Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold643.1
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: 856865
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.33
Warning! 20449 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:314240 original size:14 final size:15
Alignment explanation
Indices: 314221--314249 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
314211 TCACGAAACT
314221 TTCACACAT-ATAAA
1 TTCACACATAATAAA
314235 TTCACACATAATAAA
1 TTCACACATAATAAA
314250 CACATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:316515 original size:36 final size:36
Alignment explanation
Indices: 316475--316583 Score: 191
Period size: 36 Copynumber: 3.0 Consensus size: 36
316465 GCTAAGCTAC
*
316475 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
* *
316511 CACTTATCACTTTTTCGCTTGATCAGATAAATGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
316547 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
316583 C
1 C
316584 TAAAGTTACC
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 68 1.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (36 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
Found at i:316598 original size:46 final size:46
Alignment explanation
Indices: 316547--316665 Score: 202
Period size: 46 Copynumber: 2.6 Consensus size: 46
316537 ATAAATGTAG
* * *
316547 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGTTAC
1 CACTTATCACTTTATCTCTTGATCAGATAAGTGTAGCTAAAGCTAC
*
316593 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTATCTCTTGATCAGATAAGTGTAGCTAAAGCTAC
316639 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTATCTCTTGATCAGA
316666 AGTACTCAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 69 1.00
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.37
Consensus pattern (46 bp):
CACTTATCACTTTATCTCTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:318337 original size:24 final size:24
Alignment explanation
Indices: 318289--318335 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
318279 ACTGGTCATA
*
318289 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGAATATTTG
*
318313 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAG-GAATATT
318336 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.38, T:0.26
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGAATATTTG
Found at i:319378 original size:27 final size:27
Alignment explanation
Indices: 319338--319693 Score: 351
Period size: 27 Copynumber: 13.2 Consensus size: 27
319328 AGAGGTCGAT
319338 AAATGA-TCGAAATACCCCCATAGGGTA
1 AAATGACT-GAAATACCCCCATAGGGTA
* * * *
319365 AATTGACTAAAATAACCCCGTAGGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
* *
319392 AAATAACTGAAATACCCCCATAAGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
** *
319419 AAATGACCAAAATACCCCTATAGGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
** * *
319446 AAATGACCAAAATACCCTCATAGTGTA
1 AAATGACTGAAATACCCCCATAGGGTA
* *
319473 GAATGACTGAAATACCCCAATAGGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
* * *
319500 AAATAACCGAAATACCCCTATAGGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
* ***
319527 AAAT-AATCGAAATA-CCCCATAAAATA
1 AAATGACT-GAAATACCCCCATAGGGTA
* *
319553 AAATGACTGAAATACCTCCATAAGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
* *
319580 AAATGACCGAAATACCCCCATAAGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
* * * *
319607 GAATGACCGAAATACCCTCATAAGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
* * *
319634 GAATGA-TCGAAATATCCCCATAAGGTA
1 AAATGACT-GAAATACCCCCATAGGGTA
*
319661 AAATGACTGAAATACCCCCATAGAGTA
1 AAATGACTGAAATACCCCCATAGGGTA
319688 AAATGA
1 AAATGA
319694 TTGTTATACT
Statistics
Matches: 274, Mismatches: 49, Indels: 12
0.82 0.15 0.04
Matches are distributed among these distances:
26 19 0.07
27 253 0.92
28 2 0.01
ACGTcount: A:0.45, C:0.21, G:0.15, T:0.19
Consensus pattern (27 bp):
AAATGACTGAAATACCCCCATAGGGTA
Found at i:319482 original size:81 final size:79
Alignment explanation
Indices: 319338--319693 Score: 408
Period size: 81 Copynumber: 4.4 Consensus size: 79
319328 AGAGGTCGAT
* * * * *
319338 AAATGATCGAAATACCCCCATAGGGTAAATTGACTAAAATAACCCCGTAGGGTAAAATAACTGAA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAAT-ACCCCATA-GGTAAAATGACTGAA
319403 ATACCCCCATAAGGTA
64 ATACCCCCATAAGGTA
* * *
319419 AAATGACCAAAATACCCCTATAGGGTAAAATGACCAAAATACCCTCATAGTGTAGAATGACTGAA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCC-CATAG-GTAAAATGACTGAA
* *
319484 ATACCCCAATAGGGTA
64 ATACCCCCATAAGGTA
* * * * * **
319500 AAATAACCGAAATACCCCTATAGGGTAAAATAATCGAAATACCCCATAAAATAAAATGACTGAAA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCAT-AGGTAAAATGACTGAAA
*
319565 TACCTCCATAAGGTA
65 TACCCCCATAAGGTA
* * * *
319580 AAATGACCGAAATACCCCCATAAGGTAGAATGACCGAAATACCCTCATAAGGTAGAATGA-TCGA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCC-CAT-AGGTAAAATGACT-GA
*
319644 AATATCCCCATAAGGTA
63 AATACCCCCATAAGGTA
* *
319661 AAATGACTGAAATACCCCCATAGAGTAAAATGA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGA
319694 TTGTTATACT
Statistics
Matches: 234, Mismatches: 36, Indels: 10
0.84 0.13 0.04
Matches are distributed among these distances:
80 72 0.31
81 162 0.69
ACGTcount: A:0.45, C:0.21, G:0.15, T:0.19
Consensus pattern (79 bp):
AAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCATAGGTAAAATGACTGAAAT
ACCCCCATAAGGTA
Found at i:319964 original size:26 final size:26
Alignment explanation
Indices: 319928--320004 Score: 102
Period size: 26 Copynumber: 3.0 Consensus size: 26
319918 TTTACCACAT
*
319928 ATACTGTTACTGGTAGCTTTGCTGCG
1 ATACTGATACTGGTAGCTTTGCTGCG
* *
319954 ATACTGATACTGGCAGCTCTGCTGCG
1 ATACTGATACTGGTAGCTTTGCTGCG
*
319980 ATGCT-ATTACTGGTAGCTTTGCTGC
1 ATACTGA-TACTGGTAGCTTTGCTGC
320005 AATATTTGTG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
25 1 0.02
26 43 0.98
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (26 bp):
ATACTGATACTGGTAGCTTTGCTGCG
Found at i:320145 original size:28 final size:28
Alignment explanation
Indices: 320097--320190 Score: 120
Period size: 28 Copynumber: 3.4 Consensus size: 28
320087 TACTGCACTG
*
320097 CACTGCTACTGTATTGGGCTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
* *
320125 CATTGATT-CTGTATTGGGCTAAAGCCCA
1 CACTG-TTACTGTATTGGGCTAAGGCCCA
* *
320153 CACTGTTACTATATTGGGCTAAGGCCTA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
320181 CACTG-TACTG
1 CACTGTTACTG
320191 CCACTGAATA
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
27 6 0.11
28 49 0.88
29 1 0.02
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.30
Consensus pattern (28 bp):
CACTGTTACTGTATTGGGCTAAGGCCCA
Found at i:320992 original size:55 final size:55
Alignment explanation
Indices: 320932--321037 Score: 176
Period size: 55 Copynumber: 1.9 Consensus size: 55
320922 CTTAAACTGA
* *
320932 AATACACTGAAAGACTACTATAGATAGTAGGACTGTACTGAAACTCATTAGGTAG
1 AATACACTGAAAGACTACTATAGATAGTAGGACTATACTAAAACTCATTAGGTAG
* *
320987 AATACACTGAGAGACTACTATAGATAGTAGGACTATACTAAAACTCTTTAG
1 AATACACTGAAAGACTACTATAGATAGTAGGACTATACTAAAACTCATTAG
321038 TGAGAGTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 47 1.00
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (55 bp):
AATACACTGAAAGACTACTATAGATAGTAGGACTATACTAAAACTCATTAGGTAG
Found at i:321051 original size:55 final size:55
Alignment explanation
Indices: 320932--321053 Score: 165
Period size: 55 Copynumber: 2.2 Consensus size: 55
320922 CTTAAACTGA
* * *
320932 AATACACTGAAAGACTACTATAGATAGTAGGACTGTACTGAAACTCATTAGGTAG
1 AATAAACTGAAAGACTACTATAGATAGTAGGACTATACTAAAACTCATTAGGTAG
* * *
320987 AATACACTGAGAGACTACTATAGATAGTAGGACTATACTAAAACTCTTTA-GTGAG
1 AATAAACTGAAAGACTACTATAGATAGTAGGACTATACTAAAACTCATTAGGT-AG
*
321042 AGTAAACTGAAA
1 AATAAACTGAAA
321054 CTGTAGGAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 2 0.03
55 57 0.97
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (55 bp):
AATAAACTGAAAGACTACTATAGATAGTAGGACTATACTAAAACTCATTAGGTAG
Found at i:322882 original size:27 final size:27
Alignment explanation
Indices: 322862--323209 Score: 320
Period size: 27 Copynumber: 12.9 Consensus size: 27
322852 TAAAATAATT
** *
322862 GAAATACCCCTGTAGGGTAAAATGATC
1 GAAATACCCCCATAGGGTAAAATGACC
* * *
322889 GAAATACCACCGTATGGTAAAATGACC
1 GAAATACCCCCATAGGGTAAAATGACC
* * * *
322916 AAAATACCCTCATAGGGTAAAATAACT
1 GAAATACCCCCATAGGGTAAAATGACC
* *** **
322943 GAAATACCCTCAATAAAATAAAATGATT
1 GAAATACCC-CCATAGGGTAAAATGACC
** * * *
322971 GAAATACCCTTATCGGGTAGAATAACC
1 GAAATACCCCCATAGGGTAAAATGACC
* * *
322998 AAAATACCCCCATAGAGTAAAATGACT
1 GAAATACCCCCATAGGGTAAAATGACC
* * * * * *
323025 AAAATACCCCTATAAGATAGAATGATC
1 GAAATACCCCCATAGGGTAAAATGACC
* *
