Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 56 of 136
Found at i:18448790 original size:37 final size:37
Alignment explanation
Indices: 18448735--18448805 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
18448725 TTTAAATTAC
*
18448735 AAGTATATGGTTACTTGATATGTG-AGCGAAAATGAAT
1 AAGTATATGGTTACTTGATATATGTA-CGAAAATGAAT
*
18448772 AAGTATATGGTTATTTGATATATGTACGAAAATG
1 AAGTATATGGTTACTTGATATATGTACGAAAATG
18448806 TTCAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 30 0.97
38 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (37 bp):
AAGTATATGGTTACTTGATATATGTACGAAAATGAAT
Found at i:18449155 original size:95 final size:95
Alignment explanation
Indices: 18448986--18449161 Score: 230
Period size: 95 Copynumber: 1.9 Consensus size: 95
18448976 TCCGATAGTG
* * * *
18448986 GATACCTTACTGATGGCTAAGATTCTGCATATAATACTTATTCTTCACAGCTCATATGAGTAGCA
1 GATACCTTACCGATGGCTAAGATTCTGCATATAATACTTATTCTTCACAGCTAATATGAGCAACA
*
18449051 TCATTTAATGGTTAATGTCCCAATTTACTA
66 TCATGTAATGGTTAATGTCCCAATTTACTA
* * * *
18449081 GATACCTTACCGATGGCTAAGATTCTGCATGT-GT-TTTGAATTCTTCACAGCTAATGTGAGCAA
1 GATACCTTACCGATGGCTAAGATTCTGCATATAATACTT--ATTCTTCACAGCTAATATGAGCAA
*
18449144 CATCGTGTAATGGTTAAT
64 CATCATGTAATGGTTAAT
18449162 AGTCAATTCA
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
93 2 0.03
94 1 0.01
95 66 0.96
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (95 bp):
GATACCTTACCGATGGCTAAGATTCTGCATATAATACTTATTCTTCACAGCTAATATGAGCAACA
TCATGTAATGGTTAATGTCCCAATTTACTA
Found at i:18450363 original size:26 final size:26
Alignment explanation
Indices: 18450325--18450377 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
18450315 TTGAGGTGTC
18450325 AATTGTGGCATATTGGTTAGGCACTT
1 AATTGTGGCATATTGGTTAGGCACTT
*
18450351 AATTGTGGGATATTGGTTAGGCACTT
1 AATTGTGGCATATTGGTTAGGCACTT
18450377 A
1 A
18450378 GGATGAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.25, C:0.09, G:0.28, T:0.38
Consensus pattern (26 bp):
AATTGTGGCATATTGGTTAGGCACTT
Found at i:18455545 original size:29 final size:29
Alignment explanation
Indices: 18455500--18455618 Score: 116
Period size: 29 Copynumber: 4.1 Consensus size: 29
18455490 GTGTTAAATA
* * * *
18455500 ATGGTCGTAACCGTCCCTTTCCATATTCG
1 ATGGTCGAAACCATCCCTTTTCATAATCG
18455529 ATGGTCGAAACCATCCCTTTTCATTAATC-
1 ATGGTCGAAACCATCCCTTTTCA-TAATCG
* **
18455558 AGTGGTTGTCACCATCCCTTTTCATAATCG
1 A-TGGTCGAAACCATCCCTTTTCATAATCG
* *
18455588 ATAG-CTGAAACTATCCCTTTTCATAATCG
1 ATGGTC-GAAACCATCCCTTTTCATAATCG
18455617 AT
1 AT
18455619 AACCAAATCT
Statistics
Matches: 74, Mismatches: 12, Indels: 8
0.79 0.13 0.09
Matches are distributed among these distances:
29 50 0.68
30 24 0.32
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.35
Consensus pattern (29 bp):
ATGGTCGAAACCATCCCTTTTCATAATCG
Found at i:18455666 original size:29 final size:29
Alignment explanation
Indices: 18455571--18455659 Score: 126
Period size: 29 Copynumber: 3.1 Consensus size: 29
18455561 GGTTGTCACC
*
18455571 ATCCCTTTTCATAATCGATAGCTGAAACT
1 ATCCCTTTTCATAATCGATAGCCGAAACT
*
18455600 ATCCCTTTTCATAATCGATAACC-AAATCT
1 ATCCCTTTTCATAATCGATAGCCGAAA-CT
* *
18455629 ATCCCTTTTCATATTCGATAGCCGAAGCT
1 ATCCCTTTTCATAATCGATAGCCGAAACT
18455658 AT
1 AT
18455660 TGCTTTTTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
28 3 0.06
29 48 0.91
30 2 0.04
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (29 bp):
ATCCCTTTTCATAATCGATAGCCGAAACT
Found at i:18460219 original size:34 final size:34
Alignment explanation
Indices: 18460176--18460242 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
18460166 CAAGTATATT
* *
18460176 AAATAATAATTACTTATATT-AAATAAATAAATA
1 AAATAATAATTAATTAAATTAAAATAAATAAATA
*
18460209 AAATATATAATTAATTAAATTAAAATAATTAAAT
1 AAATA-ATAATTAATTAAATTAAAATAAATAAAT
18460243 CTATAAATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 5 0.17
34 13 0.45
35 11 0.38
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (34 bp):
AAATAATAATTAATTAAATTAAAATAAATAAATA
Found at i:18461440 original size:10 final size:10
Alignment explanation
Indices: 18461423--18461514 Score: 54
Period size: 10 Copynumber: 9.6 Consensus size: 10
18461413 TTGTAAACAA
18461423 TATTAATATAT
1 TATTAATA-AT
18461434 T-TTAATAAT
1 TATTAATAAT
*
18461443 TATTAATAAA
1 TATTAATAAT
*
18461453 TATAAATAA-
1 TATTAATAAT
18461462 TA--AA-AA-
1 TATTAATAAT
* *
18461468 TACTAAAAAT
1 TATTAATAAT
18461478 TATTAAATAAT
1 TATT-AATAAT
* *
18461489 TATAAAT-GT
1 TATTAATAAT
18461498 TATTAAATAAT
1 TATT-AATAAT
18461509 TATTAA
1 TATTAA
18461515 AAAAAGCGGA
Statistics
Matches: 65, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
6 4 0.06
7 2 0.03
8 2 0.03
9 11 0.17
10 32 0.49
11 14 0.22
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (10 bp):
TATTAATAAT
Found at i:18461491 original size:11 final size:11
Alignment explanation
Indices: 18461471--18461515 Score: 60
Period size: 10 Copynumber: 4.4 Consensus size: 11
18461461 ATAAAAATAC
18461471 TAAA-AATTAT
1 TAAATAATTAT
18461481 TAAATAATTA-
1 TAAATAATTAT
*
18461491 TAAAT-GTTAT
1 TAAATAATTAT
18461501 TAAATAATTAT
1 TAAATAATTAT
18461512 TAAA
1 TAAA
18461516 AAAAGCGGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
9 3 0.10
10 14 0.47
11 13 0.43
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (11 bp):
TAAATAATTAT
Found at i:18465175 original size:64 final size:64
Alignment explanation
Indices: 18465097--18465225 Score: 249
Period size: 64 Copynumber: 2.0 Consensus size: 64
18465087 TTTTTTCAAT
18465097 TATTTGTACAAATTAATTAAGCTCATGTTATTACATCAAAAAATATCAAAATAACTCAAAAAAA
1 TATTTGTACAAATTAATTAAGCTCATGTTATTACATCAAAAAATATCAAAATAACTCAAAAAAA
*
18465161 TATTTGTACAAATTAATTAAGCTCATGTTATTACATCAAATAATATCAAAATAACTCAAAAAAA
1 TATTTGTACAAATTAATTAAGCTCATGTTATTACATCAAAAAATATCAAAATAACTCAAAAAAA
18465225 T
1 T
18465226 TCTATTTTAT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (64 bp):
TATTTGTACAAATTAATTAAGCTCATGTTATTACATCAAAAAATATCAAAATAACTCAAAAAAA
Found at i:18465250 original size:25 final size:25
Alignment explanation
Indices: 18465216--18465367 Score: 183
Period size: 25 Copynumber: 6.3 Consensus size: 25
18465206 TCAAAATAAC
18465216 TCAAA-AAAATTCTATTTTATTACA
1 TCAAATAAAATTCTATTTTATTACA
18465240 TCAAATAAAATTCTATTTTATTACA
1 TCAAATAAAATTCTATTTTATTACA
*
18465265 TCAAATAAACTTCTATTTTATTACA
1 TCAAATAAAATTCTATTTTATTACA
* ** *
18465290 TCAAATAATA-TC-A--AAATAAC-
1 TCAAATAAAATTCTATTTTATTACA
*
18465310 TCAAA-AAAATTTCTAATTTATTACA
1 TCAAATAAAA-TTCTATTTTATTACA
*
18465335 TCAAATAAACTTCTATTTTATTACA
1 TCAAATAAAATTCTATTTTATTACA
18465360 TCAAATAA
1 TCAAATAA
18465368 CACAAAAAAA
Statistics
Matches: 108, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
19 3 0.03
20 5 0.05
21 6 0.06
22 1 0.01
23 1 0.01
24 11 0.10
25 78 0.72
26 3 0.03
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (25 bp):
TCAAATAAAATTCTATTTTATTACA
Found at i:18465330 original size:45 final size:44
Alignment explanation
Indices: 18465188--18465342 Score: 193
Period size: 45 Copynumber: 3.4 Consensus size: 44
18465178 TAAGCTCATG
18465188 TTATTACATCAAATAATATCAAAATAACTCAAAAAAATTCTATT
1 TTATTACATCAAATAATATCAAAATAACTCAAAAAAATTCTATT
* ** * *
18465232 TTATTACATCAAATAAAATTCTATTTTATTACATCAAATAAACTTCTATT
1 TTATTACATCAAATAATA-TC-A--AAATAAC-TCAAA-AAAATTCTATT
*
18465282 TTATTACATCAAATAATATCAAAATAACTCAAAAAAATTTCTAAT
1 TTATTACATCAAATAATATCAAAATAACTCAAAAAAA-TTCTATT
18465327 TTATTACATCAAATAA
1 TTATTACATCAAATAA
18465343 ACTTCTATTT
Statistics
Matches: 93, Mismatches: 11, Indels: 13
0.79 0.09 0.11
Matches are distributed among these distances:
44 20 0.22
45 29 0.31
46 5 0.05
48 5 0.05
49 7 0.08
50 27 0.29
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (44 bp):
TTATTACATCAAATAATATCAAAATAACTCAAAAAAATTCTATT
Found at i:18465354 original size:95 final size:94
Alignment explanation
Indices: 18465188--18465367 Score: 333
Period size: 95 Copynumber: 1.9 Consensus size: 94
18465178 TAAGCTCATG
*
18465188 TTATTACATCAAATAATATCAAAATAACTCAAAAAAATTCTATTTTATTACATCAAATAAAATTC
1 TTATTACATCAAATAATATCAAAATAACTCAAAAAAATTCTAATTTATTACATCAAATAAAATTC
18465253 TATTTTATTACATCAAATAAACTTCTATT
66 TATTTTATTACATCAAATAAACTTCTATT
*
18465282 TTATTACATCAAATAATATCAAAATAACTCAAAAAAATTTCTAATTTATTACATCAAATAAACTT
1 TTATTACATCAAATAATATCAAAATAACTCAAAAAAA-TTCTAATTTATTACATCAAATAAAATT
18465347 CTATTTTATTACATCAAATAA
65 CTATTTTATTACATCAAATAA
18465368 CACAAAAAAA
Statistics
Matches: 83, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
94 37 0.45
95 46 0.55
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (94 bp):
TTATTACATCAAATAATATCAAAATAACTCAAAAAAATTCTAATTTATTACATCAAATAAAATTC
TATTTTATTACATCAAATAAACTTCTATT
Found at i:18465852 original size:18 final size:18
Alignment explanation
Indices: 18465829--18465868 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
18465819 GACTCGGAAA
*
18465829 AGGATACATATAAGGGTT
1 AGGATACATATAAGGGCT
18465847 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
18465865 AGGA
1 AGGA
18465869 AACGTACCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.30, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:18466739 original size:20 final size:20
Alignment explanation
Indices: 18466702--18466739 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
18466692 TTTATTTTTA
*
18466702 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
18466722 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
18466740 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:18480709 original size:16 final size:16
Alignment explanation
Indices: 18480688--18480720 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
18480678 AACCTTGAAT
18480688 GGTTACATTAAAAATG
1 GGTTACATTAAAAATG
18480704 GGTTACATTAAAAATG
1 GGTTACATTAAAAATG
18480720 G
1 G
18480721 ATCATAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.30
Consensus pattern (16 bp):
GGTTACATTAAAAATG
Found at i:18481075 original size:26 final size:26
Alignment explanation
Indices: 18481027--18481089 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
18481017 CCTGTAAGTG
18481027 TTCTGAAACTAATACATGCTATGATA
1 TTCTGAAACTAATACATGCTATGATA
* * *
18481053 TTCTGAAACTGATATATGTTATGATA
1 TTCTGAAACTAATACATGCTATGATA
*
