Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 166 of 349
Found at i:53759907 original size:23 final size:21
Alignment explanation
Indices: 53759871--53759915 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 21
53759861 ATTTTAATAT
53759871 TTTAATTAATTAATTCCTAATTA
1 TTTAATTAATTAA-T-CTAATTA
53759894 TTTAATT-ATATAATCTAATTA
1 TTTAATTAAT-TAATCTAATTA
53759915 T
1 T
53759916 AGTTTTCGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 8 0.38
22 3 0.14
23 10 0.48
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTAATTAATTAATCTAATTA
Found at i:53759913 original size:32 final size:31
Alignment explanation
Indices: 53759844--53759914 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
53759834 TCCTAATAAA
*
53759844 AATT-ATTAATTCTAATTATTTTAATATTTT
1 AATTAATTAATTCTAATTATTTTAATATTAT
53759874 AATTAATTAATTCCTAATTA-TTTAAT-TATAT
1 AATTAATTAATT-CTAATTATTTTAATAT-TAT
53759905 AATCTAATTA
1 AAT-TAATTA
53759915 TAGTTTTCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
30 5 0.14
31 18 0.50
32 13 0.36
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.54
Consensus pattern (31 bp):
AATTAATTAATTCTAATTATTTTAATATTAT
Found at i:53761892 original size:28 final size:28
Alignment explanation
Indices: 53761846--53761919 Score: 123
Period size: 28 Copynumber: 2.6 Consensus size: 28
53761836 TGGCCCCTTT
*
53761846 AGGCCCAATCTCATTCATATGGCCCATC
1 AGGCCCAATCACATTCATATGGCCCATC
53761874 -GGCCCTAATCACATTCATATGGCCCATC
1 AGGCCC-AATCACATTCATATGGCCCATC
53761902 AGGCCCAATCACATTCAT
1 AGGCCCAATCACATTCAT
53761920 GGTCATGCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
27 5 0.12
28 33 0.77
29 5 0.12
ACGTcount: A:0.27, C:0.35, G:0.14, T:0.24
Consensus pattern (28 bp):
AGGCCCAATCACATTCATATGGCCCATC
Found at i:53770131 original size:12 final size:13
Alignment explanation
Indices: 53770107--53770135 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
53770097 GGGCTGTAAC
53770107 TATTGCATTTATT
1 TATTGCATTTATT
53770120 TATTGC-TTTATT
1 TATTGCATTTATT
53770132 TATT
1 TATT
53770136 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:53775995 original size:17 final size:18
Alignment explanation
Indices: 53775973--53776006 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53775963 CACATTGAAG
53775973 TGTTTT-ATCGAAAACCT
1 TGTTTTCATCGAAAACCT
*
53775990 TGTTTTCATTGAAAACC
1 TGTTTTCATCGAAAACC
53776007 CTTCAAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (18 bp):
TGTTTTCATCGAAAACCT
Found at i:53779248 original size:11 final size:11
Alignment explanation
Indices: 53779212--53779267 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
53779202 CATGGTATGT
53779212 ATGATATGCAC
1 ATGATATGCAC
* *
53779223 ATGACATG--T
1 ATGATATGCAC
53779232 ATGATATGCAC
1 ATGATATGCAC
*
53779243 ATGATATG--T
1 ATGATATGCAC
53779252 ATGATATGCAC
1 ATGATATGCAC
53779263 ATGAT
1 ATGAT
53779268 GTATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:53779267 original size:20 final size:20
Alignment explanation
Indices: 53779201--53779267 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
53779191 ATTTTGATAA
*
53779201 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
53779221 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
53779241 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
53779261 ACATGAT
1 ACATGAT
53779268 GTATTCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:53779343 original size:24 final size:24
Alignment explanation
Indices: 53779316--53779508 Score: 273
Period size: 24 Copynumber: 8.0 Consensus size: 24
53779306 GGAGGAAGTG
*
53779316 CAAAAGGGCTTATGCCCCAATTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
53779340 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
53779364 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
53779388 AAAAAGGGCTTATACCCCAGTTA-
1 CAAAAGGGCTTATGCCCCAGTTAT
53779411 CTAAAAGGGCTTATGCCCCAGTTAT
1 C-AAAAGGGCTTATGCCCCAGTTAT
*
53779436 TAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
53779460 TAAAAGGGCTTTTGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
53779484 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 CAAAAG-GGCTTATGCC-CCAGTTAT
53779509 TTGATAAAGC
Statistics
Matches: 156, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
24 145 0.93
25 11 0.07
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (24 bp):
CAAAAGGGCTTATGCCCCAGTTAT
Found at i:53787614 original size:20 final size:20
Alignment explanation
Indices: 53787548--53787614 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
53787538 ATTTTGATAA
* *
53787548 ACATGGTATGTATGATATAC
1 ACATGATATGTATGATATGC
*
53787568 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
53787588 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
53787608 ACATGAT
1 ACATGAT
53787615 GTATTCATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:53787695 original size:24 final size:24
Alignment explanation
Indices: 53787664--53787856 Score: 298
Period size: 24 Copynumber: 8.0 Consensus size: 24
53787654 GATGAAGTGC
* *
53787664 AAAAGGGCTTATACCCCAGTTATA
1 AAAAGGGCTTATGCCCCAGTTATT
*
53787688 AAAAGGGCTTATGCCCCAGTTACT
1 AAAAGGGCTTATGCCCCAGTTATT
*
53787712 AAAAGGGCTTATGCCCCAGTTATA
1 AAAAGGGCTTATGCCCCAGTTATT
*
53787736 AAAAGGGCTTATGCCCCAGTTACT
1 AAAAGGGCTTATGCCCCAGTTATT
53787760 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
53787784 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
53787808 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
53787832 AAAAGAGGC-TAGGCCTCCAGTTATT
1 AAAAG-GGCTTATGCC-CCAGTTATT
53787857 TGATAAAGCA
Statistics
Matches: 156, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
24 144 0.92
25 12 0.08
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:53788514 original size:12 final size:12
Alignment explanation
Indices: 53788497--53788522 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53788487 CAACACCATG
53788497 ATTATTTGATTT
1 ATTATTTGATTT
53788509 ATTATTTGATTT
1 ATTATTTGATTT
53788521 AT
1 AT
53788523 CAAAGAGGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (12 bp):
ATTATTTGATTT
Found at i:53798188 original size:28 final size:28
Alignment explanation
Indices: 53798153--53798226 Score: 107
Period size: 28 Copynumber: 2.6 Consensus size: 28
53798143 CAGCCCCTTT
53798153 AGGCCCAATCTCATTCATATGGCCCATC
1 AGGCCCAATCTCATTCATATGGCCCATC
53798181 -GGCCCCAATCAT-ATTCATATGGCCCATC
1 AGG-CCCAATC-TCATTCATATGGCCCATC
*
53798209 AGGCCCAATCACATTCAT
1 AGGCCCAATCTCATTCAT
53798227 GGTCATGCAA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
27 2 0.05
28 36 0.88
29 3 0.07
ACGTcount: A:0.27, C:0.35, G:0.14, T:0.24
Consensus pattern (28 bp):
AGGCCCAATCTCATTCATATGGCCCATC
Found at i:53800290 original size:20 final size:20
Alignment explanation
Indices: 53800262--53800300 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
53800252 AAACATACAT
* *
53800262 TTCACATACAATTTAATCAA
1 TTCAAATACAATTCAATCAA
53800282 TTCAAATACAATTCAATCA
1 TTCAAATACAATTCAATCA
53800301 CAACCAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (20 bp):
TTCAAATACAATTCAATCAA
Found at i:53802537 original size:40 final size:40
Alignment explanation
Indices: 53802333--53802537 Score: 236
Period size: 40 Copynumber: 5.1 Consensus size: 40
53802323 CGGAATTTAA
** *
53802333 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
53802373 CCGGTTATAGTAACTCTCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
53802413 CCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
53802453 CCGAATTTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
53802493 CCGGATATGGTCACCTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGT-AACTCGCACAAATGCCTTCGGGACTTAGC
53802533 CCGGA
1 CCGGA
53802538 AATCATTCAA
Statistics
Matches: 143, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
39 4 0.03
40 126 0.88
41 13 0.09
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:53809544 original size:46 final size:47
Alignment explanation
Indices: 53809468--53809669 Score: 217
Period size: 47 Copynumber: 4.3 Consensus size: 47
53809458 TTGCACATAG
* **
53809468 TCACATATCACACACTGAAGCCATAGCCCAGCCATGGTCTTACACGG-A
1 TCACATATCACAC-C-GATGCCATAGCCCAGATATGGTCTTACACGGAA
* * * *
53809516 TCACATATCACACTGATGCTATATCCCAGATATGGTCTTACACAGAA
1 TCACATATCACACCGATGCCATAGCCCAGATATGGTCTTACACGGAA
* * * * *
53809563 GCACATATCATACCGATGTCATATCCCAGATATGGTCTTATACGGAA
1 TCACATATCACACCGATGCCATAGCCCAGATATGGTCTTACACGGAA
* * * * *
53809610 GCTCATATCACACCGATGCCATAGCCTAGCTATGGTCTTATACGGAAA
1 TCACATATCACACCGATGCCATAGCCCAGATATGGTCTTACACGG-AA
53809658 TCACATATCACA
1 TCACATATCACA
53809670 TGTTGCCATG
Statistics
Matches: 130, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
46 25 0.19
47 80 0.62
48 25 0.19
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (47 bp):
TCACATATCACACCGATGCCATAGCCCAGATATGGTCTTACACGGAA
Found at i:53809762 original size:18 final size:18
Alignment explanation
Indices: 53809741--53809777 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
53809731 CTAAATCCGT
53809741 CGTTCCATCTAATTTGTA
1 CGTTCCATCTAATTTGTA
53809759 CGTTCCATCTAATTTGTA
1 CGTTCCATCTAATTTGTA
53809777 C
1 C
53809778 TTTTACTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (18 bp):
CGTTCCATCTAATTTGTA
Found at i:53810279 original size:16 final size:16
Alignment explanation
Indices: 53810260--53810290 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53810250 TTCTATCAAA
*
53810260 ATCACTTAATAAAATC
1 ATCACATAATAAAATC
53810276 ATCACATAATAAAAT
1 ATCACATAATAAAAT
53810291 AAGAACTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (16 bp):
ATCACATAATAAAATC
Found at i:53812928 original size:16 final size:16
Alignment explanation
Indices: 53812907--53812939 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
53812897 GTTTACATTA
53812907 TACT-AATATTATATAT
1 TACTAAATATT-TATAT
53812923 TACTAAATATTTATAT
1 TACTAAATATTTATAT
53812939 T
1 T
53812940 TTGTGTGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (16 bp):
TACTAAATATTTATAT
Found at i:53813215 original size:5 final size:5
Alignment explanation
Indices: 53813205--53813235 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
53813195 TATAAAAAAA
53813205 TATTT TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT TATTT T
53813236 TTAATTACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:53819993 original size:19 final size:22
Alignment explanation
Indices: 53819947--53819992 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
53819937 AAGTAGGTTG
53819947 TATATTATTTTTTGTAATATTA
1 TATATTATTTTTTGTAATATTA
53819969 TATATTATTTTTAT-TAAT-TTA
1 TATATTATTTTT-TGTAATATTA
53819990 TAT
1 TAT
53819993 TTTAATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.26
22 16 0.70
23 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TATATTATTTTTTGTAATATTA
Found at i:53820045 original size:21 final size:20
Alignment explanation
Indices: 53820016--53820055 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
53820006 ATATTAAGAA
