Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397260.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_51.0, 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: 10072460
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 70252 characters in sequence are not A, C, G, or T
File 4 of 20
Found at i:1193446 original size:20 final size:20
Alignment explanation
Indices: 1193421--1193460 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1193411 ATTTGAATTG
1193421 TTTATTCCAATTTGTTCTTA
1 TTTATTCCAATTTGTTCTTA
1193441 TTTATTCCAATTTGTTCTTA
1 TTTATTCCAATTTGTTCTTA
1193461 ATGCTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.15, G:0.05, T:0.60
Consensus pattern (20 bp):
TTTATTCCAATTTGTTCTTA
Found at i:1200423 original size:20 final size:20
Alignment explanation
Indices: 1200394--1200431 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1200384 TGTTAAGTGA
1200394 TTAATTTAAG-TATTTTTAG
1 TTAATTTAAGTTATTTTTAG
1200413 TTAATTTTAAGTTATTTTT
1 TTAA-TTTAAGTTATTTTT
1200432 TTTAAATTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 6 0.35
21 7 0.41
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (20 bp):
TTAATTTAAGTTATTTTTAG
Found at i:1225675 original size:15 final size:15
Alignment explanation
Indices: 1225655--1225698 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1225645 TTAACATTAC
1225655 AAAATTATAACTTAT
1 AAAATTATAACTTAT
1225670 AAAATTATTAA-TTAT
1 AAAATTA-TAACTTAT
*
1225685 AATATATATAACTT
1 AAAAT-TATAACTT
1225699 TGTTTATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 18 0.72
16 7 0.28
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAATTATAACTTAT
Found at i:1225848 original size:335 final size:343
Alignment explanation
Indices: 1225260--1226082 Score: 884
Period size: 335 Copynumber: 2.3 Consensus size: 343
1225250 ATTACTATTA
* * * * *
1225260 TATATATATAGTTTTAATATAAACATATCTACTTTTTATTTTGTGTTAACATTACAAAAATTGTG
1 TATATATATACTTTAAATATAAACATATTTACTTTTTATTTTGTGTTAACATTAC-AAAATTATA
* * * * *
1225325 ACTTATACAATTATTAATTATAATATATATGCCATTGTTTATATAATCTTATAATATATATACTT
65 ACTTATAAAATTATTAATTATAATATATAT-ACTTTGTTTATATAAAC-T-T-ATATATATACCT
* *
1225390 AAAGAAAGCTCTTGAGATTAGAATAGTTTTGGAACCTAAATTTTTTTTAATTTCATGAAATTAAG
126 AAAGAAAGCTCTTGAGACTAGAATAGTTTTGAAACCTAAATTTTTTTTAATTTCATGAAATTAAG
* * *
1225455 AACAAATCCTTATAATTAATTAAATTAATTCATGAAACTAACATTATTAATTAACTTGTAATGTC
191 AACAAATCCGTATAATTAATTAAATTAATTCATAAAACTAACATTATTAATTAACTTGTAATGCC
** * * *
1225520 ATTTAATGTATATAGTTTATATAT-T-GA-GTTA-A-T-TTATAAGAAATATAATTATTATTATA
256 ATTTAATACATATACTTTATATATATAGATATTAGATTATTATAAGAAATATAATTACTATTATA
1225579 TATATACTAAAATA-TTTTTA-G
321 TATATACTAAAATATTTTTTATG
*
1225600 TATATATATACTTTAAATATAAACATATTTACTTTCTATTTTGTGTTAACATTACAAAATTATAA
1 TATATATATACTTTAAATATAAACATATTTACTTTTTATTTTGTGTTAACATTACAAAATTATAA
1225665 CTTATAAAATTATTAATTATAATATATATAACTTTGTTTATATAAACTTATATA-A-ACCTAAAG
66 CTTATAAAATTATTAATTATAATATATAT-ACTTTGTTTATATAAACTTATATATATACCTAAAG
* ** * * *
1225728 AAAAG-T-TGTGAGACTAGAATAGTTCTT-AAACTTAGTTATTTTTTTAATTTTATGTAATTCAG
130 -AAAGCTCT-TGAGACTAGAATAGTT-TTGAAACCTAAAT-TTTTTTTAATTTCATGAAATTAAG
**
1225790 AACAAA-CTCGTATTGTTAATTAAATTAATTCATAAAACTATA-ATTATTAATTAACTTGTAATG
191 AACAAATC-CGTATAATTAATTAAATTAATTCATAAAACTA-ACATTATTAATTAACTTGTAATG
* *
1225853 CCTTTTAATACATATACTTTATATATATATATATTAGATTCAATTATAAGAAATATAATTACTAT
254 CCATTTAATACATATACTTTATATATATAGATATTAGATT--ATTATAAGAAATATAATTACTAT
* *
1225918 TTTATATATATTAAAATATTTTTTATG
317 TATATATATACTAAAATATTTTTTATG
* * *
1225945 TATGCGTGTGTGTGTGTGTGTACATATGTACTTTAAATATAAATAGATTTACTTTTTATTTTGTG
1 TA------------------T--ATATATACTTTAAATATAAACATATTTACTTTTTATTTTGTG
*
1226010 TTAACATTATCAAAATTATAACTTATAAAATTATTAATTACAATATATATACTTTTGTTTATATA
46 TTAACATTA-CAAAATTATAACTTATAAAATTATTAATTATAATATATATAC-TTTGTTTATATA
1226075 AACTTATA
109 AACTTATA
1226083 ACATATAAAT
Statistics
Matches: 406, Mismatches: 39, Indels: 50
0.82 0.08 0.10
Matches are distributed among these distances:
333 1 0.00
334 30 0.07
335 104 0.26
336 7 0.02
337 2 0.00
338 4 0.01
339 51 0.13
340 52 0.13
343 37 0.09
344 6 0.01
345 3 0.01
363 1 0.00
365 49 0.12
366 59 0.15
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (343 bp):
TATATATATACTTTAAATATAAACATATTTACTTTTTATTTTGTGTTAACATTACAAAATTATAA
CTTATAAAATTATTAATTATAATATATATACTTTGTTTATATAAACTTATATATATACCTAAAGA
AAGCTCTTGAGACTAGAATAGTTTTGAAACCTAAATTTTTTTTAATTTCATGAAATTAAGAACAA
ATCCGTATAATTAATTAAATTAATTCATAAAACTAACATTATTAATTAACTTGTAATGCCATTTA
ATACATATACTTTATATATATAGATATTAGATTATTATAAGAAATATAATTACTATTATATATAT
ACTAAAATATTTTTTATG
Found at i:1226041 original size:15 final size:17
Alignment explanation
Indices: 1226011--1226043 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1226001 TATTTTGTGT
1226011 TAACATTATCAAAATTA
1 TAACATTATCAAAATTA
1226028 TAAC-TTAT-AAAATTA
1 TAACATTATCAAAATTA
1226043 T
1 T
1226044 TAATTACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 4 0.25
17 4 0.25
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (17 bp):
TAACATTATCAAAATTA
Found at i:1244874 original size:17 final size:17
Alignment explanation
Indices: 1244852--1244889 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1244842 TTTATGACTT
1244852 TTAATTTAAA-ATAAAAA
1 TTAA-TTAAATATAAAAA
*
1244869 TTAATTAAATATAACAA
1 TTAATTAAATATAAAAA
1244886 TTAA
1 TTAA
1244890 AAAATTTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (17 bp):
TTAATTAAATATAAAAA
Found at i:1248076 original size:18 final size:18
Alignment explanation
Indices: 1248035--1248076 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
1248025 AAGTTAACTA
*
1248035 TTAACCATAAGAGCTTAT
1 TTAACTATAAGAGCTTAT
1248053 TTAACTATAAGAGCTTAT
1 TTAACTATAAGAGCTTAT
1248071 TTAACT
1 TTAACT
1248077 CAAAGTGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (18 bp):
TTAACTATAAGAGCTTAT
Found at i:1248763 original size:26 final size:27
Alignment explanation
Indices: 1248734--1248790 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
1248724 ATTTTAAAAA
* *
1248734 ATTTAAAT-AAATTTTTATTTTTTTAT
1 ATTTAAATCAAATTTTTATATTTATAT
*
1248760 ATTT-AATCAAGTTTTTATATTTATAT
1 ATTTAAATCAAATTTTTATATTTATAT
1248786 -TTTAA
1 ATTTAA
1248791 GTTAAATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 6 0.23
26 20 0.77
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (27 bp):
ATTTAAATCAAATTTTTATATTTATAT
Found at i:1250081 original size:11 final size:10
Alignment explanation
Indices: 1250053--1250086 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1250043 AAGTGATATT
1250053 TAATTAATAA
1 TAATTAATAA
1250063 TAATTAATCAA
1 TAATTAAT-AA
*
1250074 TCATTAATAA
1 TAATTAATAA
1250084 TAA
1 TAA
1250087 GAGTCTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (10 bp):
TAATTAATAA
Found at i:1250486 original size:16 final size:17
Alignment explanation
Indices: 1250450--1250484 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1250440 ATTTTTATGT
1250450 AATATACGTGACAAAAA
1 AATATACGTGACAAAAA
1250467 AATATACGTGACAAAAA
1 AATATACGTGACAAAAA
1250484 A
1 A
1250485 TACAAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.60, C:0.11, G:0.11, T:0.17
Consensus pattern (17 bp):
AATATACGTGACAAAAA
Found at i:1250852 original size:16 final size:18
Alignment explanation
Indices: 1250810--1250843 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1250800 ATTTTTTTTA
1250810 AAATAA-ATATTTTATTC
1 AAATAATATATTTTATTC
1250827 AAATAATATATTTTATT
1 AAATAATATATTTTATT
1250844 AGATATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATAATATATTTTATTC
Found at i:1256183 original size:29 final size:26
Alignment explanation
Indices: 1256143--1256202 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 26
1256133 TATTTTTATT
1256143 TTTAAATATTAATAATTTATAATTGATAA
1 TTTAAATATTAAT-ATTT-T-ATTGATAA
* *
1256172 TTTAAATGTTAATATTTTATTTATAA
1 TTTAAATATTAATATTTTATTGATAA
1256198 TTTAA
1 TTTAA
1256203 TCATTATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 12 0.41
27 1 0.03
28 4 0.14
29 12 0.41
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (26 bp):
TTTAAATATTAATATTTTATTGATAA
Found at i:1256250 original size:14 final size:14
Alignment explanation
Indices: 1256143--1256250 Score: 54
Period size: 14 Copynumber: 7.9 Consensus size: 14
1256133 TATTTTTATT
1256143 TTTAAATATTAATAA
1 TTTAAATATT-ATAA
*
1256158 TTTATAAT-TGATAA
1 TTTA-AATATTATAA
*
1256172 TTTAAATGTTA-ATA
1 TTTAAATATTATA-A
*
1256186 TTT-TAT-TTATAA
1 TTTAAATATTATAA
1256198 TTT-AATCATTATAA
1 TTTAAAT-ATTATAA
*
1256212 TTATATAATCTTA-ATA
1 TT-TA-AATATTATA-A
1256228 TTT---TATTATAA
1 TTTAAATATTATAA
1256239 TTTAAATATTAT
1 TTTAAATATTAT
1256251 TATGATTTTT
Statistics
Matches: 73, Mismatches: 6, Indels: 29
0.68 0.06 0.27
Matches are distributed among these distances:
11 8 0.11
12 10 0.14
13 7 0.10
14 28 0.38
15 8 0.11
16 9 0.12
17 3 0.04
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (14 bp):
TTTAAATATTATAA
Found at i:1256250 original size:41 final size:39
Alignment explanation
Indices: 1256149--1256250 Score: 118
Period size: 41 Copynumber: 2.5 Consensus size: 39
1256139 TATTTTTAAA
* *
1256149 TATTAATAATTTATAAT-TGATAATTTAAATGTTAATATTT
1 TATT-ATAATTTA-AATATTATAATTTAAATCTTAATATTT
1256189 TATTTATAATTT-AATCATTATAATTATATAATCTTAATATTT
1 TA-TTATAATTTAAAT-ATTATAATT-TA-AATCTTAATATTT
1256231 TATTATAATTTAAATATTAT
1 TATTATAATTTAAATATTAT
1256251 TATGATTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
38 3 0.06
40 16 0.30
41 18 0.33
42 17 0.31
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (39 bp):
TATTATAATTTAAATATTATAATTTAAATCTTAATATTT
Found at i:1256252 original size:17 final size:18
Alignment explanation
Indices: 1256180--1256258 Score: 61
Period size: 17 Copynumber: 4.1 Consensus size: 18
1256170 AATTTAAATG
*
1256180 TTAATATTTTATTTATAAT
1 TTAATATATTA-TTATAAT
*
1256199 TTAATCATTATAATTATATAAT
