATTATTAAATTAATATGTAGGTGGAAAACATGAAACACTATTAAAAAAAA
ATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAATATGGACACT
TTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTAGCGTTT
ATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCCATACT
TTTTTCACTGTGGAAAACATTAATTTAAGGTT
Found at i:417007 original size:46 final size:45
Alignment explanation
Indices: 416910--417007 Score: 108
Period size: 46 Copynumber: 2.1 Consensus size: 45
416900 ATAGGTAAAA
* * *
416910 ATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTTATAT-ATGTAATATCTATCATTT
* *
416956 ATATAATGTAATAGGTAGTGGTTATAT-TGTAAAGTATCTATCATTT
1 ATATAATGTAATAGGTAGCGCTTATATATGT-AA-TATCTATCATTT
*
417002 TTATAA
1 ATATAA
417008 AAGTGTCTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
44 3 0.07
45 2 0.05
46 39 0.89
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.43
Consensus pattern (45 bp):
ATATAATGTAATAGGTAGCGCTTATATATGTAATATCTATCATTT
Found at i:417376 original size:23 final size:23
Alignment explanation
Indices: 417341--417413 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
417331 ATAGGTAAAA
*
417341 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
417364 ATATAATGGAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
417387 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
417410 ATAT
1 ATAT
417414 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.37
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:417518 original size:431 final size:431
Alignment explanation
Indices: 416702--417579 Score: 1564
Period size: 431 Copynumber: 2.0 Consensus size: 431
416692 CTTTGGTTAA
* *
416702 TATTGTTAAATT-TAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTG
1 TATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTG
* *
416766 TGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGA
66 TGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTAA
*
416831 AACATAAATTACATAACTTTAAACAAAGTATCGATCCTTTTTATAAAAAATATGGACACTTTCAA
131 AACATAAATTACATAACTTTAAACAAAGTATCGATCCTTTTTATAAAAAATATGGACAATTTCAA
* * *
416896 TATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTATCGTTTATATA
196 TATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGGAATAGGTAGCGTTTATATA
* *
416961 ATGTAATAGGTAGTGGTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCTATACTTTTTT
261 ATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCCATACTTTTTT
* *
417026 CACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATT
326 CACTGTGGAAAACATTAATTTAAAGTTATATTTTGAGTGAGTTTTAAGATATTAATTTAGTAATT
*
417091 ATAGGCGTCTAATGATTTATTTTTCATGTTACGATATATAT
391 ATAGGCGTCTAATGATTTATTTTTCACGTTACGATATATAT
417132 TATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTT
1 TATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAA-TTTTTT
417197 GTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATTA
65 GTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTA
*
417261 AAACATAAATTACATAACTTTAAA-AGAAGTATCGATCCTTTTTATAAAAAGTATGGACAATTTC
130 AAACATAAATTACATAACTTTAAACA-AAGTATCGATCCTTTTTATAAAAAATATGGACAATTTC
417325 AATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGGAATAGGTAGCGTTTATA
194 AATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGGAATAGGTAGCGTTTATA
*
417390 TAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTT
259 TAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCCATACTTTT
*
417455 TTCACTGTGGAAAATATTAATTTAAAGTTATATTTTGAGTGAGTTTTAAGATATTAATTTAGTAA
324 TTCACTGTGGAAAACATTAATTTAAAGTTATATTTTGAGTGAGTTTTAAGATATTAATTTAGTAA
*
417520 TTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATAT
389 TTATAGGCGTCTAATGATTTATTTTTCACGTTACGATATATAT
417563 TATTATTAAATTAAAAA
1 TATTATTAAATTAAAAA
417580 CAATAAACAT
Statistics
Matches: 428, Mismatches: 17, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
430 12 0.03
431 357 0.83
432 59 0.14
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (431 bp):
TATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTG
TGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTAA
AACATAAATTACATAACTTTAAACAAAGTATCGATCCTTTTTATAAAAAATATGGACAATTTCAA
TATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGGAATAGGTAGCGTTTATATA
ATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCCATACTTTTTT
CACTGTGGAAAACATTAATTTAAAGTTATATTTTGAGTGAGTTTTAAGATATTAATTTAGTAATT
ATAGGCGTCTAATGATTTATTTTTCACGTTACGATATATAT
Found at i:429167 original size:28 final size:28
Alignment explanation
Indices: 429116--429171 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
429106 CATTTATGTA
429116 TGGAACCACTAAATCTTGCAATCCTGTG
1 TGGAACCACTAAATCTTGCAATCCTGTG
429144 TGGAACCACTAAATCTTGCAATCCTGTG
1 TGGAACCACTAAATCTTGCAATCCTGTG
429172 ATGCGTCACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.29
Consensus pattern (28 bp):
TGGAACCACTAAATCTTGCAATCCTGTG
Found at i:429371 original size:21 final size:21
Alignment explanation
Indices: 429345--429412 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
429335 GAACTTGAAT
*
429345 ATGAAAAAAAATAATGTTAAC
1 ATGAAAAAATATAATGTTAAC
* *
429366 ATGAAAATATATAATGTTAAT
1 ATGAAAAAATATAATGTTAAC
* * *
429387 ATGAAGAGATATAATATTAAC
1 ATGAAAAAATATAATGTTAAC
429408 ATGAA
1 ATGAA
429413 GAGATGTGAC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.56, C:0.03, G:0.12, T:0.29
Consensus pattern (21 bp):
ATGAAAAAATATAATGTTAAC
Found at i:429413 original size:21 final size:21
Alignment explanation
Indices: 429355--429694 Score: 202
Period size: 21 Copynumber: 16.0 Consensus size: 21
429345 ATGAAAAAAA
* *
429355 ATAATGTTAACATGAAAATAT
1 ATAATGTTAACATGAAGAGAT
*
429376 ATAATGTTAATATGAAGAGAT
1 ATAATGTTAACATGAAGAGAT
*
429397 ATAATATTAACATGAAGAGAT
1 ATAATGTTAACATGAAGAGAT
* * **
429418 GTGACATTAACATGAAGAGAT
1 ATAATGTTAACATGAAGAGAT
* * *
429439 GTGATGTTAAAATGAAGAGAT
1 ATAATGTTAACATGAAGAGAT
* * *
429460 A-AGATATTGACATG-A-ATAT
1 ATA-ATGTTAACATGAAGAGAT
** * *
429479 ATAATGTTAATGTGAAGTGACG
1 ATAATGTTAACATGAAGAGA-T
* * *
429501 AGTTATATTAACATAAAGAGAT
1 A-TAATGTTAACATGAAGAGAT
** *
429523 ATAAAATTACCATGAAGAGAT
1 ATAATGTTAACATGAAGAGAT
* * *
429544 ATGGA-GTTAACATAAAAGGAGGT
1 AT-AATGTTAACAT-GAA-GAGAT
* *
429567 TTAATGTTAACATGAAAAGAT
1 ATAATGTTAACATGAAGAGAT
* * *
429588 GTGATGTTAATATGAAGAGAT
1 ATAATGTTAACATGAAGAGAT
*
429609 ATGATGTTAACATGAAGAGAT
1 ATAATGTTAACATGAAGAGAT
* * *
429630 GTGATGTTAACATGAAGTGAT
1 ATAATGTTAACATGAAGAGAT
* * *
429651 GAGTGATGTTAACATAAAAAGAT
1 -A-TAATGTTAACATGAAGAGAT
* * *
429674 ATAATATTAACGTAAAGAGAT
1 ATAATGTTAACATGAAGAGAT
429695 GTGTGATGTT
Statistics
Matches: 246, Mismatches: 61, Indels: 24
0.74 0.18 0.07
Matches are distributed among these distances:
19 11 0.04
20 3 0.01
21 180 0.73
22 9 0.04
23 43 0.17
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.29
Consensus pattern (21 bp):
ATAATGTTAACATGAAGAGAT
Found at i:429657 original size:65 final size:63
Alignment explanation
Indices: 429379--429710 Score: 179
Period size: 65 Copynumber: 5.2 Consensus size: 63
429369 AAAATATATA
* * * * * * ** *
429379 ATGTTAATATGAAGAGATATAATATTAACATGAAGAGATGTGACATTAACATGAAGAGATGTG
1 ATGTTAACATGAAAAGATGTGATGTTAACATGAAGAGATATGATGTTAACATAAAGAGATGTG
* * ** * * * * ** *
429442 ATGTTAAAATGAAGAGATAAGATATTGACATG-A-ATATATAATGTTAATGTGAAGTGACGA-GT
1 ATGTTAACATGAAAAGATGTGATGTTAACATGAAGAGATATGATGTTAACAT-AA-AGA-GATGT
*
429504 T
63 G
* * * ** * * *
429505 ATATTAACAT-AAAGAGATATAAAATTACCATGAAGAGATATGGA-GTTAACATAAAAGGAGGTT
1 ATGTTAACATGAAA-AGATGTGATGTTAACATGAAGAGATAT-GATGTTAACAT-AAA-GAGATG
*
429568 TA
62 TG
* *
429570 ATGTTAACATGAAAAGATGTGATGTTAATATGAAGAGATATGATGTTAACATGAAGAGATGTG
1 ATGTTAACATGAAAAGATGTGATGTTAACATGAAGAGATATGATGTTAACATAAAGAGATGTG
** * * * * *
429633 ATGTTAACATGAAGTGATGAGTGATGTTAACATAAAAAGATATAATATTAACGTAAAGAGATGTG
1 ATGTTAACATGAAAAGAT--GTGATGTTAACATGAAGAGATATGATGTTAACATAAAGAGA--TG
429698 TG
62 TG
429700 ATGTTAACATG
1 ATGTTAACATG
429711 GTGATGTTAA
Statistics
Matches: 203, Mismatches: 51, Indels: 26
0.73 0.18 0.09
Matches are distributed among these distances:
61 10 0.05
62 4 0.02
63 74 0.36
64 8 0.04
65 88 0.43
66 4 0.02
67 15 0.07
ACGTcount: A:0.44, C:0.05, G:0.22, T:0.30
Consensus pattern (63 bp):
ATGTTAACATGAAAAGATGTGATGTTAACATGAAGAGATATGATGTTAACATAAAGAGATGTG
Found at i:429684 original size:44 final size:44
Alignment explanation
Indices: 429570--429710 Score: 178
Period size: 44 Copynumber: 3.2 Consensus size: 44
429560 AGGAGGTTTA
*
429570 ATGTTAACATGAAAAGATGTGATGTTAATATGAAGAGAT-A-TG
1 ATGTTAACATGAAAAGATGTGATGTTAACATGAAGAGATGAGTG
* *
429612 ATGTTAACATGAAGAGATGTGATGTTAACATGAAGTGATGAGTG
1 ATGTTAACATGAAAAGATGTGATGTTAACATGAAGAGATGAGTG
* * * * * * *
429656 ATGTTAACATAAAAAGATATAATATTAACGTAAAGAGATGTGTG
1 ATGTTAACATGAAAAGATGTGATGTTAACATGAAGAGATGAGTG
429700 ATGTTAACATG
1 ATGTTAACATG
429711 GTGATGTTAA
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
42 36 0.43
43 1 0.01
44 47 0.56
ACGTcount: A:0.42, C:0.04, G:0.23, T:0.30
Consensus pattern (44 bp):
ATGTTAACATGAAAAGATGTGATGTTAACATGAAGAGATGAGTG
Found at i:429716 original size:14 final size:14
Alignment explanation
Indices: 429697--429728 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
429687 AAAGAGATGT
429697 GTGATGTTAACATG
1 GTGATGTTAACATG
*
429711 GTGATGTTAATATG
1 GTGATGTTAACATG
429725 GTGA
1 GTGA
429729 GATTTGTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.31, T:0.38
Consensus pattern (14 bp):
GTGATGTTAACATG
Found at i:429930 original size:15 final size:16
Alignment explanation
Indices: 429912--429947 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
429902 TAAATTAATT
429912 TATAAAACATTAAAC-
1 TATAAAACATTAAACG
*
429927 TATAAAGCATTAAACG
1 TATAAAACATTAAACG
429943 TATAA
1 TATAA
429948 TTATAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.56, C:0.11, G:0.06, T:0.28
Consensus pattern (16 bp):
TATAAAACATTAAACG
Found at i:430196 original size:27 final size:27
Alignment explanation
Indices: 430143--430191 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
430133 CGCTACTACT
430143 ACCACCACCACCATTACTGTCGTCGCC
1 ACCACCACCACCATTACTGTCGTCGCC
430170 ACCACCACCA-CATT-C-GTCGTCG
1 ACCACCACCACCATTACTGTCGTCG
430192 TCGCCGCCGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 7 0.32
25 1 0.05
26 4 0.18
27 10 0.45
ACGTcount: A:0.22, C:0.47, G:0.12, T:0.18
Consensus pattern (27 bp):
ACCACCACCACCATTACTGTCGTCGCC
Found at i:436699 original size:217 final size:217
Alignment explanation
Indices: 436279--436701 Score: 731
Period size: 217 Copynumber: 1.9 Consensus size: 217
436269 TTATAATGTA
* *
436279 AAAAATATTAAATCAATTTACTCTATCATGATTTGGTAATATATAAAAATCAGGAATTTAAGAAT
1 AAAAATATTAAATCAATTTACTCTATCATGATTTAGTAATATATAAAAATCAGGAATTTAAGAAC
* *
436344 GCTAAAAATAATAATTAAGCTACCTTATTGTCGAACAGAACATGATTAGAGAAGCATTGGTTGCC
66 GCTAAAAACAATAATTAAGATACCTTATTGTCGAACAGAACATGATTAGAGAAGCATTGGTTGCC
* *
436409 TTTCATTGAAGATCTGTATATGAAACCCTCCAATTCTGGACAGTCGTATATTCTCAGTGACTCCA
131 TTCCATTGAAGATCTGTATATGAAACCCTCCAATTCTGGACAGTCGAATATTCTCAGTGACTCCA
*
436474 AGGTCGAAAATATTTATCTTAT
196 ACGTCGAAAATATTTATCTTAT
436496 AAAAATATTAAATCAATTTACTCTATCATGATTTAGTAATATATAAAAATCAGGAATTTAAGAAC
1 AAAAATATTAAATCAATTTACTCTATCATGATTTAGTAATATATAAAAATCAGGAATTTAAGAAC
436561 GCTAAAAACAATAATTAAGATACCTTATTGTCGAACAGAACATGATTAGAGAAGCATTGGTTGCC
66 GCTAAAAACAATAATTAAGATACCTTATTGTCGAACAGAACATGATTAGAGAAGCATTGGTTGCC
* * * *
436626 TTCCATTGAAGATCTGTATATGAAACCCTCCAATTCTGGACATTTGAATATT-TCCATTGACTTC
131 TTCCATTGAAGATCTGTATATGAAACCCTCCAATTCTGGACAGTCGAATATTCT-CAGTGACTCC
436690 AACGTCGAAAAT
195 AACGTCGAAAAT
436702 TGAATAACTT
Statistics
Matches: 194, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
216 1 0.01
217 193 0.99
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (217 bp):
AAAAATATTAAATCAATTTACTCTATCATGATTTAGTAATATATAAAAATCAGGAATTTAAGAAC
GCTAAAAACAATAATTAAGATACCTTATTGTCGAACAGAACATGATTAGAGAAGCATTGGTTGCC
