Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 129 of 141
Found at i:41358029 original size:51 final size:51
Alignment explanation
Indices: 41357967--41358160 Score: 319
Period size: 51 Copynumber: 3.9 Consensus size: 51
41357957 ACTTTCCACT
*
41357967 TGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTCCACTTGTCAC
1 TGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTTGTCAC
*
41358018 TGATCAGATAAGTGTAGCCGAAGCTATCACTCATCACTTTCCAC---T---
1 TGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTTGTCAC
*
41358063 TGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTCCACTTGTCAC
1 TGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTTGTCAC
41358114 TGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTTG
1 TGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTTG
41358161 ATCAGATAAG
Statistics
Matches: 132, Mismatches: 5, Indels: 12
0.89 0.03 0.08
Matches are distributed among these distances:
45 42 0.32
48 2 0.02
51 88 0.67
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (51 bp):
TGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTTGTCAC
Found at i:41358083 original size:96 final size:96
Alignment explanation
Indices: 41357919--41358176 Score: 507
Period size: 96 Copynumber: 2.7 Consensus size: 96
41357909 TCACTTTAGG
41357919 CACTGATCAGATAAGTGTAGCCGAAGCTATCACTCATCACTTTCCACTTGATCAGATAAGTGTAG
1 CACTGATCAGATAAGTGTAGCCGAAGCTATCACTCATCACTTTCCACTTGATCAGATAAGTGTAG
41357984 CTGAAGCTATCACTTATCACTTTCCACTTGT
66 CTGAAGCTATCACTTATCACTTTCCACTTGT
41358015 CACTGATCAGATAAGTGTAGCCGAAGCTATCACTCATCACTTTCCACTTGATCAGATAAGTGTAG
1 CACTGATCAGATAAGTGTAGCCGAAGCTATCACTCATCACTTTCCACTTGATCAGATAAGTGTAG
41358080 CTGAAGCTATCACTTATCACTTTCCACTTGT
66 CTGAAGCTATCACTTATCACTTTCCACTTGT
*
41358111 CACTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTTGATCAGATAAGTGTAG
1 CACTGATCAGATAAGTGTAGCCGAAGCTATCACTCATCACTTTCCACTTGATCAGATAAGTGTAG
41358176 C
66 C
41358177 ACTTATCACT
Statistics
Matches: 161, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 161 1.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (96 bp):
CACTGATCAGATAAGTGTAGCCGAAGCTATCACTCATCACTTTCCACTTGATCAGATAAGTGTAG
CTGAAGCTATCACTTATCACTTTCCACTTGT
Found at i:41358182 original size:35 final size:36
Alignment explanation
Indices: 41358141--41358212 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
41358131 CCGAAGCTAT
41358141 CACTTATCACTTT-CCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGCCACTTGATCAGATAAGTGTAG
*
41358176 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGCCACTTGATCAGATAAGTGTAG
41358212 C
1 C
41358213 TAAAGCTACC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 13 0.37
36 22 0.63
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (36 bp):
CACTTATCACTTTGCCACTTGATCAGATAAGTGTAG
Found at i:41362454 original size:21 final size:19
Alignment explanation
Indices: 41362426--41362473 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 19
41362416 ATTTTCATGC
41362426 TATA-TATTATAAAAAATAA
1 TATATTATTATAAAAAAT-A
*
41362445 TATACTTATTTATAACAAATA
1 TATA-TTA-TTATAAAAAATA
41362466 TATATTAT
1 TATATTAT
41362474 AATTTTTGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 5 0.20
20 3 0.12
21 7 0.28
22 10 0.40
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (19 bp):
TATATTATTATAAAAAATA
Found at i:41362457 original size:22 final size:20
Alignment explanation
Indices: 41362432--41362473 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
41362422 ATGCTATATA
41362432 TTATAAAAAATAATATACTTAT
1 TTATAAAAAAT-ATATA-TTAT
*
41362454 TTATAACAAATATATATTAT
1 TTATAAAAAATATATATTAT
41362474 AATTTTTGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 5 0.26
22 10 0.53
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (20 bp):
TTATAAAAAATATATATTAT
Found at i:41365283 original size:31 final size:30
Alignment explanation
Indices: 41365215--41365290 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 30
41365205 TGGGGTCTAA
*
41365215 TTAAAATTTTT-AAAATTCTGTGAGATTAG
1 TTAAAATTTTTAAAAATTCTGAGAGATTAG
* * *
41365244 TGATAATTTTTAAAAATT-TAAGAGAGCTTAG
1 TTAAAATTTTTAAAAATTCT--GAGAGATTAG
41365275 TTAAAATTTTCTAAAA
1 TTAAAATTTT-TAAAA
41365291 GTTTCAAGGG
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
29 10 0.27
30 6 0.16
31 16 0.43
32 5 0.14
ACGTcount: A:0.42, C:0.04, G:0.12, T:0.42
Consensus pattern (30 bp):
TTAAAATTTTTAAAAATTCTGAGAGATTAG
Found at i:41370455 original size:17 final size:18
Alignment explanation
Indices: 41370407--41370456 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 18
41370397 AAATAAATAT
41370407 ATATATATATATTTAAAAC
1 ATATATATAT-TTTAAAAC
*
41370426 ATATGAGA-A-TTTAAAA-
1 ATAT-ATATATTTTAAAAC
41370442 ATATATATATTTTAA
1 ATATATATATTTTAA
41370457 TTTTTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
15 2 0.08
16 5 0.19
17 12 0.46
19 5 0.19
20 2 0.08
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (18 bp):
ATATATATATTTTAAAAC
Found at i:41375503 original size:114 final size:114
Alignment explanation
Indices: 41375303--41375530 Score: 447
Period size: 114 Copynumber: 2.0 Consensus size: 114
41375293 GACTACAAGC
41375303 CTCCCACACTACACTTGCAAATGGACAAAAGAACAAGACATGTTCAATGGTTTTGTTTCCATTAC
1 CTCCCACACTACACTTGCAAATGGACAAAAGAACAAGACATGTTCAATGGTTTTGTTTCCATTAC
*
41375368 ACCACCTCGAGCACCTTGAGTCTTTATGCCTTGTTCTTTTTGGCCATGT
66 ACCACCTCGAGCACCTTGAGTCTTTATGCCTTGCTCTTTTTGGCCATGT
41375417 CTCCCACACTACACTTGCAAATGGACAAAAGAACAAGACATGTTCAATGGTTTTGTTTCCATTAC
1 CTCCCACACTACACTTGCAAATGGACAAAAGAACAAGACATGTTCAATGGTTTTGTTTCCATTAC
41375482 ACCACCTCGAGCACCTTGAGTCTTTATGCCTTGCTCTTTTTGGCCATGT
66 ACCACCTCGAGCACCTTGAGTCTTTATGCCTTGCTCTTTTTGGCCATGT
41375531 TGTCTTTGGT
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
114 113 1.00
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (114 bp):
CTCCCACACTACACTTGCAAATGGACAAAAGAACAAGACATGTTCAATGGTTTTGTTTCCATTAC
ACCACCTCGAGCACCTTGAGTCTTTATGCCTTGCTCTTTTTGGCCATGT
Found at i:41389868 original size:114 final size:114
Alignment explanation
Indices: 41389668--41389895 Score: 429
Period size: 114 Copynumber: 2.0 Consensus size: 114
41389658 GACTACAAGC
*
41389668 CTCCCACACTACACTTGCAAATGGACAAAAGAACAAGACATGTTCAATGGTTTTGTTTCCATTAC
1 CTCCCACACTACACTTGCAAATGGACAAAAGAACAAGACATGTTCAACGGTTTTGTTTCCATTAC
*
41389733 ACCACCTCGAGCACCTTGAGTCTTTATGCCTTGTTCTTTTTGGCCATGT
66 ACCACCTCGAGCACCTTGAGTCTTTATGCCTTGCTCTTTTTGGCCATGT
*
41389782 CTCCCACACTACACTTGCAAATGGACAAAATAACAAGACATGTTCAACGGTTTTGTTTCCATTAC
1 CTCCCACACTACACTTGCAAATGGACAAAAGAACAAGACATGTTCAACGGTTTTGTTTCCATTAC
41389847 ACCACCTCGAGCACCTTGAGTCTTTATGCCTTGCTCTTTTTGGCCATGT
66 ACCACCTCGAGCACCTTGAGTCTTTATGCCTTGCTCTTTTTGGCCATGT
41389896 TGTCTTTGGT
Statistics
Matches: 111, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 111 1.00
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.32
Consensus pattern (114 bp):
CTCCCACACTACACTTGCAAATGGACAAAAGAACAAGACATGTTCAACGGTTTTGTTTCCATTAC
ACCACCTCGAGCACCTTGAGTCTTTATGCCTTGCTCTTTTTGGCCATGT
Found at i:41392663 original size:110 final size:110
Alignment explanation
Indices: 41392460--41392769 Score: 500
Period size: 110 Copynumber: 2.8 Consensus size: 110
41392450 AAAAAAAAAC
*
41392460 AAAATTTTATAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
1 AAAATTTCA-AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
*
41392525 GGTGTCGATTTTCCTCGTTCAACCAAATGGCTTAATATCCTTCTTA
65 GGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTCTTA
* * *
41392571 AAAATTTCAAAATAGGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCTTAAGGTGTTGG
1 AAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGG
41392636 GTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTCTTA
66 GTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTCTTA
* * *
41392681 AAAATTTCAAAATAAGGCAATGTTTTGAGTTTGGAAATTCGAG-GAACGTGCCCTAAGGTGCTGG
1 AAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGG
* *
41392745 GTTTCGA--TTTCTCGTTTAACCAAAT
66 GTGTCGATTTTTCTCGTTCAACCAAAT
41392770 TGCCAAATAT
Statistics
Matches: 186, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
107 17 0.09
109 23 0.12
110 138 0.74
111 8 0.04
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (110 bp):
AAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGG
GTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTCTTA
Found at i:41395888 original size:13 final size:13
Alignment explanation
Indices: 41395870--41395894 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41395860 TGAATATACT
41395870 AATAAATAAAATA
1 AATAAATAAAATA
41395883 AATAAATAAAAT
1 AATAAATAAAAT
41395895 TATCCTCTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AATAAATAAAATA
Found at i:41396328 original size:9 final size:9
Alignment explanation
Indices: 41396300--41396337 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
41396290 AACAATTTAA
41396300 TTTTTTTCT
1 TTTTTTTCT
*
41396309 TTTTATCTCT
1 TTTT-TTTCT
41396319 TTTTTTTCT
1 TTTTTTTCT
41396328 TTTTTTTCT
1 TTTTTTTCT
41396337 T
1 T
41396338 CCCCTTTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:41397857 original size:101 final size:102
Alignment explanation
Indices: 41397733--41397937 Score: 403
Period size: 101 Copynumber: 2.0 Consensus size: 102
41397723 AGGATTTTAT
41397733 AAATTAACATTTTTTAATTTATTTTTGAAATATAAAATGTTAAAAGTATTGTAGAGGCCCCTGTA
1 AAATTAACATTTTTTAATTTATTTTTGAAATATAAAATGTTAAAAGTATTGTAGAGGCCCCTGTA
41397798 CTAGAAATTAGATTACATTTTGCCCCTCTACTAAAAA
66 CTAGAAATTAGATTACATTTTGCCCCTCTACTAAAAA
41397835 AAATTAACA-TTTTTAATTTATTTTTGAAATATAAAATGTTAAAAGTATTGTAGAGGCCCCTGTA
1 AAATTAACATTTTTTAATTTATTTTTGAAATATAAAATGTTAAAAGTATTGTAGAGGCCCCTGTA