1 TTAAT-A-TATTA-T-TATAAT
*
1256221 CTTAATATTTTATTATAAT
1 -TTAATATATTATTATAAT
*
1256240 TTAA-ATATTATTATGAT
1 TTAATATATTATTATAAT
1256257 TT
1 TT
1256259 TTTAATTTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
17 13 0.26
18 4 0.08
19 11 0.22
20 2 0.04
21 8 0.16
22 7 0.14
23 5 0.10
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (18 bp):
TTAATATATTATTATAAT
Found at i:1256384 original size:42 final size:41
Alignment explanation
Indices: 1256338--1256554 Score: 168
Period size: 42 Copynumber: 5.5 Consensus size: 41
1256328 TAAATAATAT
*
1256338 TATTTTATTTATAATTTAATGATTAATATTATAAAATCTTAA
1 TATTTTATTTATAATTTAATAATTAATATTATAAAAT-TTAA
* * * * * **
1256380 TATTTTA-TTATAGTTTAAAAATTATTATGAT--TATTTTT
1 TATTTTATTTATAATTTAATAATTAATATTATAAAATTTAA
** *
1256418 TATTTTATTT-T-ATTT--T--TTAAATATT-TGTAATTT-T
1 TATTTTATTTATAATTTAATAATT-AATATTATAAAATTTAA
* * *
1256452 TAATTTATTTATAATTTAATAATTAACATTATAAAGTATTAA
1 TATTTTATTTATAATTTAATAATTAATATTATAAAAT-TTAA
* * *
1256494 TATTTTATTTATAATTTAATAATTAACATTATAAAGTACTAA
1 TATTTTATTTATAATTTAATAATTAATATTATAAAAT-TTAA
1256536 TATTTTATTTATAATTTAA
1 TATTTTATTTATAATTTAA
1256555 ATATTATTAT
Statistics
Matches: 141, Mismatches: 21, Indels: 26
0.75 0.11 0.14
Matches are distributed among these distances:
33 3 0.02
34 14 0.10
35 5 0.04
36 4 0.03
37 3 0.02
38 11 0.08
39 9 0.06
40 5 0.04
41 21 0.15
42 66 0.47
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.56
Consensus pattern (41 bp):
TATTTTATTTATAATTTAATAATTAATATTATAAAATTTAA
Found at i:1256451 original size:17 final size:18
Alignment explanation
Indices: 1256431--1256468 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1256421 TTTATTTTAT
*
1256431 TTTTTAA-ATATTTGTAA
1 TTTTTAATATATTTATAA
*
1256448 TTTTTAATTTATTTATAA
1 TTTTTAATATATTTATAA
1256466 TTT
1 TTT
1256469 AATAATTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTTTAATATATTTATAA
Found at i:1256460 original size:18 final size:17
Alignment explanation
Indices: 1256414--1256468 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
1256404 TTATGATTAT
* *
1256414 TTTTTATTTTATTTTAT
1 TTTTTAATTTATTTTAA
*
1256431 TTTTTAA-ATATTTGTAA
1 TTTTTAATTTATTT-TAA
1256448 TTTTTAATTTATTTATAA
1 TTTTTAATTTATTT-TAA
1256466 TTT
1 TTT
1256469 AATAATTAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 5 0.16
17 15 0.48
18 11 0.35
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (17 bp):
TTTTTAATTTATTTTAA
Found at i:1256485 original size:20 final size:20
Alignment explanation
Indices: 1256460--1256527 Score: 75
Period size: 20 Copynumber: 3.3 Consensus size: 20
1256450 TTTAATTTAT
1256460 TTATAATTTAATAATTAACA
1 TTATAATTTAATAATTAACA
* * *
1256480 TTATAAAGTATTAATATTTTA-T
1 TTAT-AA-T-TTAATAATTAACA
1256502 TTATAATTTAATAATTAACA
1 TTATAATTTAATAATTAACA
1256522 TTATAA
1 TTATAA
1256528 AGTACTAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
19 9 0.24
20 11 0.29
21 4 0.11
22 5 0.13
23 9 0.24
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (20 bp):
TTATAATTTAATAATTAACA
Found at i:1256507 original size:22 final size:22
Alignment explanation
Indices: 1256480--1256549 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
1256470 ATAATTAACA
1256480 TTATAAAGTATTAATATTTTAT
1 TTATAAAGTATTAATATTTTAT
* * *
1256502 TTAT-AA-T-TTAATAATTAACA
1 TTATAAAGTATTAATATTTTA-T
*
1256522 TTATAAAGTACTAATATTTTAT
1 TTATAAAGTATTAATATTTTAT
1256544 TTATAA
1 TTATAA
1256550 TTTAAATATT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
19 9 0.24
20 5 0.14
21 4 0.11
22 11 0.30
23 8 0.22
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (22 bp):
TTATAAAGTATTAATATTTTAT
Found at i:1256536 original size:20 final size:20
Alignment explanation
Indices: 1256468--1256536 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
1256458 ATTTATAATT
1256468 TAATAATTAACATTATAAAG
1 TAATAATTAACATTATAAAG
* *** **
1256488 TATTAATATTTTATTTATAATT
1 TAATAAT-TAACA-TTATAAAG
1256510 TAATAATTAACATTATAAAG
1 TAATAATTAACATTATAAAG
*
1256530 TACTAAT
1 TAATAAT
1256537 ATTTTATTTA
Statistics
Matches: 34, Mismatches: 13, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
20 18 0.53
21 4 0.12
22 12 0.35
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (20 bp):
TAATAATTAACATTATAAAG
Found at i:1256559 original size:20 final size:20
Alignment explanation
Indices: 1256492--1256564 Score: 58
Period size: 20 Copynumber: 3.5 Consensus size: 20
1256482 ATAAAGTATT
1256492 AATATTTTATTTATAATTT-
1 AATATTTTATTTATAATTTA
* * * **
1256511 AATAATTAACATTATAAAGTA
1 AATATTTTA-TTTATAATTTA
1256532 CTAATATTTTATTTATAATTTA
1 --AATATTTTATTTATAATTTA
1256554 AATATTATTAT
1 AATATT-TTAT
1256565 GATTATTTAT
Statistics
Matches: 39, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
19 7 0.18
20 13 0.33
21 4 0.10
22 8 0.21
23 7 0.18
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (20 bp):
AATATTTTATTTATAATTTA
Found at i:1256613 original size:27 final size:28
Alignment explanation
Indices: 1256564--1256628 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 28
1256554 AATATTATTA
* *
1256564 TGATTATTTATTTTTAAATATTAATAAT
1 TGATAATTTATTTTAAAATATTAATAAT
*
1256592 TTATAATTTA-TTTAAAATATTAATAAT
1 TGATAATTTATTTTAAAATATTAATAAT
*
1256619 TGATCATTTA
1 TGATAATTTA
1256629 AATGTTAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 24 0.75
28 8 0.25
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.54
Consensus pattern (28 bp):
TGATAATTTATTTTAAAATATTAATAAT
Found at i:1260332 original size:91 final size:91
Alignment explanation
Indices: 1260172--1260354 Score: 303
Period size: 91 Copynumber: 2.0 Consensus size: 91
1260162 ATCAATTTAT
* * **
1260172 AAGATTCTTATTAATTTGCTAATGGGTTAATACTTGTTGCAATGATAATAGAGTAAAATTGCTAA
1 AAGAATCTTACTAATTTGCTAATGGGCCAATACTTGTTGCAATGATAATAGAGTAAAATTGCTAA
* *
1260237 CCATGATAGTGTGGGTTTAGTTGTTG
66 CCATGATAGTGCGGGTTTAGTTCTTG
*
1260263 AAGAATCTTACTAATTTGCTAATGGGCCAATACTTGTTGCAGTGATAATAGAGTAAAATTGCTAA
1 AAGAATCTTACTAATTTGCTAATGGGCCAATACTTGTTGCAATGATAATAGAGTAAAATTGCTAA
1260328 CCATGATAGTGCGGGTTTAGTTCTTG
66 CCATGATAGTGCGGGTTTAGTTCTTG
1260354 A
1 A
1260355 GTAGTCATTT
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 85 1.00
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (91 bp):
AAGAATCTTACTAATTTGCTAATGGGCCAATACTTGTTGCAATGATAATAGAGTAAAATTGCTAA
CCATGATAGTGCGGGTTTAGTTCTTG
Found at i:1285791 original size:29 final size:29
Alignment explanation
Indices: 1285759--1285818 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
1285749 AAATTTTCAT
1285759 AAAAA-TGAA-AAATAAAAGATTAAAAAAGA
1 AAAAAGTGAATAAATAAAAG-TT-AAAAAGA
*
1285788 AAAAAGTGAATATATAAAAGTTAAAAAGA
1 AAAAAGTGAATAAATAAAAGTTAAAAAGA
1285817 AA
1 AA
1285819 TTAATATACA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 14 0.50
30 6 0.21
31 8 0.29
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.17
Consensus pattern (29 bp):
AAAAAGTGAATAAATAAAAGTTAAAAAGA
Found at i:1285886 original size:22 final size:22
Alignment explanation
Indices: 1285835--1285905 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
1285825 TACAAAATTA
*
1285835 TATTAATGTTTTAAT-ACTAAAT
1 TATTAATATTTTAATGA-TAAAT
*
1285857 T-TTAATATGTTAATGATAAAT
1 TATTAATATTTTAATGATAAAT
* *
1285878 TATTAATATTTTATTGATAAAA
1 TATTAATATTTTAATGATAAAT
1285900 TATTAA
1 TATTAA
1285906 ATTATTACGA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
21 17 0.40
22 25 0.60
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (22 bp):
TATTAATATTTTAATGATAAAT
Found at i:1294824 original size:19 final size:20
Alignment explanation
Indices: 1294800--1294841 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
1294790 CTGTCTGGTT
1294800 CTGGTTTA-GTTTTTTTTAA
1 CTGGTTTAGGTTTTTTTTAA
1294819 CTGGTTTAGGGTTTTTTTTAA
1 CTGGTTTA-GGTTTTTTTTAA
1294840 CT
1 CT
1294842 TTTATAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.38
21 13 0.62
ACGTcount: A:0.14, C:0.07, G:0.19, T:0.60
Consensus pattern (20 bp):
CTGGTTTAGGTTTTTTTTAA
Found at i:1294853 original size:21 final size:21
Alignment explanation
Indices: 1294800--1294855 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
1294790 CTGTCTGGTT
1294800 CTGGTTT--AGTTTTTTTTAA
1 CTGGTTTAAAGTTTTTTTTAA
**
1294819 CTGGTTTAGGGTTTTTTTTAA
1 CTGGTTTAAAGTTTTTTTTAA
*
1294840 CT-TTTATAAAGTTTTT
1 CTGGTT-TAAAGTTTTT
1294856 ATGAAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 7 0.23
20 2 0.07
21 21 0.70
ACGTcount: A:0.18, C:0.05, G:0.16, T:0.61
Consensus pattern (21 bp):
CTGGTTTAAAGTTTTTTTTAA
Found at i:1301830 original size:5 final size:6
Alignment explanation
Indices: 1301819--1301849 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1301809 GAGAGAAGCG
*
1301819 AAGGGG AAGGGA AAGGGA AAGGGA AAGGGA A
1 AAGGGA AAGGGA AAGGGA AAGGGA AAGGGA A
1301850 TGTTTGGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (6 bp):
AAGGGA
Found at i:1302046 original size:29 final size:29
Alignment explanation
Indices: 1302011--1302098 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
1302001 GTCTTTAAAT
1302011 TATTTAAATAATTTTTTATATTTTTATTA
1 TATTTAAATAATTTTTTATATTTTTATTA
* *
1302040 TATTTAATTAA-ATTTTATATTTTTATTTA
1 TATTTAAATAATTTTTTATATTTTTA-TTA
* * *
1302069 AAATTAAATAAAATTTTATATATTTTTATT
1 TATTTAAAT--AATTTTTTATATTTTTATT
1302099 TTAAATCAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
28 13 0.27
29 19 0.40
31 4 0.08
32 12 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
TATTTAAATAATTTTTTATATTTTTATTA
Found at i:1302064 original size:28 final size:28
Alignment explanation
Indices: 1302024--1302102 Score: 90
Period size: 30 Copynumber: 2.8 Consensus size: 28
1302014 TTAAATAATT
*
1302024 TTTTATATTTTTATTATATTTAATTAAA
1 TTTTATATTTTTATTATATTTAATAAAA
* *
1302052 TTTTATATTTTTATTTAAAATTAAATAAAA
1 TTTTATATTTTTA-TT-ATATTTAATAAAA
*
1302082 TTTTATATATTT-TTAT-TTTAA
1 TTTTATATTTTTATTATATTTAA
1302103 ATCAAATAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 15 0.35