TTCCATTGAAGATCTGTATATGAAACCCTCCAATTCTGGACAGTCGAATATTCTCAGTGACTCCA
ACGTCGAAAATATTTATCTTAT
Found at i:440282 original size:23 final size:23
Alignment explanation
Indices: 440256--440306 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
440246 GATATGTTTA
*
440256 ATGTTTGTTTTATTGTCTTGTGG
1 ATGTTTGTTTTATTGTCTAGTGG
440279 ATGTTTGTTTTATTGTCTAGTGG
1 ATGTTTGTTTTATTGTCTAGTGG
440302 ATGTT
1 ATGTT
440307 GTTCGCTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.12, C:0.04, G:0.25, T:0.59
Consensus pattern (23 bp):
ATGTTTGTTTTATTGTCTAGTGG
Found at i:440704 original size:20 final size:19
Alignment explanation
Indices: 440681--440742 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 19
440671 AAGTTGGGAG
440681 AAAAAAATTATAAATATTTT
1 AAAAAAATTATAAA-ATTTT
** *
440701 AAAATTATGATAAGAATTTT
1 AAAAAAATTATAA-AATTTT
*
440721 AAAAAATATATTTAAAATTTT
1 AAAAAA-AT-TATAAAATTTT
440742 A
1 A
440743 GAAATAAATA
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
20 19 0.59
21 10 0.31
22 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.40
Consensus pattern (19 bp):
AAAAAAATTATAAAATTTT
Found at i:442301 original size:29 final size:29
Alignment explanation
Indices: 442243--442347 Score: 185
Period size: 29 Copynumber: 3.7 Consensus size: 29
442233 CCATTTTTCC
*
442243 AGTTTATTGCCTAACGTTTTTTCGG-TCT
1 AGTTTAGTGCCTAACGTTTTTTCGGTTCT
*
442271 AGTTTAGTGCCTAATGTTTTTTCGGTTCT
1 AGTTTAGTGCCTAACGTTTTTTCGGTTCT
442300 AGTTTAGTGCCTAACGTTTTTTCGGTTCT
1 AGTTTAGTGCCTAACGTTTTTTCGGTTCT
442329 AGTTTAGTGCCTAACGTTT
1 AGTTTAGTGCCTAACGTTT
442348 CATTCCGTCA
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
28 23 0.32
29 50 0.68
ACGTcount: A:0.15, C:0.16, G:0.20, T:0.49
Consensus pattern (29 bp):
AGTTTAGTGCCTAACGTTTTTTCGGTTCT
Found at i:443336 original size:95 final size:93
Alignment explanation
Indices: 443214--443491 Score: 355
Period size: 95 Copynumber: 3.0 Consensus size: 93
443204 AATTATCATC
* ** *
443214 AAAAATTGAAAAATATAAATAAGGAAAGAAAGACTAAGG-GTTCTCAAGTCTTAATCAATTATTA
1 AAAAATTGAAAAGTATAAATAA--AAAGAAAGACTAAGGACCTCTCAAGTCTTTATCAATTATTA
443278 TTATTATCTTTCTTTGATTTTAGTTTAATA
64 TTATTATCTTTCTTTGATTTTAGTTTAATA
*
443308 AAAAATTTGAAAAGTACAAAT--AAAGAAAGACTTAAGGACCTCTCAAGTCTTTATCAATTATTA
1 AAAAA-TTGAAAAGTATAAATAAAAAGAAAGAC-TAAGGACCTCTCAAGTCTTTATCAATTATTA
* *
443371 TTATTATCTTTCTTTAATTTTAGTGTAATA
64 TTATTATCTTTCTTTGATTTTAGTTTAATA
* * * *
443401 AAAAATTGAAAAGTATAAATAATAAAAAAAAAACTAAGGACCTCTCAAGTCTTTATCAATGATTC
1 AAAAATTGAAAAGTATAAAT-A-AAAAGAAAGACTAAGGACCTCTCAAGTCTTTATCAATTATTA
* * *
443466 TTACTATGTTTCTTTGCTTTTAGTTT
64 TTATTATCTTTCTTTGATTTTAGTTT
443492 TGGTTAGATA
Statistics
Matches: 160, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
91 10 0.06
92 19 0.12
93 55 0.34
94 5 0.03
95 63 0.39
96 8 0.05
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (93 bp):
AAAAATTGAAAAGTATAAATAAAAAGAAAGACTAAGGACCTCTCAAGTCTTTATCAATTATTATT
ATTATCTTTCTTTGATTTTAGTTTAATA
Found at i:443373 original size:93 final size:94
Alignment explanation
Indices: 443214--443491 Score: 348
Period size: 93 Copynumber: 3.0 Consensus size: 94
443204 AATTATCATC
* ** ** *
443214 AAAAATTGAAAAATATAAATAAGGAAAGAAAGACTAAGG-GTTCTCAAGTCTTAATCAATTATTA
1 AAAAATTG-AAAAGATAAATAATAAAAGAAAGACTAAGGACCTCTCAAGTCTTTATCAATTATTA
443278 TTATTATCTTTCTTTGATTTTAGTTTAATA
65 TTATTATCTTTCTTTGATTTTAGTTTAATA
*
443308 AAAAATTTGAAAAG-TACA-AAT-AAAGAAAGACTTAAGGACCTCTCAAGTCTTTATCAATTATT
1 AAAAA-TTGAAAAGATAAATAATAAAAGAAAGAC-TAAGGACCTCTCAAGTCTTTATCAATTATT
* *
443370 ATTATTATCTTTCTTTAATTTTAGTGTAATA
64 ATTATTATCTTTCTTTGATTTTAGTTTAATA
* * * *
443401 AAAAATTGAAAAGTATAAATAATAAAAAAAAAACTAAGGACCTCTCAAGTCTTTATCAATGATTC
1 AAAAATTGAAAAG-ATAAATAATAAAAGAAAGACTAAGGACCTCTCAAGTCTTTATCAATTATTA
* * *
443466 TTACTATGTTTCTTTGCTTTTAGTTT
65 TTATTATCTTTCTTTGATTTTAGTTT
443492 TGGTTAGATA
Statistics
Matches: 159, Mismatches: 18, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
91 10 0.06
92 15 0.09
93 58 0.36
94 12 0.08
95 56 0.35
96 8 0.05
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (94 bp):
AAAAATTGAAAAGATAAATAATAAAAGAAAGACTAAGGACCTCTCAAGTCTTTATCAATTATTAT
TATTATCTTTCTTTGATTTTAGTTTAATA
Found at i:444175 original size:38 final size:39
Alignment explanation
Indices: 444100--444176 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
444090 ATTATCTTTC
444100 TTTGAGTTTAGTTTAATAAAAAAATTGAAAATGATAAAT
1 TTTGAGTTTAGTTTAATAAAAAAATTGAAAATGATAAAT
*
444139 TTTGATTTTAGTTTAAT-AAAAAATTGAAAAAT-ATAAAT
1 TTTGAGTTTAGTTTAATAAAAAAATTG-AAAATGATAAAT
444177 AAATTAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
38 15 0.42
39 21 0.58
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.40
Consensus pattern (39 bp):
TTTGAGTTTAGTTTAATAAAAAAATTGAAAATGATAAAT
Found at i:444185 original size:17 final size:17
Alignment explanation
Indices: 444154--444186 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
444144 TTTTAGTTTA
444154 ATAAAAAATTGAAAAAT
1 ATAAAAAATTGAAAAAT
444171 ATAAATAAATT-AAAAA
1 ATAAA-AAATTGAAAAA
444187 AGACTAAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
ATAAAAAATTGAAAAAT
Found at i:444186 original size:18 final size:17
Alignment explanation
Indices: 444154--444187 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
444144 TTTTAGTTTA
*
444154 ATAAAAAATTGAAAAAT
1 ATAAAAAATTAAAAAAT
444171 ATAAATAAATTAAAAAA
1 ATAAA-AAATTAAAAAA
444188 GACTAAGGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
ATAAAAAATTAAAAAAT
Found at i:447771 original size:39 final size:39
Alignment explanation
Indices: 447717--447794 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
447707 AAGAAAAATT
447717 CTACAACGCTCGACAAGCACGGATGAATACCGTTAACGA
1 CTACAACGCTCGACAAGCACGGATGAATACCGTTAACGA
447756 CTACAACGCTCGACAAGCACGGATGAATACCGTTAACGA
1 CTACAACGCTCGACAAGCACGGATGAATACCGTTAACGA
447795 TGGGCACTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.36, C:0.28, G:0.21, T:0.15
Consensus pattern (39 bp):
CTACAACGCTCGACAAGCACGGATGAATACCGTTAACGA
Found at i:450186 original size:3 final size:3
Alignment explanation
Indices: 450178--450225 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
450168 AGTTAATTAG
450178 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
450226 TTTTCGACCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:450535 original size:91 final size:90
Alignment explanation
Indices: 450380--450548 Score: 302
Period size: 91 Copynumber: 1.9 Consensus size: 90
450370 CATTGTTGGA
*
450380 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTGTTGGATGAGCTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGCTCTTCTCATTATGAAC
450445 TCTCCACTGGAAATACTGATGCAAGG
66 TCTCCACT-GAAATACTGATGCAAGG
* *
450471 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTTTGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGCTCTTCTCATTATGAAC
450536 TCTCCACTGAAAT
66 TCTCCACTGAAAT
450549 GTTGATCAAC
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
90 5 0.07
91 70 0.93
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.40
Consensus pattern (90 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGCTCTTCTCATTATGAAC
TCTCCACTGAAATACTGATGCAAGG
Found at i:450644 original size:18 final size:18
Alignment explanation
Indices: 450615--450663 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
450605 TATGAACTTC
450615 TTCTTCCTCATTGGATGAG
1 TTCTT-CTCATTGGATGAG
*
450634 TTCTTCTCATTGGATGGG
1 TTCTTCTCATTGGATGAG
450652 TTCTTCTCATTG
1 TTCTTCTCATTG
450664 TGAACTCTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 24 0.83
19 5 0.17
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.47
Consensus pattern (18 bp):
TTCTTCTCATTGGATGAG
Found at i:450755 original size:129 final size:131
Alignment explanation
Indices: 450500--450773 Score: 396
Period size: 129 Copynumber: 2.1 Consensus size: 131
450490 TATGAACTTC
* *
450500 TTCTTCCTCGTTGGATGAGTTCTTCTCATTTTGAACTCTCCACTGAAATGTTGATCAACCTCTTC
1 TTCTT-CTCATTGGATGAGTTCTTCTCATTGTGAACTCTCCACTGAAATGTTGATCAACCTCTTC
*
450565 TGTGATGGAATCGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGA
65 TGTGATGGAATCGAA-CAAGG-TGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTCATTGGA
*
450630 TGAG
128 CGAG
* * *
450634 TTCTTCTCATTGGATGGGTTCTTCTCATTGTGAACTCTCCATTGAAAATGTTGATCCACCTCCTT
1 TTCTTCTCATTGGATGAGTTCTTCTCATTGTGAACTCTCCACTG-AAATGTTGATCAACCT-CTT
450699 CTGTGATGGAATCG-A-AA-G-GAACAAGTTCTTCTCATTATGAACTT-TCTATTCCTCATTGGA
64 CTGTGATGGAATCGAACAAGGTGAACAAGTTCTTCTCATTATGAACTTCT-TATTCCTCATTGGA
450759 CGAG
128 CGAG
450763 TTCTTCTCATT
1 TTCTTCTCATT
450774 ATGAACTCTT
Statistics
Matches: 130, Mismatches: 7, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
128 1 0.01
129 53 0.41
131 1 0.01
132 2 0.02
133 35 0.27
134 21 0.16
135 17 0.13
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (131 bp):
TTCTTCTCATTGGATGAGTTCTTCTCATTGTGAACTCTCCACTGAAATGTTGATCAACCTCTTCT
GTGATGGAATCGAACAAGGTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTCATTGGACGA
G
Found at i:450960 original size:136 final size:136
Alignment explanation
Indices: 450717--451611 Score: 1508
Period size: 136 Copynumber: 6.6 Consensus size: 136
450707 GAATCGAAAG
* * *
450717 GAACAAGTTCTTCTCATTATGAACTTTCTAT-T-CCTCATT-GGACGAGTTCTTCTCATTATGAA
1 GAACAAGCTCTTCTCATTATGAAC-TTCT-TCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAA
* * * *
450779 CTCTTCATTGGAAATGTCAATCCCTCGAGCGAGGCGTCACTGATTCAAAATGCCGTGAATCGAGT
64 CTCTCCATTGGAAATGTCAATCCCTCAAGCGAGGCGTCACTGATTCGAAATGTCGTGAATCGAGT
*
450844 GATAGGTC
129 GATAGGTT
450852 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACT
* * *
450917 CTCCATTGGAAATGTCAATTCCTCAAGCGATGCGTCACTGATTCGAAATGTCGTGAATTGAGTGA
66 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGCGTCACTGATTCGAAATGTCGTGAATCGAGTGA
450982 TAGGTT
131 TAGGTT
*
450988 GAACAAACTCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACT
451053 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGCGTCACTGATTCGAAATGTCGTGAATCGAGTGA
66 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGCGTCACTGATTCGAAATGTCGTGAATCGAGTGA
*
451118 TAGATT
131 TAGGTT
451124 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACT
* * * * *
451189 CTTCATTAGAAATGTCAATCCCTCAAGCGAGGCATCACTGATTCAAAATATCGTGAATCGAGTGA
66 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGCGTCACTGATTCGAAATGTCGTGAATCGAGTGA
451254 TAGGTT
131 TAGGTT
*
451260 GAACAAGCTCTTCTAATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACT
*
451325 CTCCATTGGAAATGTCAATCTCTCAAGCGAGGCGTCACTGATTCGAAATGTCGTGAATCGAGTGA
66 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGCGTCACTGATTCGAAATGTCGTGAATCGAGTGA
451390 TAGGTT
131 TAGGTT
451396 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACT
* *
451461 CTTCATTGGAAATGTCAATCCCTCAAGCGAGGCGTCACTGATTCGAAATGTCATGAATCGAGTGA
66 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGCGTCACTGATTCGAAATGTCGTGAATCGAGTGA
*
451526 TAGGTC
131 TAGGTT
* *
451532 AAACAAGCTATTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACT
**
451597 CTGTATTGGAAATGT
66 CTCCATTGGAAATGT
451612 TGATCTGTTT
Statistics
Matches: 718, Mismatches: 39, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
133 1 0.00
134 5 0.01
135 29 0.04
136 683 0.95
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (136 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACT
CTCCATTGGAAATGTCAATCCCTCAAGCGAGGCGTCACTGATTCGAAATGTCGTGAATCGAGTGA
TAGGTT
Found at i:452056 original size:76 final size:73
Alignment explanation
Indices: 451913--452081 Score: 221
Period size: 76 Copynumber: 2.3 Consensus size: 73
451903 TTGTCTCAAG
**
451913 GGTTTTAAGAAAAACCATCTCAAGTGTGATAAATTTTGTTCCAAAGGAAAACTGTCTCAAGCAAG
1 GGTTTTAAGAAAAACCATCTCAAGTGAAATAAATTTTGTTCCAAAGGAAAACTGTCTCAAGCAAG
451978 ACGAAATA
66 ACGAAATA
* * * * *
451986 GGTTTCAAGAAAAATCATCTCAAGTGAAATTCAATTTCTTGTTTCAAGGGAAAACTGTCTCAAGC