41397899 CTAGAAATTAGATTACATTTTGCCCCTCTACTAAAAA
66 CTAGAAATTAGATTACATTTTGCCCCTCTACTAAAAA
41397936 AA
1 AA
41397938 TGAACAAATT
Statistics
Matches: 103, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
101 94 0.91
102 9 0.09
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.38
Consensus pattern (102 bp):
AAATTAACATTTTTTAATTTATTTTTGAAATATAAAATGTTAAAAGTATTGTAGAGGCCCCTGTA
CTAGAAATTAGATTACATTTTGCCCCTCTACTAAAAA
Found at i:41403007 original size:17 final size:19
Alignment explanation
Indices: 41402971--41403009 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
41402961 TATTATGTTG
41402971 TTATTGTATAACTCTTATT
1 TTATTGTATAACTCTTATT
*
41402990 TTATTGT-TAA-TTTTATT
1 TTATTGTATAACTCTTATT
41403007 TTA
1 TTA
41403010 GAAGTATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 3 0.16
19 7 0.37
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (19 bp):
TTATTGTATAACTCTTATT
Found at i:41421899 original size:22 final size:22
Alignment explanation
Indices: 41421871--41421915 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
41421861 AAGAGTGTCC
41421871 AGCAAGTTTTGAGATCTGAAGG
1 AGCAAGTTTTGAGATCTGAAGG
41421893 AGCAAGTTTTGAGATCTGAAGG
1 AGCAAGTTTTGAGATCTGAAGG
41421915 A
1 A
41421916 CAATGGTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.09, G:0.31, T:0.27
Consensus pattern (22 bp):
AGCAAGTTTTGAGATCTGAAGG
Found at i:41434327 original size:21 final size:21
Alignment explanation
Indices: 41434284--41434349 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 21
41434274 GTATGGATAG
*
41434284 ATTTTTTATATTAATATT-TATA
1 ATTTTTTA-ATTAAT-TTAAATA
41434306 ATTTTTTAATTAATTTAAATAA
1 ATTTTTTAATTAATTTAAAT-A
41434328 AGTTTGTTT-ATT-ATTTAAATA
1 A-TTT-TTTAATTAATTTAAATA
41434349 A
1 A
41434350 AAGATAGATA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
20 2 0.05
21 10 0.26
22 18 0.46
23 6 0.15
24 3 0.08
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (21 bp):
ATTTTTTAATTAATTTAAATA
Found at i:41441368 original size:216 final size:221
Alignment explanation
Indices: 41440960--41441404 Score: 596
Period size: 216 Copynumber: 2.0 Consensus size: 221
41440950 TTTGTATTTG
* * * *
41440960 GTTCCCTTATGTTGGAACTTTGAAGAGATTTGAATGTATTATTATCACATGCCTTGGATACATGG
1 GTTCCATTATGTTGGAACTTTGAAGAAATTTGAATGTATTATGATCACATGCC---G-TACATGA
* *** * *
41441025 TTCTGGTGAGTTATGGTGATTAGTTTTAGATTGCATTATTTTGGAGCTGTAAGGAACCTAAATGT
62 TAC-GGTGAGTTATGGTGATTAACGTTAGATTCCATTATTTTGGAGCTGTAAGGAACCTAAAGGT
* * * *
41441090 CTTAAGGAACGTTGTTGTTACCGATAAAATATCTAAGAGATGCATATGTGATGATTGATTTTAGC
126 CTTAACGAAAGTTGTCGTTACCGATAAAATATCTAAGAGATGCATATGTGATGATCGATTTTAGC
41441155 TTCCGTTATTTAG-TAGCTTTGAGGAATTCAA
191 TTCCGTTATTTAGCT-GCTTTGAGGAATTCAA
41441186 GTTCCATTATGTTGGAACTTTGAAGAAATTTGAATGTATTATGATCACATGCC-T-CA-GATAC-
1 GTTCCATTATGTTGGAACTTTGAAGAAATTTGAATGTATTATGATCACATGCCGTACATGATACG
* * **
41441247 GTG-GTTATTGTGATTAACGTTCGATTCCATTATTTTGGAGCTGTAAGGAATTTAAAGGTCTTAA
66 GTGAGTTATGGTGATTAACGTTAGATTCCATTATTTTGGAGCTGTAAGGAACCTAAAGGTCTTAA
* * *
41441311 CGAAAGTTGTCGTTACTGATAAAATATCTAAGAGATGCGTATGTGTTGATCGATTTTAGCTTCCG
131 CGAAAGTTGTCGTTACCGATAAAATATCTAAGAGATGCATATGTGATGATCGATTTTAGCTTCCG
*
41441376 TTATTTAGCTGCTTTGTGGAATTCAA
196 TTATTTAGCTGCTTTGAGGAATTCAA
41441402 GTT
1 GTT
41441405 TTGTAATCTA
Statistics
Matches: 196, Mismatches: 22, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
216 136 0.69
217 4 0.02
219 3 0.02
220 2 0.01
221 1 0.01
226 50 0.26
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (221 bp):
GTTCCATTATGTTGGAACTTTGAAGAAATTTGAATGTATTATGATCACATGCCGTACATGATACG
GTGAGTTATGGTGATTAACGTTAGATTCCATTATTTTGGAGCTGTAAGGAACCTAAAGGTCTTAA
CGAAAGTTGTCGTTACCGATAAAATATCTAAGAGATGCATATGTGATGATCGATTTTAGCTTCCG
TTATTTAGCTGCTTTGAGGAATTCAA
Found at i:41452338 original size:2 final size:2
Alignment explanation
Indices: 41452331--41452356 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41452321 CCCAATATGT
41452331 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
41452357 ACCTTAGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41453564 original size:19 final size:19
Alignment explanation
Indices: 41453536--41453577 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
41453526 ATAAAATTCC
41453536 AAAA-ATGAAAATTTCTAA-
1 AAAATATGAAAATTT-TAAT
41453554 AAAATATGAAAATTTTAAT
1 AAAATATGAAAATTTTAAT
41453573 AAAAT
1 AAAAT
41453578 TTAAAAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (19 bp):
AAAATATGAAAATTTTAAT
Found at i:41453584 original size:19 final size:19
Alignment explanation
Indices: 41453543--41453584 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
41453533 TCCAAAAATG
*
41453543 AAAATTTCTAAAAAATATG
1 AAAATTTCTAAAAAATATA
*
41453562 AAAATTT-TAATAAAATTTA
1 AAAATTTCTAA-AAAATATA
41453581 AAAA
1 AAAA
41453585 AGTATTAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAATTTCTAAAAAATATA
Found at i:41454608 original size:7 final size:7
Alignment explanation
Indices: 41454598--41454622 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41454588 TAAAAAAATA
41454598 AAATATT
1 AAATATT
41454605 AAATATT
1 AAATATT
41454612 AAATATT
1 AAATATT
41454619 AAAT
1 AAAT
41454623 TCATATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATATT
Found at i:41456003 original size:21 final size:20
Alignment explanation
Indices: 41455958--41456010 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
41455948 TTGCAAGTCT
*
41455958 ATGTCTCGAGACACATAACTG
1 ATGTCTCAAGACACATAAC-G
41455979 ATGTCTCAAGACATCAGTAAC-
1 ATGTCTCAAGACA-CA-TAACG
*
41456000 ATGTTTCAAGA
1 ATGTCTCAAGA
41456011 TACCTAGAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 22 0.79
22 2 0.07
23 4 0.14
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (20 bp):
ATGTCTCAAGACACATAACG
Found at i:41456197 original size:93 final size:93
Alignment explanation
Indices: 41456029--41456197 Score: 198
Period size: 93 Copynumber: 1.8 Consensus size: 93
41456019 GCATGTCTTG
* * * * *
41456029 AGACTTTGCTCCCTTGGAGCAAAACTTTAGCTACTAACTTGCTTGTCTCGAGACTTAGAGTCTTA
1 AGACTTTGCCCCCTTGGAGCAAAACTTTAGCTACTAACTTACATGTCTCGAGACATAGAATCTTA
**
41456094 TGTCTCGAGACTTTTATGGCAAGTCTCA
66 TAACTCGAGACTTTTATGGCAAGTCTCA
* * *
41456122 AGACTTTGCCCCCTT-GACGTAAAGCTTT-GCTTACTAACTTACATGTCTCGAGACATATAATCT
1 AGACTTTGCCCCCTTGGA-GCAAAACTTTAGC-TACTAACTTACATGTCTCGAGACATAGAATCT
* *
41456185 TGTAACTTGAGAC
64 TATAACTCGAGAC
41456198 ATTGTTGGGA
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
92 4 0.06
93 58 0.94
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (93 bp):
AGACTTTGCCCCCTTGGAGCAAAACTTTAGCTACTAACTTACATGTCTCGAGACATAGAATCTTA
TAACTCGAGACTTTTATGGCAAGTCTCA
Found at i:41456519 original size:8 final size:9
Alignment explanation
Indices: 41456498--41456572 Score: 51
Period size: 9 Copynumber: 8.0 Consensus size: 9
41456488 CTAATCAACA
41456498 AAAAATTTT
1 AAAAATTTT
41456507 AAAAATTTT
1 AAAAATTTT
**
41456516 AAAAAATTCA
1 -AAAAATTTT
41456526 AAATAATTTT
1 AAA-AATTTT
* **
41456536 AAAAAATCC
1 AAAAATTTT
*
41456545 AAATATTTAT
1 AAAAATTT-T
*
41456555 AAAAATTTC
1 AAAAATTTT
*
41456564 AAATATTTT
1 AAAAATTTT
41456573 TTTTTAAATT
Statistics
Matches: 48, Mismatches: 15, Indels: 6
0.70 0.22 0.09
Matches are distributed among these distances:
9 27 0.56
10 21 0.44
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (9 bp):
AAAAATTTT
Found at i:41456520 original size:10 final size:10
Alignment explanation
Indices: 41456497--41456542 Score: 60
Period size: 9 Copynumber: 4.7 Consensus size: 10
41456487 TCTAATCAAC
41456497 AAAAAATTTT
1 AAAAAATTTT
41456507 -AAAAATTTT
1 AAAAAATTTT
*
41456516 AAAAAA-TTC
1 AAAAAATTTT
41456525 AAAATAATTTT
1 AAAA-AATTTT
41456536 AAAAAAT
1 AAAAAAT
41456543 CCAAATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
9 15 0.48
10 10 0.32
11 6 0.19
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (10 bp):
AAAAAATTTT
Found at i:41456548 original size:19 final size:18
Alignment explanation
Indices: 41456511--41456572 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 18
41456501 AATTTTAAAA
*
41456511 ATTTTAAAAAATTCAAAAT
1 ATTTTAAAAAA-TCCAAAT
41456530 AATTTTAAAAAATCCAAAT
1 -ATTTTAAAAAATCCAAAT
* *
41456549 ATTTATAAAAATTTCAAAT
1 ATTT-TAAAAAATCCAAAT
41456568 ATTTT
1 ATTTT
41456573 TTTTTAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 5 0.13
19 22 0.58
20 11 0.29
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTTTAAAAAATCCAAAT
Found at i:41456600 original size:14 final size:15
Alignment explanation
Indices: 41456583--41456612 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
41456573 TTTTTAAATT
41456583 ATAAAAATT-TAAAA
1 ATAAAAATTCTAAAA
41456597 ATAAAAATTCTAAAA
1 ATAAAAATTCTAAAA
41456612 A
1 A
41456613 AACTCTAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (15 bp):
ATAAAAATTCTAAAA
Found at i:41459588 original size:9 final size:10
Alignment explanation
Indices: 41459556--41459600 Score: 56
Period size: 10 Copynumber: 4.4 Consensus size: 10
41459546 AATGATTTTT
41459556 AATTTTTAAA
1 AATTTTTAAA
41459566 ATATTTTTTAAA
1 A-A-TTTTTAAA
41459578 AATTTTT-AA
1 AATTTTTAAA
*
41459587 AATTTTAAAA
1 AATTTTTAAA
41459597 AATT
1 AATT
41459601 AATTAAATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
9 8 0.26
10 12 0.39
11 2 0.06
12 9 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
AATTTTTAAA
Found at i:41463600 original size:93 final size:94
Alignment explanation
Indices: 41463489--41463677 Score: 371
Period size: 93 Copynumber: 2.0 Consensus size: 94
41463479 GATTTTTTTT
41463489 TTCCAATTGGATACTTGAACTTAGTTTCATAATTCAAATCGGTATCTGAACTTGGTTTTTTTTGT