29 2 0.05
30 21 0.49
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
TTTTATATTTTTATTATATTTAATAAAA
Found at i:1302069 original size:19 final size:20
Alignment explanation
Indices: 1302032--1302070 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1302022 TTTTTTATAT
1302032 TTTTATTATATTTAATTAAA
1 TTTTATTATATTTAATTAAA
* *
1302052 TTTTA-TATTTTTATTTAAA
1 TTTTATTATATTTAATTAAA
1302071 ATTAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTATTATATTTAATTAAA
Found at i:1302096 original size:32 final size:30
Alignment explanation
Indices: 1302014--1302112 Score: 105
Period size: 32 Copynumber: 3.3 Consensus size: 30
1302004 TTTAAATTAT
* *
1302014 TTAAAT-AATTTTTTATATTTTTA-TTATA
1 TTAAATAAAATTTTTATATTTTTATTTAAA
* *
1302042 TTTAATTAAA-TTTTATATTTTTATTTAAAA
1 TTAAATAAAATTTTTATATTTTTATTT-AAA
1302072 TTAAATAAAATTTTATATATTTTTATTTTAAA
1 TTAAATAAAATTTT-TATATTTTTA-TTTAAA
*
1302104 TCAAATAAA
1 TTAAATAAA
1302113 TTGTTATGAT
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
28 18 0.31
29 4 0.07
30 10 0.17
31 3 0.05
32 21 0.36
33 3 0.05
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (30 bp):
TTAAATAAAATTTTTATATTTTTATTTAAA
Found at i:1303845 original size:22 final size:22
Alignment explanation
Indices: 1303820--1303865 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1303810 ATGAAGTAAA
*
1303820 TTTTATGTTTTTAAATA-ATTTT
1 TTTTAT-TTATTAAATATATTTT
*
1303842 TTTTATTTATTATATATATTTT
1 TTTTATTTATTAAATATATTTT
1303864 TT
1 TT
1303866 AAATTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTTATTTATTAAATATATTTT
Found at i:1304377 original size:53 final size:53
Alignment explanation
Indices: 1304266--1304378 Score: 131
Period size: 53 Copynumber: 2.1 Consensus size: 53
1304256 AGTTCAATTG
* * *
1304266 CCAAAATTTTTAAACATTTTTATTTATTATATATATATTTTTAATAACCCCTT
1 CCAAAATTTTTAAACATTTTTATATATTAGATATATATTTTTAATAACCCCCT
* * * *
1304319 CCAAAATTTTTAAA-TTTTTTATATATTAGATACTTTTTCTTTTAATGACCCCCT
1 CCAAAATTTTTAAACATTTTTATATATTAGATA-TATAT-TTTTAATAACCCCCT
1304373 -CAAAAT
1 CCAAAAT
1304379 AATTTTTTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
52 15 0.29
53 23 0.45
54 13 0.25
ACGTcount: A:0.35, C:0.15, G:0.02, T:0.49
Consensus pattern (53 bp):
CCAAAATTTTTAAACATTTTTATATATTAGATATATATTTTTAATAACCCCCT
Found at i:1304584 original size:3 final size:3
Alignment explanation
Indices: 1304578--1304617 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1304568 TTTCTATTTA
1304578 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1304618 CCTTATAGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1304999 original size:24 final size:24
Alignment explanation
Indices: 1304972--1305018 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1304962 TATATTTAGT
*
1304972 TAAAACGAAATTATCTTGAGTATA
1 TAAAACGAAATTATCTTAAGTATA
* *
1304996 TAAAAGGAAATTTTCTTAAGTAT
1 TAAAACGAAATTATCTTAAGTAT
1305019 TTAGTCTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (24 bp):
TAAAACGAAATTATCTTAAGTATA
Found at i:1310708 original size:31 final size:30
Alignment explanation
Indices: 1310672--1310745 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 30
1310662 ATGTGCTGGT
1310672 TATTATGGATATTCAATATATCTTACTTAGC
1 TATTATGGATATT-AATATATCTTACTTAGC
** *
1310703 TATTATGGAT-TTTGTATATCTTATTTAGC
1 TATTATGGATATTAATATATCTTACTTAGC
* *
1310732 TACTATGAATATTA
1 TATTATGGATATTA
1310746 TAAATATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 22 0.61
30 4 0.11
31 10 0.28
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.49
Consensus pattern (30 bp):
TATTATGGATATTAATATATCTTACTTAGC
Found at i:1311445 original size:20 final size:21
Alignment explanation
Indices: 1311412--1311450 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1311402 AATGGAGAGA
*
1311412 AGCATCAATTAGTT-AAAGTG
1 AGCATCAATAAGTTGAAAGTG
*
1311432 AGCATTAATAAGTTGAAAG
1 AGCATCAATAAGTTGAAAG
1311451 GAGGCTAGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.28
Consensus pattern (21 bp):
AGCATCAATAAGTTGAAAGTG
Found at i:1326182 original size:13 final size:13
Alignment explanation
Indices: 1326164--1326189 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1326154 TGAGAATACC
1326164 AAAAAATAAAAAT
1 AAAAAATAAAAAT
1326177 AAAAAATAAAAAT
1 AAAAAATAAAAAT
1326190 GGAAATAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:1329319 original size:62 final size:62
Alignment explanation
Indices: 1329222--1329346 Score: 205
Period size: 62 Copynumber: 2.0 Consensus size: 62
1329212 GGATACACTC
* * * * *
1329222 TAGTAAAATATAATTAGCTGGAATGATTTAATATATTACTTTTTATGCATTTTTTGCCCCTT
1 TAGTAAAATATAATTAGCTAGAATAATTTAATATATCACTTTTCATGCATTTTTTGACCCTT
1329284 TAGTAAAATATAATTAGCTAGAATAATTTAATATATCACTTTTCATGCATTTTTTGACCCTT
1 TAGTAAAATATAATTAGCTAGAATAATTTAATATATCACTTTTCATGCATTTTTTGACCCTT
1329346 T
1 T
1329347 GTGTTACCTC
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.46
Consensus pattern (62 bp):
TAGTAAAATATAATTAGCTAGAATAATTTAATATATCACTTTTCATGCATTTTTTGACCCTT
Found at i:1332233 original size:16 final size:16
Alignment explanation
Indices: 1332214--1332275 Score: 54
Period size: 15 Copynumber: 3.8 Consensus size: 16
1332204 TATCTCGTAA
*
1332214 ATATATTTTTAATGTT
1 ATATATTTTTAATCTT
* *
1332230 ATATA-TTTTATTTTT
1 ATATATTTTTAATCTT
*
1332245 ATTTATTATTATAATCTT
1 ATATATT-TT-TAATCTT
*
1332263 ATATAGTTTTAAT
1 ATATATTTTTAAT
1332276 TTTTAATTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
15 12 0.33
16 10 0.28
17 4 0.11
18 10 0.28
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (16 bp):
ATATATTTTTAATCTT
Found at i:1332267 original size:33 final size:33
Alignment explanation
Indices: 1332217--1332357 Score: 112
Period size: 32 Copynumber: 4.2 Consensus size: 33
1332207 CTCGTAAATA
*
1332217 TATT-TTTAATGTTATA-TATTTTATTTTTATT
1 TATTATTTAATCTTATATTATTTTATTTTTATT
1332248 TATTATTATAATCTTATA-TAGTTTTAATTTTTAATT
1 TATTATT-TAATCTTATATTA-TTTT-ATTTTT-ATT
* * *
1332284 TTTTAATTTTTTATATTATATTATTTTATTTTTATT
1 TATT-A--TTTAATCTTATATTATTTTATTTTTATT
* *
1332320 TAATT-TTTAA-CTTATATTATATAATTTTTATT
1 T-ATTATTTAATCTTATATTATTTTATTTTTATT
*
1332352 TTTTAT
1 TATTAT
1332358 ATTTTATTTT
Statistics
Matches: 89, Mismatches: 10, Indels: 21
0.74 0.08 0.17
Matches are distributed among these distances:
31 6 0.07
32 23 0.26
33 15 0.17
34 4 0.04
35 6 0.07
36 10 0.11
37 9 0.10
38 12 0.13
39 4 0.04
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (33 bp):
TATTATTTAATCTTATATTATTTTATTTTTATT
Found at i:1332313 original size:5 final size:5
Alignment explanation
Indices: 1332292--1332421 Score: 59
Period size: 5 Copynumber: 25.0 Consensus size: 5
1332282 TTTTTTAATT
* * * ** * * *
1332292 TTTTA TATTA TATTA TTTTA TTTTTA TTTAA TTTTTA ACTTA TATTA TATAA
1 TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA
* *
1332344 TTTTTA TTTT- TTATA TTTTA TTTTA TTTTAA TTTTTGA TTCTTA TATTA
1 -TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A -TTTT-A TT-TTA TTTTA
* *
1332393 -TATA TTTTA TTTTAA TATT- TTTTA TTTTA
1 TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA
1332422 ATTATAACAT
Statistics
Matches: 95, Mismatches: 20, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
4 8 0.08
5 59 0.62
6 21 0.22
7 7 0.07
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.70
Consensus pattern (5 bp):
TTTTA
Found at i:1332317 original size:21 final size:21
Alignment explanation
Indices: 1332291--1332372 Score: 70
Period size: 21 Copynumber: 4.2 Consensus size: 21
1332281 ATTTTTTAAT
1332291 TTTTTATATTATATTATTTTA
1 TTTTTATATTATATTATTTTA
1332312 TTTTTAT-TTA-A-T-TTTTA
1 TTTTTATATTATATTATTTTA
** *
1332329 -ACTTATATTATATAATTTTTA
1 TTTTTATATTATATTA-TTTTA
*
1332350 TTTTT-TA-TATTTTATTTTA
1 TTTTTATATTATATTATTTTA
1332369 TTTT
1 TTTT
1332373 AATTTTTGAT
Statistics
Matches: 48, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
16 4 0.08
17 8 0.17
18 2 0.04
19 10 0.21
20 8 0.17
21 14 0.29
22 2 0.04
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTTATATTATATTATTTTA
Found at i:1332363 original size:7 final size:7
Alignment explanation
Indices: 1332231--1332421 Score: 60
Period size: 7 Copynumber: 26.3 Consensus size: 7
1332221 TTTAATGTTA
1332231 TATATTT
1 TATATTT
1332238 TAT-TTT
1 TATATTT
1332244 TATTTATTAT
1 TA--TATT-T
1332254 TATAATCTT
1 TAT-AT-TT
1332263 ATATAGTTT
1 -TATA-TTT
1332272 TA-ATTT
1 TATATTT
1332278 T-TAATTT
1 TAT-ATTT
*
1332285 TTTAATTT
1 TAT-ATTT
* *
1332293 TTTATAT
1 TATATTT
1332300 TATATTAT
1 TATATT-T
*
1332308 TTTATTT
1 TATATTT
1332315 T-TA-TT
1 TATATTT
1332320 TA-ATTT
1 TATATTT
**
1332326 T-TAACT
1 TATATTT
*
1332332 TATATTA
1 TATATTT
1332339 TATAATTTT
1 TAT-A-TTT
*
1332348 TATTTTT
1 TATATTT
1332355 TATATTT
1 TATATTT
1332362 TATTTTATTT
1 TA---TATTT
1332372 TA-ATTT
1 TATATTT
1332378 T-TGATTCT
1 TAT-ATT-T
*
1332386 TATATTA
1 TATATTT
1332393 TATATTT
1 TATATTT
1332400 TAT-TTT
1 TATATTT
*
1332406 AATATTT
1 TATATTT
*
1332413 TTTATTT
1 TATATTT
1332420 TA
1 TA
1332422 ATTATAACAT
Statistics
Matches: 140, Mismatches: 18, Indels: 52
0.67 0.09 0.25
Matches are distributed among these distances:
5 4 0.03
6 27 0.19
7 55 0.39
8 25 0.18
9 14 0.10
10 15 0.11
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.69
Consensus pattern (7 bp):
TATATTT
Found at i:1332401 original size:52 final size:54
Alignment explanation
Indices: 1332291--1332421 Score: 157
Period size: 52 Copynumber: 2.5 Consensus size: 54
1332281 ATTTTTTAAT
*
1332291 TTTTTATATT-ATATTATTTTATTTT-TATTTAATTTTTAACTTATATTATATAA
1 TTTTTATTTTAATA-TATTTTATTTTATATTTAATTTTTAACTTATATTATATAA
* *
1332344 TTTTTATTTT-TTATATTTTATTTTAT-TTTAATTTTTGATTCTTATATTATAT-A
1 TTTTTATTTTAATATATTTTATTTTATATTTAATTTTT-A-ACTTATATTATATAA
*
1332397 -TTTTATTTTAATATTTTTTATTTTA
1 TTTTTATTTTAATATATTTTATTTTA
1332422 ATTATAACAT
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
52 30 0.43
