Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 53 of 204
Found at i:17341285 original size:27 final size:27
Alignment explanation
Indices: 17341250--17341325 Score: 118
Period size: 27 Copynumber: 2.8 Consensus size: 27
17341240 TGTATGAATG
17341250 AATTAGGTTAATTCGGGTAATTCGGTT
1 AATTAGGTTAATTCGGGTAATTCGGTT
*
17341277 AATTCGGTTAATTCGGGTAATTCGGTT
1 AATTAGGTTAATTCGGGTAATTCGGTT
*
17341304 AATTTA-GTTAATTCGGTTAATT
1 AA-TTAGGTTAATTCGGGTAATT
17341326 TTTAACCAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
27 43 0.96
28 2 0.04
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.43
Consensus pattern (27 bp):
AATTAGGTTAATTCGGGTAATTCGGTT
Found at i:17341472 original size:12 final size:12
Alignment explanation
Indices: 17341455--17341479 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17341445 TGTTATTTCG
17341455 GGTCGGTTAACC
1 GGTCGGTTAACC
17341467 GGTCGGTTAACC
1 GGTCGGTTAACC
17341479 G
1 G
17341480 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:17345152 original size:20 final size:19
Alignment explanation
Indices: 17345105--17345153 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 19
17345095 ACTTAAATTT
17345105 ATTA-AAAATTAGAAAAAA
1 ATTATAAAATTAGAAAAAA
17345123 ATTATAAAATATAGAAAAAA
1 ATTATAAAAT-TAGAAAAAA
*
17345143 ATTGTAAAATT
1 ATTATAAAATT
17345154 TTATAAAGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 4 0.14
19 6 0.21
20 18 0.64
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (19 bp):
ATTATAAAATTAGAAAAAA
Found at i:17345424 original size:21 final size:21
Alignment explanation
Indices: 17345398--17345445 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
17345388 ATTAAAGGGC
17345398 TTTTTTATGCA-TTTTAT-AAT
1 TTTTTTATG-ATTTTTATAAAT
17345418 TCTTTTTATGATTTTTATAAAT
1 T-TTTTTATGATTTTTATAAAT
17345440 TTTTTT
1 TTTTTT
17345446 CTAATTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 2 0.08
21 19 0.76
22 4 0.16
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.69
Consensus pattern (21 bp):
TTTTTTATGATTTTTATAAAT
Found at i:17345452 original size:21 final size:21
Alignment explanation
Indices: 17345409--17345453 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
17345399 TTTTTATGCA
*
17345409 TTTTATAATTCTTTTTATGAT
1 TTTTATAATTCTTTTTATAAT
*
17345430 TTTTATAAATT-TTTTTCTAAT
1 TTTTAT-AATTCTTTTTATAAT
17345451 TTT
1 TTT
17345454 AATAGGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTTATAATTCTTTTTATAAT
Found at i:17345750 original size:95 final size:92
Alignment explanation
Indices: 17345613--17345784 Score: 211
Period size: 95 Copynumber: 1.8 Consensus size: 92
17345603 CAGTCAAAAT
* *
17345613 GTCTTTTTGATGCATTTTAACAATTCAAATACTTAATAGAGTGCAAAAAAAAAAAACAGGCGCTT
1 GTCTTTTTGATGCATTTGAACAATTCAAATACCTAATAGAGTGCAAAAAAAAAAAA-AGG-GCTT
17345678 AATTTTTTTATTTTTTGAAAAAGTTTAAAG
64 AATTTTTTT-TTTTTTGAAAAAGTTTAAAG
* * * * * * **
17345708 GTCTTTTTGATGCATGTTGAA-AGTTCTAGTACCTAATTGAGTGTAAAAAGAAAGTAAGGGCTTA
1 GTCTTTTTGATGCAT-TTGAACAATTCAAATACCTAATAGAGTGCAAAAAAAAAAAAAGGGCTTA
17345772 ATTTTTTTTTTTT
65 ATTTTTTTTTTTT
17345785 AAGTTTGAGA
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
92 5 0.08
93 13 0.20
94 3 0.05
95 41 0.62
96 4 0.06
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.41