53820016 TATTATTAAATTATATATTAT
1 TATTATTAAATTATA-ATTAT
*
53820037 TATTGTTAAATTATAATTA
1 TATTATTAAATTATAATTA
53820056 ATAATAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TATTATTAAATTATAATTAT
Found at i:53820118 original size:61 final size:59
Alignment explanation
Indices: 53819965--53820123 Score: 185
Period size: 61 Copynumber: 2.6 Consensus size: 59
53819955 TTTTTGTAAT
* *** **
53819965 ATTATATATTATTTTTATTAATTTATATTTTAATAATTGCTATATTAAGAATATTATTAA
1 ATTATATATTATTTTTATTAAATTATA-TTTAATAATAAATATATTAAGAATAGGATTAA
* * * *
53820025 ATTATATATTATTATTGTTAAATTATAATTAATAATAAATTTATTAA-AATAGGATTAA
1 ATTATATATTATTTTTATTAAATTATATTTAATAATAAATATATTAAGAATAGGATTAA
53820083 ATTATGTATTATTATTTTTATTAAATTATATTTAATAATAA
1 ATTA--TA-TATTATTTTTATTAAATTATATTTAATAATAA
53820124 TCCTATTAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
58 13 0.16
59 15 0.18
60 26 0.31
61 29 0.35
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (59 bp):
ATTATATATTATTTTTATTAAATTATATTTAATAATAAATATATTAAGAATAGGATTAA
Found at i:53820315 original size:16 final size:16
Alignment explanation
Indices: 53820294--53820341 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
53820284 AATTAATTTG
53820294 CTATTACAGTTCTATT
1 CTATTACAGTTCTATT
**
53820310 CTATTACAACTCTATT
1 CTATTACAGTTCTATT
* *
53820326 CCATTATAGTTCTATT
1 CTATTACAGTTCTATT
53820342 ACATTACAAC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.27, C:0.21, G:0.04, T:0.48
Consensus pattern (16 bp):
CTATTACAGTTCTATT
Found at i:53820348 original size:32 final size:32
Alignment explanation
Indices: 53820296--53820365 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
53820286 TTAATTTGCT
*
53820296 ATTACAGTTCTATTCTATTACAACTCTATTCC
1 ATTACAGTTCTATTCTATTACAACCCTATTCC
*
53820328 ATTATAGTTCTATTAC-ATTACAACCCTATTCC
1 ATTACAGTTCTATT-CTATTACAACCCTATTCC
53820360 ATTACA
1 ATTACA
53820366 CTGAACCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 33 0.97
33 1 0.03
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (32 bp):
ATTACAGTTCTATTCTATTACAACCCTATTCC
Found at i:53824036 original size:14 final size:15
Alignment explanation
Indices: 53824006--53824043 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
53823996 GCCTCTTTTG
53824006 CATTT-CATTTCATT
1 CATTTGCATTTCATT
53824020 CATTTGCATTTCA-T
1 CATTTGCATTTCATT
*
53824034 CATATGCATT
1 CATTTGCATT
53824044 AAGTTTCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.24, C:0.21, G:0.05, T:0.50
Consensus pattern (15 bp):
CATTTGCATTTCATT
Found at i:53829584 original size:189 final size:186
Alignment explanation
Indices: 53829158--53829714 Score: 611
Period size: 189 Copynumber: 3.0 Consensus size: 186
53829148 AGAAATCAAA
** * *
53829158 AATCCTATACAGCTGAAGTTGCAGTAGGTCGAATCAAATCTACCATGGCGAATCTTTTCTCCCTG
1 AATCCTATACCTCTGAAGTTGCAGTAGGTCGGATCAAATCTACCATGGCGAATCTTATCTCCCTG
* ** * * * * * * *
53829223 AAGTTGTAGTGGAGCAGATTGAAGCCGCGAACCTTATCTACCTGAAGTTTCAGTGGAGCAGGCTA
66 AAGTTGCAGAAGAGCAGATTGAAGCCACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAAGTTG
* *
53829288 AAGATAGCAAATCTTATTTCTCTGAAGTTGCAGTGGAACAGATTAAAGCTACGAGTTAC
131 AAGATAGCAAATCTTATTTCTCTGAAGTTGCAGTAGAATAGATTAAAGCTA--AG-TAC
* * * * * *
53829347 AAGTCCTATACCTCTGAAGTTGTAATAGGTCAGATCAAATCGACCATGGTGAATCTTATCTCTCT
1 AA-TCCTATACCTCTGAAGTTGCAGTAGGTCGGATCAAATCTACCATGGCGAATCTTATCTCCCT
* * *
53829412 AAAGTTGCAGAAGAGCAGATTAAAGCCACAAACAACAAATCTCATCTCCCTAAAGTTGCAGTGGA
65 GAAGTTGCAGAAGAGCAGATTGAAGCCACAAAC--C---T-T-ATCTCCCTGAAGTTGCAGTGGA
* * * * *
53829477 GCAAGTTGAAGTTA-CAAGTCTTATATCTCTGAAGTTGCAGTAAAATAGATTAAAGCT-A-T-G
123 GCAAGTTGAAGATAGCAAATCTTATTTCTCTGAAGTTGCAGTAGAATAGATTAAAGCTAAGTAC
* *
53829537 AATCCTATACCTCTGAAGTTGCAGCAGGTTGGATCAAATCTACCATGGCGAATCTTATCTCCCTG
1 AATCCTATACCTCTGAAGTTGCAGTAGGTCGGATCAAATCTACCATGGCGAATCTTATCTCCCTG
* * * * *
53829602 AAGTTACAGTAA-AGCAGATTGAAGCCCCAAACCTTATCTCCCTGAAGTTGCAGTGAAGTAAATT
66 AAGTTGCAG-AAGAGCAGATTGAAGCCACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAAGTT
* * *
53829666 GAAGATAGCAAATATTATTTCCCTGAAGTTGCAGTAGAATAGACTAAAG
130 GAAGATAGCAAATCTTATTTCTCTGAAGTTGCAGTAGAATAGATTAAAG
53829715 GTACAGATTA
Statistics
Matches: 305, Mismatches: 53, Indels: 26
0.79 0.14 0.07
Matches are distributed among these distances:
182 31 0.10
183 36 0.12
184 1 0.00
187 1 0.00
189 82 0.27
190 82 0.27
191 1 0.00
192 1 0.00
193 1 0.00
195 1 0.00
196 39 0.13
197 29 0.10
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (186 bp):
AATCCTATACCTCTGAAGTTGCAGTAGGTCGGATCAAATCTACCATGGCGAATCTTATCTCCCTG
AAGTTGCAGAAGAGCAGATTGAAGCCACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAAGTTG
AAGATAGCAAATCTTATTTCTCTGAAGTTGCAGTAGAATAGATTAAAGCTAAGTAC
Found at i:53831594 original size:26 final size:25
Alignment explanation
Indices: 53831518--53831594 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 25
53831508 ATTTAGACGG
53831518 TTTTTATACATTATTTATTTCAAATTTA
1 TTTTTATAC-TTATTTATTT-AAA-TTA
53831546 TTTTTCATA-TTATTTATTCTAAA-TA
1 TTTTT-ATACTTATTTATT-TAAATTA
53831571 TTTTTATACGTTATTTATGTTAAA
1 TTTTTATAC-TTATTTAT-TTAAA
53831595 CCATTATATA
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
24 3 0.07
25 7 0.16
26 12 0.27
27 13 0.30
28 6 0.14
29 3 0.07
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (25 bp):
TTTTTATACTTATTTATTTAAATTA
Found at i:53831909 original size:46 final size:47
Alignment explanation
Indices: 53831792--53831915 Score: 121
Period size: 46 Copynumber: 2.7 Consensus size: 47
53831782 ATTTTTCACA
* * *
53831792 TATTATTTATTTTAGACTTTCTA-TGTTTTCTTTTAAATTGTTATATG
1 TATTAATTATTTTAGACTTT-TATTATTTTATTTTAAATTGTTATATG
* ** * *
53831839 TATT-ATTCATTTTA-AGTTGCATTATTTTATTTTAAATTGTTTTGTG
1 TATTAATT-ATTTTAGACTTTTATTATTTTATTTTAAATTGTTATATG
*
53831885 TATTAATTATTTTAGA-TTTTATTATATTATT
1 TATTAATTATTTTAGACTTTTATTATTTTATT
53831916 CCCTTTAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
45 1 0.02
46 47 0.76
47 14 0.23
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.62
Consensus pattern (47 bp):
TATTAATTATTTTAGACTTTTATTATTTTATTTTAAATTGTTATATG
Found at i:53836279 original size:34 final size:34
Alignment explanation
Indices: 53836240--53836309 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
53836230 TCAAATAAAC
53836240 ACCAAAATTAATACATTTCAAAGCCAAAACACTA
1 ACCAAAATTAATACATTTCAAAGCCAAAACACTA
53836274 ACCAAAATTAATACATTTCAAAGCCAAAACACTA
1 ACCAAAATTAATACATTTCAAAGCCAAAACACTA
53836308 AC
1 AC
53836310 TCACATAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.53, C:0.24, G:0.03, T:0.20
Consensus pattern (34 bp):
ACCAAAATTAATACATTTCAAAGCCAAAACACTA
Found at i:53837298 original size:21 final size:21
Alignment explanation
Indices: 53837272--53837311 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
53837262 CCGTGTGTCA
53837272 CACACGGTCTAGACACATGCC
1 CACACGGTCTAGACACATGCC
53837293 CACACGGTCTAGACACATG
1 CACACGGTCTAGACACATG
53837312 TCTGTGTGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.35, G:0.20, T:0.15
Consensus pattern (21 bp):
CACACGGTCTAGACACATGCC
Found at i:53842111 original size:17 final size:18
Alignment explanation
Indices: 53842089--53842123 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
53842079 CATAACAGCC
53842089 CACATTTTCCT-TCCTTT
1 CACATTTTCCTATCCTTT
*
53842106 CACATTTTTCTATCCTTT
1 CACATTTTCCTATCCTTT
53842124 TCTACAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.14, C:0.31, G:0.00, T:0.54
Consensus pattern (18 bp):
CACATTTTCCTATCCTTT
Found at i:53845119 original size:28 final size:28
Alignment explanation
Indices: 53845056--53845209 Score: 256
Period size: 28 Copynumber: 5.5 Consensus size: 28
53845046 AAATTAAGTC
* *
53845056 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
53845083 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
53845111 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
53845139 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAACT
*
53845167 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
53845195 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
53845210 GTACAATTTA
Statistics
Matches: 121, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
27 22 0.18
28 99 0.82
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:53845146 original size:56 final size:56
Alignment explanation
Indices: 53845056--53845234 Score: 261
Period size: 56 Copynumber: 3.2 Consensus size: 56
53845046 AAATTAAGTC
* *
53845056 CGCACACTCAGTGCTATATAATC-AACTCGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTATATAATCAAACT
* *
53845111 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTATATAATCAAACT
* * * * *
53845167 CGCACACTTAGTGCTACATAATCAAGCTCGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTATATAA-TCAAACT
53845224 CGCACACTTAG
1 CGCACACTTAG
53845235 CGCCAATCTC
Statistics
Matches: 111, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
55 21 0.19
56 75 0.68
57 15 0.14
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (56 bp):
CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTATATAATCAAACT
Found at i:53853296 original size:28 final size:28
Alignment explanation
Indices: 53853239--53853389 Score: 247
Period size: 28 Copynumber: 5.5 Consensus size: 28
53853229 AAATTAAGTC
* *
53853239 CGCACACTCAGTGCTATATAATC-AA-T
1 CGCACACTTAGTGCTACATAATCAAACT
*
53853265 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
53853293 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
53853321 CGCACACTTAGTGCTAC-TAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
53853348 CGCACACTTAGTGCTACATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
53853375 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
53853390 GTCAATTTAA
Statistics
Matches: 120, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
26 22 0.18
27 48 0.40
28 50 0.42
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:53853314 original size:54 final size:54
Alignment explanation
Indices: 53853239--53853389 Score: 250
Period size: 54 Copynumber: 2.8 Consensus size: 54
53853229 AAATTAAGTC
* *
53853239 CGCACACTCAGTGCTATATAATCAA-TCGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTA-ATAATCAAACT
*
53853293 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACTAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACTCGCACACTTAGTGCTAATAATCAAACT
53853348 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCT
53853390 GTCAATTTAA
Statistics
Matches: 92, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
54 40 0.43
55 35 0.38
56 17 0.18
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTAATAATCAAACT
Found at i:53853409 original size:54 final size:53
Alignment explanation
Indices: 53853239--53853412 Score: 226
Period size: 54 Copynumber: 3.2 Consensus size: 53
53853229 AAATTAAGTC
* * *
53853239 CGCACACTCAGTGCTATATAATCAA-TCGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCT-T-CAATCAAACT
*
53853293 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACTAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACTCGCACACTTAGTGCTTC-AATCAAACT
