Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 29 of 106
Found at i:11377783 original size:44 final size:44
Alignment explanation
Indices: 11377734--11377817 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
11377724 AAAAAGAGTG
*
11377734 AAAACTTTGGAGAGCAAAATGGTAATTTTACCATTAAAGTTGTC
1 AAAACTTTGGAGAGCAAAATAGTAATTTTACCATTAAAGTTGTC
* * **
11377778 AAAACTTTGGAGGGTAAAATAGTAATTTTTTCATTAAAGT
1 AAAACTTTGGAGAGCAAAATAGTAATTTTACCATTAAAGT
11377818 GGTTAAAGGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (44 bp):
AAAACTTTGGAGAGCAAAATAGTAATTTTACCATTAAAGTTGTC
Found at i:11380390 original size:16 final size:17
Alignment explanation
Indices: 11380369--11380412 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
11380359 TTGGTTAAAA
*
11380369 TTTCCCACCA-GTTCGT
1 TTTCCCACCATGTTAGT
* *
11380385 TTTCCCATCATTTTAGT
1 TTTCCCACCATGTTAGT
11380402 TTTCCCACCAT
1 TTTCCCACCAT
11380413 TGACCCAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.16, C:0.34, G:0.07, T:0.43
Consensus pattern (17 bp):
TTTCCCACCATGTTAGT
Found at i:11380684 original size:27 final size:27
Alignment explanation
Indices: 11380654--11380844 Score: 195
Period size: 27 Copynumber: 7.0 Consensus size: 27
11380644 TATAACAACT
* * * *
11380654 TTTTCATCATGATGTATAATAACTAAA
1 TTTTCAACATGACGTGTAACAACTAAA
* *
11380681 TTTTTCAACATAACGTGTAACGACTAAA
1 -TTTTCAACATGACGTGTAACAACTAAA
* * *
11380709 TCTTT-AACATGACGTATAACGACTATAT
1 T-TTTCAACATGACGTGTAACAACTA-AA
11380737 TTTTCAACATGACGTGTAACAACTAAA
1 TTTTCAACATGACGTGTAACAACTAAA
* * * * *
11380764 TTTTCAATATAATGTATAACAACTACAT
1 TTTTCAACATGACGTGTAACAACTA-AA
* *
11380792 TTTTTAACATGACGTGTAACAGCTAAA
1 TTTTCAACATGACGTGTAACAACTAAA
11380819 TTTTCAACATGACGTGTAACAACTAA
1 TTTTCAACATGACGTGTAACAACTAA
11380845 TGTAGACACT
Statistics
Matches: 133, Mismatches: 26, Indels: 9
0.79 0.15 0.05
Matches are distributed among these distances:
27 69 0.52
28 64 0.48
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (27 bp):
TTTTCAACATGACGTGTAACAACTAAA
Found at i:11380739 original size:55 final size:54
Alignment explanation
Indices: 11380654--11380844 Score: 231
Period size: 55 Copynumber: 3.5 Consensus size: 54
11380644 TATAACAACT
* * * *
11380654 TTTTCATCATGATGTATAATAACTAAATTTTTCAACATAACGTGTAACGACTAAA
1 TTTTCAACATGACGTATAACAACTAAATTTTTCAACATGACGTGTAAC-ACTAAA
* *
11380709 TCTTT-AACATGACGTATAACGACTATATTTTTCAACATGACGTGTAACAACTAAA
1 T-TTTCAACATGACGTATAACAACTAAATTTTTCAACATGACGTGTAAC-ACTAAA
* * * * *
11380764 TTTTCAATATAATGTATAACAACTACATTTTTTAACATGACGTGTAACAGCTAAA
1 TTTTCAACATGACGTATAACAACTAAATTTTTCAACATGACGTGTAACA-CTAAA
*
11380819 TTTTCAACATGACGTGTAACAACTAA
1 TTTTCAACATGACGTATAACAACTAA
11380845 TGTAGACACT
Statistics
Matches: 115, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
54 4 0.03
55 108 0.94
56 3 0.03
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (54 bp):
TTTTCAACATGACGTATAACAACTAAATTTTTCAACATGACGTGTAACACTAAA
Found at i:11382839 original size:2 final size:2
Alignment explanation
Indices: 11382832--11382865 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
11382822 CATTATGATG
11382832 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11382866 NNNNNNNNNN
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11383084 original size:2 final size:2
Alignment explanation
Indices: 11383077--11383127 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
11383067 NNNNNNNNNN
11383077 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
11383119 TA TA AA TA T
1 TA TA TA TA T
11383128 CTATGTTTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:11387089 original size:28 final size:27
Alignment explanation
Indices: 11387045--11387229 Score: 95
Period size: 27 Copynumber: 6.8 Consensus size: 27
11387035 AAATCTCCAG
* **
11387045 CATGGTGTGTAACAATTACGTTTTTCAA
1 CATGGTATGTAACAATTA-AATTTTCAA
*
11387073 CATGGTATGTAATAATTAAATTTTCAA
1 CATGGTATGTAACAATTAAATTTTCAA
*** * *
11387100 CATGACGTGTAATAACTAAATTTTCAA
1 CATGGTATGTAACAATTAAATTTTCAA
*** * * *
11387127 CATCACATGTAATAACTATATTTTTCAA
1 CATGGTATGTAACAATTA-AATTTTCAA
* *
11387155 TATGACGTA--TAACAACTAAATTTTCAA
1 CATG--GTATGTAACAATTAAATTTTCAA
* *** *
11387182 TATGACGTGTAACAATTATATTTTCAA
1 CATGGTATGTAACAATTAAATTTTCAA
** *
11387209 CATGGCGTGTAATAATTAAAT
1 CATGGTATGTAACAATTAAAT
11387230 GTTAGAACAT
Statistics
Matches: 126, Mismatches: 26, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
27 91 0.72
28 34 0.27
30 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.37
Consensus pattern (27 bp):
CATGGTATGTAACAATTAAATTTTCAA
Found at i:11387110 original size:27 final size:27
Alignment explanation
Indices: 11387066--11387259 Score: 183
Period size: 27 Copynumber: 7.1 Consensus size: 27
11387056 ACAATTACGT
*** *
11387066 TTTTCAACATGGTATGTAATAATTAAA
1 TTTTCAACATGACGTGTAATAACTAAA
11387093 TTTTCAACATGACGTGTAATAACTAAA
1 TTTTCAACATGACGTGTAATAACTAAA
* * *
11387120 TTTTCAACATCACATGTAATAACTATAT
1 TTTTCAACATGACGTGTAATAACTA-AA
* * *
11387148 TTTTCAATATGACGTATAACAACTAAA
1 TTTTCAACATGACGTGTAATAACTAAA
* * * *
11387175 TTTTCAATATGACGTGTAACAATTATA
1 TTTTCAACATGACGTGTAATAACTAAA
* *
11387202 TTTTCAACATGGCGTGTAATAATTAAA
1 TTTTCAACATGACGTGTAATAACTAAA
** * *
11387229 TGTTAGAACATGACGTATAAT-ACTATA
1 T-TTTCAACATGACGTGTAATAACTAAA
11387256 TTTT
1 TTTT
11387260 TTCAAGCTGC
Statistics
Matches: 138, Mismatches: 27, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
26 2 0.01
27 100 0.72
28 36 0.26
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.38
Consensus pattern (27 bp):
TTTTCAACATGACGTGTAATAACTAAA
Found at i:11387160 original size:55 final size:55
Alignment explanation
Indices: 11387066--11387260 Score: 198
Period size: 55 Copynumber: 3.6 Consensus size: 55
11387056 ACAATTACGT
** * *
11387066 TTTTCAACATGGTATGTAATAATTA-AATTTTCAACATGACGTGTAATAACTAAA
1 TTTTCAACATGACATGTAATAACTATATTTTTCAACATGACGTGTAATAACTAAA
* * * *
11387120 TTTTCAACATCACATGTAATAACTATATTTTTCAATATGACGTATAACAACTAAA
1 TTTTCAACATGACATGTAATAACTATATTTTTCAACATGACGTGTAATAACTAAA
* * * * * *
11387175 TTTTCAATATGACGTGTAACAATTATA-TTTTCAACATGGCGTGTAATAATTAAA
1 TTTTCAACATGACATGTAATAACTATATTTTTCAACATGACGTGTAATAACTAAA
** * *
11387229 TGTTAGAACATGACGTATAAT-ACTATATTTTT
1 T-TTTCAACATGACATGTAATAACTATATTTTT
11387261 TCAAGCTGCC
Statistics
Matches: 114, Mismatches: 24, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
54 49 0.43
55 65 0.57
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.38
Consensus pattern (55 bp):
TTTTCAACATGACATGTAATAACTATATTTTTCAACATGACGTGTAATAACTAAA
Found at i:11387242 original size:82 final size:82
Alignment explanation
Indices: 11387089--11387248 Score: 203
Period size: 82 Copynumber: 2.0 Consensus size: 82
11387079 ATGTAATAAT
* * * *
11387089 TAAATTTTCAACATGACGTGTAATAACTAAATTTTCAACATCACATGTAATAACTATATTTTTCA
1 TAAATTTTCAACATGACGTGTAACAACTAAATTTTCAACATCACATGTAATAACTAAATGTTACA
*
11387154 ATATGACGTATAACAAC
66 ACATGACGTATAACAAC
* * * ** * * *
11387171 TAAATTTTCAATATGACGTGTAACAATTATATTTTCAACATGGCGTGTAATAATTAAATGTTAGA
1 TAAATTTTCAACATGACGTGTAACAACTAAATTTTCAACATCACATGTAATAACTAAATGTTACA
11387236 ACATGACGTATAA
66 ACATGACGTATAA
11387249 TACTATATTT
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
82 65 1.00
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.36
Consensus pattern (82 bp):
TAAATTTTCAACATGACGTGTAACAACTAAATTTTCAACATCACATGTAATAACTAAATGTTACA
ACATGACGTATAACAAC
Found at i:11409654 original size:17 final size:15
Alignment explanation
Indices: 11409640--11409673 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
11409630 GGCACTGTGA
11409640 GCTTTCCTTCTCTGT
1 GCTTTCCTTCTCTGT
* *
11409655 TCTTTCCTTCTCTCT
1 GCTTTCCTTCTCTGT
11409670 GCTT
1 GCTT
11409674 CAATCATTGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.35, G:0.09, T:0.56
Consensus pattern (15 bp):
GCTTTCCTTCTCTGT
Found at i:11416765 original size:2 final size:2
Alignment explanation
Indices: 11416758--11416812 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
11416748 ACAATCAATT
11416758 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11416800 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
11416813 NNNNNNNNNN
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11420798 original size:43 final size:43
Alignment explanation
Indices: 11420731--11420900 Score: 225
Period size: 43 Copynumber: 4.0 Consensus size: 43
11420721 TGTGATAATA
* * * * *
11420731 ATGACCCAGCTATATGAGGTGTGGGAGTGTACATGAGCTGATG
1 ATGACCCAACTATGTGCGATGTGGGAGTGCACATGAGCTGATG
* *
11420774 ATGACTCAACTATGTGTGATGTGGGAGTGCACATGAGCTGATG
1 ATGACCCAACTATGTGCGATGTGGGAGTGCACATGAGCTGATG
* *
11420817 ATGACCCAACTATGTGCGATGTGGGAGTGCACATAAGCTAATG
1 ATGACCCAACTATGTGCGATGTGGGAGTGCACATGAGCTGATG
* *
11420860 ATGACCCGACTATGTGCGAAT-AGGGAGTGCACATGAGCTGA
1 ATGACCCAACTATGTGCG-ATGTGGGAGTGCACATGAGCTGA
11420901 GTGTGGCAGA
Statistics
Matches: 112, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
43 110 0.98
44 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.32, T:0.24
Consensus pattern (43 bp):
ATGACCCAACTATGTGCGATGTGGGAGTGCACATGAGCTGATG
Found at i:11421106 original size:21 final size:22
Alignment explanation
Indices: 11421075--11421115 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
11421065 TAAATTGCTC
**
11421075 TATTTCTCGCTGTAGCGAGATT
1 TATTTCTCGCTACAGCGAGATT
11421097 TATTT-TCGCTACAGCGAGA
1 TATTTCTCGCTACAGCGAGA
11421116 AACTCTCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (22 bp):
TATTTCTCGCTACAGCGAGATT
Found at i:11422876 original size:21 final size:21
Alignment explanation
Indices: 11422852--11422900 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
11422842 AGATAGAAAG
11422852 TTTCTCGTTGCAACAAGATTC
1 TTTCTCGTTGCAACAAGATTC
11422873 TTTCTCGTTGCAACAAGATTC
1 TTTCTCGTTGCAACAAGATTC
*
11422894 ATTCTCG
1 TTTCTCG
11422901 CTACAGTGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.39
Consensus pattern (21 bp):
TTTCTCGTTGCAACAAGATTC
Found at i:11423291 original size:42 final size:42
Alignment explanation
Indices: 11423245--11423329 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
11423235 GGTCAGCATA
11423245 AGCTCATATGCACCCCTACACGCACATGGCTAGATCATCATC
1 AGCTCATATGCACCCCTACACGCACATGGCTAGATCATCATC
* * ** * * * *
11423287 AGCTCATGTGTACTTCTGCACGCACATGGTTGGGTCATCATC
1 AGCTCATATGCACCCCTACACGCACATGGCTAGATCATCATC