1 TTCCAATTGGATACTTGAACTTAGTTTCATAATTCAAATCGGTATCTGAACTTGGTTTTTTTTGT
41463554 CCAAATTAGTACTTACTTATTTGAACCAA
66 CCAAATTAGTACTTACTTATTTGAACCAA
41463583 TTCCAA-TGGATACTTGAACTTAGTTTCATAATTCAAATCGGTATCTGAACTTGGTTTTTTTTGT
1 TTCCAATTGGATACTTGAACTTAGTTTCATAATTCAAATCGGTATCTGAACTTGGTTTTTTTTGT
41463647 CCAAATTAGTACTTACTTATTTGAACCAA
66 CCAAATTAGTACTTACTTATTTGAACCAA
41463676 TT
1 TT
41463678 TGAACAAAAA
Statistics
Matches: 95, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
93 89 0.94
94 6 0.06
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.43
Consensus pattern (94 bp):
TTCCAATTGGATACTTGAACTTAGTTTCATAATTCAAATCGGTATCTGAACTTGGTTTTTTTTGT
CCAAATTAGTACTTACTTATTTGAACCAA
Found at i:41468413 original size:18 final size:17
Alignment explanation
Indices: 41468383--41468416 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
41468373 TGAAAGCAAG
*
41468383 AAAAAGAATAAGGAAAA
1 AAAAAGAAAAAGGAAAA
41468400 AAAAGAGAAAAAGGAAA
1 AAAA-AGAAAAAGGAAA
41468417 GTACCAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (17 bp):
AAAAAGAAAAAGGAAAA
Found at i:41471805 original size:233 final size:234
Alignment explanation
Indices: 41471387--41471854 Score: 929
Period size: 233 Copynumber: 2.0 Consensus size: 234
41471377 TCAAATTGAA
41471387 TTTTATGAAGATTTTATATTAATTACTTAAAAAATATTTAAAATTTATATTTCATATATCATAAT
1 TTTTATGAAGATTTTATATTAATTACTTAAAAAATATTTAAAATTTATATTTCATATATCATAAT
41471452 ATTAACAACGAATTGTAGTAAATTATTTGTTAAGCTTAATATATACGTAGTGGAGGTAATTTGGT
66 ATTAACAACGAATTGTAGTAAATTATTTGTTAAGCTTAATATATACGTAGTGGAGGTAATTTGGT
41471517 GTTTCAAAAATTTGGAAGAAAAATGGTAATAAAAAAACAACAGGTCGTAATTGTTTACCTCTACT
131 GTTTCAAAAATTTGGAAGAAAAATGGTAATAAAAAAACAACAGGTCGTAATTGTTTACCTCTACT
41471582 ATCTTATCTTGCCATAACTAAAAATTTTCTTAATTTTCT
196 ATCTTATCTTGCCATAACTAAAAATTTTCTTAATTTTCT
41471621 TTTTATGAAG-TTTTATATTAATTACTTAAAAAATATTTAAAATTTATATTTCATATATCATAAT
1 TTTTATGAAGATTTTATATTAATTACTTAAAAAATATTTAAAATTTATATTTCATATATCATAAT
41471685 ATTAACAACGAATTGTAGTAAATTATTTGTTAAGCTTAATATATACGTAGTGGAGGTAATTTGGT
66 ATTAACAACGAATTGTAGTAAATTATTTGTTAAGCTTAATATATACGTAGTGGAGGTAATTTGGT
41471750 GTTTCAAAAATTTGGAAGAAAAATGGTAATAAAAAAACAACAGGTCGTAATTGTTTACCTCTACT
131 GTTTCAAAAATTTGGAAGAAAAATGGTAATAAAAAAACAACAGGTCGTAATTGTTTACCTCTACT
41471815 ATCTTATCTTGCCATAACTAAAAATTTTCTTAATTTTCT
196 ATCTTATCTTGCCATAACTAAAAATTTTCTTAATTTTCT
41471854 T
1 T
41471855 AATTTAAGGT
Statistics
Matches: 234, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
233 224 0.96
234 10 0.04
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (234 bp):
TTTTATGAAGATTTTATATTAATTACTTAAAAAATATTTAAAATTTATATTTCATATATCATAAT
ATTAACAACGAATTGTAGTAAATTATTTGTTAAGCTTAATATATACGTAGTGGAGGTAATTTGGT
GTTTCAAAAATTTGGAAGAAAAATGGTAATAAAAAAACAACAGGTCGTAATTGTTTACCTCTACT
ATCTTATCTTGCCATAACTAAAAATTTTCTTAATTTTCT
Found at i:41472966 original size:20 final size:21
Alignment explanation
Indices: 41472907--41472960 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
41472897 TTTAGTTTAT
*
41472907 AATATATATTAAATAATAATTA
1 AATATATATT-TATAATAATTA
* *
41472929 AAAATATATTTATGATAA-TA
1 AATATATATTTATAATAATTA
41472949 AATATATATTTA
1 AATATATATTTA
41472961 CTATAACATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 13 0.46
21 6 0.21
22 9 0.32
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
AATATATATTTATAATAATTA
Found at i:41475377 original size:154 final size:154
Alignment explanation
Indices: 41475094--41476088 Score: 1560
Period size: 154 Copynumber: 6.5 Consensus size: 154
41475084 AAAAATATAG
41475094 AGGGCCCAACCGGGTTCGAACCGGTGACCTCTTGATCTGCAGTCAAATGCTCTACCACTGAGCTA
1 AGGGCCCAACCGGGTTCGAACCGGTGACCTCTTGATCTGCAGTCAAATGCTCTACCACTGAGCTA
* *
41475159 TGGACCCCATTGAGAAGCAGTTTTACTTTGGTTACTACATGTATAAACTATGGAAGTTTAGGACG
66 TGGACCCCATTGAGAAGCAATTTTACTTTGGTTACTACATGTATAAACTATGGAAGTTTTGGACG
*
41475224 GACTTGGCAAAATTAAGTAAAAGC
131 GACTTGGCAAAAATAAGTAAAAGC
41475248 AGGGCCCAACCGGGTTCGAACCGGTGACCTCTTGATCTGCAGTCAAATGCTCTACCACTGAGCTA
1 AGGGCCCAACCGGGTTCGAACCGGTGACCTCTTGATCTGCAGTCAAATGCTCTACCACTGAGCTA
*
41475313 TGGACCCCATTGTGAAGC-ATTTTCACTTTGGTTACTACATGTATAAACTATGGAAGTTTTGGAC
66 TGGACCCCATTGAGAAGCAATTTT-ACTTTGGTTACTACATGTATAAACTATGGAAGTTTTGGAC
**
41475377 GGACTTGGCAAAAGCAAGTAAAAGC
130 GGACTTGGCAAAAATAAGTAAAAGC
41475402 AGGGCCCAACCGGGTTCGAACCGGTGACCTCTTGATCTGCAGTCAAATGCTCTACCACTGAGCTA
1 AGGGCCCAACCGGGTTCGAACCGGTGACCTCTTGATCTGCAGTCAAATGCTCTACCACTGAGCTA
* * *
41475467 TGGACCGCATTGAGAAGCAATTTTCCTTTGGTTACTACATGTATAAATTATGGAAGTTTTGGACG
66 TGGACCCCATTGAGAAGCAATTTTACTTTGGTTACTACATGTATAAACTATGGAAGTTTTGGACG
** *
41475532 GACTTGGCAAAAGCAAGTGAAAGC
131 GACTTGGCAAAAATAAGTAAAAGC
*
41475556 AGGGCCCAACCGGGTTCGAACCGGTGACATCTTGATCTGCAGTCAAATGCTCTACCACTGAGCTA
1 AGGGCCCAACCGGGTTCGAACCGGTGACCTCTTGATCTGCAGTCAAATGCTCTACCACTGAGCTA
* * *
41475621 TGGACCCCGTTGAGAAGCAATTTTGCTTTGGTTACTACATGTATAAACTATGGAAGTTTAGGACG
66 TGGACCCCATTGAGAAGCAATTTTACTTTGGTTACTACATGTATAAACTATGGAAGTTTTGGACG
*
41475686 GACTTGGCAAAATTAAGT--AAGC
131 GACTTGGCAAAAATAAGTAAAAGC
41475708 AGGGCCCAACCGGGTTCGAACCGGTGACCTCTTGATCTGCAGTCAAATGCTCTACCACTGAGCTA
1 AGGGCCCAACCGGGTTCGAACCGGTGACCTCTTGATCTGCAGTCAAATGCTCTACCACTGAGCTA
* * *
41475773 TGGACCCCATTCAGAAGCAATTCTACTTTGGTTAGTACATGTATAAACTATGGAAGTTTTGGACG
66 TGGACCCCATTGAGAAGCAATTTTACTTTGGTTACTACATGTATAAACTATGGAAGTTTTGGACG
* **
41475838 GACTTGGCAAAAATAGGTAAAATT
131 GACTTGGCAAAAATAAGTAAAAGC
*
41475862 AGGGCCCAACCGGGTTCAAACCGGTGACCTCTTGATCTGCAGTCAAATGCTCTACCACTGAGCTA
1 AGGGCCCAACCGGGTTCGAACCGGTGACCTCTTGATCTGCAGTCAAATGCTCTACCACTGAGCTA
* * **** * *
41475927 TGGACCCCATTGAGATGCAATGTTACTTTGACCGCTAGATGTATAAACTAAGG-A----TGGACG
66 TGGACCCCATTGAGAAGCAATTTTACTTTGGTTACTACATGTATAAACTATGGAAGTTTTGGACG
* *
41475987 GACTCGGCAAAAATATA-TAAACA-A
131 GACTTGGCAAAAATA-AGTAAA-AGC
*
41476011 AGGGCCCAACCGGGTTCGAACCAGTGACCTCTTGATCTGCAGTCAAATGCTCTACCACTGAGCTA
1 AGGGCCCAACCGGGTTCGAACCGGTGACCTCTTGATCTGCAGTCAAATGCTCTACCACTGAGCTA
* *
41476076 TAGACCCCGTTGA
66 TGGACCCCATTGA
41476089 ATTTTTAATA
Statistics
Matches: 787, Mismatches: 48, Indels: 17
0.92 0.06 0.02
Matches are distributed among these distances:
149 98 0.12
150 1 0.00
152 143 0.18
153 5 0.01
154 535 0.68
155 5 0.01
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (154 bp):
AGGGCCCAACCGGGTTCGAACCGGTGACCTCTTGATCTGCAGTCAAATGCTCTACCACTGAGCTA
TGGACCCCATTGAGAAGCAATTTTACTTTGGTTACTACATGTATAAACTATGGAAGTTTTGGACG
GACTTGGCAAAAATAAGTAAAAGC
Found at i:41480282 original size:25 final size:25
Alignment explanation
Indices: 41480253--41480304 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
41480243 CATTATCCAT
41480253 AGCTCCTCTTCAACCCATAAATAGG
1 AGCTCCTCTTCAACCCATAAATAGG
41480278 AGCTCCTCTTCAACCCATAAATAGG
1 AGCTCCTCTTCAACCCATAAATAGG
41480303 AG
1 AG
41480305 GATAATCAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.31, G:0.13, T:0.23
Consensus pattern (25 bp):
AGCTCCTCTTCAACCCATAAATAGG
Found at i:41485296 original size:11 final size:11
Alignment explanation
Indices: 41485280--41485307 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
41485270 GTATGTTATG
41485280 GCTTTGTGTGT
1 GCTTTGTGTGT
41485291 GCTTTGTGTGT
1 GCTTTGTGTGT
41485302 GCTTTG
1 GCTTTG
41485308 CGCGTGCTTA
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:0.00, C:0.11, G:0.36, T:0.54
Consensus pattern (11 bp):
GCTTTGTGTGT
Found at i:41487474 original size:16 final size:16
Alignment explanation
Indices: 41487453--41487494 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
41487443 TTATTAAATT
*
41487453 ATATATTTTAATTATA
1 ATATATTTTAATAATA
41487469 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
41487484 AT-TATGTTTAA
1 ATATAT-TTTAA
41487495 NNNNNNNNNN
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:41487479 original size:15 final size:15
Alignment explanation
Indices: 41487444--41487485 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
41487434 TTAAGAATTT
*
41487444 TATTAAATTAT-ATA
1 TATTTAATTATAATA
41487458 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
41487472 TATTTAATAATAAT
1 TATTTAATTATAAT
41487486 TATGTTTAAN
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:41487672 original size:45 final size:44
Alignment explanation
Indices: 41487586--41487680 Score: 145
Period size: 45 Copynumber: 2.1 Consensus size: 44
41487576 TTACACCTCT
*
41487586 ATTACATTCAACCAAACACAGGATTGCTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACACAGGATTGCTATTACACCTCTATTCC
***
41487630 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACACAGGA-TTGCTATTACACCTCTATTCC
41487675 ATTACA
1 ATTACA
41487681 CCTCTAATCC
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 20 0.43
45 26 0.57
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (44 bp):
ATTACATTCAACCAAACACAGGATTGCTATTACACCTCTATTCC
Found at i:41487680 original size:16 final size:16
Alignment explanation
Indices: 41487659--41487728 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
41487649 TTGATTTGCT
*
41487659 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
41487675 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
41487691 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
*
41487707 ATTACGCCTCTAATCC
1 ATTACACCTCTAATCC
*
41487723 AATACA
1 ATTACA
41487729 GCGAACCAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:41487700 original size:32 final size:32
Alignment explanation
Indices: 41487659--41487728 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
41487649 TTGATTTGCT
41487659 ATTACACCTCTATTCCATTACACCTCTAATCC
1 ATTACACCTCTATTCCATTACACCTCTAATCC
*
41487691 ATTACACCTCTATTCCATTACGCCTCTAATCC
1 ATTACACCTCTATTCCATTACACCTCTAATCC
*
41487723 AATACA
1 ATTACA