323052 GAAATACCCCCCATAAGGTAAAATGACA
1 GAAATA-CCCCCATAGGGTAAAATGACC
*
323080 GAAATACCCCCATAGGGTAAAATGATC
1 GAAATACCCCCATAGGGTAAAATGACC
*
323107 GAAATACCCCCATAGGGTAAAATGACT
1 GAAATACCCCCATAGGGTAAAATGACC
* *
323134 GAAATACCCCCATAGGGTAAAATAACT
1 GAAATACCCCCATAGGGTAAAATGACC
* *
323161 GAAATACCCCC-TAGGATAAAATGATC
1 GAAATACCCCCATAGGGTAAAATGACC
*
323187 GAAATACCCCCATAAGGTAAAAT
1 GAAATACCCCCATAGGGTAAAAT
323210 AACTATTATA
Statistics
Matches: 256, Mismatches: 62, Indels: 6
0.79 0.19 0.02
Matches are distributed among these distances:
26 22 0.09
27 192 0.75
28 42 0.16
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.20
Consensus pattern (27 bp):
GAAATACCCCCATAGGGTAAAATGACC
Found at i:323056 original size:109 final size:109
Alignment explanation
Indices: 322851--323209 Score: 370
Period size: 109 Copynumber: 3.3 Consensus size: 109
322841 CCCTTACAGG
* * * * *
322851 ATAAAATAATTGAAATACCCCTGTAGGGTAAAATGATCGAAATACCACCGTATGGTAAAATGACC
1 ATAAAATGATTGAAATACCCCTATAGGGTAAAATGATCGAAATACCCCCATA-GGTAAAATGACT
* * *
322916 AAAATA-CCCTCATAGGGTAAAATAACTGAAATACCCTCAATAAA
65 AAAATACCCCTCATAAGATAAAATAACTGAAATACCCCCAATAAA
* * * * * *
322960 ATAAAATGATTGAAATACCCTTATCGGGTAGAATAACCAAAATACCCCCATAGAGTAAAATGACT
1 ATAAAATGATTGAAATACCCCTATAGGGTAAAATGATCGAAATACCCCCATAG-GTAAAATGACT
* * * *
323025 AAAATACCCCT-ATAAGATAGAATGA-TCGAAATACCCCCCATAAG
65 AAAATACCCCTCATAAGATAAAATAACT-GAAATACCCCCAATAAA
* ** *
323069 GTAAAATGACAGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATGACT
1 ATAAAATGATTGAAATACCCCTATAGGGTAAAATGATCGAAATACCCCCATA-GGTAAAATGACT
* * * **
323134 GAAATACCCC-CATAGGGTAAAATAACTGAAATACCCCC--TAGG
65 AAAATACCCCTCATAAGATAAAATAACTGAAATACCCCCAATAAA
* * *
323176 ATAAAATGATCGAAATACCCCCATAAGGTAAAAT
1 ATAAAATGATTGAAATACCCCTATAGGGTAAAAT
323210 AACTATTATA
Statistics
Matches: 206, Mismatches: 38, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
107 33 0.16
108 2 0.01
109 165 0.80
110 6 0.03
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.20
Consensus pattern (109 bp):
ATAAAATGATTGAAATACCCCTATAGGGTAAAATGATCGAAATACCCCCATAGGTAAAATGACTA
AAATACCCCTCATAAGATAAAATAACTGAAATACCCCCAATAAA
Found at i:323513 original size:23 final size:24
Alignment explanation
Indices: 323464--323513 Score: 57
Period size: 26 Copynumber: 2.0 Consensus size: 24
323454 GTGATATTGA
*
323464 TACTGGCAGCTTTGTTGCGATGCTAT
1 TACTGGCAGCTTTGCTGCGA--CTAT
*
323490 TACTGGTAGCTTTGCTGCGA-TAT
1 TACTGGCAGCTTTGCTGCGACTAT
323513 T
1 T
323514 GGTGTGTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 4 0.18
26 18 0.82
ACGTcount: A:0.16, C:0.18, G:0.26, T:0.40
Consensus pattern (24 bp):
TACTGGCAGCTTTGCTGCGACTAT
Found at i:323668 original size:28 final size:28
Alignment explanation
Indices: 323616--323707 Score: 116
Period size: 28 Copynumber: 3.3 Consensus size: 28
323606 TGCACTGCAT
* *
323616 TGTTACTGTATTGGGCAAAGACCCACAC
1 TGTTACTGTATTGGGCTAAGGCCCACAC
*
323644 TGATT-TTGTATTGGGCTAAGGCCCACAC
1 TG-TTACTGTATTGGGCTAAGGCCCACAC
* *
323672 TGTTACTGTATTAGGCTAAGGCCCAAAC
1 TGTTACTGTATTGGGCTAAGGCCCACAC
323700 TG-TACTGT
1 TGTTACTGT
323708 CACTGAATAG
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
27 8 0.14
28 46 0.82
29 2 0.04
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (28 bp):
TGTTACTGTATTGGGCTAAGGCCCACAC
Found at i:325376 original size:23 final size:23
Alignment explanation
Indices: 325345--325420 Score: 118
Period size: 23 Copynumber: 3.3 Consensus size: 23
325335 GCACATAAGT
325345 GCTA-CACTGATATGTAGCCGAA
1 GCTACCACTGATATGTAGCCGAA
*
325367 GCTACCACTGATATGTAGCCGTA
1 GCTACCACTGATATGTAGCCGAA
* *
325390 GCTACCACTGAAATGTAGCTGAA
1 GCTACCACTGATATGTAGCCGAA
325413 GCTACCAC
1 GCTACCAC
325421 AGATCAATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 4 0.08
23 45 0.92
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.22
Consensus pattern (23 bp):
GCTACCACTGATATGTAGCCGAA
Found at i:333920 original size:30 final size:30
Alignment explanation
Indices: 333886--333945 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
333876 GAATTGGATC
333886 AAATCAAAATTTCATGTATAAAATTACACA
1 AAATCAAAATTTCATGTATAAAATTACACA
* *
333916 AAATCAAATTTTCATGTATACAATTACACA
1 AAATCAAAATTTCATGTATAAAATTACACA
333946 TATTAAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.50, C:0.15, G:0.03, T:0.32
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAAATTACACA
Found at i:335021 original size:30 final size:32
Alignment explanation
Indices: 334944--335008 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
334934 ACAGGTCGTT
334944 ACCATCATTATTTTAGCAGGTCGCACTCTTTC
1 ACCATCATTATTTTAGCAGGTCGCACTCTTTC
* *
334976 NACCATCATTATTTTAGCAGGTCTCATTCTTTC
1 -ACCATCATTATTTTAGCAGGTCGCACTCTTTC
335009 CCTGTTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.22, C:0.26, G:0.11, T:0.40
Consensus pattern (32 bp):
ACCATCATTATTTTAGCAGGTCGCACTCTTTC
Found at i:335248 original size:50 final size:50
Alignment explanation
Indices: 335173--335274 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
335163 TATGGTTCTA
335173 TTACTTGTTTATTCTATTGCATGTTTGATTGATTCTGTTGATAAGGCACT
1 TTACTTGTTTATTCTATTGCATGTTTGATTGATTCTGTTGATAAGGCACT
335223 TTACTTGTTTATTCTATTGCATGTTTGATTGATTCTGTTGATAAGGCACT
1 TTACTTGTTTATTCTATTGCATGTTTGATTGATTCTGTTGATAAGGCACT
335273 TT
1 TT
335275 GGTTTCCCTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.20, C:0.12, G:0.18, T:0.51
Consensus pattern (50 bp):
TTACTTGTTTATTCTATTGCATGTTTGATTGATTCTGTTGATAAGGCACT
Found at i:339361 original size:49 final size:49
Alignment explanation
Indices: 339304--339407 Score: 172
Period size: 49 Copynumber: 2.1 Consensus size: 49
339294 TCATGTGTTA
* * *
339304 TAATTTTATAAAGTGTTGATCTTTTGATTCATGATATTGAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
*
339353 TAATTTTATAAAGTTTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
339402 TAATTT
1 TAATTT
339408 GTTTTTTTCT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.32, C:0.08, G:0.09, T:0.52
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
Found at i:340830 original size:21 final size:21
Alignment explanation
Indices: 340789--340831 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
340779 AATAAAGTAG
*
340789 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
340810 ATTATATATTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
340831 A
1 A
340832 AATTCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:340896 original size:28 final size:28
Alignment explanation
Indices: 340860--341060 Score: 83
Period size: 28 Copynumber: 6.9 Consensus size: 28
340850 TAATATTAAG
*
340860 AATTTTATTAAATTATATATTTTTATTA
1 AATTATATTAAATTATATATTTTTATTA
* * *
340888 AATTATATTTAATAATA-ATTATT-TTA
1 AATTATATTAAATTATATATTTTTATTA
*
340914 AATTATATT---TTATAGTATTATATATTA
1 AATTATATTAAATTATA-TATT-TTTATTA
* * * *
340941 TGATTTTAGTAAATTCATATAAGAATATTAATATTAA
1 -AATTATATTAAATT-ATAT----AT-TT-TTATT-A
*
340978 GAATTTTATTAAATTATATATTTTTATTA
1 -AATTATATTAAATTATATATTTTTATTA
* * * *
341007 AATTATATTTAA-TA-ATAATTATGTTA
1 AATTATATTAAATTATATATTTTTATTA
* *
341033 AAATATGATTAAATTATTTATTATTTAT
1 AATTAT-ATTAAATTATATATT-TTTAT
341061 ATTAATAATC
Statistics
Matches: 128, Mismatches: 25, Indels: 38
0.67 0.13 0.20
Matches are distributed among these distances:
23 4 0.03
25 3 0.02
26 27 0.21
27 15 0.12
28 32 0.25
29 4 0.03
30 7 0.05
31 5 0.04
32 5 0.04
35 3 0.02
36 10 0.08
37 13 0.10
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (28 bp):
AATTATATTAAATTATATATTTTTATTA
Found at i:340919 original size:119 final size:119
Alignment explanation
Indices: 340796--341034 Score: 453
Period size: 119 Copynumber: 2.0 Consensus size: 119
340786 TAGATTATAT
340796 ATTAT-TTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATA-TTAATATTAAG
*
340860 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
65 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
340915 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTAATATTAAGA
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTAATATTAAGA
340980 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
66 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
341034 A
1 A
341035 ATATGATTAA
Statistics
Matches: 118, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
119 71 0.60
120 47 0.40
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.52
Consensus pattern (119 bp):
ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTAATATTAAGA
ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
Found at i:340989 original size:18 final size:18
Alignment explanation
Indices: 340966--341013 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
340956 CATATAAGAA
340966 TATTAATATTA-AGAATTT
1 TATTAA-ATTATAGAATTT
* *
340984 TATTAAATTATATATTTT