1 GGTTTTAAGAAAAACCATCTCAAGTGAAA-T-AAATT-TTGTTCCAAAGGAAAACTGTCTCAAGC
* * *
452051 GAGACGAAGTT
63 AAGACGAAATA
452062 GGTTTTAAGAAAAACCATCT
1 GGTTTTAAGAAAAACCATCT
452082 TAAGAGAGAC
Statistics
Matches: 81, Mismatches: 12, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
73 25 0.31
74 1 0.01
75 4 0.05
76 51 0.63
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (73 bp):
GGTTTTAAGAAAAACCATCTCAAGTGAAATAAATTTTGTTCCAAAGGAAAACTGTCTCAAGCAAG
ACGAAATA
Found at i:452131 original size:28 final size:28
Alignment explanation
Indices: 452092--452177 Score: 145
Period size: 28 Copynumber: 3.0 Consensus size: 28
452082 TAAGAGAGAC
452092 AAAACTTTGTTTCAAGAGAAACTGTCTCA
1 AAAAC-TTGTTTCAAGAGAAACTGTCTCA
452121 AAAACTTGTTTCAAGAGAAACTGTCTCA
1 AAAACTTGTTTCAAGAGAAACTGTCTCA
* *
452149 AAAACTTGTTTCAAAAGAAACTATCTCA
1 AAAACTTGTTTCAAGAGAAACTGTCTCA
452177 A
1 A
452178 GGGAGACAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
28 50 0.91
29 5 0.09
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (28 bp):
AAAACTTGTTTCAAGAGAAACTGTCTCA
Found at i:452164 original size:13 final size:13
Alignment explanation
Indices: 452118--452164 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
452108 AGAAACTGTC
452118 TCAAAAACTTGTT
1 TCAAAAACTTGTT
*
452131 TCAAGAGAAAC-TGTC
1 TC-A-A-AAACTTGTT
452146 TCAAAAACTTGTT
1 TCAAAAACTTGTT
452159 TCAAAA
1 TCAAAA
452165 GAAACTATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 4 0.14
13 12 0.43
14 2 0.07
15 6 0.21
16 4 0.14
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.30
Consensus pattern (13 bp):
TCAAAAACTTGTT
Found at i:452215 original size:15 final size:15
Alignment explanation
Indices: 452103--452218 Score: 64
Period size: 15 Copynumber: 7.6 Consensus size: 15
452093 AAACTTTGTT
452103 TCAAGAGAAACTGTC
1 TCAAGAGAAACTGTC
*
452118 TC-A-A-AAACTTGTT
1 TCAAGAGAAAC-TGTC
452131 TCAAGAGAAACTGTC
1 TCAAGAGAAACTGTC
*
452146 TC-A-A-AAACTTGTT
1 TCAAGAGAAAC-TGTC
* *
452159 TCAAAAGAAACTATC
1 TCAAGAGAAACTGTC
* *
452174 TCAAGGGAGACAAAATTTGTT
1 TCAA--GAG---AAA-CTGTC
452195 TCAAGAGAAACTGTC
1 TCAAGAGAAACTGTC
452210 TCAAGAGAA
1 TCAAGAGAA
452219 GAAAAAAAAT
Statistics
Matches: 76, Mismatches: 11, Indels: 28
0.66 0.10 0.24
Matches are distributed among these distances:
12 8 0.11
13 12 0.16
14 4 0.05
15 27 0.36
16 11 0.14
17 2 0.03
19 3 0.04
20 3 0.04
21 6 0.08
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.25
Consensus pattern (15 bp):
TCAAGAGAAACTGTC
Found at i:452251 original size:39 final size:39
Alignment explanation
Indices: 452165--452341 Score: 137
Period size: 39 Copynumber: 4.6 Consensus size: 39
452155 TGTTTCAAAA
* * * *
452165 GAAACTATCTCAAG-G-GA-GACAAAATTTGTTTCAAGA
1 GAAACTATCTCAAGAGAGATAAAAAAATTTGTTTCGAGG
*
452201 GAAACTGTCTCAAGAGAAGA-AAAAAAATTTGTTTCGAGG
1 GAAACTATCTCAAGAG-AGATAAAAAAATTTGTTTCGAGG
* * *** *
452240 GAAATTATCTCAAGCGAGATAAAATCTTTTGTTTTGAGG
1 GAAACTATCTCAAGAGAGATAAAAAAATTTGTTTCGAGG
* ** *
452279 GAAACTATCTCAAGTGAGATAAAATCATTTGTTTCAAGG
1 GAAACTATCTCAAGAGAGATAAAAAAATTTGTTTCGAGG
* * ** *
452318 AAAACAATCTTGAGCGAGATAAAA
1 GAAACTATCTCAAGAGAGATAAAA
452342 TCTTTTGTTT
Statistics
Matches: 115, Mismatches: 22, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
36 13 0.11
37 1 0.01
38 3 0.03
39 98 0.85
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (39 bp):
GAAACTATCTCAAGAGAGATAAAAAAATTTGTTTCGAGG
Found at i:452310 original size:78 final size:78
Alignment explanation
Indices: 452201--452351 Score: 196
Period size: 78 Copynumber: 1.9 Consensus size: 78
452191 TGTTTCAAGA
* * * **
452201 GAAACTGTCTCAAGAGAAGAAAAAAAATTTGTTTCGAGGGAAATTATCTCAAGCGAGATAAAATC
1 GAAACTATCTCAAGAGAAGAAAAAAAATTTGTTTCAAGGAAAACAATCTCAAGCGAGATAAAATC
452266 TTTTGTTTTGAGG
66 TTTTGTTTTGAGG
* ** **
452279 GAAACTATCTCAAGTG-AGATAAAATCATTTGTTTCAAGGAAAACAATCTTGAGCGAGATAAAAT
1 GAAACTATCTCAAGAGAAGA-AAAAAAATTTGTTTCAAGGAAAACAATCTCAAGCGAGATAAAAT
452343 CTTTTGTTT
65 CTTTTGTTT
452352 CAAGGAAAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
77 3 0.05
78 59 0.95
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.31
Consensus pattern (78 bp):
GAAACTATCTCAAGAGAAGAAAAAAAATTTGTTTCAAGGAAAACAATCTCAAGCGAGATAAAATC
TTTTGTTTTGAGG
Found at i:452376 original size:40 final size:40
Alignment explanation
Indices: 452252--452651 Score: 556
Period size: 40 Copynumber: 10.0 Consensus size: 40
452242 AATTATCTCA
* ** * * **
452252 AGCGAGATAAAATCTTTTGTTTTGAGG-GAAACTATCTCA
1 AGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
*
452291 AGTGAGATAAAATCATT-TGTTTCAAGG-AAAACAATCTTG
1 AGCGAGATAAAATC-TTCTGTTTCAAGGAAAAACAATCTTG
*
452330 AGCGAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTG
1 AGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
*
452370 AACGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
1 AGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
** *
452410 AATGAAATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
1 AGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
* * *
452450 AGTGAGATAAAATCTTATGTTTCAAGGAAAAACAATATTG
1 AGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
* *
452490 AGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTT
1 AGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
* *
452530 AGTGAGATAAAATCTTCTGTTTCAAGGAAAAAAAAATCTTG
1 AGCGAGATAAAATCTTCTGTTTCAAGG-AAAAACAATCTTG
452571 AGCGAGATAAAATCTTCTGTTTCAAGGAAAAA-AATCTTG
1 AGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
*
452610 AGCGAGATAAAAATCTTATGTTTCAAGGAAAAACAATCTTG
1 AGCGAGAT-AAAATCTTCTGTTTCAAGGAAAAACAATCTTG
452651 A
1 A
452652 ATCAAATAAA
Statistics
Matches: 332, Mismatches: 23, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
38 2 0.01
39 67 0.20
40 218 0.66
41 45 0.14
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.30
Consensus pattern (40 bp):
AGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
Found at i:452406 original size:23 final size:23
Alignment explanation
Indices: 452380--452448 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
452370 AACGAGATAA
452380 AATCTTCTGTTTCAAGGAAAAAC
1 AATCTTCTGTTTCAAGGAAAAAC
*
452403 AATC-T-TG----AATGAAATAA-
1 AATCTTCTGTTTCAAGGAAA-AAC
452420 AATCTTCTGTTTCAAGGAAAAAC
1 AATCTTCTGTTTCAAGGAAAAAC
452443 AATCTT
1 AATCTT
452449 GAGTGAGATA
Statistics
Matches: 36, Mismatches: 2, Indels: 16
0.67 0.04 0.30
Matches are distributed among these distances:
17 10 0.28
18 3 0.08
19 2 0.06
21 2 0.06
22 3 0.08
23 16 0.44
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (23 bp):
AATCTTCTGTTTCAAGGAAAAAC
Found at i:452733 original size:76 final size:74
Alignment explanation
Indices: 452628--452799 Score: 204
Period size: 76 Copynumber: 2.3 Consensus size: 74
452618 AAAAATCTTA
* * *
452628 TGTTTCAAGGAAAAACAATCTTGAATCAAATAAAATGTCTTGTTT-TGAATAAAACATGTCTCTA
1 TGTTTTAA-GAAAAACAATCTTGAATCAAATAAAATGTCTTCTTTCTG--TAAAACA-GTCTCAA
452692 GCGAGACAAA-TC
62 GCGAGACAAAGTC
* * * *
452704 TTGTTTTGAGAAAAACAATCTTGAGTCAAATGAAATGTCTTCTTTCCTGTAAAACAGTCTCAAGT
1 -TGTTTTAAGAAAAACAATCTTGAATCAAATAAAATGTCTTCTTT-CTGTAAAACAGTCTCAAGC
452769 GAGACAAAGTC
64 GAGACAAAGTC
*
452780 TGTTTTAAGAAAAATAATCT
1 TGTTTTAAGAAAAACAATCT
452800 CCAGTGAGAT
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
75 33 0.40
76 42 0.51
77 6 0.07
78 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (74 bp):
TGTTTTAAGAAAAACAATCTTGAATCAAATAAAATGTCTTCTTTCTGTAAAACAGTCTCAAGCGA
GACAAAGTC
Found at i:454217 original size:10 final size:9
Alignment explanation
Indices: 454204--454330 Score: 109
Period size: 10 Copynumber: 13.8 Consensus size: 9
454194 TTTTCGTCCC
454204 TTTTTCTTT
1 TTTTTCTTT
*
454213 GTTTT-TTT
1 TTTTTCTTT
*
454221 TTTCTCTTT
1 TTTTTCTTT
*
454230 TTTTT-TCT
1 TTTTTCTTT
454238 TTTTTCTTT
1 TTTTTCTTT
*
454247 TTTCT-TTT
1 TTTTTCTTT
454255 TTTTTCTTTT
1 TTTTTC-TTT
454265 TCTTTTCTTT
1 T-TTTTCTTT
454275 TCTTTTCTTT
1 T-TTTTCTTT
*
454285 TCTTTTTTTT
1 T-TTTTCTTT
454295 TCTTTTCTTT
1 T-TTTTCTTT
*
454305 TTTCTT-TTC
1 TTT-TTCTTT
454314 TTTTTCTCTT
1 TTTTTCT-TT
454324 TTTTTCT
1 TTTTTCT
454331 GATGGATAAG
Statistics
Matches: 98, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
8 22 0.22
9 25 0.26
10 46 0.47
11 5 0.05
ACGTcount: A:0.00, C:0.15, G:0.01, T:0.84
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:454218 original size:1 final size:1
Alignment explanation
Indices: 454204--454328 Score: 79
Period size: 1 Copynumber: 125.0 Consensus size: 1
454194 TTTTCGTCCC
* * * * * * * * *
454204 TTTTTCTTTGTTTTTTTTTTCTCTTTTTTTTTCTTTTTTCTTTTTTCTTTTTTTTTCTTTTTCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * * * *
454269 TTCTTTTCTTTTCTTTTCTTTTTTTTTCTTTTCTTTTTTCTTTTCTTTTTCTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
454329 CTGATGGATA
Statistics
Matches: 86, Mismatches: 38, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 86 1.00
ACGTcount: A:0.00, C:0.14, G:0.01, T:0.85
Consensus pattern (1 bp):
T
Found at i:454224 original size:15 final size:14
Alignment explanation
Indices: 454204--454330 Score: 123
Period size: 15 Copynumber: 8.5 Consensus size: 14
454194 TTTTCGTCCC
454204 TTTTTCTTTGTTTTT
1 TTTTTCTTT-TTTTT
*
454219 TTTTTC--TCTTTT
1 TTTTTCTTTTTTTT
*
454231 TTTTTCTTTTTTCT
1 TTTTTCTTTTTTTT
454245 TTTTTCTTTTTTTTT
1 TTTTTC-TTTTTTTT
454260 CTTTTTCTTTTCTTTT
1 -TTTTTCTTTT-TTTT
*
454276 CTTTTCTTTTCTTTT
1 TTTTTCTTTT-TTTT
454291 TTTTTCTTTTCTTTTT
1 TTTTTC-TTT-TTTTT
454307 TCTTTTCTTTTTCTCTT
1 T-TTTTCTTTTT-T-TT
454324 TTTTTCT
1 TTTTTCT
454331 GATGGATAAG
Statistics
Matches: 96, Mismatches: 6, Indels: 19
0.79 0.05 0.16
Matches are distributed among these distances:
12 10 0.10
13 1 0.01
14 10 0.10
15 38 0.40
16 28 0.29
17 9 0.09
ACGTcount: A:0.00, C:0.15, G:0.01, T:0.84
Consensus pattern (14 bp):
TTTTTCTTTTTTTT
Found at i:454242 original size:20 final size:20
Alignment explanation
Indices: 454217--454327 Score: 102
Period size: 21 Copynumber: 5.3 Consensus size: 20
454207 TTCTTTGTTT
454217 TTTTTTTCTCTTTTTTTTTC
1 TTTTTTTCTCTTTTTTTTTC
*
454237 -TTTTTTCT-TTTTTCTTTTT
1 TTTTTTTCTCTTTTT-TTTTC
* *
454256 TTTTCTTTTTCTTTTCTTTTC
1 TTTT-TTTCTCTTTTTTTTTC
454277 TTTTCTTT-TCTTTTTTTTTC
1 TTTT-TTTCTCTTTTTTTTTC
*
454297 TTTTCTTTTTTCTTTTCTTTTTC
1 -TTT-TTTTCTCTTTT-TTTTTC
454320 TCTTTTTT
1 T-TTTTTT
454328 TCTGATGGAT
Statistics
Matches: 77, Mismatches: 5, Indels: 16
0.79 0.05 0.16
Matches are distributed among these distances:
18 5 0.06
19 12 0.16
20 14 0.18
21 22 0.29
22 16 0.21
23 8 0.10
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTTTTCTCTTTTTTTTTC
Found at i:459036 original size:15 final size:16
Alignment explanation
Indices: 459016--459053 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
459006 AACGTCTTTT
459016 AAAAAT-AATTTTAAG
1 AAAAATCAATTTTAAG
*
459031 AAAAATCATTTTTAAG
1 AAAAATCAATTTTAAG
459047 ACAAAAT
1 A-AAAAT
459054 TTGGTCTTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 9 0.45
17 5 0.25
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (16 bp):
AAAAATCAATTTTAAG
Found at i:460876 original size:20 final size:20
Alignment explanation
Indices: 460833--460876 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
460823 GTTTAAGATT
* *
460833 TGTTTAATGGATTTGTGGTT
1 TGTTTAATGGATTTGTAGTG
* *
460853 TGTTTAGTGGATTTTTAGTG
1 TGTTTAATGGATTTGTAGTG
460873 TGTT
1 TGTT
460877 AGGTTTGATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (20 bp):
TGTTTAATGGATTTGTAGTG
Found at i:461059 original size:3 final size:3
Alignment explanation
Indices: 461051--461077 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
461041 AGTTAATTAG
461051 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
461078 TTTTCGACCC
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):
AAT
Found at i:465688 original size:18 final size:18
Alignment explanation