11423329 A
1 A
11423330 TCACACAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.26
Consensus pattern (42 bp):
AGCTCATATGCACCCCTACACGCACATGGCTAGATCATCATC
Found at i:11425469 original size:15 final size:15
Alignment explanation
Indices: 11425446--11425507 Score: 58
Period size: 15 Copynumber: 4.3 Consensus size: 15
11425436 CATTTAAATT
*
11425446 ATATATAAAATATTA
1 ATATTTAAAATATTA
*
11425461 ATATTTAAATTATTA
1 ATATTTAAAATATTA
*
11425476 ATATTTTAAATA--A
1 ATATTTAAAATATTA
* *
11425489 AT-TATAAATTATTA
1 ATATTTAAAATATTA
11425503 ATATT
1 ATATT
11425508 GATGAAATAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
12 6 0.17
13 3 0.08
14 3 0.08
15 24 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATTTAAAATATTA
Found at i:11425502 original size:42 final size:40
Alignment explanation
Indices: 11425373--11425507 Score: 116
Period size: 42 Copynumber: 3.3 Consensus size: 40
11425363 TTTAAGTTTT
* *
11425373 TTATTATATATTATAAA-AATAATATTTAAA-AATTTA-AAA
1 TTATTA-ATATT-TAAATTATAATATTTAAATAAATTATAAA
** *
11425412 TTATTAATATTTTCATTATAATGACATTTAAAT-TATATATAAA
1 TTATTAATATTTAAATTATAAT---ATTTAAATAAAT-TATAAA
*
11425455 ATATTAATATTTAAATTATTAATATTTTAAATAAATTATAAA
1 TTATTAATATTTAAATTA-TAATA-TTTAAATAAATTATAAA
11425497 TTATTAATATT
1 TTATTAATATT
11425508 GATGAAATAA
Statistics
Matches: 76, Mismatches: 10, Indels: 17
0.74 0.10 0.17
Matches are distributed among these distances:
37 2 0.03
38 10 0.13
39 6 0.08
41 9 0.12
42 25 0.33
43 20 0.26
44 4 0.05
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (40 bp):
TTATTAATATTTAAATTATAATATTTAAATAAATTATAAA
Found at i:11425522 original size:27 final size:26
Alignment explanation
Indices: 11425466--11425523 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
11425456 TATTAATATT
*
11425466 TAAATTATTAATATTTTAAATAAATTA
1 TAAATTATTAATATTTGAAATAAA-TA
11425493 TAAATTATTAATATTGATGAAATAAA-A
1 TAAATTATTAATATT--TGAAATAAATA
11425520 TAAA
1 TAAA
11425524 ATAAAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 20 0.71
29 8 0.29
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (26 bp):
TAAATTATTAATATTTGAAATAAATA
Found at i:11427275 original size:3 final size:3
Alignment explanation
Indices: 11427267--11427295 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
11427257 ATGGTTTCAT
11427267 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
11427296 CGTATGGATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:11430154 original size:2 final size:2
Alignment explanation
Indices: 11430106--11430137 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
11430096 CACCAAATTA
11430106 AT AT -T AT AT AT AT A- AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11430138 TTTTTATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11435820 original size:26 final size:28
Alignment explanation
Indices: 11435763--11435820 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 28
11435753 TCATAAACAA
*
11435763 ACAAA-TATTATATATATTTTTTATATT
1 ACAAATTATTATATATATTTTATATATT
*
11435790 -TAAATTATT-TATATATTTTATA-ATT
1 ACAAATTATTATATATATTTTATATATT
11435815 ACAAAT
1 ACAAAT
11435821 AAAATTTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
25 3 0.12
26 19 0.73
27 4 0.15
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (28 bp):
ACAAATTATTATATATATTTTATATATT
Found at i:11442931 original size:36 final size:36
Alignment explanation
Indices: 11442880--11442959 Score: 142
Period size: 36 Copynumber: 2.2 Consensus size: 36
11442870 GTGAGAATAT
*
11442880 GGCTAATTGCAACATGAAACAGCGTATGCATCTATA
1 GGCTAATTGCAACATGAAACAGCGTACGCATCTATA
*
11442916 GGCTAATTGCGACATGAAACAGCGTACGCATCTATA
1 GGCTAATTGCAACATGAAACAGCGTACGCATCTATA
11442952 GGCTAATT
1 GGCTAATT
11442960 CCCAAACCTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (36 bp):
GGCTAATTGCAACATGAAACAGCGTACGCATCTATA
Found at i:11445705 original size:17 final size:16
Alignment explanation
Indices: 11445671--11445708 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
11445661 TTAATTATAA
*
11445671 TATATATACTTTTGTT
1 TATATAAACTTTTGTT
11445687 TATATAAACTTTT-TT
1 TATATAAACTTTTGTT
*
11445702 TTTATAA
1 TATATAA
11445709 TTGGGGGAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (16 bp):
TATATAAACTTTTGTT
Found at i:11446932 original size:11 final size:11
Alignment explanation
Indices: 11446903--11446934 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
11446893 CAAATAACAT
11446903 TTGTTACAAAA
1 TTGTTACAAAA
11446914 -TG-TACAAAA
1 TTGTTACAAAA
11446923 TTGTTACAAAA
1 TTGTTACAAAA
11446934 T
1 T
11446935 GGAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 7 0.37
10 4 0.21
11 8 0.42
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.34
Consensus pattern (11 bp):
TTGTTACAAAA
Found at i:11446942 original size:20 final size:20
Alignment explanation
Indices: 11446903--11446942 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
11446893 CAAATAACAT
* *
11446903 TTGTTACAAAATGTACAAAA
1 TTGTTACAAAATGGAAAAAA
11446923 TTGTTACAAAATGGAAAAAA
1 TTGTTACAAAATGGAAAAAA
11446943 AAATTTGTAT
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:0.53, C:0.07, G:0.12, T:0.28
Consensus pattern (20 bp):
TTGTTACAAAATGGAAAAAA
Found at i:11451837 original size:13 final size:13
Alignment explanation
Indices: 11451819--11451843 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11451809 TTTCAGAAAA
11451819 TTTATAAAATCAT
1 TTTATAAAATCAT
11451832 TTTATAAAATCA
1 TTTATAAAATCA
11451844 CAATTTCTCT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:11453242 original size:19 final size:19
Alignment explanation
Indices: 11453218--11453255 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
11453208 CTACCAAACC
*
11453218 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
11453237 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
11453256 AGTTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:11459355 original size:16 final size:15
Alignment explanation
Indices: 11459335--11459363 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
11459325 CTACTTCTAT
11459335 TTTTTTGGTTTATAC
1 TTTTTTGGTTTATAC
11459350 TTTTTTGGTTTATA
1 TTTTTTGGTTTATA
11459364 GAGCATGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.03, G:0.14, T:0.69
Consensus pattern (15 bp):
TTTTTTGGTTTATAC
Found at i:11462331 original size:27 final size:27
Alignment explanation
Indices: 11462301--11462406 Score: 90
Period size: 27 Copynumber: 3.8 Consensus size: 27
11462291 AGTCTCATAC
*
11462301 CCATTGTTGTTGTAGTTGCTGGCGTAG
1 CCATTGTTGTTGTAGTTGCTGGAGTAG
* * * * *
11462328 CCATTAG-TCTTATAGCTACTTGAGTAG
1 CCATT-GTTGTTGTAGTTGCTGGAGTAG
*
11462355 CCATTGTTGTTGTAGTTGCTGGTGGTGTAG
1 CCATTGTTGTTGTAGTTGC---TGGAGTAG
11462385 CCATTGTTGTTGT-GATTGCTGG
1 CCATTGTTGTTGTAG-TTGCTGG
11462407 TGGTGTAGCC
Statistics
Matches: 61, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
26 1 0.02
27 35 0.57
28 1 0.02
29 1 0.02
30 23 0.38
ACGTcount: A:0.14, C:0.14, G:0.30, T:0.42
Consensus pattern (27 bp):
CCATTGTTGTTGTAGTTGCTGGAGTAG
Found at i:11462387 original size:30 final size:30
Alignment explanation
Indices: 11462351--11462462 Score: 163
Period size: 30 Copynumber: 3.6 Consensus size: 30
11462341 AGCTACTTGA
11462351 GTAGCCATTGTTGTTGTAGTTGCTGGTGGT
1 GTAGCCATTGTTGTTGTAGTTGCTGGTGGT
11462381 GTAGCCATTGTTGTTGT-GATTGCTGGTGGT
1 GTAGCCATTGTTGTTGTAG-TTGCTGGTGGT
* *
11462411 GTAGCCGTTGTTGTAGTTGTAGTTTCTGGTGGT
1 GTAGCCATTG-T-T-GTTGTAGTTGCTGGTGGT
11462444 GTAGCCATTGTTGTTGTAG
1 GTAGCCATTGTTGTTGTAG
11462463 CTGTTTTTCT
Statistics
Matches: 74, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
29 1 0.01
30 44 0.59
31 2 0.03
32 2 0.03
33 24 0.32
34 1 0.01
ACGTcount: A:0.11, C:0.10, G:0.36, T:0.44
Consensus pattern (30 bp):
GTAGCCATTGTTGTTGTAGTTGCTGGTGGT
Found at i:11463774 original size:2 final size:2
Alignment explanation
Indices: 11463767--11463800 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
11463757 GACACATACG
11463767 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11463801 GCATGCTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:11465809 original size:2 final size:2
Alignment explanation
Indices: 11465802--11465833 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
11465792 TAGGCTTTAG
11465802 GA GA GA GA GA GA GA GA GA GA GA GA GTA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G-A GA GA G
11465834 GAGCCGTCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03
Consensus pattern (2 bp):
GA
Found at i:11471583 original size:33 final size:32
Alignment explanation
Indices: 11471539--11471604 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 32
11471529 ACGCTCTCTC
11471539 TCTCTCTCTCTATATATATATATATATATATA
1 TCTCTCTCTCTATATATATATATATATATATA
11471571 TCNTCTCTCTCTATATATATATATATATATATA
1 TC-TCTCTCTCTATATATATATATATATATATA
11471604 T
1 T
11471605 ATCCTCTATG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 2 0.06
33 31 0.94
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.50
Consensus pattern (32 bp):
TCTCTCTCTCTATATATATATATATATATATA
Found at i:11471622 original size:35 final size:34
Alignment explanation
Indices: 11471549--11471629 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 34
11471539 TCTCTCTCTC
* *
11471549 TATATATATATATATATATATATCNTCTCTCTCTA
1 TATATATATATATATATATATATC-TCTCTATCGA
11471584 TATATATATATATATATATATATC-CTCTATGCAGA
1 TATATATATATATATATATATATCTCTCTAT-C-GA
11471619 TATATACTATA
1 TATATA-TATA
11471630 GCATGAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
33 5 0.12
34 1 0.02
35 31 0.76
36 4 0.10
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.46
Consensus pattern (34 bp):
TATATATATATATATATATATATCTCTCTATCGA
Found at i:11471624 original size:2 final size:2
Alignment explanation
Indices: 11471549--11471606 Score: 62
Period size: 2 Copynumber: 28.5 Consensus size: 2
11471539 TCTCTCTCTC
* * * * *
11471549 TA TA TA TA TA TA TA TA TA TA TA TCN TC TC TC TC TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA
11471592 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
11471607 CCTCTATGCA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
2 51 0.98
3 1 0.02
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11473784 original size:22 final size:22
Alignment explanation