53 27 0.39
54 12 0.17
ACGTcount: A:0.27, C:0.02, G:0.01, T:0.70
Consensus pattern (54 bp):
TTTTTATTTTAATATATTTTATTTTATATTTAATTTTTAACTTATATTATATAA
Found at i:1332426 original size:33 final size:34
Alignment explanation
Indices: 1332364--1332427 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 34
1332354 TTATATTTTA
*
1332364 TTTTATTTT-A-ATTTTTGATTCTTATATTATATA-
1 TTTTATTTTAATATTTTTTATT-TTA-ATTATATAT
1332397 TTTTATTTTAATATTTTTTATTTTAATTATA
1 TTTTATTTTAATATTTTTTATTTTAATTATA
1332428 ACATATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 15 0.54
34 4 0.14
35 9 0.32
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (34 bp):
TTTTATTTTAATATTTTTTATTTTAATTATATAT
Found at i:1333027 original size:7 final size:7
Alignment explanation
Indices: 1333015--1333058 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
1333005 TTAATATTTT
1333015 AATAATA
1 AATAATA
1333022 AATAATA
1 AATAATA
*
1333029 AATAATT
1 AATAATA
1333036 AATAATA
1 AATAATA
* *
1333043 ATTATTA
1 AATAATA
1333050 AATTAATA
1 AA-TAATA
1333058 A
1 A
1333059 TATTTTAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
7 25 0.83
8 5 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (7 bp):
AATAATA
Found at i:1333039 original size:21 final size:22
Alignment explanation
Indices: 1333013--1333060 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
1333003 TATTAATATT
1333013 TTAATAATAAATAATAAA-TAA
1 TTAATAATAAATAATAAATTAA
* *
1333034 TTAATAATAATTATTAAATTAA
1 TTAATAATAAATAATAAATTAA
1333056 -TAATA
1 TTAATA
1333061 TTTTAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAATAATAAATAATAAATTAA
Found at i:1333822 original size:3 final size:3
Alignment explanation
Indices: 1333816--1333841 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1333806 ATCTTCCTCC
1333816 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
1333842 ATCGTCCTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:1360400 original size:22 final size:22
Alignment explanation
Indices: 1360375--1360419 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1360365 CATTTTCATT
1360375 CGTTGCGTGACCCAATATTAGG
1 CGTTGCGTGACCCAATATTAGG
* *
1360397 CGTTGCGTGACCCCATGTTAGG
1 CGTTGCGTGACCCAATATTAGG
1360419 C
1 C
1360420 ACTAGGTGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.27, G:0.29, T:0.27
Consensus pattern (22 bp):
CGTTGCGTGACCCAATATTAGG
Found at i:1363472 original size:42 final size:42
Alignment explanation
Indices: 1363398--1363484 Score: 129
Period size: 42 Copynumber: 2.1 Consensus size: 42
1363388 TGTCATAAAT
* * *
1363398 ATGGTCATCACACTTAACATTTTCTAAGACAATAGTTGTGGC
1 ATGGTCATCACACTGAACATTTCCTAACACAATAGTTGTGGC
* *
1363440 ATGGTCATCGCACTGAACCTTTCCTAACACAATAGTTGTGGC
1 ATGGTCATCACACTGAACATTTCCTAACACAATAGTTGTGGC
1363482 ATG
1 ATG
1363485 TTCTGTAGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (42 bp):
ATGGTCATCACACTGAACATTTCCTAACACAATAGTTGTGGC
Found at i:1364955 original size:129 final size:129
Alignment explanation
Indices: 1364713--1364975 Score: 316
Period size: 129 Copynumber: 2.0 Consensus size: 129
1364703 CATTCCTAAT
*
1364713 AAGT-AGTCATGCAATGCCTAATATCCAATCACACATCCTAATATCCAATGACTCAATGCCTAAA
1 AAGTCAGTCATGCAATGCCTAATATCCAATCACACACCCTAATATCCAATGACTCAATGCCTAAA
* * * *
1364777 AAATATTAACGAATTGCTTAATAACTAATTGATTTCGCCACTCAAAGCTAGGTCTAAGTTGCCA
66 AAAAATTAACGAATTCCTTAATAACTAATTGATTTCACCACTCAAAGCTAGGTCTAAGTTGCAA
* * * ** *
1364841 AAGTCAGTCATGCAATGCCTAATATCTAGTCAGACACCCTAATATCCTGTGACGT-AATGTCTAA
1 AAGTCAGTCATGCAATGCCTAATATCCAATCACACACCCTAATATCCAATGAC-TCAATGCCTAA
* * * * ** * *
1364905 AAAAAATTCATGACTTACCTT-ATAACTAATTGATTTCACTACTCTCAGCTAGGTTTAAGTTTCA
65 AAAAAATTAACGAATT-CCTTAATAACTAATTGATTTCACCACTCAAAGCTAGGTCTAAGTTGCA
1364969 A
129 A
1364970 AAGTCA
1 AAGTCA
1364976 TATAATTTAC
Statistics
Matches: 113, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
128 4 0.04
129 105 0.93
130 4 0.04
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (129 bp):
AAGTCAGTCATGCAATGCCTAATATCCAATCACACACCCTAATATCCAATGACTCAATGCCTAAA
AAAAATTAACGAATTCCTTAATAACTAATTGATTTCACCACTCAAAGCTAGGTCTAAGTTGCAA
Found at i:1381886 original size:35 final size:34
Alignment explanation
Indices: 1381844--1381910 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
1381834 ACCATTATTG
*
1381844 TAAGGGTTCTGCTTGCTATCGTGAAATAGTGTTAT
1 TAAGGGTTCCGCTTGCTATCGTGAAA-AGTGTTAT
* * *
1381879 TAAGGGTTCCGTTTGCTCTTGTGAAAAGTGTT
1 TAAGGGTTCCGCTTGCTATCGTGAAAAGTGTT
1381911 GTGAGGGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 6 0.21
35 22 0.79
ACGTcount: A:0.21, C:0.12, G:0.27, T:0.40
Consensus pattern (34 bp):
TAAGGGTTCCGCTTGCTATCGTGAAAAGTGTTAT
Found at i:1385040 original size:19 final size:19
Alignment explanation
Indices: 1385003--1385046 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1384993 TTTTTTTTTT
*
1385003 GTAAAAAATGAATAAAAAA
1 GTAAAAAATGAAAAAAAAA
1385022 GTAAAAAAT-AAAAATAAAA
1 GTAAAAAATGAAAAA-AAAA
*
1385041 ATAAAA
1 GTAAAA
1385047 CAAATGGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (19 bp):
GTAAAAAATGAAAAAAAAA
Found at i:1389748 original size:211 final size:211
Alignment explanation
Indices: 1389379--1389789 Score: 705
Period size: 211 Copynumber: 1.9 Consensus size: 211
1389369 ACAAGCTTAA
* * *
1389379 AGCTGACAACAGACTTTAAGCCTCATTGCATCCCCTGAAATGGCGGTTGCTTCCCAAGACACCTG
1 AGCTAACAACAGACTTTAAGCCTCATTCCATCCCCTGAAATGGCGGTTGCTTCCCAAGACACCTA
*
1389444 AAGTTGCCAATACAGGTGCAAATGTTAATTATTGGGAAAAAGGAAGATGTCTGTTTACTTGATAG
66 AAGTTGCCAATACAGGTGCAAATGTTAATTATTGGGAAAAAGGAAGATGTCTATTTACTTGATAG
*
1389509 TGCAACGACACATACCATACTTTGTAGCAAGCAATTTTTCTCAAGTGTGACATTGTGTAAGGAAA
131 TGCAACGACACATAACATACTTTGTAGCAAGCAATTTTTCTCAAGTGTGACATTGTGTAAGGAAA
1389574 ATGTCAACAGGTTTAT
196 ATGTCAACAGGTTTAT
* * *
1389590 AGCTAACAACAGACTTTGAGCCTCATTCCATCCCCTGAAGTGGTGGTTGCTTCCCAAGACACCTA
1 AGCTAACAACAGACTTTAAGCCTCATTCCATCCCCTGAAATGGCGGTTGCTTCCCAAGACACCTA
* *
1389655 AAGTTGCCAATACATGTGTAAATGTTAATTATTGGGAAAAAGGAAGATGTCTATTTACTTGATAG
66 AAGTTGCCAATACAGGTGCAAATGTTAATTATTGGGAAAAAGGAAGATGTCTATTTACTTGATAG
* * *
1389720 TGCAACGACACATAACATACTTTGTAGCAAGCACTTTTTCTCAAGTGTGACATTGTGTGAGGCAA
131 TGCAACGACACATAACATACTTTGTAGCAAGCAATTTTTCTCAAGTGTGACATTGTGTAAGGAAA
1389785 ATGTC
196 ATGTC
1389790 CATACAATAT
Statistics
Matches: 187, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
211 187 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.29
Consensus pattern (211 bp):
AGCTAACAACAGACTTTAAGCCTCATTCCATCCCCTGAAATGGCGGTTGCTTCCCAAGACACCTA
AAGTTGCCAATACAGGTGCAAATGTTAATTATTGGGAAAAAGGAAGATGTCTATTTACTTGATAG
TGCAACGACACATAACATACTTTGTAGCAAGCAATTTTTCTCAAGTGTGACATTGTGTAAGGAAA
ATGTCAACAGGTTTAT
Found at i:1394274 original size:20 final size:20
Alignment explanation
Indices: 1394236--1394274 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1394226 TGTGTTCTCT
* *
1394236 ACTCTAACTAAGTACGAGAG
1 ACTCTAACCAAGTAAGAGAG
*
1394256 ACTCTAACCAATTAAGAGA
1 ACTCTAACCAAGTAAGAGA
1394275 TCTTTGTCTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.21
Consensus pattern (20 bp):
ACTCTAACCAAGTAAGAGAG
Found at i:1410544 original size:17 final size:16
Alignment explanation
Indices: 1410515--1410569 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 16
1410505 TTTGTTTATG
*
1410515 TTTTTCTTGTTTTTCC
1 TTTTTCTTCTTTTTCC
*
1410531 TTTTATCTTCTTTTTTC
1 TTTT-TCTTCTTTTTCC
* *
1410548 TTTTTTTTTTTATTTCC
1 TTTTTCTTCTT-TTTCC
1410565 TTTTT
1 TTTTT
1410570 TAATTCTTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
16 9 0.28
17 23 0.72
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.80
Consensus pattern (16 bp):
TTTTTCTTCTTTTTCC
Found at i:1410558 original size:24 final size:26
Alignment explanation
Indices: 1410515--1410570 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 26
1410505 TTTGTTTATG
1410515 TTTTTCTTGTTTTTCCTTTTATCTT-CT
1 TTTTTCTTGTTTTT-CTTTTAT-TTCCT
1410542 TTTTTCTT-TTTTT-TTTTATTTCCT
1 TTTTTCTTGTTTTTCTTTTATTTCCT
1410566 TTTTT
1 TTTTT
1410571 AATTCTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
23 2 0.07
24 13 0.46
26 5 0.18
27 8 0.29
ACGTcount: A:0.04, C:0.14, G:0.02, T:0.80
Consensus pattern (26 bp):
TTTTTCTTGTTTTTCTTTTATTTCCT
Found at i:1410568 original size:12 final size:11
Alignment explanation
Indices: 1410531--1410591 Score: 50
Period size: 12 Copynumber: 5.3 Consensus size: 11
1410521 TTGTTTTTCC
1410531 TTTTATCTTCTT
1 TTTTAT-TTCTT
* *
1410543 TTTTCTTTTTTT
1 TTTT-ATTTCTT
1410555 TTTTATTTCCTT
1 TTTTATTT-CTT
*
1410567 TTTTAATTCTT
1 TTTTATTTCTT
* *
1410578 TCTTCTTTCTT
1 TTTTATTTCTT
1410589 TTT
1 TTT
1410592 CTCACATCCT
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
11 16 0.42
12 21 0.55
13 1 0.03
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTATTTCTT
Found at i:1417636 original size:21 final size:23
Alignment explanation
Indices: 1417610--1417665 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 23
1417600 GATCGTATAT
1417610 TATTTTTATTATTTAA-AA-TAA
1 TATTTTTATTATTTAATAATTAA
* *
1417631 TATTTTAATTA-ATAATAATTAA
1 TATTTTTATTATTTAATAATTAA
1417653 T-TTTTTATT-TTTA
1 TATTTTTATTATTTA
1417666 TAAAGTCAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
20 3 0.11
21 21 0.75
22 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TATTTTTATTATTTAATAATTAA
Found at i:1420259 original size:21 final size:22
Alignment explanation
Indices: 1420224--1420267 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1420214 CTCTTAAAGT
1420224 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
1420246 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
1420267 A
1 A
1420268 TTAATCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:1430586 original size:10 final size:10
Alignment explanation
Indices: 1430571--1430603 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1430561 TAATTTAAAA
1430571 TAAAATAACC
1 TAAAATAACC
1430581 TAAAATAA-C