* *
53853348 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTGTCAATTTAAACC
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCT-TCAA-TCAAACT
53853403 CG-ACACTTAG
1 CGCACACTTAG
53853413 CGCCAATCTC
Statistics
Matches: 108, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
54 50 0.46
55 42 0.39
56 16 0.15
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.26
Consensus pattern (53 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTTCAATCAAACT
Found at i:53858792 original size:32 final size:31
Alignment explanation
Indices: 53858749--53858809 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 31
53858739 AGCCCGGTTA
*
53858749 TAGTAATTCGCAAAATGCCTTCGGGACTTAAC
1 TAGTAACTCGCAAAATGCCTTC-GGACTTAAC
*
53858781 TAGTAACTCGCACAATGCCTTCGGACTTA
1 TAGTAACTCGCAAAATGCCTTCGGACTTA
53858810 CCCGGATAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 7 0.26
32 20 0.74
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.28
Consensus pattern (31 bp):
TAGTAACTCGCAAAATGCCTTCGGACTTAAC
Found at i:53858906 original size:39 final size:38
Alignment explanation
Indices: 53858781--53858977 Score: 168
Period size: 39 Copynumber: 4.9 Consensus size: 38
53858771 GGGACTTAAC
*
53858781 TAGTAACTCGCACAATGCCTTCGGACTTA-CCCGGATAGT
1 TAGTAACTCGCACAATGCCTTCGGGCTTAGCCCGGA-A-T
* * *
53858820 AACTTAAACACTCGCACAAATGCCTTCGGGACTTAACCCGGAAT
1 TA-GT--A-ACTCGCAC-AATGCCTTCGGG-CTTAGCCCGGAAT
53858864 TAGTAATCTCGCACAATGCCTTCGGGCTTAGCCCGGAAT
1 TAGTAA-CTCGCACAATGCCTTCGGGCTTAGCCCGGAAT
* *
53858903 TAGT-ACTCGCACAATGCCTTCGGATCTTAGTCCGG-A-
1 TAGTAACTCGCACAATGCCTTCGG-GCTTAGCCCGGAAT
* * *
53858939 TATGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 TA-GTAAC-TCGCACAATGCCTTCGGG-CTTAGCCCGGA
53858978 CAGCATTCAA
Statistics
Matches: 132, Mismatches: 12, Indels: 27
0.77 0.07 0.16
Matches are distributed among these distances:
36 2 0.02
37 21 0.16
38 12 0.09
39 41 0.31
40 14 0.11
41 8 0.06
42 1 0.01
43 9 0.07
44 13 0.10
45 5 0.04
46 6 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (38 bp):
TAGTAACTCGCACAATGCCTTCGGGCTTAGCCCGGAAT
Found at i:53858938 original size:77 final size:78
Alignment explanation
Indices: 53858829--53858977 Score: 182
Period size: 77 Copynumber: 1.9 Consensus size: 78
53858819 TAACTTAAAC
* *
53858829 ACTCGCACAAATGCCTTCGGGACTTAACCCGGA-ATTAGTAA-TCTCGCACAATGCCTTCGGG-C
1 ACTCGCACAAATGCCTTCGGGACTTAACCCGGATA-T-GTAACT-TAGCACAAAGCCTTCGGGAC
53858891 TTAGCCCGGAATTAGT
63 TTAGCCCGGAATTAGT
** *
53858907 ACTCGCAC-AATGCCTTC-GGATCTTAGTCCGGATATGTCACTTAGCACAAAGCCTTCGGGACTT
1 ACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATGTAACTTAGCACAAAGCCTTCGGGACTT
53858970 AGCCCGGA
65 AGCCCGGA
53858978 CAGCATTCAA
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
76 22 0.35
77 31 0.50
78 9 0.15
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (78 bp):
ACTCGCACAAATGCCTTCGGGACTTAACCCGGATATGTAACTTAGCACAAAGCCTTCGGGACTTA
GCCCGGAATTAGT
Found at i:53866032 original size:40 final size:40
Alignment explanation
Indices: 53865988--53866251 Score: 333
Period size: 40 Copynumber: 6.7 Consensus size: 40
53865978 GCTCCTCGTT
* * *
53865988 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
53866028 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
53866068 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
53866108 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * * *
53866148 CAAATGCCTTCGGG-CTTAGCCCGAAATTAGTATCTTGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * *
53866187 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGAT-TTAGTAAC-TCGCA
*
53866228 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
53866252 CAGCATTCAA
Statistics
Matches: 203, Mismatches: 15, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
38 2 0.01
39 47 0.23
40 145 0.71
41 9 0.04
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:53871516 original size:41 final size:40
Alignment explanation
Indices: 53871471--53871632 Score: 109
Period size: 41 Copynumber: 3.9 Consensus size: 40
53871461 TCTTGGCACC
53871471 GGCTCAAAAGCCCTTCAAGACCAAGCTCGGATTAGACTACT
1 GGCTCAAAAGCCCTTCAAGACCAAGCTCGGATTAGAC-ACT
* * * ** *
53871512 GGCTCGAAGGCCCTTC-GGAATTAAG-TCCGG-TTATGTCACT
1 GGCTCAAAAGCCCTTCAAG-ACCAAGCT-CGGATTA-GACACT
* * *
53871552 GGCTCTAAAAAGCCCTTCGAA-ACTAAGTTCAGTTATTAG-CACT
1 GGCTC--AAAAGCCCTTC-AAGACCAAGCTC-G-GATTAGACACT
*
53871595 GGCTCAAAAGCCCTTCGAGACCAAGCTCGGATTTAGAC
1 GGCTCAAAAGCCCTTCAAGACCAAGCTCGGA-TTAGAC
53871633 CCCGATTAGC
Statistics
Matches: 92, Mismatches: 15, Indels: 28
0.68 0.11 0.21
Matches are distributed among these distances:
39 1 0.01
40 19 0.21
41 42 0.46
42 15 0.16
43 11 0.12
44 1 0.01
45 3 0.03
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (40 bp):
GGCTCAAAAGCCCTTCAAGACCAAGCTCGGATTAGACACT
Found at i:53871570 original size:42 final size:40
Alignment explanation
Indices: 53871509--53871612 Score: 111
Period size: 42 Copynumber: 2.5 Consensus size: 40
53871499 GGATTAGACT
* * * * *
53871509 ACTGGCTCGAAGGCCCTTCGGAATTAAGTCCGGTTATGT-C
1 ACTGGCTCAAAAGCCCTTCGAAACTAAGTCCAGTTAT-TAC
*
53871549 ACTGGCTCTAAAAAGCCCTTCGAAACTAAGTTCAGTTATTAGC
1 ACTGGCTC--AAAAGCCCTTCGAAACTAAGTCCAGTTATTA-C
53871592 ACTGGCTCAAAAGCCCTTCGA
1 ACTGGCTCAAAAGCCCTTCGA
53871613 GACCAAGCTC
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
40 8 0.15
41 14 0.26
42 23 0.43
43 9 0.17
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (40 bp):
ACTGGCTCAAAAGCCCTTCGAAACTAAGTCCAGTTATTAC
Found at i:53873907 original size:10 final size:10
Alignment explanation
Indices: 53873888--53873936 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
53873878 GCAAATCTGC
*
53873888 CAAAAATAAT
1 CAAAATTAAT
53873898 CAAAATTAAT
1 CAAAATTAAT
53873908 CAAAATTAATT
1 CAAAATTAA-T
*
53873919 ATAAAATTAAT
1 -CAAAATTAAT
*
53873930 TAAAATT
1 CAAAATT
53873937 CATTATGTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 25 0.71
11 2 0.06
12 8 0.23
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (10 bp):
CAAAATTAAT
Found at i:53873927 original size:22 final size:22
Alignment explanation
Indices: 53873899--53873942 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
53873889 AAAAATAATC
53873899 AAAATTAATCAAAATTAATTAT
1 AAAATTAATCAAAATTAATTAT
* *
53873921 AAAATTAATTAAAATTCATTAT
1 AAAATTAATCAAAATTAATTAT
53873943 GTTAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATTAATCAAAATTAATTAT
Found at i:53876871 original size:26 final size:27
Alignment explanation
Indices: 53876821--53876871 Score: 70
Period size: 25 Copynumber: 1.9 Consensus size: 27
53876811 AGTTCATAAA
*
53876821 TTCTCTTCGAGTTTTCTTTTTAAGAAT
1 TTCTCTTCGAGTTTTCTTTTGAAGAAT
53876848 TTCTCTT-GAG-TTTCTTTTAGAAGA
1 TTCTCTTCGAGTTTTCTTTT-GAAGA
53876872 GTTTTAGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 8 0.36
26 7 0.32
27 7 0.32
ACGTcount: A:0.20, C:0.14, G:0.14, T:0.53
Consensus pattern (27 bp):
TTCTCTTCGAGTTTTCTTTTGAAGAAT
Found at i:53879285 original size:49 final size:49
Alignment explanation
Indices: 53879209--53879397 Score: 211
Period size: 49 Copynumber: 3.9 Consensus size: 49
53879199 ATCATAGTTA
* ** *
53879209 ATGAGATCCCGTGTAAGATTATGTCTGGGACATGGCATCGGCATTCGAG
1 ATGAGATCCCATGTAAGACCATATCTGGGACATGGCATCGGCATTCGAG
* * *
53879258 ATGAGATCCCATGTAAGACCATATCTGGGACATGGCATTGACATCCGAG
1 ATGAGATCCCATGTAAGACCATATCTGGGACATGGCATCGGCATTCGAG
* ** * * *
53879307 ATGAGAGCCGGTGTAAGACCATATTTGGGACATGGCATCGGCGTT-GAT
1 ATGAGATCCCATGTAAGACCATATCTGGGACATGGCATCGGCATTCGAG
* * *
53879355 ATGTG-TGCTAGTGTAAGACCATATCTGGGACATGGCATCGGCA
1 ATGAGATCCCA-TGTAAGACCATATCTGGGACATGGCATCGGCA
53879398 CCAATATGTC
Statistics
Matches: 116, Mismatches: 23, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
47 1 0.01
48 36 0.31
49 79 0.68
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (49 bp):
ATGAGATCCCATGTAAGACCATATCTGGGACATGGCATCGGCATTCGAG
Found at i:53879405 original size:48 final size:48
Alignment explanation
Indices: 53879232--53879618 Score: 196
Period size: 48 Copynumber: 8.3 Consensus size: 48
53879222 TAAGATTATG
* * * *
53879232 TCTGGGACATGGCATCGGCATTCGAGATGAGATCCCA-TGTAAGACCATA
1 TCTGGGACATGGCATCGGCA-CCGATATGTGA-GCCAGTGTAAGACCATA
* * * * *
53879281 TCTGGGACATGGCATTGACATCCGAGATGAGAGCCGGTGTAAGACCATA
1 TCTGGGACATGGCATCGGCA-CCGATATGTGAGCCAGTGTAAGACCATA
* *** * *
53879330 TTTGGGACATGGCATCGGCGTTGATATGTGTGCTAGTGTAAGACCATA
1 TCTGGGACATGGCATCGGCACCGATATGTGAGCCAGTGTAAGACCATA
* * * * *
53879378 TCTGGGACATGGCATCGGCACCAATATGTCATCCTGTATAAGACCATA
1 TCTGGGACATGGCATCGGCACCGATATGTGAGCCAGTGTAAGACCATA
** * * * * * **** * *
53879426 TCAAGGATATGGCTTCGGCATCGTTAAGTGATTTTGTATAAGACCATG
1 TCTGGGACATGGCATCGGCACCGATATGTGAGCCAGTGTAAGACCATA
* * * *
53879474 TCTGGGACATGGCAT---CA---ATATGAG-GTCCCGTATAAGACCATG
1 TCTGGGACATGGCATCGGCACCGATATGTGAG-CCAGTGTAAGACCATA
* * * *
53879516 TCTGGGATATGGCATCGGCACTGATATGAGA-CTTC-GTATAAGACCATA
1 TCTGGGACATGGCATCGGCACCGATATGTGAGC--CAGTGTAAGACCATA
* * *
53879564 TCTGGGATATGGCATC-G-A--TATACG-G-GCCCA-TGTAAGACCATA
1 TCTGGGACATGGCATCGGCACCGATATGTGAG-CCAGTGTAAGACCATA
53879606 TCTGGGACATGGC
1 TCTGGGACATGGC
53879619 TTTGGCACTC
Statistics
Matches: 268, Mismatches: 56, Indels: 35
0.75 0.16 0.10
Matches are distributed among these distances:
42 55 0.21
43 1 0.00
44 5 0.02
45 4 0.01
46 1 0.00
47 2 0.01
48 142 0.53
49 58 0.22
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (48 bp):
TCTGGGACATGGCATCGGCACCGATATGTGAGCCAGTGTAAGACCATA
Found at i:53879507 original size:42 final size:42
Alignment explanation
Indices: 53879461--53879618 Score: 140
Period size: 42 Copynumber: 3.6 Consensus size: 42
53879451 AAGTGATTTT
* *
53879461 GTATAAGACCATGTCTGGGACATGGCATCAATATGAGGTCCC
1 GTATAAGACCATATCTGGGACATGGCATCAATATGAGGACCC
* * *
53879503 GTATAAGACCATGTCTGGGATATGGCATCGGCACTGATATGA-GACTTC
1 GTATAAGACCATATCTGGGACATGGCAT---CA---ATATGAGGAC-CC
* * *
53879551 GTATAAGACCATATCTGGGATATGGCATCGATAT-ACGGGCCC
1 GTATAAGACCATATCTGGGACATGGCATCAATATGA-GGACCC
* *
53879593 ATGTAAGACCATATCTGGGACATGGC
1 GTATAAGACCATATCTGGGACATGGC
53879619 TTTGGCACTC
Statistics
Matches: 97, Mismatches: 10, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
41 1 0.01
42 55 0.57
43 2 0.02
45 3 0.03
47 2 0.02
48 34 0.35
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (42 bp):
GTATAAGACCATATCTGGGACATGGCATCAATATGAGGACCC
Found at i:53879534 original size:90 final size:90
Alignment explanation
Indices: 53879413--53879627 Score: 236
Period size: 90 Copynumber: 2.4 Consensus size: 90
53879403 ATGTCATCCT
** * * * * * *
53879413 GTATAAGACCATATCAAGGATATGGCTTCGGCA-TCGTTAAGTGATTTTGTATAAGACCATGTCT
1 GTATAAGACCATATCTGGGATATGGCATCGGCACT-GATAAGAGACTTCGTATAAGACCATATCT
*
53879477 GGGACATGGCATCAATATGA-GGTCCC
65 GGGACATGGCATCAATAT-ACGGGCCC
* *
53879503 GTATAAGACCATGTCTGGGATATGGCATCGGCACTGATATGAGACTTCGTATAAGACCATATCTG
1 GTATAAGACCATATCTGGGATATGGCATCGGCACTGATAAGAGACTTCGTATAAGACCATATCTG
* *
53879568 GGATATGGCATCGATATACGGGCCC
66 GGACATGGCATCAATATACGGGCCC
* * * * *
53879593 ATGTAAGACCATATCTGGGACATGGCTTTGGCACT