Indices: 11473759--11473813 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
11473749 GTGTGATTAA
*
11473759 TTTTTAGGCATTACGTGA-TTG
1 TTTTTAGGCATTACGTGACTAG
*
11473780 GTTTTAGGCATTACGTGACTAG
1 TTTTTAGGCATTACGTGACTAG
*
11473802 TTTTTAGACATT
1 TTTTTAGGCATT
11473814 GCATGACTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.45
Consensus pattern (22 bp):
TTTTTAGGCATTACGTGACTAG
Found at i:11473820 original size:22 final size:22
Alignment explanation
Indices: 11473758--11473829 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
11473748 TGTGTGATTA
* * *
11473758 ATTTTTAGGCATTACGTGATTG
1 ATTTTTAGACATTACATGACTG
* * *
11473780 -GTTTTAGGCATTACGTGACT-
1 ATTTTTAGACATTACATGACTG
*
11473800 AGTTTTTAGACATTGCATGACTG
1 A-TTTTTAGACATTACATGACTG
11473823 ATTTTTA
1 ATTTTTA
11473830 AGCAATGCCT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
21 18 0.44
22 22 0.54
23 1 0.02
ACGTcount: A:0.24, C:0.11, G:0.21, T:0.44
Consensus pattern (22 bp):
ATTTTTAGACATTACATGACTG
Found at i:11474026 original size:26 final size:25
Alignment explanation
Indices: 11473841--11474235 Score: 270
Period size: 23 Copynumber: 16.6 Consensus size: 25
11473831 GCAATGCCTA
* *
11473841 AGTCACACAATGCCTTA-C-TAACT
1 AGTCACGCAATGCCTTATCAAAACT
* * *
11473864 AGTCACGTAATGCCTTA-C-TAACA
1 AGTCACGCAATGCCTTATCAAAACT
* *
11473887 AGTCACGCAATGCCTTA-C-TAACA
1 AGTCACGCAATGCCTTATCAAAACT
* * *
11473910 AGTCACGTAATG-C-T-TCACTAACA
1 AGTCACGCAATGCCTTATCA-AAACT
* *
11473933 AGTCACGCAATG-C-T-TCACTAACA
1 AGTCACGCAATGCCTTATCA-AAACT
* * *
11473956 AGTCACGCAATGCCTCA-C-TAACA
1 AGTCACGCAATGCCTTATCAAAACT
11473979 AGTCACGCAATGCC-TATC--AACT
1 AGTCACGCAATGCCTTATCAAAACT
11474001 AGTCACGCAATGCCTTATCAGAAACT
1 AGTCACGCAATGCCTTATCA-AAACT
* *
11474027 AGTTACGCAATACCTTATCAAAAACT
1 AGTCACGCAATGCCTTATC-AAAACT
11474053 AGTCACGCAATGCC-TATC--AACT
1 AGTCACGCAATGCCTTATCAAAACT
* * *
11474075 AGTCACGTAATGTCTTATTAGAAACT
1 AGTCACGCAATGCCTTATCA-AAACT
*
11474101 AGTCATGCAATGCCTTATCAAAAACT
1 AGTCACGCAATGCCTTATC-AAAACT
* *
11474127 AGTCACGCAATG-----TCCAAAGT
1 AGTCACGCAATGCCTTATCAAAACT
*
11474147 CAATCACGCAATGCC-TAT--AAACT
1 -AGTCACGCAATGCCTTATCAAAACT
* *
11474170 AGTCACGCAATGTCTTATTAGAAACT
1 AGTCACGCAATGCCTTATCA-AAACT
*
11474196 AGTCACGCAATGCCTTATCAAAAATT
1 AGTCACGCAATGCCTTATC-AAAACT
11474222 AGTCACGCAATGCC
1 AGTCACGCAATGCC
11474236 CAAAGTCAGT
Statistics
Matches: 315, Mismatches: 30, Indels: 51
0.80 0.08 0.13
Matches are distributed among these distances:
20 4 0.01
21 15 0.05
22 47 0.15
23 126 0.40
24 1 0.00
25 6 0.02
26 113 0.36
27 3 0.01
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.25
Consensus pattern (25 bp):
AGTCACGCAATGCCTTATCAAAACT
Found at i:11474065 original size:74 final size:73
Alignment explanation
Indices: 11473841--11474235 Score: 306
Period size: 69 Copynumber: 5.5 Consensus size: 73
11473831 GCAATGCCTA
* * *
11473841 AGTCACACAATGCCT-TACTAACTAGTCACGTAATGCCTTACT---AACAAGTCACGCAATGCCT
1 AGTCACGCAATGCCTAT-C-AACTAGTCACGCAATGCCTTA-TAGAAACTAGTCACGCAATGCCT
* *
11473902 TA-C--TAACA
63 TATCAAAAACT
* * * * ** *
11473910 AGTCACGTAATGCTTCA-CTAACAAGTCACGCAATG-CTT-CACTAACAAGTCACGCAATGCC--
1 AGTCACGCAATGCCT-ATC-AACTAGTCACGCAATGCCTTATAGAAACTAGTCACGCAATGCCTT
** *
11473970 -TCACTAACA
64 ATCAAAAACT
* *
11473979 AGTCACGCAATGCCTATCAACTAGTCACGCAATGCCTTATCAGAAACTAGTTACGCAATACCTTA
1 AGTCACGCAATGCCTATCAACTAGTCACGCAATGCCTTAT-AGAAACTAGTCACGCAATGCCTTA
11474044 TCAAAAACT
65 TCAAAAACT
* * *
11474053 AGTCACGCAATGCCTATCAACTAGTCACGTAATGTCTTATTAGAAACTAGTCATGCAATGCCTTA
1 AGTCACGCAATGCCTATCAACTAGTCACGCAATGCCTTA-TAGAAACTAGTCACGCAATGCCTTA
11474118 TCAAAAACT
65 TCAAAAACT
* * *
11474127 AGTCACGCAATGTCC-A--AAGTCAATCACGCAATGCC-TAT--AAACTAGTCACGCAATGTCTT
1 AGTCACGCAATG-CCTATCAACT-AGTCACGCAATGCCTTATAGAAACTAGTCACGCAATGCCTT
* *
11474186 ATTAGAAACT
64 ATCAAAAACT
*
11474196 AGTCACGCAATGCCTTATCAAAAATTAGTCACGCAATGCC
1 AGTCACGCAATGCC-TATC---AACTAGTCACGCAATGCC
11474236 CAAAGTCAGT
Statistics
Matches: 268, Mismatches: 33, Indels: 45
0.77 0.10 0.13
Matches are distributed among these distances:
67 1 0.00
68 21 0.08
69 107 0.40
70 1 0.00
71 17 0.06
72 5 0.02
73 11 0.04
74 99 0.37
75 6 0.02
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.25
Consensus pattern (73 bp):
AGTCACGCAATGCCTATCAACTAGTCACGCAATGCCTTATAGAAACTAGTCACGCAATGCCTTAT
CAAAAACT
Found at i:11474189 original size:95 final size:95
Alignment explanation
Indices: 11473997--11474253 Score: 352
Period size: 95 Copynumber: 2.7 Consensus size: 95
11473987 AATGCCTATC
* * * ** *
11473997 AACTAGTCACGCAATGCCTTATCAGAAACTAGTTACGCAATACCTTATCAAAAACTAGTCACGCA
1 AACTAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAATGCC----CAAAGTC-AATCACGCA
* *
11474062 ATGCCTATCAACTAGTCACGTAATGTCTTATTAGA
61 ATGCCTATAAACTAGTCACGCAATGTCTTATTAGA
* *
11474097 AACTAGTCATGCAATGCCTTATCAAAAACTAGTCACGCAATGTCCAAAGTCAATCACGCAATGCC
1 AACTAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAATGCCCAAAGTCAATCACGCAATGCC
11474162 TATAAACTAGTCACGCAATGTCTTATTAGA
66 TATAAACTAGTCACGCAATGTCTTATTAGA
* * *
11474192 AACTAGTCACGCAATGCCTTATCAAAAATTAGTCACGCAATGCCCAAAGTCAGTCATGCAAT
1 AACTAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAATGCCCAAAGTCAATCACGCAAT
11474254 ATCCAAAGTC
Statistics
Matches: 142, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
95 98 0.69
96 5 0.04
100 39 0.27
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.25
Consensus pattern (95 bp):
AACTAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAATGCCCAAAGTCAATCACGCAATGCC
TATAAACTAGTCACGCAATGTCTTATTAGA
Found at i:11474246 original size:21 final size:21
Alignment explanation
Indices: 11474222--11474277 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
11474212 ATCAAAAATT
*
11474222 AGTCACGCAATGCCCAAAGTC
1 AGTCACGCAATACCCAAAGTC
* *
11474243 AGTCATGCAATATCCAAAGTC
1 AGTCACGCAATACCCAAAGTC
*
11474264 AGTCACACAATACC
1 AGTCACGCAATACC
11474278 TAAAAACTAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.38, C:0.30, G:0.14, T:0.18
Consensus pattern (21 bp):
AGTCACGCAATACCCAAAGTC
Found at i:11477868 original size:17 final size:19
Alignment explanation
Indices: 11477846--11477889 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
11477836 TAGTAACTAT
11477846 TTTATATTGATA-GGAT-C
1 TTTATATTGATACGGATGC
*
11477863 TTTATATT-ATACGGTTGC
1 TTTATATTGATACGGATGC
11477881 TTTATATTG
1 TTTATATTG
11477890 TATAACTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 3 0.13
17 11 0.48
18 9 0.39
ACGTcount: A:0.25, C:0.07, G:0.16, T:0.52
Consensus pattern (19 bp):
TTTATATTGATACGGATGC
Found at i:11481415 original size:17 final size:16
Alignment explanation
Indices: 11481387--11481418 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
11481377 TGATAATAAA
11481387 AAATAAAATAATGATT
1 AAATAAAATAATGATT
11481403 AAATAATAATAATGAT
1 AAATAA-AATAATGAT
11481419 AAGAATAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (16 bp):
AAATAAAATAATGATT
Found at i:11485891 original size:92 final size:90
Alignment explanation
Indices: 11485733--11485915 Score: 312
Period size: 92 Copynumber: 2.0 Consensus size: 90
11485723 ATGTAATCGA
11485733 ACTCTGTCTTGTTTCAGATGTGGTTATACCCCAAAAATTCAAAGTTTCAGACTTTGAAAAGTATG
1 ACTCTGTCTTGTTTCAGATGTGGTTATACCCCAAAAATTCAAAGTTTCAGACTTTGAAAAGTATG
11485798 ATGGAACCAAGTGCCCGGTCACACAC
66 ATGGAA-CAAGTGCCCGGTCACACAC
* *
11485824 ANCTCTGTCTTGTTTCAGATGTGGTTATACCCCCAAAATTCAAAGTTTCTGACTTTGAAAAGTAT
1 A-CTCTGTCTTGTTTCAGATGTGGTTATACCCCAAAAATTCAAAGTTTCAGACTTTGAAAAGTAT
* *
11485889 GATGGAACAAGTGCTCGGTCACGCAC
65 GATGGAACAAGTGCCCGGTCACACAC
11485915 A
1 A
11485916 TCACTATGTA
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
91 19 0.22
92 68 0.78
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (90 bp):
ACTCTGTCTTGTTTCAGATGTGGTTATACCCCAAAAATTCAAAGTTTCAGACTTTGAAAAGTATG
ATGGAACAAGTGCCCGGTCACACAC
Found at i:11492620 original size:14 final size:13
Alignment explanation
Indices: 11492601--11492633 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
11492591 TATTTTGCAT
11492601 AAAAAAAAAGAAGA
1 AAAAAAAAAG-AGA
11492615 AAAAAAAAAGAGA
1 AAAAAAAAAGAGA
11492628 AAAAAA
1 AAAAAA
11492634 TAAATTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAGA
Found at i:11492645 original size:15 final size:15
Alignment explanation
Indices: 11492627--11492662 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
11492617 AAAAAAAGAG
11492627 AAAAAAAT-AAATTA
1 AAAAAAATAAAATTA
11492641 AAAAAAATAAAATTA
1 AAAAAAATAAAATTA
11492656 AAAAAAA
1 AAAAAAA
11492663 ATTTCAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAAAATAAAATTA
Found at i:11493586 original size:38 final size:38
Alignment explanation
Indices: 11493545--11494060 Score: 428
Period size: 38 Copynumber: 13.6 Consensus size: 38
11493535 GTTTTGTTAT
* *
11493545 CTCAGTTTTGAGGAATTCATTTTTAAAAGTTTCGTTGT
1 CTCAGCTTTGAGGAATTCATTTTTAAAAGTTTCGTTGC
* * *
11493583 CTCAACTTTGAGGAGTTCA-TTTTAAAAGTTCCAG-TGC
1 CTCAGCTTTGAGGAATTCATTTTTAAAAGTTTC-GTTGC
* * *
11493620 CTCAGCTTTGAGGAGTTAATTTTTAAAAAGTTTCATTGC
1 CTCAGCTTTGAGGAATTCATTTTT-AAAAGTTTCGTTGC
* * *
11493659 CTCCGCTTTGAGGAGTTCATTTTTAAAAGTTTTGTTGC
1 CTCAGCTTTGAGGAATTCATTTTTAAAAGTTTCGTTGC
* * * * **
11493697 CTTAGCTTTAAGG-AGTCACATTTTAAAAGTCCCGTTGC
1 CTCAGCTTTGAGGAATTCA-TTTTTAAAAGTTTCGTTGC
* *
11493735 CTCAACTTTGAGGAGTTCATTTTTAGAAA-TTTCGTTGC
1 CTCAGCTTTGAGGAATTCATTTTTA-AAAGTTTCGTTGC
* * * *
11493773 CTCAACTTTGA-AAAGTTCATTTTTAAACGTCTCGTTGC
1 CTCAGCTTTGAGGAA-TTCATTTTTAAAAGTTTCGTTGC
* *
11493811 CTCAGCTTTGAGG-AGTCATATTTTTAAAGTTAT-GTTGC
1 CTCAGCTTTGAGGAATTCAT-TTTTAAAAGTT-TCGTTGC
* *
11493849 CTCAGCTTTGGGGAGTTTCATTTTT-AAAGTTTCGTTGC
1 CTCAGCTTTGAGGA-ATTCATTTTTAAAAGTTTCGTTGC
* * *
11493887 CTTAGTTTTGAGGAGTTTCATTTTT-AAAGTTAT-GTTGC
1 CTCAGCTTTGAGGA-ATTCATTTTTAAAAGTT-TCGTTGC
* *
11493925 CTCAGCTTTGGGGAGTTTCATTTTT-AAAGTTTCGTTGC
1 CTCAGCTTTGAGGA-ATTCATTTTTAAAAGTTTCGTTGC
** * * * *
11493963 CTCATTTTTGAGGAGTTTTATTTTT-AAAGTTTCATAGC
1 CTCAGCTTTGAGGA-ATTCATTTTTAAAAGTTTCGTTGC
* ** * *
11494001 CACAATTTTGAGGAGTTCATTTTTAAAA-TTTCATTGC
1 CTCAGCTTTGAGGAATTCATTTTTAAAAGTTTCGTTGC
*
11494038 CTCAGCTTTAAGGAATCTCATTT
1 CTCAGCTTTGAGGAAT-TCATTT
11494061 AAAAAAAAAA
Statistics
Matches: 394, Mismatches: 65, Indels: 38
0.79 0.13 0.08
Matches are distributed among these distances:
37 70 0.18
38 275 0.70
39 45 0.11