1 TAAAATAACC
*
1430590 TAAAATAACT
1 TAAAATAACC
1430600 TAAA
1 TAAA
1430604 TTAATCACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (10 bp):
TAAAATAACC
Found at i:1430594 original size:9 final size:9
Alignment explanation
Indices: 1430571--1430604 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
1430561 TAATTTAAAA
1430571 TAAAATAACC
1 TAAAATAA-C
1430581 TAAAATAAC
1 TAAAATAAC
1430590 TAAAATAAC
1 TAAAATAAC
*
1430599 TTAAAT
1 TAAAAT
1430605 TAATCACTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.26
Consensus pattern (9 bp):
TAAAATAAC
Found at i:1430970 original size:32 final size:31
Alignment explanation
Indices: 1430928--1430999 Score: 108
Period size: 32 Copynumber: 2.3 Consensus size: 31
1430918 CATCATAAAC
* *
1430928 GCCAAGGTGCAATGGGGATTGTACATTGCTA
1 GCCAAGGTGCAATAGGGATTCTACATTGCTA
1430959 GTCCAAGGTGCAATAGGGATTCTACATTGCTA
1 G-CCAAGGTGCAATAGGGATTCTACATTGCTA
1430991 GCCTAAGGT
1 GCC-AAGGT
1431000 TGATGGGGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
31 3 0.08
32 34 0.92
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.26
Consensus pattern (31 bp):
GCCAAGGTGCAATAGGGATTCTACATTGCTA
Found at i:1437468 original size:95 final size:95
Alignment explanation
Indices: 1437305--1437495 Score: 355
Period size: 95 Copynumber: 2.0 Consensus size: 95
1437295 TATACTTAAT
*
1437305 GGTAAACACCCATTTACACCCTATAGAACTCTTACCTTCAGGTAACTCCATTACATCCCAAGTTT
1 GGTAAACACCCATTTACACCCTACAGAACTCTTACCTTCAGGTAACTCCATTACATCCCAAGTTT
1437370 CATTCATTTTTAGGGCTCTCATTTCTTCAA
66 CATTCATTTTTAGGGCTCTCATTTCTTCAA
*
1437400 GGTAAACACCCATTTACACCCTACAGAACTCTTACCTTCAGGTAACTCCATTTCATCCCAAGTTT
1 GGTAAACACCCATTTACACCCTACAGAACTCTTACCTTCAGGTAACTCCATTACATCCCAAGTTT
*
1437465 CATTCATTTTTAGGGCTTTCATTTCTTCAA
66 CATTCATTTTTAGGGCTCTCATTTCTTCAA
1437495 G
1 G
1437496 TACAGTAACC
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 93 1.00
ACGTcount: A:0.27, C:0.28, G:0.10, T:0.35
Consensus pattern (95 bp):
GGTAAACACCCATTTACACCCTACAGAACTCTTACCTTCAGGTAACTCCATTACATCCCAAGTTT
CATTCATTTTTAGGGCTCTCATTTCTTCAA
Found at i:1453064 original size:21 final size:21
Alignment explanation
Indices: 1453039--1453081 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1453029 AAAGATTTTA
1453039 TTTTTC-AAGAATCAACTTCTT
1 TTTTTCTAAGAATCAA-TTCTT
*
1453060 TTTTTCTCAGAATCAATTCTT
1 TTTTTCTAAGAATCAATTCTT
1453081 T
1 T
1453082 ACCATTGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.26, C:0.19, G:0.05, T:0.51
Consensus pattern (21 bp):
TTTTTCTAAGAATCAATTCTT
Found at i:1456323 original size:79 final size:80
Alignment explanation
Indices: 1456162--1456351 Score: 204
Period size: 79 Copynumber: 2.4 Consensus size: 80
1456152 AGTGTCTACA
* * * * *
1456162 CTTGGTAACTAAAAACCACAACACAAGGATATTGGGTTATTAACCTTGGAACCACCGCACCAGAA
1 CTTGGTAACTTAAAATCACAATACAAGGATATTGGGATATTAACCTTGGAACCACCACACCAGAA
* *
1456227 GTTTTACCTATCATC
66 GATTCACCTATCATC
* * * * * *
1456242 CTTGGTAACTTATAATCACAATATAAGGATATT-GGATATTAACCTTGGAACTACCATACTA-AG
1 CTTGGTAACTTAAAATCACAATACAAGGATATTGGGATATTAACCTTGGAACCACCACACCAGAA
*
1456305 GATTCAGCCTATTATC
66 GATTCA-CCTATCATC
* *
1456321 CTTGGTAATTTAAAATCACAATTCCAAGGAT
1 CTTGGTAACTTAAAATCACAA-TACAAGGAT
1456352 TTTGCCTATT
Statistics
Matches: 90, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 5 0.06
79 50 0.56
80 35 0.39
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (80 bp):
CTTGGTAACTTAAAATCACAATACAAGGATATTGGGATATTAACCTTGGAACCACCACACCAGAA
GATTCACCTATCATC
Found at i:1457710 original size:17 final size:18
Alignment explanation
Indices: 1457688--1457721 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1457678 TTTGTAGGTG
1457688 TTTAAT-GAAAGAAGAAT
1 TTTAATGGAAAGAAGAAT
*
1457705 TTTAATGGAGAGAAGAA
1 TTTAATGGAAAGAAGAA
1457722 AAAAACTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (18 bp):
TTTAATGGAAAGAAGAAT
Found at i:1461006 original size:17 final size:17
Alignment explanation
Indices: 1460984--1461030 Score: 94
Period size: 17 Copynumber: 2.8 Consensus size: 17
1460974 TAGATAGACC
1460984 CATTTATCAATAATGAA
1 CATTTATCAATAATGAA
1461001 CATTTATCAATAATGAA
1 CATTTATCAATAATGAA
1461018 CATTTATCAATAA
1 CATTTATCAATAA
1461031 ATGTTCTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (17 bp):
CATTTATCAATAATGAA
Found at i:1462738 original size:73 final size:73
Alignment explanation
Indices: 1462625--1462763 Score: 163
Period size: 73 Copynumber: 1.9 Consensus size: 73
1462615 CTACCAATAG
* * * * * *
1462625 CCATTTTAAGAAGGGGGTAATTATCATTCATACTCACATCATAAGAAATAGGCAATCATACATCC
1 CCATTTTAAGAAGGGGGCAAATATCATCCACACTCACATCACAAGAAATAGGAAATCATACATCC
1462690 ATTAGTAT
66 ATTAGTAT
** * * *
1462698 CCATTTTAAG-AGGTGGGCAAATATCATCCACACTGGCATCACAAGAAGTGGGAAATTATACATC
1 CCATTTTAAGAAGG-GGGCAAATATCATCCACACTCACATCACAAGAAATAGGAAATCATACATC
1462762 CA
65 CA
1462764 CATTGGCAAT
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
72 3 0.06
73 51 0.94
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (73 bp):
CCATTTTAAGAAGGGGGCAAATATCATCCACACTCACATCACAAGAAATAGGAAATCATACATCC
ATTAGTAT
Found at i:1466499 original size:15 final size:15
Alignment explanation
Indices: 1466467--1466511 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
1466457 TATTGGATTA
*
1466467 AAATTT-AAGATTTT
1 AAATTTAAAAATTTT
1466481 -AATTTAAAAATTTT
1 AAATTTAAAAATTTT
1466495 AAATTTAAAAATTTT
1 AAATTTAAAAATTTT
1466510 AA
1 AA
1466512 GATATGTGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 5 0.18
14 7 0.25
15 16 0.57
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (15 bp):
AAATTTAAAAATTTT
Found at i:1474897 original size:23 final size:23
Alignment explanation
Indices: 1474524--1475035 Score: 187
Period size: 23 Copynumber: 22.5 Consensus size: 23
1474514 GATAGAGTGG
*
1474524 GAATATGTGACA-CACCATGGAGA
1 GAATATGTGACATGA-CATGGAGA
*
1474547 GAATATGTGAGATGACATGGTA-A
1 GAATATGTGACATGACATGG-AGA
* * * *
1474570 GAATATGTGTCACGTCAAGGTA-A
1 GAATATGTGACATGACATGG-AGA
* * **
1474593 GAATATGTGAGACGTTATGGAG-
1 GAATATGTGACATGACATGGAGA
* * * * *
1474615 GAAACATGTGACACGTCAAGGTGA
1 G-AATATGTGACATGACATGGAGA
* *
1474639 GTATATGTGACA-CACCATGGAG-
1 GAATATGTGACATGA-CATGGAGA
* * * *
1474661 GAAATATGTGACACGAGATGAAAA
1 G-AATATGTGACATGACATGGAGA
* * *
1474685 GAAAATGTGACATGGCATGGTGA
1 GAATATGTGACATGACATGGAGA
* * *
1474708 GAATATGTGAGACGACATGGAGG
1 GAATATGTGACATGACATGGAGA
* *
1474731 GAATATGTGACACT-CCATGGAGG
1 GAATATGTGACA-TGACATGGAGA
* * *
1474754 GAATGTATG--AT-ACA--GAGG
1 GAATATGTGACATGACATGGAGA
* *
1474772 GAATATGTGACA-CACCATGGTGA
1 GAATATGTGACATGA-CATGGAGA
* *
1474795 GAATATGTGAGATGACATGGTGA
1 GAATATGTGACATGACATGGAGA
* * *
1474818 GAATATATAACATGAGA-GGATGA
1 GAATATGTGACATGACATGGA-GA
* * * *
1474841 AAATATGTGACACGCCATGGTGA
1 GAATATGTGACATGACATGGAGA
* * * *
1474864 GAATTTGTGAGATGCCATGGAGG
1 GAATATGTGACATGACATGGAGA
* ** * *
1474887 GAATATGTGAGATGATGTTGTGA
1 GAATATGTGACATGACATGGAGA
* * *
1474910 GAATAAGTGACACGACATGGAGG
1 GAATATGTGACATGACATGGAGA
* * * *
1474933 GAATATGTGAAATGCCATGAAAA
1 GAATATGTGACATGACATGGAGA
* *
1474956 GAATATGTGACACGATATGGATG-
1 GAATATGTGACATGACATGGA-GA
* *
1474979 GAATCTGT-ACACT-CCAT-GATGA
1 GAATATGTGACA-TGACATGGA-GA
* * * *
1475001 AAATATATGAGATGACATGGAGG
1 GAATATGTGACATGACATGGAGA
1475024 GAATATGTGACA
1 GAATATGTGACA
1475036 CGGCATAAAT
Statistics
Matches: 353, Mismatches: 111, Indels: 50
0.69 0.22 0.10
Matches are distributed among these distances:
18 11 0.03
20 5 0.01
21 7 0.02
22 16 0.05
23 304 0.86
24 10 0.03
ACGTcount: A:0.37, C:0.11, G:0.30, T:0.23
Consensus pattern (23 bp):
GAATATGTGACATGACATGGAGA
Found at i:1474920 original size:69 final size:70
Alignment explanation
Indices: 1474772--1475035 Score: 257
Period size: 69 Copynumber: 3.8 Consensus size: 70
1474762 GATACAGAGG
* * * * *
1474772 GAATATGTGACACACCATGGTGAGAATATGTGAGATGACATGGTGAGAATATATAACATGA-GAG
1 GAATATGTGACACGCCATGGTGAGAATATGTGAGATGACATGGAGAGAATATGTGACATGATGTG
1474836 GATGA
66 GATGA
* * * * * *
1474841 AAATATGTGACACGCCATGGTGAGAATTTGTGAGATGCCATGGAGGGAATATGTGAGATGATGTT
1 GAATATGTGACACGCCATGGTGAGAATATGTGAGATGACATGGAGAGAATATGTGACATGATGTG
1474906 G-TGA
66 GATGA
* * * * * * * * * *
1474910 GAATAAGTGACACGACATGGAGGGAATATGTGAAATGCCATGAAAAGAATATGTGACACGATATG
1 GAATATGTGACACGCCATGGTGAGAATATGTGAGATGACATGGAGAGAATATGTGACATGATGTG
1474975 GATG-
66 GATGA
* * * * * *
1474979 GAATCTGT-ACACTCCATGATGAAAATATATGAGATGACATGGAGGGAATATGTGACA
1 GAATATGTGACACGCCATGGTGAGAATATGTGAGATGACATGGAGAGAATATGTGACA
1475036 CGGCATAAAT
Statistics
Matches: 154, Mismatches: 39, Indels: 5
0.78 0.20 0.03
Matches are distributed among these distances:
68 37 0.24
69 113 0.73
70 4 0.03
ACGTcount: A:0.37, C:0.10, G:0.29, T:0.24
Consensus pattern (70 bp):
GAATATGTGACACGCCATGGTGAGAATATGTGAGATGACATGGAGAGAATATGTGACATGATGTG
GATGA
Found at i:1476816 original size:23 final size:25
Alignment explanation
Indices: 1476789--1476840 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 25
1476779 TATTCCATAT
1476789 ATATAAATATTATT-AATA-TATTA
1 ATATAAATATTATTAAATATTATTA
*
1476812 ATATAAATATTGTTAAATATTATTA
1 ATATAAATATTATTAAATATTATTA
1476837 ATAT
1 ATAT
1476841 TGTTACTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 13 0.50
24 4 0.15
25 9 0.35
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
ATATAAATATTATTAAATATTATTA
Found at i:1476841 original size:19 final size:19
Alignment explanation
Indices: 1476792--1476845 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
1476782 TCCATATATA
*
1476792 TAAATATTATTAATA-TAT
1 TAAATATTATTAATATTGT
1476810 T-AATA-TA--AATATTGT
1 TAAATATTATTAATATTGT
1476825 TAAATATTATTAATATTGT
1 TAAATATTATTAATATTGT
1476844 TA
1 TA
1476846 CTTAATATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
14 4 0.13
15 3 0.10
16 6 0.20
17 6 0.20
18 1 0.03
19 10 0.33
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (19 bp):
TAAATATTATTAATATTGT