1 GTATAAGACCATATCTGGGATATGGCATCGGCACT
53879628 CTATTTGGTG
Statistics
Matches: 104, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
89 1 0.01
90 102 0.98
91 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (90 bp):
GTATAAGACCATATCTGGGATATGGCATCGGCACTGATAAGAGACTTCGTATAAGACCATATCTG
GGACATGGCATCAATATACGGGCCC
Found at i:53887946 original size:18 final size:20
Alignment explanation
Indices: 53887925--53887967 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
53887915 AATTTTCCGG
*
53887925 AAATAT-TTTTTTTTCAAA-
1 AAATATGTTTTTATTCAAAC
53887943 AAAT-TGTTTTTATTCAAAC
1 AAATATGTTTTTATTCAAAC
53887962 AAATAT
1 AAATAT
53887968 AGTATGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 15 0.71
19 4 0.19
20 1 0.05
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (20 bp):
AAATATGTTTTTATTCAAAC
Found at i:53890467 original size:22 final size:23
Alignment explanation
Indices: 53890426--53890468 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
53890416 AATTAATAAC
53890426 ATATAATTGATATATCATATTTA
1 ATATAATTGATATATCATATTTA
53890449 ATAT-ATTAGATA-ATCATATT
1 ATATAATT-GATATATCATATT
53890469 GTTTTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (23 bp):
ATATAATTGATATATCATATTTA
Found at i:53899122 original size:20 final size:20
Alignment explanation
Indices: 53899097--53899136 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
53899087 TGTATTTATA
* *
53899097 AAATTTTAGAATTTTTCATT
1 AAATTTTACAACTTTTCATT
53899117 AAATTTTACAACTTTTCATT
1 AAATTTTACAACTTTTCATT
53899137 TTAGTCCCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (20 bp):
AAATTTTACAACTTTTCATT
Found at i:53901672 original size:27 final size:27
Alignment explanation
Indices: 53901634--53901892 Score: 338
Period size: 27 Copynumber: 9.6 Consensus size: 27
53901624 CGTACCTGAA
*
53901634 CCCTCATGTGATAAAATGATGATTTTG
1 CCCTCATGTGATAAAATGACGATTTTG
*
53901661 CCCTCATGTGATAAAATGACGATTTTT
1 CCCTCATGTGATAAAATGACGATTTTG
*
53901688 CCCTCATGTGATAAACTGACGATTTTG
1 CCCTCATGTGATAAAATGACGATTTTG
*
53901715 CCCTCATGTGATAAAATGACAATTTTG
1 CCCTCATGTGATAAAATGACGATTTTG
* * **
53901742 CCCTTAGGTGATAAAATGAAAATTTTG
1 CCCTCATGTGATAAAATGACGATTTTG
* *
53901769 CCCTTATGTGATAAAATGACGATTTTA
1 CCCTCATGTGATAAAATGACGATTTTG
*
53901796 CCCTCATGTGATAAAATGATGATTTTG
1 CCCTCATGTGATAAAATGACGATTTTG
* * * *
53901823 CCTTTAGGTGATAAAATGACAATTTTG
1 CCCTCATGTGATAAAATGACGATTTTG
* ** *
53901850 CCCTTATGTGATAAAATGATAATTTTT
1 CCCTCATGTGATAAAATGACGATTTTG
*
53901877 CCCTTATGTGATAAAA
1 CCCTCATGTGATAAAA
53901893 AGACTGAAAT
Statistics
Matches: 207, Mismatches: 25, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 207 1.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Consensus pattern (27 bp):
CCCTCATGTGATAAAATGACGATTTTG
Found at i:53901778 original size:81 final size:81
Alignment explanation
Indices: 53901633--53901892 Score: 385
Period size: 81 Copynumber: 3.2 Consensus size: 81
53901623 GCGTACCTGA
* * * * *
53901633 ACCCTCATGTGATAAAATGATGATTTTGCCCTCATGTGATAAAATGACGATTTTTCCCTCATGTG
1 ACCCTCATGTGATAAAATGATGATTTTGCCCTTAGGTGATAAAATGACAATTTTGCCCTTATGTG
*
53901698 ATAAACTGACGATTTT
66 ATAAAATGACGATTTT
* ** *
53901714 GCCCTCATGTGATAAAATGACAATTTTGCCCTTAGGTGATAAAATGAAAATTTTGCCCTTATGTG
1 ACCCTCATGTGATAAAATGATGATTTTGCCCTTAGGTGATAAAATGACAATTTTGCCCTTATGTG
53901779 ATAAAATGACGATTTT
66 ATAAAATGACGATTTT
*
53901795 ACCCTCATGTGATAAAATGATGATTTTGCCTTTAGGTGATAAAATGACAATTTTGCCCTTATGTG
1 ACCCTCATGTGATAAAATGATGATTTTGCCCTTAGGTGATAAAATGACAATTTTGCCCTTATGTG
**
53901860 ATAAAATGATAATTTT
66 ATAAAATGACGATTTT
* *
53901876 TCCCTTATGTGATAAAA
1 ACCCTCATGTGATAAAA
53901893 AGACTGAAAT
Statistics
Matches: 160, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 160 1.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Consensus pattern (81 bp):
ACCCTCATGTGATAAAATGATGATTTTGCCCTTAGGTGATAAAATGACAATTTTGCCCTTATGTG
ATAAAATGACGATTTT
Found at i:53901919 original size:81 final size:81
Alignment explanation
Indices: 53901633--53901922 Score: 243
Period size: 81 Copynumber: 3.6 Consensus size: 81
53901623 GCGTACCTGA
* * * * ** * *
53901633 ACCCTCATGTGATAAAATGATGATTTTGCCCTCAT--GTGATAAAATGACGATTTTTCCCTCATG
1 ACCCTCATGTGATAAAAAGATGAATATG-CCT-ATAGGAGATAAAATGAAAATTTTGCCCTTATG
* *
53901696 TGATAAACTGACGATTTT
64 TGATAAAATGACAATTTT
* * * * *
53901714 GCCCTCATGTGATAAAATGA-CAATTTTGCCCT-TAGGTGATAAAATGAAAATTTTGCCCTTATG
1 ACCCTCATGTGATAAAAAGATGAA-TATG-CCTATAGGAGATAAAATGAAAATTTTGCCCTTATG
*
53901777 TGATAAAATGACGATTTT
64 TGATAAAATGACAATTTT
* * * * * *
53901795 ACCCTCATGTGATAAAATGATGATTTTGCCTTTAGGTGATAAAATGACAATTTTGCCCTTATGTG
1 ACCCTCATGTGATAAAAAGATGAATATGCCTATAGGAGATAAAATGAAAATTTTGCCCTTATGTG
*
53901860 ATAAAATGATAATTTT
66 ATAAAATGACAATTTT
* *
53901876 TCCCTTATGTGATAAAAAGACTGAAATAT-CCTCATA-GAG-TAAAATGA
1 ACCCTCATGTGATAAAAAGA-TG-AATATGCCT-ATAGGAGATAAAATGA
53901923 TTGAAATACC
Statistics
Matches: 180, Mismatches: 21, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
79 1 0.01
80 4 0.02
81 162 0.90
82 8 0.04
83 5 0.03
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (81 bp):
ACCCTCATGTGATAAAAAGATGAATATGCCTATAGGAGATAAAATGAAAATTTTGCCCTTATGTG
ATAAAATGACAATTTT
Found at i:53901984 original size:27 final size:27
Alignment explanation
Indices: 53901888--53902003 Score: 99
Period size: 27 Copynumber: 4.3 Consensus size: 27
53901878 CCTTATGTGA
* * * *
53901888 TAAAAAGACTGAAATATCCTCATAGAG
1 TAAAATGACTGAAATACCCTCGTAGGG
* *
53901915 TAAAATGATTGAAATACCCTCATAGGG
1 TAAAATGACTGAAATACCCTCGTAGGG
* **
53901942 TAGAATGACCAAAATACCC-CTGTAGGG
1 TAAAATGACTGAAATACCCTC-GTAGGG
* * * *
53901969 TAAAATGACTGTAATACCTTGGTAAGG
1 TAAAATGACTGAAATACCCTCGTAGGG
53901996 TAAAATGA
1 TAAAATGA
53902004 TAGATTTGTT
Statistics
Matches: 71, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
26 1 0.01
27 70 0.99
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (27 bp):
TAAAATGACTGAAATACCCTCGTAGGG
Found at i:53902082 original size:23 final size:23
Alignment explanation
Indices: 53902039--53902088 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
53902029 CTGTATTTGA
53902039 GCATGCCATGTTATATGTATGTT
1 GCATGCCATGTTATATGTATGTT
53902062 GCAT-CCATGTATAATAT-TATGTT
1 GCATGCCATGT-T-ATATGTATGTT
53902085 GCAT
1 GCAT
53902089 TGCATGGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.24
23 15 0.60
24 4 0.16
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (23 bp):
GCATGCCATGTTATATGTATGTT
Found at i:53902986 original size:30 final size:30
Alignment explanation
Indices: 53902952--53903011 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
53902942 TATCATGTCT
53902952 TATGGAAAACACTTCAATGTGGCATCGCCA
1 TATGGAAAACACTTCAATGTGGCATCGCCA
*
53902982 TATGGAAAACACTTCAATGTGGCATTGCCA
1 TATGGAAAACACTTCAATGTGGCATCGCCA
53903012 GATTCGGCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (30 bp):
TATGGAAAACACTTCAATGTGGCATCGCCA
Found at i:53912557 original size:50 final size:50
Alignment explanation
Indices: 53912450--53912602 Score: 148
Period size: 52 Copynumber: 3.0 Consensus size: 50
53912440 CGGAAAAGAT
** * * ** *
53912450 ATGATATGTGCGCCCGTTTAAGACCATAGCTGGGCTATGGCATCAGTGCAAT
1 ATGATATGTGTTCCCGTATAAGACCA-AGCT-GGCTATGGCATCGGTGTGAC
*
53912502 GTGATATGTGTTCCCGTATAAGACC-AGCTGTGCTATGGCATCGGTGTGAC
1 ATGATATGTGTTCCCGTATAAGACCAAGCTG-GCTATGGCATCGGTGTGAC
*
53912552 ATGATAATGTGATT-CCGTATAAGACCATATCTGGCATATGGCATCGGTGTG
1 ATGAT-ATGTG-TTCCCGTATAAGACCA-AGCTGGC-TATGGCATCGGTGTG
53912603 TGATGTGATC
Statistics
Matches: 85, Mismatches: 10, Indels: 11
0.80 0.09 0.10
Matches are distributed among these distances:
49 1 0.01
50 23 0.27
51 17 0.20
52 25 0.29
53 19 0.22
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.29
Consensus pattern (50 bp):
ATGATATGTGTTCCCGTATAAGACCAAGCTGGCTATGGCATCGGTGTGAC
Found at i:53912622 original size:46 final size:47
Alignment explanation
Indices: 53912558--53912652 Score: 122
Period size: 46 Copynumber: 2.0 Consensus size: 47
53912548 TGACATGATA
* * **
53912558 ATGTGATTCCGTATAAGACCATA-TCTGGCATATGGCATCGGTGTGTG
1 ATGTGATTCCATAAAAGACCATAGTAGGGC-TATGGCATCGGTGTGTG
*
53912605 ATGTGA-TCCATAAAAGACCATAGTAGGGCTATGGCTTCGGTGTGTG
1 ATGTGATTCCATAAAAGACCATAGTAGGGCTATGGCATCGGTGTGTG
53912651 AT
1 AT
53912653 ATGTGAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
46 32 0.76
47 10 0.24
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (47 bp):
ATGTGATTCCATAAAAGACCATAGTAGGGCTATGGCATCGGTGTGTG
Found at i:53921252 original size:34 final size:34
Alignment explanation
Indices: 53921208--53921275 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
53921198 GAACAGTTGA
* * *
53921208 ACAGTCTTGGGGCTAAGCCCTTTTCAGTATCAGTG
1 ACAGTCTTGGGCCTAAGCCCATCTCAGTA-CAGTG
*
53921243 ACAGT-TTGGGCCTTAGCCCATCTCAGTACAGTG
1 ACAGTCTTGGGCCTAAGCCCATCTCAGTACAGTG
53921276 TGAAAAATGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 5 0.17
34 19 0.66
35 5 0.17
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (34 bp):
ACAGTCTTGGGCCTAAGCCCATCTCAGTACAGTG
Found at i:53926564 original size:9 final size:9
Alignment explanation
Indices: 53926550--53926618 Score: 51
Period size: 9 Copynumber: 8.0 Consensus size: 9
53926540 GACACCTGCA
53926550 ATTAAACAC
1 ATTAAACAC
53926559 ATTAAA-AC
1 ATTAAACAC
*
53926567 ---AAACAT
1 ATTAAACAC
53926573 ATTAAACAC
1 ATTAAACAC
53926582 ATTTAAACAC
1 A-TTAAACAC
53926592 TTATTAAACAC
1 --ATTAAACAC
53926603 A--AAACAC
1 ATTAAACAC
*
53926610 TTTAAACAC
1 ATTAAACAC
53926619 TTATCTTAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 18
0.70 0.04 0.26
Matches are distributed among these distances:
5 3 0.06
6 1 0.02
7 6 0.12
8 2 0.04
9 19 0.40
10 8 0.17
11 8 0.17
12 1 0.02
ACGTcount: A:0.55, C:0.20, G:0.00, T:0.25
Consensus pattern (9 bp):
ATTAAACAC
Found at i:53926598 original size:11 final size:11
Alignment explanation
Indices: 53926550--53926603 Score: 58
Period size: 10 Copynumber: 4.9 Consensus size: 11
53926540 GACACCTGCA
53926550 ATTAAACACAT
1 ATTAAACACAT
*
53926561 -TAAAACAAACAT
1 ATTAAAC--ACAT
53926573 ATTAAACACAT
1 ATTAAACACAT
*
53926584 -TTAAACACTT
1 ATTAAACACAT
53926594 ATTAAACACA
1 ATTAAACACA
53926604 AAACACTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 14 0.40
11 12 0.34
12 4 0.11
13 5 0.14
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.26
Consensus pattern (11 bp):
ATTAAACACAT
Found at i:53926598 original size:21 final size:22
Alignment explanation
Indices: 53926550--53926603 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
53926540 GACACCTGCA
53926550 ATTAAACACATTAAAACAAACAT
1 ATTAAACACATTAAAAC-AACAT
* *
53926573 ATTAAACACATTTAAAC-ACTT
1 ATTAAACACATTAAAACAACAT
53926594 ATTAAACACA
1 ATTAAACACA
53926604 AAACACTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 13 0.45
23 16 0.55
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.26
Consensus pattern (22 bp):
ATTAAACACATTAAAACAACAT
Found at i:53926609 original size:18 final size:19
Alignment explanation
Indices: 53926572--53926611 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