Indices: 465656--465699 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
465646 TTAAGAGATA
*
465656 GTTAGAAGTTTGTTAATCT
1 GTTAG-AGTTGGTTAATCT
*
465675 GTTAGAGTTGGTTACTCT
1 GTTAGAGTTGGTTAATCT
465693 GTTAGAG
1 GTTAGAG
465700 CTGTTGAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.23, C:0.07, G:0.27, T:0.43
Consensus pattern (18 bp):
GTTAGAGTTGGTTAATCT
Found at i:469363 original size:12 final size:12
Alignment explanation
Indices: 469346--469375 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
469336 AGCCCATGCA
469346 CACCACGCATAT
1 CACCACGCATAT
*
469358 CACCACGTATAT
1 CACCACGCATAT
469370 CACCAC
1 CACCAC
469376 TTGCATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.43, G:0.07, T:0.17
Consensus pattern (12 bp):
CACCACGCATAT
Found at i:473465 original size:21 final size:21
Alignment explanation
Indices: 473441--473480 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
473431 GTTGGAGCTT
* *
473441 TAGGATTAATGTAGACATCTC
1 TAGGATGAATCTAGACATCTC
473462 TAGGATGAATCTAGACATC
1 TAGGATGAATCTAGACATC
473481 CATTTGTCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (21 bp):
TAGGATGAATCTAGACATCTC
Found at i:473954 original size:18 final size:18
Alignment explanation
Indices: 473903--473957 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
473893 CTAACTTACT
* * *
473903 TAAATTAACTAGCATACT
1 TAAATGAACTAGCATGCA
* *
473921 TAAATGAAATATCATGCA
1 TAAATGAACTAGCATGCA
473939 TAAATGAACTAGCATGCA
1 TAAATGAACTAGCATGCA
473957 T
1 T
473958 CTTTATTCAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (18 bp):
TAAATGAACTAGCATGCA
Found at i:481644 original size:60 final size:60
Alignment explanation
Indices: 481572--481684 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
481562 TATAGGATAC
* ** *
481572 TATTTTGTTGAGTCTTTCAACTATTAAAAGTTATAAAATGGTTCA-TCAACTATAAGAAGT
1 TATTTTGATGAGTCCATCAACTATTAAAAGTTACAAAATGG-TCACTCAACTATAAGAAGT
*
481632 TATTTTGATGAGTCCATCGACTATTAAAAGTTACAAAATGGTCACTCAACTAT
1 TATTTTGATGAGTCCATCAACTATTAAAAGTTACAAAATGGTCACTCAACTAT
481685 TCATTATTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 3 0.06
60 44 0.94
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37
Consensus pattern (60 bp):
TATTTTGATGAGTCCATCAACTATTAAAAGTTACAAAATGGTCACTCAACTATAAGAAGT
Found at i:481663 original size:31 final size:31
Alignment explanation
Indices: 481572--481664 Score: 84
Period size: 31 Copynumber: 3.1 Consensus size: 31
481562 TATAGGATAC
* **
481572 TATTTTGTTGAGTCTTTCAACTATTAAAAGT
1 TATTTTGATGAGTCCATCAACTATTAAAAGT
*** *
481603 TA-TAAAATG-GTTCATCAACTA-TAAGAAGT
1 TATTTTGATGAGTCCATCAACTATTAA-AAGT
*
481632 TATTTTGATGAGTCCATCGACTATTAAAAGT
1 TATTTTGATGAGTCCATCAACTATTAAAAGT
481663 TA
1 TA
481665 CAAAATGGTC
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
28 3 0.07
29 15 0.33
30 7 0.15
31 18 0.39
32 3 0.07
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (31 bp):
TATTTTGATGAGTCCATCAACTATTAAAAGT
Found at i:483042 original size:18 final size:19
Alignment explanation
Indices: 483000--483043 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
482990 TTATTTGACT
* *
483000 TTATTTATAATTTTTTATA
1 TTATTTATAATTTTTAAAA
483019 TATATTTATAA-TTTTAAAA
1 T-TATTTATAATTTTTAAAA
483038 TTATTT
1 TTATTT
483044 TATATGCCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 8 0.36
20 9 0.41
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATTTATAATTTTTAAAA
Found at i:483117 original size:12 final size:12
Alignment explanation
Indices: 483102--483126 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
483092 CCCGTCCCCA
483102 TCCCCGTATCCG
1 TCCCCGTATCCG
483114 TCCCCGTATCCG
1 TCCCCGTATCCG
483126 T
1 T
483127 GCAACATAGA
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:0.08, C:0.48, G:0.16, T:0.28
Consensus pattern (12 bp):
TCCCCGTATCCG
Found at i:484158 original size:21 final size:21
Alignment explanation
Indices: 484132--484579 Score: 317
Period size: 21 Copynumber: 21.0 Consensus size: 21
484122 TATGAAAAAA
* *
484132 ATAATGTTAACATGAAAATAT
1 ATAATGTTAACATGAAGAGAT
* *
484153 ATAATGTTAATATGAGGAGAT
1 ATAATGTTAACATGAAGAGAT
*
484174 ATAATATTAACATGAAGAGAT
1 ATAATGTTAACATGAAGAGAT
*
484195 GTAATGTTAA-AGTGAAGAGAT
1 ATAATGTTAACA-TGAAGAGAT
* * * * *
484216 ATGATATTGACATGAATATAT
1 ATAATGTTAACATGAAGAGAT
*
484237 ATAATGTTAACATGAAGTGAT
1 ATAATGTTAACATGAAGAGAT
* * *
484258 AAGTGATGTTAACCTAAAGAGAT
1 -A-TAATGTTAACATGAAGAGAT
**
484281 ATAAAATTAACATGAAGAGAT
1 ATAATGTTAACATGAAGAGAT
* *
484302 ATAGA-GTTAATAT-AAAAGGATGT
1 ATA-ATGTTAACATGAAGA-GA--T
* * * * *
484325 TTGATGTTATCATAAAAAGAT
1 ATAATGTTAACATGAAGAGAT
* * * *
484346 GTGATGTTAATATGGAGAGAT
1 ATAATGTTAACATGAAGAGAT
* *
484367 ATGATATTAACATGAAGAGAT
1 ATAATGTTAACATGAAGAGAT
* * *
484388 GTGATGTTAACATGAAGTGAT
1 ATAATGTTAACATGAAGAGAT
* * *
484409 GAGTGATGTTAACATAAAGATAT
1 -A-TAATGTTAACATGAAGAGAT
*
484432 ATAAAGTTAACATGAAGAGAT
1 ATAATGTTAACATGAAGAGAT
* *
484453 GAGTGATGTTAACATAAAGAGAT
1 -A-TAATGTTAACATGAAGAGAT
* *
484476 ATACTGTTAACATGAAGAGTT
1 ATAATGTTAACATGAAGAGAT
* * * *
484497 GTGATGTTAATATGGAGAGAT
1 ATAATGTTAACATGAAGAGAT
**
484518 ATGTTGTTAACATGAAGAGAT
1 ATAATGTTAACATGAAGAGAT
* * *
484539 ATGATGTTAACATAAAGAGAC
1 ATAATGTTAACATGAAGAGAT
*
484560 ATAATATTAACATGAAGAGA
1 ATAATGTTAACATGAAGAGA
484580 AGTTCATTTC
Statistics
Matches: 332, Mismatches: 81, Indels: 28
0.75 0.18 0.06
Matches are distributed among these distances:
20 4 0.01
21 256 0.77
22 8 0.02
23 60 0.18
24 4 0.01
ACGTcount: A:0.44, C:0.04, G:0.21, T:0.30
Consensus pattern (21 bp):
ATAATGTTAACATGAAGAGAT
Found at i:484294 original size:65 final size:63
Alignment explanation
Indices: 484135--484579 Score: 342
Period size: 65 Copynumber: 6.9 Consensus size: 63
484125 GAAAAAAATA
* * * * * * *
484135 ATGTTAACATGAAA-ATATATAATGTTAATATGAGGAGATATAATATTAACATGAAGAGATGTA
1 ATGTTAACAT-AAAGAGATATGATATTAACATGAAGAGATATAATGTTAACATGAAGAGATGTG
* * * * *
484198 ATGTTAA-AGTGAAGAGATATGATATTGACATGAATATATATAATGTTAACATGAAGTGATAAGT
1 ATGTTAACA-TAAAGAGATATGATATTAACATGAAGAGATATAATGTTAACATGAAGAGAT--GT
484262 G
63 G
* * * * *
484263 ATGTTAACCTAAAGAGATATAAAATTAACATGAAGAGATATAGA-GTTAATAT-AAAAGGATGTT
1 ATGTTAACATAAAGAGATATGATATTAACATGAAGAGATATA-ATGTTAACATGAAGA-GATG--
484326 TG
62 TG
* * * * * * * *
484328 ATGTTATCATAAAAAGATGTGATGTTAATATGGAGAGATATGATATTAACATGAAGAGATGTG
1 ATGTTAACATAAAGAGATATGATATTAACATGAAGAGATATAATGTTAACATGAAGAGATGTG
* * * * * *
484391 ATGTTAACATGAAGTGATGAGTGATGTTAACATAAAGATATATAAAGTTAACATGAAGAGATGAG
1 ATGTTAACATAAAGAGAT-A-TGATATTAACATGAAGAGATATAATGTTAACATGAAGAGAT--G
484456 TG
62 TG
* * * * * * *
484458 ATGTTAACATAAAGAGATAT-ACTGTTAACATGAAGAGTTGTGATGTTAATATGGAGAGATATG
1 ATGTTAACATAAAGAGATATGA-TATTAACATGAAGAGATATAATGTTAACATGAAGAGATGTG
* * * * * *
484521 TTGTTAACATGAAGAGATATGATGTTAACATAAAGAGACATAATATTAACATGAAGAGA
1 ATGTTAACATAAAGAGATATGATATTAACATGAAGAGATATAATGTTAACATGAAGAGA
484580 AGTTCATTTC
Statistics
Matches: 297, Mismatches: 68, Indels: 34
0.74 0.17 0.09
Matches are distributed among these distances:
62 3 0.01
63 110 0.37
64 5 0.02
65 155 0.52
66 5 0.02
67 19 0.06
ACGTcount: A:0.44, C:0.04, G:0.21, T:0.30
Consensus pattern (63 bp):
ATGTTAACATAAAGAGATATGATATTAACATGAAGAGATATAATGTTAACATGAAGAGATGTG
Found at i:484370 original size:151 final size:151
Alignment explanation
Indices: 484169--484551 Score: 463
Period size: 151 Copynumber: 2.5 Consensus size: 151
484159 TTAATATGAG
* * * * * * * *
484169 GAGATATAATATTAACATGAAGAGATGTAATGTTAA-AGTGAAGAGATATGATATTGACATGAAT
1 GAGATATACTGTTAACATAAAAAGATGTGATGTTAATA-TGGAGAGATATGATATTAACATGAAG
* * *
484233 ATATATAATGTTAACATGAAGTGATAAGTGATGTTAACCTAAAGAGATATAAAATTAACATGAAG
65 AGATATGATGTTAACATGAAGTGATAAGTGATGTTAACATAAAGAGATATAAAATTAACATGAAG
*
484298 AGAT-A-TAGA-GTTAATATAAA
130 AGATGAGT-GATGTTAACATAAA
* *
484318 -AGGATGTTTGA-TGTTATCATAAAAAGATGTGATGTTAATATGGAGAGATATGATATTAACATG
1 GA-GA--TAT-ACTGTTAACATAAAAAGATGTGATGTTAATATGGAGAGATATGATATTAACATG
* * * *
484381 AAGAGATGTGATGTTAACATGAAGTGATGAGTGATGTTAACATAAAGATATATAAAGTTAACATG
62 AAGAGATATGATGTTAACATGAAGTGATAAGTGATGTTAACATAAAGAGATATAAAATTAACATG
484446 AAGAGATGAGTGATGTTAACATAAA
127 AAGAGATGAGTGATGTTAACATAAA
* * * * *
484471 GAGATATACTGTTAACATGAAGAGTTGTGATGTTAATATGGAGAGATATGTTGTTAACATGAAGA
1 GAGATATACTGTTAACATAAAAAGATGTGATGTTAATATGGAGAGATATGATATTAACATGAAGA
484536 GATATGATGTTAACAT
66 GATATGATGTTAACAT
484552 AAAGAGACAT
Statistics
Matches: 199, Mismatches: 25, Indels: 18
0.82 0.10 0.07
Matches are distributed among these distances:
148 1 0.01
149 2 0.01
150 1 0.01
151 176 0.88
152 5 0.03
153 13 0.07
154 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.31
Consensus pattern (151 bp):
GAGATATACTGTTAACATAAAAAGATGTGATGTTAATATGGAGAGATATGATATTAACATGAAGA
GATATGATGTTAACATGAAGTGATAAGTGATGTTAACATAAAGAGATATAAAATTAACATGAAGA
GATGAGTGATGTTAACATAAA
Found at i:484416 original size:86 final size:85
Alignment explanation
Indices: 484169--484576 Score: 290
Period size: 86 Copynumber: 4.8 Consensus size: 85
484159 TTAATATGAG
* * * * * * * *
484169 GAGATATAATATTAACATGAAGAGATGTAATGTTAA-AGTGAAGAGATATGATATTGACATGAA-
1 GAGATATGATGTTAACATGAAGAGATATGATATTAACA-TAAAGAGATATGATGTTAACATGAAG
* * * * * *
484232 TATATATAATGTTAACATGAA
65 GATGTGTGATGTTATCATAAA
* * * * * * * *
484253 GTGATAAGTGATGTTAACCTAAAGAGATATAAAATTAACATGAAGAGATATAGA-GTTAATATAA
1 GAGAT-A-TGATGTTAACATGAAGAGATATGATATTAACATAAAGAGATAT-GATGTTAACAT-G
*
484317 AAGGATGTTTGATGTTATCATAAA
62 AAGGATGTGTGATGTTATCATAAA
* * * * * *
484341 AAGATGTGATGTTAATATGGAGAGATATGATATTAACATGAAGAGATGTGATGTTAACATGAAGT
1 GAGATATGATGTTAACATGAAGAGATATGATATTAACATAAAGAGATATGATGTTAACATGAAG-
* *
484406 GATGAGTGATGTTAACATAAA
65 GATGTGTGATGTTATCATAAA
* * * *
484427 GATATATAAAGTTAACATGAAGAGATGAGTGATGTTAACATAAAGAGATAT-ACTGTTAACATGA
1 GAGATATGATGTTAACATGAAGAGAT-A-TGATATTAACATAAAGAGATATGA-TGTTAACATGA
**
484491 A-GA-GTTGTGATGTTAAT-ATGGA
63 AGGATG-TGTGATGTT-ATCATAAA
* * * * *
484513 GAGATATGTTGTTAACATGAAGAGATATGATGTTAACATAAAGAGACATAATATTAACATGAAG
1 GAGATATGATGTTAACATGAAGAGATATGATATTAACATAAAGAGATATGATGTTAACATGAAG
484577 AGAAGTTCAT
Statistics
Matches: 256, Mismatches: 53, Indels: 29
0.76 0.16 0.09
Matches are distributed among these distances:
84 36 0.14
85 9 0.04
86 154 0.60
87 8 0.03
88 49 0.19
ACGTcount: A:0.44, C:0.04, G:0.22, T:0.30
Consensus pattern (85 bp):
GAGATATGATGTTAACATGAAGAGATATGATATTAACATAAAGAGATATGATGTTAACATGAAGG
ATGTGTGATGTTATCATAAA
Found at i:484737 original size:15 final size:16
Alignment explanation
Indices: 484719--484754 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
484709 TAAATTAATT
484719 TATAAAACATTAAAC-
1 TATAAAACATTAAACG
*
484734 TATAAAATATTAAACG
1 TATAAAACATTAAACG
484750 TATAA
1 TATAA
484755 TTATAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.31
Consensus pattern (16 bp):
TATAAAACATTAAACG
Found at i:490452 original size:29 final size:30
Alignment explanation
Indices: 490419--490488 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
490409 TTAAAAATAT
490419 AAAATAAATATTAA-ATTA-TAATT-TTATTA
1 AAAATAAATA--AACATTATTAATTGTTATTA
*
490448 AAAATAAATAAACATTATTAATTGTTGTTA
1 AAAATAAATAAACATTATTAATTGTTATTA
490478 AAAAT-AATAAA
1 AAAATAAATAAA
490489 TAATAAATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
27 2 0.05
28 4 0.11
29 21 0.57
30 10 0.27
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (30 bp):
AAAATAAATAAACATTATTAATTGTTATTA
Found at i:490457 original size:33 final size:32
Alignment explanation
Indices: 490402--490503 Score: 88
Period size: 33 Copynumber: 3.2 Consensus size: 32
490392 TTTCTAATAT
490402 TAATTTTTTAAAAATATAAAATAAATATTAAATTA
1 TAATTTTTT-AAAA-AT-AAATAAATATTAAATTA
*
490437 TAATTTTATTAAAAATAAATAAACATT--A-T-
1 TAATTTT-TTAAAAATAAATAAATATTAAATTA
* *
490466 TAATTGTTGTTAAAAAT-AATAAATAATAAATAA
1 TAATT-TT-TTAAAAATAAATAAATATTAAATTA
490499 TAATT