40 4 0.01
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (38 bp):
CTCAGCTTTGAGGAATTCATTTTTAAAAGTTTCGTTGC
Found at i:11493672 original size:76 final size:75
Alignment explanation
Indices: 11493545--11494065 Score: 477
Period size: 76 Copynumber: 6.9 Consensus size: 75
11493535 GTTTTGTTAT
* * * *
11493545 CTCAGTTTTGAGGAATTCATTTTTAAAAGTTTCGTTGTCTCAACTTTGAGGAGTTCATTTTAAAA
1 CTCAGCTTTGAGGAGTTCATTTTTAAAAGTTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTAAAA
11493610 GTTCCAG-TGC
66 GTT-CAGTTGC
* * *
11493620 CTCAGCTTTGAGGAGTTAATTTTTAAAAAGTTTCATTGCCTCCGCTTTGAGGAGTTCATTTTTAA
1 CTCAGCTTTGAGGAGTTCATTTTT-AAAAGTTTCGTTGCCTCAGCTTTGAGGAGTTCA-TTTTAA
**
11493685 AAGTTTTGTTGC
64 AAGTTCAGTTGC
* * * ** *
11493697 CTTAGCTTTAAGGAG-TCACATTTTAAAAGTCCCGTTGCCTCAACTTTGAGGAGTTCATTTTTAG
1 CTCAGCTTTGAGGAGTTCA-TTTTTAAAAGTTTCGTTGCCTCAGCTTTGAGGAGTTCA-TTTTA-
*
11493761 AAATTTC-GTTGC
63 AAAGTTCAGTTGC
* ** * * *
11493773 CTCAACTTTGAAAAGTTCATTTTTAAACGTCTCGTTGCCTCAGCTTTGAGGAG-TCATATTTTTA
1 CTCAGCTTTGAGGAGTTCATTTTTAAAAGTTTCGTTGCCTCAGCTTTGAGGAGTTC--ATTTTAA
11493837 AAGTT-ATGTTGC
64 AAGTTCA-GTTGC
* * * *
11493849 CTCAGCTTTGGGGAGTTTCATTTTT-AAAGTTTCGTTGCCTTAGTTTTGAGGAGTTTCATTTTTA
1 CTCAGCTTTGAGGAG-TTCATTTTTAAAAGTTTCGTTGCCTCAGCTTTGAGGAG-TTCATTTTAA
11493913 AAGTT-ATGTTGC
64 AAGTTCA-GTTGC
* ** * *
11493925 CTCAGCTTTGGGGAGTTTCATTTTT-AAAGTTTCGTTGCCTCATTTTTGAGGAGTTTTATTTTTA
1 CTCAGCTTTGAGGAG-TTCATTTTTAAAAGTTTCGTTGCCTCAGCTTTGAGGAG-TTCATTTTAA
*
11493989 AAGTTTCA-TAGC
64 AAG-TTCAGTTGC
* ** * * * *
11494001 CACAATTTTGAGGAGTTCATTTTTAAAA-TTTCATTGCCTCAGCTTTAAGGAATCTCATTTAAAA
1 CTCAGCTTTGAGGAGTTCATTTTTAAAAGTTTCGTTGCCTCAGCTTTGAGGAGT-TCATTTTAAA
11494065 A
65 A
11494066 AAAAACAAAC
Statistics
Matches: 374, Mismatches: 55, Indels: 34
0.81 0.12 0.07
Matches are distributed among these distances:
74 1 0.00
75 64 0.17
76 255 0.68
77 51 0.14
78 3 0.01
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.42
Consensus pattern (75 bp):
CTCAGCTTTGAGGAGTTCATTTTTAAAAGTTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTAAAA
GTTCAGTTGC
Found at i:11493775 original size:114 final size:114
Alignment explanation
Indices: 11493551--11494065 Score: 524
Period size: 114 Copynumber: 4.5 Consensus size: 114
11493541 TTATCTCAGT
* * *
11493551 TTTGAGGAATTCATTTTTAAAAGTTTCGTTGTCTCAACTTTGAGGAGT-TCATTTTAAAAGTTCC
1 TTTGAGGAGTTCATTTTTAAAAGTTTCGTTGCCTCAGCTTTGAGGAGTCTCATTTTAAAAG-TCC
* * **
11493615 AG-TGCCTCAGCTTTGAGGAG-TTAATTTTTAAAAAGTTTCATTGCCTCCGC
65 CGTTGCCTCAGCTTTGAGGAGTTTCATTTTT-AAAA-TTTCATTGCCTCAAC
* * * *
11493665 TTTGAGGAGTTCATTTTTAAAAGTTTTGTTGCCTTAGCTTTAAGGAGTCACATTTTAAAAGTCCC
1 TTTGAGGAGTTCATTTTTAAAAGTTTCGTTGCCTCAGCTTTGAGGAGTCTCATTTTAAAAGTCCC
* *
11493730 GTTGCCTCAACTTTGAGGAG-TTCATTTTTAGAAATTTCGTTGCCTCAAC
66 GTTGCCTCAGCTTTGAGGAGTTTCATTTTTA-AAATTTCATTGCCTCAAC
** * * * **
11493779 TTTGAAAAGTTCATTTTTAAACGTCTCGTTGCCTCAGCTTTGAGGAGTCAT-ATTTTTAAAGTTA
1 TTTGAGGAGTTCATTTTTAAAAGTTTCGTTGCCTCAGCTTTGAGGAGTC-TCATTTTAAAAGTCC
* * * * * **
11493843 TGTTGCCTCAGCTTTGGGGAGTTTCATTTTTAAAGTTTCGTTGCCTTAGT
65 CGTTGCCTCAGCTTTGAGGAGTTTCATTTTTAAAATTTCATTGCCTCAAC
* * * *
11493893 TTTGAGGAGTTTCATTTTT-AAAGTTAT-GTTGCCTCAGCTTTGGGGAGTTTCATTTTTAAAGTT
1 TTTGAGGAG-TTCATTTTTAAAAGTT-TCGTTGCCTCAGCTTTGAGGAGTCTCATTTTAAAAGTC
* ** * * * * *
11493956 TCGTTGCCTCATTTTTGAGGAGTTTTATTTTTAAAGTTTCATAGCCACAAT
64 CCGTTGCCTCAGCTTTGAGGAGTTTCATTTTTAAAATTTCATTGCCTCAAC
* * * *
11494007 TTTGAGGAGTTCATTTTTAAAA-TTTCATTGCCTCAGCTTTAAGGAATCTCATTTAAAAA
1 TTTGAGGAGTTCATTTTTAAAAGTTTCGTTGCCTCAGCTTTGAGGAGTCTCATTTTAAAA
11494066 AAAAACAAAC
Statistics
Matches: 336, Mismatches: 55, Indels: 21
0.82 0.13 0.05
Matches are distributed among these distances:
112 1 0.00
113 38 0.11
114 238 0.71
115 59 0.18
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.43
Consensus pattern (114 bp):
TTTGAGGAGTTCATTTTTAAAAGTTTCGTTGCCTCAGCTTTGAGGAGTCTCATTTTAAAAGTCCC
GTTGCCTCAGCTTTGAGGAGTTTCATTTTTAAAATTTCATTGCCTCAAC
Found at i:11496591 original size:17 final size:16
Alignment explanation
Indices: 11496563--11496594 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
11496553 TGATAATAAA
11496563 AAATAAAATAATGATT
1 AAATAAAATAATGATT
11496579 AAATAATAATAATGAT
1 AAATAA-AATAATGAT
11496595 AAGAATAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (16 bp):
AAATAAAATAATGATT
Found at i:11498678 original size:30 final size:30
Alignment explanation
Indices: 11498644--11498704 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
11498634 AGGATAAAGT
*
11498644 TAATTTTCTTCAAATAAAAGACAATTATAA
1 TAATTTTATTCAAATAAAAGACAATTATAA
* *
11498674 TAATTTTATTCTAATAAAAGACTATTATAA
1 TAATTTTATTCAAATAAAAGACAATTATAA
11498704 T
1 T
11498705 TGAAAGACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (30 bp):
TAATTTTATTCAAATAAAAGACAATTATAA
Found at i:11499247 original size:2 final size:2
Alignment explanation
Indices: 11499242--11499280 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
11499232 TTTAAACCGA
*
11499242 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11499281 ACAAATGATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:11501325 original size:26 final size:26
Alignment explanation
Indices: 11501296--11501390 Score: 64
Period size: 26 Copynumber: 3.3 Consensus size: 26
11501286 AGAGAACAAC
11501296 CAGAACAAGTGAAGTGTTACTTCACG
1 CAGAACAAGTGAAGTGTTACTTCACG
* *
11501322 CAGAATAACTAGAACAAGTGAAGCGTTACTTCACG
1 CAGAACAAGT-G---AAGT-----GTTACTTCACG
***
11501357 CAGAACAAGTGAAGCACTACTTCACG
1 CAGAACAAGTGAAGTGTTACTTCACG
11501383 CAGAACAA
1 CAGAACAA
11501391 TTAGAATAAG
Statistics
Matches: 53, Mismatches: 7, Indels: 18
0.68 0.09 0.23
Matches are distributed among these distances:
26 25 0.47
27 1 0.02
30 4 0.08
31 3 0.06
34 1 0.02
35 19 0.36
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (26 bp):
CAGAACAAGTGAAGTGTTACTTCACG
Found at i:11501343 original size:35 final size:35
Alignment explanation
Indices: 11501288--11501364 Score: 127
Period size: 35 Copynumber: 2.2 Consensus size: 35
11501278 TATTATATAG
*
11501288 AGAACAACCAGAACAAGTGAAGTGTTACTTCACGC
1 AGAACAACCAGAACAAGTGAAGCGTTACTTCACGC
* *
11501323 AGAATAACTAGAACAAGTGAAGCGTTACTTCACGC
1 AGAACAACCAGAACAAGTGAAGCGTTACTTCACGC
11501358 AGAACAA
1 AGAACAA
11501365 GTGAAGCACT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (35 bp):
AGAACAACCAGAACAAGTGAAGCGTTACTTCACGC
Found at i:11501364 original size:61 final size:61
Alignment explanation
Indices: 11501296--11501425 Score: 170
Period size: 61 Copynumber: 2.1 Consensus size: 61
11501286 AGAGAACAAC
*** * * * *
11501296 CAGAACAAGTGAAGTGTTACTTCACGCAGAATAACTAGAACAAGTGAAGCGTTACTTCACG
1 CAGAACAAGTGAAGCACTACTTCACGCAGAACAACTAGAACAAGTGAAGCATTACTTAAAG
* * *
11501357 CAGAACAAGTGAAGCACTACTTCACGCAGAACAATTAGAATAAGTGAAGTATTACTTAAAG
1 CAGAACAAGTGAAGCACTACTTCACGCAGAACAACTAGAACAAGTGAAGCATTACTTAAAG
11501418 CAGAACAA
1 CAGAACAA
11501426 TTAGAAAAAG
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.20
Consensus pattern (61 bp):
CAGAACAAGTGAAGCACTACTTCACGCAGAACAACTAGAACAAGTGAAGCATTACTTAAAG
Found at i:11501413 original size:35 final size:35
Alignment explanation
Indices: 11501358--11501446 Score: 115
Period size: 35 Copynumber: 2.5 Consensus size: 35
11501348 TACTTCACGC
* * * * *
11501358 AGAACAAGTGAAGCACTACTTCACGCAGAACAATT
1 AGAAAAAGTGAAGTATTACTTAAAGCAGAACAATT
*
11501393 AGAATAAGTGAAGTATTACTTAAAGCAGAACAATT
1 AGAAAAAGTGAAGTATTACTTAAAGCAGAACAATT
*
11501428 AGAAAAAGTAAAGTATTAC
1 AGAAAAAGTGAAGTATTAC
11501447 CCCATATAGA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 47 1.00
ACGTcount: A:0.48, C:0.13, G:0.17, T:0.21
Consensus pattern (35 bp):
AGAAAAAGTGAAGTATTACTTAAAGCAGAACAATT
Found at i:11501715 original size:29 final size:28
Alignment explanation
Indices: 11501683--11501752 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
11501673 CTCGTATACT
*
11501683 TATTCATGTACAGCTTATTCTCTTGTACC
1 TATTC-TGTACAGCTTATTCTCTCGTACC
* * *
11501712 TATTCTCATATAGCTTCTTCTCTCGTACC
1 TATTCT-GTACAGCTTATTCTCTCGTACC
11501741 TATTCTTGTACA
1 TATTC-TGTACA
11501753 CCTCTTCTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
28 1 0.03
29 31 0.94
30 1 0.03
ACGTcount: A:0.20, C:0.26, G:0.09, T:0.46
Consensus pattern (28 bp):
TATTCTGTACAGCTTATTCTCTCGTACC
Found at i:11501990 original size:13 final size:13
Alignment explanation
Indices: 11501972--11501996 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11501962 ACTTGAGAGC
11501972 TTCTCTCTCTAAA
1 TTCTCTCTCTAAA
11501985 TTCTCTCTCTAA
1 TTCTCTCTCTAA
11501997 TTATCTTGTA
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:0.20, C:0.32, G:0.00, T:0.48
Consensus pattern (13 bp):
TTCTCTCTCTAAA
Found at i:11507291 original size:102 final size:102
Alignment explanation
Indices: 11507139--11507363 Score: 256
Period size: 102 Copynumber: 2.2 Consensus size: 102
11507129 CCAAGAAATG
* * * * *
11507139 AGCGATAAAGCTAGCGGCCAATAGCATAACATCATTACAGCCAAATTATGAGCGATAAAGCAAGC
1 AGCGATAAAGCTTGCGACCAAAAGCAGAACATCATTACAGCCAAAATATGAGCGATAAAGCAAGC
* * *
11507204 -AGCTGGAA-TATGAGTAATAAATTATGGTCAAAGAATA
66 GA-CT-GAAGTAAGAATAATAAACTATGGTCAAAGAATA
* * * * * **
11507241 AGCGATAAAGCTTGCGACCAAAAGTAGAATATTATTGCAGCCAAAATATGAGCGTTAAAGCTTGC
1 AGCGATAAAGCTTGCGACCAAAAGCAGAACATCATTACAGCCAAAATATGAGCGATAAAGCAAGC
* *
11507306 GACTGAAGTAAGAATGATGAACTATGGTCAAAGAATA
66 GACTGAAGTAAGAATAATAAACTATGGTCAAAGAATA
*
11507343 AGCAATAAAGCTTGCGACCAA
1 AGCGATAAAGCTTGCGACCAA
11507364 TAAAAAAAAA
Statistics
Matches: 103, Mismatches: 18, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
101 3 0.03
102 99 0.96
103 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (102 bp):
AGCGATAAAGCTTGCGACCAAAAGCAGAACATCATTACAGCCAAAATATGAGCGATAAAGCAAGC
GACTGAAGTAAGAATAATAAACTATGGTCAAAGAATA
Found at i:11508684 original size:29 final size:28
Alignment explanation
Indices: 11508616--11508685 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
11508606 AGAAAAGAGG
*
11508616 TGTACAAGAATAGGTACGAGAGAAGAAGC
1 TGTAC-AGAATAGGTACAAGAGAAGAAGC
* * *
11508645 TATATGAGAATAGGTACAAGAGAATAAGC
1 TGTA-CAGAATAGGTACAAGAGAAGAAGC
11508674 TGTACATGAATA
1 TGTACA-GAATA
11508686 AGTATACGAG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
28 1 0.03
29 32 0.97
ACGTcount: A:0.46, C:0.09, G:0.26, T:0.20
Consensus pattern (28 bp):
TGTACAGAATAGGTACAAGAGAAGAAGC