53926562 AAAACAAACA
53926572 TATTAAACACATTTAAACACT
1 TATTAAACACA--TAAACACT
53926593 TATTAAACACA-AAACACT
1 TATTAAACACATAAACACT
53926611 T
1 T
53926612 TAAACACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
21 11 0.58
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (19 bp):
TATTAAACACATAAACACT
Found at i:53930821 original size:45 final size:45
Alignment explanation
Indices: 53930696--53930910 Score: 253
Period size: 45 Copynumber: 4.9 Consensus size: 45
53930686 TTTTATCAAA
* * * **
53930696 TCACCGGCATT-CAGCCTGCTAGGTTTAAAAACCCGAAT--TCAT-
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAAT-ATC
* *
53930738 TCACCGGCATT-TCGCCTGCTAGGCTC-GAGGCCCGAATAATATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
* * *
53930781 TCACCAGTATTATAGCCTGCTAGGCTTAAAGGCCCGAATAATATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
* * *
53930826 TCACTGGCATTATAGCCTGCTAGGGTCAAAGGCCTGAATAATATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
*
53930871 TCACCGGCATTATAGCCTGCTAGACTCAAAGGCCCGAATA
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATA
53930911 GTACTGTACA
Statistics
Matches: 146, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
41 8 0.05
42 24 0.16
43 10 0.07
44 13 0.09
45 91 0.62
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
Found at i:53935596 original size:37 final size:37
Alignment explanation
Indices: 53935496--53935744 Score: 241
Period size: 40 Copynumber: 6.7 Consensus size: 37
53935486 TTGAATGATG
* *
53935496 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGT-ACTA-A
* *
53935536 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAA
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAG-TACTAA
53935575 TTCC-GGCTAAG-CCGAAGGCATTTGTGCGAGTACTAA
1 -TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTACTAA
53935611 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTACT-A
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTACTAA
53935647 -----G-TAAG-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAG-TACT-AA
*
53935679 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAG-TACTA-A
* *
53935719 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAG-CCCGAAGGCATTTG
53935745 AACGAGGAGC
Statistics
Matches: 183, Mismatches: 9, Indels: 34
0.81 0.04 0.15
Matches are distributed among these distances:
29 19 0.10
30 8 0.04
31 1 0.01
32 1 0.01
35 3 0.02
36 14 0.08
37 43 0.23
38 4 0.02
39 8 0.04
40 74 0.40
41 8 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (37 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTACTAA
Found at i:53935659 original size:66 final size:70
Alignment explanation
Indices: 53935582--53935716 Score: 233
Period size: 66 Copynumber: 2.0 Consensus size: 70
53935572 TAATTCCGGC
53935582 TAAGCCGAAGGCATTTGTGCGAG-TACT-AATCCGGGCTAAG-CCCGAAGGCATTTGTGCGAG-T
1 TAAGCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTT
53935643 ACTAG
66 ACTAG
*
53935648 TAAGCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTT
1 TAAGCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTT
53935713 ACTA
66 ACTA
53935717 TAACCGGGCT
Statistics
Matches: 64, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
66 23 0.36
67 4 0.06
68 12 0.19
69 20 0.31
70 5 0.08
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (70 bp):
TAAGCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTT
ACTAG
Found at i:53935661 original size:29 final size:31
Alignment explanation
Indices: 53935618--53935676 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 31
53935608 TAATCCGGGC
53935618 TAAGCCCGAAGGCATTTGTGCGAG-TACTAG
1 TAAGCCCGAAGGCATTTGTGCGAGTTACTAG
53935648 TAAG-CCGAAGGCATTTGTGCGAGTTACTA
1 TAAGCCCGAAGGCATTTGTGCGAGTTACTA
53935677 AATCCGGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (31 bp):
TAAGCCCGAAGGCATTTGTGCGAGTTACTAG
Found at i:53935758 original size:40 final size:40
Alignment explanation
Indices: 53935652--53935763 Score: 111
Period size: 40 Copynumber: 2.8 Consensus size: 40
53935642 TACTAGTAAG
** * *
53935652 CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGTTAAGTC
1 CCGAAGGCATTTGAACGAGTGACTATAA-CCGGGCTAAGTC
** * *
53935692 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTC
1 CCGAAGGCATTTGAACGAGTGACTATAACCGGGCTAAGTC
*
53935732 CCGAAGGCATTTGAACGAG-GAGCTATATCCGG
1 CCGAAGGCATTTGAACGAGTGA-CTATAACCGG
53935764 TTAAATTCCG
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
39 1 0.02
40 61 0.95
41 2 0.03
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTTGAACGAGTGACTATAACCGGGCTAAGTC
Found at i:53943569 original size:40 final size:40
Alignment explanation
Indices: 53943424--53943646 Score: 264
Period size: 40 Copynumber: 5.7 Consensus size: 40
53943414 TTGAATGATG
* *
53943424 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
53943463 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAA-
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
53943503 TCCGGGCTAAG--CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
53943541 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
53943581 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
53943620 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
53943647 AACGAGGAGC
Statistics
Matches: 164, Mismatches: 11, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
37 26 0.16
38 11 0.07
39 11 0.07
40 104 0.63
41 11 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:53943627 original size:80 final size:79
Alignment explanation
Indices: 53943424--53943646 Score: 294
Period size: 80 Copynumber: 2.8 Consensus size: 79
53943414 TTGAATGATG
* * * *
53943424 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATATCCGGGCTAAG-TCCCGAAGGCAT
53943487 TTGTGCGAGATACTAA
64 TTGTGCGAGATACTAA
*
53943503 TCCGGGCTAAG--CCGAAGGCATTTGTGCGAGATACTA-ATTCCGGGCTAAGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCCCGAAGGCATT
*
53943565 TGTGCGAGTTACTAAA
65 TGTGCGAGATACT-AA
* * *
53943581 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTT
53943646 G
66 G
53943647 AACGAGGAGC
Statistics
Matches: 127, Mismatches: 10, Indels: 13
0.85 0.07 0.09
Matches are distributed among these distances:
76 2 0.02
77 46 0.36
78 19 0.15
79 11 0.09
80 48 0.38
81 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAA
Found at i:53945865 original size:40 final size:40
Alignment explanation
Indices: 53945810--53946027 Score: 343
Period size: 40 Copynumber: 5.5 Consensus size: 40
53945800 CGGATGATAA
* *
53945810 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
53945850 CCGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
53945890 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
53945930 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
53945970 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
53946010 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
53946028 TACTCGGTTT
Statistics
Matches: 168, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
39 17 0.10
40 150 0.89
41 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:53949643 original size:46 final size:46
Alignment explanation
Indices: 53949593--53949763 Score: 204
Period size: 46 Copynumber: 3.7 Consensus size: 46
53949583 TGGTTGAGCA
*
53949593 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * *
53949639 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
*
53949686 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
53949732 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACT
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT
53949764 AAGGGGCGGG
Statistics
Matches: 104, Mismatches: 14, Indels: 14
0.79 0.11 0.11
Matches are distributed among these distances:
43 5 0.05
45 3 0.03
46 60 0.58
47 29 0.28
48 3 0.03
50 4 0.04
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:53949749 original size:93 final size:93
Alignment explanation
Indices: 53949590--53949760 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
53949580 GGATGGTTGA
* *
53949590 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
53949655 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
53949683 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
53949748 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
53949761 ACTAAGGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:53956804 original size:40 final size:40
Alignment explanation
Indices: 53956749--53956966 Score: 316
Period size: 40 Copynumber: 5.5 Consensus size: 40
53956739 CGGATGATAA
* *
53956749 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
53956789 CCGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
53956829 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
53956869 CCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
** *
53956909 CCGGGCTAAGTTTCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
53956949 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
53956967 TACTCGGTTT
Statistics
Matches: 162, Mismatches: 14, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
39 15 0.09
40 146 0.90
41 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:53962809 original size:48 final size:47
Alignment explanation
Indices: 53962739--53962964 Score: 168
Period size: 48 Copynumber: 4.7 Consensus size: 47
53962729 TATGTGTGCT
** * *
53962739 AGTGTAAGACCACATCTAGGACATAGCATCGGCCACGATGTGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG-CACGATGTGAGAGCC
* * *
53962787 AGTGTAAGACCATGTCTGGGACATGGGATTGGCA--ATGTAACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGATGT---GAGAGCC
* ** * ** *
53962835 AGTGTAAGACCATGTTTGGGACATGGCATCGGCATTAAGACAAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGATG-TGAGAGCC
* * ** *
53962883 AGTGTAAGACCATGTCTGGGACATGGCATTGGCCTCGACATGTGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG-CACGATGTGAGAGCC
* * ** *
53962931 AATGTAAGACCATGTTTGAAACATGGCATTGGCA
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCA
53962965 ATTCACCCTC
Statistics
Matches: 142, Mismatches: 29, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
45 4 0.03
47 3 0.02
48 131 0.92
49 2 0.01
50 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.22
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGATGTGAGAGCC
Found at i:53962937 original size:96 final size:96
Alignment explanation
Indices: 53962781--53962964 Score: 246
Period size: 96 Copynumber: 1.9 Consensus size: 96
53962771 CCACGATGTG
* * *
53962781 AGAGCCAGTGTAAGACCATGTCTGGGACATGGGATTGGCAATGTAACGAGAGCTAGTGTAAGACC
1 AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCAATGTAACGAGAGCCAATGTAAGACC
**
53962846 ATGTTTGGGACATGGCATCGGCATTAAGACA
66 ATGTTTGAAACATGGCATCGGCATTAAGACA
* * * *
53962877 AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATTGGC-CTCG-ACATGTGAGCCAATGTAAGA
1 AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCAAT-GTA-ACGAGAGCCAATGTAAGA
*
53962940 CCATGTTTGAAACATGGCATTGGCA
64 CCATGTTTGAAACATGGCATCGGCA
53962965 ATTCACCCTC