41487729 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.33
Consensus pattern (32 bp):
ATTACACCTCTATTCCATTACACCTCTAATCC
Found at i:41490625 original size:13 final size:13
Alignment explanation
Indices: 41490607--41490633 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41490597 CTTGAAGTAT
41490607 AAACAATTTTTAA
1 AAACAATTTTTAA
41490620 AAACAATTTTTAA
1 AAACAATTTTTAA
41490633 A
1 A
41490634 CAAAAAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (13 bp):
AAACAATTTTTAA
Found at i:41490881 original size:25 final size:26
Alignment explanation
Indices: 41490853--41490901 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
41490843 GTATGATTAT
*
41490853 TTGGTTTGAACAATA-TGTAGTATCA
1 TTGGTATGAACAATATTGTAGTATCA
41490878 TTGGTATGAACAATATTGTAGTAT
1 TTGGTATGAACAATATTGTAGTAT
41490902 TATGTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (26 bp):
TTGGTATGAACAATATTGTAGTATCA
Found at i:41494632 original size:7 final size:7
Alignment explanation
Indices: 41494620--41494648 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
41494610 TTTAAACATA
41494620 TAATTAT
1 TAATTAT
41494627 TAATTAT
1 TAATTAT
41494634 TAATTA-
1 TAATTAT
41494640 TAATTAT
1 TAATTAT
41494647 TA
1 TA
41494649 TATTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
TAATTAT
Found at i:41497072 original size:3 final size:3
Alignment explanation
Indices: 41497066--41497094 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
41497056 AGAAGAAGAA
41497066 GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
41497095 AGATATGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:41498642 original size:31 final size:30
Alignment explanation
Indices: 41498603--41498703 Score: 96
Period size: 31 Copynumber: 3.3 Consensus size: 30
41498593 TTATATTTAT
41498603 ATAGAAATCAATAATTGAGTTATAAATAAA
1 ATAGAAATCAATAATTGAGTTATAAATAAA
*** * ** * * *
41498633 ATAGTAAATCAGGCATTAAAATAT-ATTTAT
1 ATAG-AAATCAATAATTGAGTTATAAATAAA
41498663 ATAGAAATCAATAATTGAGTTATAAATAAA
1 ATAGAAATCAATAATTGAGTTATAAATAAA
41498693 ATAGTAAATCA
1 ATAG-AAATCA
41498704 TTTATGATTA
Statistics
Matches: 50, Mismatches: 18, Indels: 5
0.68 0.25 0.07
Matches are distributed among these distances:
29 13 0.26
30 18 0.36
31 19 0.38
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.32
Consensus pattern (30 bp):
ATAGAAATCAATAATTGAGTTATAAATAAA
Found at i:41498669 original size:60 final size:61
Alignment explanation
Indices: 41498583--41498703 Score: 235
Period size: 60 Copynumber: 2.0 Consensus size: 61
41498573 TCAGAAAAAT
41498583 GGCATTAAAATTATATTTATATAGAAATCAATAATTGAGTTATAAATAAAATAGTAAATCA
1 GGCATTAAAATTATATTTATATAGAAATCAATAATTGAGTTATAAATAAAATAGTAAATCA
41498644 GGCATTAAAA-TATATTTATATAGAAATCAATAATTGAGTTATAAATAAAATAGTAAATCA
1 GGCATTAAAATTATATTTATATAGAAATCAATAATTGAGTTATAAATAAAATAGTAAATCA
41498704 TTTATGATTA
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 50 0.83
61 10 0.17
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.34
Consensus pattern (61 bp):
GGCATTAAAATTATATTTATATAGAAATCAATAATTGAGTTATAAATAAAATAGTAAATCA
Found at i:41498686 original size:29 final size:29
Alignment explanation
Indices: 41498593--41498686 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
41498583 GGCATTAAAA
41498593 TTATATTTATATAGAAATCAATAATTGAG
1 TTATATTTATATAGAAATCAATAATTGAG
* * * *** * *
41498622 TTATAAATAAAATAGTAAATCAGGCATTAAA
1 TTAT-ATTTATATAG-AAATCAATAATTGAG
*
41498653 ATATATTTATATAGAAATCAATAATTGAG
1 TTATATTTATATAGAAATCAATAATTGAG
41498682 TTATA
1 TTATA
41498687 AATAAAATAG
Statistics
Matches: 45, Mismatches: 18, Indels: 4
0.67 0.27 0.06
Matches are distributed among these distances:
29 18 0.40
30 14 0.31
31 13 0.29
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.37
Consensus pattern (29 bp):
TTATATTTATATAGAAATCAATAATTGAG
Found at i:41500935 original size:59 final size:60
Alignment explanation
Indices: 41500816--41500935 Score: 143
Period size: 60 Copynumber: 2.0 Consensus size: 60
41500806 TGGGTGACCA
* * * *
41500816 ATTTATAATTTTTCATAGTTGGGTGACCAAAAAAAGAAATTAACTATTAATTGAGTGACT
1 ATTTATAACTTTTCATAGTTGGATGACCAAAAAAAGAAATTAACTAATAATTGAGCGACT
* ** * * *
41500876 ATTTGTAACTTTTCATAGTTGGATGATTAAAAATA-AAATTTACTAATAATTGGGCGACT
1 ATTTATAACTTTTCATAGTTGGATGACCAAAAAAAGAAATTAACTAATAATTGAGCGACT
41500935 A
1 A
41500936 CTAGTACAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
59 21 0.42
60 29 0.58
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (60 bp):
ATTTATAACTTTTCATAGTTGGATGACCAAAAAAAGAAATTAACTAATAATTGAGCGACT
Found at i:41504991 original size:27 final size:27
Alignment explanation
Indices: 41504953--41505029 Score: 120
Period size: 27 Copynumber: 2.9 Consensus size: 27
41504943 TAGTATTGGC
41504953 GCCTATCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
41504980 GCCTACCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
41505007 GCC-ATTCTGAGAGGCGCCAATGG
1 GCCTA-TCTGGGAGGCGCCAATGG
41505030 GCCGGGCCGG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 45 0.98
ACGTcount: A:0.17, C:0.25, G:0.39, T:0.19
Consensus pattern (27 bp):
GCCTATCTGGGAGGCGCCAATGGTGGT
Found at i:41505272 original size:19 final size:19
Alignment explanation
Indices: 41505250--41505287 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
41505240 AATTTAATTT
*
41505250 ATTAGTAATAAATTACTAA
1 ATTACTAATAAATTACTAA
*
41505269 ATTACTAATAAGTTACTAA
1 ATTACTAATAAATTACTAA
41505288 TAAATTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (19 bp):
ATTACTAATAAATTACTAA
Found at i:41505567 original size:19 final size:19
Alignment explanation
Indices: 41505545--41505582 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
41505535 TATAAATTTA
*
41505545 TTAGTAACTTATTAGTAAT
1 TTAGTAACTTATTACTAAT
*
41505564 TTAGTAATTTATTACTAAT
1 TTAGTAACTTATTACTAAT
41505583 AAATTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (19 bp):
TTAGTAACTTATTACTAAT
Found at i:41505841 original size:27 final size:28
Alignment explanation
Indices: 41505803--41505879 Score: 115
Period size: 27 Copynumber: 2.9 Consensus size: 28
41505793 CCGGCCCGGC
*
41505803 CCATTGGCGCCTCTCAGAAT-GGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
*
41505830 CCATTGGCGCCTCCCAG-GTAGGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
41505857 CCATTGGCGCCTCCCAG-ATAGGC
1 CCATTGGCGCCTCCCAGAATAGGC
41505880 GCCAATACTA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 45 0.98
ACGTcount: A:0.19, C:0.39, G:0.25, T:0.17
Consensus pattern (28 bp):
CCATTGGCGCCTCCCAGAATAGGCACCA
Found at i:41509774 original size:43 final size:43
Alignment explanation
Indices: 41509719--41509806 Score: 144
Period size: 43 Copynumber: 2.0 Consensus size: 43
41509709 GTCTAAACTC
41509719 AAAAAATAATCTTATTTG-TTTCAAAATAAAAAT-AAACAATTA
1 AAAAAATAATCTTATTTGCTTT-AAAATAAAAATAAAACAATTA
41509761 AAAAATATAATCTTATTTGCTTTAAAATAAAAATAAAACAATTA
1 AAAAA-ATAATCTTATTTGCTTTAAAATAAAAATAAAACAATTA
41509805 AA
1 AA
41509807 TTAAATTCAG
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
42 5 0.12
43 24 0.56
44 14 0.33
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (43 bp):
AAAAAATAATCTTATTTGCTTTAAAATAAAAATAAAACAATTA
Found at i:41510339 original size:28 final size:28
Alignment explanation
Indices: 41510292--41510354 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 28
41510282 CATTTTGGAA
*
41510292 TTATAAAAAAAACATAAAAATA-AAA-T
1 TTATAAAAAAAAAATAAAAATATAAATT
*
41510318 TTATAAAAAAATATAATTAAAATATAAATT
1 TTATAAAAAAA-A-AATAAAAATATAAATT
41510348 TTATAAA
1 TTATAAA
41510355 CATTAGTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 11 0.35
27 1 0.03
28 8 0.26
29 3 0.10
30 8 0.26
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (28 bp):
TTATAAAAAAAAAATAAAAATATAAATT
Found at i:41522906 original size:16 final size:15
Alignment explanation
Indices: 41522877--41522910 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
41522867 TTAAAAGTAA
41522877 AATAATATAACATAC
1 AATAATATAACATAC
*
41522892 AATAACTATATCATAC
1 AATAA-TATAACATAC
41522908 AAT
1 AAT
41522911 TATTCAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (15 bp):
AATAATATAACATAC
Found at i:41537448 original size:34 final size:34
Alignment explanation
Indices: 41537405--41537477 Score: 146
Period size: 34 Copynumber: 2.1 Consensus size: 34
41537395 AAGACCAAAC
41537405 CATGATGGTGAAACTTGTCCAATACAATATCTAT
1 CATGATGGTGAAACTTGTCCAATACAATATCTAT
41537439 CATGATGGTGAAACTTGTCCAATACAATATCTAT
1 CATGATGGTGAAACTTGTCCAATACAATATCTAT
41537473 CATGA
1 CATGA
41537478 CTTGTTCTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.32
Consensus pattern (34 bp):
CATGATGGTGAAACTTGTCCAATACAATATCTAT
Found at i:41537592 original size:31 final size:30
Alignment explanation
Indices: 41537557--41537654 Score: 83
Period size: 31 Copynumber: 3.2 Consensus size: 30
41537547 ATTGAATATT
41537557 ATTTGATATCTAATTTTAATTTTAATGTTCA
1 ATTTGATATCTAA-TTTAATTTTAATGTTCA
**
41537588 ATTTGATA-CTTCAATTT-ATTTTTTTGTTCTA
1 ATTTGATATC-T-AATTTAATTTTAATGTTC-A
* * *
41537619 ATTTGATATTTAAGTTTAAGTTCAATGTTCA
1 ATTTGATATCTAA-TTTAATTTTAATGTTCA
*
41537650 CTTTG
1 ATTTG
41537655 GCACATGAGT
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
30 13 0.25
31 30 0.57
32 10 0.19
ACGTcount: A:0.28, C:0.08, G:0.09, T:0.55
Consensus pattern (30 bp):
ATTTGATATCTAATTTAATTTTAATGTTCA
Found at i:41538415 original size:18 final size:19
Alignment explanation
Indices: 41538376--41538421 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
41538366 GATAATTTTT
41538376 TTTATAAATTAAATACACTA
1 TTTA-AAATTAAATACACTA
41538396 -TTAAAATCTAAATACA-TA
1 TTTAAAAT-TAAATACACTA
41538414 TTTAAAAT
1 TTTAAAAT