1 TAATT
490504 CATTTGATCC
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
29 13 0.23
30 11 0.20
31 2 0.04
33 15 0.27
34 2 0.04
35 11 0.20
36 2 0.04
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (32 bp):
TAATTTTTTAAAAATAAATAAATATTAAATTA
Found at i:495962 original size:7 final size:7
Alignment explanation
Indices: 495946--495983 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
495936 GTCAAAGAAA
*
495946 GTCAATG
1 GTCAACG
495953 GTCAACG
1 GTCAACG
495960 GTCAACG
1 GTCAACG
*
495967 GTCAACA
1 GTCAACG
495974 GTCAACG
1 GTCAACG
495981 GTC
1 GTC
495984 GGGTCGGGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:495990 original size:5 final size:5
Alignment explanation
Indices: 495980--496032 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
495970 AACAGTCAAC
* *
495980 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG
496029 GGTC
1 GGTC
496033 AGACCGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:495996 original size:17 final size:17
Alignment explanation
Indices: 495974--496033 Score: 75
Period size: 17 Copynumber: 3.2 Consensus size: 17
495964 ACGGTCAACA
495974 GTCAACGGTCGGGTCGG
1 GTCAACGGTCGGGTCGG
495991 GTCAACGGTCGGGTCGGGTCGG
1 GTCAA----C-GGTCGGGTCGG
496013 GTCAACGGTCGGGTCGG
1 GTCAACGGTCGGGTCGG
496030 GTCA
1 GTCA
496034 GACCGGTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
17 20 0.53
18 1 0.03
21 1 0.03
22 16 0.42
ACGTcount: A:0.12, C:0.23, G:0.47, T:0.18
Consensus pattern (17 bp):
GTCAACGGTCGGGTCGG
Found at i:496008 original size:22 final size:22
Alignment explanation
Indices: 495980--496032 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
495970 AACAGTCAAC
495980 GGTCGGGTCGGGTCAACGGTCG
1 GGTCGGGTCGGGTCAACGGTCG
496002 GGTCGGGTCGGGTCAACGGTCG
1 GGTCGGGTCGGGTCAACGGTCG
496024 GGTCGGGTC
1 GGTCGGGTC
496033 AGACCGGTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (22 bp):
GGTCGGGTCGGGTCAACGGTCG
Found at i:496047 original size:9 final size:9
Alignment explanation
Indices: 496029--496127 Score: 81
Period size: 9 Copynumber: 10.3 Consensus size: 9
496019 GGTCGGGTCG
*
496029 GGTCAGACC
1 GGTCAAACC
496038 GGTCAAACC
1 GGTCAAACC
* *
496047 GATTCAGACC
1 G-GTCAAACC
496057 GGTCAAACC
1 GGTCAAACC
*
496066 GGTTCGAACC
1 GG-TCAAACC
*
496076 GGTTGAAACC
1 GG-TCAAACC
496086 GGTCAAACC
1 GGTCAAACC
496095 GGTCAGAACC
1 GGTCA-AACC
*
496105 GGTTGAAAACC
1 GG-T-CAAACC
*
496116 GGTTAAACC
1 GGTCAAACC
496125 GGT
1 GGT
496128 TTCCAGCAGC
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
9 36 0.49
10 30 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:496086 original size:29 final size:31
Alignment explanation
Indices: 496054--496128 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
496044 ACCGATTCAG
496054 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
496083 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
496113 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
496129 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:496106 original size:19 final size:19
Alignment explanation
Indices: 496029--496127 Score: 80
Period size: 19 Copynumber: 5.2 Consensus size: 19
496019 GGTCGGGTCG
496029 GGTCAG-ACCGGTCAAACC
1 GGTCAGAACCGGTCAAACC
*
496047 GATTCAG-ACCGGTCAAACC
1 G-GTCAGAACCGGTCAAACC
*
496066 GGTTC-GAACCGGTTGAAACC
1 GG-TCAGAACCGG-TCAAACC
496086 GGTCA-AACCGGTCAGAACC
1 GGTCAGAACCGGTCA-AACC
* * *
496105 GGTTGAAAACCGGTTAAACC
1 GG-TCAGAACCGGTCAAACC
496125 GGT
1 GGT
496128 TTCCAGCAGC
Statistics
Matches: 67, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
18 4 0.06
19 39 0.58
20 16 0.24
21 8 0.12
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (19 bp):
GGTCAGAACCGGTCAAACC
Found at i:503297 original size:7 final size:7
Alignment explanation
Indices: 503281--503311 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
503271 GTCAAAGAAA
*
503281 GTCAATG
1 GTCAACG
503288 GTCAACG
1 GTCAACG
503295 GTCAACG
1 GTCAACG
503302 GTCAACG
1 GTCAACG
503309 GTC
1 GTC
503312 GGGTCGGGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:503318 original size:5 final size:5
Alignment explanation
Indices: 503308--503365 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
503298 AACGGTCAAC
* *
503308 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
503357 GGTCG GGTC
1 GGTCG GGTC
503366 AGACCGGTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.07, C:0.22, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:503327 original size:22 final size:22
Alignment explanation
Indices: 503301--503365 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
503291 AACGGTCAAC
503301 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
503323 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
503345 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
503366 AGACCGGTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:503409 original size:19 final size:19
Alignment explanation
Indices: 503368--503431 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
503358 GTCGGGTCAG
*
503368 ACCGGTCAAACCGATTC-A
1 ACCGGTCAAACCGGTTCGA
503386 GACCGGTCAAACCGGTTCGA
1 -ACCGGTCAAACCGGTTCGA
*
503406 ACCGGTTGAAACCGG-TCAGA
1 ACCGG-TCAAACCGGTTC-GA
503426 ACCGGT
1 ACCGGT
503432 TAAAAACCGG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
19 24 0.60
20 16 0.40
ACGTcount: A:0.28, C:0.30, G:0.27, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCGA
Found at i:503419 original size:20 final size:21
Alignment explanation
Indices: 503394--503452 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
503384 CAGACCGGTC
*
503394 AAACCGGTTCGAACCGGTT-G
1 AAACCGGTTCGAACCGGTTAA
503414 AAACCGG-TCAGAACCGGTTAA
1 AAACCGGTTC-GAACCGGTTAA
*
503435 AAACCGGTT-AAACCGGTT
1 AAACCGGTTCGAACCGGTT
503453 TCCAGCAGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 2 0.06
20 24 0.71
21 7 0.21
22 1 0.03
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (21 bp):
AAACCGGTTCGAACCGGTTAA
Found at i:509047 original size:29 final size:29
Alignment explanation
Indices: 508985--509064 Score: 135
Period size: 28 Copynumber: 2.8 Consensus size: 29
508975 ATATCCATTT
* *
508985 TTCCAGTTTATTGCCTAACGTTTTTTTGG
1 TTCCAGTTTAGTGCCTAACGTTTTTTCGG
509014 -TCCAGTTTAGTGCCTAACGTTTTTTCGG
1 TTCCAGTTTAGTGCCTAACGTTTTTTCGG
509042 TTCCAGTTTAGTGCCTAACGTTT
1 TTCCAGTTTAGTGCCTAACGTTT
509065 CATTCCGTCA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 26 0.54
29 22 0.46
ACGTcount: A:0.15, C:0.20, G:0.19, T:0.46
Consensus pattern (29 bp):
TTCCAGTTTAGTGCCTAACGTTTTTTCGG
Found at i:517652 original size:52 final size:52
Alignment explanation
Indices: 517565--517671 Score: 187
Period size: 52 Copynumber: 2.1 Consensus size: 52
517555 TGGTTTTGGC
*
517565 GTGTGCAGCATTTTTTCCACGTGAGGAGTGCTTTGTGTTTAGCATTTCGGCA
1 GTGTGCAGCATTTTTTCCACGTGAGAAGTGCTTTGTGTTTAGCATTTCGGCA
* *
517617 GTGTGCAGCATTTTTTCCATGTGAGAAGTGTTTTGTGTTTAGCATTTCGGCA
1 GTGTGCAGCATTTTTTCCACGTGAGAAGTGCTTTGTGTTTAGCATTTCGGCA
517669 GTG
1 GTG
517672 CTTTGAAGTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.16, C:0.15, G:0.29, T:0.40
Consensus pattern (52 bp):
GTGTGCAGCATTTTTTCCACGTGAGAAGTGCTTTGTGTTTAGCATTTCGGCA
Found at i:521995 original size:21 final size:21
Alignment explanation
Indices: 521971--522010 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
521961 GTTGGAGCTT
* *
521971 TAGGATTAATGTAGACATCTC
1 TAGGATGAATCTAGACATCTC
521992 TAGGATGAATCTAGACATC
1 TAGGATGAATCTAGACATC
522011 CATTTTTCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (21 bp):
TAGGATGAATCTAGACATCTC
Found at i:522479 original size:18 final size:18
Alignment explanation
Indices: 522426--522480 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
522416 AATAAACTAA
*
522426 CTTAAATGAACTAACATA
1 CTTAAATGAACTAACATG
* *
522444 CTTAAATGACCTATCATG
1 CTTAAATGAACTAACATG
*
522462 CTTAAATGAACTAGCATG
1 CTTAAATGAACTAACATG
522480 C
1 C
522481 ATCTTTATTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (18 bp):
CTTAAATGAACTAACATG
Found at i:523582 original size:15 final size:16
Alignment explanation
Indices: 523564--523593 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
523554 GTGGCAGATC
523564 AAAATCCAG-ACGGGG
1 AAAATCCAGAACGGGG
523579 AAAATCCAGAACGGG
1 AAAATCCAGAACGGG
523594 AAAGAAAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.43, C:0.20, G:0.30, T:0.07
Consensus pattern (16 bp):
AAAATCCAGAACGGGG
Found at i:540171 original size:43 final size:43
Alignment explanation
Indices: 540104--540189 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
540094 TGGCTTTAGA
* *
540104 GAAGTTAGGAGGGAAAGTTATCCCCTATATGTAAAGTTTTGTT
1 GAAGTTAGGACGGAAAGATATCCCCTATATGTAAAGTTTTGTT
* *
540147 GAAGTTAGGACTGAAAGATGTCCCCTATATGTAAAGTTTTGTT
1 GAAGTTAGGACGGAAAGATATCCCCTATATGTAAAGTTTTGTT
540190 TGATGCACGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.35
Consensus pattern (43 bp):
GAAGTTAGGACGGAAAGATATCCCCTATATGTAAAGTTTTGTT
Found at i:543367 original size:2 final size:2
Alignment explanation
Indices: 543360--543411 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
543350 TTATCCTTTA
543360 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
543402 AT AT AT AT AT
1 AT AT AT AT AT
543412 CCTTTGTTGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:543725 original size:23 final size:23
Alignment explanation
Indices: 543698--543742 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
543688 TATTATACTC
543698 ATCCAGCAAAGAAAGAAAAAAAA
1 ATCCAGCAAAGAAAGAAAAAAAA
*
543721 ATCCAGCAAAGAAAGGAAAAAA
1 ATCCAGCAAAGAAAGAAAAAAA
543743 GAAAAAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.67, C:0.13, G:0.16, T:0.04
Consensus pattern (23 bp):
ATCCAGCAAAGAAAGAAAAAAAA
Found at i:543758 original size:10 final size:9
Alignment explanation
Indices: 543737--543801 Score: 55
Period size: 9 Copynumber: 7.3 Consensus size: 9
543727 CAAAGAAAGG
543737 AAAAA-AGA
1 AAAAAGAGA
543745 AAAAAGAGGA
1 AAAAAGA-GA
*
543755 AAAAAGAAA
1 AAAAAGAGA
543764 AAAAAG-GA
1 AAAAAGAGA
*
543772 AAGAAATAGA
1 AA-AAAGAGA
* *
543782 AAAAAAACA
1 AAAAAGAGA
543791 AAAAAGA-A
1 AAAAAGAGA
543799 AAA
1 AAA
543802 GAAAAAAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
8 12 0.26
9 22 0.47
10 13 0.28
ACGTcount: A:0.82, C:0.02, G:0.15, T:0.02
Consensus pattern (9 bp):
AAAAAGAGA
Found at i:543782 original size:20 final size:17
Alignment explanation
Indices: 543732--543801 Score: 88
Period size: 17 Copynumber: 4.0 Consensus size: 17
543722 TCCAGCAAAG
543732 AAAGGAAAAAAGAAAAA
1 AAAGGAAAAAAGAAAAA
*
543749 AGAGGAAAAAAGAAAAA
1 AAAGGAAAAAAGAAAAA
543766 AAAGGAAAGAAATAGAAAAA
1 AAAGG-AA-AAA-AGAAAAA
*
543786 AAA-CAAAAAAGAAAAA
1 AAAGGAAAAAAGAAAAA
543802 GAAAAAAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
16 7 0.15
17 23 0.49
18 4 0.09
19 3 0.06
20 10 0.21
ACGTcount: A:0.80, C:0.01, G:0.17, T:0.01
Consensus pattern (17 bp):
AAAGGAAAAAAGAAAAA
Found at i:548843 original size:22 final size:22
Alignment explanation
Indices: 548815--548936 Score: 219
Period size: 22 Copynumber: 5.6 Consensus size: 22
548805 ACATCTACAT
548815 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
548837 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
548859 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
548881 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
548903 TTTTTAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
548925 T-TTCAAAGATGA
1 TCTTCAAAGATGA
548937 AAGCTTTATT
Statistics
Matches: 97, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
21 10 0.10
22 87 0.90
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:549779 original size:114 final size:114
Alignment explanation
Indices: 549348--550125 Score: 1018
Period size: 115 Copynumber: 6.9 Consensus size: 114
549338 CCATCATTCA
* ** * *