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
95 2 0.03
96 74 0.97
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23
Consensus pattern (96 bp):
AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCAATGTAACGAGAGCCAATGTAAGACC
ATGTTTGAAACATGGCATCGGCATTAAGACA
Found at i:53964179 original size:21 final size:20
Alignment explanation
Indices: 53964155--53964194 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
53964145 GTTAAATAGG
53964155 CACACGAGCGTGTCGCCCTTC
1 CACACGAGCGTGT-GCCCTTC
* *
53964176 CACATGGGCGTGTGCCCTT
1 CACACGAGCGTGTGCCCTT
53964195 ATCTACTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.12, C:0.38, G:0.28, T:0.23
Consensus pattern (20 bp):
CACACGAGCGTGTGCCCTTC
Found at i:53966094 original size:22 final size:22
Alignment explanation
Indices: 53966066--53966130 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
53966056 GTAAATACGT
*
53966066 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
*
53966088 TTGGCACAGAGCCATATAT-AGG
1 TTGGCACAAAGCCATA-ATCAGG
**
53966110 TTGGTGCAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
53966131 AATAGTTGGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.05
22 33 0.89
23 2 0.05
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.22
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:53966329 original size:41 final size:41
Alignment explanation
Indices: 53966272--53966394 Score: 192
Period size: 41 Copynumber: 3.0 Consensus size: 41
53966262 TAAAAGTCAC
* * *
53966272 CGGTGGATTCACGGTCGTCAAGCAACCATACGATCCTTAAT
1 CGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAAT
*
53966313 CGGTGGATCCACGGTCGTCAAGCAACCATGCGATTCTCAAT
1 CGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAAT
**
53966354 CGGTGGATCCACAATCGTCAAGCAACCATGCGATCCTCAAT
1 CGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAAT
53966395 TTCTTCCTCC
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 75 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (41 bp):
CGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAAT
Found at i:53966684 original size:27 final size:27
Alignment explanation
Indices: 53966654--53966706 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
53966644 GGTAAATCTA
53966654 CAAACCAAGGGTATTTCAATAATTTTG
1 CAAACCAAGGGTATTTCAATAATTTTG
* *
53966681 CAAACCAATGGTATTTCTATAATTTT
1 CAAACCAAGGGTATTTCAATAATTTT
53966707 TGAAAGTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (27 bp):
CAAACCAAGGGTATTTCAATAATTTTG
Found at i:53966743 original size:27 final size:27
Alignment explanation
Indices: 53966660--53966815 Score: 138
Period size: 27 Copynumber: 5.7 Consensus size: 27
53966650 TCTACAAACC
** * **
53966660 AAGGGTATTTCAATAATTTTGCAAACC
1 AAGGGTATTTCTGTAATTTTGTAAATT
* *
53966687 AATGGTATTTCTATAATTTT-TGAAAGTT
1 AAGGGTATTTCTGTAATTTTGT-AAA-TT
53966715 AAGGGTATTTCTGTAATTTTGTAAATT
1 AAGGGTATTTCTGTAATTTTGTAAATT
* *
53966742 AAGGGTGTTTATGTAATTTTGTAAATT
1 AAGGGTATTTCTGTAATTTTGTAAATT
** *
53966769 -AGGAGTATTTCTGTAATTTTCCAAATC
1 AAGG-GTATTTCTGTAATTTTGTAAATT
*
53966796 AGGGGTATTT-TGGTAATTTT
1 AAGGGTATTTCT-GTAATTTT
53966816 AAAAGTCGAG
Statistics
Matches: 108, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
26 4 0.04
27 80 0.74
28 23 0.21
29 1 0.01
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.45
Consensus pattern (27 bp):
AAGGGTATTTCTGTAATTTTGTAAATT
Found at i:53966812 original size:54 final size:54
Alignment explanation
Indices: 53966754--53966993 Score: 240
Period size: 54 Copynumber: 4.4 Consensus size: 54
53966744 GGGTGTTTAT
**
53966754 GTAATTTTGTAAAT-TAGGAGTATTTCT-GTAATTTTCCAAATCAGGGGTATTTTG
1 GTAATTTTACAAATCTAGG-GTATTT-TGGTAATTTTCCAAATCAGGGGTATTTTG
* * * * *
53966808 GTAATTTTA-AAAGTCGAGGGTATTTTAGTAATTTTCCGAATCAGGGGTGTTTTA
1 GTAATTTTACAAA-TCTAGGGTATTTTGGTAATTTTCCAAATCAGGGGTATTTTG
* * * *
53966862 GTAATTTTACAAGTCAAGGGTATTTTGGTAATTTTACAAA-CTAGGGATATTTTG
1 GTAATTTTACAAATCTAGGGTATTTTGGTAATTTTCCAAATC-AGGGGTATTTTG
***
53966916 GTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTGTTAATC-GAGGGTATTTTG
1 GTAATTTTACAAATCTA-GGGTATTTTGGTAATTTTCCAAATCAG-GGGTATTTTG
* *
53966970 GTAATTTTACTAATCGAGGGTATT
1 GTAATTTTACAAATCTAGGGTATT
53966994 CAATAATTTT
Statistics
Matches: 156, Mismatches: 21, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
53 8 0.05
54 140 0.90
55 8 0.05
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.42
Consensus pattern (54 bp):
GTAATTTTACAAATCTAGGGTATTTTGGTAATTTTCCAAATCAGGGGTATTTTG
Found at i:53966828 original size:27 final size:26
Alignment explanation
Indices: 53966773--53966993 Score: 173
Period size: 27 Copynumber: 8.2 Consensus size: 26
53966763 TAAATTAGGA
*
53966773 GTATTTCT-GTAATTTTCCAAATC-AGGG
1 GTATTT-TGGTAATTTT-AAAATCGA-GG
53966800 GTATTTTGGTAATTTTAAAAGTCGAGG
1 GTATTTTGGTAATTTTAAAA-TCGAGG
* **
53966827 GTATTTTAGTAATTTTCCGAATC-AGGG
1 GTATTTTGGTAATTTT-AAAATCGA-GG
* * * *
53966854 GTGTTTTAGTAATTTTACAAGTCAAGG
1 GTATTTTGGTAATTTTA-AAATCGAGG
*
53966881 GTATTTTGGTAATTTTACAAA-CTAGG
1 GTATTTTGGTAATTTTA-AAATCGAGG
*
53966907 GATATTTTGGTAATTTTACAAA-CTAGGG
1 G-TATTTTGGTAATTTTA-AAATCGA-GG
**
53966935 GTATTTTGGTAATTTTGTTAATCGAGG
1 GTATTTTGGTAATTTT-AAAATCGAGG
*
53966962 GTATTTTGGTAATTTTACTAATCGAGG
1 GTATTTTGGTAATTTTA-AAATCGAGG
53966989 GTATT
1 GTATT
53966994 CAATAATTTT
Statistics
Matches: 166, Mismatches: 16, Indels: 24
0.81 0.08 0.12
Matches are distributed among these distances:
26 10 0.06
27 147 0.89
28 9 0.05
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.43
Consensus pattern (26 bp):
GTATTTTGGTAATTTTAAAATCGAGG
Found at i:53966839 original size:81 final size:81
Alignment explanation
Indices: 53966635--53966993 Score: 255
Period size: 81 Copynumber: 4.4 Consensus size: 81
53966625 CACCCTACAA
* * * * * * * ** **
53966635 GGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAATAATTTTGCAAACCAATGGTATTTCTA
1 GGGTATTTTGGTAATTTTACAAATCGAGGGTATTTTAGTAATTTTGCAAATTAGGGGTATTT-TA
** * *
53966700 -TAATTTTTGAAAGTTAA
65 GTAATTTTACAAA-TCAG
** ** * * *
53966717 GGGTATTTCT-GTAATTTTGTAAATTAAGGGT-GTTTATGTAATTTTGTAAATTAGGAGTATTTC
1 GGGTATTT-TGGTAATTTTACAAATCGAGGGTATTTTA-GTAATTTTGCAAATTAGGGGTATTT-
*
53966780 T-GTAATTTTCCAAATCAG
63 TAGTAATTTTACAAATCAG
* * * *
53966798 GGGTATTTTGGTAATTTTA-AAAGTCGAGGGTATTTTAGTAATTTTCCGAATCAGGGGTGTTTTA
1 GGGTATTTTGGTAATTTTACAAA-TCGAGGGTATTTTAGTAATTTTGCAAATTAGGGGTATTTTA
* *
53966862 GTAATTTTACAAGTCAA
65 GTAATTTTACAAATCAG
* * * * *
53966879 GGGTATTTTGGTAATTTTACAAA-CTAGGGATATTTTGGTAATTTTACAAACTAGGGGTATTTTG
1 GGGTATTTTGGTAATTTTACAAATCGAGGG-TATTTTAGTAATTTTGCAAATTAGGGGTATTTTA
***
53966943 GTAATTTTGTTAATC-G
65 GTAATTTTACAAATCAG
*
53966959 AGGGTATTTTGGTAATTTTACTAATCGAGGGTATT
1 -GGGTATTTTGGTAATTTTACAAATCGAGGGTATT
53966994 CAATAATTTT
Statistics
Matches: 218, Mismatches: 48, Indels: 23
0.75 0.17 0.08
Matches are distributed among these distances:
80 10 0.05
81 143 0.66
82 64 0.29
83 1 0.00
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (81 bp):
GGGTATTTTGGTAATTTTACAAATCGAGGGTATTTTAGTAATTTTGCAAATTAGGGGTATTTTAG
TAATTTTACAAATCAG
Found at i:53967093 original size:27 final size:27
Alignment explanation
Indices: 53967013--53967081 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 27
53967003 TGTAAACCAA
*
53967013 GGGTATTTCAATAATTCTACCCTACAG
1 GGGTATTTCAGTAATTCTACCCTACAG
* * *
53967040 GGGCATTTTAGTAATTCTATCCTACAG
1 GGGTATTTCAGTAATTCTACCCTACAG
53967067 GGGTATTTCAGTAAT
1 GGGTATTTCAGTAAT
53967082 AGTAGCCTAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (27 bp):
GGGTATTTCAGTAATTCTACCCTACAG
Found at i:53969780 original size:32 final size:32
Alignment explanation
Indices: 53969738--53969838 Score: 94
Period size: 32 Copynumber: 3.2 Consensus size: 32
53969728 ATGCAGCTCT
* *
53969738 AAGCCTTCAGTAGCGGTATTATAATTGGCACA
1 AAGCCATCAGTAACGGTATTATAATTGGCACA
* **
53969770 AAGCCATCAGTAACTGTATTATGTTTGGCACA
1 AAGCCATCAGTAACGGTATTATAATTGGCACA
* *** * *
53969802 TAGCCATCAACGACGGTAATATAATCGGCACA
1 AAGCCATCAGTAACGGTATTATAATTGGCACA
*
53969834 CAGCC
1 AAGCC
53969839 TTGGGCAAAT
Statistics
Matches: 54, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (32 bp):
AAGCCATCAGTAACGGTATTATAATTGGCACA
Found at i:53970334 original size:27 final size:27
Alignment explanation
Indices: 53970304--53970390 Score: 131
Period size: 27 Copynumber: 3.2 Consensus size: 27
53970294 CAAAACAGTT
*
53970304 ATTTTACCCTACAAGGGTATTTCGGTA
1 ATTTTACACTACAAGGGTATTTCGGTA
*
53970331 ATTTTACACTACAAAGGTATGTT-GGTA
1 ATTTTACACTACAAGGGTAT-TTCGGTA
*
53970358 AGTTTACACTACAAGGGTATTTCGGTA
1 ATTTTACACTACAAGGGTATTTCGGTA
53970385 ATTTTA
1 ATTTTA
53970391 AAAATTGGGG
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
26 2 0.04
27 49 0.92
28 2 0.04
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (27 bp):
ATTTTACACTACAAGGGTATTTCGGTA
Found at i:53970452 original size:27 final size:26
Alignment explanation
Indices: 53970317--53970481 Score: 102
Period size: 27 Copynumber: 6.2 Consensus size: 26
53970307 TTACCCTACA
* * *
53970317 AGGGTATTTCGGTAATTTTACACTACA
1 AGGGTATTTCGGTAATTTTAAAAT-CG
* * * * *
53970344 AAGGTATGTT-GGTAAGTTTACACTACA
1 AGGGTAT-TTCGGTAATTTTAAAAT-CG
*
53970371 AGGGTATTTCGGTAATTTTAAAAATTG
1 AGGGTATTTCGGTAATTTT-AAAATCG
* * * *
53970398 GGGGCA-TTCAGTAATTTTACAATCCG
1 AGGGTATTTCGGTAATTTTAAAAT-CG
53970424 AGGGTATTTCGGTAATTTTATAAATCG
1 AGGGTATTTCGGTAATTTTA-AAATCG
* * *
53970451 AGAGTATTTTGATAATTTTACAAATCG
1 AGGGTATTTCGGTAATTTTA-AAATCG
53970478 -GGGT
1 AGGGT
53970482 CTTAACGACC
Statistics
Matches: 110, Mismatches: 22, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
25 4 0.04
26 21 0.19
27 77 0.70
28 8 0.07
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (26 bp):
AGGGTATTTCGGTAATTTTAAAATCG
Found at i:53975930 original size:64 final size:64
Alignment explanation
Indices: 53975850--53976033 Score: 178
Period size: 67 Copynumber: 2.8 Consensus size: 64
53975840 AGACATTATG
* * *
53975850 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGTGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
53975914 ATGTAGCTAGGTCGCATGCGTGGCT-CCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGA
1 ATGTAGCTAGGTCGCATGGGT-GATACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGA
53975978 TAA
62 TAA
* * * *
53975981 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGATACT-ATGTGTACACCATGTAG-ACAAGAGAGC
53976034 CGAACTCTAT
Statistics
Matches: 97, Mismatches: 16, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
62 1 0.01
63 19 0.20
64 23 0.24
65 4 0.04
66 18 0.19
67 32 0.33
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:53977322 original size:820 final size:820
Alignment explanation
Indices: 53975742--53977384 Score: 3241
Period size: 820 Copynumber: 2.0 Consensus size: 820
53975732 AGAGAGAAAT
53975742 CCCGGTTGAACCTTCGGAAAGATTGGATGATACAGATAGTATGTAGCTAGGTCACATGTATGGTG
1 CCCGGTTGAACCTTCGGAAAGATTGGATGATACAGATAGTATGTAGCTAGGTCACATGTATGGTG
53975807 CTGAGTGCACATCATGTGTACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTG
66 CTGAGTGCACATCATGTGTACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTG
53975872 ATACTATGTGTACACCATGTAGACAAGAGTGCTACGGGATATATGTAGCTAGGTCGCATGCGTGG
131 ATACTATGTGTACACCATGTAGACAAGAGTGCTACGGGATATATGTAGCTAGGTCGCATGCGTGG
*
53975937 CTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGATAAATTGGCTAGGTCACATGGGTG
196 CTCCAGGTGAAGGACACCATGTAAACAAGAGAGCTACGAGATAAATTGGCTAGGTCACATGGGTG
53976002 GTACTGAGTGTTCACCATGTGTACAAGAGAGCCGAACTCTATGATGGGTGGAGCTATGTGCTGAA
261 GTACTGAGTGTTCACCATGTGTACAAGAGAGCCGAACTCTATGATGGGTGGAGCTATGTGCTGAA
53976067 ACCACCAAGTATCGAGGATTGGTCCGAAGTGTTCAACGGGAGACTCTCTATGTATTACTTTGTGA
326 ACCACCAAGTATCGAGGATTGGTCCGAAGTGTTCAACGGGAGACTCTCTATGTATTACTTTGTGA
53976132 GTTTTGTGATGAATAAGTGCATGAACTTGGTTATGTGAATGACGTGTTCATTAAGTGACCAGGAT
391 GTTTTGTGATGAATAAGTGCATGAACTTGGTTATGTGAATGACGTGTTCATTAAGTGACCAGGAT
53976197 GTGGTAAGGTTATAAACAAGTAAGTTATACATGAGGATGATTTTATGGTGACCTTGTGATCATGG
456 GTGGTAAGGTTATAAACAAGTAAGTTATACATGAGGATGATTTTATGGTGACCTTGTGATCATGG
* *
53976262 GCCTATACTTGTGATGTATGAAATGTGGTGAAAATGATTTGTGATATGTATGTTAAAATGATATT
521 GCCTATACTTCTGATGTATGAAATGTGGTGAAAATGATTTGTGATATGTATGTTAAAATGAGATT
53976327 AATAAAAAGAAAGTGTGAAAGAGTGAATTAGCAATAAAACTGTTTTGGATAGTAGTAATGACGTG
586 AATAAAAAGAAAGTGTGAAAGAGTGAATTAGCAATAAAACTGTTTTGGATAGTAGTAATGACGTG
53976392 ATTTTGAAAAATCACCAAAAATAGTAGAAATTGAATCAGAGACTGAATGAGATAGTAAATTAAAT
651 ATTTTGAAAAATCACCAAAAATAGTAGAAATTGAATCAGAGACTGAATGAGATAGTAAATTAAAT
53976457 CTTAATGAGTCTATTTTCATATAAAAGAAACAGAGCAAGAAAAGGAGTTCTATATTTTGACATAT
716 CTTAATGAGTCTATTTTCATATAAAAGAAACAGAGCAAGAAAAGGAGTTCTATATTTTGACATAT
53976522 TTATGTTTTTGTGAGACTGGTTTAGAATGATTACGTGATC
781 TTATGTTTTTGTGAGACTGGTTTAGAATGATTACGTGATC
53976562 CCCGGTTGAACCTTCGGAAAGATTGGATGATACAGATAGTATGTAGCTAGGTCACATGTATGGTG
1 CCCGGTTGAACCTTCGGAAAGATTGGATGATACAGATAGTATGTAGCTAGGTCACATGTATGGTG
53976627 CTGAGTGCACATCATGTGTACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTG
66 CTGAGTGCACATCATGTGTACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTG
53976692 ATACTATGTGTACACCATGTAGACAAGAGTGCTACGGGATATATGTAGCTAGGTCGCATGCGTGG
131 ATACTATGTGTACACCATGTAGACAAGAGTGCTACGGGATATATGTAGCTAGGTCGCATGCGTGG
53976757 CTCCAGGTGAAGGACACCATGTAAACAAGAGAGCTACGAGATAAATTGGCTAGGTCACATGGGTG
196 CTCCAGGTGAAGGACACCATGTAAACAAGAGAGCTACGAGATAAATTGGCTAGGTCACATGGGTG
53976822 GTACTGAGTGTTCACCATGTGTACAAGAGAGCCGAACTCTATGATGGGTGGAGCTATGTGCTGAA
261 GTACTGAGTGTTCACCATGTGTACAAGAGAGCCGAACTCTATGATGGGTGGAGCTATGTGCTGAA
53976887 ACCACCAAGTATCGAGGATTGGTCCGAAGTGTTCAACGGGAGACTCTCTATGTATTACTTTGTGA
326 ACCACCAAGTATCGAGGATTGGTCCGAAGTGTTCAACGGGAGACTCTCTATGTATTACTTTGTGA
53976952 GTTTTGTGATGAATAAGTGCATGAACTTGGTTATGTGAATGACGTGTTCATTAAGTGACCAGGAT
391 GTTTTGTGATGAATAAGTGCATGAACTTGGTTATGTGAATGACGTGTTCATTAAGTGACCAGGAT
53977017 GTGGTAAGGTTATAAACAAGTAAGTTATACATGAGGATGATTTTATGGTGACCTTGTGATCATGG
456 GTGGTAAGGTTATAAACAAGTAAGTTATACATGAGGATGATTTTATGGTGACCTTGTGATCATGG
53977082 GCCTATACTTCTGATGTATGAAATGTGGTGAAAATGATTTGTGATATGTATGTTAAAATGAGATT
521 GCCTATACTTCTGATGTATGAAATGTGGTGAAAATGATTTGTGATATGTATGTTAAAATGAGATT
53977147 AATAAAAAGAAAGTGTGAAAGAGTGAATTAGCAATAAAACTGTTTTGGATAGTAGTAATGACGTG
586 AATAAAAAGAAAGTGTGAAAGAGTGAATTAGCAATAAAACTGTTTTGGATAGTAGTAATGACGTG
*
53977212 ATTTTGAAAAATCACCAAAAATAGTAGAAATTGAATCAGAGACTGAATGAGATATTAAATTAAAT
651 ATTTTGAAAAATCACCAAAAATAGTAGAAATTGAATCAGAGACTGAATGAGATAGTAAATTAAAT
*
53977277 CTTAATGAGTCTATTTTCATATAAAAGAAACAGAGCAAGAAAAGGAGTTCTATATTTTGATATAT
716 CTTAATGAGTCTATTTTCATATAAAAGAAACAGAGCAAGAAAAGGAGTTCTATATTTTGACATAT
53977342 TTATGTTTTTGTGAGACTGGTTTAGAATGATTACGTGATC
781 TTATGTTTTTGTGAGACTGGTTTAGAATGATTACGTGATC
53977382 CCC
1 CCC
53977385 TGTTCTAACT
Statistics
Matches: 818, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
820 818 1.00
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (820 bp):
CCCGGTTGAACCTTCGGAAAGATTGGATGATACAGATAGTATGTAGCTAGGTCACATGTATGGTG
CTGAGTGCACATCATGTGTACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTG
ATACTATGTGTACACCATGTAGACAAGAGTGCTACGGGATATATGTAGCTAGGTCGCATGCGTGG
CTCCAGGTGAAGGACACCATGTAAACAAGAGAGCTACGAGATAAATTGGCTAGGTCACATGGGTG
GTACTGAGTGTTCACCATGTGTACAAGAGAGCCGAACTCTATGATGGGTGGAGCTATGTGCTGAA
ACCACCAAGTATCGAGGATTGGTCCGAAGTGTTCAACGGGAGACTCTCTATGTATTACTTTGTGA
GTTTTGTGATGAATAAGTGCATGAACTTGGTTATGTGAATGACGTGTTCATTAAGTGACCAGGAT
GTGGTAAGGTTATAAACAAGTAAGTTATACATGAGGATGATTTTATGGTGACCTTGTGATCATGG
GCCTATACTTCTGATGTATGAAATGTGGTGAAAATGATTTGTGATATGTATGTTAAAATGAGATT
AATAAAAAGAAAGTGTGAAAGAGTGAATTAGCAATAAAACTGTTTTGGATAGTAGTAATGACGTG
ATTTTGAAAAATCACCAAAAATAGTAGAAATTGAATCAGAGACTGAATGAGATAGTAAATTAAAT
CTTAATGAGTCTATTTTCATATAAAAGAAACAGAGCAAGAAAAGGAGTTCTATATTTTGACATAT
TTATGTTTTTGTGAGACTGGTTTAGAATGATTACGTGATC
Found at i:53981190 original size:46 final size:46
Alignment explanation
Indices: 53981137--53981308 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
53981127 TGGGTATCCA
53981137 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTCCG
*
53981183 AACTCGTTGAGTTGAGTCCGAGTT--C-GA-GAGATGT-AACTAGGCATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGTGAA-T--G--TCCG
* * * *
53981230 AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTCCG
*
53981276 AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53981309 GCGTGTTACA
Statistics
Matches: 109, Mismatches: 6, Indels: 22
0.80 0.04 0.16
Matches are distributed among these distances:
42 3 0.03
43 7 0.06
44 1 0.01
45 1 0.01
46 60 0.55
47 27 0.25
48 1 0.01
49 1 0.01
50 5 0.05
51 3 0.03
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.29
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTCCG
Found at i:53984919 original size:13 final size:13
Alignment explanation
Indices: 53984901--53984925 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53984891 TTTCTGTGAA
53984901 AGTAGTAAAAATG
1 AGTAGTAAAAATG
53984914 AGTAGTAAAAAT
1 AGTAGTAAAAAT
53984926 CTGAATTGAA
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:0.56, C:0.00, G:0.20, T:0.24
Consensus pattern (13 bp):
AGTAGTAAAAATG
Found at i:53985553 original size:48 final size:48
Alignment explanation
Indices: 53985346--53985576 Score: 217
Period size: 48 Copynumber: 4.9 Consensus size: 48
53985336 GGGACATGCA
*
53985346 TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAAAATG
1 TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATG
* * *
53985394 TGACCCCATGTAAGACCATCTATGGGACATGGCATTGGCATCAATATG
1 TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATG
* *** * *
53985442 AGA-CATTGTGTAAGACCATAG-CTGGG-CTAT--CA---GCTTCGATATG
1 TGATC-CCATGTAAGACCAT-GTCTGGGAC-ATGGCATTGGCATCAATATG
* *
53985485 CATGATCCCATGTTAGACCATGTCTGGGACATGGCATTGGCATCGATATG
1 --TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATG
* * * *
53985535 TGATCCCATGTAATACCATATCTGGGATATGGAATTGGCATC
1 TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC
53985577 CTACTATGTG
Statistics
Matches: 147, Mismatches: 23, Indels: 26
0.75 0.12 0.13
Matches are distributed among these distances:
43 9 0.06
44 1 0.01
45 19 0.13
46 4 0.03
47 4 0.03
48 100 0.68
50 10 0.07
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (48 bp):
TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATG
Found at i:53988347 original size:24 final size:24
Alignment explanation
Indices: 53988258--53988350 Score: 84
Period size: 24 Copynumber: 3.9 Consensus size: 24
53988248 GAGCTAACGG
53988258 ACAGTAAGCTC-TACTGAGCTG-AA
1 ACAGTAAGCTCTTAC-GAGCTGAAA
* *
53988281 ACGGTAAGCT-TTGACGAGCTGGAA
1 ACAGTAAGCTCTT-ACGAGCTGAAA
* ** *
53988305 ATAGTAAGCTCCAATGAGCTGAAA
1 ACAGTAAGCTCTTACGAGCTGAAA
*
53988329 ACAATAAGCTCTTACGAGCTGA
1 ACAGTAAGCTCTTACGAGCTGA
53988351 TATATCGGTA
Statistics
Matches: 54, Mismatches: 12, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
23 16 0.30
24 38 0.70
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (24 bp):
ACAGTAAGCTCTTACGAGCTGAAA
Found at i:53992367 original size:35 final size:35
Alignment explanation
Indices: 53992324--53992437 Score: 133
Period size: 35 Copynumber: 3.3 Consensus size: 35
53992314 CATAGGTAAG
53992324 TACATGTGAGCTTATATTGAACTTGTATATTCGGC
1 TACATGTGAGCTTATATTGAACTTGTATATTCGGC
* * **
53992359 TGCATGTGAGGTTATATTGAACTTG-AGTATAT-GAT
1 TACATGTGAGCTTATATTGAACTTGTA-TAT-TCGGC
* *
53992394 TACATGTGAGCTTATATTGAACTGGTATATTCGGT
1 TACATGTGAGCTTATATTGAACTTGTATATTCGGC
*
53992429 TATATGTGA
1 TACATGTGA
53992438 AGTTATCTTG
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
34 2 0.03
35 62 0.94
36 2 0.03
ACGTcount: A:0.27, C:0.10, G:0.23, T:0.40
Consensus pattern (35 bp):
TACATGTGAGCTTATATTGAACTTGTATATTCGGC
Found at i:53995121 original size:47 final size:47
Alignment explanation
Indices: 53995067--53995304 Score: 359
Period size: 47 Copynumber: 5.1 Consensus size: 47
53995057 TTAGGATTTT
** * * *
53995067 ATGTGATGAATGTGAATGTGTATATATGAGATGAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
53995114 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
53995161 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
53995208 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
53995255 ATGTGATGAATGTGAACATGTATATATGTGGTAAGGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
53995302 ATG
1 ATG
53995305 CGAAACGTGT
Statistics
Matches: 179, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 179 1.00
ACGTcount: A:0.32, C:0.11, G:0.31, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:53995191 original size:25 final size:25
Alignment explanation
Indices: 53995162--53995239 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
53995152 GAATGGCCAA
53995162 TGTGATGAATGTGAACATGCGTATG
1 TGTGATGAATGTGAACATGCGTATG
* * * *
53995187 TGTGAT-AAGGCCG-A-ATG-GCCA-A
1 TGTGATGAATG-TGAACATGCG-TATG
53995209 TGTGATGAATGTGAACATGCGTATG
1 TGTGATGAATGTGAACATGCGTATG
53995234 TGTGAT
1 TGTGAT
53995240 AAGGCCGAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 14
0.63 0.13 0.23
Matches are distributed among these distances:
22 8 0.21
23 8 0.21
24 8 0.21
25 14 0.37
ACGTcount: A:0.28, C:0.10, G:0.32, T:0.29
Consensus pattern (25 bp):
TGTGATGAATGTGAACATGCGTATG
Found at i:53995344 original size:46 final size:46
Alignment explanation
Indices: 53995278--53995368 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
53995268 GAACATGTAT
* * *
53995278 ATATGTGGTAAGGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATGG
* * *
53995324 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATG
53995369 TGTATATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.33, C:0.09, G:0.32, T:0.26
Consensus pattern (46 bp):
ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATGG
Found at i:54003384 original size:15 final size:15
Alignment explanation
Indices: 54003364--54003394 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
54003354 GCAAGTTTTA
54003364 TGCCGGTGATTTATT
1 TGCCGGTGATTTATT
54003379 TGCCGGTGATTTATT
1 TGCCGGTGATTTATT
54003394 T
1 T
54003395 CAACTCTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.26, T:0.48
Consensus pattern (15 bp):
TGCCGGTGATTTATT
Found at i:54003598 original size:35 final size:33