41538422 ATAATTAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (19 bp):
TTTAAAATTAAATACACTA
Found at i:41541893 original size:19 final size:19
Alignment explanation
Indices: 41541871--41541908 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
41541861 TTTGAATTGA
41541871 TTTATAATTT-TTATAATTT
1 TTTATAATTTATTA-AATTT
*
41541890 TTTATTATTTATTAAATTT
1 TTTATAATTTATTAAATTT
41541909 AGTATTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATAATTTATTAAATTT
Found at i:41543388 original size:1 final size:1
Alignment explanation
Indices: 41543382--41543440 Score: 118
Period size: 1 Copynumber: 59.0 Consensus size: 1
41543372 TTTTGGGGTT
41543382 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
41543441 AAGGAAAGGT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:41548339 original size:6 final size:6
Alignment explanation
Indices: 41548330--41548364 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
41548320 TATATATTTA
41548330 TATGCT TATGCT TATGCT TATGCT TATGCT TATGC
1 TATGCT TATGCT TATGCT TATGCT TATGCT TATGC
41548365 GTTGGTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (6 bp):
TATGCT
Found at i:41556479 original size:26 final size:25
Alignment explanation
Indices: 41556426--41556480 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
41556416 ATTTTCTGTC
* * **
41556426 AATTTGATTCTTATTTTTTAAATTA
1 AATTTGATTATTATCTTTTAAAAAA
41556451 AATTTGATTATTAATCTTTTAAAAAA
1 AATTTGATTATT-ATCTTTTAAAAAA
41556477 AATT
1 AATT
41556481 AAATCTCTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (25 bp):
AATTTGATTATTATCTTTTAAAAAA
Found at i:41559950 original size:54 final size:54
Alignment explanation
Indices: 41559846--41559950 Score: 122
Period size: 54 Copynumber: 1.9 Consensus size: 54
41559836 ATGTTAAAAG
* * ****
41559846 ATTAAAGTATAAGGATTAAATCTTAAATATAAGCATATTGTGGTTAAAATTGAA
1 ATTAAACTATAAGGATTAAATCTTAAATATAAGCATACTAAAATTAAAATTGAA
* *
41559900 ATTAAACTATAAGGATTAAATCTT-AATTTAAGCATAACTAAAATTGAAATT
1 ATTAAACTATAAGGATTAAATCTTAAATATAAGCAT-ACTAAAATTAAAATT
41559951 AAAGTATAAG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
53 10 0.24
54 32 0.76
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.35
Consensus pattern (54 bp):
ATTAAACTATAAGGATTAAATCTTAAATATAAGCATACTAAAATTAAAATTGAA
Found at i:41566362 original size:40 final size:40
Alignment explanation
Indices: 41566316--41566397 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
41566306 ATATAATTAT
*
41566316 TATATTTAAGAACTTATTCAATTACTCTAATATAAAATTG
1 TATATTTAAGAACTGATTCAATTACTCTAATATAAAATTG
41566356 TATATTTAAGAACTGATTCAATTACTCTAATATAAAATTG
1 TATATTTAAGAACTGATTCAATTACTCTAATATAAAATTG
41566396 TA
1 TA
41566398 CTTTTATAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (40 bp):
TATATTTAAGAACTGATTCAATTACTCTAATATAAAATTG
Found at i:41567824 original size:27 final size:27
Alignment explanation
Indices: 41567786--41567854 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 27
41567776 GGTCGGGTGG
41567786 GCCTCATAGGGAGGCACCATTAAAAGT
1 GCCTCATAGGGAGGCACCATTAAAAGT
*
41567813 GCCTTATAGGGAGGCACCATTAAAAGT
1 GCCTCATAGGGAGGCACCATTAAAAGT
*
41567840 GCATCATAGGGAGGC
1 GCCTCATAGGGAGGC
41567855 GCCAATGAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.32, C:0.20, G:0.29, T:0.19
Consensus pattern (27 bp):
GCCTCATAGGGAGGCACCATTAAAAGT
Found at i:41567912 original size:19 final size:19
Alignment explanation
Indices: 41567863--41568004 Score: 121
Period size: 19 Copynumber: 7.3 Consensus size: 19
41567853 GCGCCAATGA
*
41567863 GTAATTTTGTATGTATATT
1 GTAATTTTGTATGAATATT
41567882 GTAACTTTTTGTATGAATATT
1 GTAA--TTTTGTATGAATATT
41567903 GTAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
** *
41567922 GTAA-TTAATATTGTAATTTT
1 GTAATTTTGTA-TG-AATATT
* *
41567942 GT-A--TGGATATTGTAATTTT
1 GTAATTTTG-TA-TG-AATATT
*
41567961 GTAATTTTATATGAATATT
1 GTAATTTTGTATGAATATT
*
41567980 ATAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
41567999 GTAATT
1 GTAATT
41568005 ATTTTATAAT
Statistics
Matches: 103, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
18 5 0.05
19 67 0.65
20 10 0.10
21 20 0.19
22 1 0.01
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.54
Consensus pattern (19 bp):
GTAATTTTGTATGAATATT
Found at i:41567932 original size:31 final size:31
Alignment explanation
Indices: 41567897--41567985 Score: 123
Period size: 31 Copynumber: 3.0 Consensus size: 31
41567887 TTTTTGTATG
41567897 AATATTGTAATTTTGTATGAATATTGTAATT
1 AATATTGTAATTTTGTATGAATATTGTAATT
*
41567928 AATATTGTAATTTTGTATGGATATTGTAA-T
1 AATATTGTAATTTTGTATGAATATTGTAATT
* *
41567958 --T-TTGTAATTTTATATGAATATTATAATT
1 AATATTGTAATTTTGTATGAATATTGTAATT
41567986 TTGTATGAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
27 22 0.42
28 2 0.04
30 1 0.02
31 28 0.53
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (31 bp):
AATATTGTAATTTTGTATGAATATTGTAATT
Found at i:41567965 original size:27 final size:27
Alignment explanation
Indices: 41567901--41567990 Score: 117
Period size: 27 Copynumber: 3.2 Consensus size: 27
41567891 TGTATGAATA
41567901 TTGTAATTTTGTATGAATATTGTAATTAAT
1 TTGTAATTTTGTATGAATATTGTAA-T--T
*
41567931 ATTGTAATTTTGTATGGATATTGTAATT
1 -TTGTAATTTTGTATGAATATTGTAATT
* *
41567959 TTGTAATTTTATATGAATATTATAATT
1 TTGTAATTTTGTATGAATATTGTAATT
41567986 TTGTA
1 TTGTA
41567991 TGAATATTGT
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
27 29 0.53
28 1 0.02
30 1 0.02
31 24 0.44
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.54
Consensus pattern (27 bp):
TTGTAATTTTGTATGAATATTGTAATT
Found at i:41568050 original size:61 final size:61
Alignment explanation
Indices: 41567983--41568126 Score: 261
Period size: 61 Copynumber: 2.4 Consensus size: 61
41567973 GAATATTATA
* *
41567983 ATTTTGTATGAATATTGTAATTATTTTATAATTAGTTTTATATTTATAGTTTTTTATTAGT
1 ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTATATTTATAGTTTTTGATTAGT
*
41568044 ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAGT
1 ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTATATTTATAGTTTTTGATTAGT
41568105 ATTTTGTATGAATATTGTAATT
1 ATTTTGTATGAATATTGTAATT
41568127 TTGTANNNNN
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 80 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (61 bp):
ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTATATTTATAGTTTTTGATTAGT
Found at i:41568671 original size:15 final size:16
Alignment explanation
Indices: 41568635--41568676 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
41568625 CTCATTTAAT
*
41568635 TTTTATATAATGTAAC
1 TTTTATATTATGTAAC
41568651 TTTTATATTATGTAA-
1 TTTTATATTATGTAAC
*
41568666 TTTTATTTTAT
1 TTTTATATTAT
41568677 TTTGTATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (16 bp):
TTTTATATTATGTAAC
Found at i:41569313 original size:23 final size:23
Alignment explanation
Indices: 41569264--41569314 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
41569254 ACTTGTTTAA
* * *
41569264 GTGGACAAATATGGGGCTGACAC
1 GTGGACAAATAAGGGGATAACAC
* *
41569287 GTGGAGAAATAAGGGGATAACAT
1 GTGGACAAATAAGGGGATAACAC
41569310 GTGGA
1 GTGGA
41569315 TGCATCTTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.10, G:0.37, T:0.18
Consensus pattern (23 bp):
GTGGACAAATAAGGGGATAACAC
Found at i:41569506 original size:18 final size:19
Alignment explanation
Indices: 41569467--41569506 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
41569457 TTAAAATTTC
* *
41569467 TAAAAAAATTAAATAGGTT
1 TAAAAAAATTAAAAAGGGT
41569486 TAAAAAAA-TAAAAAGGGT
1 TAAAAAAATTAAAAAGGGT
41569504 TAA
1 TAA
41569507 TTTTTGGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (19 bp):
TAAAAAAATTAAAAAGGGT
Found at i:41569761 original size:25 final size:25
Alignment explanation
Indices: 41569716--41569773 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
41569706 ATGACTTCTT
*
41569716 TTTTAAATTTTTTGTGCATTTTTAAA
1 TTTTAAATTTTTTAT-CATTTTTAAA
*
41569742 TTTTAAATTTTTATAT-ATTTTTAGA
1 TTTTAAATTTTT-TATCATTTTTAAA
41569767 TTTTAAA
1 TTTTAAA
41569774 AAATTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 15 0.52
26 12 0.41
27 2 0.07
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (25 bp):
TTTTAAATTTTTTATCATTTTTAAA
Found at i:41569780 original size:25 final size:25
Alignment explanation
Indices: 41569733--41569780 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
41569723 TTTTTTGTGC
***
41569733 ATTTTTAAATTTTAAATTTTTATAT
1 ATTTTTAAATTTTAAAAAATTATAT
*
41569758 ATTTTTAGATTTTAAAAAATTAT
1 ATTTTTAAATTTTAAAAAATTAT
41569781 TTTTATTTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
ATTTTTAAATTTTAAAAAATTATAT
Found at i:41569821 original size:82 final size:82
Alignment explanation
Indices: 41569758--41569947 Score: 276
Period size: 82 Copynumber: 2.3 Consensus size: 82
41569748 ATTTTTATAT
*
41569758 ATTTTTAG-A-TTTTAAAAAATTATTTTTATTTTTTGTAAGTTGAATATTTAAAGATAATATTTT
1 ATTTTTAGAATTTTTAAAAAA--ATGTTTATTTTTTG-AAGTTGAATATTTAAAGATAATATTTT
41569821 AAATGTTAAAATTTAACTTA
63 AAATGTTAAAATTTAACTTA
* **
41569841 ATTTTTTGAATTTTTTCAAAAATGTTTATTTTTTGAAGTTGAATATTTAAAGATAATATTTTAAA
1 ATTTTTAGAATTTTTAAAAAAATGTTTATTTTTTGAAGTTGAATATTTAAAGATAATATTTTAAA
41569906 TGTTAAAATTTAACTTA
66 TGTTAAAATTTAACTTA
* **
41569923 ATTTTTTGAATTTTTTCAAAAATGT
1 ATTTTTAGAATTTTTAAAAAAATGT
41569948 AAGCTTTTTT
Statistics
Matches: 101, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
82 72 0.71
83 20 0.20
84 1 0.01
85 8 0.08
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (82 bp):
ATTTTTAGAATTTTTAAAAAAATGTTTATTTTTTGAAGTTGAATATTTAAAGATAATATTTTAAA
TGTTAAAATTTAACTTA
Found at i:41569847 original size:27 final size:28
Alignment explanation