1 TATTAAATTATAGAATTT
341002 TATTAAATTATA
1 TATTAAATTATA
341014 TTTAATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 4 0.15
18 23 0.85
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
TATTAAATTATAGAATTT
Found at i:342977 original size:18 final size:20
Alignment explanation
Indices: 342942--342982 Score: 50
Period size: 18 Copynumber: 2.1 Consensus size: 20
342932 ATATTATTTT
*
342942 AAAATATATATAATACATCA
1 AAAATATATATAAAACATCA
*
342962 AAAATAT-TA-AAAACATTA
1 AAAATATATATAAAACATCA
342980 AAA
1 AAA
342983 TAAATGTTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 10 0.53
19 2 0.11
20 7 0.37
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (20 bp):
AAAATATATATAAAACATCA
Found at i:346215 original size:31 final size:33
Alignment explanation
Indices: 346172--346235 Score: 114
Period size: 31 Copynumber: 2.0 Consensus size: 33
346162 GAGTCTCTTT
346172 TTTTTCCCTAATTTGGTACCTAAACTTG-AAAA
1 TTTTTCCCTAATTTGGTACCTAAACTTGTAAAA
346204 TTTTT-CCTAATTTGGTACCTAAACTTGTAAAA
1 TTTTTCCCTAATTTGGTACCTAAACTTGTAAAA
346236 CATATACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 22 0.71
32 9 0.29
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.42
Consensus pattern (33 bp):
TTTTTCCCTAATTTGGTACCTAAACTTGTAAAA
Found at i:347144 original size:20 final size:19
Alignment explanation
Indices: 347119--347160 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
347109 AAATAATTTC
*
347119 TAGAAAATATTAATTTTTTT
1 TAGAAAA-ATTAATATTTTT
*
347139 TAGAAAAGTTAATATTTTT
1 TAGAAAAATTAATATTTTT
347158 TAG
1 TAG
347161 TGTTTGGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (19 bp):
TAGAAAAATTAATATTTTT
Found at i:348980 original size:19 final size:18
Alignment explanation
Indices: 348940--348980 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
348930 ATTGCCTCTA
348940 AATAATAACAAAATTAAC
1 AATAATAACAAAATTAAC
348958 AATAA-AACAAAAGTTATAC
1 AATAATAACAAAA-TTA-AC
348977 AATA
1 AATA
348981 TCCAAACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.33
18 8 0.38
19 6 0.29
ACGTcount: A:0.66, C:0.10, G:0.02, T:0.22
Consensus pattern (18 bp):
AATAATAACAAAATTAAC
Found at i:358106 original size:23 final size:24
Alignment explanation
Indices: 358076--358141 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
358066 GCGCATTCTA
* *
358076 TTTGGCCTGTGTGGTGTA-TTTTG
1 TTTGGCCTTTGTGGTGTACTTATG
*
358099 TTTGGCCTTTGTGGCGTACTTATG
1 TTTGGCCTTTGTGGTGTACTTATG
*
358123 TTTGGCCTTTGTGATGTAC
1 TTTGGCCTTTGTGGTGTAC
358142 CCTATATGTC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 16 0.43
24 21 0.57
ACGTcount: A:0.08, C:0.14, G:0.30, T:0.48
Consensus pattern (24 bp):
TTTGGCCTTTGTGGTGTACTTATG
Found at i:358129 original size:24 final size:24
Alignment explanation
Indices: 358076--358190 Score: 90
Period size: 23 Copynumber: 4.8 Consensus size: 24
358066 GCGCATTCTA
* * *
358076 TTTGGCCTGTGTGGTGTA-TTTTG
1 TTTGGCCTTTGTGGCGTACTTATG
358099 TTTGGCCTTTGTGGCGTACTTATG
1 TTTGGCCTTTGTGGCGTACTTATG
** * *
358123 TTTGGCCTTTGTGATGTACCCTATA
1 TTTGGCCTTTGTGGCGTA-CTTATG
* * * * *
358148 TGTCGTCTTTGTGGCATA-TTCTG
1 TTTGGCCTTTGTGGCGTACTTATG
*
358171 TTGGGCCTTTGTGGCGTACT
1 TTTGGCCTTTGTGGCGTACT
358191 CTGCTAAGTT
Statistics
Matches: 68, Mismatches: 21, Indels: 5
0.72 0.22 0.05
Matches are distributed among these distances:
23 31 0.46
24 21 0.31
25 16 0.24
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (24 bp):
TTTGGCCTTTGTGGCGTACTTATG
Found at i:366026 original size:27 final size:27
Alignment explanation
Indices: 365996--366060 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
365986 ACAACAATTC
**
365996 CAACAGCAACAACTCCTCCAACAACAA
1 CAACAGCAACAACAACTCCAACAACAA
** *
366023 CAACAGCAACTGCAACTTCAACAACAA
1 CAACAGCAACAACAACTCCAACAACAA
*
366050 CAAGAGCAACA
1 CAACAGCAACA
366061 TGAACAACAG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.49, C:0.35, G:0.08, T:0.08
Consensus pattern (27 bp):
CAACAGCAACAACAACTCCAACAACAA
Found at i:366058 original size:21 final size:21
Alignment explanation
Indices: 366014--366069 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
366004 ACAACTCCTC
* * *
366014 CAACAACAACAACAGCAACTG
1 CAACATCAACAACAACAACAG
* *
366035 CAACTTCAACAACAACAAGAG
1 CAACATCAACAACAACAACAG
*
366056 CAACATGAACAACA
1 CAACATCAACAACA
366070 GTTACAGTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.54, C:0.30, G:0.09, T:0.07
Consensus pattern (21 bp):
CAACATCAACAACAACAACAG
Found at i:368740 original size:23 final size:24
Alignment explanation
Indices: 368693--368738 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
368683 GAAAAATATT
368693 AAATATATATATTTTTTATTTTTA
1 AAATATATATATTTTTTATTTTTA
368717 AAATATA-ATAATTTTTTATTTT
1 AAATATATAT-ATTTTTTATTTT
368739 AAGTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
AAATATATATATTTTTTATTTTTA
Found at i:368849 original size:9 final size:9
Alignment explanation
Indices: 368835--368862 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
368825 TTTTGTTACA
368835 ACAATTAAT
1 ACAATTAAT
368844 ACAATTAAT
1 ACAATTAAT
368853 ACAATTAAT
1 ACAATTAAT
368862 A
1 A
368863 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:368884 original size:68 final size:68
Alignment explanation
Indices: 368805--369082 Score: 515
Period size: 68 Copynumber: 4.1 Consensus size: 68
368795 TCAAGTTTGT
*
368805 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
368870 AAA
66 AAA
368873 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
368938 AAA
66 AAA
*
368941 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
369006 AAA
66 AAA
369009 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
369072 AAT
66 AAA
369075 TTTACTAA
1 TTTACTAA
369083 CAATTAATTT
Statistics
Matches: 207, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
66 27 0.13
67 1 0.00
68 179 0.86
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:368915 original size:9 final size:9
Alignment explanation
Indices: 368903--368930 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
368893 TTTTATTACA
368903 ACAATTAAT
1 ACAATTAAT
368912 ACAATTAAT
1 ACAATTAAT
368921 ACAATTAAT
1 ACAATTAAT
368930 A
1 A
368931 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:369092 original size:16 final size:16
Alignment explanation
Indices: 369071--369112 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
369061 AATAATTTGA
*
369071 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
369087 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
369103 TAGTTTTAAT
1 TAATTTTAAT
369113 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:387179 original size:14 final size:14
Alignment explanation
Indices: 387162--387203 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
387152 TCACTCAAAA
387162 TTCAAAATTCAAGT
1 TTCAAAATTCAAGT
* *
387176 TTCAAATTTCAAAT
1 TTCAAAATTCAAGT
387190 TTCAAAAGTTCAAG
1 TTCAAAA-TTCAAG
387204 AATATCCCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
TTCAAAATTCAAGT
Found at i:387976 original size:13 final size:13
Alignment explanation
Indices: 387932--387981 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
387922 ATTTAAGAAT
*
387932 ATTTTAATTGATA
1 ATTTTAATTTATA
* *
387945 ATTTTTAAAATTATT
1 A-TTTT-AATTTATA
387960 ATTTTAATTTATA
1 ATTTTAATTTATA
387973 ATTTTAATT
1 ATTTTAATT
387982 AAAAAAATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
13 16 0.53
14 8 0.27
15 6 0.20
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (13 bp):
ATTTTAATTTATA
Found at i:391232 original size:28 final size:28
Alignment explanation
Indices: 391198--391254 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
391188 AGTAGTACGC
391198 TGGGACAGTAAACAC-AGATAAAGTTTGT
1 TGGGACAGTAAACACGAGATAAA-TTTGT
*
391226 TGGGACAGTAAACACGAGGTAAATTTGT
1 TGGGACAGTAAACACGAGATAAATTTGT
391254 T
1 T
391255 AGGAGGCGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 21 0.78
29 6 0.22
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (28 bp):
TGGGACAGTAAACACGAGATAAATTTGT
Found at i:392298 original size:35 final size:35
Alignment explanation
Indices: 392247--392316 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
392237 GACCTAGTTA
*
392247 AAGAACTTACTAAGTTCATTTGAACTTACAGTAGT
1 AAGAACTCACTAAGTTCATTTGAACTTACAGTAGT
*
392282 AAGAACTCACTTAGTTCATTTGAACTTACAGTAGT
1 AAGAACTCACTAAGTTCATTTGAACTTACAGTAGT
392317 GTGGCTGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (35 bp):
AAGAACTCACTAAGTTCATTTGAACTTACAGTAGT
Found at i:393672 original size:15 final size:15
Alignment explanation
Indices: 393652--393683 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
393642 TAAACTATTG
393652 AAATAATGAAGCTTC
1 AAATAATGAAGCTTC
393667 AAATAATGAAGCTTC
1 AAATAATGAAGCTTC
393682 AA
1 AA