Found at i:1476854 original size:19 final size:19
Alignment explanation
Indices: 1476808--1476854 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
1476798 TTATTAATAT
*
1476808 ATTAATATAAATATTGTTA
1 ATTAATATTAATATTGTTA
* *
1476827 AATATTATTAATATTGTTA
1 ATTAATATTAATATTGTTA
*
1476846 CTTAATATT
1 ATTAATATT
1476855 TTTATATAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (19 bp):
ATTAATATTAATATTGTTA
Found at i:1492208 original size:15 final size:15
Alignment explanation
Indices: 1492167--1492209 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
1492157 AAACAAAAGA
1492167 ATATAAAAATAATA-
1 ATATAAAAATAATAT
**
1492181 ATACCAAAA-AATAT
1 ATATAAAAATAATAT
1492195 ATATAAAAATAATAT
1 ATATAAAAATAATAT
1492210 TTTAAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 4 0.17
14 14 0.61
15 5 0.22
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (15 bp):
ATATAAAAATAATAT
Found at i:1492220 original size:28 final size:28
Alignment explanation
Indices: 1492151--1492208 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
1492141 TTTAGAAAAT
*
1492151 TAATACAAACAAAAGA-ATATAAAAATAA
1 TAATACAAA-AAAATATATATAAAAATAA
*
1492179 TAATACCAAAAAATATATATAAAAATAA
1 TAATACAAAAAAATATATATAAAAATAA
1492207 TA
1 TA
1492209 TTTTAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.69, C:0.07, G:0.02, T:0.22
Consensus pattern (28 bp):
TAATACAAAAAAATATATATAAAAATAA
Found at i:1493196 original size:21 final size:21
Alignment explanation
Indices: 1493158--1493197 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1493148 TCATAATAAA
*
1493158 TACAAAAGATAAATATTTAGT
1 TACAAAAGAAAAATATTTAGT
1493179 TACAAAA-AAAAATGATTTA
1 TACAAAAGAAAAAT-ATTTA
1493198 TAAGGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.30
Consensus pattern (21 bp):
TACAAAAGAAAAATATTTAGT
Found at i:1498634 original size:2 final size:2
Alignment explanation
Indices: 1498627--1498659 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1498617 ATATGTATAA
1498627 GT GT GT GT GT GT GT GT GT GT G- GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1498660 TTATGTATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:1505699 original size:21 final size:21
Alignment explanation
Indices: 1505675--1505714 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1505665 AGCAGAGGAA
* *
1505675 AAGAAGCAGAGGAAGATGATG
1 AAGAACCAGAAGAAGATGATG
*
1505696 AAGAACCAGAAGCAGATGA
1 AAGAACCAGAAGAAGATGA
1505715 AGCTGCAGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.10, G:0.33, T:0.07
Consensus pattern (21 bp):
AAGAACCAGAAGAAGATGATG
Found at i:1505724 original size:12 final size:12
Alignment explanation
Indices: 1505707--1505740 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1505697 AGAACCAGAA
1505707 GCAGATGAAGCT
1 GCAGATGAAGCT
1505719 GCAGATGAAGCT
1 GCAGATGAAGCT
*
1505731 GCAAATGAAG
1 GCAGATGAAG
1505741 ATGGCAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.38, C:0.15, G:0.32, T:0.15
Consensus pattern (12 bp):
GCAGATGAAGCT
Found at i:1507056 original size:18 final size:18
Alignment explanation
Indices: 1507033--1507075 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1507023 CAATCCATAG
*
1507033 ACCAGAACCGGAAGCAGA
1 ACCAGAACCAGAAGCAGA
*
1507051 ACCAGAACCAGAAGGAGA
1 ACCAGAACCAGAAGCAGA
*
1507069 AGCAGAA
1 ACCAGAA
1507076 GAAGAATAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.49, C:0.23, G:0.28, T:0.00
Consensus pattern (18 bp):
ACCAGAACCAGAAGCAGA
Found at i:1514039 original size:60 final size:60
Alignment explanation
Indices: 1513933--1514045 Score: 145
Period size: 60 Copynumber: 1.9 Consensus size: 60
1513923 ATTTTCAGCG
* * * * *
1513933 TTTTGGAGTAGTTTTTGATACATGAAGAAAAACCTTTGAGCGTTTTGAGCATTGTAAGTA
1 TTTTGGAGTAATTTTTGATACATAAAGAAAAACCTTTAAACATTTTGAGCATTGTAAGTA
* ** *
1513993 TTTTGGAGTAATTTTTGCTATGTAAAGAAAAACTTTTAAACATTTTGAGCATT
1 TTTTGGAGTAATTTTTGATACATAAAGAAAAACCTTTAAACATTTTGAGCATT
1514046 TTTAACTAAG
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 44 1.00
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (60 bp):
TTTTGGAGTAATTTTTGATACATAAAGAAAAACCTTTAAACATTTTGAGCATTGTAAGTA
Found at i:1514294 original size:23 final size:23
Alignment explanation
Indices: 1514268--1514328 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
1514258 TTAATAGAGT
* *
1514268 ATTGCGTGATTAGTTAGTAAGGC
1 ATTGCGTGATTAGTTACTAAGAC
* *
1514291 ATTGGGTGACTAGTTACTAAGAC
1 ATTGCGTGATTAGTTACTAAGAC
*
1514314 ATTGCGTAATTAGTT
1 ATTGCGTGATTAGTT
1514329 TTTAAGCATT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.28, C:0.10, G:0.26, T:0.36
Consensus pattern (23 bp):
ATTGCGTGATTAGTTACTAAGAC
Found at i:1514334 original size:23 final size:22
Alignment explanation
Indices: 1514147--1514339 Score: 82
Period size: 22 Copynumber: 8.6 Consensus size: 22
1514137 AGTTTTAGTT
** *
1514147 GTTTTTAAGCATTATGTAATCA
1 GTTTTTAAGCATTGCGTAATTA
* *
1514169 GTTTTT-GGACATTGCGTGATTA
1 GTTTTTAAG-CATTGCGTAATTA
** ** *
1514191 GTTTTTAAATATTATGTAACTA
1 GTTTTTAAGCATTGCGTAATTA
* * *
1514213 ATTTTTAAGCATTACGTAACTA
1 GTTTTTAAGCATTGCGTAATTA
* * * * *
1514235 ATTTTTAAGTATTACGTGATTG
1 GTTTTTAAGCATTGCGTAATTA
** * *
1514257 GTTAATAGAGTATTGCGTGATTA
1 GTTTTTA-AGCATTGCGTAATTA
** * * *
1514280 GTTAGTAAGGCATTGGGTGACTA
1 GTTTTTAA-GCATTGCGTAATTA
**
1514303 GTTACTAAGACATTGCGTAATTA
1 GTTTTTAAG-CATTGCGTAATTA
1514326 GTTTTTAAGCATTG
1 GTTTTTAAGCATTG
1514340 TGTGACATAG
Statistics
Matches: 131, Mismatches: 35, Indels: 10
0.74 0.20 0.06
Matches are distributed among these distances:
21 1 0.01
22 76 0.58
23 54 0.41
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (22 bp):
GTTTTTAAGCATTGCGTAATTA
Found at i:1514501 original size:22 final size:21
Alignment explanation
Indices: 1514455--1514516 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 21
1514445 TTAAGTCACG
* *
1514455 TAATATTTAAAAATCAGTTTAA
1 TAATATTTAAAAATCA-ATGAA
1514477 TAATATTTAAAAATCAATGACA
1 TAATATTTAAAAATCAATGA-A
* * *
1514499 TAATGTCTAAAAACCAAT
1 TAATATTTAAAAATCAAT
1514517 ACTGTAATAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 2 0.06
22 32 0.94
ACGTcount: A:0.52, C:0.10, G:0.05, T:0.34
Consensus pattern (21 bp):
TAATATTTAAAAATCAATGAA
Found at i:1514808 original size:19 final size:20
Alignment explanation
Indices: 1514774--1514811 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1514764 AATCATGTCA
*
1514774 AAAATTGATTAAAAATAATT
1 AAAATTGATGAAAAATAATT
1514794 AAAATT-ATGAAAAATAAT
1 AAAATTGATGAAAAATAAT
1514812 ATTTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (20 bp):
AAAATTGATGAAAAATAATT
Found at i:1517425 original size:19 final size:18
Alignment explanation
Indices: 1517384--1517427 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1517374 AGGTCTTATA
*
1517384 ATTAATAATTAAATAATT
1 ATTATTAATTAAATAATT
1517402 ATTATTAATTATAAT-ATT
1 ATTATTAATTA-AATAATT
1517420 ACTTATTA
1 A-TTATTA
1517428 TTTTATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTATTAATTAAATAATT
Found at i:1518954 original size:2 final size:2
Alignment explanation
Indices: 1518906--1518946 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1518896 AAATGAGACA
1518906 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1518947 CCTATATACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1525466 original size:26 final size:25
Alignment explanation
Indices: 1525431--1525493 Score: 117
Period size: 26 Copynumber: 2.5 Consensus size: 25
1525421 CAATAACCTC
1525431 AGTGCATAGATTGGAGGACTTTGAT
1 AGTGCATAGATTGGAGGACTTTGAT
1525456 AGTGCTATAGATTGGAGGACTTTGAT
1 AGTGC-ATAGATTGGAGGACTTTGAT
1525482 AGTGCATAGATT
1 AGTGCATAGATT
1525494 CTGCTGGTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 12 0.32
26 25 0.68
ACGTcount: A:0.29, C:0.08, G:0.30, T:0.33
Consensus pattern (25 bp):
AGTGCATAGATTGGAGGACTTTGAT
Found at i:1536409 original size:37 final size:37
Alignment explanation
Indices: 1536341--1536429 Score: 90
Period size: 37 Copynumber: 2.4 Consensus size: 37
1536331 AAGTAACTGG
* * * *
1536341 TGAAAAGTCAAATCATGCTTAATGCCAAAGCAATTGA
1 TGAAGAGTCAAATCATGCTCAATGCCAAAGCAACTAA
* *
1536378 TGAAGAGTCAAATCATGGC-CAATGTCGAAGCAACTAA
1 TGAAGAGTCAAATCAT-GCTCAATGCCAAAGCAACTAA
* *
1536415 TGGAGAATCAAATCA
1 TGAAGAGTCAAATCA
1536430 CGCCTAGCAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
37 41 0.95
38 2 0.05
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.21
Consensus pattern (37 bp):
TGAAGAGTCAAATCATGCTCAATGCCAAAGCAACTAA
Found at i:1536463 original size:37 final size:37
Alignment explanation
Indices: 1536379--1536504 Score: 99
Period size: 37 Copynumber: 3.4 Consensus size: 37
1536369 AGCAATTGAT
* * *** **
1536379 GAAGAGTCAAATCATGGCCAATGTCGAAGCAACTAAT
1 GAAGAGTCAAATCACGCCCACCATCGAAGCAACTAGC
* * * * *
1536416 GGAGAATCAAATCACGCCTAGCATCGAGGCAACTAGC
1 GAAGAGTCAAATCACGCCCACCATCGAAGCAACTAGC
** * * *
1536453 GAAGAGTCAAATCGTGCCCACCATCTAAGTAACTAGT
1 GAAGAGTCAAATCACGCCCACCATCGAAGCAACTAGC
1536490 GAAGAGTCAAATCAC
1 GAAGAGTCAAATCAC
1536505 ACATGATGCC
Statistics
Matches: 66, Mismatches: 23, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.17
Consensus pattern (37 bp):
GAAGAGTCAAATCACGCCCACCATCGAAGCAACTAGC
Found at i:1537007 original size:73 final size:73
Alignment explanation
Indices: 1536924--1537090 Score: 199
Period size: 73 Copynumber: 2.3 Consensus size: 73
1536914 GATCAAGAGA
* *
1536924 CATTGTTAGTCGACTAAGAGCTTACTACCAAAAATTGAGTACAGAGACAGAAACGACTTAATCAA
1 CATTGTTAGTCGACTAAGAGCTTACCACCAAAAACTGAGTACAGAGACAGAAACGACTTAATCAA
1536989 CTAAGAAG
66 CTAAGAAG
* * ** * * * * * *
1536997 TATTGTTAGTCGACTAAGAGCTTGCCGTCAGAAACTGGGTTCAGAGACATAAATGACTTAATCGA
1 CATTGTTAGTCGACTAAGAGCTTACCACCAAAAACTGAGTACAGAGACAGAAACGACTTAATCAA
* *
1537062 TTAAGTAG
66 CTAAGAAG
*
1537070 CAATGTTAGTCGACTAAGAGC
1 CATTGTTAGTCGACTAAGAGC
1537091 ATTCTGTTTG
Statistics
Matches: 78, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