18481079 TTCTAAAACTA
1 TTCTGAAACTA
18481090 GTGTAGGTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (26 bp):
TTCTGAAACTAATACATGCTATGATA
Found at i:18491567 original size:25 final size:25
Alignment explanation
Indices: 18491539--18491594 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
18491529 TATGCTAACT
* * *
18491539 CAAGCTATAGATCGGTCTGCTCTCA
1 CAAGCTATAAATCAGTATGCTCTCA
18491564 CAAGCTATAAATCAGTATGCTCTCA
1 CAAGCTATAAATCAGTATGCTCTCA
*
18491589 CGAGCT
1 CAAGCT
18491595 GTGGGTCGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (25 bp):
CAAGCTATAAATCAGTATGCTCTCA
Found at i:18498081 original size:64 final size:64
Alignment explanation
Indices: 18497980--18498130 Score: 266
Period size: 64 Copynumber: 2.4 Consensus size: 64
18497970 AACACATACT
*
18497980 CAACAATAATGAATTAGAAAATGGTAGCATACTACATCTAAAATTACGGCACAAATCAGGTTTC
1 CAACAATAATGAATTAGAAAATGGCAGCATACTACATCTAAAATTACGGCACAAATCAGGTTTC
* *
18498044 CAACAATAATGAATTAGAAAATGGCAGCATACTACATCTAAACTTACGGCACAAATCGGGTTTC
1 CAACAATAATGAATTAGAAAATGGCAGCATACTACATCTAAAATTACGGCACAAATCAGGTTTC
*
18498108 CAACAATAATGAATCAGAAAATG
1 CAACAATAATGAATTAGAAAATG
18498131 ACATTTCTAT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 83 1.00
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.23
Consensus pattern (64 bp):
CAACAATAATGAATTAGAAAATGGCAGCATACTACATCTAAAATTACGGCACAAATCAGGTTTC
Found at i:18506612 original size:21 final size:21
Alignment explanation
Indices: 18506588--18506630 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
18506578 TAGAACTACA
*
18506588 ATCA-AAGCAAGATGCATCCAC
1 ATCAGAAGC-AGATGCAGCCAC
*
18506609 ATCAGAATCAGATGCAGCCAC
1 ATCAGAAGCAGATGCAGCCAC
18506630 A
1 A
18506631 ACACTCTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.42, C:0.28, G:0.16, T:0.14
Consensus pattern (21 bp):
ATCAGAAGCAGATGCAGCCAC
Found at i:18508414 original size:16 final size:17
Alignment explanation
Indices: 18508393--18508427 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
18508383 AATTAGAGGA
*
18508393 GGGATTTTTG-GGATTT
1 GGGATTGTTGCGGATTT
18508409 GGGATTGTTGCGGATTT
1 GGGATTGTTGCGGATTT
18508426 GG
1 GG
18508428 TGAGAGTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.11, C:0.03, G:0.43, T:0.43
Consensus pattern (17 bp):
GGGATTGTTGCGGATTT
Found at i:18509531 original size:54 final size:54
Alignment explanation
Indices: 18509384--18509666 Score: 333
Period size: 54 Copynumber: 5.3 Consensus size: 54
18509374 AGACCCCAAA
** * *
18509384 ATAGGGTAAAACAACTAAAATACCCCTAT-AGGATAAAATGATCGAAATACCCCT
1 ATAGGGTAAAATGACCAAAATACCCCTATAAGG-TAAAATGATCGAAATACCCCC
* * * *
18509438 ACA-GGTAAAATGACCAAAATACCCCTATAGGGTAGAATGATCAAAATACCCCC
1 ATAGGGTAAAATGACCAAAATACCCCTATAAGGTAAAATGATCGAAATACCCCC
* * * * *
18509491 ATAGGGTAAAATGACTAAAATACCCCCATAAGGTAAAATGACCGAAATATCCCT
1 ATAGGGTAAAATGACCAAAATACCCCTATAAGGTAAAATGATCGAAATACCCCC
* * *
18509545 ATAGGGTAAAATGACCAAAATACCCCTATAGGGTAAAATGAACAAAATACCCCC
1 ATAGGGTAAAATGACCAAAATACCCCTATAAGGTAAAATGATCGAAATACCCCC
* * *
18509599 ATAGGGTAAAATGACCGAAATAACACC-ATAAGGTAGAAA-GATCGAAATA-CTCC
1 ATAGGGTAAAATGACCAAAAT-ACCCCTATAAGGTA-AAATGATCGAAATACCCCC
18509652 ATAGGGTAAAATGAC
1 ATAGGGTAAAATGAC
18509667 TGTTATACCC
Statistics
Matches: 195, Mismatches: 30, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
53 60 0.31
54 128 0.66
55 7 0.04
ACGTcount: A:0.46, C:0.20, G:0.16, T:0.18
Consensus pattern (54 bp):
ATAGGGTAAAATGACCAAAATACCCCTATAAGGTAAAATGATCGAAATACCCCC
Found at i:18509619 original size:27 final size:27
Alignment explanation
Indices: 18509384--18509666 Score: 302
Period size: 27 Copynumber: 10.6 Consensus size: 27
18509374 AGACCCCAAA
** * *
18509384 ATAGGGTAAAACAACTAAAATACCCCT
1 ATAGGGTAAAATGACCAAAATACCCCC
* * * *
18509411 ATAGGATAAAATGATCGAAATACCCCT
1 ATAGGGTAAAATGACCAAAATACCCCC
* *
18509438 ACA-GGTAAAATGACCAAAATACCCCT
1 ATAGGGTAAAATGACCAAAATACCCCC
* *
18509464 ATAGGGTAGAATGATCAAAATACCCCC
1 ATAGGGTAAAATGACCAAAATACCCCC
*
18509491 ATAGGGTAAAATGACTAAAATACCCCC
1 ATAGGGTAAAATGACCAAAATACCCCC
* * * *
18509518 ATAAGGTAAAATGACCGAAATATCCCT
1 ATAGGGTAAAATGACCAAAATACCCCC
*
18509545 ATAGGGTAAAATGACCAAAATACCCCT
1 ATAGGGTAAAATGACCAAAATACCCCC
*
18509572 ATAGGGTAAAATGAACAAAATACCCCC
1 ATAGGGTAAAATGACCAAAATACCCCC
* * *
18509599 ATAGGGTAAAATGACCGAAATAACACC
1 ATAGGGTAAAATGACCAAAATACCCCC
* * * *
18509626 ATAAGGTAGAAA-GATCGAAATA-CTCC
1 ATAGGGTA-AAATGACCAAAATACCCCC
18509652 ATAGGGTAAAATGAC
1 ATAGGGTAAAATGAC
18509667 TGTTATACCC
Statistics
Matches: 217, Mismatches: 36, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
25 3 0.01
26 34 0.16
27 177 0.82
28 3 0.01
ACGTcount: A:0.46, C:0.20, G:0.16, T:0.18
Consensus pattern (27 bp):
ATAGGGTAAAATGACCAAAATACCCCC
Found at i:18518021 original size:19 final size:19
Alignment explanation
Indices: 18517997--18518035 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
18517987 TTGTGAGCAC
18517997 TTAGCATTCTATTGAATAT
1 TTAGCATTCTATTGAATAT
18518016 TTAGCATTCTATTGAATAT
1 TTAGCATTCTATTGAATAT
18518035 T
1 T
18518036 CACGTTGGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (19 bp):
TTAGCATTCTATTGAATAT
Found at i:18524665 original size:33 final size:33
Alignment explanation
Indices: 18524604--18524894 Score: 269
Period size: 33 Copynumber: 8.8 Consensus size: 33
18524594 TGGAATCCAT
* * * * *
18524604 AGAGGTAGTCTGTTGCGATAGTAAACACAGAAC
1 AGAGATAGTCCGTTGGGACAGTAAACACATAAC
* *** *
18524637 AAAGATAGTTTATTGGGACAGTAAACACATAAT
1 AGAGATAGTCCGTTGGGACAGTAAACACATAAC
* *
18524670 AGAGATAGTCTGCTGGGACAGTAAACACATAAC
1 AGAGATAGTCCGTTGGGACAGTAAACACATAAC
* * * * * *
18524703 AGAGATAGTTCATTGTGATAGTAAACACAGAAT
1 AGAGATAGTCCGTTGGGACAGTAAACACATAAC
*
18524736 AGAGATAGTCCGTTGGGACAATAAACACA-ACAC
1 AGAGATAGTCCGTTGGGACAGTAAACACATA-AC
* * * * * *
18524769 AAAGATAGTCCGCTAGGATAATAAACACATGAC
1 AGAGATAGTCCGTTGGGACAGTAAACACATAAC
* *
18524802 AGAGATAGTCCGTTAGGATAGTAAACACATAAC
1 AGAGATAGTCCGTTGGGACAGTAAACACATAAC
* *
18524835 AGAGATAGTCTGTTGGGACAGTAAATACATAAC
1 AGAGATAGTCCGTTGGGACAGTAAACACATAAC
* * * *
18524868 AAAAATAGTCTGTTGGGACAATAAACA
1 AGAGATAGTCCGTTGGGACAGTAAACA
18524895 TATATAGAGT
Statistics
Matches: 212, Mismatches: 44, Indels: 4
0.82 0.17 0.02
Matches are distributed among these distances:
32 1 0.00
33 211 1.00
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.22
Consensus pattern (33 bp):
AGAGATAGTCCGTTGGGACAGTAAACACATAAC
Found at i:18524794 original size:99 final size:99
Alignment explanation
Indices: 18524620--18524894 Score: 329
Period size: 99 Copynumber: 2.8 Consensus size: 99
18524610 AGTCTGTTGC
* * * * * * *
18524620 GATAGTAAACACAGAACAAAGATAGTTTATTGGGACAGTAAACACATAATAGAGATAGTCTGCTG
1 GATAGTAAACACAGAACAGAGATAGTCTGTTGGGACAGTAAACACATAACAAAGATAGTCCGCTA
* *
18524685 GGACAGTAAACACATAACAGAGATAGTTCATT-G
66 GGACAATAAACACATAACAGAGATAGTCCATTAG
* * *
18524718 TGATAGTAAACACAGAATAGAGATAGTCCGTTGGGACAATAAACACA-ACACAAAGATAGTCCGC
1 -GATAGTAAACACAGAACAGAGATAGTCTGTTGGGACAGTAAACACATA-ACAAAGATAGTCCGC
* * *
18524782 TAGGATAATAAACACATGACAGAGATAGTCCGTTAG
64 TAGGACAATAAACACATAACAGAGATAGTCCATTAG
* * * * * *
18524818 GATAGTAAACACATAACAGAGATAGTCTGTTGGGACAGTAAATACATAACAAAAATAGTCTGTTG
1 GATAGTAAACACAGAACAGAGATAGTCTGTTGGGACAGTAAACACATAACAAAGATAGTCCGCTA
18524883 GGACAATAAACA
66 GGACAATAAACA
18524895 TATATAGAGT
Statistics
Matches: 148, Mismatches: 25, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
98 1 0.01
99 145 0.98
100 2 0.01
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.21
Consensus pattern (99 bp):
GATAGTAAACACAGAACAGAGATAGTCTGTTGGGACAGTAAACACATAACAAAGATAGTCCGCTA
GGACAATAAACACATAACAGAGATAGTCCATTAG
Found at i:18528956 original size:27 final size:28
Alignment explanation
Indices: 18528922--18528984 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
18528912 AAAAAATAAT
*
18528922 CAAAATATTAT-AACTTTTTTTATTTAC
1 CAAAATATTATAAAATTTTTTTATTTAC
18528949 CAAAATATTATAAAATTTTTTTATTTAC
1 CAAAATATTATAAAATTTTTTTATTTAC
18528977 CAAAATAT
1 CAAAATAT
18528985 ACCAAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 11 0.32
28 23 0.68
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.48
Consensus pattern (28 bp):
CAAAATATTATAAAATTTTTTTATTTAC
Found at i:18530034 original size:28 final size:30
Alignment explanation
Indices: 18530003--18530068 Score: 91
Period size: 28 Copynumber: 2.3 Consensus size: 30
18529993 TTTTTGGTAT
** *
18530003 ATTTTGGTAAATAA-AAAAATTA-TATAAC
1 ATTTTGGTAAATAATAAAAAAAAGGATAAC
18530031 ATTTTGGTAAATAATAAAAAAAAGGATAAC
1 ATTTTGGTAAATAATAAAAAAAAGGATAAC
18530061 ATTTTGGT
1 ATTTTGGT
18530069 TATTTTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 14 0.42
29 6 0.18
30 13 0.39
ACGTcount: A:0.50, C:0.03, G:0.12, T:0.35
Consensus pattern (30 bp):
ATTTTGGTAAATAATAAAAAAAAGGATAAC
Found at i:18530240 original size:9 final size:9
Alignment explanation
Indices: 18530228--18530258 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
18530218 GTTAAACGAG
18530228 TCGAGTTAT
1 TCGAGTTAT
*
18530237 TCGAGTTAA
1 TCGAGTTAT
18530246 TCGAGTTAT
1 TCGAGTTAT
18530255 TCGA
1 TCGA
18530259 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:18530329 original size:9 final size:9
Alignment explanation
Indices: 18530312--18530348 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
18530302 TGAGTTTTCG
18530312 AATTCGAAT
1 AATTCGAAT
*
18530321 AACTCGAAT
1 AATTCGAAT
18530330 AATTCGAAT
1 AATTCGAAT
18530339 AATTCGAAT
1 AATTCGAAT
18530348 A
1 A
18530349 TCAAATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:18530639 original size:25 final size:25
Alignment explanation
Indices: 18530611--18530662 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
18530601 TTACATTTAA
*
18530611 AATGATGGGAATTATTTTAAAATAT
1 AATGATGGGAATTATTGTAAAATAT
18530636 AATGATGGGAATTATTGTAAAATAT
1 AATGATGGGAATTATTGTAAAATAT
18530661 AA
1 AA
18530663 AGTAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (25 bp):
AATGATGGGAATTATTGTAAAATAT
Found at i:18550859 original size:75 final size:75
Alignment explanation
Indices: 18550736--18550883 Score: 287
Period size: 75 Copynumber: 2.0 Consensus size: 75
18550726 TAGTGAGTCG
*
18550736 TATATTTTGATACAGTCAAAACATATACTGTAATAGGTTGTACTATAAAGACTGATGTTGGGTAT