393684 GTGAGTTCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.25
Consensus pattern (15 bp):
AAATAATGAAGCTTC
Found at i:394155 original size:58 final size:58
Alignment explanation
Indices: 394063--394196 Score: 144
Period size: 58 Copynumber: 2.3 Consensus size: 58
394053 ATACGTAGCT
* * * * * * *
394063 TAAGACAATGGATGAAAGTCGCCATGACAGCATGGTATAAGGTAAAATGTATATGGCG
1 TAAGACCATAGATGAAAGGCGCCATGACAGCATGGTACAAAGTAAAAGGTATATGACG
* * *
394121 TAAGACCATAGATGAAAGGCGCCATGGC-GACATGGTACAAAGTATAAGGTATATGATG
1 TAAGACCATAGATGAAAGGCGCCATGACAG-CATGGTACAAAGTAAAAGGTATATGACG
* *
394179 TAAAACCATAGACGAAAG
1 TAAGACCATAGATGAAAG
394197 ATGTTATGGC
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
57 1 0.02
58 62 0.98
ACGTcount: A:0.40, C:0.13, G:0.26, T:0.20
Consensus pattern (58 bp):
TAAGACCATAGATGAAAGGCGCCATGACAGCATGGTACAAAGTAAAAGGTATATGACG
Found at i:395565 original size:15 final size:16
Alignment explanation
Indices: 395528--395566 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
395518 TTATTTTTTA
*
395528 TTTTATTATTAGATTG
1 TTTTATTATTAGACTG
*
395544 TTTTATTTTTAGACTG
1 TTTTATTATTAGACTG
395560 -TTTATTA
1 TTTTATTA
395567 GCAGCTGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.23, C:0.03, G:0.10, T:0.64
Consensus pattern (16 bp):
TTTTATTATTAGACTG
Found at i:397227 original size:17 final size:16
Alignment explanation
Indices: 397180--397227 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
397170 GGCATATAAT
*
397180 ATTTGGATAGATTATTG
1 ATTT-GATAGATTATTA
*
397197 ATTTGATAAAATTAGTTA
1 ATTTGAT-AGATTA-TTA
397215 ATTTGATAGATTA
1 ATTTGATAGATTA
397228 ACTAATTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 3 0.12
17 14 0.54
18 9 0.35
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.46
Consensus pattern (16 bp):
ATTTGATAGATTATTA
Found at i:397797 original size:21 final size:21
Alignment explanation
Indices: 397736--397814 Score: 81
Period size: 21 Copynumber: 3.9 Consensus size: 21
397726 GGTGGATCAA
* *
397736 CTCTTACAAGCTCCTGTTCAG
1 CTCTTACGAGCTTCTGTTCAG
*
397757 CTCTTACGAGCTTCTATTCAG
1 CTCTTACGAGCTTCTGTTCAG
* * *
397778 CTCTTATGAGTTTTTGTTCA-
1 CTCTTACGAGCTTCTGTTCAG
*
397798 C-CTTTCGAGCTTCTGTT
1 CTCTTACGAGCTTCTGTT
397815 GGCGTATTCA
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
19 12 0.26
20 1 0.02
21 34 0.72
ACGTcount: A:0.15, C:0.27, G:0.15, T:0.43
Consensus pattern (21 bp):
CTCTTACGAGCTTCTGTTCAG
Found at i:406058 original size:29 final size:31
Alignment explanation
Indices: 406026--406089 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 31
406016 AAAAACTCAT
*
406026 TAAAAATATATAAAAATTAT-TAAAA-TTAA
1 TAAAAATATATAAAAATTATAAAAAAGTTAA
* * *
406055 TAAATATGTATAAATATTATAAAAAAGTTAA
1 TAAAAATATATAAAAATTATAAAAAAGTTAA
406086 TAAA
1 TAAA
406090 TTATAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 17 0.59
30 4 0.14
31 8 0.28
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (31 bp):
TAAAAATATATAAAAATTATAAAAAAGTTAA
Found at i:406910 original size:16 final size:16
Alignment explanation
Indices: 406889--406921 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
406879 TTAAATGATT
406889 TTTTTATAATTTATAA
1 TTTTTATAATTTATAA
*
406905 TTTTTATAATTTTTAA
1 TTTTTATAATTTATAA
406921 T
1 T
406922 AGTTTTGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTATAATTTATAA
Found at i:406927 original size:10 final size:9
Alignment explanation
Indices: 406889--407152 Score: 101
Period size: 10 Copynumber: 28.0 Consensus size: 9
406879 TTAAATGATT
406889 TTTTTATAA
1 TTTTTATAA
406898 --TTTATAA
1 TTTTTATAA
406905 TTTTTATAA
1 TTTTTATAA
*
406914 TTTTTAATAG
1 TTTTT-ATAA
*
406924 TTTTGAT-A
1 TTTTTATAA
406932 TTTTTAT-A
1 TTTTTATAA
*
406940 TTTTTACAA
1 TTTTTATAA
* *
406949 GCTTTTATGAC
1 -TTTTTAT-AA
*
406960 TTTTTATACG
1 TTTTTATA-A
406970 TTTTTATAA
1 TTTTTATAA
406979 GTTTTTATATA
1 -TTTTTATA-A
* *
406990 TTTTAAGTATG
1 TTTTTA-TA-A
407001 TTTTTATTAAA
1 TTTTTA-T-AA
* *
407012 TTTATAAAA
1 TTTTTATAA
407021 TCTTTTATAA
1 T-TTTTATAA
* *
407031 TATATTATAGC
1 T-TTTTATA-A
* * *
407042 TTATTAGAT
1 TTTTTATAA
407051 TTTTTATAA
1 TTTTTATAA
*
407060 TATTTATAA
1 TTTTTATAA
*
407069 CTTTTTTATTA
1 --TTTTTATAA
407080 TTTTTATAA
1 TTTTTATAA
*
407089 GTTTATATTAA
1 -TTTTTA-TAA
* *
407100 TGTTAAT-A
1 TTTTTATAA
407108 TTTGTTA-AA
1 TTT-TTATAA
**
407117 TTTAAATAA
1 TTTTTATAA
407126 -TTTTATAA
1 TTTTTATAA
*
407134 TTTTTTATGA
1 -TTTTTATAA
407144 TTTTTATAA
1 TTTTTATAA
407153 GAAAATATAA
Statistics
Matches: 189, Mismatches: 44, Indels: 44
0.68 0.16 0.16
Matches are distributed among these distances:
7 7 0.04
8 23 0.12
9 58 0.31
10 73 0.39
11 27 0.14
12 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (9 bp):
TTTTTATAA
Found at i:413787 original size:25 final size:24
Alignment explanation
Indices: 413728--413788 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
413718 AGGAGAGGTG
* * *
413728 TTTTTCAATATTAATATAATTATT
1 TTTTTAAATATTAATATAAATAAT
*
413752 TTTATTTAATATTAATATAAAATAAT
1 TTT-TTAAATATTAATAT-AAATAAT
413778 TTTTTAAATAT
1 TTTTTAAATAT
413789 ATTAATATCC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 3 0.10
25 20 0.65
26 8 0.26
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTTTAAATATTAATATAAATAAT
Found at i:419207 original size:18 final size:17
Alignment explanation
Indices: 419174--419212 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
419164 TTTTATAAAT
419174 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
419192 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
419209 TGTG
1 TGTG
419213 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:419467 original size:23 final size:23
Alignment explanation
Indices: 419441--419498 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
419431 GTTATTGATT
* *
419441 AGTGGTAGCTTCGGCTACATTTC
1 AGTGGTAGCTTCAGCTACATATC
*
419464 AGTGGTAGCTACAGCTACATATC
1 AGTGGTAGCTTCAGCTACATATC
419487 AGTGGTAGCTTC
1 AGTGGTAGCTTC
419499 TTAGAGAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (23 bp):
AGTGGTAGCTTCAGCTACATATC
Found at i:436460 original size:20 final size:19
Alignment explanation
Indices: 436413--436462 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
436403 TTACAAAAAT
*
436413 AAAATA-AAATAATTTTTA
1 AAAATATAAATTATTTTTA
* *
436431 AAATTTTAAATTATTTATTA
1 AAAATATAAATTATTT-TTA
436451 AAAATATAAATT
1 AAAATATAAATT
436463 TACATAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 4 0.16
19 8 0.32
20 13 0.52
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAATATAAATTATTTTTA
Found at i:437235 original size:26 final size:25
Alignment explanation
Indices: 437183--437237 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
437173 AATTTTAAAA
* * *
437183 TATTTTTAAAATACTTTTTATTTTT
1 TATTTTTAAAATAATTTTTAGTGTT
*
437208 TATTTTTAAAATAAATTTTTGGTGTT
1 TATTTTTAAAAT-AATTTTTAGTGTT
437234 TATT
1 TATT
437238 AAAAAAATGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (25 bp):
TATTTTTAAAATAATTTTTAGTGTT
Found at i:439107 original size:20 final size:20
Alignment explanation
Indices: 439079--439155 Score: 83
Period size: 18 Copynumber: 4.1 Consensus size: 20
439069 GAAGATATAT
439079 AAATAGTAAAAATATATAAA
1 AAATAGTAAAAATATATAAA
* * *
439099 AAATTGTAAAATTTTAT-AA
1 AAATAGTAAAAATATATAAA
439118 AAATAGTAAAAA-ATA-AAA
1 AAATAGTAAAAATATATAAA
*
439136 AAATA-TAGAAATATA-AAA
1 AAATAGTAAAAATATATAAA
439154 AA
1 AA
439156 CTATAAATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
17 5 0.10
18 17 0.35
19 12 0.25
20 14 0.29
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (20 bp):
AAATAGTAAAAATATATAAA
Found at i:439162 original size:10 final size:9
Alignment explanation
Indices: 439079--439162 Score: 57
Period size: 10 Copynumber: 9.0 Consensus size: 9
439069 GAAGATATAT
439079 AAATAGTAAA
1 AAATA-TAAA
439089 AATATATAAA
1 AA-ATATAAA
*
439099 AAAT-TGTAA
1 AAATAT-AAA
* *
439108 AATTTTATAA
1 AAATATA-AA
439118 AAATAGTAAA
1 AAATA-TAAA
439128 AAATA-AAA
1 AAATATAAA
*
439136 AAATAT-AG
1 AAATATAAA
439144 AAATATAAA
1 AAATATAAA
439153 AAACTATAAA
1 AAA-TATAAA
439163 TTTTATAAAG
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
8 16 0.27
9 11 0.19
10 27 0.46
11 5 0.08
ACGTcount: A:0.68, C:0.01, G:0.05, T:0.26
Consensus pattern (9 bp):
AAATATAAA
Found at i:439467 original size:26 final size:27
Alignment explanation
Indices: 439432--439530 Score: 85
Period size: 26 Copynumber: 3.5 Consensus size: 27
439422 TAAAAAAAAA
*
439432 TTAATTTTTAATAAATTTTAAT-TTTT
1 TTAATATTTAATAAATTTTAATATTTT
*
439458 TTAATATTTATTAAATTTTAATATTTTTT
1 TTAATATTTAATAAATTTTAATA--TTTT
**
439487 TCTAA-ATTTTAATATTTTTTTAATATTTT
1 T-TAATA-TTTAATA-AATTTTAATATTTT
*
439516 TTAAATTTTTAATAA
1 TT-AATATTTAATAA
439531 GAGCAGGAGC