73 78 1.00
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (73 bp):
CATTGTTAGTCGACTAAGAGCTTACCACCAAAAACTGAGTACAGAGACAGAAACGACTTAATCAA
CTAAGAAG
Found at i:1539675 original size:36 final size:36
Alignment explanation
Indices: 1539626--1539724 Score: 103
Period size: 36 Copynumber: 2.8 Consensus size: 36
1539616 CAATTTTCCT
*
1539626 TTTTAACAAGATCAAGCGTAACCTTTACAACATGCC
1 TTTTAACAGGATCAAGCGTAACCTTTACAACATGCC
* ** *
1539662 TTTTAACAGGATCATGCGTAACCTCCATAACATGCC
1 TTTTAACAGGATCAAGCGTAACCTTTACAACATGCC
* * *
1539698 GTTT-ATAGGCTC-AGACGTAACCTTTAC
1 TTTTAACAGGATCAAG-CGTAACCTTTAC
1539725 CAAGACATTA
Statistics
Matches: 50, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
34 1 0.02
35 15 0.30
36 34 0.68
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.29
Consensus pattern (36 bp):
TTTTAACAGGATCAAGCGTAACCTTTACAACATGCC
Found at i:1541524 original size:30 final size:30
Alignment explanation
Indices: 1541477--1541538 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
1541467 AGGGGTGAAG
1541477 TTGTAATTATCAAAAG-TTAAAAGATCAAT
1 TTGTAATTATCAAAAGTTTAAAAGATCAAT
* * *
1541506 TTGTAATTTATGAAAAGTTTGAAAGTTCAAT
1 TTGTAA-TTATCAAAAGTTTAAAAGATCAAT
1541537 TT
1 TT
1541539 AAAAAGGATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 6 0.21
30 9 0.32
31 13 0.46
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.40
Consensus pattern (30 bp):
TTGTAATTATCAAAAGTTTAAAAGATCAAT
Found at i:1546962 original size:21 final size:21
Alignment explanation
Indices: 1546938--1546984 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
1546928 TTTATTAAGG
1546938 TTATTTTAAATTTATTT-TTAT
1 TTATTTT-AATTTATTTATTAT
*
1546959 TTATCTTAATTTATTTATTAT
1 TTATTTTAATTTATTTATTAT
1546980 TTATT
1 TTATT
1546985 AGTTTTTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (21 bp):
TTATTTTAATTTATTTATTAT
Found at i:1550626 original size:18 final size:17
Alignment explanation
Indices: 1550591--1550624 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1550581 TTCTTGATAA
1550591 AATAAAACTCCTTATTT
1 AATAAAACTCCTTATTT
1550608 AATAATAACT-CTTATTT
1 AATAA-AACTCCTTATTT
1550625 TATTATTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (17 bp):
AATAAAACTCCTTATTT
Found at i:1550888 original size:29 final size:28
Alignment explanation
Indices: 1550765--1550932 Score: 149
Period size: 29 Copynumber: 5.8 Consensus size: 28
1550755 TTAAGATAAC
*
1550765 TCTTGTCTTTAATTAAGACAAAAATATTTT
1 TCTTGTC-TAAATTAAGACAAAAATA-TTT
* * * *
1550795 ATCTTATTTAAATTGAGACAAATATATTT
1 -TCTTGTCTAAATTAAGACAAAAATATTT
*
1550824 TCTTGTCTAGATTAAGGTA-AAAAATAATTT
1 TCTTGTCTAAATTAA-G-ACAAAAAT-ATTT
* * *
1550854 TGTTGTCTTAAATTAAGATAAATATATTT
1 TCTTGTC-TAAATTAAGACAAAAATATTT
* *
1550883 TCTTGTCTAAATTAAGACCAAACATGTTT
1 TCTTGTCTAAATTAAGA-CAAAAATATTT
*
1550912 TCTTGTCTAAATTAATACAAA
1 TCTTGTCTAAATTAAGACAAA
1550933 CATGTAAAAG
Statistics
Matches: 113, Mismatches: 18, Indels: 15
0.77 0.12 0.10
Matches are distributed among these distances:
28 25 0.22
29 44 0.39
30 32 0.28
31 12 0.11
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.43
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAAAATATTT
Found at i:1552158 original size:16 final size:17
Alignment explanation
Indices: 1552137--1552185 Score: 64
Period size: 16 Copynumber: 2.8 Consensus size: 17
1552127 CATTTTGTTC
1552137 TTAATTAATTATTTAG-
1 TTAATTAATTATTTAGA
1552153 TTAATTAATTATTTTTAGA
1 TTAATTAATTA--TTTAGA
*
1552172 TTAATTAATCATTT
1 TTAATTAATTATTT
1552186 GAAATTGAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 11 0.38
17 3 0.10
18 5 0.17
19 10 0.34
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (17 bp):
TTAATTAATTATTTAGA
Found at i:1552177 original size:19 final size:18
Alignment explanation
Indices: 1552137--1552185 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 18
1552127 CATTTTGTTC
1552137 TTAATTAATTA--TTTAG
1 TTAATTAATTATTTTTAG
1552153 TTAATTAATTATTTTTAG
1 TTAATTAATTATTTTTAG
*
1552171 ATTAATTAATCATTT
1 -TTAATTAATTATTT
1552186 GAAATTGAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 11 0.38
18 5 0.17
19 13 0.45
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (18 bp):
TTAATTAATTATTTTTAG
Found at i:1564447 original size:58 final size:56
Alignment explanation
Indices: 1564375--1564493 Score: 168
Period size: 58 Copynumber: 2.1 Consensus size: 56
1564365 CATAGTAATC
* * * *
1564375 CAAAGTAGTTTGCATGTGATATATTTATTTTATGCA-ATTTAATAAATGCTATGCAATG
1 CAAAGTAGTATGCATGTAACAGATTTATTTTATG-AGA-TTAATAAATGCTATGC-ATG
1564433 CAAAGTAGTATGCATGTAACAGATTTATTTTATGAGATTAATAAATGCTATGCATG
1 CAAAGTAGTATGCATGTAACAGATTTATTTTATGAGATTAATAAATGCTATGCATG
1564489 CAAAG
1 CAAAG
1564494 ATGAGACCTT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
56 8 0.14
57 17 0.30
58 31 0.55
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (56 bp):
CAAAGTAGTATGCATGTAACAGATTTATTTTATGAGATTAATAAATGCTATGCATG
Found at i:1567971 original size:16 final size:16
Alignment explanation
Indices: 1567950--1567983 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1567940 TTAGAATAGA
* *
1567950 ATGTGTGTATGTATAT
1 ATGTGTATATATATAT
1567966 ATGTGTATATATATAT
1 ATGTGTATATATATAT
1567982 AT
1 AT
1567984 ATATAGTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (16 bp):
ATGTGTATATATATAT
Found at i:1568859 original size:34 final size:34
Alignment explanation
Indices: 1568816--1568885 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
1568806 GTGATAATAT
*
1568816 TTAGAGACATTGAAG-ATGATGATATGCCCTCACA
1 TTAGAGACATT-AAGAATGATGATATGCCATCACA
*
1568850 TTAGAGACATTAAGAATGATGATATTCCATCACA
1 TTAGAGACATTAAGAATGATGATATGCCATCACA
1568884 TT
1 TT
1568886 GAAGACCTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 3 0.09
34 30 0.91
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (34 bp):
TTAGAGACATTAAGAATGATGATATGCCATCACA
Found at i:1570567 original size:15 final size:15
Alignment explanation
Indices: 1570543--1570573 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1570533 TAATATAAAA
1570543 TTAAACTAAAATAAC
1 TTAAACTAAAATAAC
*
1570558 TTAAATTAAAATAAC
1 TTAAACTAAAATAAC
1570573 T
1 T
1570574 CAACATGATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (15 bp):
TTAAACTAAAATAAC
Found at i:1574378 original size:35 final size:34
Alignment explanation
Indices: 1574295--1574434 Score: 176
Period size: 35 Copynumber: 4.0 Consensus size: 34
1574285 NNNNNNNNNN
1574295 GTTTAATTAAGTTATTGAGCCTAATTGATTAAATTT
1 GTTTAATTAAGTTATTG-GCCTAATTGATTAAA-TT
* *
1574331 GTTTAATCAAGTTATTGGCCTTAATTGATCAAATT
1 GTTTAATTAAGTTATTGGCC-TAATTGATTAAATT
1574366 GTTTAATTAAGTTATTGGGCCTAATT-AGTTAAATT
1 GTTTAATTAAGTTATT-GGCCTAATTGA-TTAAATT
* *
1574401 GTTT-CTTAAGTTATTGGGTCTAATTGATTAAATT
1 GTTTAATTAAGTTATT-GGCCTAATTGATTAAATT
1574435 AAACAATTAA
Statistics
Matches: 94, Mismatches: 6, Indels: 10
0.85 0.05 0.09
Matches are distributed among these distances:
34 27 0.29
35 36 0.38
36 31 0.33
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.46
Consensus pattern (34 bp):
GTTTAATTAAGTTATTGGCCTAATTGATTAAATT
Found at i:1574388 original size:71 final size:69
Alignment explanation
Indices: 1574295--1574434 Score: 185
Period size: 71 Copynumber: 2.0 Consensus size: 69
1574285 NNNNNNNNNN
1574295 GTTTAATTAAGTTATTGAGCCTAATT-GATTAAATTTGTTTAATCAAGTTATTGGC-CTTAATTG
1 GTTTAATTAAGTTATTGAGCCTAATTAG-TTAAA-TTGTTT-ATCAAGTTATTGGCTC-TAATTG
1574358 ATCAAATT
62 ATCAAATT
* * * * *
1574366 GTTTAATTAAGTTATTGGGCCTAATTAGTTAAATTGTTTCTTAAGTTATTGGGTCTAATTGATTA
1 GTTTAATTAAGTTATTGAGCCTAATTAGTTAAATTGTTTATCAAGTTATTGGCTCTAATTGATCA
1574431 AATT
66 AATT
1574435 AAACAATTAA
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
69 24 0.39
70 7 0.11
71 30 0.48
72 1 0.02
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.46
Consensus pattern (69 bp):
GTTTAATTAAGTTATTGAGCCTAATTAGTTAAATTGTTTATCAAGTTATTGGCTCTAATTGATCA
AATT
Found at i:1574447 original size:69 final size:71
Alignment explanation
Indices: 1574299--1574455 Score: 178
Period size: 69 Copynumber: 2.2 Consensus size: 71
1574289 NNNNNNGTTT
*
1574299 AATTAAGTTATTGAGCCTAATTGATTAAATTTGTTTAATCAAGTTATTGGCCTTAATTGATCAAA
1 AATTAAGTTATTGGGCCTAATTGATTAAATTTGTTTAATCAAGTTATTGGCCTTAATTGATCAAA
****
1574364 TTGTTT
66 TTAAAC
* * * *
1574370 AATTAAGTTATTGGGCCTAATT-AGTTAAA-TTGTTT-CTTAAGTTATTGG-GTCTAATTGATTA
1 AATTAAGTTATTGGGCCTAATTGA-TTAAATTTGTTTAATCAAGTTATTGGCCT-TAATTGATCA
1574431 AATTAAAC
64 AATTAAAC
1574439 AATTAAGTTAATTGGGC
1 AATTAAGTT-ATTGGGC
1574456 TTCTTAAAGA
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
68 1 0.01
69 33 0.45
70 14 0.19
71 26 0.35
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (71 bp):
AATTAAGTTATTGGGCCTAATTGATTAAATTTGTTTAATCAAGTTATTGGCCTTAATTGATCAAA
TTAAAC
Found at i:1577124 original size:18 final size:18
Alignment explanation
Indices: 1577101--1577140 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
1577091 AGTTATATTT
1577101 TCTCAAAAAGAT-CTCCTC
1 TCTCAAAAA-ATACTCCTC
1577119 TCTCAAAAAATACTCCTC
1 TCTCAAAAAATACTCCTC
1577137 TCTC
1 TCTC
1577141 TCTATCAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.30
Consensus pattern (18 bp):
TCTCAAAAAATACTCCTC
Found at i:1578214 original size:22 final size:21
Alignment explanation
Indices: 1578176--1578216 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1578166 TTCAAATGAT
* *
1578176 TATTTATTAAAATTTTAAAAA
1 TATTCATTAAAACTTTAAAAA
1578197 TATTCATTAAAAACTTTAAA
1 TATTCATT-AAAACTTTAAA
1578217 TAAAGTAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (21 bp):
TATTCATTAAAACTTTAAAAA
Found at i:1578610 original size:18 final size:18
Alignment explanation
Indices: 1578584--1578620 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1578574 TATGACATTT
*
1578584 TCAATTTTCAAATTAATG
1 TCAACTTTCAAATTAATG
*
1578602 TCAACTTTCAAGTTAATG
1 TCAACTTTCAAATTAATG
1578620 T
1 T