1 TATATTTTGATACAGTCAAAACATATACTGTAATAGGTTGTACTATAAAAACTGATGTTGGGTAT
18550801 GCCACAATTT
66 GCCACAATTT
18550811 TATATTTTGATACAGTCAAAACATATACTGTAATAGGTTGTACTATAAAAACTGATGTTGGGTAT
1 TATATTTTGATACAGTCAAAACATATACTGTAATAGGTTGTACTATAAAAACTGATGTTGGGTAT
18550876 GCCACAAT
66 GCCACAAT
18550884 CTATGTAGTG
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (75 bp):
TATATTTTGATACAGTCAAAACATATACTGTAATAGGTTGTACTATAAAAACTGATGTTGGGTAT
GCCACAATTT
Found at i:18561737 original size:25 final size:25
Alignment explanation
Indices: 18561703--18561773 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
18561693 CCTTTACATA
*
18561703 TATGCTCACACGAGATGTGAATAAG
1 TATGCTCACACGAGCTGTGAATAAG
* *
18561728 TATGCTCACACGAGCTATGACTAAG
1 TATGCTCACACGAGCTGTGAATAAG
*
18561753 TATGCTCACATGAGCTGTGAA
1 TATGCTCACACGAGCTGTGAA
18561774 AATGGGCATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (25 bp):
TATGCTCACACGAGCTGTGAATAAG
Found at i:18573385 original size:242 final size:241
Alignment explanation
Indices: 18572961--18573432 Score: 847
Period size: 242 Copynumber: 2.0 Consensus size: 241
18572951 AGAAAAGATG
* * *
18572961 AGTTTTTATCTTAATAAAAATGGAAAATAATAATTTAATATGCATTATATTATTTATTATTTATT
1 AGTTTTTATCTTAATAAAAATGAAAAATAATAATTTAATATGCATTATATTAATTATTAATTATT
*
18573026 ATTTACTTTGAGTAGAATTAGAACTTAGAATTTGTACGAATTCTACTCTAGCTCCTACTCCTTTC
66 ATTTACTTTGAGTAGAATTAGAACTTAGAATTTGTAAGAATTCTACTCTAGCTCCTACTCCTTTC
18573091 ACTATAAATTCCACCCATCTATTCTTATTTTTTTTCATTCATACACCATTCCCTCCAAAAACACC
131 ACTATAAATTCCACCCATCTATTCTTATTTTTTTTCATTCATACACCATTCCCTCCAAAAACACC
18573156 AAAACCCTTAAGTGTCGAAACCTCTTAACAATTCCTTTATTCGATA
196 AAAACCCTTAAGTGTCGAAACCTCTTAACAATTCCTTTATTCGATA
* *
18573202 AGTTTTTATCTTAATAAATTAAT-AAAAATAATAATTTAGTATGCATTATATTAATTATTAATTG
1 AGTTTTTATCTTAATAAA--AATGAAAAATAATAATTTAATATGCATTATATTAATTATTAATTA
* *
18573266 TTATTTACTTTGAGTAGAATTAGAACTTAGAATTTTTAAGAATTCTACTCTAGCTCTTACTCCTT
64 TTATTTACTTTGAGTAGAATTAGAACTTAGAATTTGTAAGAATTCTACTCTAGCTCCTACTCCTT
18573331 TCACTATAAATTCCACCCATCTATTCTTATTTTTTTTCATTCATACACCATTCCCTCCAAAAACA
129 TCACTATAAATTCCACCCATCTATTCTTATTTTTTTTCATTCATACACCATTCCCTCCAAAAACA
18573396 CCAAAACCCTTAAGTGTCGAAACCTCTTAACAATTCC
194 CCAAAACCCTTAAGTGTCGAAACCTCTTAACAATTCC
18573433 ATAGCCACAA
Statistics
Matches: 221, Mismatches: 8, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
241 18 0.08
242 200 0.90
243 3 0.01
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.40
Consensus pattern (241 bp):
AGTTTTTATCTTAATAAAAATGAAAAATAATAATTTAATATGCATTATATTAATTATTAATTATT
ATTTACTTTGAGTAGAATTAGAACTTAGAATTTGTAAGAATTCTACTCTAGCTCCTACTCCTTTC
ACTATAAATTCCACCCATCTATTCTTATTTTTTTTCATTCATACACCATTCCCTCCAAAAACACC
AAAACCCTTAAGTGTCGAAACCTCTTAACAATTCCTTTATTCGATA
Found at i:18576146 original size:91 final size:91
Alignment explanation
Indices: 18575991--18576158 Score: 336
Period size: 91 Copynumber: 1.8 Consensus size: 91
18575981 CCAAAGGTCC
18575991 GATTGAAGCTGAGTCTAGGGTTTAAAAGCCTAAATTTATCTATCTTTTACCTACCTCTAGCCTAG
1 GATTGAAGCTGAGTCTAGGGTTTAAAAGCCTAAATTTATCTATCTTTTACCTACCTCTAGCCTAG
18576056 CTACGTTACAACCTTTTTAAAGATCT
66 CTACGTTACAACCTTTTTAAAGATCT
18576082 GATTGAAGCTGAGTCTAGGGTTTAAAAGCCTAAATTTATCTATCTTTTACCTACCTCTAGCCTAG
1 GATTGAAGCTGAGTCTAGGGTTTAAAAGCCTAAATTTATCTATCTTTTACCTACCTCTAGCCTAG
18576147 CTACGTTACAAC
66 CTACGTTACAAC
18576159 NNNNNNNNNN
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 77 1.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (91 bp):
GATTGAAGCTGAGTCTAGGGTTTAAAAGCCTAAATTTATCTATCTTTTACCTACCTCTAGCCTAG
CTACGTTACAACCTTTTTAAAGATCT
Found at i:18578186 original size:15 final size:15
Alignment explanation
Indices: 18578166--18578195 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18578156 TAATTAATCT
*
18578166 AACACAGTTATGTCA
1 AACACAATTATGTCA
18578181 AACACAATTATGTCA
1 AACACAATTATGTCA
18578196 TCTTGATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (15 bp):
AACACAATTATGTCA
Found at i:18585465 original size:54 final size:54
Alignment explanation
Indices: 18585398--18585507 Score: 202
Period size: 54 Copynumber: 2.0 Consensus size: 54
18585388 CGGCCTCTGA
*
18585398 ATCTTAAACAATCATTAGCATCAACTCAAAACTCTGAATCAAAATTCAAATCAC
1 ATCTTAAACAATCATTAGCATCAACTCAAAACTCTAAATCAAAATTCAAATCAC
*
18585452 ATCTTAAACAATCATTAGCATCAACTCAAAACTCTAAATCAGAATTCAAATCAC
1 ATCTTAAACAATCATTAGCATCAACTCAAAACTCTAAATCAAAATTCAAATCAC
18585506 AT
1 AT
18585508 TGAGTCTGTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.46, C:0.24, G:0.04, T:0.26
Consensus pattern (54 bp):
ATCTTAAACAATCATTAGCATCAACTCAAAACTCTAAATCAAAATTCAAATCAC
Found at i:18594326 original size:25 final size:25
Alignment explanation
Indices: 18594262--18594327 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
18594252 TTGAAAGTTC
* *
18594262 ACTAGGGGTAAAATCGTCAAAATTTT
1 ACTA-GGGTAAAATTGTCAAAACTTT
* * *
18594288 ATTGGGGTAAAATTTTCAAAACTTT
1 ACTAGGGTAAAATTGTCAAAACTTT
18594313 ACTAGGGTAAAATTG
1 ACTAGGGTAAAATTG
18594328 GGGTGAGAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
25 30 0.94
26 2 0.06
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (25 bp):
ACTAGGGTAAAATTGTCAAAACTTT
Found at i:18595382 original size:12 final size:12
Alignment explanation
Indices: 18595365--18595393 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
18595355 TTTATCACAC
18595365 ATTTTGAAAGGA
1 ATTTTGAAAGGA
18595377 ATTTTGAAAGGA
1 ATTTTGAAAGGA
18595389 ATTTT
1 ATTTT
18595394 TTTCATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (12 bp):
ATTTTGAAAGGA
Found at i:18601723 original size:24 final size:24
Alignment explanation
Indices: 18601675--18601721 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
18601665 ACTAGTCATA
*
18601675 GAGAGATTTGAGGAGGGATATTTG
1 GAGAGATTTGAGGAGGAATATTTG
*
18601699 GAGATATTTGAGGAGAGAATATT
1 GAGAGATTTGAGGAG-GAATATT
18601722 GGGTTTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.34, C:0.00, G:0.36, T:0.30
Consensus pattern (24 bp):
GAGAGATTTGAGGAGGAATATTTG
Found at i:18602499 original size:81 final size:81
Alignment explanation
Indices: 18602355--18602758 Score: 531
Period size: 81 Copynumber: 5.0 Consensus size: 81
18602345 TACAGTGAGA
* * * * *
18602355 CCCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGATCAAAATA-CCCTCATAGG
1 CCCCTATAGGGTAAAATGACCGTAATACCCCCATAGGGTTAAATGATCGAAATACCCCT-ATAAG
** *
18602419 GTAAAATGACCAAAATA
65 GTAAAATGACCGTAATG
* * * * * * *
18602436 CCCTTATAGGGTAAAATGACTGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCTATAGGG
1 CCCCTATAGGGTAAAATGACCGTAATACCCCCATAGGGTTAAATGATCGAAATACCCCTATAAGG
18602501 TAAAATGACCGTAATG
66 TAAAATGACCGTAATG
* * *
18602517 CCCCTATAGGGTAAAATGATCGTAATACCCCCATAGGGTTATATGATCGAAATACCCCTGTAAGG
1 CCCCTATAGGGTAAAATGACCGTAATACCCCCATAGGGTTAAATGATCGAAATACCCCTATAAGG
*
18602582 TAAAATGACCGTAGTG
66 TAAAATGACCGTAATG
* * ** * *
18602598 CCCATATAGGGTAATATGACCGTAATACCTTCATAGGGTTAAATGACCGAAATACCCCTGTAAGG
1 CCCCTATAGGGTAAAATGACCGTAATACCCCCATAGGGTTAAATGATCGAAATACCCCTATAAGG
*
18602663 TAAAATGACTGTAATG
66 TAAAATGACCGTAATG
* * *
18602679 CCCCTATAGGGTAAAATGACCGTAATACCCCCATAGGGTTAAATGATTGAAATACCCCTGTTAGG
1 CCCCTATAGGGTAAAATGACCGTAATACCCCCATAGGGTTAAATGATCGAAATACCCCTATAAGG
18602744 TAAAATGACCGTAAT
66 TAAAATGACCGTAAT
18602759 ACCTCTGGAG
Statistics
Matches: 287, Mismatches: 35, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
81 283 0.99
82 4 0.01
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (81 bp):
CCCCTATAGGGTAAAATGACCGTAATACCCCCATAGGGTTAAATGATCGAAATACCCCTATAAGG
TAAAATGACCGTAATG
Found at i:18602772 original size:27 final size:27
Alignment explanation
Indices: 18602354--18602778 Score: 417
Period size: 27 Copynumber: 15.8 Consensus size: 27
18602344 CTACAGTGAG
*
18602354 ACCCCCATAGGGTAAAATGACCGAAAT
1 ACCCCTATAGGGTAAAATGACCGAAAT
* * *
18602381 ACCCCCATAGGGTAAAATGATCAAAAT
1 ACCCCTATAGGGTAAAATGACCGAAAT
*
18602408 A-CCCTCATAGGGTAAAATGACCAAAAT
1 ACCCCT-ATAGGGTAAAATGACCGAAAT
* *
18602435 ACCCTTATAGGGTAAAATGACTGAAAT
1 ACCCCTATAGGGTAAAATGACCGAAAT
* *
18602462 ACCCCCATAGGGTAAAATGACCAAAAT
1 ACCCCTATAGGGTAAAATGACCGAAAT
*
18602489 ACCCCTATAGGGTAAAATGACCGTAAT
1 ACCCCTATAGGGTAAAATGACCGAAAT
* * *
18602516 GCCCCTATAGGGTAAAATGATCGTAAT
1 ACCCCTATAGGGTAAAATGACCGAAAT
* * * *
18602543 ACCCCCATAGGGTTATATGATCGAAAT
1 ACCCCTATAGGGTAAAATGACCGAAAT
* * * *
18602570 ACCCCTGTAAGGTAAAATGACCGTAGT
1 ACCCCTATAGGGTAAAATGACCGAAAT
* * * *
18602597 GCCCATATAGGGTAATATGACCGTAAT
1 ACCCCTATAGGGTAAAATGACCGAAAT
* *
18602624 A-CCTTCATAGGGTTAAATGACCGAAAT
1 ACCCCT-ATAGGGTAAAATGACCGAAAT
* * * *
18602651 ACCCCTGTAAGGTAAAATGACTGTAAT
1 ACCCCTATAGGGTAAAATGACCGAAAT
* *
18602678 GCCCCTATAGGGTAAAATGACCGTAAT
1 ACCCCTATAGGGTAAAATGACCGAAAT
* * **
18602705 ACCCCCATAGGGTTAAATGATTGAAAT
1 ACCCCTATAGGGTAAAATGACCGAAAT
* *
18602732 ACCCCTGTTA-GGTAAAATGACCGTAAT
1 ACCCCT-ATAGGGTAAAATGACCGAAAT
* **
18602759 ACCTCTGGAGGGT-AAATGAC
1 ACCCCTATAGGGTAAAATGAC
18602779 TATTTTTCCC
Statistics
Matches: 327, Mismatches: 65, Indels: 13
0.81 0.16 0.03
Matches are distributed among these distances:
26 14 0.04
27 305 0.93
28 8 0.02
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (27 bp):
ACCCCTATAGGGTAAAATGACCGAAAT
Found at i:18602821 original size:11 final size:11
Alignment explanation
Indices: 18602805--18602874 Score: 50
Period size: 11 Copynumber: 6.0 Consensus size: 11
18602795 TGTAAATGAT
*
18602805 TGATTTGTCTG
1 TGATTTGTATG
**
18602816 TGATTTAAATG
1 TGATTTGTATG
*
18602827 ACTGATTTGTTTG
1 --TGATTTGTATG
*
18602840 TGATTGGTATG
1 TGATTTGTATG
*
18602851 ACTGATTTGTCTG
1 --TGATTTGTATG
18602864 TGATTTGTATG
1 TGATTTGTATG
18602875 ACTGATTTTG
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
11 27 0.61
13 17 0.39
ACGTcount: A:0.19, C:0.06, G:0.26, T:0.50
Consensus pattern (11 bp):
TGATTTGTATG
Found at i:18602832 original size:24 final size:24
Alignment explanation
Indices: 18602797--18602882 Score: 109
Period size: 24 Copynumber: 3.6 Consensus size: 24
18602787 CCCTCGAGTG
*
18602797 TAAATGATTGATTTGTCTGTGATT
1 TAAATGACTGATTTGTCTGTGATT
*
18602821 TAAATGACTGATTTGTTTGTGATT
1 TAAATGACTGATTTGTCTGTGATT
***
18602845 GGTATGACTGATTTGTCTGTGATT
1 TAAATGACTGATTTGTCTGTGATT
**
18602869 TGTATGACTGATTT
1 TAAATGACTGATTT