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
26 20 0.34
28 1 0.02
29 20 0.34
30 9 0.16
31 8 0.14
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (27 bp):
TTAATATTTAATAAATTTTAATATTTT
Found at i:439516 original size:20 final size:18
Alignment explanation
Indices: 439456--439515 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 18
439446 ATTTTAATTT
*
439456 TTTTAATA-TTTATTAAA
1 TTTTAATATTTTTTTAAA
439473 TTTTAATATTTTTTTCTAAA
1 TTTTAATA-TTTTTT-TAAA
439493 TTTTAATATTTTTTTAATA
1 TTTTAATATTTTTTTAA-A
439512 TTTT
1 TTTT
439516 TTAAATTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
17 8 0.21
18 3 0.08
19 15 0.39
20 12 0.32
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTAATATTTTTTTAAA
Found at i:439524 original size:8 final size:10
Alignment explanation
Indices: 439436--439529 Score: 74
Period size: 10 Copynumber: 9.9 Consensus size: 10
439426 AAAAAATTAA
*
439436 TTTTTAATAA
1 TTTTTAATAT
*
439446 ATTTTAAT-T
1 TTTTTAATAT
439455 TTTTTAATAT
1 TTTTTAATAT
*
439465 TTATTAA-A-
1 TTTTTAATAT
439473 -TTTTAATAT
1 TTTTTAATAT
** *
439482 TTTTTTCTAA
1 TTTTTAATAT
*
439492 ATTTTAATATT
1 TTTTTAATA-T
439503 TTTTTAATAT
1 TTTTTAATAT
439513 TTTTTAA-A-
1 TTTTTAATAT
439521 TTTTTAATA
1 TTTTTAATA
439530 AGAGCAGGAG
Statistics
Matches: 65, Mismatches: 13, Indels: 13
0.71 0.14 0.14
Matches are distributed among these distances:
7 5 0.08
8 8 0.12
9 10 0.15
10 34 0.52
11 8 0.12
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTTAATAT
Found at i:457586 original size:30 final size:30
Alignment explanation
Indices: 457545--457613 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
457535 AAATTACACC
* *
457545 AACAATCACTCAATATTGA-GAAAATAATAA
1 AACAGTCACTCAAT-TTGAGGAAAATAACAA
*
457575 AACAGTCACTCAATTTTAGGAAAATAACAA
1 AACAGTCACTCAATTTGAGGAAAATAACAA
457605 AACAGTCAC
1 AACAGTCAC
457614 CCGCTAACAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 3 0.09
30 32 0.91
ACGTcount: A:0.52, C:0.17, G:0.09, T:0.22
Consensus pattern (30 bp):
AACAGTCACTCAATTTGAGGAAAATAACAA
Found at i:458388 original size:22 final size:23
Alignment explanation
Indices: 458343--458388 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
458333 GAGTTAAGAA
*
458343 AAAAGGAAAAAAAAGAGGAGAAG
1 AAAAGGAAAAAAAAGAGGAAAAG
458366 AAAA-GAAAAAAAAG-GGACAAAG
1 AAAAGGAAAAAAAAGAGGA-AAAG
458388 A
1 A
458389 TTCAACGGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 3 0.14
22 14 0.67
23 4 0.19
ACGTcount: A:0.72, C:0.02, G:0.26, T:0.00
Consensus pattern (23 bp):
AAAAGGAAAAAAAAGAGGAAAAG
Found at i:460841 original size:30 final size:29
Alignment explanation
Indices: 460806--460880 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 29
460796 AAGAAGTACA
* *
460806 ACTAAATTGATAGAATG-TGTAAAGTTGAGG
1 ACTAAATTGATA-AATGATGTAAAATT-AAG
* *
460836 ACTAAATTTATTAAATGATTTAAAATTAAG
1 ACTAAATTGA-TAAATGATGTAAAATTAAG
460866 ACTAAATTGATAAAT
1 ACTAAATTGATAAAT
460881 ATTATAAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
29 5 0.13
30 24 0.63
31 9 0.24
ACGTcount: A:0.47, C:0.04, G:0.15, T:0.35
Consensus pattern (29 bp):
ACTAAATTGATAAATGATGTAAAATTAAG
Found at i:464216 original size:34 final size:35
Alignment explanation
Indices: 464166--464232 Score: 127
Period size: 34 Copynumber: 1.9 Consensus size: 35
464156 CTTCGACTTC
464166 GAGTCATTACTAGCAAACACAAAATGCATCAGTCG
1 GAGTCATTACTAGCAAACACAAAATGCATCAGTCG
464201 GAGTCATT-CTAGCAAACACAAAATGCATCAGT
1 GAGTCATTACTAGCAAACACAAAATGCATCAGT
464233 TGATATTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 24 0.75
35 8 0.25
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.21
Consensus pattern (35 bp):
GAGTCATTACTAGCAAACACAAAATGCATCAGTCG
Found at i:468955 original size:78 final size:78
Alignment explanation
Indices: 468826--468981 Score: 312
Period size: 78 Copynumber: 2.0 Consensus size: 78
468816 AGCCATAAGA
468826 TTCAAAGTTTTAAGCAAAATACCTGAAGGGTATTGCAGAGGGCAGAATGAAACTGAAATGGGTTT
1 TTCAAAGTTTTAAGCAAAATACCTGAAGGGTATTGCAGAGGGCAGAATGAAACTGAAATGGGTTT
468891 ACAGATCTTGGGG
66 ACAGATCTTGGGG
468904 TTCAAAGTTTTAAGCAAAATACCTGAAGGGTATTGCAGAGGGCAGAATGAAACTGAAATGGGTTT
1 TTCAAAGTTTTAAGCAAAATACCTGAAGGGTATTGCAGAGGGCAGAATGAAACTGAAATGGGTTT
468969 ACAGATCTTGGGG
66 ACAGATCTTGGGG
468982 GCAGTTGTAG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.26
Consensus pattern (78 bp):
TTCAAAGTTTTAAGCAAAATACCTGAAGGGTATTGCAGAGGGCAGAATGAAACTGAAATGGGTTT
ACAGATCTTGGGG
Found at i:469423 original size:21 final size:21
Alignment explanation
Indices: 469397--469437 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
469387 TTTTAGAAAT
*
469397 TTTAGAA-TTTTTAACAATTTC
1 TTTAGAAGATTTTAA-AATTTC
469418 TTTAGAAGATTTTAAAATTT
1 TTTAGAAGATTTTAAAATTT
469438 TGTACTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (21 bp):
TTTAGAAGATTTTAAAATTTC
Found at i:469768 original size:20 final size:19
Alignment explanation
Indices: 469739--469778 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
469729 AAAATTATAA
469739 AAAATTAAA-TTAATCTTTT
1 AAAATTAAATTTAAT-TTTT
469758 AAAATTAAAATTTAATTTTT
1 AAAATT-AAATTTAATTTTT
469778 A
1 A
469779 CCCCTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 8 0.42
21 5 0.26
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAATTAAATTTAATTTTT
Found at i:470211 original size:11 final size:10
Alignment explanation
Indices: 470196--470290 Score: 76
Period size: 10 Copynumber: 9.6 Consensus size: 10
470186 AATTTTTTTA
*
470196 ATTTTGAAAT
1 ATTTTTAAAT
470206 ATTTTTAAAAT
1 ATTTTT-AAAT
*
470217 ATTTTTTTAA-
1 A-TTTTTAAAT
470227 ATTTTT-AA-
1 ATTTTTAAAT
470235 ATTTTTAAAT
1 ATTTTTAAAT
470245 ATTTTTAAAAT
1 ATTTTT-AAAT
470256 ACATTTTTAAAT
1 --ATTTTTAAAT
470268 -TTTTT-AAT
1 ATTTTTAAAT
*
470276 -TTTTAAAAT
1 ATTTTTAAAT
470285 ATTTTT
1 ATTTTT
470291 TTAGTATTTA
Statistics
Matches: 72, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
8 15 0.21
9 15 0.21
10 16 0.22
11 11 0.15
12 9 0.12
13 6 0.08
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (10 bp):
ATTTTTAAAT
Found at i:470233 original size:8 final size:8
Alignment explanation
Indices: 470220--470282 Score: 60
Period size: 8 Copynumber: 8.0 Consensus size: 8
470210 TTAAAATATT
470220 TTTTTAAA
1 TTTTTAAA
470228 TTTTTAAA
1 TTTTTAAA
470236 TTTTTAAATA
1 TTTTT-AA-A
470246 TTTTTAAA
1 TTTTTAAA
* *
470254 ---ATACA
1 TTTTTAAA
470259 TTTTTAAA
1 TTTTTAAA
*
470267 TTTTTTAA
1 TTTTTAAA
470275 TTTTTAAA
1 TTTTTAAA
470283 ATATTTTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
5 3 0.07
8 31 0.70
9 4 0.09
10 6 0.14
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (8 bp):
TTTTTAAA
Found at i:470265 original size:31 final size:29
Alignment explanation
Indices: 470227--470285 Score: 91
Period size: 31 Copynumber: 2.0 Consensus size: 29
470217 ATTTTTTTAA
470227 ATTTTTAAATTTTTAAATATTTTTAAAATAC
1 ATTTTTAAATTTTT-AA-ATTTTTAAAATAC
*
470258 ATTTTTAAATTTTTTAATTTTTAAAATA
1 ATTTTTAAATTTTTAAATTTTTAAAATA
470286 TTTTTTTAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 12 0.44
30 1 0.04
31 14 0.52
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (29 bp):
ATTTTTAAATTTTTAAATTTTTAAAATAC
Found at i:470306 original size:40 final size:38
Alignment explanation
Indices: 470178--470290 Score: 163
Period size: 39 Copynumber: 2.9 Consensus size: 38
470168 TAAATATATT
* *
470178 TATTTTTTAATTTTTTTAATTTTGAAATATTTTTAAAA
1 TATTTTTTAAATTTTTTAATTTTTAAATATTTTTAAAA
*
470216 TATTTTTTTAAATTTTTAAATTTTTAAATATTTTTAAAA
1 TA-TTTTTTAAATTTTTTAATTTTTAAATATTTTTAAAA
*
470255 TACATTTTTAAATTTTTTAATTTTTAAAATATTTTT
1 TA-TTTTTTAAATTTTTTAATTTTT-AAATATTTTT
470291 TTAGTATTTA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
38 2 0.03
39 55 0.82
40 10 0.15
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (38 bp):
TATTTTTTAAATTTTTTAATTTTTAAATATTTTTAAAA
Found at i:475881 original size:22 final size:21
Alignment explanation
Indices: 475853--475901 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
475843 AAAAAACTAT
*
475853 AATTTTTTAAATATAAATTTTG
1 AATTTTTT-AATACAAATTTTG
* *
475875 AATTTTTTTATACATATTTTG
1 AATTTTTTAATACAAATTTTG
475896 AATTTT
1 AATTTT
475902 AAAATTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (21 bp):
AATTTTTTAATACAAATTTTG
Found at i:475947 original size:20 final size:19
Alignment explanation
Indices: 475889--475952 Score: 110
Period size: 19 Copynumber: 3.3 Consensus size: 19
475879 TTTTTATACA
475889 TATTTTGAATTTTAAAATT
1 TATTTTGAATTTTAAAATT
475908 TATTTTGAATTTTAAAATT
1 TATTTTGAATTTTAAAATT
*
475927 TATTTTGAATATTTGAAATT
1 TATTTTGAAT-TTTAAAATT
475947 TATTTT
1 TATTTT
475953 AAAATTTATT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
19 29 0.67
20 14 0.33
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.59
Consensus pattern (19 bp):