Indices: 41569812--41569929 Score: 61
Period size: 27 Copynumber: 4.3 Consensus size: 28
41569802 TATTTAAAGA
*
41569812 TAATATTTTAAATGTT-AAAATTTAACT
1 TAATTTTTTAAATGTTAAAAATTTAACT
* * *
41569839 TAATTTTTTGAATTTTTTCAAAAATGT---T
1 TAATTTTTT-AA-ATGTT-AAAAATTTAACT
* * * **
41569867 T-ATTTTTTGAA-GTTGAATATTTAAAGA
1 TAATTTTTTAAATGTTAAAAATTT-AACT
*
41569894 TAATATTTTAAATGTT-AAAATTTAACT
1 TAATTTTTTAAATGTTAAAAATTTAACT
41569921 TAATTTTTT
1 TAATTTTTT
41569930 GAATTTTTTC
Statistics
Matches: 64, Mismatches: 17, Indels: 20
0.63 0.17 0.20
Matches are distributed among these distances:
23 5 0.08
24 2 0.03
26 1 0.02
27 26 0.41
28 18 0.28
29 6 0.09
31 6 0.09
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (28 bp):
TAATTTTTTAAATGTTAAAAATTTAACT
Found at i:41569956 original size:82 final size:83
Alignment explanation
Indices: 41569787--41569956 Score: 299
Period size: 82 Copynumber: 2.1 Consensus size: 83
41569777 TTATTTTTAT
41569787 TTTTTGTAAGTTGAATATTTAAAGATAATATTTTAAATGTTAAAATTTAACTTAATTTTTTGAAT
1 TTTTTGTAAGTTGAATATTTAAAGATAATATTTTAAATGTTAAAATTTAACTTAATTTTTTGAAT
* *
41569852 TTTTTCAAAAATGTTTAT
66 TTTTTCAAAAATGTTAAC
41569870 TTTTTG-AAGTTGAATATTTAAAGATAATATTTTAAATGTTAAAATTTAACTTAATTTTTTGAAT
1 TTTTTGTAAGTTGAATATTTAAAGATAATATTTTAAATGTTAAAATTTAACTTAATTTTTTGAAT
41569934 TTTTTCAAAAATG-TAAGC
66 TTTTTCAAAAATGTTAA-C
41569952 TTTTT
1 TTTTT
41569957 TTTTTTTAAG
Statistics
Matches: 84, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
81 2 0.02
82 76 0.90
83 6 0.07
ACGTcount: A:0.37, C:0.03, G:0.09, T:0.51
Consensus pattern (83 bp):
TTTTTGTAAGTTGAATATTTAAAGATAATATTTTAAATGTTAAAATTTAACTTAATTTTTTGAAT
TTTTTCAAAAATGTTAAC
Found at i:41574083 original size:15 final size:15
Alignment explanation
Indices: 41574065--41574096 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
41574055 ATAGAAATAT
41574065 GTGGTAATAAAATCA
1 GTGGTAATAAAATCA
41574080 GTGGTAATAAAATCA
1 GTGGTAATAAAATCA
41574095 GT
1 GT
41574097 AAAAATTTGA
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:0.44, C:0.06, G:0.22, T:0.28
Consensus pattern (15 bp):
GTGGTAATAAAATCA
Found at i:41580902 original size:19 final size:21
Alignment explanation
Indices: 41580875--41580913 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
41580865 AAATAAGAAT
41580875 TTTCGAAT-ATAA-CTTAAAA
1 TTTCGAATAATAACCTTAAAA
*
41580894 TTTCTAATAATAACCTTAAA
1 TTTCGAATAATAACCTTAAA
41580914 TGTAATTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 4 0.24
21 6 0.35
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (21 bp):
TTTCGAATAATAACCTTAAAA
Found at i:41585970 original size:2 final size:2
Alignment explanation
Indices: 41585912--41585950 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
41585902 ACTAAAACAA
41585912 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 A
41585951 AGAAAAAANN
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41595102 original size:100 final size:102
Alignment explanation
Indices: 41594932--41595148 Score: 411
Period size: 100 Copynumber: 2.1 Consensus size: 102
41594922 TCATCAAAAA
41594932 TTAACATCAAAACAGTTGCATTTGACAAAATCAATGGCATTAGGTCATAACTCTAACCAAAAAAA
1 TTAACATCAAAACAGTTGCATTTGACAAAATCAATGGCATTAGGTCATAACTCTAACCAAAAAAA
41594997 AAAAAACCTAAAATTGACAGAAATTAGAACAAACAT-
66 AAAAAACCTAAAATTGACAGAAATTAGAACAAACATG
41595033 TTAACATCAAAACAGTTGCA-TTGACAAAATCAATGGCATTAGGTCATAACTCTAACCAAAAAAA
1 TTAACATCAAAACAGTTGCATTTGACAAAATCAATGGCATTAGGTCATAACTCTAACCAAAAAAA
41595097 AAAAAACCTAAAATTGACAGAAATTAGAACAAACATG
66 AAAAAACCTAAAATTGACAGAAATTAGAACAAACATG
41595134 TTAACATCATAAACA
1 TTAACATCA-AAACA
41595149 ACCCAAATCA
Statistics
Matches: 114, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
100 80 0.70
101 29 0.25
102 5 0.04
ACGTcount: A:0.52, C:0.17, G:0.10, T:0.22
Consensus pattern (102 bp):
TTAACATCAAAACAGTTGCATTTGACAAAATCAATGGCATTAGGTCATAACTCTAACCAAAAAAA
AAAAAACCTAAAATTGACAGAAATTAGAACAAACATG
Found at i:41597979 original size:31 final size:31
Alignment explanation
Indices: 41597904--41597979 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
41597894 AAATGTGATC
*
41597904 GATTACAGGGTATG-ATAGGTAAATGTAAAT
1 GATTACAGGGTATGAATAGGTAAATATAAAT
* * * * *
41597934 GATTACATGATATGAATATGTGAATATGAAT
1 GATTACAGGGTATGAATAGGTAAATATAAAT
*
41597965 GATTATAGGGTATGA
1 GATTACAGGGTATGA
41597980 TAATGCAAAT
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
30 12 0.33
31 24 0.67
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (31 bp):
GATTACAGGGTATGAATAGGTAAATATAAAT
Found at i:41598558 original size:23 final size:24
Alignment explanation
Indices: 41598514--41598560 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
41598504 AAGTATATAA
41598514 AAGATTATGCGATCCATTTAGAAT
1 AAGATTATGCGATCCATTTAGAAT
41598538 AAGATTATGCGAT-CATTTAGAAT
1 AAGATTATGCGATCCATTTAGAAT
41598561 CGAGCCTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (24 bp):
AAGATTATGCGATCCATTTAGAAT
Found at i:41605262 original size:73 final size:74
Alignment explanation
Indices: 41605171--41605317 Score: 287
Period size: 73 Copynumber: 2.0 Consensus size: 74
41605161 AAATATTTAC
41605171 ACTTAAATTTTATTAATATTTTTATAATTCGATAAATCGTACTTTGATTCAAAAAATTAAAATTT
1 ACTTAAATTTTATTAATATTTTTATAATTCGATAAATCGTACTTTGATTCAAAAAATTAAAATTT
41605236 TATAGATCT
66 TATAGATCT
41605245 ACTTAAA-TTTATTAATATTTTTATAATTCGATAAATCGTACTTTGATTCAAAAAATTAAAATTT
1 ACTTAAATTTTATTAATATTTTTATAATTCGATAAATCGTACTTTGATTCAAAAAATTAAAATTT
41605309 TATAGATCT
66 TATAGATCT
41605318 CTACTTTATA
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 66 0.90
74 7 0.10
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (74 bp):
ACTTAAATTTTATTAATATTTTTATAATTCGATAAATCGTACTTTGATTCAAAAAATTAAAATTT
TATAGATCT
Found at i:41610866 original size:86 final size:86
Alignment explanation
Indices: 41610742--41611938 Score: 2358
Period size: 86 Copynumber: 13.9 Consensus size: 86
41610732 AAGTGTCCGG
41610742 TAAGCCTCCCCGAGGGAGGTATGGAGGGGTAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
1 TAAGCCTCCCCGAGGGAGGTATGGAGGGGTAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
41610807 TTGTTTGCACGGGATTTAATA
66 TTGTTTGCACGGGATTTAATA
41610828 TAAGCCTCCCCGAGGGAGGTATGGAGGGGTAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
1 TAAGCCTCCCCGAGGGAGGTATGGAGGGGTAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
41610893 TTGTTTGCACGGGATTTAATA
66 TTGTTTGCACGGGATTTAATA
41610914 TAAGCCTCCCCGAGGGAGGTATGGAGGGGTAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
1 TAAGCCTCCCCGAGGGAGGTATGGAGGGGTAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
41610979 TTGTTTGCACGGGATTTAATA
66 TTGTTTGCACGGGATTTAATA
41611000 TAAGCCTCCCCGAGGGAGGTATGGAGGGGTAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
1 TAAGCCTCCCCGAGGGAGGTATGGAGGGGTAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
41611065 TTGTTTGCACGGGATTTAATA
66 TTGTTTGCACGGGATTTAATA
41611086 TAAGCCTCCCCGAGGGAGGTATGGAGGGGTAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
1 TAAGCCTCCCCGAGGGAGGTATGGAGGGGTAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
41611151 TTGTTTGCACGGGATTTAATA
66 TTGTTTGCACGGGATTTAATA
41611172 TAAGCCTCCCCGAGGGAGGTATGGAGGGGTAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
1 TAAGCCTCCCCGAGGGAGGTATGGAGGGGTAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
41611237 TTGTTTGCACGGGATTTAATA
66 TTGTTTGCACGGGATTTAATA
41611258 TAAGCCTCCCCGAGGGAGGTATGGAGGGGTAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
1 TAAGCCTCCCCGAGGGAGGTATGGAGGGGTAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
41611323 TTGTTTGCACGGGATTTAATA
66 TTGTTTGCACGGGATTTAATA
41611344 TAAGCCTCCCCGAGGGAGGTATGGAGGGGTAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
1 TAAGCCTCCCCGAGGGAGGTATGGAGGGGTAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
41611409 TTGTTTGCACGGGATTTAATA
66 TTGTTTGCACGGGATTTAATA
41611430 TAAGCCTCCCCGAGGGAGGTATGGAGGGGTAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
1 TAAGCCTCCCCGAGGGAGGTATGGAGGGGTAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
41611495 TTGTTTGCACGGGATTTAATA
66 TTGTTTGCACGGGATTTAATA
41611516 TAAGCCTCCCCGAGGGAGGTATGGAGGGGTAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
1 TAAGCCTCCCCGAGGGAGGTATGGAGGGGTAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
41611581 TTGTTTGCACGGGATTTAATA
66 TTGTTTGCACGGGATTTAATA
*
41611602 TAAGCCTCCCCGAGGGAGGTATGGAGGGGGAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
1 TAAGCCTCCCCGAGGGAGGTATGGAGGGGTAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
41611667 TTGTTTGCACGGGATTTAATA
66 TTGTTTGCACGGGATTTAATA
*
41611688 TAAGCCTCCCCGAGGGAGGTATGGAGGGGGAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
1 TAAGCCTCCCCGAGGGAGGTATGGAGGGGTAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
41611753 TTGTTTGCACGGGATTTAATA
66 TTGTTTGCACGGGATTTAATA
*
41611774 TAAGCCTCCCCGAGGGAGGTATGGAGGGGGAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
1 TAAGCCTCCCCGAGGGAGGTATGGAGGGGTAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
41611839 TTGTTTGCACGGGATTTAATA
66 TTGTTTGCACGGGATTTAATA
*
41611860 TAAGCCTCCCCGAGGGAGGTATGGAGGGGGAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
1 TAAGCCTCCCCGAGGGAGGTATGGAGGGGTAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
41611925 TTGTTTGCACGGGA
66 TTGTTTGCACGGGA
41611939 GAGATCACAC
Statistics
Matches: 1110, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 1110 1.00
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.32
Consensus pattern (86 bp):
TAAGCCTCCCCGAGGGAGGTATGGAGGGGTAACGTTCCTAGTGTAGTTATAGTGTTGTTACCCTC
TTGTTTGCACGGGATTTAATA