18602883 TGAGCAAGGC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.22, C:0.06, G:0.23, T:0.49
Consensus pattern (24 bp):
TAAATGACTGATTTGTCTGTGATT
Found at i:18603006 original size:27 final size:27
Alignment explanation
Indices: 18602950--18603006 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
18602940 GGAAGTACTG
* *
18602950 TACTGGTGGCTCTGCCATAATCACTGT
1 TACTGGTGGCTCTGCCACAATCACTAT
18602977 TACTGGTGGCT-TGGCCACATAT-ACTAT
1 TACTGGTGGCTCT-GCCACA-ATCACTAT
18603004 TAC
1 TAC
18603007 GGGCAGCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 1 0.04
27 23 0.88
28 2 0.08
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (27 bp):
TACTGGTGGCTCTGCCACAATCACTAT
Found at i:18603062 original size:26 final size:26
Alignment explanation
Indices: 18603008--18603062 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
18602998 TACTATTACG
** *
18603008 GGCAGCTTTGTTGCGATACTGTTGTT
1 GGCAGCTTTGTTGCGATACTACTGAT
*
18603034 GGCAGCTTTGTTGCGATGCTACTGAT
1 GGCAGCTTTGTTGCGATACTACTGAT
18603060 GGC
1 GGC
18603063 TTTGTGCCGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.18, G:0.33, T:0.36
Consensus pattern (26 bp):
GGCAGCTTTGTTGCGATACTACTGAT
Found at i:18603094 original size:32 final size:32
Alignment explanation
Indices: 18603053--18603209 Score: 179
Period size: 32 Copynumber: 4.9 Consensus size: 32
18603043 GTTGCGATGC
*
18603053 TACTGATGGCTTTGTGCCGATCATATTACCAT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * * *
18603085 TACTGATGGCTTTATACCGATCACAATACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * *
18603117 TACTGATGGCTTTGTACCAATCATAATACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * * * * *
18603149 TACTGATGGCTGTGTGCTGATAATATCACTGC
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
*
18603181 TACTGATGGCTTTGTGCCAATCATATTAC
1 TACTGATGGCTTTGTGCCGATCATATTAC
18603210 TGTACTTATT
Statistics
Matches: 103, Mismatches: 22, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 103 1.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACCGT
Found at i:18603899 original size:49 final size:49
Alignment explanation
Indices: 18603836--18603933 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
18603826 TTAATTGGGC
18603836 TTTTGCCTATTTACTTTAAATTGCTAGTTTAGGGAAGACGAATTTTCAA
1 TTTTGCCTATTTACTTTAAATTGCTAGTTTAGGGAAGACGAATTTTCAA
18603885 TTTTGCCCTA-TTACTTTAAATTGCTAGTTTAGGGAAGACGAATTTTCAA
1 TTTTG-CCTATTTACTTTAAATTGCTAGTTTAGGGAAGACGAATTTTCAA
18603934 AATAATAACT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
49 44 0.92
50 4 0.08
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (49 bp):
TTTTGCCTATTTACTTTAAATTGCTAGTTTAGGGAAGACGAATTTTCAA
Found at i:18605870 original size:14 final size:15
Alignment explanation
Indices: 18605846--18605879 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
18605836 TGTGATTATT
18605846 TTGATGATTGATATG
1 TTGATGATTGATATG
*
18605861 TTGA-GATTGATATT
1 TTGATGATTGATATG
18605875 TTGAT
1 TTGAT
18605880 ATGTATGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (15 bp):
TTGATGATTGATATG
Found at i:18605879 original size:22 final size:22
Alignment explanation
Indices: 18605853--18605902 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
18605843 ATTTTGATGA
18605853 TTGATATGT-TGAGATTGATATT
1 TTGATATGTATGAGATT-ATATT
*
18605875 TTGATATGTATGCGATTATATT
1 TTGATATGTATGAGATTATATT
18605897 TGTGAT
1 T-TGAT
18605903 GATCTCACAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.26, C:0.02, G:0.22, T:0.50
Consensus pattern (22 bp):
TTGATATGTATGAGATTATATT
Found at i:18606326 original size:16 final size:16
Alignment explanation
Indices: 18606305--18606374 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
18606295 TTTGGTTCGT
* *
18606305 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
* *
18606321 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
18606337 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
18606353 CGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
18606369 TGTAAT
1 TGTAAT
18606375 AGCAAATCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.31, C:0.01, G:0.36, T:0.31
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:18606408 original size:45 final size:44
Alignment explanation
Indices: 18606354--18606447 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 44
18606344 GAATAGAGGC
*
18606354 GTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGC-AATCAACTGTTTGGTTGAAT
***
18606399 GTAATGGAATAGAGGCGTAATAGCAATCCTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGCAATCAACTGTTTGGTTGAAT
18606443 GTAAT
1 GTAAT
18606448 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 22 0.49
45 23 0.51
ACGTcount: A:0.33, C:0.07, G:0.28, T:0.32
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGCAATCAACTGTTTGGTTGAAT
Found at i:18606628 original size:18 final size:17
Alignment explanation
Indices: 18606607--18606641 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
18606597 TTATTATTAA
*
18606607 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
18606625 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
18606642 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:18616086 original size:50 final size:50
Alignment explanation
Indices: 18615987--18616226 Score: 273
Period size: 50 Copynumber: 4.7 Consensus size: 50
18615977 AATGAGATCT
* * *
18615987 CATGTAAGACCATGTCTGAGACATGGAATTGGCATCATTGAGATTATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCA---AG---ATGAGAGGTCC
*
18616043 CATGTAAGACCATGTTTGGGACATGGCATTGGCACCAAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATGAGAGGTCC
* * * *
18616093 CATGTAAGATCATGTCTGGGACATAGCGTTGGCACCGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATGAGAGGTCC
** * * * **
18616143 CCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATGAGAGGTCC
* *
18616193 CATGTAAGACCATATCTGGGATATGGCATTGGCA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA
18616227 GTACAGAAAA
Statistics
Matches: 161, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
50 126 0.78
53 2 0.01
56 33 0.20
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATGAGAGGTCC
Found at i:18616462 original size:12 final size:12
Alignment explanation
Indices: 18616445--18616483 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
18616435 ATGAGTTATT
18616445 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
18616457 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
18616469 TAAGTGAGTAAG
1 TAAGTAAGCAAG
18616481 TAA
1 TAA
18616484 AGAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:18621933 original size:6 final size:6
Alignment explanation
Indices: 18621924--18621948 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
18621914 ACTTCATAGT
18621924 CATCGC CATCGC CATCGC CATCGC C
1 CATCGC CATCGC CATCGC CATCGC C
18621949 GCTGCTTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.52, G:0.16, T:0.16
Consensus pattern (6 bp):
CATCGC
Found at i:18622571 original size:25 final size:25
Alignment explanation
Indices: 18622534--18622589 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
18622524 ATTAGCGATT
* *
18622534 GTGATATGTGGCTTTTTTCTTTCTA
1 GTGATACGAGGCTTTTTTCTTTCTA
*
18622559 GTGATACGAGGCTTTTTTTTTTCTA
1 GTGATACGAGGCTTTTTTCTTTCTA
18622584 GTGATA
1 GTGATA
18622590 TGTGGCCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.16, C:0.11, G:0.21, T:0.52
Consensus pattern (25 bp):
GTGATACGAGGCTTTTTTCTTTCTA
Found at i:18628058 original size:106 final size:106
Alignment explanation
Indices: 18627873--18628472 Score: 1200
Period size: 106 Copynumber: 5.7 Consensus size: 106
18627863 ACATGCGAAA
18627873 GCCATGTCCCAGACATGGTCTTACATGGGACCCCTCATCTCGGTGCCAACGCCATGTCCTAGACA
1 GCCATGTCCCAGACATGGTCTTACATGGGACCCCTCATCTCGGTGCCAACGCCATGTCCTAGACA
18627938 TGGTCTTCCATAGGCCCTCTCATGATTTCAAGGATGCCAAT
66 TGGTCTTCCATAGGCCCTCTCATGATTTCAAGGATGCCAAT
18627979 GCCATGTCCCAGACATGGTCTTACATGGGACCCCTCATCTCGGTGCCAACGCCATGTCCTAGACA
1 GCCATGTCCCAGACATGGTCTTACATGGGACCCCTCATCTCGGTGCCAACGCCATGTCCTAGACA
18628044 TGGTCTTCCATAGGCCCTCTCATGATTTCAAGGATGCCAAT
66 TGGTCTTCCATAGGCCCTCTCATGATTTCAAGGATGCCAAT
18628085 GCCATGTCCCAGACATGGTCTTACATGGGACCCCTCATCTCGGTGCCAACGCCATGTCCTAGACA
1 GCCATGTCCCAGACATGGTCTTACATGGGACCCCTCATCTCGGTGCCAACGCCATGTCCTAGACA
18628150 TGGTCTTCCATAGGCCCTCTCATGATTTCAAGGATGCCAAT
66 TGGTCTTCCATAGGCCCTCTCATGATTTCAAGGATGCCAAT
18628191 GCCATGTCCCAGACATGGTCTTACATGGGACCCCTCATCTCGGTGCCAACGCCATGTCCTAGACA
1 GCCATGTCCCAGACATGGTCTTACATGGGACCCCTCATCTCGGTGCCAACGCCATGTCCTAGACA
18628256 TGGTCTTCCATAGGCCCTCTCATGATTTCAAGGATGCCAAT
66 TGGTCTTCCATAGGCCCTCTCATGATTTCAAGGATGCCAAT
18628297 GCCATGTCCCAGACATGGTCTTACATGGGACCCCTCATCTCGGTGCCAACGCCATGTCCTAGACA
1 GCCATGTCCCAGACATGGTCTTACATGGGACCCCTCATCTCGGTGCCAACGCCATGTCCTAGACA
18628362 TGGTCTTCCATAGGCCCTCTCATGATTTCAAGGATGCCAAT
66 TGGTCTTCCATAGGCCCTCTCATGATTTCAAGGATGCCAAT
18628403 GCCATGTCCCAGACATGGTCTTACATGGGACCCCTCATCTCGGTGCCAACGCCATGTCCTAGACA
1 GCCATGTCCCAGACATGGTCTTACATGGGACCCCTCATCTCGGTGCCAACGCCATGTCCTAGACA
18628468 TGGTC
66 TGGTC
18628473 CCATATTCAT
Statistics
Matches: 494, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 494 1.00
ACGTcount: A:0.21, C:0.32, G:0.21, T:0.25
Consensus pattern (106 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCCCTCATCTCGGTGCCAACGCCATGTCCTAGACA
TGGTCTTCCATAGGCCCTCTCATGATTTCAAGGATGCCAAT
Found at i:18635613 original size:50 final size:51
Alignment explanation
Indices: 18635559--18635664 Score: 153
Period size: 50 Copynumber: 2.1 Consensus size: 51
18635549 AAATGGGAGT
* * *
18635559 TCTCATA-TCGGTGCCCATGCCATGTCCCAAACATGGTCTTACGGGGGACC
1 TCTCATACTCGGTGCCAACGCCATGTCCCAAACATGGTCTTACAGGGGACC
* *
18635609 TCTCA-ACTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACC
1 TCTCATACTCGGTGCCAACGCCATGTCCCAAACATGGTCTTACAGGGGACC
18635659 TCTCAT
1 TCTCAT
18635665 NNNNNNNNNN
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.02
50 48 0.98
ACGTcount: A:0.21, C:0.33, G:0.22, T:0.25
Consensus pattern (51 bp):
TCTCATACTCGGTGCCAACGCCATGTCCCAAACATGGTCTTACAGGGGACC
Found at i:18647689 original size:17 final size:17
Alignment explanation
Indices: 18647667--18647708 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
18647657 TGTGTCTCAA