TATTTTGAATTTTAAAATT
Found at i:475957 original size:32 final size:34
Alignment explanation
Indices: 475916--475981 Score: 118
Period size: 32 Copynumber: 2.0 Consensus size: 34
475906 TTTATTTTGA
475916 ATTTTAAAATTTATTTTGAATA-TTTGAA-ATTT
1 ATTTTAAAATTTATTTTGAATATTTTGAATATTT
475948 ATTTTAAAATTTATTTTGAATATTTTGAATATTT
1 ATTTTAAAATTTATTTTGAATATTTTGAATATTT
475982 TAAATATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 22 0.69
33 6 0.19
34 4 0.12
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (34 bp):
ATTTTAAAATTTATTTTGAATATTTTGAATATTT
Found at i:475973 original size:9 final size:9
Alignment explanation
Indices: 475959--475988 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
475949 TTTTAAAATT
475959 TATTTTGAA
1 TATTTTGAA
475968 TATTTTGAA
1 TATTTTGAA
*
475977 TATTTTAAA
1 TATTTTGAA
475986 TAT
1 TAT
475989 AAATTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (9 bp):
TATTTTGAA
Found at i:476005 original size:41 final size:39
Alignment explanation
Indices: 475903--476022 Score: 91
Period size: 41 Copynumber: 2.9 Consensus size: 39
475893 TTGAATTTTA
475903 AAATTTATTTTGAATTTTAAAATTTATTTTGAATATTTGAAATT
1 AAATTTATTTTG-ATTTT--AA--TATTTTGAATATTTGAAATT
* * * *
475947 TATTTTAAAATTT-ATTTTGAATATTTTGAATATTTTAAATAT
1 AAATTT--ATTTTGATTTT-AATATTTTGAATATTTGAAAT-T
* *
475989 AAATTTATTTTGATTTTCATATTTT-CATATTTGA
1 AAATTTATTTTGATTTTAATATTTTGAATATTTGA
476023 CAATGACCAA
Statistics
Matches: 61, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
39 7 0.11
40 11 0.18
41 23 0.38
42 5 0.08
43 2 0.03
44 9 0.15
46 4 0.07
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.57
Consensus pattern (39 bp):
AAATTTATTTTGATTTTAATATTTTGAATATTTGAAATT
Found at i:480680 original size:22 final size:21
Alignment explanation
Indices: 480655--480697 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
480645 AATTTTTTCC
*
480655 TTTTTATATATCTTGAATTTTT
1 TTTTTAAATATCTT-AATTTTT
*
480677 TTTTTAAATTTCTTAATTTTT
1 TTTTTAAATATCTTAATTTTT
480698 AAAGATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (21 bp):
TTTTTAAATATCTTAATTTTT
Found at i:480912 original size:11 final size:11
Alignment explanation
Indices: 480896--480923 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
480886 ATATACTTAT
480896 ATTTAAAAATA
1 ATTTAAAAATA
480907 ATTTAAAAATA
1 ATTTAAAAATA
480918 ATTTAA
1 ATTTAA
480924 TTAATACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
ATTTAAAAATA
Found at i:486788 original size:56 final size:56
Alignment explanation
Indices: 486702--486813 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
486692 TCTTTGATAC
486702 AAATTAGAATTCGTAGGCATAAAATTATTTACAAATTTCCATACTGTAATTTTCAT
1 AAATTAGAATTCGTAGGCATAAAATTATTTACAAATTTCCATACTGTAATTTTCAT
486758 AAATTAGAATTCGTAGGCATAAAATTATTTACAAATTTCCATACTGTAATTTTCAT
1 AAATTAGAATTCGTAGGCATAAAATTATTTACAAATTTCCATACTGTAATTTTCAT
486814 TCTTTCCGAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (56 bp):
AAATTAGAATTCGTAGGCATAAAATTATTTACAAATTTCCATACTGTAATTTTCAT
Found at i:487863 original size:7 final size:7
Alignment explanation
Indices: 487851--487903 Score: 52
Period size: 7 Copynumber: 7.1 Consensus size: 7
487841 AAAAGTTATT
487851 TTAAAAA
1 TTAAAAA
487858 TTAAAAA
1 TTAAAAA
487865 TTATAAAA
1 TTA-AAAA
*
487873 TATATAAAT
1 T-TA-AAAA
*
487882 TTAAAAT
1 TTAAAAA
487889 TTAAAAA
1 TTAAAAA
*
487896 GTAAAAA
1 TTAAAAA
487903 T
1 T
487904 AATATAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
7 26 0.65
8 7 0.17
9 7 0.17
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (7 bp):
TTAAAAA
Found at i:487885 original size:31 final size:31
Alignment explanation
Indices: 487850--487911 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
487840 GAAAAGTTAT
*
487850 TTTAAAAATTAAAAATTATAAAAT-ATATAAA
1 TTTAAAAATTAAAAAGTA-AAAATAATATAAA
*
487881 TTTAAAATTTAAAAAGTAAAAATAATATAAA
1 TTTAAAAATTAAAAAGTAAAAATAATATAAA
487912 AAGATTGCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 5 0.18
31 23 0.82
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (31 bp):
TTTAAAAATTAAAAAGTAAAAATAATATAAA
Found at i:488864 original size:13 final size:13
Alignment explanation
Indices: 488848--488880 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
488838 ATTTTCATTG
488848 ATAATTTTTGAAA
1 ATAATTTTTGAAA
*
488861 ATAAATTTTGAAA
1 ATAATTTTTGAAA
488874 ATAATTT
1 ATAATTT
488881 CGAAACATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (13 bp):
ATAATTTTTGAAA
Found at i:488867 original size:14 final size:13
Alignment explanation
Indices: 488848--488891 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
488838 ATTTTCATTG
*
488848 ATAATTTTTGAAA
1 ATAAATTTTGAAA
488861 ATAAATTTTGAAA
1 ATAAATTTTGAAA
*
488874 AT-AATTTCGAAA
1 ATAAATTTTGAAA
488886 CATAAA
1 -ATAAA
488892 AATAAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 9 0.33
13 16 0.59
14 2 0.07
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (13 bp):
ATAAATTTTGAAA
Found at i:501053 original size:15 final size:15
Alignment explanation
Indices: 501033--501061 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
501023 TTTTTTTAAT
501033 AATAATTAGAAAAAG
1 AATAATTAGAAAAAG
501048 AATAATTAGAAAAA
1 AATAATTAGAAAAA
501062 CATACCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (15 bp):
AATAATTAGAAAAAG
Found at i:503226 original size:26 final size:26
Alignment explanation
Indices: 503190--503241 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
503180 CAACTTGGTC
503190 ATAGGAGGGAAAAAGGTATGACCGTT
1 ATAGGAGGGAAAAAGGTATGACCGTT
*
503216 ATAGGAGGGAAAAATGTATGACCGTT
1 ATAGGAGGGAAAAAGGTATGACCGTT
503242 TCGTTGAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.33, T:0.21
Consensus pattern (26 bp):
ATAGGAGGGAAAAAGGTATGACCGTT
Found at i:516956 original size:27 final size:27
Alignment explanation
Indices: 516926--516983 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
516916 AATTTTAAAG
*
516926 AAATATATAAATA-ATTTTAATAAAATA
1 AAATATA-AAATATATTATAATAAAATA
* * *
516953 AAATTTAAAATATATTATAATTAAATT
1 AAATATAAAATATATTATAATAAAATA
516980 AAAT
1 AAAT
516984 TAATTTCTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
AAATATAAAATATATTATAATAAAATA
Found at i:516984 original size:27 final size:26
Alignment explanation
Indices: 516934--516984 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
516924 AGAAATATAT
*
516934 AAATAATTTTAATAAAATAAAATTTA
1 AAATAATTATAATAAAATAAAATTTA
* *
516960 AAATATATTATAATTAAATTAAATT
1 AAATA-ATTATAATAAAATAAAATT
516985 AATTTCTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 5 0.24
27 16 0.76
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
AAATAATTATAATAAAATAAAATTTA
Found at i:521951 original size:3 final size:3
Alignment explanation
Indices: 521943--521995 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
521933 ACCAATAACA
* *
521943 AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
521991 AAT AA
1 AAT AA
521996 AGGAAGAAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:522828 original size:14 final size:16
Alignment explanation
Indices: 522797--522830 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
522787 TAAAAGAAAT
522797 TTATAAACGTTATATA
1 TTATAAACGTTATATA
522813 TTATAAA-GTT-TATA
1 TTATAAACGTTATATA
522827 TTAT
1 TTAT
522831 TTTTTAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 3 0.17
16 7 0.39
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (16 bp):
TTATAAACGTTATATA
Found at i:526836 original size:20 final size:21
Alignment explanation
Indices: 526798--526841 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
526788 GGTTGTATAG
* *
526798 AAAAAATTAATATTTAAGGAT
1 AAAAAATTAAAATTAAAGGAT
*
526819 AAAAAA-TAAAATTAAAGGTT
1 AAAAAATTAAAATTAAAGGAT
526839 AAA
1 AAA
526842 TGTTGCTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (21 bp):
AAAAAATTAAAATTAAAGGAT
Found at i:528265 original size:102 final size:102
Alignment explanation
Indices: 528089--528291 Score: 397
Period size: 102 Copynumber: 2.0 Consensus size: 102
528079 CCATCCATGG
528089 CTTCCCCGCACAAGTCCATACCCAAACCAGGTCTTTCATCTCCGTCTTCATCATCATTACAATCA
1 CTTCCCCGCACAAGTCCATACCCAAACCAGGTCTTTCATCTCCGTCTTCATCATCATTACAATCA
528154 ATCAAATCTTGATCATCACCATCATCATCGAGAAATA
66 ATCAAATCTTGATCATCACCATCATCATCGAGAAATA
*
528191 CTTCCCTGCACAAGTCCATACCCAAACCAGGTCTTTCATCTCCGTCTTCATCATCATTACAATCA
1 CTTCCCCGCACAAGTCCATACCCAAACCAGGTCTTTCATCTCCGTCTTCATCATCATTACAATCA
528256 ATCAAATCTTGATCATCACCATCATCATCGAGAAAT
66 ATCAAATCTTGATCATCACCATCATCATCGAGAAAT
528292 TTAAGAATTG
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 100 1.00
ACGTcount: A:0.31, C:0.33, G:0.08, T:0.28
Consensus pattern (102 bp):
CTTCCCCGCACAAGTCCATACCCAAACCAGGTCTTTCATCTCCGTCTTCATCATCATTACAATCA