549348 ATGGATCAACATTTT-CAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAG-AAGAAGAAG
1 ATGGATCAACCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAG
* * * *
549411 TTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCCCTCG
66 TTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTAAATTCATCACTTG
* ** ** * * *
549460 GTGGATCAATATTTT-CAGTTAGAGTTCATAATGAGAAGAAATCATCTGAAGAAGAAAAAGAAGA
1 ATGGATCAACCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAG--GAGAAAGAAGA
* * *
549524 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCG
64 AGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTAAATTCATCACTTG
* * ** * ** * * **
549575 GTGGATC-AGCAGTGCCAGTTAGAGTTCATAATGAAAAGAACTCATCTGAAAAAG-AAGAAGAAG
1 ATGGATCAACCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAG
*
549638 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTTG
66 TTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTAAATTCATCACTTG
*
549687 ATGGATCAA-CTTTTCTAGAAAAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAA
1 ATGGATCAACCTTTTCCAG-AAAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAA
549751 GTTCATAATGAGAAGAACTTGTTTAACCTTTTG-TTCAAATTCATCACTTG
65 GTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTT-AAATTCATCACTTG
* * *
549801 ATGGATCAAGCTTTTCCAGAAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
1 ATGGATCAACCTTTTCCAGAAAA-AGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAA
* * *
549866 GTTCATAATGAGAAGAATTTGTTTAACCTTTTGCTCAAATCCATCACTTG
65 GTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTAAATTCATCACTTG
* *
549916 ATGGATC-AGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCTTCTGAAGGAGAAAGAAGAA
1 ATGGATCAACCTTTTCCAG-AAAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAA
549980 GTTCATAATGAGAAGAACTTGTTTAACCTTTTG-TTCAAATTCATCACTTG
65 GTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTT-AAATTCATCACTTG
* *
550030 ATGGATCAACC-TTTACAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAG
1 ATGGATCAACCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAG
* *
550094 TTCATAATGAGAAGAGCTTATTTAACCTTTTG
66 TTCATAATGAGAAGAACTTGTTTAACCTTTTG
550126 AATGACTCTT
Statistics
Matches: 604, Mismatches: 48, Indels: 27
0.89 0.07 0.04
Matches are distributed among these distances:
112 115 0.19
113 109 0.18
114 177 0.29
115 202 0.33
116 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (114 bp):
ATGGATCAACCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAG
TTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTAAATTCATCACTTG
Found at i:549938 original size:229 final size:228
Alignment explanation
Indices: 549368--550125 Score: 1082
Period size: 229 Copynumber: 3.3 Consensus size: 228
549358 ATTTTCAGTT
549368 AGAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * * * * * ** *
549432 TCAACTTTTTGCTTAAATTCATCCCTCGGTGGATCAATATTTTCAG-TTAGAGTTCATAATGAGA
66 TCAACCTTTTGCTTAAATTCATCACTTGATGGATCACT-TTTCCAGAAAAAAGTTCATAATGAGA
* * * *
549496 AGAAATCATCTGAAGAAGAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
130 AGAACTCATCTGAAG--GAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTG-TT
* * * * **
549561 -AAATTCATCACTCGGTGGATC-AGCAGTGCCAG-TT
192 CAAATTCATCACTTGATGGATCAAGCATTTCCAGAAA
* *
549595 AGAGTTCATAATGAAAAGAACTCATCTGAA-AAAGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
*
549659 TCAACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCTAGAAAAAAGTTCATAATGAGA
66 TCAACCTTTTGCTTAAATTCATCACTTGATGGATC-ACTTTTCCAGAAAAAAGTTCATAATGAGA
549724 AGAACTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGTTCAA
130 AGAACTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGTTCAA
*
549789 ATTCATCACTTGATGGATCAAGCTTTTCCAGAAA
195 ATTCATCACTTGATGGATCAAGCATTTCCAGAAA
*
549823 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * *
549888 TTAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGA
66 TCAACCTTTTGCTTAAATTCATCACTTGATGGATCA-CTTTTCCAGAAAAAAGTTCATAATGAGA
*
549953 AGAACTCTTCTGAAGGAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGTTCAA
130 AGAACTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGTTCAA
* * *
550018 ATTCATCACTTGATGGATCAA-CCTTTACAGAGA
195 ATTCATCACTTGATGGATCAAGCATTTCCAGAAA
* * * *
550051 A-AGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGAAGAGCTTAT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
*
550115 TTAACCTTTTG
66 TCAACCTTTTG
550126 AATGACTCTT
Statistics
Matches: 485, Mismatches: 38, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
225 2 0.00
226 63 0.13
227 173 0.36
228 71 0.15
229 176 0.36
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (228 bp):
AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
TCAACCTTTTGCTTAAATTCATCACTTGATGGATCACTTTTCCAGAAAAAAGTTCATAATGAGAA
GAACTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGTTCAAA
TTCATCACTTGATGGATCAAGCATTTCCAGAAA
Found at i:550360 original size:6 final size:6
Alignment explanation
Indices: 550349--550419 Score: 54
Period size: 6 Copynumber: 11.3 Consensus size: 6
550339 TTTACCCATT
* * * * *
550349 TTATTA TTATTA TAATTA TTATCA TAATAA TTATTA TTATAA TTATTA
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA
550397 -TATATA TATATATA TATATTA TT
1 TTAT-TA T-TAT-TA T-TATTA TT
550420 TAAAAAATAT
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
5 3 0.06
6 36 0.68
7 3 0.06
8 11 0.21
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (6 bp):
TTATTA
Found at i:550368 original size:12 final size:13
Alignment explanation
Indices: 550351--550419 Score: 76
Period size: 12 Copynumber: 5.5 Consensus size: 13
550341 TACCCATTTT
550351 ATTATTAT-TATA
1 ATTATTATATATA
550363 ATTATTATCATAATA
1 ATTATTAT-AT-ATA
550378 ATTATTAT-TATA
1 ATTATTATATATA
550390 ATTATTATATAT-
1 ATTATTATATATA
550402 A-TA-TATATATA
1 ATTATTATATATA
550413 TATTATT
1 -ATTATT
550420 TAAAAAATAT
Statistics
Matches: 49, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
10 7 0.14
11 2 0.04
12 21 0.43
13 6 0.12
14 2 0.04
15 11 0.22
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTATTATATATA
Found at i:550369 original size:15 final size:15
Alignment explanation
Indices: 550349--550446 Score: 74
Period size: 15 Copynumber: 6.4 Consensus size: 15
550339 TTTACCCATT
*
550349 TTATTATTATTATAA
1 TTATTATTATAATAA
*
550364 TTATTATCATAATAA
1 TTATTATTATAATAA
*
550379 TTATTATTATAATTA
1 TTATTATTATAATAA
550394 TTA-TATATATATATATA
1 TTATTAT-TATA-ATA-A
*
550411 TATATTATT-TAAAAA
1 T-TATTATTATAATAA
* * *
550426 ATATAATAATAATAA
1 TTATTATTATAATAA
*
550441 TAATTA
1 TTATTA
550447 CAAACAGGCC
Statistics
Matches: 64, Mismatches: 13, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
14 8 0.12
15 42 0.66
16 4 0.06
17 4 0.06
18 3 0.05
19 3 0.05
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATTATTATAATAA
Found at i:550882 original size:17 final size:17
Alignment explanation
Indices: 550856--550893 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
550846 AGAGACCAGC
* *
550856 AAAAATAGAGAAGAAAA
1 AAAAACAGAGAACAAAA
550873 AAAAACAGAGAACAAAA
1 AAAAACAGAGAACAAAA
550890 AAAA
1 AAAA
550894 GAAAACCTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.79, C:0.05, G:0.13, T:0.03
Consensus pattern (17 bp):
AAAAACAGAGAACAAAA
Found at i:554387 original size:28 final size:28
Alignment explanation
Indices: 554356--554410 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
554346 TGCATTTATG
554356 TGTGGAACCACTAAATCTTGCAATCCTA
1 TGTGGAACCACTAAATCTTGCAATCCTA
554384 TGTGGAACCACTAAATCTTGCAATCCT
1 TGTGGAACCACTAAATCTTGCAATCCT
554411 GTGATGCGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (28 bp):
TGTGGAACCACTAAATCTTGCAATCCTA
Found at i:554621 original size:21 final size:21
Alignment explanation
Indices: 554595--554662 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
554585 GAACTTGAAT
*
554595 ATGAAAAAAAATAATGTTAAC
1 ATGAAAAAATATAATGTTAAC
* *
554616 ATGAAAATATATAATGTTAAT
1 ATGAAAAAATATAATGTTAAC
* * *
554637 ATGAAGAGATATAATATTAAC
1 ATGAAAAAATATAATGTTAAC
554658 ATGAA
1 ATGAA
554663 GAGATGTGAC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.56, C:0.03, G:0.12, T:0.29
Consensus pattern (21 bp):
ATGAAAAAATATAATGTTAAC
Found at i:554663 original size:21 final size:21
Alignment explanation
Indices: 554608--554960 Score: 226
Period size: 21 Copynumber: 16.5 Consensus size: 21
554598 AAAAAAAATA
* * *
554608 ATGTTAACATGAAAATATATA
1 ATGTTAACATGAAGAGATATG
* *
554629 ATGTTAATATGAAGAGATATA
1 ATGTTAACATGAAGAGATATG
* *
554650 ATATTAACATGAAGAGATGTG
1 ATGTTAACATGAAGAGATATG
** *
554671 ACATTAACATGAAGAGATGTG
1 ATGTTAACATGAAGAGATATG
* *
554692 ATGTTAAAATGAAGAGATACG
1 ATGTTAACATGAAGAGATATG
* * * *
554713 ATATTGACATG-A-ATATATA
1 ATGTTAACATGAAGAGATATG
** * * *
554732 ATGTTAATGTGAAGTGACGAGTT
1 ATGTTAACATGAAGAGA-TA-TG
* * *
554755 ATATTAACATAAAGAGATATA
1 ATGTTAACATGAAGAGATATG
* *
554776 AAGTTACCATGAAGAGATATGG
1 ATGTTAACATGAAGAGATAT-G
* * * *
554798 A-GTTAACATAAAAGGAGGTTTA
1 ATGTTAACAT-GAA-GAGATATG
* *
554820 ATGTTAACATGAAAAGATGTG
1 ATGTTAACATGAAGAGATATG
* *
554841 ATGTTAATATGGAGAGATATG
1 ATGTTAACATGAAGAGATATG
*
554862 ATGTTAACATGAAGAGATGTG
1 ATGTTAACATGAAGAGATATG
*
554883 ATGTTAACATGAAGTGATGAGTG
1 ATGTTAACATGAAGAGAT-A-TG
* * *
554906 ATGTTAACATAAAAAGATATA
1 ATGTTAACATGAAGAGATATG
* * *
554927 ATGTTAACGTAAAGAGATGTGTG
1 ATGTTAACATGAAGAGA--TATG
554950 ATGTTAACATG
1 ATGTTAACATG
554961 GTGATGTTAA
Statistics
Matches: 252, Mismatches: 68, Indels: 22
0.74 0.20 0.06
Matches are distributed among these distances:
19 11 0.04
20 2 0.01
21 176 0.70
22 9 0.04
23 54 0.21
ACGTcount: A:0.43, C:0.05, G:0.22, T:0.30
Consensus pattern (21 bp):
ATGTTAACATGAAGAGATATG
Found at i:554907 original size:65 final size:64
Alignment explanation
Indices: 554820--554960 Score: 167
Period size: 65 Copynumber: 2.2 Consensus size: 64
554810 AGGAGGTTTA
* ** * * *
554820 ATGTTAACATGAAAAGATGTGATGTTAATATGGAGAGATATGATGTTAACATGAAGAGA-TGTG
1 ATGTTAACATGAAAAGATGTGATGTTAACATAAAAAGATATAATGTTAACATAAAGAGAGTGTG
** *
554883 ATGTTAACATGAAGTGATGAGTGATGTTAACATAAAAAGATATAATGTTAACGTAAAGAGATGTG
1 ATGTTAACATGAAAAGAT--GTGATGTTAACATAAAAAGATATAATGTTAACATAAAGAGA-GTG
554948 TG
63 TG
554950 ATGTTAACATG
1 ATGTTAACATG
554961 GTGATGTTAA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
63 16 0.25
65 34 0.52
67 15 0.23
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.30
Consensus pattern (64 bp):
ATGTTAACATGAAAAGATGTGATGTTAACATAAAAAGATATAATGTTAACATAAAGAGAGTGTG
Found at i:554931 original size:44 final size:44
Alignment explanation
Indices: 554820--554960 Score: 178
Period size: 44 Copynumber: 3.2 Consensus size: 44
554810 AGGAGGTTTA
* *
554820 ATGTTAACATGAAAAGATGTGATGTTAATATGGAGAGAT-A-TG
1 ATGTTAACATGAAAAGATGTGATGTTAACATGAAGAGATGAGTG
* *
554862 ATGTTAACATGAAGAGATGTGATGTTAACATGAAGTGATGAGTG
1 ATGTTAACATGAAAAGATGTGATGTTAACATGAAGAGATGAGTG
* * * * * *
554906 ATGTTAACATAAAAAGATATAATGTTAACGTAAAGAGATGTGTG
1 ATGTTAACATGAAAAGATGTGATGTTAACATGAAGAGATGAGTG
554950 ATGTTAACATG
1 ATGTTAACATG
554961 GTGATGTTAA
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
42 35 0.42
43 1 0.01
44 48 0.57
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.30
Consensus pattern (44 bp):
ATGTTAACATGAAAAGATGTGATGTTAACATGAAGAGATGAGTG
Found at i:554943 original size:86 final size:86
Alignment explanation
Indices: 554758--554960 Score: 203
Period size: 86 Copynumber: 2.3 Consensus size: 86
554748 ACGAGTTATA
* * * **
554758 TTAACATAAAGAGATATAAAGTTACCATGAAGAGATATGGAGTTAACATAAAAGGAGGTTTAATG
1 TTAACATAAAGAGATATGATGTTAACATGAAGAGATATGGAGTTAACATAAAAGGAGGAGTAATG
* * *
554823 TTAACATGAAAAGATGTGATG
66 TTAACATAAAAAGATATAATG
* ** * * * *
554844 TTAATATGGAGAGATATGATGTTAACATGAAGAGATGT-GATGTTAACAT-GAAGTGATGAGTGA
1 TTAACATAAAGAGATATGATGTTAACATGAAGAGATATGGA-GTTAACATAAAAG-GAGGAGTAA
554907 TGTTAACATAAAAAGATATAATG
64 TGTTAACATAAAAAGATATAATG