1578621 TACGTGGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (18 bp):
TCAACTTTCAAATTAATG
Found at i:1582065 original size:2 final size:2
Alignment explanation
Indices: 1582058--1582100 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
1582048 ATCTTACATT
* * *
1582058 TA TA TA TA TA TA TA TA TA TA CA CA CA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1582100 T
1 T
1582101 TTTGAATTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1583369 original size:2 final size:2
Alignment explanation
Indices: 1583362--1583390 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1583352 CCCAAATTAT
1583362 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1583391 TCAAGCATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1589599 original size:14 final size:14
Alignment explanation
Indices: 1589580--1589607 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1589570 CCAATTACTA
1589580 GTGTGTGTATATAT
1 GTGTGTGTATATAT
1589594 GTGTGTGTATATAT
1 GTGTGTGTATATAT
1589608 ATATATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (14 bp):
GTGTGTGTATATAT
Found at i:1589682 original size:20 final size:21
Alignment explanation
Indices: 1589657--1589698 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1589647 TATCTTGATG
1589657 ATTTATGT-AGGGATGAAATT
1 ATTTATGTCAGGGATGAAATT
1589677 ATTTATGTCAGGGATGAAATT
1 ATTTATGTCAGGGATGAAATT
1589698 A
1 A
1589699 GAAATAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (21 bp):
ATTTATGTCAGGGATGAAATT
Found at i:1590425 original size:257 final size:257
Alignment explanation
Indices: 1589959--1590468 Score: 690
Period size: 257 Copynumber: 2.0 Consensus size: 257
1589949 ACCCATTAAA
*
1589959 TTAACAATACATAACAATAACTAAACTACAAAATCTTTTATAAATTCAAATATTACTAATATAAA
1 TTAACAATACATAACAATAACTAAACTACAAAATCATTTATAAATTCAAATATTACTAATATAAA
* * *
1590024 AGAAATGCAAAAATTAAAATTGACTTGGGATTTGAGAATTAAAGAAACTTTATCTATGAATTATG
66 ACAAATGCAAAAATTAAAATTGACTTGGGATTGGAGAATTAAAGAAACATTATCTATGAATTATG
* *
1590089 ATAGATTAATAATAAAAGTTAGGAATTTCAAAATTTATATGAGCTAAATGGTTTAATATAATTAT
131 ATAGATTAATAATAAAAGTTAAGAATTTCAAAATTTATATGAGCTAAAGGGTTTAATATAATTAT
* * *
1590154 TTGTTCAAAAAGAAAATATTTTTTTTGACTGATTCAC-CAAAAAGAAAATATGAGAAAACCAT
196 TTGTTCAAAAAGAAAA-AGTTTTTTTGACTGATTCACGAAAAAAGAAAATAGGAGAAAACCAT
* * * *
1590216 TTAAGAATACATAACAATAACTGATCTA-AACTATCATTTATAAATTCAAATATTACTAATATAA
1 TTAACAATACATAACAATAACTAAACTACAA-AATCATTTATAAATTCAAATATTACTAATATAA
*
1590280 AACAAATGTAAAAATTAAAATTGGA-TTGGGATTGGA-AATTAAAGAAACATTA-CTTATGAATT
65 AACAAATGCAAAAATTAAAATT-GACTTGGGATTGGAGAATTAAAGAAACATTATC-TATGAATT
* * * ** *
1590342 ATGATAGATTAATAATAAATA-TTAAGCATTTCAAAATTTATGTGAGTTAAAGGGTTTCGTATAG
128 ATGATAGATTAATAATAAA-AGTTAAGAATTTCAAAATTTATATGAGCTAAAGGGTTTAATATAA
* *** * *
1590406 TTGTTTGATTTGGAAAGAAAAAGTTTTTTTGATTGATTCACGAAAAAAGAGAATAGGAGAAAA
192 TTATTTG-TTCAAAAAGAAAAAGTTTTTTTGACTGATTCACGAAAAAAGAAAATAGGAGAAAA
1590469 GGATTTTAAA
Statistics
Matches: 221, Mismatches: 26, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
255 1 0.00
256 103 0.47
257 115 0.52
258 2 0.01
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.34
Consensus pattern (257 bp):
TTAACAATACATAACAATAACTAAACTACAAAATCATTTATAAATTCAAATATTACTAATATAAA
ACAAATGCAAAAATTAAAATTGACTTGGGATTGGAGAATTAAAGAAACATTATCTATGAATTATG
ATAGATTAATAATAAAAGTTAAGAATTTCAAAATTTATATGAGCTAAAGGGTTTAATATAATTAT
TTGTTCAAAAAGAAAAAGTTTTTTTGACTGATTCACGAAAAAAGAAAATAGGAGAAAACCAT
Found at i:1592211 original size:253 final size:252
Alignment explanation
Indices: 1591757--1592685 Score: 1004
Period size: 252 Copynumber: 3.7 Consensus size: 252
1591747 AGTTTAACAA
* * * * *
1591757 TGTTTCACTTTTATGATTTTTCACATTAATTCTTATAAATTTACATACAA-A-TTTTCAATTACT
1 TGTTTCACCTTTATAATTTTTTACATTAATTCTTATAAGTTTACAT-CAAGATTTTTCAATTGCT
* * * ** *
1591820 AATTTTCACTAAAATTATTTTGTATCCTTATTATTATTCATTCT-TAAATTAAACTTTGTAACTC
65 AATTTTCACTATAATTATTTTGTATACTTATTATTATTCATT-TATAAATTAAAATTCATAAATC
* * *
1591884 ATTAAATACTTTTAG-TTCGAGAATATAAAATTAAATGTATAATTTTCAAATAAATTAAATCTAT
129 ATTAAATACTTTTAGCTT-GAGAATATAAATTTAAATGTTTAATTTTCAAA-AAATTAAATATAT
* * *
1591948 CTTGACTTAATGAACTTTTTATGATAACTCTCACACATTTACATCAATATTTTAATAATGCT
192 TTTGACTTAATGAACTTGTTAT-ATAAATCTCACACATTTACATCAATATTTTAATAATGCT
* * *
1592010 TGTTTCACCTTTATAATTTTTGATC-TTAATTCTTATAAGTTAACATCAATG-TTTTTTAATTGC
1 TGTTTCACCTTTATAATTTTTTA-CATTAATTCTTATAAGTTTACATCAA-GATTTTTCAATTGC
* * * *
1592073 TAATTTTCACGATAACTATTTT-TATACTTATTATTATTCATTTACAAATTAAAATTTATAAATC
64 TAATTTTCACTATAATTATTTTGTATACTTATTATTATTCATTTATAAATTAAAATTCATAAATC
* * * *
1592137 GTCAAATACTTTTAGCTTGAGAATATAAATTTAAATGTTTAATTTTCATAAAAATTAGATTTATT
129 ATTAAATACTTTTAGCTTGAGAATATAAATTTAAATGTTTAATTTTCA-AAAAATTAAATATATT
* **
1592202 TTAACTTAATTG-ACTTGTTATATCAAATCTCACACATTTACATCAATATTTTAA-AAAACT
193 TTGACTTAA-TGAACTTGTTATAT-AAATCTCACACATTTACATCAATATTTTAATAATGCT
* ** *
1592262 TGTTCCACCTTTATAATTTTTTACATTAATTCTTAT-AGTTTTATGTCAAGATTTTTCAATTGTT
1 TGTTTCACCTTTATAATTTTTTACATTAATTCTTATAAG-TTTACATCAAGATTTTTCAATTGCT
* * *
1592326 AATTTTCACTATAATTATTTT-TATATTTATTATTATTCATTTATAAATTAAAATTCACAAA-GA
65 AATTTTCACTATAATTATTTTGTATACTTATTATTATTCATTTATAAATTAAAATTCATAAATCA
* * * *
1592389 GTTAAATACTTTTAGC-TGAAAATATAAATTTAAATGTTTGATTTTCACAAAATTTATATATATT
130 -TTAAATACTTTTAGCTTGAGAATATAAATTTAAATGTTTAATTTTCA-AAAAATTAAATATATT
* * * * * * **
1592453 GTGACTTAAT-AGACTTGCTACATTAAATCTTATACATTTACGTCAATATTAAAATAATGCT
193 TTGACTTAATGA-ACTTGTTATA-TAAATCTCACACATTTACATCAATATTTTAATAATGCT
** ** * * * * * *
1592514 TGTTTCATTTTTATAATTTTTTATGTTAATTCTTCTAGGTTTATATTAAGATATTTCAATTGATA
1 TGTTTCACCTTTATAATTTTTTACATTAATTCTTATAAGTTTACATCAAGATTTTTCAATTGCTA
* * * * *
1592579 ATTTTCACAATAATTATTTTGTTTCCTTATTAGTATTTTTATTTATAAATTAAAATTCATAAATC
66 ATTTTCACTATAATTATTTTGTATACTTATTA-T-TATTCATTTATAAATTAAAATTCATAAATC
* *
1592644 ATTAAATACTTTTAGCTTGAGAATATAAATATAAATGCTTAA
129 ATTAAATACTTTTAGCTTGAGAATATAAATTTAAATGTTTAA
1592686 ACAAAATAAT
Statistics
Matches: 570, Mismatches: 83, Indels: 43
0.82 0.12 0.06
Matches are distributed among these distances:
250 1 0.00
251 86 0.15
252 205 0.36
253 180 0.32
254 36 0.06
255 40 0.07
256 22 0.04
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (252 bp):
TGTTTCACCTTTATAATTTTTTACATTAATTCTTATAAGTTTACATCAAGATTTTTCAATTGCTA
ATTTTCACTATAATTATTTTGTATACTTATTATTATTCATTTATAAATTAAAATTCATAAATCAT
TAAATACTTTTAGCTTGAGAATATAAATTTAAATGTTTAATTTTCAAAAAATTAAATATATTTTG
ACTTAATGAACTTGTTATATAAATCTCACACATTTACATCAATATTTTAATAATGCT
Found at i:1592529 original size:504 final size:505
Alignment explanation
Indices: 1591710--1592685 Score: 1141
Period size: 504 Copynumber: 1.9 Consensus size: 505
1591700 CTTATTACGA
* * * * * * *
1591710 TGACTAGTTATATTAACTATCACACATTTACGTAAATAGTTTAACAATGTTTCACTTTTATGATT
1 TGACTAGTTATATCAAATATCACACATTTACATAAATAGTTTAAAAATGTTCCACCTTTATAATT
1591775 TTTCACATTAATTCTTATAAATTTACATACAAATTTTCAATTACTAATTTTCACTAAAATTATTT
66 TTTCACATTAATTCTTATAAATTTACATACAAATTTTCAATTACTAATTTTCACTAAAATTATTT
* * *** * * *
1591840 TGTATCCTTATTATTATTCATTCTTAAATTAAACTTTGTAACTCATTAAATACTTTTAGTTCGAG
131 TGTATACTTATTATTATTCATTCTTAAATTAAAATTCACAACACATTAAATACTTTTAGCTCGAA
* **
1591905 AATATAAAATTAAATGTATAATTTTCAAATAAATTAAATCTATCTTGACTTAATGAACTTTTTAT
196 AATATAAAATTAAATGTATAATTTTCAAATAAATTAAATATATCTTGACTTAATGAACTTGCTAT
* * **
1591970 GATAACTCTCACACATTTACATCAATATTTTAATAATGCTTGTTTCACCTTTATAATTTTTGATC
261 CATAAATCTCACACATTTACATCAATATTAAAATAATGCTTGTTTCACCTTTATAATTTTTGATC
* * * *
1592035 TTAATTCTTATAAGTTAACATCAATG-TTTTTTAATTGCTAATTTTCACGATAACTATTTT-TAT
326 TTAATTCTTATAAGTTAACATCAA-GATATTTCAATTGATAATTTTCACAATAACTATTTTGTAT
* *
1592098 ACTTATTA-T-TATTCATTTACAAATTAAAATTTATAAATCGTCAAATACTTTTAGCTTGAGAAT
390 ACTTATTAGTATATTCATTTACAAATTAAAATTCATAAATCATCAAATACTTTTAGCTTGAGAAT
* *
1592161 ATAAATTTAAATGTTTAATTTTCATAAAAATTAGATTTATTTTAACTTAAT
455 ATAAATATAAATGCTTAATTTTCATAAAAATTAGATTTATTTTAACTTAAT
* * * *
1592212 TGACTTGTTATATCAAATCTCACACATTTACATCAATATTTTAAAAAACTTGTTCCACCTTTATA
1 TGACTAGTTATATCAAATATCACACATTTACATAAATAGTTT-AAAAA--TGTTCCACCTTTATA
* ** ** ** *
1592277 ATTTTTTACATTAATTCTTATAGTTTTATGT-CAAGATTTTTCAATTGTTAATTTTCACTATAAT
63 ATTTTTCACATTAATTCTTATAAATTTACATACAA-A-TTTTCAATTACTAATTTTCACTAAAAT
* *
1592341 TATTTT-TATATTTATTATTATTCATT-TATAAATTAAAATTCACAA-AGAGTTAAATACTTTTA
126 TATTTTGTATACTTATTATTATTCATTCT-TAAATTAAAATTCACAACACA-TTAAATACTTTTA
* * * * *
1592403 GCT-GAAAATATAAATTTAAATGTTTGATTTTCACAA-AATTTATATATAT-TGTGACTTAAT-A
189 GCTCGAAAATATAAAATTAAATGTATAATTTTCA-AATAAATTAAATATATCT-TGACTTAATGA
* * * **
1592464 GACTTGCTA-CATTAAATCTTATACATTTACGTCAATATTAAAATAATGCTTGTTTCATTTTTAT
252 -ACTTGCTATCA-TAAATCTCACACATTTACATCAATATTAAAATAATGCTTGTTTCACCTTTAT
* * * * * * * *
1592528 AATTTTTTATGTTAATTCTTCTAGGTTTATATTAAGATATTTCAATTGATAATTTTCACAATAAT
315 AATTTTTGATCTTAATTCTTATAAGTTAACATCAAGATATTTCAATTGATAATTTTCACAATAAC
* * * * * *
1592593 TATTTTGTTTCCTTATTAGTATTTTTATTTATAAATTAAAATTCATAAATCATTAAATACTTTTA
380 TATTTTGTATACTTATTAGTATATTCATTTACAAATTAAAATTCATAAATCATCAAATACTTTTA
1592658 GCTTGAGAATATAAATATAAATGCTTAA
445 GCTTGAGAATATAAATATAAATGCTTAA
1592686 ACAAAATAAT
Statistics
Matches: 391, Mismatches: 68, Indels: 25
0.81 0.14 0.05
Matches are distributed among these distances:
502 35 0.09
503 8 0.02
504 157 0.40
505 96 0.25
506 31 0.08
507 64 0.16
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (505 bp):
TGACTAGTTATATCAAATATCACACATTTACATAAATAGTTTAAAAATGTTCCACCTTTATAATT
TTTCACATTAATTCTTATAAATTTACATACAAATTTTCAATTACTAATTTTCACTAAAATTATTT
TGTATACTTATTATTATTCATTCTTAAATTAAAATTCACAACACATTAAATACTTTTAGCTCGAA
AATATAAAATTAAATGTATAATTTTCAAATAAATTAAATATATCTTGACTTAATGAACTTGCTAT
CATAAATCTCACACATTTACATCAATATTAAAATAATGCTTGTTTCACCTTTATAATTTTTGATC
TTAATTCTTATAAGTTAACATCAAGATATTTCAATTGATAATTTTCACAATAACTATTTTGTATA
CTTATTAGTATATTCATTTACAAATTAAAATTCATAAATCATCAAATACTTTTAGCTTGAGAATA
TAAATATAAATGCTTAATTTTCATAAAAATTAGATTTATTTTAACTTAAT
Done.