ATCAAATCTTGATCATCACCATCATCATCGAGAAATA
Found at i:529897 original size:21 final size:21
Alignment explanation
Indices: 529837--529897 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
529827 AATATTTTTC
* *
529837 AATTCTAGTCAAGTAAAATGA
1 AATTCGAGTCGAGTAAAATGA
* *
529858 AATTCGAGTAGGGTAAAATGA
1 AATTCGAGTCGAGTAAAATGA
*
529879 AATTCGAGTCGAGTCAAAT
1 AATTCGAGTCGAGTAAAAT
529898 CAAGTGAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (21 bp):
AATTCGAGTCGAGTAAAATGA
Found at i:530101 original size:18 final size:17
Alignment explanation
Indices: 530078--530121 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
530068 TTTTTTTAAA
530078 TATAAAATTTGAAATTCT
1 TATAAAATTTGAAATT-T
*
530096 TATAAATATTTTAAATTT
1 TATAAA-ATTTGAAATTT
530114 TA-AAAATT
1 TATAAAATT
530122 ATTTGATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 3 0.12
17 3 0.12
18 9 0.38
19 9 0.38
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (17 bp):
TATAAAATTTGAAATTT
Found at i:530111 original size:19 final size:18
Alignment explanation
Indices: 530078--530127 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
530068 TTTTTTTAAA
530078 TATAAA-ATTTGAAATTCT
1 TATAAATATTTGAAATT-T
*
530096 TATAAATATTTTAAATTT
1 TATAAATATTTGAAATTT
*
530114 TAAAAATTATTTGA
1 TATAAA-TATTTGA
530128 TTTTTTGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (18 bp):
TATAAATATTTGAAATTT
Found at i:530133 original size:19 final size:20
Alignment explanation
Indices: 530111--530153 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
530101 ATATTTTAAA
530111 TTTTAAAAATTA-TTTGATT
1 TTTTAAAAATTATTTTGATT
**
530130 TTTTGGAAATTATTTTGATT
1 TTTTAAAAATTATTTTGATT
530150 TTTT
1 TTTT
530154 TTTGTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (20 bp):
TTTTAAAAATTATTTTGATT
Found at i:531836 original size:11 final size:11
Alignment explanation
Indices: 531793--531830 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
531783 CATAGTTAAA
531793 AAATTAAAATT
1 AAATTAAAATT
*
531804 -AAGTATAAATT
1 AAATTA-AAATT
531815 AAATTAAAATT
1 AAATTAAAATT
531826 AAATT
1 AAATT
531831 TTAATTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 4 0.17
11 15 0.65
12 4 0.17
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
AAATTAAAATT
Found at i:535606 original size:22 final size:24
Alignment explanation
Indices: 535578--535621 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
535568 CGATATATAT
*
535578 ATTATTA-AATT-ATAAAAAAACC
1 ATTATTAGAATTGAAAAAAAAACC
535600 ATTATTAGAATTGAAAAAAAAA
1 ATTATTAGAATTGAAAAAAAAA
535622 ACAAAAACGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 4 0.21
24 8 0.42
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (24 bp):
ATTATTAGAATTGAAAAAAAAACC
Found at i:540585 original size:27 final size:27
Alignment explanation
Indices: 540543--540594 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
540533 ATCTAAATAA
*
540543 TCCAACACTTGTGTTTCGC-CACCAAAG
1 TCCAACACTTGAGTTTC-CTCACCAAAG
540570 TCCAACACTTGAGTTTCCTCACCAA
1 TCCAACACTTGAGTTTCCTCACCAA
540595 GGTTTAGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.27, C:0.35, G:0.12, T:0.27
Consensus pattern (27 bp):
TCCAACACTTGAGTTTCCTCACCAAAG
Found at i:541324 original size:14 final size:15
Alignment explanation
Indices: 541296--541325 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
541286 TCATCTATTC
541296 TCTCAATTATTTTAT
1 TCTCAATTATTTTAT
541311 TCTCAATT-TTTTAT
1 TCTCAATTATTTTAT
541325 T
1 T
541326 TAATTTCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.63
Consensus pattern (15 bp):
TCTCAATTATTTTAT
Found at i:542328 original size:94 final size:94
Alignment explanation
Indices: 542208--542395 Score: 376
Period size: 94 Copynumber: 2.0 Consensus size: 94
542198 GTAATAAAGT
542208 AAGATTCAGTTAATAATATAATTATCATATTATTTTTTCATTATTATATTTTTTAAATAATATAT
1 AAGATTCAGTTAATAATATAATTATCATATTATTTTTTCATTATTATATTTTTTAAATAATATAT
542273 TATTTGAGTAAATAGAATAATGACGCGAG
66 TATTTGAGTAAATAGAATAATGACGCGAG
542302 AAGATTCAGTTAATAATATAATTATCATATTATTTTTTCATTATTATATTTTTTAAATAATATAT
1 AAGATTCAGTTAATAATATAATTATCATATTATTTTTTCATTATTATATTTTTTAAATAATATAT
542367 TATTTGAGTAAATAGAATAATGACGCGAG
66 TATTTGAGTAAATAGAATAATGACGCGAG
542396 TTATGTGGGT
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (94 bp):
AAGATTCAGTTAATAATATAATTATCATATTATTTTTTCATTATTATATTTTTTAAATAATATAT
TATTTGAGTAAATAGAATAATGACGCGAG
Found at i:548905 original size:19 final size:18
Alignment explanation
Indices: 548872--549001 Score: 68
Period size: 19 Copynumber: 6.9 Consensus size: 18
548862 ATTATAATAA
* *
548872 ATAAAAATAAATAAAAGTT
1 ATAAAAAT-TATAAAATTT
548891 ATAAAAATTAGT-AAATTT
1 ATAAAAATTA-TAAAATTT
*
548909 A-AAAAAATATTAAAAATTT
1 ATAAAAATTA-T-AAAATTT
***
548928 ATTAAAAATTATAAAAACC
1 A-TAAAAATTATAAAATTT
* *
548947 ATAAAAGAATAAAAAATTT
1 ATAAAA-ATTATAAAATTT
*
548966 -TAAAATTTTATAAATATTAT
1 ATAAAA-ATTATAAA-ATT-T
*
548986 AAAAAAATTATAAAAT
1 ATAAAAATTATAAAAT
549002 ACATAAAAAA
Statistics
Matches: 83, Mismatches: 19, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
17 8 0.10
18 22 0.27
19 33 0.40
20 9 0.11
21 11 0.13
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (18 bp):
ATAAAAATTATAAAATTT
Found at i:548942 original size:9 final size:9
Alignment explanation
Indices: 548858--549000 Score: 71
Period size: 9 Copynumber: 15.4 Consensus size: 9
548848 CAGGTGGCAA
548858 AAAAATTAT
1 AAAAATTAT
*
548867 AATAA--AT
1 AAAAATTAT
*
548874 AAAAATAAAT
1 AAAAAT-TAT
*
548884 AAAAGTTAT
1 AAAAATTAT
548893 AAAAATTAGT
1 AAAAATTA-T
*
548903 -AAATTTA-
1 AAAAATTAT
*
548910 AAAAAATATT
1 AAAAATTA-T
548920 AAAAATTTATT
1 AAAAA-TTA-T
548931 AAAAATTAT
1 AAAAATTAT
**
548940 AAAAACCAT
1 AAAAATTAT
*
548949 AAAAGAATA-
1 AAAA-ATTAT
*
548958 AAAAATTTT
1 AAAAATTAT
*
548967 AAAATTTTAT
1 AAAA-ATTAT
*
548977 AAATATTAT
1 AAAAATTAT
548986 AAAAAAATTAT
1 --AAAAATTAT
548997 AAAA
1 AAAA
549001 TACATAAAAA
Statistics
Matches: 101, Mismatches: 20, Indels: 26
0.69 0.14 0.18
Matches are distributed among these distances:
7 6 0.06
8 7 0.07
9 47 0.47
10 24 0.24
11 17 0.17
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:548996 original size:20 final size:20
Alignment explanation
Indices: 548893--549012 Score: 58
Period size: 20 Copynumber: 6.2 Consensus size: 20
548883 TAAAAGTTAT
548893 AAAAATTAGTAAAT-TTA-AA
1 AAAAATTA-TAAATATTATAA
* *
548912 AAAATATTAAAAAT-TTAT-T
1 AAAA-ATTATAAATATTATAA
* **
548931 AAAAATTATAAAAACCATAA
1 AAAAATTATAAATATTATAA
* * *
548951 AAGAA-TA-AAAAATT-TTA
1 AAAAATTATAAATATTATAA
**
548968 AAATTTTATAAATATTATAA
1 AAAAATTATAAATATTATAA
*
548988 AAAAATTATAAA-ATACATAA
1 AAAAATTATAAATAT-TATAA
549008 AAAAA
1 AAAAA
549013 AAACCCTTTA
Statistics
Matches: 74, Mismatches: 19, Indels: 15
0.69 0.18 0.14
Matches are distributed among these distances:
17 4 0.05
18 14 0.19
19 27 0.36
20 29 0.39
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAAATTATAAATATTATAA
Found at i:560149 original size:2 final size:2
Alignment explanation
Indices: 560142--560168 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
560132 CTGGTTTCTT
560142 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
560169 AATAGTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:574673 original size:21 final size:23
Alignment explanation
Indices: 574635--574687 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 23
574625 GATTTCTTTT
* *
574635 TAATTATTTATAGCATTT-TA-A
1 TAATTTTTTATAGCATTTGCATA
**
574656 TAATTTTTTATATTATTTGCATA
1 TAATTTTTTATAGCATTTGCATA
574679 TAATTTTTT
1 TAATTTTTT
574688 TAATTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 15 0.58
22 1 0.04
23 10 0.38
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (23 bp):
TAATTTTTTATAGCATTTGCATA
Found at i:574759 original size:7 final size:7
Alignment explanation
Indices: 574747--574786 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
574737 TACTCCAAAC
574747 CTTAAAT
1 CTTAAAT
574754 CTTAAAT
1 CTTAAAT
574761 AC-TAAAT
1 -CTTAAAT
574768 CTTAAA-
1 CTTAAAT
574774 CTTAAAT
1 CTTAAAT
574781 CTTAAA
1 CTTAAA
574787 CCTTGAACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
6 7 0.23
7 22 0.73
8 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (7 bp):
CTTAAAT
Found at i:574786 original size:20 final size:20
Alignment explanation
Indices: 574743--574797 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
574733 TTTATACTCC
574743 AAACCTTAAATCTTAAATACT
1 AAACCTTAAA-CTTAAATACT
*
574764 AAATCTTAAACTTAAAT-CTT
1 AAACCTTAAACTTAAATAC-T
*
574784 AAACCTTGAACTTA
1 AAACCTTAAACTTA
574798 GATTTAGGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 1 0.03
20 20 0.67
21 9 0.30
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (20 bp):
AAACCTTAAACTTAAATACT
Found at i:574797 original size:13 final size:13