Found at i:11510706 original size:13 final size:13
Alignment explanation
Indices: 11510688--11510722 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 13
11510678 ATGCTGCGTG
11510688 TTTGGTTGCAATT
1 TTTGGTTGCAATT
11510701 TTTGGTGTTGCAATT
1 TTT-G-GTTGCAATT
11510716 TTTGGTT
1 TTTGGTT
11510723 TTTATTCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 6 0.30
14 2 0.10
15 12 0.60
ACGTcount: A:0.11, C:0.06, G:0.26, T:0.57
Consensus pattern (13 bp):
TTTGGTTGCAATT
Found at i:11510712 original size:15 final size:15
Alignment explanation
Indices: 11510692--11510721 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
11510682 TGCGTGTTTG
11510692 GTTGCAATTTTTGGT
1 GTTGCAATTTTTGGT
11510707 GTTGCAATTTTTGGT
1 GTTGCAATTTTTGGT
11510722 TTTTATTCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.07, G:0.27, T:0.53
Consensus pattern (15 bp):
GTTGCAATTTTTGGT
Found at i:11510943 original size:32 final size:29
Alignment explanation
Indices: 11510867--11510987 Score: 110
Period size: 29 Copynumber: 4.2 Consensus size: 29
11510857 GTATTAACAT
* * * *
11510867 TGTAACAA-AAT-GTTTTTGAATATGTCG
1 TGTAACAACAATATTTTTTCAACATGGCG
*
11510894 TGTAACAACAATATTTTTTCAACATGGTG
1 TGTAACAACAATATTTTTTCAACATGGCG
*
11510923 TGTAACAACAATATTTTTTTTTCAACATTGCG
1 TGTAACAACAATA---TTTTTTCAACATGGCG
11510955 TGTAACAAC---ATTTTTT-AACTATGGCG
1 TGTAACAACAATATTTTTTCAAC-ATGGCG
11510981 TGTAACA
1 TGTAACA
11510988 TGTTTTTATA
Statistics
Matches: 80, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
25 3 0.04
26 18 0.22
27 8 0.10
28 3 0.04
29 25 0.31
32 23 0.29
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (29 bp):
TGTAACAACAATATTTTTTCAACATGGCG
Found at i:11510993 original size:23 final size:23
Alignment explanation
Indices: 11510961--11511112 Score: 103
Period size: 24 Copynumber: 6.4 Consensus size: 23
11510951 TGCGTGTAAC
* *
11510961 AACATTTTTTA-ACTATGGCGTGT
1 AACATGTTTTATAC-ATGACGTGT
11510984 AACATGTTTTTATACATGACGTGT
1 AACATG-TTTTATACATGACGTGT
*
11511008 CACATGTTTT-TGCACATGACGTGT
1 AACATGTTTTAT--ACATGACGTGT
* *
11511032 CACATGTTTTTGTACATGACGTGT
1 AACATG-TTTTATACATGACGTGT
* *
11511056 CACATGTTTTTGTACAT-AGCGTGT
1 AACATG-TTTTATACATGA-CGTGT
* * * *
11511080 CATATGTTTCTGTACATGGCGTGT
1 AACATGTTT-TATACATGACGTGT
*
11511104 CACATGTTT
1 AACATGTTT
11511113 CTGTACATAG
Statistics
Matches: 114, Mismatches: 6, Indels: 17
0.83 0.04 0.12
Matches are distributed among these distances:
22 1 0.01
23 13 0.11
24 93 0.82
25 6 0.05
26 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.41
Consensus pattern (23 bp):
AACATGTTTTATACATGACGTGT
Found at i:11511006 original size:24 final size:24
Alignment explanation
Indices: 11510979--11511120 Score: 205
Period size: 24 Copynumber: 5.9 Consensus size: 24
11510969 TTAACTATGG
* *
11510979 CGTGTAACATGTTTTTATACATGA
1 CGTGTCACATGTTTTTGTACATGA
*
11511003 CGTGTCACATGTTTTTGCACATGA
1 CGTGTCACATGTTTTTGTACATGA
11511027 CGTGTCACATGTTTTTGTACATGA
1 CGTGTCACATGTTTTTGTACATGA
11511051 CGTGTCACATGTTTTTGTACAT-A
1 CGTGTCACATGTTTTTGTACATGA
* * *
11511074 GCGTGTCATATGTTTCTGTACATGG
1 -CGTGTCACATGTTTTTGTACATGA
*
11511099 CGTGTCACATGTTTCTGTACAT
1 CGTGTCACATGTTTTTGTACAT
11511121 AGTGAAAACA
Statistics
Matches: 108, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
23 1 0.01
24 107 0.99
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (24 bp):
CGTGTCACATGTTTTTGTACATGA
Found at i:11514958 original size:15 final size:15
Alignment explanation
Indices: 11514938--11514968 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
11514928 TGTTATCTTC
11514938 CCTGCAATCACATTA
1 CCTGCAATCACATTA
11514953 CCTGCAATCACATTA
1 CCTGCAATCACATTA
11514968 C
1 C
11514969 ATTGTGAAGT
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:0.32, C:0.35, G:0.06, T:0.26
Consensus pattern (15 bp):
CCTGCAATCACATTA
Found at i:11525808 original size:18 final size:18
Alignment explanation
Indices: 11525781--11525820 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
11525771 AATCGTTAAT
**
11525781 TTATGAGTTATTTATGAA
1 TTATGAGTTACCTATGAA
*
11525799 TTATGTGTTACCTATGAA
1 TTATGAGTTACCTATGAA
11525817 TTAT
1 TTAT
11525821 TTGTGAAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.05, G:0.15, T:0.50
Consensus pattern (18 bp):
TTATGAGTTACCTATGAA
Found at i:11537050 original size:22 final size:22
Alignment explanation
Indices: 11537007--11537050 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
11536997 TTTAAAACAA
* *
11537007 CTTTAAAACTAAAAACTTTGAT
1 CTTTAAAACCAAAAACTCTGAT
* *
11537029 CTTTAGAACCAAAAGCTCTGAT
1 CTTTAAAACCAAAAACTCTGAT
11537051 ACCAATCGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (22 bp):
CTTTAAAACCAAAAACTCTGAT
Found at i:11539667 original size:20 final size:20
Alignment explanation
Indices: 11539642--11539687 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
11539632 CTTCTAAACC
*
11539642 TCAAATCATACTGCAATAAG
1 TCAAATCATACTCCAATAAG
*
11539662 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
11539682 TCAAAT
1 TCAAAT
11539688 GGGGCCAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.46, C:0.20, G:0.07, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:11541527 original size:20 final size:19
Alignment explanation
Indices: 11541499--11541536 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
11541489 ACTCATTAAC
*
11541499 ATTTTAATTAATTTAAATA
1 ATTTTAATTAATCTAAATA
11541518 ATTTTAAATTAATCTAAAT
1 ATTTT-AATTAATCTAAAT
11541537 TCACTACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTTAATTAATCTAAATA
Found at i:11541613 original size:119 final size:120
Alignment explanation
Indices: 11541379--11541614 Score: 325
Period size: 123 Copynumber: 1.9 Consensus size: 120
11541369 TAATACAACC
* *
11541379 TTAATTAATTTAAATAATTTAAAATTAATCTAAATTTACTAATCTAATTATTTGCTCAATTACTT
1 TTAATTAATTTAAATAATTTAAAATTAATCTAAATTCACTAATCTAATTAATTGCTCAATTAC-T
* * *
11541444 AGTTATAACACATATCATTACTTACTTAACTATATTATTTAATTAACTCATTAACATT
65 --TTATAACACATATCATTACTTAATCAACTAAATTATTTAATTAACTCATTAACATT
* * *
11541502 TTAATTAATTTAAATAATTTTAAATTAATCTAAATTCACTACTTTAATTAATTGCTTC-ATTAC-
1 TTAATTAATTTAAATAATTTAAAATTAATCTAAATTCACTAATCTAATTAATTGC-TCAATTACT
*
11541565 TTATAACACAT-TACATTACTTAATCAACTAAATTATTTATTTAACTCATT
65 TTATAACACATAT-CATTACTTAATCAACTAAATTATTTAATTAACTCATT
11541615 CACACCTTAT
Statistics
Matches: 102, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
118 1 0.01
119 44 0.43
123 55 0.54
124 2 0.02
ACGTcount: A:0.40, C:0.13, G:0.01, T:0.46
Consensus pattern (120 bp):
TTAATTAATTTAAATAATTTAAAATTAATCTAAATTCACTAATCTAATTAATTGCTCAATTACTT
TATAACACATATCATTACTTAATCAACTAAATTATTTAATTAACTCATTAACATT
Found at i:11544553 original size:19 final size:20
Alignment explanation
Indices: 11544526--11544571 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
11544516 AGGAGACAAG
*
11544526 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
11544545 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
11544564 ATAATATT
1 ATAATATT
11544572 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:11546403 original size:13 final size:13
Alignment explanation
Indices: 11546385--11546409 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11546375 AGAGAAATTG
11546385 TGATTTTATAAAA
1 TGATTTTATAAAA
11546398 TGATTTTATAAA
1 TGATTTTATAAA
11546410 TTTTCTGAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:11560691 original size:20 final size:20
Alignment explanation
Indices: 11560646--11560683 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
11560636 TTTTTTACCC
11560646 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
11560666 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
11560684 AGATTTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:11561924 original size:13 final size:13
Alignment explanation
Indices: 11561906--11561930 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11561896 TGAATAAATG
11561906 TGATTTTATAAAA
1 TGATTTTATAAAA
11561919 TGATTTTATAAA
1 TGATTTTATAAA
11561931 TTTTCTGAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:11562994 original size:26 final size:25
Alignment explanation
Indices: 11562958--11563008 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 25
11562948 TTTCACTTCA
11562958 AATGAACGTTTTAGATACTTAATTT
1 AATGAACGTTTTAGATACTTAATTT
*
11562983 NAATGAACGTTTTAGATATTTAATTT
1 -AATGAACGTTTTAGATACTTAATTT
11563009 GTTTTTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.45
Consensus pattern (25 bp):
AATGAACGTTTTAGATACTTAATTT
Found at i:11573557 original size:12 final size:11
Alignment explanation
Indices: 11573540--11573567 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
11573530 CCAAATTGTC
11573540 AAAAAAAAAAG
1 AAAAAAAAAAG
11573551 AAAAAAAAAAG
1 AAAAAAAAAAG
11573562 AAAAAA
1 AAAAAA
11573568 GTTGAGAGGA
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:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:11573760 original size:24 final size:26
Alignment explanation
Indices: 11573713--11573772 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 26
11573703 TCAATATGGA
11573713 GTGTAACAACTTTTTTTAACCATGAC
1 GTGTAACAACTTTTTTTAACCATGAC
** **
11573739 GTGTAACATGTTTTTTT-A-CATGGT
1 GTGTAACAACTTTTTTTAACCATGAC
11573763 GTGTAACAAC
1 GTGTAACAAC
11573773 AGTATTTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
24 12 0.43
25 1 0.04
26 15 0.54
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (26 bp):
GTGTAACAACTTTTTTTAACCATGAC
Found at i:11573844 original size:45 final size:45
Alignment explanation
Indices: 11573793--11573881 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
11573783 TTTAACATAG
*
11573793 CGTGTAACAACCTAACCATGGCTTGTCACAGGTTTTTGTACATGA
1 CGTGTAACAACCTAACCATAGCTTGTCACAGGTTTTTGTACATGA
* *
11573838 CGTGTAACAAGCTAACCATAGCTTGTCATAGGTTTTTGTACATG
1 CGTGTAACAACCTAACCATAGCTTGTCACAGGTTTTTGTACATG
11573882 GCCTGCCACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (45 bp):
CGTGTAACAACCTAACCATAGCTTGTCACAGGTTTTTGTACATGA
Found at i:11573914 original size:114 final size:114
Alignment explanation
Indices: 11573781--11574074 Score: 423
Period size: 114 Copynumber: 2.6 Consensus size: 114
11573771 ACAGTATTTT
*
11573781 TTTTTA-ACATAGCGTGTAACAACCTAACCATGGCTTGTCACAGGTTTTTGTACATGACGTGTAA
1 TTTTTATACATAGCATGTAACAACCTAACCATGGCTTGTCACAGGTTTTTGTACATGACGTGTAA