Found at i:41613725 original size:11 final size:11
Alignment explanation
Indices: 41613709--41613742 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
41613699 TTTTGTCTCA
41613709 CGCTACAGTAT
1 CGCTACAGTAT
41613720 CGCTACAGTAT
1 CGCTACAGTAT
*
41613731 CGCTACAATAT
1 CGCTACAGTAT
41613742 C
1 C
41613743 TAATCTCACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (11 bp):
CGCTACAGTAT
Found at i:41614323 original size:17 final size:20
Alignment explanation
Indices: 41614289--41614327 Score: 57
Period size: 17 Copynumber: 2.1 Consensus size: 20
41614279 GATAATTTAG
41614289 TTTTTAACATTTACATTTTT
1 TTTTTAACATTTACATTTTT
41614309 TTTTTAA-A-TTA-ATTTTT
1 TTTTTAACATTTACATTTTT
41614326 TT
1 TT
41614328 CTTTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 3 0.16
19 1 0.05
20 7 0.37
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTTAACATTTACATTTTT
Found at i:41614626 original size:31 final size:31
Alignment explanation
Indices: 41614591--41614652 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
41614581 TAAAATGGGG
*
41614591 TTTTAGGTTCCTTAAAAGTTGG-AGAAATTTT
1 TTTTAGGTCCCTTAAAAGTTGGTA-AAATTTT
41614622 TTTTAGGTCCCTTAAAAGTTGGTAAAATTTT
1 TTTTAGGTCCCTTAAAAGTTGGTAAAATTTT
41614653 ATTCTTAACC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (31 bp):
TTTTAGGTCCCTTAAAAGTTGGTAAAATTTT
Found at i:41614972 original size:2 final size:2
Alignment explanation
Indices: 41614967--41614991 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41614957 AAAAAAAAAA
41614967 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
41614992 AACATTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41616936 original size:20 final size:20
Alignment explanation
Indices: 41616911--41616951 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
41616901 CCTTTCTCTT
41616911 TTACTTCTTCAACATTTGGG
1 TTACTTCTTCAACATTTGGG
*
41616931 TTACTTCTTCAAGATTTGGG
1 TTACTTCTTCAACATTTGGG
41616951 T
1 T
41616952 AAAGGGTGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.46
Consensus pattern (20 bp):
TTACTTCTTCAACATTTGGG
Found at i:41617043 original size:63 final size:63
Alignment explanation
Indices: 41616935--41617062 Score: 220
Period size: 63 Copynumber: 2.0 Consensus size: 63
41616925 TTTGGGTTAC
* * *
41616935 TTCTTCAAGATTTGGGTAAAGGGTGAGTTTAGATTGACGGCGAATTATATGTTAAGGATGTGT
1 TTCTTCAAGATTTGGGTAAAAGGTGAGTTTAGATTAACGGCGAATTATATGTTAAGGATGGGT
*
41616998 TTCTTCAAGATTTGGGTAAAAGGTGAGTTTAGATTAACGGTGAATTATATGTTAAGGATGGGT
1 TTCTTCAAGATTTGGGTAAAAGGTGAGTTTAGATTAACGGCGAATTATATGTTAAGGATGGGT
41617061 TT
1 TT
41617063 AGATGGAGGA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.28, C:0.05, G:0.29, T:0.38
Consensus pattern (63 bp):
TTCTTCAAGATTTGGGTAAAAGGTGAGTTTAGATTAACGGCGAATTATATGTTAAGGATGGGT
Found at i:41630259 original size:12 final size:12
Alignment explanation
Indices: 41630244--41630284 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
41630234 TACTTTATGT
41630244 TTTTTTTTATAA
1 TTTTTTTTATAA
41630256 TTTTTTTTA-ATA
1 TTTTTTTTATA-A
*
41630268 TTTGTTTTATAA
1 TTTTTTTTATAA
41630280 TTTTT
1 TTTTT
41630285 AAATTATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 1 0.04
12 23 0.92
13 1 0.04
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (12 bp):
TTTTTTTTATAA
Found at i:41630292 original size:23 final size:23
Alignment explanation
Indices: 41630248--41630295 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
41630238 TTATGTTTTT
*
41630248 TTTTATAATTTTTTTTAATATTTG
1 TTTTATAA-TTTTTTAAATATTTG
41630272 TTTTATAA-TTTTTAAATTATTTG
1 TTTTATAATTTTTTAAA-TATTTG
41630295 T
1 T
41630296 CGACGTGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 7 0.32
24 8 0.36
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (23 bp):
TTTTATAATTTTTTAAATATTTG
Found at i:41630819 original size:61 final size:61
Alignment explanation
Indices: 41630746--41630877 Score: 144
Period size: 60 Copynumber: 2.2 Consensus size: 61
41630736 CAATATGGTC
* * *
41630746 CTAAATCT-AAAAATTCAACAAATTCAGCCCTCAA-TGTTTATAAAATTTGTC-ATTTAATT
1 CTAATTCTAAAAAAATCAACAAATTCAGCCCTCAACT-TTTACAAAATTTGTCAATTTAATT
* * * * * *
41630805 CTAATTCTAAAAAAATCAATAAATTTAGCCTTGAACTTTTACAGAATTTTTCAATTTAATT
1 CTAATTCTAAAAAAATCAACAAATTCAGCCCTCAACTTTTACAAAATTTGTCAATTTAATT
*
41630866 CTAATTTTAAAA
1 CTAATTCTAAAA
41630878 GTAAAAAAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
59 7 0.12
60 33 0.55
61 20 0.33
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.39
Consensus pattern (61 bp):
CTAATTCTAAAAAAATCAACAAATTCAGCCCTCAACTTTTACAAAATTTGTCAATTTAATT
Found at i:41650658 original size:29 final size:29
Alignment explanation
Indices: 41650616--41650673 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
41650606 CGACTCAAGG
41650616 GATAGTTCATAGGTTGTCTTGCCCACATA
1 GATAGTTCATAGGTTGTCTTGCCCACATA
41650645 GATAGTTCATAGGTTGTCTTGCCCACATA
1 GATAGTTCATAGGTTGTCTTGCCCACATA
41650674 CATCCAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (29 bp):
GATAGTTCATAGGTTGTCTTGCCCACATA
Found at i:41665186 original size:29 final size:28
Alignment explanation
Indices: 41665153--41665246 Score: 90
Period size: 24 Copynumber: 3.4 Consensus size: 28
41665143 AAGTTTTCAC
41665153 TTATTTATAGTAGTAAACTTTATAGTATT
1 TTATTTATAGTA-TAAACTTTATAGTATT
41665182 TTATTTATAGTAT----TTTATAGTATT
1 TTATTTATAGTATAAACTTTATAGTATT
**
41665206 TTATTTTATTTAAAATAAACTTTATAGTA-T
1 TTA-TTTA--TAGTATAAACTTTATAGTATT
41665236 TTATTATATAG
1 TTATT-TATAG
41665247 ATTTGATAGT
Statistics
Matches: 54, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
24 14 0.26
25 4 0.07
27 4 0.07
28 3 0.06
29 14 0.26
30 6 0.11
31 9 0.17
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.55
Consensus pattern (28 bp):
TTATTTATAGTATAAACTTTATAGTATT
Found at i:41665190 original size:14 final size:14
Alignment explanation
Indices: 41665171--41665199 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41665161 AGTAGTAAAC
41665171 TTTATAGTATTTTA
1 TTTATAGTATTTTA
41665185 TTTATAGTATTTTA
1 TTTATAGTATTTTA
41665199 T
1 T
41665200 AGTATTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (14 bp):
TTTATAGTATTTTA
Found at i:41665216 original size:10 final size:10
Alignment explanation
Indices: 41665185--41665209 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
41665175 TAGTATTTTA
41665185 TTTATAGTAT
1 TTTATAGTAT
41665195 TTTATAGTAT
1 TTTATAGTAT
41665205 TTTAT
1 TTTAT
41665210 TTTATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (10 bp):
TTTATAGTAT
Found at i:41666363 original size:26 final size:25
Alignment explanation
Indices: 41666332--41666410 Score: 77
Period size: 28 Copynumber: 3.0 Consensus size: 25
41666322 TTAAATTTGA
*
41666332 AATTTAATTCTTATACTTTAATTTC
1 AATTTAATCCTTATACTTTAATTTC
* * * *
41666357 AATTTTAGTCCTAATATGCTTAAATTTG
1 AA-TTTAATCCT--TATACTTTAATTTC
41666385 AGATTTAATCCTTATACTTTAATTTC
1 A-ATTTAATCCTTATACTTTAATTTC
41666411 TAGCATCATT
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
25 2 0.05
26 18 0.44
28 20 0.49
29 1 0.02
ACGTcount: A:0.32, C:0.13, G:0.05, T:0.51
Consensus pattern (25 bp):
AATTTAATCCTTATACTTTAATTTC
Found at i:41666384 original size:54 final size:55
Alignment explanation
Indices: 41666294--41666410 Score: 182
Period size: 54 Copynumber: 2.1 Consensus size: 55
41666284 AAATTGGTTA
*
41666294 AATTTCAACTTTAGTCCTTTTAATATGCTTAAATTTGAAATTTAATTCTTATACTTT
1 AATTTCAACTTTAGTCC--TTAATATGCTTAAATTTGAAATTTAATCCTTATACTTT
* *
41666351 AATTTCAATTTTAGTCC-TAATATGCTTAAATTTGAGATTTAATCCTTATACTTT
1 AATTTCAACTTTAGTCCTTAATATGCTTAAATTTGAAATTTAATCCTTATACTTT
41666405 AATTTC
1 AATTTC
41666411 TAGCATCATT
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
54 41 0.72
57 16 0.28
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.50
Consensus pattern (55 bp):
AATTTCAACTTTAGTCCTTAATATGCTTAAATTTGAAATTTAATCCTTATACTTT
Found at i:41666391 original size:28 final size:27
Alignment explanation
Indices: 41666314--41666396 Score: 80
Period size: 28 Copynumber: 3.0 Consensus size: 27
41666304 TTAGTCCTTT
*
41666314 TAATATGCTTAAATTTGAAATTTAATTC
1 TAATATGCTTAAATTTG-AATTTAATCC
* * * *
41666342 T--TATACTTTAATTTCAATTTTAGTCC
1 TAATATGCTTAAATTTGAA-TTTAATCC
41666368 TAATATGCTTAAATTTGAGATTTAATCC
1 TAATATGCTTAAATTTGA-ATTTAATCC
41666396 T
1 T
41666397 TATACTTTAA
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
25 2 0.05
26 18 0.43
28 21 0.50
29 1 0.02
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (27 bp):
TAATATGCTTAAATTTGAATTTAATCC
Found at i:41672374 original size:23 final size:22
Alignment explanation
Indices: 41672342--41672403 Score: 88
Period size: 22 Copynumber: 2.7 Consensus size: 22
41672332 GCCCGGCCCT
*
41672342 TTTTTAATTAAAATTAAAATTATA
1 TTTTT-ATTAAAATTAAAACTA-A
41672366 TTTTTATTAAAATTAAAACTAA
1 TTTTTATTAAAATTAAAACTAA
*
41672388 TTGTTATTAAAATTAA
1 TTTTTATTAAAATTAA
41672404 TTGTTATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.44
23 15 0.42
24 5 0.14
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTATTAAAATTAAAACTAA
Found at i:41672398 original size:16 final size:16
Alignment explanation
Indices: 41672377--41672430 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
41672367 TTTTATTAAA
*
41672377 ATTAAAACTAATTGTT
1 ATTAAAATTAATTGTT
41672393 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
*
41672409 ATCAAAATTAATTGTT
1 ATTAAAATTAATTGTT
41672425 ATTAAA
1 ATTAAA
41672431 GTTGTATCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTAAAATTAATTGTT
Found at i:41673355 original size:51 final size:49
Alignment explanation
Indices: 41673300--41673416 Score: 130
Period size: 51 Copynumber: 2.3 Consensus size: 49
41673290 TTTTGGCCCT
*