* *
554930 TTAACGTAAAGAGATGTGTGATGTTAACATG
1 TTAACATAAAGAGA--TATGATGTTAACATG
554961 GTGATGTTAA
Statistics
Matches: 93, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
85 5 0.05
86 74 0.80
88 14 0.15
ACGTcount: A:0.42, C:0.05, G:0.24, T:0.29
Consensus pattern (86 bp):
TTAACATAAAGAGATATGATGTTAACATGAAGAGATATGGAGTTAACATAAAAGGAGGAGTAATG
TTAACATAAAAAGATATAATG
Found at i:554966 original size:14 final size:14
Alignment explanation
Indices: 554947--554978 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
554937 AAAGAGATGT
554947 GTGATGTTAACATG
1 GTGATGTTAACATG
*
554961 GTGATGTTAATATG
1 GTGATGTTAACATG
554975 GTGA
1 GTGA
554979 GATTTGTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.31, T:0.38
Consensus pattern (14 bp):
GTGATGTTAACATG
Found at i:555438 original size:24 final size:27
Alignment explanation
Indices: 555393--555446 Score: 78
Period size: 24 Copynumber: 2.1 Consensus size: 27
555383 CGCTACTACT
555393 ACCACCACCACCATTACTGTCGTCGCC
1 ACCACCACCACCATTACTGTCGTCGCC
*
555420 ACCACCACCA-CATT-C-GTCGTCGTC
1 ACCACCACCACCATTACTGTCGTCGCC
555444 ACC
1 ACC
555447 GCCGCCGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 11 0.42
25 1 0.04
26 4 0.15
27 10 0.38
ACGTcount: A:0.22, C:0.48, G:0.11, T:0.19
Consensus pattern (27 bp):
ACCACCACCACCATTACTGTCGTCGCC
Found at i:559482 original size:5 final size:5
Alignment explanation
Indices: 559472--559504 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
559462 AACACTAAAC
559472 AGAAG AGAAG AGAAG AGAAG AGAAG AGAAG AGA
1 AGAAG AGAAG AGAAG AGAAG AGAAG AGAAG AGA
559505 GTGACCTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (5 bp):
AGAAG
Found at i:561815 original size:2 final size:2
Alignment explanation
Indices: 561808--561839 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
561798 CGTTTGCAAT
561808 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
561840 CATACATACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:564407 original size:12 final size:12
Alignment explanation
Indices: 564390--564426 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
564380 ATAAGAACCC
564390 TCTTCTCCTGAT
1 TCTTCTCCTGAT
564402 TCTTCTCCTGAT
1 TCTTCTCCTGAT
*
564414 TCTTCTCTTGAT
1 TCTTCTCCTGAT
564426 T
1 T
564427 TAACCTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.08, C:0.30, G:0.08, T:0.54
Consensus pattern (12 bp):
TCTTCTCCTGAT
Found at i:570923 original size:43 final size:44
Alignment explanation
Indices: 570852--571309 Score: 481
Period size: 43 Copynumber: 10.6 Consensus size: 44
570842 TGAGAACCAA
* * * *
570852 AAACGCCGCTATAGTTCAAGATCTATAGCGGCGTTTTTGGA-AC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGATAC
* * * *
570895 AAACGTCGCAAAAGGTCGATATATATAGCGGCGTTTTTAGA-AC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGATAC
* * *
570938 AAACGCCGCAAAAAGGTCAAGATCTCTAGCGGCGTTTATGGA-AC
1 AAACGCCGC-AAAAGGTCGAGATCTATAGCGGCGTTTTTGGATAC
* *
570982 AAATGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGTA-AC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGATAC
* * * *
571025 AAACGTCGCAAAAGGT-TAGATATTTAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGATAC
* *
571068 AAATGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGTA-AC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGATAC
* * * *
571111 AAACGTCGCAAAAGGT-TAGATATTTAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGATAC
* * * * * *
571154 AAATGCTGCAAAAGGAC-AGATCTATAGTGGCATTTTTGGACAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGATAC
* * * *
571197 AAACGTCGCAAAAGGT-TAGATATTTAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGATAC
* *
571240 AAAACGCTGCAAAA-GTACG-GATCTATAGCGGCGTTTTTGGACAC
1 -AAACGCCGCAAAAGGT-CGAGATCTATAGCGGCGTTTTTGGATAC
*
571284 AAACGCCGCAAAAAGTC-AGATCTATA
1 AAACGCCGCAAAAGGTCGAGATCTATA
571310 ATTACCATTC
Statistics
Matches: 341, Mismatches: 63, Indels: 22
0.80 0.15 0.05
Matches are distributed among these distances:
42 40 0.12
43 210 0.62
44 91 0.27
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (44 bp):
AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGATAC
Found at i:571088 original size:86 final size:86
Alignment explanation
Indices: 570877--571296 Score: 580
Period size: 86 Copynumber: 4.9 Consensus size: 86
570867 TCAAGATCTA
* * * * *
570877 TAGCGGCGTTTTTGGA-ACAAACGTCGCAAAAGGTCGATATATATAGCGGCGTTTTTAGAACAAA
1 TAGCGGCGTTTTTGGATACAAATGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAA
* * * *
570941 CGCCGCAAAAAGGTCAAGATCTC
66 CGTCGC-AAAAGGT-TAGATATT
* *
570964 TAGCGGCGTTTATGGA-ACAAATGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGTAACAAA
1 TAGCGGCGTTTTTGGATACAAATGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAA
571028 CGTCGCAAAAGGTTAGATATT
66 CGTCGCAAAAGGTTAGATATT
*
571049 TAGCGGCGTTTTTGGATACAAATGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGTAACAAA
1 TAGCGGCGTTTTTGGATACAAATGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAA
571114 CGTCGCAAAAGGTTAGATATT
66 CGTCGCAAAAGGTTAGATATT
* * * *
571135 TAGCGGCGTTTTTGGATACAAATGCTGCAAAAGGAC-AGATCTATAGTGGCATTTTTGGACACAA
1 TAGCGGCGTTTTTGGATACAAATGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGA-ACAA
571199 ACGTCGCAAAAGGTTAGATATT
65 ACGTCGCAAAAGGTTAGATATT
* *
571221 TAGCGGCGTTTTTGGATACAAAACGCTGCAAAA-GTACG-GATCTATAGCGGCGTTTTTGGACAC
1 TAGCGGCGTTTTTGGATAC-AAATGCCGCAAAAGGT-CGAGATCTATAGCGGCGTTTTTGGA-AC
*
571284 AAACGCCGCAAAA
63 AAACGTCGCAAAA
571297 AGTCAGATCT
Statistics
Matches: 306, Mismatches: 22, Indels: 10
0.91 0.07 0.03
Matches are distributed among these distances:
85 40 0.13
86 156 0.51
87 110 0.36
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (86 bp):
TAGCGGCGTTTTTGGATACAAATGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAA
CGTCGCAAAAGGTTAGATATT
Found at i:572189 original size:26 final size:26
Alignment explanation
Indices: 572160--572209 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
572150 ATAATTAATG
572160 ATTAAAATCACAAAATGCAGGGAATA
1 ATTAAAATCACAAAATGCAGGGAATA
572186 ATTAAAATCACAAAATGCAGGGAA
1 ATTAAAATCACAAAATGCAGGGAA
572210 ACAAGATACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.54, C:0.12, G:0.16, T:0.18
Consensus pattern (26 bp):
ATTAAAATCACAAAATGCAGGGAATA
Found at i:573994 original size:41 final size:41
Alignment explanation
Indices: 573949--574533 Score: 526
Period size: 41 Copynumber: 14.3 Consensus size: 41
573939 TTAGCCGCAG
* * *
573949 AAACGCCACTAAAGTACGGGTCTTTGGCGGCGTTTGCATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* *
573990 AAACGCCACTAAAGTACGGGTCTTTGGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
*
574031 AAACGCCACT-AAGTAC-AGGTCTTTGGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGA-GTCTTTAGCGGCGTTTGTATAA
* * *
574071 AAACGTCGCTAAAGTACGAGTCTTTGGCGGCG-TTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * *
574111 AAACGTCGCTAAAGTACGAGTCTTTGGCGGCGTTTTTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* *
574152 AAACGCCACTAAAGTACGTG-CATTTAGCGGCGTTTGTATAG
1 AAACGCCACTAAAGTACGAGTC-TTTAGCGGCGTTTGTATAA
* ** * *
574193 AAACGCCACTAAAGTATGAGAATTTAGCGGCGTTTGTGCTTA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGT-ATAA
* * * * *
574235 AAATGCCACTAAAGTA-TAGTATTTAGCGGCGTTTATACAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* *
574275 AAACGCCACTAAAGTACGAG-CATTTAGCGGCGTTTGTGCTTA
1 AAACGCCACTAAAGTACGAGTC-TTTAGCGGCGTTTGT-ATAA
* * * * * *
574317 AAACGTCACTATAGTAC-ATTATTTAGCGGCGTTTATATAG
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * *
574357 AAACGCCACTAAAGTACGAG-CATTTAGTGGCGTTTGTGCTTA
1 AAACGCCACTAAAGTACGAGTC-TTTAGCGGCGTTTGT-ATAA
** * * * **
574399 AAACGCCACTATTGTAC-ATTATTTAGCGGCGTTTATACGA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
*** * *
574439 AAACGCCACTAAAGTAC-AGTAGGTAGCGGCGTTTATATAC
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
** * * *
574479 AAACGCCACTAAAACACAAGTATTTACCGGCGTTTGT-TCAAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTAT--AA
*
574521 AAACGCCGCTAAA
1 AAACGCCACTAAA
574534 AGTGCCGCTA
Statistics
Matches: 453, Mismatches: 73, Indels: 35
0.81 0.13 0.06
Matches are distributed among these distances:
40 158 0.35
41 233 0.51
42 62 0.14
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
Found at i:574504 original size:122 final size:123
Alignment explanation
Indices: 573975--574533 Score: 368
Period size: 122 Copynumber: 4.6 Consensus size: 123
573965 CGGGTCTTTG
** * ** ** * * *
573975 GCGGCGTTTGCATAAAAACGCCACTAAAGTACGGGTCTTTGGCGGCGTTTGTATAAAAACGCCAC
1 GCGGCGTTTATATACAAACGCCACTAAAACACAAGTATTTAGCGGCGTTTGTACAAAAACGCCAC
* * * * * *** *
574040 T-AAGTAC-AGGTC-TTTGGCGGCGTTTGTA-TAAAAACGTCGCTAAAGTACGAGTCTTTG
66 TAAAGTACGA-G-CATTTAGCGGCGTTTATACTGAAAACGCCACTAAAGTAC-AGTAGGTA
* * ** * * * * *
574097 GCGGCGTTGTATA-A-AAACGTCGCTAAAGTACGAGTCTTTGGCGGCGTTTTTATAAAAACGCCA
1 GCGGCGTT-TATATACAAACGCCACTAAAACACAAGTATTTAGCGGCGTTTGTACAAAAACGCCA
* * * * **
574160 CTAAAGTACGTGCATTTAGCGGCGTTTGTA-T-AGAAACGCCACTAAAGTATGAGAATTTA
65 CTAAAGTACGAGCATTTAGCGGCGTTTATACTGA-AAACGCCACTAAAGTA-CAGTAGGTA
* * * ** * *
574219 GCGGCGTTTGTGCTTA-AAATGCCACTAAAGTA-TAGTATTTAGCGGCGTTTATACAAAAACGCC
1 GCGGCGTTTAT--ATACAAACGCCACTAAAACACAAGTATTTAGCGGCGTTTGTACAAAAACGCC
* * * * * * **
574282 ACTAAAGTACGAGCATTTAGCGGCGTTTGTGCTTAAAACGTCACTATAGTACATTATTTA
64 ACTAAAGTACGAGCATTTAGCGGCGTTTATACTGAAAACGCCACTAAAGTACAGTAGGTA
* ** * * * * *
574342 GCGGCGTTTATATAGAAACGCCACTAAAGTACGAGCATTTAGTGGCGTTTGTGCTTAAAACGCCA
1 GCGGCGTTTATATACAAACGCCACTAAAACACAAGTATTTAGCGGCGTTTGTAC-AAAAACGCCA
** **
574407 CTATTGTAC-ATTATTTAGCGGCGTTTATAC-GAAAACGCCACTAAAGTACAGTAGGTA
65 CTAAAGTACGAGCATTTAGCGGCGTTTATACTGAAAACGCCACTAAAGTACAGTAGGTA
* * *
574464 GCGGCGTTTATATACAAACGCCACTAAAACACAAGTATTTACCGGCGTTTGTTCAAAAAACGCCG
1 GCGGCGTTTATATACAAACGCCACTAAAACACAAGTATTTAGCGGCGTTTGTAC-AAAAACGCCA
574529 CTAAA
65 CTAAA
574534 AGTGCCGCTA
Statistics
Matches: 358, Mismatches: 65, Indels: 28
0.79 0.14 0.06
Matches are distributed among these distances:
121 53 0.15
122 152 0.42
123 107 0.30
124 45 0.13
125 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (123 bp):
GCGGCGTTTATATACAAACGCCACTAAAACACAAGTATTTAGCGGCGTTTGTACAAAAACGCCAC
TAAAGTACGAGCATTTAGCGGCGTTTATACTGAAAACGCCACTAAAGTACAGTAGGTA
Found at i:574834 original size:2 final size:2
Alignment explanation
Indices: 574811--574953 Score: 85
Period size: 2 Copynumber: 73.5 Consensus size: 2
574801 GATTCTGTAG
*
574811 TA TA T- TA TA TA TG TA TA GTA TA TA TCA TA TA TA GTA TA TA CTA
1 TA TA TA TA TA TA TA TA TA -TA TA TA T-A TA TA TA -TA TA TA -TA
* *
574854 TA T- TA TT TA GTA TA T- TG T- TA TA TA GTA T- TA TA T- 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
* *
574893 T- TA TA GTA TA TA TT TA T- TA TA T- TA TA TA TA T- TA TA GTA TT
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
574933 TA TA T- TA T- TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
574954 CGTAGTATTT
Statistics
Matches: 113, Mismatches: 8, Indels: 40
0.70 0.05 0.25
Matches are distributed among these distances:
1 12 0.11
2 85 0.75
3 16 0.14
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (2 bp):
TA
Found at i:574952 original size:30 final size:30
Alignment explanation
Indices: 574874--575030 Score: 155
Period size: 30 Copynumber: 5.3 Consensus size: 30
574864 TATATTGTTA
* *
574874 TATAGTATTATAT-TATATATTATAGTATA
1 TATATTATTATATATATATATTATAGTATT
574903 TAT-TTATTATATTATATATATTATAGTATT
1 TATATTATTATA-TATATATATTATAGTATT
**
574933 TATATTATTATATATATATATCGTAGTATT
1 TATATTATTATATATATATATTATAGTATT
* *
574963 TATATTATTATAGAGTATACCATTATAGT-TGT
1 TATATTATTATATA-TATA-TATTATAGTAT-T
* * *
574995 TATA-TATTAGA-AT-TATATTATATTATA
1 TATATTATTATATATATATATTATAGTATT
575022 TATATTATT
1 TATATTATT
575031 TATTTCGTTA
Statistics
Matches: 108, Mismatches: 12, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