11573845 CAAGCTAACCATAGCTTGTCATAGGTTTTTGTACATGGCCTGCCACATA
66 CAAGCTAACCATAGCTTGTCATAGGTTTTTGTACATGGCCTGCCACATA
* * * **
11573894 TTTTTGTACATGGCATGTAACAAGCTAACCATGGCTTGTCACATATTTTTGTACAT-AGCGTGTA
1 TTTTTATACATAGCATGTAACAACCTAACCATGGCTTGTCACAGGTTTTTGTACATGA-CGTGTA
* * * *
11573958 ACACGCTAACCATGGCTTGTCATAGGTTTTTGTACATGGCGTGTCACATA
65 ACAAGCTAACCATAGCTTGTCATAGGTTTTTGTACATGGCCTGCCACATA
* * * *
11574008 TTTTTATACATAGCGTGTAAC-ACGTTAACCACGGCTTGTCACAGGTTTTTGTACATGGCGTGTA
1 TTTTTATACATAGCATGTAACAAC-CTAACCATGGCTTGTCACAGGTTTTTGTACATGACGTGTA
11574072 ACA
65 ACA
11574075 TCATAACGTG
Statistics
Matches: 158, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
113 7 0.04
114 151 0.96
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (114 bp):
TTTTTATACATAGCATGTAACAACCTAACCATGGCTTGTCACAGGTTTTTGTACATGACGTGTAA
CAAGCTAACCATAGCTTGTCATAGGTTTTTGTACATGGCCTGCCACATA
Found at i:11573942 original size:45 final size:45
Alignment explanation
Indices: 11573878--11573997 Score: 168
Period size: 45 Copynumber: 2.7 Consensus size: 45
11573868 GGTTTTTGTA
* *
11573878 CATGGCCTGCCACATATTTTTGTACATGGCATGTAACAAGCTAAC
1 CATGGCTTGTCACATATTTTTGTACATGGCATGTAACAAGCTAAC
* * *
11573923 CATGGCTTGTCACATATTTTTGTACATAGCGTGTAACACGCTAAC
1 CATGGCTTGTCACATATTTTTGTACATGGCATGTAACAAGCTAAC
* **
11573968 CATGGCTTGTCATAGGTTTTTGTACATGGC
1 CATGGCTTGTCACATATTTTTGTACATGGC
11573998 GTGTCACATA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 66 1.00
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (45 bp):
CATGGCTTGTCACATATTTTTGTACATGGCATGTAACAAGCTAAC
Found at i:11573996 original size:69 final size:69
Alignment explanation
Indices: 11573923--11574075 Score: 252
Period size: 69 Copynumber: 2.2 Consensus size: 69
11573913 ACAAGCTAAC
* * * *
11573923 CATGGCTTGTCACATATTTTTGTACATAGCGTGTAACACGCTAACCATGGCTTGTCATAGGTTTT
1 CATGGCGTGTCACATATTTTTATACATAGCGTGTAACACGCTAACCACGGCTTGTCACAGGTTTT
11573988 TGTA
66 TGTA
*
11573992 CATGGCGTGTCACATATTTTTATACATAGCGTGTAACACGTTAACCACGGCTTGTCACAGGTTTT
1 CATGGCGTGTCACATATTTTTATACATAGCGTGTAACACGCTAACCACGGCTTGTCACAGGTTTT
11574057 TGTA
66 TGTA
*
11574061 CATGGCGTGTAACAT
1 CATGGCGTGTCACAT
11574076 CATAACGTGT
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 78 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (69 bp):
CATGGCGTGTCACATATTTTTATACATAGCGTGTAACACGCTAACCACGGCTTGTCACAGGTTTT
TGTA
Found at i:11577995 original size:43 final size:41
Alignment explanation
Indices: 11577907--11577995 Score: 97
Period size: 43 Copynumber: 2.1 Consensus size: 41
11577897 GTGAACATAT
* * * *
11577907 TTTTCTCTTATCTTGTTCTCTTGTGTTTTTTCACATATACT
1 TTTTCTCTTATCTTGTTCTCTTGTATATTTTCACATAAACC
* **
11577948 TTTTCTCTTATACCTTGTTCTCTTTTATATTTTCATGTAAACC
1 TTTTCTCTTAT--CTTGTTCTCTTGTATATTTTCACATAAACC
11577991 TTTTC
1 TTTTC
11577996 CCTTTTACTT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 11 0.28
43 28 0.72
ACGTcount: A:0.15, C:0.20, G:0.06, T:0.60
Consensus pattern (41 bp):
TTTTCTCTTATCTTGTTCTCTTGTATATTTTCACATAAACC
Found at i:11588891 original size:26 final size:26
Alignment explanation
Indices: 11588854--11589060 Score: 147
Period size: 26 Copynumber: 8.1 Consensus size: 26
11588844 GGGTTACGGC
11588854 ATCCATCTACTTCTAATGGTAAAATT
1 ATCCATCTACTTCTAATGGTAAAATT
* *
11588880 ATCCATCCACTTCTAGTGGTAAAATT
1 ATCCATCTACTTCTAATGGTAAAATT
* * * * *
11588906 TTTC-T-TAAATTCAAATGATAAAATT
1 ATCCATCT-ACTTCTAATGGTAAAATT
* *
11588931 ATCCATCCACTTCTAGTGGTAAAATT
1 ATCCATCTACTTCTAATGGTAAAATT
* * * * *
11588957 ATTC-T-TAAATTCAAATGATAAATTT
1 ATCCATCT-ACTTCTAATGGTAAAATT
*
11588982 ATCCATCTACTTCTGATGGTAAAATT
1 ATCCATCTACTTCTAATGGTAAAATT
** * * *
11589008 AT-TGT-TAGATTTTGATGGTAAAATT
1 ATCCATCTA-CTTCTAATGGTAAAATT
* *
11589033 ATCCATTTACTTCTAGTGGTAAAATT
1 ATCCATCTACTTCTAATGGTAAAATT
11589059 AT
1 AT
11589061 TCTTAAAATT
Statistics
Matches: 133, Mismatches: 39, Indels: 18
0.70 0.21 0.09
Matches are distributed among these distances:
24 2 0.02
25 52 0.39
26 76 0.57
27 3 0.02
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (26 bp):
ATCCATCTACTTCTAATGGTAAAATT
Found at i:11588932 original size:51 final size:51
Alignment explanation
Indices: 11588868--11589067 Score: 276
Period size: 51 Copynumber: 3.9 Consensus size: 51
11588858 ATCTACTTCT
* *
11588868 AATGGTAAAATTATCCATCCACTTCTAGTGGTAAAATTTTTCTTAAATTCA
1 AATGATAAAATTATCCATCCACTTCTAGTGGTAAAATTATTCTTAAATTCA
11588919 AATGATAAAATTATCCATCCACTTCTAGTGGTAAAATTATTCTTAAATTCA
1 AATGATAAAATTATCCATCCACTTCTAGTGGTAAAATTATTCTTAAATTCA
* * * * **
11588970 AATGATAAATTTATCCATCTACTTCT-GATGGTAAAATTATTGTTAGATTTT
1 AATGATAAAATTATCCATCCACTTCTAG-TGGTAAAATTATTCTTAAATTCA
* * **
11589021 GATGGTAAAATTATCCATTTACTTCTAGTGGTAAAATTATTCTTAAA
1 AATGATAAAATTATCCATCCACTTCTAGTGGTAAAATTATTCTTAAA
11589068 ATTAAAATAG
Statistics
Matches: 133, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
50 1 0.01
51 131 0.98
52 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (51 bp):
AATGATAAAATTATCCATCCACTTCTAGTGGTAAAATTATTCTTAAATTCA
Found at i:11601211 original size:123 final size:122
Alignment explanation
Indices: 11601069--11601841 Score: 701
Period size: 123 Copynumber: 6.3 Consensus size: 122
11601059 AATTATTTCA
* * * * * * *
11601069 TGCCAATGTAACTAGACTTAAATATCTTAGATGTCAATTTGATTGGACTTAAACTCTTTTGTGGC
1 TGCCAACGTAACTAGACTTATACATCTTGGATG-CAATTTGATTGGGCTTAAAATCTTTTGTGCC
*
11601134 AAAGTAACTGGACTT-TAACATCTTAGATGCTAGTTTGATTGGGCTTAAACTCTTTTTG
65 AAAGTAACTGGACTTAT-ACATCTTGGATGCTAGTTTGATTGGGCTTAAACTCTTTTTG
11601192 TGCCAACGTAAC-AGAACTTATACATCTTGGATGCCAATTTGATTTGGGCTTAAAATCATTTTGT
1 TGCCAACGTAACTAG-ACTTATACATCTTGGATG-CAATTTGA-TTGGGCTTAAAATC-TTTTGT
* * * * *
11601256 GCCAATGTATCTGGACTTAAACATCTTAGATGCCAGTTAT-ATTGGGCTTAAACTCTTTTTG
62 GCCAAAGTAACTGGACTTATACATCTTGGATGCTAGTT-TGATTGGGCTTAAACTCTTTTTG
* * ** ** *
11601317 TGCCAATGTAACTAGACTTATACATCTTGAATGCTAGGTAAATTGGGCTTAAACTCTTTTTGTGC
1 TGCCAACGTAACTAGACTTATACATCTTGGATGC-AATTTGATTGGGCTTAAAATC-TTTTGTGC
* * * ** * *
11601382 TAACGTAACTGGACTTATACATCTTGGATGCTAGGTAAATTAGGCTTAAACTCCTTTTG
64 CAAAGTAACTGGACTTATACATCTTGGATGCTAGTTTGATTGGGCTTAAACTCTTTTTG
* * * * *
11601441 TGCCAACATAA-TTGAACTTATATATCTTGGATGC--TTGGTAAATTGGGCTTAAATTCTTTCT-
1 TGCCAACGTAACTAG-ACTTATACATCTTGGATGCAATT--T-GATTGGGCTTAAAATCTTT-TG
* * * *
11601502 TACCAACA-TAACTAGAGTTATACATCTTGGATGCTAGTTTGATTGGGCTTAAAATCATTTTT-
61 TGCCAA-AGTAACTGGACTTATACATCTTGGATGCTAGTTTGATTGGGCTTAAACTC-TTTTTG
* * * **
11601564 TGCCAACGTAACTGGACTTATACATCTTGGATGCCAACTTGATTAGGCTTAAAATCTTTTGTGTT
1 TGCCAACGTAACTAGACTTATACATCTTGGATG-CAATTTGATTGGGCTTAAAATCTTTTGTGCC
* * * *
11601629 AACA-TAACTGGACTTATATATCTTGGATGCTAGTTTGATTGGGTTTAAAATCATTTTG
65 AA-AGTAACTGGACTTATACATCTTGGATGCTAGTTTGATTGGGCTTAAACTCTTTTTG
* * ** ** *
11601687 TACCAACGTAACTAGACTTATACATCTTTTG-TGCTAGCTAAATTGGGCTTAAATTCTTTTGTGC
1 TGCCAACGTAACTAGACTTATACATC-TTGGATGC-AATTTGATTGGGCTTAAAATCTTTTGTGC
* * ** * *
11601751 CAACA-TAACTGGACTTAGACATCTTGGAT-TTCA-ACTAAATGGGCTTAAACTCTTTTTG
64 CAA-AGTAACTGGACTTATACATCTTGGATGCT-AGTTTGATTGGGCTTAAACTCTTTTTG
* * *
11601809 TGCCAATGTAACTGGCCTTATACATCTTGGATG
1 TGCCAACGTAACTAGACTTATACATCTTGGATG
11601842 TTAGCTAATT
Statistics
Matches: 536, Mismatches: 89, Indels: 51
0.79 0.13 0.08
Matches are distributed among these distances:
121 4 0.01
122 51 0.10
123 252 0.47
124 135 0.25
125 90 0.17
126 4 0.01
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (122 bp):
TGCCAACGTAACTAGACTTATACATCTTGGATGCAATTTGATTGGGCTTAAAATCTTTTGTGCCA
AAGTAACTGGACTTATACATCTTGGATGCTAGTTTGATTGGGCTTAAACTCTTTTTG
Found at i:11601225 original size:62 final size:62
Alignment explanation
Indices: 11601069--11601841 Score: 722
Period size: 62 Copynumber: 12.5 Consensus size: 62
11601059 AATTATTTCA
* * * * * * *
11601069 TGCCAATGTAACTAGACTTAAATATCTTAGATG-TCAATTTGATTGGACTTAAACTC-TTTTG
1 TGCCAACGTAACTGGACTTATACATCTTGGATGCT-AGTTTGATTGGGCTTAAACTCTTTTTG
* * *
11601130 TGGCAAAGTAACTGGACTT-TAACATCTTAGATGCTAGTTTGATTGGGCTTAAACTCTTTTTG
1 TGCCAACGTAACTGGACTTAT-ACATCTTGGATGCTAGTTTGATTGGGCTTAAACTCTTTTTG
* * * * * *
11601192 TGCCAACGTAACAGAACTTATACATCTTGGATGCCAATTTGATTTGGGCTTAAAATCATTTTG
1 TGCCAACGTAACTGGACTTATACATCTTGGATGCTAGTTTGA-TTGGGCTTAAACTCTTTTTG
* * * * *
11601255 TGCCAATGTATCTGGACTTAAACATCTTAGATGCCAGTTAT-ATTGGGCTTAAACTCTTTTTG
1 TGCCAACGTAACTGGACTTATACATCTTGGATGCTAGTT-TGATTGGGCTTAAACTCTTTTTG
* * * * **
11601317 TGCCAATGTAACTAGACTTATACATCTTGAATGCTAGGTAAATTGGGCTTAAACTCTTTTTG
1 TGCCAACGTAACTGGACTTATACATCTTGGATGCTAGTTTGATTGGGCTTAAACTCTTTTTG
* * ** * *
11601379 TGCTAACGTAACTGGACTTATACATCTTGGATGCTAGGTAAATTAGGCTTAAACTCCTTTTG
1 TGCCAACGTAACTGGACTTATACATCTTGGATGCTAGTTTGATTGGGCTTAAACTCTTTTTG
* * * * * * ** * *
11601441 TGCCAACATAATTGAACTTATATATCTTGGATGCTTGGTAAATTGGGCTTAAATTCTTTCT-
1 TGCCAACGTAACTGGACTTATACATCTTGGATGCTAGTTTGATTGGGCTTAAACTCTTTTTG
* * * * *
11601502 TACCAACATAACTAGAGTTATACATCTTGGATGCTAGTTTGATTGGGCTTAAAATCATTTTT-
1 TGCCAACGTAACTGGACTTATACATCTTGGATGCTAGTTTGATTGGGCTTAAACTC-TTTTTG
* ** * *
11601564 TGCCAACGTAACTGGACTTATACATCTTGGATGCCAACTTGATTAGGCTTAAAATC-TTTTG
1 TGCCAACGTAACTGGACTTATACATCTTGGATGCTAGTTTGATTGGGCTTAAACTCTTTTTG
** * * * * *
11601625 TGTTAACATAACTGGACTTATATATCTTGGATGCTAGTTTGATTGGGTTTAAAATCATTTTG
1 TGCCAACGTAACTGGACTTATACATCTTGGATGCTAGTTTGATTGGGCTTAAACTCTTTTTG
* * * * ** *
11601687 TACCAACGTAACTAGACTTATACATCTTTTG-TGCTAGCTAAATTGGGCTTAAATTC-TTTTG
1 TGCCAACGTAACTGGACTTATACATC-TTGGATGCTAGTTTGATTGGGCTTAAACTCTTTTTG
* * * ** * *
11601748 TGCCAACATAACTGGACTTAGACATCTTGGAT-TTCA-ACTAAATGGGCTTAAACTCTTTTTG
1 TGCCAACGTAACTGGACTTATACATCTTGGATGCT-AGTTTGATTGGGCTTAAACTCTTTTTG
* *
11601809 TGCCAATGTAACTGGCCTTATACATCTTGGATG
1 TGCCAACGTAACTGGACTTATACATCTTGGATG
11601842 TTAGCTAATT
Statistics
Matches: 592, Mismatches: 105, Indels: 29
0.82 0.14 0.04
Matches are distributed among these distances:
60 22 0.04
61 200 0.34
62 314 0.53
63 55 0.09
64 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (62 bp):
TGCCAACGTAACTGGACTTATACATCTTGGATGCTAGTTTGATTGGGCTTAAACTCTTTTTG
Found at i:11601290 original size:31 final size:31
Alignment explanation
Indices: 11601068--11601290 Score: 93
Period size: 31 Copynumber: 7.2 Consensus size: 31
11601058 AAATTATTTC
* * *
11601068 ATGCCAATGTAACTAGACTTAAATATCTTAG
1 ATGCCAATGTATCTGGACTTAAACATCTTAG
* * *
11601099 ATGTCAATTTGAT-TGGACTTAAAC-TCTTTTG