41673300 TTTTCGTATTTT-TCTTATTTTCAG-ATTTTATTACTTTCAGTAAATATACTA
1 TTTTCGTATTTTAT-TTATTTTC-GTATTTTATTACTTTCA-TAAACATA-TA
* ** *
41673351 TTTTCGTATTTTATTTCTTTTCGTATTTTATTTTTTTCATAAACATATT
1 TTTTCGTATTTTATTTATTTTCGTATTTTATTACTTTCATAAACATATA
41673400 TTTTCGGTATTTTATTT
1 TTTTC-GTATTTTATTT
41673417 TTAATACTAT
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
49 6 0.10
50 19 0.33
51 32 0.55
52 1 0.02
ACGTcount: A:0.21, C:0.10, G:0.06, T:0.62
Consensus pattern (49 bp):
TTTTCGTATTTTATTTATTTTCGTATTTTATTACTTTCATAAACATATA
Found at i:41673373 original size:17 final size:16
Alignment explanation
Indices: 41673351--41673388 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
41673341 AAATATACTA
41673351 TTTTCGTATTTTATTT
1 TTTTCGTATTTTATTT
41673367 CTTTTCGTATTTTATTT
1 -TTTTCGTATTTTATTT
41673384 TTTTC
1 TTTTC
41673389 ATAAACATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.11, C:0.11, G:0.05, T:0.74
Consensus pattern (16 bp):
TTTTCGTATTTTATTT
Found at i:41673509 original size:27 final size:27
Alignment explanation
Indices: 41673471--41673534 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
41673461 ATAAATGGGG
*
41673471 GGTGCCGCCTCTGCCACTGGTACCATT
1 GGTGCCGCCTCTGCCACTGGCACCATT
41673498 GGTGCCGCCTCTGCCACTGGCACCATT
1 GGTGCCGCCTCTGCCACTGGCACCATT
41673525 GGTGCCGCCT
1 GGTGCCGCCT
41673535 GTGGCAATCC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.09, C:0.39, G:0.28, T:0.23
Consensus pattern (27 bp):
GGTGCCGCCTCTGCCACTGGCACCATT
Found at i:41673686 original size:28 final size:28
Alignment explanation
Indices: 41673622--41673687 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
41673612 ACCAAAAAAA
41673622 GTCCATTTTTTAAAAAATTACGGAAATG
1 GTCCATTTTTTAAAAAATTACGGAAATG
* ** *
41673650 GGCCGATTTTTTAATTATTTACCGG-AATG
1 GTCC-ATTTTTTAAAAAATTA-CGGAAATG
41673679 GTCCATTTT
1 GTCCATTTT
41673688 CCGTGAAATC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
28 8 0.26
29 20 0.65
30 3 0.10
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.41
Consensus pattern (28 bp):
GTCCATTTTTTAAAAAATTACGGAAATG
Found at i:41677841 original size:28 final size:28
Alignment explanation
Indices: 41677801--41678030 Score: 249
Period size: 23 Copynumber: 8.7 Consensus size: 28
41677791 NNNNNNNNNN
41677801 GTTAGGGTTTTTAATTAAATTAAGTTAG
1 GTTAGGGTTTTTAATTAAATTAAGTTAG
41677829 GTTAGGG--TTT--TT-AATTAAGTTAG
1 GTTAGGGTTTTTAATTAAATTAAGTTAG
* * *
41677852 GTTACGATTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAAGTTA-G
*
41677881 GTTAGGGTTTTTAATTAAATTAAGTTAT
1 GTTAGGGTTTTTAATTAAATTAAGTTAG
*
41677909 GTTAGGGTTTTT-ATTAAGTTAAGTTA-
1 GTTAGGGTTTTTAATTAAATTAAGTTAG
41677935 G--A--GTTTTTAATTAAATTAAGTTAG
1 GTTAGGGTTTTTAATTAAATTAAGTTAG
*
41677959 GTTAGGG--TTT--TT-AATTAAGTTAA
1 GTTAGGGTTTTTAATTAAATTAAGTTAG
*
41677982 GTTAGGGTTTTTAATTAAATTAGGTTAG
1 GTTAGGGTTTTTAATTAAATTAAGTTAG
* *
41678010 AGTTACGGTTTTTAATCAAAT
1 -GTTAGGGTTTTTAATTAAAT
41678031 AATGTCAAAA
Statistics
Matches: 170, Mismatches: 14, Indels: 35
0.78 0.06 0.16
Matches are distributed among these distances:
22 6 0.04
23 46 0.27
24 6 0.04
25 6 0.04
26 8 0.05
27 17 0.10
28 38 0.22
29 43 0.25
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (28 bp):
GTTAGGGTTTTTAATTAAATTAAGTTAG
Found at i:41680194 original size:22 final size:22
Alignment explanation
Indices: 41680169--41680212 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
41680159 TTTATGAGAG
41680169 TTTGAGAGAATTTTGGAAGGAA
1 TTTGAGAGAATTTTGGAAGGAA
*
41680191 TTTGAGAGAATTTTTGAAGGAA
1 TTTGAGAGAATTTTGGAAGGAA
41680213 ATTAATATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.30, T:0.34
Consensus pattern (22 bp):
TTTGAGAGAATTTTGGAAGGAA
Found at i:41680871 original size:14 final size:14
Alignment explanation
Indices: 41680834--41680876 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
41680824 CCAACCTTTA
41680834 GTCTTTATTCTAGTTT
1 GTCTTTATT-T-GTTT
*
41680850 -TTTTTATTTGTTT
1 GTCTTTATTTGTTT
41680863 GTCTTTATTTGTTT
1 GTCTTTATTTGTTT
41680877 ATTTTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 4 0.17
14 13 0.54
15 7 0.29
ACGTcount: A:0.09, C:0.07, G:0.12, T:0.72
Consensus pattern (14 bp):
GTCTTTATTTGTTT
Found at i:41681960 original size:45 final size:45
Alignment explanation
Indices: 41681903--41682003 Score: 166
Period size: 45 Copynumber: 2.2 Consensus size: 45
41681893 AGAAATACAA
* *
41681903 AAAAATTTCAAAACACACAGAGAAGCAATCAGAAACCAAAATACT
1 AAAAATTTCAAAACACACAGAGAAGAAATCAAAAACCAAAATACT
* *
41681948 AAAAATTTCAAAACACATAGAGAAGAAATCAAAAACCAGAATACT
1 AAAAATTTCAAAACACACAGAGAAGAAATCAAAAACCAAAATACT
41681993 AAAAATTTCAA
1 AAAAATTTCAA
41682004 GGGTGATTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.59, C:0.17, G:0.08, T:0.16
Consensus pattern (45 bp):
AAAAATTTCAAAACACACAGAGAAGAAATCAAAAACCAAAATACT
Found at i:41682892 original size:4 final size:4
Alignment explanation
Indices: 41682883--41682915 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
41682873 CTTTCATGAA
*
41682883 ATTT ATTT ATTT ATGT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A
41682916 CTTACTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (4 bp):
ATTT
Found at i:41689073 original size:45 final size:46
Alignment explanation
Indices: 41689024--41689121 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
41689014 AGATAGAAAC
*
41689024 CAAAATATTATCTCTTAAAC-TTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
41689069 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
*
41689115 GAAAATA
1 CAAAATA
41689122 GATATACACA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 19 0.38
46 31 0.62
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (46 bp):
CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
Found at i:41690381 original size:11 final size:11
Alignment explanation
Indices: 41690365--41690389 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41690355 AAATAAGCAG
41690365 AAAAAAAAAGA
1 AAAAAAAAAGA
41690376 AAAAAAAAAGA
1 AAAAAAAAAGA
41690387 AAA
1 AAA
41690390 TCTGAAACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:41694165 original size:9 final size:10
Alignment explanation
Indices: 41694148--41694185 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
41694138 AAAAACAATG
41694148 AATATAAAAA
1 AATATAAAAA
41694158 AA-ATAAAAA
1 AATATAAAAA
*
41694167 AATATAAAAC
1 AATATAAAAA
*
41694177 TATATAAAA
1 AATATAAAA
41694186 GAAAAATGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (10 bp):
AATATAAAAA
Found at i:41698423 original size:14 final size:14
Alignment explanation
Indices: 41698360--41698424 Score: 51
Period size: 14 Copynumber: 4.5 Consensus size: 14
41698350 TTGTTATAAG
* *
41698360 TTTAATATTTAATA
1 TTTAATTTTTAAAA
41698374 TTT-ATTTTTAAAA
1 TTTAATTTTTAAAA
***
41698387 TTTTAATTTTATTATCT
1 -TTTAA-TTT-TTAAAA
41698404 TTTAATTTTTAAAA
1 TTTAATTTTTAAAA
41698418 TTTAATT
1 TTTAATT
41698425 CTAATTATGT
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
13 8 0.21
14 16 0.41
15 4 0.10
16 8 0.21
17 3 0.08
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTAATTTTTAAAA
Found at i:41698441 original size:31 final size:31
Alignment explanation
Indices: 41698377--41698444 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
41698367 TTTAATATTT
* **
41698377 ATTTTTAAAATTTTAATTTTATTATCTTTTA
1 ATTTTTAAAATTTTAATTTAATTATCTAATA
*
41698408 ATTTTTAAAA-TTTAATTCTAATTATGTAATA
1 ATTTTTAAAATTTTAATT-TAATTATCTAATA
41698439 ATTTTT
1 ATTTTT
41698445 TATTAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 7 0.22
31 25 0.78
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.60
Consensus pattern (31 bp):
ATTTTTAAAATTTTAATTTAATTATCTAATA
Found at i:41699313 original size:59 final size:60
Alignment explanation
Indices: 41699149--41699315 Score: 159
Period size: 59 Copynumber: 2.7 Consensus size: 60
41699139 TTTAAAATCA
* *
41699149 TTTGAATAAAAAATATTATAAAATA-AATAATAAACAATTAAAAAATAAATATTCAAAAAATG
1 TTTGAATAAAAAATATTATAAAATATAATAATATAC-ATTAAAAAATAAATA-T-AAAAAACG
* *
41699211 TTTGAATAAACAAATATTATAAAACA-AATAATAAATA-ATTTAAAAAAT-AA-A-AAAAAGCG
1 TTTGAATAAA-AAATATTATAAAATATAATAAT--ATACA-TTAAAAAATAAATATAAAAAACG
41699270 TTTGAATAAAAATATATTATAAAATATTTAA-AATATACATTAAAAA
1 TTTGAATAAAAA-ATATTATAAAATA--TAATAATATACATTAAAAA
41699316 TATTATAAAA
Statistics
Matches: 91, Mismatches: 5, Indels: 21
0.78 0.04 0.18
Matches are distributed among these distances:
58 2 0.02
59 38 0.42
60 1 0.01
61 3 0.03
62 13 0.14
63 23 0.25
64 9 0.10
65 2 0.02
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (60 bp):
TTTGAATAAAAAATATTATAAAATATAATAATATACATTAAAAAATAAATATAAAAAACG
Found at i:41699324 original size:23 final size:24
Alignment explanation
Indices: 41699275--41699327 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
41699265 AAGCGTTTGA
*
41699275 ATAAAA-ATATATTATAAAATATT
1 ATAAAATATACATTATAAAATATT
41699298 -TAAAATATACATTA-AAAATATT
1 ATAAAATATACATTATAAAATATT
41699320 ATAAAATA
1 ATAAAATA
41699328 AATAATAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 13 0.48
23 14 0.52
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
ATAAAATATACATTATAAAATATT
Found at i:41699366 original size:19 final size:19
Alignment explanation
Indices: 41699320--41699367 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
41699310 TAAAAATATT
*
41699320 ATAAAATAAATAATAAACAA
1 ATAAAA-AAAAAATAAACAA
* **
41699340 TTTTAAAAAAAATAAACAA
1 ATAAAAAAAAAATAAACAA
41699359 ATAAAAAAA
1 ATAAAAAAA
41699368 CTAGAATAAA
Statistics
Matches: 21, Mismatches: 7, Indels: 1
0.72 0.24 0.03
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (19 bp):
ATAAAAAAAAAATAAACAA
Done.