* *
18647667 CCGTGTGCGGCACACGG
1 CCGTGTGAGCCACACGG
18647684 CCGTGTGAGCCACACGG
1 CCGTGTGAGCCACACGG
*
18647701 CCGCGTGA
1 CCGTGTGA
18647709 CCCATGCAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.14, C:0.36, G:0.38, T:0.12
Consensus pattern (17 bp):
CCGTGTGAGCCACACGG
Found at i:18649183 original size:57 final size:57
Alignment explanation
Indices: 18649103--18649217 Score: 203
Period size: 57 Copynumber: 2.0 Consensus size: 57
18649093 ATTGCTCGAA
*
18649103 AAGGCTCAGACTACTCGATCGAGTAATACAACTGTGAAAGGGAGACCACCTCGAAAC
1 AAGGCTCAGACTACTCGACCGAGTAATACAACTGTGAAAGGGAGACCACCTCGAAAC
* *
18649160 AAGGCTTAGACTACTCGACCGAGTAATACAGCTGTGAAAGGGAGACCACCTCGAAAC
1 AAGGCTCAGACTACTCGACCGAGTAATACAACTGTGAAAGGGAGACCACCTCGAAAC
18649217 A
1 A
18649218 CTAGAAATAC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.37, C:0.24, G:0.23, T:0.16
Consensus pattern (57 bp):
AAGGCTCAGACTACTCGACCGAGTAATACAACTGTGAAAGGGAGACCACCTCGAAAC
Found at i:18658185 original size:30 final size:30
Alignment explanation
Indices: 18658149--18658211 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
18658139 ACTTGATGCC
18658149 TAAGTCTATTTTCAAGATGTTAGGGATAGG
1 TAAGTCTATTTTCAAGATGTTAGGGATAGG
18658179 TAAGTCTATTTTCAAGATGTTAGGGATAGG
1 TAAGTCTATTTTCAAGATGTTAGGGATAGG
18658209 TAA
1 TAA
18658212 AGTAAGACCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.37
Consensus pattern (30 bp):
TAAGTCTATTTTCAAGATGTTAGGGATAGG
Found at i:18663582 original size:13 final size:13
Alignment explanation
Indices: 18663564--18663599 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
18663554 TTTGGGTTTT
18663564 AATTGATTAAGTA
1 AATTGATTAAGTA
*
18663577 AATTGATTAATTA
1 AATTGATTAAGTA
*
18663590 AATTGGTTAA
1 AATTGATTAA
18663600 ATTATATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (13 bp):
AATTGATTAAGTA
Found at i:18667476 original size:51 final size:50
Alignment explanation
Indices: 18667421--18667611 Score: 192
Period size: 51 Copynumber: 3.8 Consensus size: 50
18667411 CTGGTTCACA
* * * *
18667421 TAGTAGCCTACACACAGTACTACACATGTGACCATCACTATCCGATACATG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCG-TACACG
* * * *
18667472 TAGTAGTCTGCACATAGTACTACACACGTGATCGA--AGCTATTTCGTACACA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTA-TCCGTACACG
* * *
18667523 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATC-CGTACACG
*
18667573 TAGTAGCCTGCACATAGTACTACACACGTGACTATCACT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
18667612 TTCACTTTCA
Statistics
Matches: 114, Mismatches: 18, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
49 5 0.04
50 39 0.34
51 64 0.56
52 5 0.04
53 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGTACACG
Found at i:18667598 original size:101 final size:102
Alignment explanation
Indices: 18667417--18667603 Score: 288
Period size: 101 Copynumber: 1.8 Consensus size: 102
18667407 GATACTGGTT
* * *
18667417 CACATAGTAGCCTACACACAGTACTACACATGTGACCATCACTATCCGATACATGTAGTAGTCTG
1 CACATAGTAGCCTACACACAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTG
18667482 CACATAGTACTACACACGTGATCGAAGCTATTTCGTA
66 CACATAGTACTACACACGTGATCGAAGCTATTTCGTA
* * * *
18667519 CACATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAGCCT
1 CACATAGTAGCCTACACACAGTACTACACATGCGACC-ATCACTATCCGATACACGTAGTAGCCT
18667582 GCACATAGTACTACACACGTGA
65 GCACATAGTACTACACACGTGA
18667604 CTATCACTTT
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
101 38 0.49
102 35 0.45
103 4 0.05
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.25
Consensus pattern (102 bp):
CACATAGTAGCCTACACACAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTG
CACATAGTACTACACACGTGATCGAAGCTATTTCGTA
Found at i:18667624 original size:101 final size:102
Alignment explanation
Indices: 18667414--18667641 Score: 277
Period size: 101 Copynumber: 2.2 Consensus size: 102
18667404 AATGATACTG
* * *
18667414 GTTCACATAGTAGCCTACACACAGTACTACACATGTGACCATCACTATCCGATACATGTAGTAGT
1 GTTCACATAGTAGCCTACACACAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGC
*
18667479 CTGCACATAGTACTACACACGTGATCGAAGCTATTTC
66 CTGCACATAGTACTACACACGTGATCGAAGCTATTAC
* * * * *
18667516 GTACACATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAG
1 GTTCACATAGTAGCCTACACACAGTACTACACATGCGACC-ATCACTATCCGATACACGTAGTAG
*
18667579 CCTGCACATAGTACTACACACGTGA-CTATCA-CT-TTCAC
65 CCTGCACATAGTACTACACACGTGATCGA--AGCTATT-AC
* *
18667617 TTTCACATAGTGGCCTACACACAGT
1 GTTCACATAGTAGCCTACACACAGT
18667642 CCATGCCACA
Statistics
Matches: 107, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
100 4 0.04
101 61 0.57
102 38 0.36
103 4 0.04
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (102 bp):
GTTCACATAGTAGCCTACACACAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGC
CTGCACATAGTACTACACACGTGATCGAAGCTATTAC
Found at i:18672115 original size:17 final size:17
Alignment explanation
Indices: 18672079--18672117 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
18672069 ATGGTAGTTT
*
18672079 GTTAA-CCGAGTTGCAT
1 GTTAAGCCGAGTTGCAA
*
18672095 GTTAAGCCGAGTTGTAA
1 GTTAAGCCGAGTTGCAA
18672112 GTTAAG
1 GTTAAG
18672118 TCGACTTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (17 bp):
GTTAAGCCGAGTTGCAA
Found at i:18679824 original size:43 final size:43
Alignment explanation
Indices: 18679771--18679950 Score: 346
Period size: 43 Copynumber: 4.2 Consensus size: 43
18679761 CGGGCCGTGT
18679771 AGGTCACACGGCTGTATGGTAGGCCTTTTGGTAGACCGTGTGG
1 AGGTCACACGGCTGTATGGTAGGCCTTTTGGTAGACCGTGTGG
18679814 AGGTCACACGGCTGTATGGTAGGCCTTTTGGTAGACCGTGTGG
1 AGGTCACACGGCTGTATGGTAGGCCTTTTGGTAGACCGTGTGG
18679857 AGGTCACACGGCTGTATGGTAGGCCTTTTGGTAGACCGTGTGG
1 AGGTCACACGGCTGTATGGTAGGCCTTTTGGTAGACCGTGTGG
18679900 AGGTCACACGGCTGTATGGTAGGCCTTTTGGTAGACCGTGT-G
1 AGGTCACACGGCTGTATGGTAGGCCTTTTGGTAGACCGTGTGG
18679942 -GGTCACACG
1 AGGTCACACG
18679951 ACCATGTGGT
Statistics
Matches: 137, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
41 9 0.07
42 1 0.01
43 127 0.93
ACGTcount: A:0.17, C:0.19, G:0.37, T:0.27
Consensus pattern (43 bp):
AGGTCACACGGCTGTATGGTAGGCCTTTTGGTAGACCGTGTGG
Found at i:18681671 original size:40 final size:40
Alignment explanation
Indices: 18681609--18681777 Score: 121
Period size: 40 Copynumber: 4.2 Consensus size: 40
18681599 TTTGGATAAC
* ** *
18681609 AAATGCCGCTATAGGTTTAGCATTAGAGGCGCTTTTGGAA
1 AAATGCCGCTATAGATAGAGCATTAGAGGCGCTTTTTGAA
* * *
18681649 AAATGCCGCTATAGATAGAGCATTAGTGGTG-TTTTTTAA
1 AAATGCCGCTATAGATAGAGCATTAGAGGCGCTTTTTGAA
* * * * * *
18681688 GAA-GCACCGCTATAGATCGAGCATTAGCGGTGGTTCTTGAA
1 AAATG--CCGCTATAGATAGAGCATTAGAGGCGCTTTTTGAA
* * * *
18681729 AAACGTCGCTATAGGTCA-ACCATTAGTA-GCGCTTTTTGAA
1 AAATGCCGCTATAGAT-AGAGCATTAG-AGGCGCTTTTTGAA
18681769 AAATGCCGC
1 AAATGCCGC
18681778 AAAAAAATTA
Statistics
Matches: 100, Mismatches: 23, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
38 1 0.01
39 8 0.08
40 82 0.82
41 8 0.08
42 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (40 bp):
AAATGCCGCTATAGATAGAGCATTAGAGGCGCTTTTTGAA
Found at i:18681997 original size:22 final size:24
Alignment explanation
Indices: 18681962--18682022 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 24
18681952 GCCCGGCCCG
18681962 TTTTTAATTAAAATTAAAATTATT
1 TTTTTAATTAAAATTAAAATTATT
*
18681986 TTTTTAA-T-AAATTAAAATTA-A
1 TTTTTAATTAAAATTAAAATTATT
*
18682007 TTGTT-ATTAAAATTAA
1 TTTTTAATTAAAATTAA
18682023 TTGTTAGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 5 0.15
22 19 0.58
23 1 0.03
24 7 0.21
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
TTTTTAATTAAAATTAAAATTATT
Found at i:18682015 original size:16 final size:16
Alignment explanation
Indices: 18681996--18682037 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
18681986 TTTTTAATAA
18681996 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
18682012 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
*
18682028 AGTAAAATTA
1 ATTAAAATTA
18682038 TCAAATTCCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (16 bp):
ATTAAAATTAATTGTT
Found at i:18682475 original size:7 final size:7
Alignment explanation
Indices: 18682424--18682674 Score: 116
Period size: 7 Copynumber: 35.7 Consensus size: 7
18682414 AATATATATA
18682424 TTTAGGG
1 TTTAGGG
*
18682431 TTTATGG
1 TTTAGGG
*
18682438 TGTA-GG
1 TTTAGGG
18682444 TTT-GTGG
1 TTTAG-GG
*
18682451 TTTGGGG
1 TTTAGGG
***
18682458 TTTAAAT
1 TTTAGGG
18682465 TTTAGGG
1 TTTAGGG
* *
18682472 TTTATGA
1 TTTAGGG
*
18682479 TTTAGTG
1 TTTAGGG
* *
18682486 TTAAGAG
1 TTTAGGG
*
18682493 TTTAGTG
1 TTTAGGG
* *
18682500 TTTACGA
1 TTTAGGG
18682507 TTTAGGG
1 TTTAGGG
*
18682514 TGTA-GG
1 TTTAGGG
**
18682520 TTTATTG
1 TTTAGGG
*
18682527 TTTAGTG
1 TTTAGGG
**
18682534 TTTAATG
1 TTTAGGG
*
18682541 TTTAGAG
1 TTTAGGG
* *
18682548 TTTAAAGT
1 TTT-AGGG
18682556 TTTAGGG
1 TTTAGGG
18682563 TTTAAGGG
1 TTT-AGGG
18682571 TTATA-GG
1 TT-TAGGG
*
18682578 CTTAGGG
1 TTTAGGG
18682585 TTTATGGG
1 TTTA-GGG
18682593 -TTACGGG
1 TTTA-GGG
* *
18682600 CTTAAGG
1 TTTAGGG
18682607 TTTAGGG
1 TTTAGGG
18682614 TTTAGGG
1 TTTAGGG
* *
18682621 TTTATGT
1 TTTAGGG
*
18682628 TTTAAGG
1 TTTAGGG
*
18682635 TTTATGG
1 TTTAGGG
*
18682642 TTTAGGC
1 TTTAGGG
18682649 TTTAGGG
1 TTTAGGG
*
18682656 TTTAGTG
1 TTTAGGG
*
18682663 TTTATGG
1 TTTAGGG
18682670 TTTAG
1 TTTAG
18682675 CTAAAAACAT
Statistics
Matches: 180, Mismatches: 54, Indels: 20
0.71 0.21 0.08
Matches are distributed among these distances:
6 11 0.06
7 150 0.83
8 18 0.10
9 1 0.01
ACGTcount: A:0.19, C:0.02, G:0.31, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:18682582 original size:22 final size:22
Alignment explanation
Indices: 18682557--18682619 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 22
18682547 GTTTAAAGTT
18682557 TTAGGGTTTAAGGGTTATAGGC
1 TTAGGGTTTAAGGGTTATAGGC
* **
18682579 TTAGGGTTTATGGGTTACGGGC
1 TTAGGGTTTAAGGGTTATAGGC
*
18682601 TTAAGGTTT-AGGGTT-TAGG
1 TTAGGGTTTAAGGGTTATAGG
18682620 GTTTATGTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 2 0.06
21 5 0.15
22 27 0.79
ACGTcount: A:0.19, C:0.05, G:0.38, T:0.38
Consensus pattern (22 bp):
TTAGGGTTTAAGGGTTATAGGC
Found at i:18682588 original size:29 final size:29
Alignment explanation