1 ATGCCAATGT-ATCTGGACTTAAACATC-TTAG
* * * *
11601130 -TGGCAAAGTAACTGGACTTTAACATCTTAG
1 ATGCCAATGTATCTGGACTTAAACATCTTAG
* * * * *
11601160 ATGCTAGTTTGAT-TGGGCTTAAAC-TCTTTTTG
1 ATGCCAATGT-ATCTGGACTTAAACATC--TTAG
* * * * * *
11601192 -TGCCAACGTAACAGAACTTATACATCTTGG
1 ATGCCAATGTATCTGGACTTAAACATCTTAG
* * * *
11601222 ATGCCAATTTGATTTGGGCTTAAA-ATCATTTTG
1 ATGCCAATGT-ATCTGGACTTAAACATC--TTAG
11601255 -TGCCAATGTATCTGGACTTAAACATCTTAG
1 ATGCCAATGTATCTGGACTTAAACATCTTAG
11601285 ATGCCA
1 ATGCCA
11601291 GTTATATTGG
Statistics
Matches: 132, Mismatches: 44, Indels: 32
0.63 0.21 0.15
Matches are distributed among these distances:
29 1 0.01
30 30 0.23
31 73 0.55
32 25 0.19
33 3 0.02
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (31 bp):
ATGCCAATGTATCTGGACTTAAACATCTTAG
Found at i:11601321 original size:31 final size:30
Alignment explanation
Indices: 11601223--11601326 Score: 86
Period size: 31 Copynumber: 3.3 Consensus size: 30
11601213 ACATCTTGGA
* *
11601223 TGCCAATTTGATTTGGGCTTAAAATCATTTTG
1 TGCCAATGT-ATTTGGGCTTAAACTC-TTTTG
* * *
11601255 TGCCAATGTATCTGGACTTAAACATC-TTAG
1 TGCCAATGTATTTGGGCTTAAAC-TCTTTTG
*
11601285 ATGCCAGT-TATATTGGGCTTAAACTCTTTTTG
1 -TGCCAATGTAT-TTGGGCTTAAACTC-TTTTG
11601317 TGCCAATGTA
1 TGCCAATGTA
11601327 ACTAGACTTA
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
30 8 0.14
31 33 0.59
32 15 0.27
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.39
Consensus pattern (30 bp):
TGCCAATGTATTTGGGCTTAAACTCTTTTG
Found at i:11608381 original size:15 final size:16
Alignment explanation
Indices: 11608350--11608382 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11608340 TATTTTTCAA
*
11608350 ATAAGTCCTTAATATT
1 ATAACTCCTTAATATT
11608366 ATAACTCCTT-ATATT
1 ATAACTCCTTAATATT
11608381 AT
1 AT
11608383 TGACCTAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.45
Consensus pattern (16 bp):
ATAACTCCTTAATATT
Found at i:11613516 original size:16 final size:16
Alignment explanation
Indices: 11613497--11613527 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
11613487 ATTAAATGAG
11613497 TAATTAATCAATAAAT
1 TAATTAATCAATAAAT
11613513 TAATTAATCAATAAA
1 TAATTAATCAATAAA
11613528 ATAACCATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATTAATCAATAAAT
Found at i:11621910 original size:15 final size:15
Alignment explanation
Indices: 11621890--11621935 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
11621880 TTCTTAAAAC
11621890 AACTTTAAAACCAAA
1 AACTTTAAAACCAAA
11621905 AACTTTAAAATCC-AA
1 AACTTTAAAA-CCAAA
* *
11621920 AGCTTTAAAATCAAA
1 AACTTTAAAACCAAA
11621935 A
1 A
11621936 CCTCTGATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 1 0.04
15 24 0.89
16 2 0.07
ACGTcount: A:0.57, C:0.17, G:0.02, T:0.24
Consensus pattern (15 bp):
AACTTTAAAACCAAA
Found at i:11628361 original size:14 final size:14
Alignment explanation
Indices: 11628342--11628368 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11628332 ACCTAACCTG
11628342 ACTTAACTTAACTA
1 ACTTAACTTAACTA
11628356 ACTTAACTTAACT
1 ACTTAACTTAACT
11628369 TAGCTTAGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.22, G:0.00, T:0.37
Consensus pattern (14 bp):
ACTTAACTTAACTA
Found at i:11628376 original size:5 final size:5
Alignment explanation
Indices: 11628342--11628375 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
11628332 ACCTAACCTG
*
11628342 ACTTA ACTTA AC-TA ACTTA ACTTA ACTTA GCTTA
1 ACTTA ACTTA ACTTA ACTTA ACTTA ACTTA ACTTA
11628376 GGCTACGCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (5 bp):
ACTTA
Found at i:11628429 original size:15 final size:15
Alignment explanation
Indices: 11628409--11628454 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
11628399 TTCTTAAAAC
11628409 AACTTTAAAACCAAA
1 AACTTTAAAACCAAA
11628424 AACTTTAAAATCC-AA
1 AACTTTAAAA-CCAAA
*
11628439 AACTTTAAAATCAAA
1 AACTTTAAAACCAAA
11628454 A
1 A
11628455 TCTCTGATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 1 0.04
15 25 0.89
16 2 0.07
ACGTcount: A:0.59, C:0.17, G:0.00, T:0.24
Consensus pattern (15 bp):
AACTTTAAAACCAAA
Found at i:11640676 original size:18 final size:18
Alignment explanation
Indices: 11640653--11640693 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
11640643 AATACGTTTA
11640653 TTTAATCGTGTTATCGTG
1 TTTAATCGTGTTATCGTG
*
11640671 TTTAATCGTGTTATTGTG
1 TTTAATCGTGTTATCGTG
11640689 TTTAA
1 TTTAA
11640694 ACGTATATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.54
Consensus pattern (18 bp):
TTTAATCGTGTTATCGTG
Found at i:11657491 original size:234 final size:233
Alignment explanation
Indices: 11657079--11657520 Score: 627
Period size: 234 Copynumber: 1.9 Consensus size: 233
11657069 TGTAAATAAT
* * * * *
11657079 GCAGGTTAAAAAATGAAGAATGAATGGAAAGAGCTGTTTCTATTTAGTCCATTCAATTTCATTTT
1 GCAGGTTAAAAAATGAAGAATAAATGAAAAGAGCTGTTTCTAATTAGTCCATTCAACTTCATTAT
** *
11657144 ACTAAATACTCAAGTATTTAACAGCCATATAACATTCACCATATGAAAGCACCTAACAGACAATT
66 ACTAAATAAACAAGTATTTAACAGCCATATAAAATTCACCATATGAAAGCACCTAACAGACAATT
* * ** * * * *
11657209 TAAGACTGGCCATCTAATATGCTTTCTATCTGGTATTGGTGTAGCAGAAACTCTAAATATTCCAA
131 TAAGACTCGCCATCCAATATGCTTTCTATCTGGTATCAGTGCAGCAGAAAAT-AAAATATACCAA
11657274 TCATAAGATACAGAGTAGATGGATGAGCGTGGAAATCGG
195 TCATAAGATACAGAGTAGATGGATGAGCGTGGAAATCGG
** *
11657313 GCAGGTTGAAAATTTGAGGAATAAATGAAAAGAGCTGTTTCTAATTAGTCCATTCAACTTCATTA
1 GCAGGTT-AAAAAATGAAGAATAAATGAAAAGAGCTGTTTCTAATTAGTCCATTCAACTTCATTA
* *
11657378 TAC-CAATAAACAAGTATTTATCAGCCATATAAAATTCACCATATGAAAGCACCTAACAGACAAT
65 TACTAAATAAACAAGTATTTAACAGCCATATAAAATTCACCATATGAAAGCACCTAACAGACAAT
* *
11657442 TTAAGAGTCGCCATCCAATAT-CTTTTCTATCTGGTATCAGTGCAGCAGAAAATAAAATATACTA
130 TTAAGACTCGCCATCCAATATGC-TTTCTATCTGGTATCAGTGCAGCAGAAAATAAAATATACCA
*
11657506 ATCATATGATACAGA
194 ATCATAAGATACAGA
11657521 AAAGATGAAT
Statistics
Matches: 182, Mismatches: 24, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
233 23 0.13
234 107 0.59
235 52 0.29
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (233 bp):
GCAGGTTAAAAAATGAAGAATAAATGAAAAGAGCTGTTTCTAATTAGTCCATTCAACTTCATTAT
ACTAAATAAACAAGTATTTAACAGCCATATAAAATTCACCATATGAAAGCACCTAACAGACAATT
TAAGACTCGCCATCCAATATGCTTTCTATCTGGTATCAGTGCAGCAGAAAATAAAATATACCAAT
CATAAGATACAGAGTAGATGGATGAGCGTGGAAATCGG
Found at i:11664431 original size:24 final size:24
Alignment explanation
Indices: 11664389--11664435 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
11664379 TTACTACTCG
*
11664389 TCCTCCTACTTCTGCTGCTACCCC
1 TCCTCCTACTTCAGCTGCTACCCC
11664413 TCCTCCTACTTCAAG-TGCTACCC
1 TCCTCCTACTTC-AGCTGCTACCC
11664436 TCCATGTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.13, C:0.47, G:0.09, T:0.32
Consensus pattern (24 bp):
TCCTCCTACTTCAGCTGCTACCCC
Found at i:11664667 original size:69 final size:69
Alignment explanation
Indices: 11664552--11664702 Score: 221
Period size: 69 Copynumber: 2.2 Consensus size: 69
11664542 ACAGACGAAT
* * * *
11664552 ATGCAGATGCAGATGTAGTCAATGCAGATGGAAATCCAGCAATCAATGCAATTGGAGATCTAGTG
1 ATGCAGATGCAGATGCAGTCAATGCAGATGGAAATCCAACAATCAATGCAATTGGAGATCCAGCG
11664617 GGCG
66 GGCG
* * * * *
11664621 ATGTAGATGTAGATGCAGTCAATGTAGTTGGAGATCCAACAATCAATGCAATTGGAGATCCAGCG
1 ATGCAGATGCAGATGCAGTCAATGCAGATGGAAATCCAACAATCAATGCAATTGGAGATCCAGCG
11664686 GGCG
66 GGCG
11664690 ATGCAGATGCAGA
1 ATGCAGATGCAGA
11664703 GGCAATCACT
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (69 bp):
ATGCAGATGCAGATGCAGTCAATGCAGATGGAAATCCAACAATCAATGCAATTGGAGATCCAGCG
GGCG
Found at i:11666298 original size:26 final size:25
Alignment explanation
Indices: 11666260--11666316 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 25
11666250 CATTATTCTG
* * *
11666260 TATCATCTCCATATTATTCTTTGTTA
1 TATCATTTACATACTATTCTTTG-TA
11666286 TATCATTTACATACTATTCTTTGTA
1 TATCATTTACATACTATTCTTTGTA
11666311 T-TCATT
1 TATCATT
11666317 CATGTGATAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 5 0.18
25 3 0.11
26 20 0.71
ACGTcount: A:0.25, C:0.18, G:0.04, T:0.54
Consensus pattern (25 bp):
TATCATTTACATACTATTCTTTGTA
Found at i:11666941 original size:23 final size:23
Alignment explanation
Indices: 11666915--11666971 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
11666905 TTCTTATTGA
* *
11666915 ATCGCGTGACTATATGATATGGG
1 ATCGCGTGACTAGATGATATGGC
* * *
11666938 ATCGCGTCACTAGATGATCTTGC
1 ATCGCGTGACTAGATGATATGGC
11666961 ATCGCGTGACT
1 ATCGCGTGACT
11666972 CACCTATTCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (23 bp):
ATCGCGTGACTAGATGATATGGC
Found at i:11668884 original size:31 final size:31
Alignment explanation
Indices: 11668846--11668909 Score: 112
Period size: 32 Copynumber: 2.1 Consensus size: 31
11668836 ACATTTCAAA
11668846 GCAAAGCATGG-TTTTTGGGGTTGAGGGTCT
1 GCAAAGCATGGTTTTTTGGGGTTGAGGGTCT
11668876 NGCAAAGCATGGTTTTTTGGGGTTGAGGGTCT
1 -GCAAAGCATGGTTTTTTGGGGTTGAGGGTCT
11668908 GC
1 GC
11668910 TGCTTCTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 13 0.41
32 19 0.59
ACGTcount: A:0.16, C:0.11, G:0.39, T:0.33
Consensus pattern (31 bp):
GCAAAGCATGGTTTTTTGGGGTTGAGGGTCT
Found at i:11669014 original size:13 final size:12
Alignment explanation
Indices: 11668996--11669029 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
11668986 AAATCTCCCA
11668996 TTCTTCTTTTTCT
1 TTCTTCTTTTT-T
11669009 TTCTTCTTTTTT
1 TTCTTCTTTTTT
11669021 TATCTTCTT
1 T-TCTTCTT
11669030 CTTGTATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 2 0.10
13 18 0.90
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (12 bp):
TTCTTCTTTTTT
Found at i:11674873 original size:111 final size:110
Alignment explanation
Indices: 11674599--11675029 Score: 429
Period size: 111 Copynumber: 3.8 Consensus size: 110
11674589 AATATATAAT
* * * * *
11674599 AACAAGTCACGTAATACATAAAAATCAGTAATGCAATCCTAAAAAACTACTGAACAAAAGCCTCT
1 AACAAGTAACGCAATATATAAAAATCAGTCACGCAA-CCTAAAAAACTACTGAACAAAAGCCTCT
* * ** *
11674664 AAACAACACATGAATTGCACATGTCACATTCAACCACTCTCGCAATACATAAC
65 AAACAACACATGAATTGCACAAGTCATACGCCACCA-TCT-----TACAT-AC
* * * *
11674717 AACAAGTAACGCAATATATAAAAATCGGTCACGCAACTGTTAAAAACTACTGAACAAAAGCCTTT
1 AACAAGTAACGCAATATATAAAAATCAGTCACGCAAC-CTAAAAAACTACTGAACAAAAGCCTCT
* * *
11674782 AAACAATACATGAATTACACAAGTCATGCGCCACCAT-TTACAGTAC
65 AAACAACACATGAATTGCACAAGTCATACGCCACCATCTTACA-TAC
* * * *
11674828 AACAAGTAACGCAATATATAAAAATCAGTCACGCAAGCCTAAAAAATTATTGAAGAAAAGCCTCA