Alignment explanation
Indices: 54003488--54003598 Score: 123
Period size: 35 Copynumber: 3.2 Consensus size: 33
54003478 AGGTAAGTAC
**
54003488 ATGTGAGCTTATATTGAACTTGTATATTCGGCTGC
1 ATGTGAGCTTATATTGAACTTG-ATATTCGG-TTA
* * *
54003523 ATGTGAGGTTATATTGAACTTGAGTATTTGATTA
1 ATGTGAGCTTATATTGAACTTGA-TATTCGGTTA
54003557 ATTGTGAGCTTATATTGAACTTGCATATTCGGTTA
1 A-TGTGAGCTTATATTGAACTTG-ATATTCGGTTA
54003592 TATGTGA
1 -ATGTGA
54003599 AGTTATCTTG
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
34 3 0.05
35 59 0.92
36 2 0.03
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.42
Consensus pattern (33 bp):
ATGTGAGCTTATATTGAACTTGATATTCGGTTA
Found at i:54006265 original size:40 final size:40
Alignment explanation
Indices: 54006210--54006368 Score: 259
Period size: 40 Copynumber: 4.0 Consensus size: 40
54006200 GATTTATTGA
*
54006210 CATTTGTGCTAGTGACTATATCTGGGCTAAGTCCCGAAGG
1 CATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGG
54006250 CATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGG
1 CATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGG
*
54006290 CATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGG
1 CATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGG
* *
54006330 CATTTGTGCGAGTTG-CTATATCC-GGCTAAATCCCGAAGG
1 CATTTGTGCTAG-TGACTATATCCGGGCTAAGTCCCGAAGG
54006369 TACTTGGGTT
Statistics
Matches: 113, Mismatches: 5, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
39 14 0.12
40 97 0.86
41 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (40 bp):
CATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGG
Found at i:54010424 original size:68 final size:68
Alignment explanation
Indices: 54010279--54010430 Score: 172
Period size: 68 Copynumber: 2.3 Consensus size: 68
54010269 CACCTCGAAC
* * * *
54010279 CACACATGCAACCTAGCTACATC--AA--TCTCGTAGCTCTCTTGTCTACATGGTGTACACATAG
1 CACACATGCGACCTAGCTACCTCATAATGTCTCGTAGCTCTCTTGTCTACATGGTATACACACAG
54010340 TAT
66 TAT
*
54010343 CACCCATGCGACCTAGCTACCTCATAATGTCTCGTAGCTCTCTTGTAC-ACATGGTATACATC-C
1 CACACATGCGACCTAGCTACCTCATAATGTCTCGTAGCTCTCTTGT-CTACATGGTATACA-CAC
*
54010406 CGTAT
64 AGTAT
* *
54010411 TACACATGTGACCTAGCTAC
1 CACACATGCGACCTAGCTAC
54010431 ATACCATCTG
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
64 20 0.27
66 2 0.03
68 49 0.67
69 2 0.03
ACGTcount: A:0.26, C:0.30, G:0.14, T:0.29
Consensus pattern (68 bp):
CACACATGCGACCTAGCTACCTCATAATGTCTCGTAGCTCTCTTGTCTACATGGTATACACACAG
TAT
Found at i:54010927 original size:30 final size:30
Alignment explanation
Indices: 54010893--54010953 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
54010883 TCCTTAACCC
54010893 AAACTTTGGAAAAATTACAATTTTTCCCCT
1 AAACTTTGGAAAAATTACAATTTTTCCCCT
* * * * *
54010923 AAACTTTTGCATATTTACACTTTTTCCCCT
1 AAACTTTGGAAAAATTACAATTTTTCCCCT
54010953 A
1 A
54010954 GGCTCGAGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTTCCCCT
Found at i:54016776 original size:36 final size:36
Alignment explanation
Indices: 54016727--54016801 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 36
54016717 AAAACCATGC
*
54016727 AAAGAAAACGAATTTTATAGCGCTCTATTCTAATGT
1 AAAGAAAACGAATTTTATAGCGCTCTAATCTAATGT
* *
54016763 AAAGAAAATGAATTTTATAGCTCTCTAATCTAATGT
1 AAAGAAAACGAATTTTATAGCGCTCTAATCTAATGT
54016799 AAA
1 AAA
54016802 TGGTGTGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (36 bp):
AAAGAAAACGAATTTTATAGCGCTCTAATCTAATGT
Found at i:54030160 original size:43 final size:43
Alignment explanation
Indices: 54030041--54030160 Score: 116
Period size: 43 Copynumber: 2.8 Consensus size: 43
54030031 ATTAGGTTAT
* * * *
54030041 CGATATGTGCTTACATGTAAGACCATGTCTAGGACATTGGCAT
1 CGATATGTGATTACATGTAAGACCATGTCTGGGACAGTGGCAC
* * * * * *
54030084 CGTTAAT-CGATTTCGTGTAAGACCTTGTTTGGGACAGTGGCAC
1 CGAT-ATGTGATTACATGTAAGACCATGTCTGGGACAGTGGCAC
* *
54030127 CGATATGTGATAACATGTAAGACCATATCTGGGA
1 CGATATGTGATTACATGTAAGACCATGTCTGGGA
54030161 TATGGCATTA
Statistics
Matches: 57, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
42 2 0.04
43 53 0.93
44 2 0.04
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (43 bp):
CGATATGTGATTACATGTAAGACCATGTCTGGGACAGTGGCAC
Found at i:54035630 original size:28 final size:28
Alignment explanation
Indices: 54035598--54035653 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
54035588 TTGAATAAGA
54035598 GTAAATTGTACAATTATGATGTTTTACC
1 GTAAATTGTACAATTATGATGTTTTACC
54035626 GTAAATTGTACAATTATGATGTTTTACC
1 GTAAATTGTACAATTATGATGTTTTACC
54035654 TTTAAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (28 bp):
GTAAATTGTACAATTATGATGTTTTACC
Found at i:54040462 original size:29 final size:29
Alignment explanation
Indices: 54040407--54040462 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
54040397 ATTTACGAGC
*
54040407 CTAGGGGAAAAATGTAATTTTGACAAAGT
1 CTAGGGGAAAAATGTAATTGTGACAAAGT
*
54040436 CTAGGGGCAAAATTGTAATTGTG-CAAA
1 CTAGGGG-AAAAATGTAATTGTGACAAA
54040463 AATATGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.39, C:0.09, G:0.25, T:0.27
Consensus pattern (29 bp):
CTAGGGGAAAAATGTAATTGTGACAAAGT
Found at i:54042121 original size:28 final size:28
Alignment explanation
Indices: 54042089--54042144 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
54042079 TTGAACAAGA
*
54042089 GTAAATTGTACAATTATGATGTTTTACC
1 GTAAATTGTACAATCATGATGTTTTACC
54042117 GTAAATTGTACAATCATGATGTTTTACC
1 GTAAATTGTACAATCATGATGTTTTACC
54042145 TTTAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.41
Consensus pattern (28 bp):
GTAAATTGTACAATCATGATGTTTTACC
Found at i:54048113 original size:14 final size:11
Alignment explanation
Indices: 54048080--54048107 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
54048070 GGTTGAAAAT
54048080 TTATTTTAATA
1 TTATTTTAATA
54048091 TTATTTTAATA
1 TTATTTTAATA
54048102 TTATTT
1 TTATTT
54048108 CGTTAAGAAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:54059885 original size:13 final size:13
Alignment explanation
Indices: 54059850--54059897 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
54059840 ATTTAATTAA
54059850 ATGCTAAATATAT
1 ATGCTAAATATAT
54059863 ATGCTGAAATGATAT
1 ATGCT-AAAT-ATAT
54059878 ATG-TAAATTTATAT
1 ATGCTAAA--TATAT
54059892 ATGCTA
1 ATGCTA
54059898 TAGCCGAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
13 8 0.27
14 12 0.40
15 10 0.33
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (13 bp):
ATGCTAAATATAT
Found at i:54060137 original size:43 final size:43
Alignment explanation
Indices: 54060045--54060126 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
54060035 GAGTAAGACC
**
54060045 ATGGCATCCATATGTGTTTACGAGTAAGACCCTGTCTGGAACA
1 ATGGCATCCATATGTGACTACGAGTAAGACCCTGTCTGGAACA
*
54060088 ATGGCATCGATATGTGACTAC-ATGTAAGACCAC-GTCTGG
1 ATGGCATCCATATGTGACTACGA-GTAAGACC-CTGTCTGG
54060127 GACGTTGGCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 1 0.03
43 32 0.94
44 1 0.03
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (43 bp):
ATGGCATCCATATGTGACTACGAGTAAGACCCTGTCTGGAACA
Found at i:54063137 original size:29 final size:29
Alignment explanation
Indices: 54063097--54063184 Score: 115
Period size: 29 Copynumber: 3.1 Consensus size: 29
54063087 ATGTGACTGA
*
54063097 GCCTAACGGGCCATATAAATGTGATTTGG
1 GCCTAATGGGCCATATAAATGTGATTTGG
* *
54063126 GCCTAATGGGCCATATATAGGTGATTTGG
1 GCCTAATGGGCCATATAAATGTGATTTGG
* * *
54063155 GTCTAATGGGCCATATGAATATGA-TTGG
1 GCCTAATGGGCCATATAAATGTGATTTGG
54063183 GC
1 GC
54063185 TTAGTAGGCC
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 5 0.10
29 45 0.90
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (29 bp):
GCCTAATGGGCCATATAAATGTGATTTGG
Found at i:54064320 original size:17 final size:18
Alignment explanation
Indices: 54064287--54064321 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
54064277 ATTTAAGAAG
*
54064287 GGTTTTCATTGAAAACAC
1 GGTTTTCACTGAAAACAC
54064305 GGTTTTCACT-AAAACAC
1 GGTTTTCACTGAAAACAC
54064322 TTCAATGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (18 bp):
GGTTTTCACTGAAAACAC
Found at i:54070933 original size:38 final size:37
Alignment explanation
Indices: 54070878--54070949 Score: 126
Period size: 38 Copynumber: 1.9 Consensus size: 37
54070868 ACTATGTCCG
54070878 AAAACCCCGTATGAACCTTAGGAATAGATAGGATTCA
1 AAAACCCCGTATGAACCTTAGGAATAGATAGGATTCA
*
54070915 AAAAGCCCCGTATGAACCTTAGGAATAGTTAGGAT
1 AAAA-CCCCGTATGAACCTTAGGAATAGATAGGAT
54070950 ACATATGTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 4 0.12
38 29 0.88
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.22
Consensus pattern (37 bp):
AAAACCCCGTATGAACCTTAGGAATAGATAGGATTCA
Found at i:54071758 original size:12 final size:12
Alignment explanation
Indices: 54071741--54071766 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54071731 ATTATGATAC
54071741 TATAATTTAGTT
1 TATAATTTAGTT
54071753 TATAATTTAGTT
1 TATAATTTAGTT
54071765 TA
1 TA
54071767 GTTTAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (12 bp):
TATAATTTAGTT
Found at i:54077629 original size:5 final size:5
Alignment explanation
Indices: 54077619--54077649 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
54077609 TAACTTATAC
54077619 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA G
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA G
54077650 CTTATTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:54083020 original size:47 final size:47
Alignment explanation
Indices: 54082966--54083207 Score: 331
Period size: 47 Copynumber: 5.1 Consensus size: 47
54082956 TTAGGATTTT
** * *
54082966 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCAA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
*
54083013 ATGTGATGAATGTGAACCTGTATATATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATG--TATATA--TGTGATAAGGCCGAATGGCCA
** *
54083064 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
* *
54083111 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
* * *
54083158 ATGTGATGAATGTGAACATGTATATATGTGGTAAGGCTGAATGGCTA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
54083205 ATG
1 ATG
54083208 CGAAACGTGT
Statistics
Matches: 175, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
47 128 0.73
49 9 0.05
51 38 0.22
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.28
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
Found at i:54083068 original size:24 final size:24
Alignment explanation
Indices: 54083040--54083115 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
54083030 CTGTATATAT
54083040 ATGTGTGATAAGGCCGAATGGCCA
1 ATGTGTGATAAGGCCGAATGGCCA
* * **
54083064 ATGTGATGA-ATGTG--AACAT-GCGT
1 ATGTG-TGATAAG-GCCGA-ATGGCCA
54083087 ATGTGTGATAAGGCCGAATGGCCA
1 ATGTGTGATAAGGCCGAATGGCCA
54083111 ATGTG
1 ATGTG
54083116 ATGAATGTGA
Statistics
Matches: 37, Mismatches: 8, Indels: 14
0.63 0.14 0.24
Matches are distributed among these distances:
22 4 0.11
23 12 0.32
24 17 0.46
25 4 0.11
ACGTcount: A:0.29, C:0.13, G:0.33, T:0.25
Consensus pattern (24 bp):
ATGTGTGATAAGGCCGAATGGCCA
Done.