Indices: 18682556--18682624 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
18682546 AGTTTAAAGT
18682556 TTTAGGGTTTAAGGG-TTATAGGCTTAGGG
1 TTTAGGGTTTAAGGGCTTA-AGGCTTAGGG
* *
18682585 TTTATGGG-TTACGGGCTTAAGGTTTAGGG
1 TTTA-GGGTTTAAGGGCTTAAGGCTTAGGG
18682614 TTTAGGGTTTA
1 TTTAGGGTTTA
18682625 TGTTTTAAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 3 0.09
29 26 0.74
30 6 0.17
ACGTcount: A:0.19, C:0.04, G:0.36, T:0.41
Consensus pattern (29 bp):
TTTAGGGTTTAAGGGCTTAAGGCTTAGGG
Found at i:18682884 original size:41 final size:42
Alignment explanation
Indices: 18682812--18682890 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
18682802 AAGGTTAATT
*
18682812 AAGTTGAGCAATAATGGCGTTTTTGGCTCAAAACGCCGGAAA
1 AAGTTGAACAATAATGGCGTTTTTGGCTCAAAACGCCGGAAA
** *
18682854 AAGTTGAACAATTGTGGTGTTTTTGG-TCAAAACGCCG
1 AAGTTGAACAATAATGGCGTTTTTGGCTCAAAACGCCG
18682891 CAAATATGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
41 11 0.33
42 22 0.67
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (42 bp):
AAGTTGAACAATAATGGCGTTTTTGGCTCAAAACGCCGGAAA
Found at i:18683258 original size:16 final size:16
Alignment explanation
Indices: 18683237--18683272 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
18683227 CCAGCGGCCG
*
18683237 CTCTGTCACCCGCTTC
1 CTCTGTCACCCGCATC
*
18683253 CTCTGTCGCCCGCATC
1 CTCTGTCACCCGCATC
18683269 CTCT
1 CTCT
18683273 ATTCACGGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.50, G:0.14, T:0.31
Consensus pattern (16 bp):
CTCTGTCACCCGCATC
Found at i:18684751 original size:38 final size:38
Alignment explanation
Indices: 18684700--18685051 Score: 576
Period size: 38 Copynumber: 9.4 Consensus size: 38
18684690 NNNNNNNNNN
18684700 TAACTTAATAACTTATATATATCATATCATAACTTACA
1 TAACTTAATAACTTATATATATCATATCATAACTTACA
18684738 TAACTTAATAACTTATATATATCATATCATAACTTACA
1 TAACTTAATAACTTATATATATCATATCATAACTTACA
18684776 TAACTTAATAACTTATATATATCATATCATAACTTACA
1 TAACTTAATAACTTATATATATCATATCATAACTTACA
18684814 TAACTTAATAACTTATATATATCATATCATAACTTACA
1 TAACTTAATAACTTATATATATCATATCATAACTTACA
18684852 TAACTTAATAACTTATATATATCATATCATAACTTACA
1 TAACTTAATAACTTATATATATCATATCATAACTTACA
18684890 TAACTTAATAACTTATATATATCATATCATAACTTACA
1 TAACTTAATAACTTATATATATCATATCATAACTTACA
18684928 TAACTTAATAACTTATATATATCATATCATAACTTACA
1 TAACTTAATAACTTATATATATCATATCATAACTTACA
* * *
18684966 TAACTTACATAACTCACATA-A-CTTA-CATAACTTACA
1 TAACTTA-ATAACTTATATATATCATATCATAACTTACA
18685002 TAA--TACATAA---ATATATATCATATCATAACTTACA
1 TAACTTA-ATAACTTATATATATCATATCATAACTTACA
* *
18685036 TTACTCACATAACTTA
1 TAACTTA-ATAACTTA
18685052 CATAACTTAA
Statistics
Matches: 298, Mismatches: 7, Indels: 17
0.93 0.02 0.05
Matches are distributed among these distances:
31 4 0.01
32 1 0.00
33 3 0.01
34 20 0.07
36 20 0.07
37 3 0.01
38 236 0.79
39 11 0.04
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (38 bp):
TAACTTAATAACTTATATATATCATATCATAACTTACA
Found at i:18685051 original size:61 final size:64
Alignment explanation
Indices: 18684841--18685076 Score: 204
Period size: 61 Copynumber: 3.6 Consensus size: 64
18684831 TATATCATAT
* * * *
18684841 CATAACTTACATAACTTA-ATAACTTATATATA-TCATATCATAACTTA-CATAACTTA-ATAAC
1 CATAACTCACATAACTTACATAACTTA-ATA-ACTCATA-AATATCATATCATAAC-TACATAAC
18684902 TTA
62 TTA
* * *
18684905 TATATA-TCATATCATAACTTACATAACTTAATAACTTATATATATCATATCATAACTTACATAA
1 CATA-ACTC--A-CATAACTTACATAACTTAATAACTCATAAATATCATATCATAAC-TACATAA
18684969 CTTA
61 CTTA
18684973 CATAACTCACATAACTTACATAACTTACATAA-TACATAAATAT-ATATCAT-A-T-CATAACTT
1 CATAACTCACATAACTTACATAACTTA-ATAACT-CATAAATATCATATCATAACTACATAACTT
18685033 A
64 A
* *
18685034 CATTACTCACATAACTTACATAACTTAACTATACTTATAAATA
1 CATAACTCACATAACTTACATAACTTAA-TA-ACTCATAAATA
18685077 AACAACTTAC
Statistics
Matches: 147, Mismatches: 11, Indels: 30
0.78 0.06 0.16
Matches are distributed among these distances:
60 1 0.01
61 37 0.25
62 9 0.06
63 1 0.01
64 5 0.03
65 27 0.18
66 20 0.14
67 26 0.18
68 21 0.14
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (64 bp):
CATAACTCACATAACTTACATAACTTAATAACTCATAAATATCATATCATAACTACATAACTTA
Found at i:18695143 original size:29 final size:27
Alignment explanation
Indices: 18695110--18695241 Score: 97
Period size: 28 Copynumber: 4.6 Consensus size: 27
18695100 CAGAGATTGT
18695110 CACAAAGGATTACCTTTCCAAAATTTTGC
1 CACAAAGG-TTACCTTT-CAAAATTTTGC
* * *
18695139 CACAAAGGTTGTCCTTT-AACAAGTTCGC
1 CACAAAGGTT-ACCTTTCAA-AATTTTGC
* * *
18695167 CACAAAGGCTTACCTTTCTAGAGTTTTCC
1 CACAAAGG-TTACCTTTC-AAAATTTTGC
* *
18695196 CACAAAGGTTGTCCTTT-AACAGTTTTGC
1 CACAAAGGTT-ACCTTTCAA-AATTTTGC
18695224 CACAAAGGCTTACCTTTC
1 CACAAAGG-TTACCTTTC
18695242 CAAAGGTTTT
Statistics
Matches: 81, Mismatches: 13, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
27 3 0.04
28 43 0.53
29 34 0.42
30 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (27 bp):
CACAAAGGTTACCTTTCAAAATTTTGC
Found at i:18695172 original size:57 final size:56
Alignment explanation
Indices: 18695110--18695299 Score: 238
Period size: 57 Copynumber: 3.3 Consensus size: 56
18695100 CAGAGATTGT
* *
18695110 CACAAAGGATTACCTTTCCAAAATTTTGCCACAAAGGTTGTCCTTTAACAAGTTCGC
1 CACAAAGGCTTACCTTTCCAAAGTTTT-CCACAAAGGTTGTCCTTTAACAAGTTCGC
* * *
18695167 CACAAAGGCTTACCTTTCTAGAGTTTTCCCACAAAGGTTGTCCTTTAAC-AGTTTTGC
1 CACAAAGGCTTACCTTTCCAAAGTTTT-CCACAAAGGTTGTCCTTTAACAAG-TTCGC
* * * **
18695224 CACAAAGGCTTACCTTTCCAAAGGTTTTCCATAAAGGTTTTCCTTTAACAGGTTCAT
1 CACAAAGGCTTACCTTTCCAAA-GTTTTCCACAAAGGTTGTCCTTTAACAAGTTCGC
*
18695281 CACAGAGGCTTACCTTTCC
1 CACAAAGGCTTACCTTTCC
18695300 TGGTGATCCA
Statistics
Matches: 115, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
56 2 0.02
57 107 0.93
58 6 0.05
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (56 bp):
CACAAAGGCTTACCTTTCCAAAGTTTTCCACAAAGGTTGTCCTTTAACAAGTTCGC
Found at i:18697184 original size:49 final size:46
Alignment explanation
Indices: 18697115--18697217 Score: 136
Period size: 49 Copynumber: 2.2 Consensus size: 46
18697105 AATAAGAAAG
* *
18697115 GGCAAAACTACGTCGTTTTGATAAATGTTTA-CCTTTTCTAAAGTTAAAA
1 GGCAAAATTACGTCGTTTTGATAAATGTTTATCC--AT-T-AAGTTAAAA
*
18697164 GGCAAAATTACTTCGTTTTGATAAATGTTTATCCATTAAGTTAAAA
1 GGCAAAATTACGTCGTTTTGATAAATGTTTATCCATTAAGTTAAAA
18697210 GGCAAAAT
1 GGCAAAAT
18697218 CATTATATTG
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
46 17 0.34
47 1 0.02
48 1 0.02
49 29 0.58
50 2 0.04
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.36
Consensus pattern (46 bp):
GGCAAAATTACGTCGTTTTGATAAATGTTTATCCATTAAGTTAAAA
Found at i:18697364 original size:15 final size:15
Alignment explanation
Indices: 18697305--18697368 Score: 51
Period size: 15 Copynumber: 4.1 Consensus size: 15
18697295 GAGTATAAAT
18697305 AATAGGATTTGTTAA
1 AATAGGATTTGTTAA
* *
18697320 AATAGAATTCAGTTTGATTA
1 AATAGGATT-TG-TT-A--A
18697340 AATA--ATTTGTTAA
1 AATAGGATTTGTTAA
18697353 AATAGGATTTGTTAA
1 AATAGGATTTGTTAA
18697368 A
1 A
18697369 TAATTTGTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
13 5 0.13
15 19 0.49
16 3 0.08
17 3 0.08
18 4 0.10
20 5 0.13
ACGTcount: A:0.42, C:0.02, G:0.16, T:0.41
Consensus pattern (15 bp):
AATAGGATTTGTTAA
Found at i:18697376 original size:12 final size:12
Alignment explanation
Indices: 18697332--18697376 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 12
18697322 TAGAATTCAG
18697332 TTTGATTAAATAA
1 TTTG-TTAAATAA
18697345 TTTGTTAAAATAGGA
1 TTTGTT-AAATA--A
18697360 TTTGTTAAATAA
1 TTTGTTAAATAA
18697372 TTTGT
1 TTTGT
18697377 ACTTCATCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
12 8 0.28
13 9 0.31
14 5 0.17
15 7 0.24
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (12 bp):
TTTGTTAAATAA
Found at i:18697731 original size:24 final size:23
Alignment explanation
Indices: 18697668--18697733 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 23
18697658 CTAAAAACCC
* *
18697668 AAAACTCTAAACTTTAAACTTTAA
1 AAAAC-CTAAACCTTAAACTCTAA
* *
18697692 AAAACATAAAATCTTAAACTCTAA
1 AAAACCT-AAACCTTAAACTCTAA
18697716 AAAATCCTAAACCTTAAA
1 AAAA-CCTAAACCTTAAA
18697734 AATTCGAGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
23 1 0.03
24 31 0.91
25 2 0.06
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (23 bp):
AAAACCTAAACCTTAAACTCTAA
Found at i:18697736 original size:16 final size:17
Alignment explanation
Indices: 18697699--18697736 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
18697689 TAAAAAACAT
*
18697699 AAAATCTTAAACTCTAA
1 AAAATCCTAAACTCTAA
*
18697716 AAAATCCTAAAC-CTTA
1 AAAATCCTAAACTCTAA
18697732 AAAAT
1 AAAAT
18697737 TCGAGAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATCCTAAACTCTAA
Found at i:18701895 original size:47 final size:47
Alignment explanation
Indices: 18701844--18701936 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 47
18701834 GGAAATCTGC
* *
18701844 CAAACAGCAGAAAA-TATTTTACACAGATTCAATCAAATACCAGAAAT
1 CAAACAGCA-AAAACCATTTTACACAAATTCAATCAAATACCAGAAAT
*
18701891 CAAACAGCAAAAACCATTTTACACAAATTCAATCAAATACTAGAAA
1 CAAACAGCAAAAACCATTTTACACAAATTCAATCAAATACCAGAAA
18701937 ATATTTTCCA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
46 4 0.10
47 38 0.90
ACGTcount: A:0.53, C:0.20, G:0.06, T:0.20
Consensus pattern (47 bp):
CAAACAGCAAAAACCATTTTACACAAATTCAATCAAATACCAGAAAT
Found at i:18701992 original size:14 final size:14
Alignment explanation
Indices: 18701969--18702006 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
18701959 ACAGAAAAGT
18701969 AAAACATTTTCCAG
1 AAAACATTTTCCAG
* *
18701983 AAATCATTTTCCGG
1 AAAACATTTTCCAG
18701997 AAAACATTTT
1 AAAACATTTT
18702007 ACTGTCAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.34
Consensus pattern (14 bp):
AAAACATTTTCCAG
Found at i:18702082 original size:22 final size:23
Alignment explanation
Indices: 18702046--18702089 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
18702036 CTCGAAATAA
18702046 ACTAAAATTTAAGTCAAACTTAC
1 ACTAAAATTTAAGTCAAACTTAC
18702069 ACTAAAA-TTAAGTCAAACTTA
1 ACTAAAATTTAAGTCAAACTTA
18702090 TTATAGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.50, C:0.16, G:0.05, T:0.30
Consensus pattern (23 bp):
ACTAAAATTTAAGTCAAACTTAC
Found at i:18702569 original size:6 final size:6
Alignment explanation