1 AACAAGTAACGCAATATATAAAAATCAGTCACGCAA-CCTAAAAAACTACTGAACAAAAGCCTCT
* * * *
11674893 AAACAGCACATGAATTGCAC-AGTCACACGCCCCCACTCTTGC-TAC
65 AAACAACACATGAATTGCACAAGTCATACGCCACCA-TCTTACATAC
** *
11674938 AACAAGTAACGCAATATATAAAAATCAGTCACGCACTATTTAAAAAACTACTGAACAAAAGTCTC
1 AACAAGTAACGCAATATATAAAAATCAGTCACGCA--ACCTAAAAAACTACTGAACAAAAGCCTC
* *
11675003 -AAAGCAACACATAAATTGCATAAGTCA
64 TAAA-CAACACATGAATTGCACAAGTCA
11675030 GTCATGTACT
Statistics
Matches: 263, Mismatches: 41, Indels: 24
0.80 0.12 0.07
Matches are distributed among these distances:
110 53 0.20
111 114 0.43
112 11 0.04
116 1 0.00
117 2 0.01
118 82 0.31
ACGTcount: A:0.45, C:0.24, G:0.11, T:0.20
Consensus pattern (110 bp):
AACAAGTAACGCAATATATAAAAATCAGTCACGCAACCTAAAAAACTACTGAACAAAAGCCTCTA
AACAACACATGAATTGCACAAGTCATACGCCACCATCTTACATAC
Found at i:11675701 original size:30 final size:30
Alignment explanation
Indices: 11675665--11675721 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
11675655 TCTCCTGCTG
*
11675665 GAATATGTGCAACTGGTCCCTCGCACTCAA
1 GAATATGTGCAACTGGTCCCTCACACTCAA
*
11675695 GAATATGTGCAATTGGTCCCTCACACT
1 GAATATGTGCAACTGGTCCCTCACACT
11675722 TAAAGGCACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.26
Consensus pattern (30 bp):
GAATATGTGCAACTGGTCCCTCACACTCAA
Found at i:11679629 original size:190 final size:190
Alignment explanation
Indices: 11679300--11679676 Score: 619
Period size: 190 Copynumber: 2.0 Consensus size: 190
11679290 GCGCCGCAGT
* * * *
11679300 GCTCCACTTTTCTATTTTAGGGCCATTGTTCAGTGCCGCGGCTCTCCCTTTGAGGGCCCCGATGC
1 GCTCAACTTTTCTATTTTAGGGCCATTGTTCAGTGCCGCGGCACTCCCTTTAAGGGCCACGATGC
* * * * ** * *
11679365 TGAAATATTCTGTTCCAACGGCTATTTTTTTGCTTAGTCCAGCGCTGTGGCTCTTCTTTTGAGAG
66 TGAAACATTATGTTCCAACGGCTATTTTTTTGCTTAATCAAAAGCTGTGGCTCTCCCTTTGAGAG
* *
11679430 TCTCGACGCTGAAACATTCTGTTTCAGCTACTGTCTCTTGCATATTTTAGGGTCACGAGC
131 TCGCGACGCTGAAACATTCTGTTTCAGCTACTGTCTCTTGCATATTTCAGGGTCACGAGC
*
11679490 GCTCAACTTTTCTATTTTAGGGCCATTGTTCAGTGCTGCGGCACTCCCTTTAAGGGCCACGATGC
1 GCTCAACTTTTCTATTTTAGGGCCATTGTTCAGTGCCGCGGCACTCCCTTTAAGGGCCACGATGC
11679555 TGAAACATTATGTTCCAACGGCTATTTTTTTGCTTAATCAAAAGCTGTGGCTCTCCCTTTGAGAG
66 TGAAACATTATGTTCCAACGGCTATTTTTTTGCTTAATCAAAAGCTGTGGCTCTCCCTTTGAGAG
11679620 TCGCGACGCTGAAACATTCTGTTTCAGCTACTGTCTCTTGCATATTTCAGGGTCACG
131 TCGCGACGCTGAAACATTCTGTTTCAGCTACTGTCTCTTGCATATTTCAGGGTCACG
11679677 GCTTTCAATT
Statistics
Matches: 172, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
190 172 1.00
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.35
Consensus pattern (190 bp):
GCTCAACTTTTCTATTTTAGGGCCATTGTTCAGTGCCGCGGCACTCCCTTTAAGGGCCACGATGC
TGAAACATTATGTTCCAACGGCTATTTTTTTGCTTAATCAAAAGCTGTGGCTCTCCCTTTGAGAG
TCGCGACGCTGAAACATTCTGTTTCAGCTACTGTCTCTTGCATATTTCAGGGTCACGAGC
Found at i:11682652 original size:14 final size:14
Alignment explanation
Indices: 11682635--11682661 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11682625 CAAAATTAAT
11682635 TAATTAACTAAAAC
1 TAATTAACTAAAAC
11682649 TAATTAACTAAAA
1 TAATTAACTAAAA
11682662 TTAAAACCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (14 bp):
TAATTAACTAAAAC
Found at i:11684402 original size:48 final size:48
Alignment explanation
Indices: 11684332--11684506 Score: 151
Period size: 48 Copynumber: 3.5 Consensus size: 48
11684322 GTAACGCCTA
*
11684332 TCATGCAA--CTCTAACAAATATTCAGTCACGTAATGCCTATAAAGAAC
1 TCATGCAATGCTC-AACAAATATTCAATCACGTAATGCCTATAAAGAAC
* ** *
11684379 TCATGCAATGCTCAACAAATATTCAATCAGGTAAT-ATTCAGTCACATATTAAC
1 TCATGCAATGCTCAACAAATATTCAATCACGTAATGCCT-A-T-A-A-A-GAAC
* *
11684432 TGTCATGCAACGCTCAACATAA-ATTCAATCACATAATGCCTATAAAGAAC
1 --TCATGCAATGCTCAACA-AATATTCAATCACGTAATGCCTATAAAGAAC
* *
11684482 TCACGCAATGCTCAATAAATATTCA
1 TCATGCAATGCTCAACAAATATTCA
11684507 GGCACCTAAT
Statistics
Matches: 101, Mismatches: 14, Indels: 25
0.72 0.10 0.18
Matches are distributed among these distances:
47 11 0.11
48 40 0.40
49 4 0.04
50 4 0.04
51 2 0.02
52 2 0.02
53 4 0.04
54 1 0.01
55 30 0.30
56 3 0.03
ACGTcount: A:0.41, C:0.23, G:0.10, T:0.27
Consensus pattern (48 bp):
TCATGCAATGCTCAACAAATATTCAATCACGTAATGCCTATAAAGAAC
Found at i:11684438 original size:102 final size:103
Alignment explanation
Indices: 11684277--11684506 Score: 302
Period size: 102 Copynumber: 2.2 Consensus size: 103
11684267 TACAAATAGG
* ** ** *
11684277 TCACGCAATGCTCAACAAATATTCAGTCACGTAATATTAAGTCAGGTAACGCCTATCATGCAACT
1 TCACGCAATGCTCAACAAATATTCAATCACGTAATATTAAGTCACATAACAACTATCATGCAACG
* *
11684342 CT-AACA-AATATTCAGTCACGTAATGCCTATAAAGAAC
66 CTCAACATAA-ATTCAATCACATAATGCCTATAAAGAAC
* * * ** *
11684379 TCATGCAATGCTCAACAAATATTCAATCAGGTAATATTCAGTCACATATTAACTGTCATGCAACG
1 TCACGCAATGCTCAACAAATATTCAATCACGTAATATTAAGTCACATAACAACTATCATGCAACG
11684444 CTCAACATAAATTCAATCACATAATGCCTATAAAGAAC
66 CTCAACATAAATTCAATCACATAATGCCTATAAAGAAC
*
11684482 TCACGCAATGCTCAATAAATATTCA
1 TCACGCAATGCTCAACAAATATTCA
11684507 GGCACCTAAT
Statistics
Matches: 110, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
102 55 0.50
103 53 0.48
104 2 0.02
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.27
Consensus pattern (103 bp):
TCACGCAATGCTCAACAAATATTCAATCACGTAATATTAAGTCACATAACAACTATCATGCAACG
CTCAACATAAATTCAATCACATAATGCCTATAAAGAAC
Found at i:11689008 original size:101 final size:101
Alignment explanation
Indices: 11688832--11689033 Score: 271
Period size: 101 Copynumber: 2.0 Consensus size: 101
11688822 ATGCCCTAGG
* ** * * *** *
11688832 ATGAGATGTGAATACATCATTGGTTGTAAACGTTGCTTATGTCAATATTATTATACTTCTGGTAT
1 ATGAGATATGAATACATCATTGGTCATAAACCTTGCTTATGTCAACATTATTATACTTCCAATAC
* *
11688897 ATTAAATTTTTGTTTTAAATTTACTGTTTTATGGTA
66 ATCAAATTTTTGTTTTAAATTCACTGTTTTATGGTA
* *
11688933 ATGAGATATTAATCCATCATTGGTCATAAACCTTGCTTATGTCAACATTATTATACTTCCAATAC
1 ATGAGATATGAATACATCATTGGTCATAAACCTTGCTTATGTCAACATTATTATACTTCCAATAC
11688998 A-CAAATTTTTTGTTTTAAATTCACTGTTTTATGGTA
66 ATCAAA-TTTTTGTTTTAAATTCACTGTTTTATGGTA
11689034 TTTAAAAGAT
Statistics
Matches: 87, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
100 3 0.03
101 84 0.97
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (101 bp):
ATGAGATATGAATACATCATTGGTCATAAACCTTGCTTATGTCAACATTATTATACTTCCAATAC
ATCAAATTTTTGTTTTAAATTCACTGTTTTATGGTA
Found at i:11691263 original size:2 final size:2
Alignment explanation
Indices: 11691256--11691280 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11691246 TCATACATAC
11691256 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
11691281 AACAATTCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11693678 original size:41 final size:40
Alignment explanation
Indices: 11693608--11693685 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 40
11693598 AAATAAATAA
*
11693608 AACTTCTACCATTTGATAAAAAAGTGACAACCAATAAGAGT
1 AACTTCTACCATTAGATAAAAAAG-GACAACCAATAAGAGT
* *
11693649 AACTTCTACCATCTAAGCTAAAAAA-GACAACTAATAA
1 AACTTCTACCAT-T-AGATAAAAAAGGACAACCAATAA
11693686 AAGTTAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
41 23 0.72
42 1 0.03
43 8 0.25
ACGTcount: A:0.49, C:0.19, G:0.09, T:0.23
Consensus pattern (40 bp):
AACTTCTACCATTAGATAAAAAAGGACAACCAATAAGAGT
Found at i:11702408 original size:2 final size:2
Alignment explanation
Indices: 11702396--11702485 Score: 101
Period size: 2 Copynumber: 45.0 Consensus size: 2
11702386 TAATACATAG
*
11702396 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * ** *
11702438 A- AA AG ANN NN NT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11702480 AT AT AT
1 AT AT AT
11702486 GAAAAGATTA
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.01
2 78 0.99
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.46
Consensus pattern (2 bp):
AT
Found at i:11711047 original size:23 final size:23
Alignment explanation
Indices: 11711017--11711062 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
11711007 TAGAATAACA
*
11711017 ATTCCTAATTCTATTAGGATAAG
1 ATTCCTAATTATATTAGGATAAG
11711040 ATTCCTAATTATATTAGGATAAG
1 ATTCCTAATTATATTAGGATAAG
11711063 GTTATTGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (23 bp):
ATTCCTAATTATATTAGGATAAG
Found at i:11717212 original size:23 final size:23
Alignment explanation
Indices: 11717173--11717229 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
11717163 TATAATATAA
*
11717173 AAAATTATATTAAAAAATGAAAA-T
1 AAAA-TATATAAAAAAAT-AAAAGT
11717197 AAAATATATAATAAAAATAAAAGT
1 AAAATATATAA-AAAAATAAAAGT
11717221 AAAATATAT
1 AAAATATAT
11717230 GATATTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 10 0.33
24 20 0.67
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (23 bp):
AAAATATATAAAAAAATAAAAGT
Found at i:11717480 original size:15 final size:15
Alignment explanation
Indices: 11717443--11717482 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
11717433 ATATTATTTT
*
11717443 TTTATAACTACATTA
1 TTTATAATTACATTA
*
11717458 CTTATAATTACATTA
1 TTTATAATTACATTA
11717473 TTTATAATTA
1 TTTATAATTA
11717483 TACTACATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTATAATTACATTA
Found at i:11725950 original size:26 final size:26
Alignment explanation
Indices: 11725909--11725958 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
11725899 CTTTAGGATC
11725909 TTGTTTTTCTTCTTTTCG-GTTTAAGA
1 TTGTTTTTCTTCTTTT-GAGTTTAAGA
* *
11725935 TTGTTTTTTTTTTTTTGAGTTTAA
1 TTGTTTTTCTTCTTTTGAGTTTAA
11725959 AGTGTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 20 0.95
ACGTcount: A:0.12, C:0.06, G:0.14, T:0.68
Consensus pattern (26 bp):
TTGTTTTTCTTCTTTTGAGTTTAAGA
Found at i:11727575 original size:15 final size:15
Alignment explanation
Indices: 11727555--11727585 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11727545 CACCCTCTCA
*
11727555 AAGAAAAAGAAGAAG
1 AAGAAAAAGAAAAAG
11727570 AAGAAAAAGAAAAAG
1 AAGAAAAAGAAAAAG
11727585 A
1 A
11727586 CTGCAGCTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAGAAAAAGAAAAAG
Found at i:11737321 original size:2 final size:2
Alignment explanation
Indices: 11737303--11737356 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
11737293 TACATACAAC
* *
11737303 AT AT AT -T AT AA AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11737344 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
11737357 GAGTAGTCCT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Done.