Alignment explanation
Indices: 574747--574787 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
574737 TACTCCAAAC
574747 CTTAAATCTTAAA
1 CTTAAATCTTAAA
574760 -TACTAAATCTTAAA
1 CT--TAAATCTTAAA
574774 CTTAAATCTTAAA
1 CTTAAATCTTAAA
574787 C
1 C
574788 CTTGAACTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.04
13 12 0.48
14 11 0.44
15 1 0.04
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (13 bp):
CTTAAATCTTAAA
Found at i:580578 original size:36 final size:36
Alignment explanation
Indices: 580476--580578 Score: 86
Period size: 36 Copynumber: 2.9 Consensus size: 36
580466 GAAAGATAAA
* * **
580476 GTGCC-AAGAAAGACGAAGGATAG-TTAAAAAGGTTGT
1 GTGCCTAA-AAAGATGAAGGAT-GCTTAAAAAGGCTAC
* * * *
580512 GTGCCTGAAAATG-TGAAGTATGCCTGAAAAGGCTAC
1 GTGCCT-AAAAAGATGAAGGATGCTTAAAAAGGCTAC
580548 GTGCCTAAAAAGATGAAGGATGCTTAAAAAG
1 GTGCCTAAAAAGATGAAGGATGCTTAAAAAG
580579 ATTATATTTG
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
35 6 0.12
36 40 0.78
37 3 0.06
38 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.28, T:0.20
Consensus pattern (36 bp):
GTGCCTAAAAAGATGAAGGATGCTTAAAAAGGCTAC
Found at i:580831 original size:19 final size:20
Alignment explanation
Indices: 580799--580838 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
580789 AAGAAGTGAA
**
580799 ATGTGCTTGGAAAGAC-AAT
1 ATGTGCTTAAAAAGACTAAT
580818 ATGTGCTTAAAAAGACTAAT
1 ATGTGCTTAAAAAGACTAAT
580838 A
1 A
580839 ATCTAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (20 bp):
ATGTGCTTAAAAAGACTAAT
Found at i:583868 original size:20 final size:19
Alignment explanation
Indices: 583845--583901 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
583835 AATTTCAATT
583845 TTAATAATTAATTAAATTTA
1 TTAATAATT-ATTAAATTTA
*
583865 TTAATAAATTATTTAATTTA
1 TTAAT-AATTATTAAATTTA
* * *
583885 ATAATAAATATAAAATT
1 TTAATAATTATTAAATT
583902 ATACACTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 9 0.29
20 18 0.58
21 4 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAATAATTATTAAATTTA
Found at i:584467 original size:24 final size:24
Alignment explanation
Indices: 584438--584485 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
584428 CTAATGACAT
* * *
584438 TATAAAAATTGAGGTACTAAATTA
1 TATAAAAATTAAAGTACAAAATTA
584462 TATAAAAATTAAAGTACAAAATTA
1 TATAAAAATTAAAGTACAAAATTA
584486 AATCACAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.31
Consensus pattern (24 bp):
TATAAAAATTAAAGTACAAAATTA
Found at i:584613 original size:29 final size:30
Alignment explanation
Indices: 584579--584635 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
584569 TACATCAAGA
*
584579 TAGTCCCTT-TATTATT-AAATGAATTAATT
1 TAGT-CCTTATATTATTAAAAAGAATTAATT
584608 TAGTCCTTATATTATTAAAAAGAATTAA
1 TAGTCCTTATATTATTAAAAAGAATTAA
584636 ATGAGTCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 4 0.16
29 11 0.44
30 10 0.40
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (30 bp):
TAGTCCTTATATTATTAAAAAGAATTAATT
Found at i:586644 original size:3 final size:3
Alignment explanation
Indices: 586636--586664 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
586626 TATAGTAAAT
586636 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
586665 ACACTTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:587243 original size:9 final size:9
Alignment explanation
Indices: 587227--587269 Score: 68
Period size: 9 Copynumber: 4.8 Consensus size: 9
587217 GGTATTTTTC
587227 GGTAATTCG
1 GGTAATTCG
*
587236 GTTAATTCG
1 GGTAATTCG
*
587245 GTTAATTCG
1 GGTAATTCG
587254 GGTAATTCG
1 GGTAATTCG
587263 GGTAATT
1 GGTAATT
587270 TTTAACCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.23, C:0.09, G:0.28, T:0.40
Consensus pattern (9 bp):
GGTAATTCG
Found at i:587447 original size:12 final size:12
Alignment explanation
Indices: 587430--587454 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
587420 AGTAATTTCG
587430 GGTCGGTTAACC
1 GGTCGGTTAACC
587442 GGTCGGTTAACC
1 GGTCGGTTAACC
587454 G
1 G
587455 AATGAACACC
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:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:592895 original size:42 final size:42
Alignment explanation
Indices: 592845--592975 Score: 112
Period size: 42 Copynumber: 3.1 Consensus size: 42
592835 TTAAAATGAC
592845 TTTTTATTAAAAGTTTAAATTTAGGCAGGTTACTAACAATTT
1 TTTTTATTAAAAGTTTAAATTTAGGCAGGTTACTAACAATTT
* ** **
592887 TTTTTATTAAATATTAATTTAATATTTA---ATATT--TAA-AATGAC
1 TTTTTATT-AA-A--AGTTTAA-ATTTAGGCAGGTTACTAACAAT-TT
*
592929 TTTTTATTAAAAGTTTAAATTTAGGCAGGTTACTAACAAATT
1 TTTTTATTAAAAGTTTAAATTTAGGCAGGTTACTAACAATTT
592971 TTTTT
1 TTTTT
592976 GTCTATGTAG
Statistics
Matches: 66, Mismatches: 11, Indels: 24
0.65 0.11 0.24
Matches are distributed among these distances:
37 5 0.08
38 6 0.09
40 4 0.06
41 5 0.08
42 27 0.41
43 4 0.06
44 4 0.06
46 6 0.09
47 5 0.08
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.49
Consensus pattern (42 bp):
TTTTTATTAAAAGTTTAAATTTAGGCAGGTTACTAACAATTT
Found at i:592906 original size:84 final size:83
Alignment explanation
Indices: 592808--592975 Score: 309
Period size: 84 Copynumber: 2.0 Consensus size: 83
592798 AGTTGGCTTA
*
592808 TATTAATTTTAATTTAATATTTAATATTTAAAATGACTTTTTATTAAAAGTTTAAATTTAGGCAG
1 TATTAATATTAATTTAATATTTAATATTTAAAATGACTTTTTATTAAAAGTTTAAATTTAGGCAG
*
592873 GTTACTAACAATTTTTTT
66 GTTACTAACAAATTTTTT
592891 TATTAAATATTAATTTAATATTTAATATTTAAAATGACTTTTTATTAAAAGTTTAAATTTAGGCA
1 TATT-AATATTAATTTAATATTTAATATTTAAAATGACTTTTTATTAAAAGTTTAAATTTAGGCA
592956 GGTTACTAACAAATTTTTT
65 GGTTACTAACAAATTTTTT
592975 T
1 T
592976 GTCTATGTAG
Statistics
Matches: 82, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
83 4 0.05
84 78 0.95
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (83 bp):
TATTAATATTAATTTAATATTTAATATTTAAAATGACTTTTTATTAAAAGTTTAAATTTAGGCAG
GTTACTAACAAATTTTTT
Found at i:593398 original size:16 final size:15
Alignment explanation
Indices: 593363--593398 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
593353 AAAAATTTTA
*
593363 TATTAAAATAATATT
1 TATTAAAATAATAAT
593378 TATTAAAATATATAAT
1 TATTAAAATA-ATAAT
593394 TATTA
1 TATTA
593399 TATTTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATTAAAATAATAAT
Found at i:596840 original size:41 final size:41
Alignment explanation
Indices: 596760--596893 Score: 182
Period size: 41 Copynumber: 3.3 Consensus size: 41
596750 ATCTCGGTTC
* * *
596760 CGCA-ACTTAGTGCCCGTTA-TTAACATAATTATTTGGTTT
1 CGCACACTTAGTGCTCGTTATTTAACATCATTATTTAGTTT
* * *
596799 CACACAATTAGTGCTCGTTATTTAACATCATTACTTAGTTT
1 CGCACACTTAGTGCTCGTTATTTAACATCATTATTTAGTTT
* *
596840 CGCACACTTAGTGCTCGTTATTCAACATCATTATTTAATTT
1 CGCACACTTAGTGCTCGTTATTTAACATCATTATTTAGTTT
596881 CGCACACTTAGTG
1 CGCACACTTAGTG
596894 TCAAGCATAT
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
39 3 0.04
40 13 0.16
41 66 0.80
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.40
Consensus pattern (41 bp):
CGCACACTTAGTGCTCGTTATTTAACATCATTATTTAGTTT
Found at i:602011 original size:42 final size:42
Alignment explanation
Indices: 601910--602029 Score: 125
Period size: 42 Copynumber: 2.9 Consensus size: 42
601900 TGGGTTTATA
* * * * * *
601910 CTTCAGTTTAGCTAATGATGCACTTATATGCCAGTATATTTT
1 CTTCAGTTTATCTGATGATGCACTTATGTGCTAGTACATTTC
* * * *
601952 GTTCGGTTCAT-TCGATGATGCATTTATGTGCTAGTACATTTC
1 CTTCAGTTTATCT-GATGATGCACTTATGTGCTAGTACATTTC
*
601994 CTTCAGTTTATCTGATGATGTACTTATGTGCTAGTA
1 CTTCAGTTTATCTGATGATGCACTTATGTGCTAGTA
602030 TAATTGATTC
Statistics
Matches: 61, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
41 1 0.02
42 59 0.97
43 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (42 bp):
CTTCAGTTTATCTGATGATGCACTTATGTGCTAGTACATTTC
Found at i:602041 original size:42 final size:41
Alignment explanation
Indices: 601911--602120 Score: 122
Period size: 42 Copynumber: 5.0 Consensus size: 41
601901 GGGTTTATAC
* * * *
601911 TTCAGTTTAGCTAATGATGCACTTATATGCCAGTATATTTTG
1 TTCAGTTTATCTGATGATGCACTTATGTGCTAGTATA-TTTG
* * * * *
601953 TTCGGTTCAT-TCGATGATGCATTTATGTGCTAGTACATTTCC
1 TTCAGTTTATCT-GATGATGCACTTATGTGCTAGTATATTT-G
* *
601995 TTCAGTTTATCTGATGATGTACTTATGTGCTAGTATAATTG
1 TTCAGTTTATCTGATGATGCACTTATGTGCTAGTATATTTG
* * * ** *
602036 ATTCAGCTTGTCT-AGTAATGCACCTCGTGTGTCT-GTATGATTTC
1 -TTCAGTTTATCTGA-TGATGCA-CTTATGTG-CTAGTAT-ATTTG
** *
602080 TTCAGTTTATCCAATGATGCAC-TATGTATGCTAGTTTATTT
1 TTCAGTTTATCTGATGATGCACTTATG--TGCTAGTATATTT
602121 CCTTTGAAAA
Statistics
Matches: 125, Mismatches: 31, Indels: 24
0.69 0.17 0.13
Matches are distributed among these distances:
41 7 0.06
42 81 0.65
43 31 0.25
44 6 0.05
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (41 bp):
TTCAGTTTATCTGATGATGCACTTATGTGCTAGTATATTTG
Done.