Indices: 18702558--18702596 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
18702548 TACTTACTTT
*
18702558 AACAAA AACAAA AACAAA ACCAAA AACAAA AA-AAA AACA
1 AACAAA AACAAA AACAAA AACAAA AACAAA AACAAA AACA
18702597 TAAATTCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (6 bp):
AACAAA
Found at i:18704320 original size:23 final size:21
Alignment explanation
Indices: 18704292--18704337 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
18704282 ATTTCAATGA
* * * *
18704292 TAAAATATCATTCGATTTTTT
1 TAAAAAATAATTCAATTTTAT
18704313 TAAAAAATAATTCAATTTTAT
1 TAAAAAATAATTCAATTTTAT
18704334 TAAA
1 TAAA
18704338 TATTTTTCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (21 bp):
TAAAAAATAATTCAATTTTAT
Found at i:18711036 original size:2 final size:2
Alignment explanation
Indices: 18711029--18711058 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
18711019 GACTCTCCCT
18711029 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
18711059 TACTCTCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:18711066 original size:2 final size:2
Alignment explanation
Indices: 18711061--18711093 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
18711051 CACACACATA
18711061 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
18711094 CATGTTTCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:18711674 original size:45 final size:45
Alignment explanation
Indices: 18711625--18711713 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 45
18711615 GTTCTCACCC
*
18711625 ATTTTCATCATGACGCCATAACATCTTTCAACTATGGTCGTACTA
1 ATTTTCAGCATGACGCCATAACATCTTTCAACTATGGTCGTACTA
* * * * *
18711670 ATTTTTAGCATGATGCCATAGCATCTTTCAGCTATGGTCTTACT
1 ATTTTCAGCATGACGCCATAACATCTTTCAACTATGGTCGTACT
18711714 CAGTTTAGAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.38
Consensus pattern (45 bp):
ATTTTCAGCATGACGCCATAACATCTTTCAACTATGGTCGTACTA
Found at i:18718420 original size:17 final size:20
Alignment explanation
Indices: 18718384--18718422 Score: 57
Period size: 17 Copynumber: 2.1 Consensus size: 20
18718374 TTATATTGTG
18718384 TGTTAATATATGATATTAAT
1 TGTTAATATATGATATTAAT
18718404 TGTT-ATATAT-ATA-TAAT
1 TGTTAATATATGATATTAAT
18718421 TG
1 TG
18718423 CATAGAACCG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 3 0.16
19 6 0.32
20 4 0.21
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.51
Consensus pattern (20 bp):
TGTTAATATATGATATTAAT
Found at i:18724438 original size:51 final size:52
Alignment explanation
Indices: 18724382--18724489 Score: 157
Period size: 51 Copynumber: 2.1 Consensus size: 52
18724372 ATGTAATTTT
* * *
18724382 CATTTTTATTTTTGAGAAAACCACATTCATTTCCAAATGATTT-C-ATTTCTC
1 CATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATG-TTTCCTATTTCTC
*
18724433 CATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGTTTCCTATTTCTC
1 CATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGTTTCCTATTTCTC
18724485 CATTT
1 CATTT
18724490 CATCATATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
50 3 0.06
51 36 0.71
52 12 0.24
ACGTcount: A:0.29, C:0.20, G:0.06, T:0.44
Consensus pattern (52 bp):
CATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGTTTCCTATTTCTC
Found at i:18729674 original size:27 final size:27
Alignment explanation
Indices: 18729634--18729912 Score: 285
Period size: 27 Copynumber: 10.3 Consensus size: 27
18729624 AATGGGCCTC
* *
18729634 TAAAATGATCGAAATACCCTTGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* **
18729661 TAAAATTATTGAAATACCCTCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
** * * *
18729688 TAAAACAACTGAAATACCCACGAAAGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* *
18729715 TAAAATAACTGAAATACCCTCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* *
18729742 TAAAATGAACAAAATACCCTCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
*
18729769 TAAAATGACCGAAATACCCTCGATGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* * * *
18729796 TAAAATTATCGAAATACCCTTGATGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* * *
18729823 TAAAATGACCAAAATACCCCCAAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* *
18729850 TAAAATTACCGAAATACCC-CTGAAAGG
1 TAAAATGACCGAAATACCCTC-GAAGGG
*
18729877 TAAAATGATCGAAATACTCC-C-ATAGGG
1 TAAAATGACCGAAATAC-CCTCGA-AGGG
18729904 TAAAATGAC
1 TAAAATGAC
18729913 TGTTATATCC
Statistics
Matches: 213, Mismatches: 36, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
26 2 0.01
27 208 0.98
28 3 0.01
ACGTcount: A:0.44, C:0.19, G:0.18, T:0.19
Consensus pattern (27 bp):
TAAAATGACCGAAATACCCTCGAAGGG
Found at i:18730117 original size:26 final size:26
Alignment explanation
Indices: 18730092--18730188 Score: 124
Period size: 26 Copynumber: 3.7 Consensus size: 26
18730082 ACAAACACTG
* *
18730092 TTACTGGCAGCTTTGCTGCGTTACTGA
1 TTACTGGCAGCTCTGCTGCATTACT-A
* *
18730119 -TGCTGGTAGCTCTGCTGCATTACTA
1 TTACTGGCAGCTCTGCTGCATTACTA
*
18730144 TTACTGGCAGCTCTGCTACATTACTA
1 TTACTGGCAGCTCTGCTGCATTACTA
*
18730170 TTACTGGCAGCTTTGCTGC
1 TTACTGGCAGCTCTGCTGC
18730189 GATATTGGTG
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
25 1 0.02
26 59 0.98
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (26 bp):
TTACTGGCAGCTCTGCTGCATTACTA
Found at i:18730374 original size:30 final size:30
Alignment explanation
Indices: 18730295--18730367 Score: 112
Period size: 30 Copynumber: 2.4 Consensus size: 30
18730285 ACTGCATTTG
18730295 CACTGTTACTGTATTGGGCTAAGGCCCACA
1 CACTGTTACTGTATTGGGCTAAGGCCCACA
*
18730325 CTCTGTTACTGTATTGGGCTATA-GCCCACA
1 CACTGTTACTGTATTGGGCTA-AGGCCCACA
*
18730355 CACTGCTACTGTA
1 CACTGTTACTGTA
18730368 CAGGGCTCAG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
30 38 0.97
31 1 0.03
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (30 bp):
CACTGTTACTGTATTGGGCTAAGGCCCACA
Found at i:18739403 original size:33 final size:33
Alignment explanation
Indices: 18739361--18739516 Score: 99
Period size: 33 Copynumber: 4.6 Consensus size: 33
18739351 AAAATACGGT
18739361 GGAATCAGCACTTAGCAACCACCAATGAATCGG
1 GGAATCAGCACTTAGCAACCACCAATGAATCGG
** *
18739394 GGAATCAGCACACAGCAACC-CC--T---TGGG
1 GGAATCAGCACTTAGCAACCACCAATGAATCGG
* *
18739421 GGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGG
1 GGAATCAGCACTTAGCAA-CCAC---CA-A--T-GAAT-CGG
* *
18739463 TGGAATCAGCACTTAGCAACCACTAATGAATAGG
1 -GGAATCAGCACTTAGCAACCACCAATGAATCGG
**
18739497 GGAATCAGCACACAGCAACC
1 GGAATCAGCACTTAGCAACC
18739517 CCTTTATATG
Statistics
Matches: 95, Mismatches: 12, Indels: 32
0.68 0.09 0.23
Matches are distributed among these distances:
27 19 0.20
28 2 0.02
29 1 0.01
30 1 0.01
32 3 0.03
33 36 0.38
34 2 0.02
35 3 0.03
36 1 0.01
37 1 0.01
38 1 0.01
39 1 0.01
41 1 0.01
42 5 0.05
43 18 0.19
ACGTcount: A:0.35, C:0.28, G:0.20, T:0.17
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATGAATCGG
Found at i:18739492 original size:103 final size:103
Alignment explanation
Indices: 18739164--18739520 Score: 603
Period size: 102 Copynumber: 3.5 Consensus size: 103
18739154 GGTGGATTTC
*
18739164 GCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGGGAATCAGCACT
1 GCACTTAGCAACCACCAATGAATAGGGGAATCAGCACACAGCAACCCCTTGGGGGAATCAGCACT
* * *
18739229 TAGCAACCCCC-TTCACATTTCAGATGCGGTGGAATCA
66 TAGCAACCCCCTTTCACATTTAAAATACGGTGGAATCA
* **
18739266 GCACTTAGCAACCACCAATGAATAGGGGAATTAGCACTTAGCAACCCCTCT-GGGGAATCAGCAC
1 GCACTTAGCAACCACCAATGAATAGGGGAATCAGCACACAGCAACCCCT-TGGGGGAATCAGCAC
18739330 TTA-CAACCCCCTTTCACATTTAAAATACGGTGGAATCA
65 TTAGCAACCCCCTTTCACATTTAAAATACGGTGGAATCA
*
18739368 GCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGGGAATCAGCACT
1 GCACTTAGCAACCACCAATGAATAGGGGAATCAGCACACAGCAACCCCTTGGGGGAATCAGCACT
18739433 TAGCAACCCCCTTTCACATTTAAAATACGGTGGAATCA
66 TAGCAACCCCCTTTCACATTTAAAATACGGTGGAATCA
*
18739471 GCACTTAGCAACCACTAATGAATAGGGGAATCAGCACACAGCAACCCCTT
1 GCACTTAGCAACCACCAATGAATAGGGGAATCAGCACACAGCAACCCCTT
18739521 TATATGCAAT
Statistics
Matches: 238, Mismatches: 13, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
101 9 0.04
102 145 0.61
103 84 0.35
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19
Consensus pattern (103 bp):
GCACTTAGCAACCACCAATGAATAGGGGAATCAGCACACAGCAACCCCTTGGGGGAATCAGCACT
TAGCAACCCCCTTTCACATTTAAAATACGGTGGAATCA
Found at i:18747630 original size:103 final size:103
Alignment explanation
Indices: 18747451--18747859 Score: 800
Period size: 103 Copynumber: 4.0 Consensus size: 103
18747441 TAACCGTTAT
* *
18747451 CGGTGGATTCCGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
18747516 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
66 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
18747554 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
18747619 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
66 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
18747657 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
18747722 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
66 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
18747760 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
18747825 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAA
66 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAA
18747860 TCTATAATAG
Statistics
Matches: 304, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 304 1.00
ACGTcount: A:0.32, C:0.30, G:0.20, T:0.19
Consensus pattern (103 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
Found at i:18751726 original size:10 final size:10
Alignment explanation
Indices: 18751711--18751736 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
18751701 TAATGAAATT
18751711 GAAATGATTA
1 GAAATGATTA
18751721 GAAATGATTA
1 GAAATGATTA
18751731 GAAATG
1 GAAATG
18751737 TTAATATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (10 bp):
GAAATGATTA
Found at i:18751768 original size:16 final size:16
Alignment explanation
Indices: 18751723--18751784 Score: 94
Period size: 16 Copynumber: 4.1 Consensus size: 16
18751713 AATGATTAGA
18751723 AATGATTAGAAATGTT
1 AATGATTAGAAATGTT
*
18751739 AAT-A-TA-ATATGTT
1 AATGATTAGAAATGTT
18751752 AATGATTAGAAATGTT
1 AATGATTAGAAATGTT
18751768 AATGATTAGAAATGTT
1 AATGATTAGAAATGTT
18751784 A
1 A