27 11 0.10
28 14 0.13
29 5 0.05
30 48 0.44
31 19 0.18
32 11 0.10
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (30 bp):
TATATTATTATATATATATATTATAGTATT
Found at i:574967 original size:44 final size:45
Alignment explanation
Indices: 574808--574970 Score: 110
Period size: 44 Copynumber: 3.7 Consensus size: 45
574798 AATGATTCTG
* * *
574808 TAGTATATTATATATGTATAGTATATATCA-TATA-TAGTATATACTA
1 TAGTATA-TATATAT-CATAGTATATAT-ATTATAGTATTATATATTA
* * *
574854 TA-T-TATTTAGTAT-ATTGT-TATATAGTATTA-TATTATATATTA
1 TAGTATATATA-TATCATAGTATATATATTA-TAGTATTATATATTA
* * *
574896 TAGTATATATTTATTATATTATATATATTATAGTATT-TATATTA
1 TAGTATATATATATCATAGTATATATATTATAGTATTATATATTA
* *
574940 TTA-TATATATATATCGTAGTATTTATATTAT
1 -TAGTATATATATATCATAGTATATATATTAT
574971 TATAGAGTAT
Statistics
Matches: 94, Mismatches: 14, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
40 1 0.01
41 7 0.07
42 18 0.19
43 7 0.07
44 44 0.47
45 15 0.16
46 2 0.02
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (45 bp):
TAGTATATATATATCATAGTATATATATTATAGTATTATATATTA
Found at i:578488 original size:2 final size:2
Alignment explanation
Indices: 578481--578505 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
578471 CCTATTCTAA
578481 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
578506 AACAGTGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:579465 original size:28 final size:29
Alignment explanation
Indices: 579433--579508 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 29
579423 TAGAAGACAG
579433 AAGACGCATTGTGGTCAT-CGTCTTTCTA
1 AAGACGCATTGTGGTCATCCGTCTTTCTA
* * *
579461 AAGACGTATTGTGGTCGTCGCGTCTTTCTG
1 AAGACGCATTGTGGTCATC-CGTCTTTCTA
* *
579491 AAGACACATTGTGTTCAT
1 AAGACGCATTGTGGTCAT
579509 TGCTCCCGGT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 16 0.41
30 23 0.59
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.36
Consensus pattern (29 bp):
AAGACGCATTGTGGTCATCCGTCTTTCTA
Found at i:585903 original size:33 final size:33
Alignment explanation
Indices: 585861--585923 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
585851 ATCCAAAGAA
*
585861 CACGAGGTATTCGAGATTGTTTTCTCCTTCAGT
1 CACGAGGTATTCGAGATTGTTTCCTCCTTCAGT
585894 CACGAGGTATTCGAGATTGTTTCCTCCTTC
1 CACGAGGTATTCGAGATTGTTTCCTCCTTC
585924 GGCATCAGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (33 bp):
CACGAGGTATTCGAGATTGTTTCCTCCTTCAGT
Found at i:586502 original size:112 final size:114
Alignment explanation
Indices: 586348--586570 Score: 432
Period size: 112 Copynumber: 2.0 Consensus size: 114
586338 CTGTAAATCA
586348 AAACCTCTCATGGCACTGAAAATGCAAAGCTTAGATAATAATATTAAAAATATGCAATAATTAAA
1 AAACCTCTCATGGCACTGAAAATGCAAAGCTTAGATAATAATATTAAAAATATGCAATAATTAAA
586413 GTGTTTAACCAGAATTTTTTACTGTGTTTTCACATGT-AGAAAAAAGTG
66 GTGTTTAACCAGAATTTTTTACTGTGTTTTCACATGTGAGAAAAAAGTG
586461 AAACCTCTCATGGCACTG-AAATGCAAAGCTTAGATAATAATATTAAAAATATGCAATAATTAAA
1 AAACCTCTCATGGCACTGAAAATGCAAAGCTTAGATAATAATATTAAAAATATGCAATAATTAAA
586525 GTGTTTAACCAGAATTTTTTACTGTGTTTTCACATGTGAGAAAAAA
66 GTGTTTAACCAGAATTTTTTACTGTGTTTTCACATGTGAGAAAAAA
586571 TAGTGTATAA
Statistics
Matches: 109, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
112 83 0.76
113 26 0.24
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.32
Consensus pattern (114 bp):
AAACCTCTCATGGCACTGAAAATGCAAAGCTTAGATAATAATATTAAAAATATGCAATAATTAAA
GTGTTTAACCAGAATTTTTTACTGTGTTTTCACATGTGAGAAAAAAGTG
Found at i:593040 original size:7 final size:7
Alignment explanation
Indices: 593028--593060 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
593018 ATAACTGATT
593028 AAAAAGG
1 AAAAAGG
593035 AAAAAGG
1 AAAAAGG
593042 AAAAAGG
1 AAAAAGG
593049 AAAAAGG
1 AAAAAGG
593056 AAAAA
1 AAAAA
593061 TATACTCACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (7 bp):
AAAAAGG
Found at i:594811 original size:33 final size:33
Alignment explanation
Indices: 594746--594812 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
594736 TTTGTCCTCC
*
594746 TTATTTTCTATGGTTAATTATATTTTGCCCCCT
1 TTATTTTCTATGGTTAATTATATTTTACCCCCT
* * *
594779 TTATTTTTTATGGTTAGTTATATTTTATCCCCT
1 TTATTTTCTATGGTTAATTATATTTTACCCCCT
594812 T
1 T
594813 GAATTGGGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.18, C:0.15, G:0.09, T:0.58
Consensus pattern (33 bp):
TTATTTTCTATGGTTAATTATATTTTACCCCCT
Found at i:600677 original size:31 final size:31
Alignment explanation
Indices: 600614--600745 Score: 97
Period size: 31 Copynumber: 4.3 Consensus size: 31
600604 ATATAATAAT
* * * * *
600614 TTTAAACATGTGATA-ATGTCATGTCATTAC
1 TTTAAACATATAATATATATCACGTCATCAC
* * *
600644 TTTAATCATATTATGATAT-TCACGTTATCAC
1 TTTAAACATATAAT-ATATATCACGTCATCAC
600675 TTTAAACATATAATATATATCACGTCATCAC
1 TTTAAACATATAATATATATCACGTCATCAC
* * * ** * * *
600706 TCTGAACACATAGCATATGTCATGTCATTAC
1 TTTAAACATATAATATATATCACGTCATCAC
600737 TTTAAACAT
1 TTTAAACAT
600746 GTGACATGTA
Statistics
Matches: 79, Mismatches: 20, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
30 15 0.19
31 62 0.78
32 2 0.03
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (31 bp):
TTTAAACATATAATATATATCACGTCATCAC
Found at i:600839 original size:18 final size:18
Alignment explanation
Indices: 600796--600839 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
600786 TCACGAAATG
*
600796 TAAGATTATCGGCGGGAA
1 TAAGATTACCGGCGGGAA
*
600814 T-GGAATTACCGGCGGGAA
1 TAAG-ATTACCGGCGGGAA
600832 TAAGATTA
1 TAAGATTA
600840 TTGGGAATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
17 1 0.05
18 19 0.90
19 1 0.05
ACGTcount: A:0.34, C:0.11, G:0.32, T:0.23
Consensus pattern (18 bp):
TAAGATTACCGGCGGGAA
Found at i:601242 original size:20 final size:20
Alignment explanation
Indices: 601148--601516 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
601138 GATTTTCCAT
* ** *
601148 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
601168 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
601188 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
601208 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
601228 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
601248 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
601268 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
601288 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
601308 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
601328 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
601348 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
601368 AATTGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
601388 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
601408 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
601428 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
601448 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
601468 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
601488 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
601508 AATCACAAC
1 AATCGCAAC
601517 ACTGAAATTT
Statistics
Matches: 303, Mismatches: 38, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
19 3 0.01
20 297 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:602229 original size:24 final size:24
Alignment explanation
Indices: 602190--602236 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
602180 AAATTTGGTC
602190 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
602214 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
602237 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:602428 original size:12 final size:12
Alignment explanation
Indices: 602411--602435 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
602401 ATATAATCCT
602411 GAAGAAGAAAAA
1 GAAGAAGAAAAA
602423 GAAGAAGAAAAA
1 GAAGAAGAAAAA
602435 G
1 G
602436 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:604756 original size:19 final size:19
Alignment explanation
Indices: 604734--605039 Score: 349
Period size: 19 Copynumber: 17.4 Consensus size: 19
604724 CGGAAAATAC
*
604734 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
604753 AATCCCAA--C---ATG-A
1 AATCGCAATGCGAAATGAA
604766 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
604786 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
604800 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
604819 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
604838 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
604852 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
604871 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
604890 AATCG-AA-CCGACAT---
1 AATCGCAATGCGAAATGAA
*
604904 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
604923 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
604942 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
604961 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
604980 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
604994 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
605013 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
605032 AATCGCAA
1 AATCGCAA
605040 CGAGATAATC
Statistics
Matches: 247, Mismatches: 13, Indels: 54
0.79 0.04 0.17
Matches are distributed among these distances:
13 8 0.03
14 36 0.15
15 5 0.02
16 15 0.06
17 15 0.06
18 5 0.02
19 154 0.62
20 9 0.04
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:604785 original size:33 final size:33
Alignment explanation
Indices: 604734--605061 Score: 147
Period size: 33 Copynumber: 9.5 Consensus size: 33
604724 CGGAAAATAC
*
604734 AATCGCAACGCGAAATGAAAATCCCAAC-ATGA-
1 AATCGCAATGCGAAATGAAAATCCCAACGA-GAG
*
604766 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCCCAACGAGAG
* * *
604800 AATCGCAATGCGAAATGAAAATCGCAATGCGA-
1 AATCGCAATGCGAAATGAAAATCCCAACGAGAG
* * * * *
604832 AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCGAAATGA-A-AATCCCAA--CG--A-GAG
* * *
604871 AATCGCAATGCGAAATGAAAAT-CGAACCGACAT
1 AATCGCAATGCGAAATGAAAATCCCAA-CGAGAG
* * *
604904 AATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAAAATC-CCA-ACG--A-GAG
* *
604942 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--CG--A-GAG
* *
604980 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--CG--A-GAG
* *
605013 AATCGCAATGCGAAATGAAAATCGCAACGAGAT
1 AATCGCAATGCGAAATGAAAATCCCAACGAGAG
605046 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
605062 TATAAACGCA
Statistics
Matches: 244, Mismatches: 25, Indels: 53
0.76 0.08 0.16
Matches are distributed among these distances:
31 7 0.03
32 17 0.07
33 112 0.46
34 14 0.06
35 11 0.05
36 12 0.05
37 4 0.02
38 53 0.22
39 7 0.03
40 7 0.03
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCCCAACGAGAG
Found at i:604793 original size:52 final size:52
Alignment explanation
Indices: 604765--605039 Score: 321
Period size: 52 Copynumber: 5.2 Consensus size: 52
604755 TCCCAACATG
*
604765 AAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
1 AAATCGCAATGC-GAAATGAAAATCGCAACGCGAGAATCGCAATGCGAAATGA
*
604818 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGAAAATCGCAACGCGAGAATCGCAATGCGAAATGA
* *
604870 AAATCGCAATGCGAAATGAAAATCG-AAC-CGACATAATCGCAATGCGAAATTA
1 AAATCGCAATGCGAAATGAAAATCGCAACGCG--AGAATCGCAATGCGAAATGA
* *
604922 AAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGAAAATCGCAACGCG--A-G--AATCGCAATGCGAAATGA
*
604979 AAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGAAAATCGCAACGCG--A-G--AATCGCAATGCGAAATGA
605031 AAATCGCAA
1 AAATCGCAA
605040 CGAGATAATC
Statistics
Matches: 207, Mismatches: 8, Indels: 15
0.90 0.03 0.07
Matches are distributed among these distances:
50 1 0.00
51 3 0.01
52 153 0.74
53 14 0.07
54 5 0.02
55 5 0.02
57 26 0.13
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
AAATCGCAATGCGAAATGAAAATCGCAACGCGAGAATCGCAATGCGAAATGA
Done.