18751785 TATAAAACAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
13 9 0.22
14 3 0.07
15 3 0.07
16 26 0.63
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (16 bp):
AATGATTAGAAATGTT
Found at i:18753580 original size:16 final size:17
Alignment explanation
Indices: 18753553--18753584 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
18753543 TACTTTAAAA
18753553 AATATATATTATTTTAT
1 AATATATATTATTTTAT
18753570 AATAT-TATTATTTTA
1 AATATATATTATTTTA
18753585 CATTATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
AATATATATTATTTTAT
Found at i:18753591 original size:16 final size:16
Alignment explanation
Indices: 18753553--18753591 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
18753543 TACTTTAAAA
*
18753553 AATATATATTATTTTAT
1 AATAT-TATTATTTTAC
18753570 AATATTATTATTTTAC
1 AATATTATTATTTTAC
*
18753586 ATTATT
1 AATATT
18753592 TTAGTACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
AATATTATTATTTTAC
Found at i:18753779 original size:16 final size:17
Alignment explanation
Indices: 18753760--18753791 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
18753750 TAAAATAATG
18753760 TAAAATAATA-ATATTA
1 TAAAATAATATATATTA
18753776 TAAAATAATATATATT
1 TAAAATAATATATATT
18753792 TTTTAAAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAATAATATATATTA
Found at i:18754391 original size:153 final size:153
Alignment explanation
Indices: 18754121--18754458 Score: 475
Period size: 153 Copynumber: 2.2 Consensus size: 153
18754111 AGAATATAAG
* * *
18754121 TTAAAAGTAATAAAATCCGGGGAAAAAAATAAGAACAAATGGCCGAAATAAGGGTTTTCTACTAA
1 TTAAAAGTAATAAAATCC--GGAAAAAAATAAGAAAAAATGACCGAAATAAGGATTTTCTACTAA
* * *
18754186 ATTTATTTAAAAAGCACAATTAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATA
64 ATTTATTTAAAAAACACAATAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATA
* *
18754251 ATAAAATACGAAAATAATATATTTTT
129 AGAAAATAAGAAAATAATATA-TTTT
* * *
18754277 ATTAAAAGTAATAAAATCCAGGAAAAAAATAAGAAAAAATGACTG-AATAAGGATTTT-T-TTTA
1 -TTAAAAGTAATAAAATCC-GGAAAAAAATAAGAAAAAATGACCGAAATAAGGATTTTCTACTAA
*
18754339 ATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATA
64 ATTTATTTAAAAAACACAATAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATA
*
18754404 AGAAAATAAGAAAATAGTATATTTT
129 AGAAAATAAGAAAATAATATATTTT
*
18754429 TTAAAAGTAATAAAATTCGAGAAAAAAATA
1 TTAAAAGTAATAAAATCCG-GAAAAAAATA
18754459 CGAATAAAGG
Statistics
Matches: 165, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
150 1 0.01
151 27 0.16
152 4 0.02
153 81 0.49
154 1 0.01
155 11 0.07
156 22 0.13
157 18 0.11
ACGTcount: A:0.54, C:0.07, G:0.10, T:0.29
Consensus pattern (153 bp):
TTAAAAGTAATAAAATCCGGAAAAAAATAAGAAAAAATGACCGAAATAAGGATTTTCTACTAAAT
TTATTTAAAAAACACAATAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAAG
AAAATAAGAAAATAATATATTTT
Found at i:18756050 original size:20 final size:19
Alignment explanation
Indices: 18756008--18756058 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
18755998 GCCAAGTGTC
* *
18756008 AAAGTCCAAAACCA-AAATT
1 AAAGTCCAAAA-GATAAATG
18756027 AAAGTCCATAAAGATAAATG
1 AAAGTCCA-AAAGATAAATG
18756047 AAAGTCCAAAAG
1 AAAGTCCAAAAG
18756059 CCCATACTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.57, C:0.16, G:0.12, T:0.16
Consensus pattern (19 bp):
AAAGTCCAAAAGATAAATG
Found at i:18759026 original size:9 final size:9
Alignment explanation
Indices: 18759012--18759042 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
18759002 GTTAAACGAA
18759012 TCGAGTTAT
1 TCGAGTTAT
*
18759021 TCGAGTTAA
1 TCGAGTTAT
18759030 TCGAGTTAT
1 TCGAGTTAT
18759039 TCGA
1 TCGA
18759043 ATCAACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:18759498 original size:17 final size:18
Alignment explanation
Indices: 18759473--18759530 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 18
18759463 TACTCCCCTA
*
18759473 TTTATTTTCCCTCAAACT
1 TTTATTTTCCCTAAAACT
18759491 TTTA-TTTCCC-AAAACT
1 TTTATTTTCCCTAAAACT
*
18759507 TTTAATTTTTCCCTTAAACT
1 TTT-A-TTTTCCCTAAAACT
18759527 TTTA
1 TTTA
18759531 CTTATCACCC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
16 8 0.24
17 7 0.21
18 4 0.12
19 7 0.21
20 8 0.24
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTATTTTCCCTAAAACT
Found at i:18763098 original size:40 final size:40
Alignment explanation
Indices: 18763043--18763164 Score: 172
Period size: 40 Copynumber: 3.0 Consensus size: 40
18763033 TGAATATGCC
* *
18763043 TTTAGGGGTATCGAAGTACTAATAGGGGCACGTATGTGCA
1 TTTAGGGGTACCGAAGTACAAATAGGGGCACGTATGTGCA
* *
18763083 TTTAGGGGTACCGAAGTACAAATAGGGCCACGTATGTACA
1 TTTAGGGGTACCGAAGTACAAATAGGGGCACGTATGTGCA
* * * *
18763123 TTCAAGGGTACCAAAGTACAAACAGGGGCACGTATGTGCA
1 TTTAGGGGTACCGAAGTACAAATAGGGGCACGTATGTGCA
18763163 TT
1 TT
18763165 CAGACAATAA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 72 1.00
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (40 bp):
TTTAGGGGTACCGAAGTACAAATAGGGGCACGTATGTGCA
Found at i:18766421 original size:6 final size:6
Alignment explanation
Indices: 18766410--18766453 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
18766400 TAAGTCTAAG
* *
18766410 AAAATA ACAATA AACATA AAAATA AAAATA AAAAT- AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAA
18766454 CAAATAGACT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:18772524 original size:12 final size:11
Alignment explanation
Indices: 18772507--18772531 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18772497 AACTCACTGA
18772507 TTTTTTTTTCC
1 TTTTTTTTTCC
18772518 TTTTTTTTTCC
1 TTTTTTTTTCC
18772529 TTT
1 TTT
18772532 ACATTGCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTTTCC
Found at i:18773171 original size:11 final size:11
Alignment explanation
Indices: 18773155--18773187 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
18773145 TACATTTTCA
18773155 TTATTTATTAT
1 TTATTTATTAT
18773166 TTATTTATTAT
1 TTATTTATTAT
18773177 TT-TTTA-TAT
1 TTATTTATTAT
18773186 TT
1 TT
18773188 TCTAAGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 5 0.23
10 4 0.18
11 13 0.59
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTATTTATTAT
Found at i:18781203 original size:20 final size:21
Alignment explanation
Indices: 18781170--18781208 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
18781160 AGCTCAATGG
18781170 AGCTCAATTCAGCTCAATTCT
1 AGCTCAATTCAGCTCAATTCT
*
18781191 AGCTC-ATTGAGCTCAATT
1 AGCTCAATTCAGCTCAATT
18781209 TTATCCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (21 bp):
AGCTCAATTCAGCTCAATTCT
Found at i:18781287 original size:16 final size:16
Alignment explanation
Indices: 18781266--18781300 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
18781256 GTCTTATTTT
18781266 TGCTGGAACAATTTCA
1 TGCTGGAACAATTTCA
*
18781282 TGCTGGAATAATTTCA
1 TGCTGGAACAATTTCA
18781298 TGC
1 TGC
18781301 GTCTAGCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (16 bp):
TGCTGGAACAATTTCA
Found at i:18786979 original size:23 final size:24
Alignment explanation
Indices: 18786953--18787005 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
18786943 GTGTTTTTCG
* *
18786953 AGTGATTTCTTCAATCTTCTT-TA
1 AGTGATCTCTTAAATCTTCTTCTA
*
18786976 AGTGCTCTCTTAAATCTTCTTCTA
1 AGTGATCTCTTAAATCTTCTTCTA
*
18787000 ATTGAT
1 AGTGAT
18787006 ATTTATAGAC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.23, C:0.19, G:0.09, T:0.49
Consensus pattern (24 bp):
AGTGATCTCTTAAATCTTCTTCTA
Found at i:18792471 original size:40 final size:39
Alignment explanation
Indices: 18792416--18792539 Score: 176
Period size: 40 Copynumber: 3.1 Consensus size: 39
18792406 TGAATATGCC
* *
18792416 TTCAAGAGTACCGAAGTACTAATAGAGGCACGTATGTGCA
1 TTCAAGGGTACCGAAGTACAAATAG-GGCACGTATGTGCA
*
18792456 TTCAAGGGTACCGAAGTACAAATAGGGTCACGTATGTACA
1 TTCAAGGGTACCGAAGTACAAATAGGG-CACGTATGTGCA
* *
18792496 TTCAAGGGTATCGAAGTACAAACAGGGGCACGTATGTGCA
1 TTCAAGGGTACCGAAGTACAAATA-GGGCACGTATGTGCA
18792536 TTCA
1 TTCA
18792540 GAAAATAATT
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
39 2 0.03
40 71 0.93
41 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.23
Consensus pattern (39 bp):
TTCAAGGGTACCGAAGTACAAATAGGGCACGTATGTGCA
Found at i:18795665 original size:51 final size:50
Alignment explanation
Indices: 18795586--18795771 Score: 205
Period size: 51 Copynumber: 3.7 Consensus size: 50
18795576 GAACACGTGG
*
18795586 GTAGTACTATGTGAAGGCTACTACGTGTATCGATAAA-TAATGGTCACATGT
1 GTAGTACTATGTGAAGGCTACTACGTGTACCGA-AAACT-ATGGTCACATGT
* * * *
18795637 GTAGTACTAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACGTGT
1 GTAGTACTATGTGAAGGCTACTACGTGTACCGAAAA-CTATGGTCACATGT
* * * ** * *
18795688 GTAGTACTATGTGGAGGCTACTACGTGGACCGTAAAACT-TGATTGCGTTT
1 GTAGTACTATGTGAAGGCTACTACGTGTACCG-AAAACTATGGTCACATGT
*
18795738 GTAGTACTATGTGAAGGCTACTACGTGTATCGAA
1 GTAGTACTATGTGAAGGCTACTACGTGTACCGAA
18795772 TGATAATAAT
Statistics
Matches: 116, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
49 2 0.02
50 39 0.34
51 70 0.60
52 5 0.04
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (50 bp):
GTAGTACTATGTGAAGGCTACTACGTGTACCGAAAACTATGGTCACATGT
Found at i:18808097 original size:36 final size:33
Alignment explanation
Indices: 18808032--18808098 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 33
18808022 GTGAATGAAG
*
18808032 TGAGTGAAAAAGAGAGAGAGCTTAAACAAGGAA
1 TGAGTGAAAAAGAGAGAGAGCTAAAACAAGGAA
* *
18808065 TGAGTGAAGAAGAAGAGAGTGCTCAAACACAAGG
1 TGAGTGAAAAAG-AGAGAGAGCT-AAA-ACAAGG
18808099 GAGGAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 11 0.39
34 9 0.32
35 2 0.07
36 6 0.21
ACGTcount: A:0.48, C:0.09, G:0.31, T:0.12
Consensus pattern (33 bp):
TGAGTGAAAAAGAGAGAGAGCTAAAACAAGGAA
Found at i:18810768 original size:32 final size:32
Alignment explanation
Indices: 18810701--18810769 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
18810691 CTATTCCAAT
* * *
18810701 TCACA-CCAATGGATCATTCAATACTTAGTGT
1 TCACACCCAATGAACCATTCAATACTTAGTGA
*
18810732 TCACACCCAATGAACCATTCAA-ATTTGAGTGA
1 TCACACCCAATGAACCATTCAATACTT-AGTGA
18810764 TCACAC
1 TCACAC
18810770 GAAAGACCCT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 8 0.25
32 24 0.75
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.28
Consensus pattern (32 bp):
TCACACCCAATGAACCATTCAATACTTAGTGA
Done.