Consensus pattern (92 bp):
GTCTTTTTGATGCATTTGAACAATTCAAATACCTAATAGAGTGCAAAAAAAAAAAAAGGGCTTAA
TTTTTTTTTTTTTGAAAAAGTTTAAAG
Found at i:17346007 original size:62 final size:63
Alignment explanation
Indices: 17345894--17346019 Score: 209
Period size: 62 Copynumber: 2.0 Consensus size: 63
17345884 AATTGAGTAA
*
17345894 AAGGTGATACCAATTCAATCAAAATTTTAAATAATAGTATAAATAAATTATATAACCCTCACC
1 AAGGTGATACCAATTCAATCAAAACTTTAAATAATAGTATAAATAAATTATATAACCCTCACC
* * *
17345957 AAGGTGATACCAATTCAGTC-AAACTTTAAATAATAGTGTAAATAACTTATATAACCCTCACC
1 AAGGTGATACCAATTCAATCAAAACTTTAAATAATAGTATAAATAAATTATATAACCCTCACC
17346019 A
1 A
17346020 CTACAAAAGT
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
62 40 0.68
63 19 0.32
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.29
Consensus pattern (63 bp):
AAGGTGATACCAATTCAATCAAAACTTTAAATAATAGTATAAATAAATTATATAACCCTCACC
Found at i:17349135 original size:16 final size:16
Alignment explanation
Indices: 17349114--17349150 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
17349104 ATTTCCAAAC
*
17349114 CAATCTCGAGGGACCA
1 CAATCTCGAGAGACCA
17349130 CAATCTCGAGAGACCA
1 CAATCTCGAGAGACCA
17349146 CAATC
1 CAATC
17349151 CCTAACAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.35, C:0.32, G:0.19, T:0.14
Consensus pattern (16 bp):
CAATCTCGAGAGACCA
Found at i:17355998 original size:22 final size:23
Alignment explanation
Indices: 17355937--17356001 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
17355927 GATAAACTCC
* *
17355937 TGAGCTGATAAACAGTAGGCTCTAT
1 TGAGCTG--AAACAGTAAGCTCTAA
17355962 TGAGCTGAAACAGTAAGCTCTAA
1 TGAGCTGAAACAGTAAGCTCTAA
17355985 TGAGCTG-AACAGTAAGC
1 TGAGCTGAAACAGTAAGC
17356002 CCATACGAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
22 10 0.26
23 21 0.55
25 7 0.18
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (23 bp):
TGAGCTGAAACAGTAAGCTCTAA
Found at i:17356011 original size:22 final size:23
Alignment explanation
Indices: 17355963--17356038 Score: 75
Period size: 22 Copynumber: 3.2 Consensus size: 23
17355953 AGGCTCTATT
* *
17355963 GAGCTGAAACAGTAAGCTC-TAAT
1 GAGCTGAAACAGTAAGCCCAT-AC
17355986 GAGCTG-AACAGTAAGCCCATAC
1 GAGCTGAAACAGTAAGCCCATAC
*
17356008 GAGCTGAAATATCGGTAAGCCCATAC
1 GAGCTG-AA-A-CAGTAAGCCCATAC
17356034 GAGCT
1 GAGCT
17356039 ATGGTGAGTC
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
22 18 0.40
23 7 0.16
24 1 0.02
25 1 0.02
26 18 0.40
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (23 bp):
GAGCTGAAACAGTAAGCCCATAC
Found at i:17356263 original size:67 final size:67
Alignment explanation
Indices: 17356186--17356641 Score: 698
Period size: 67 Copynumber: 6.8 Consensus size: 67
17356176 AATAATTCAA
* * * * *
17356186 TTTCTCAAATCACATATATATAATCTATTCAATTAAATACATACATTTAAATACTCAATTTGCAT
1 TTTCTCAAATCATATACATATAATCAATTCAATTAAATACATACATTTAATTACTCAATTCGCAT
17356251 AC
66 AC
* * * * *
17356253 CTTCTCAAATCATATACATATAATCGATTTAATTAAATACATACATTTAAATACTCAATTCGAAT
1 TTTCTCAAATCATATACATATAATCAATTCAATTAAATACATACATTTAATTACTCAATTCGCAT
17356318 AC
66 AC
* * * * *
17356320 TTTCTCAAATCACATATATATAATCGATTTAATT-AATACATACATTTAAATACTCAATTCGCAT
1 TTTCTCAAATCATATACATATAATCAATTCAATTAAATACATACATTTAATTACTCAATTCGCAT
17356384 AC
66 AC
* *
17356386 TTTCTCAAATCATATACATATAATCCATTCAATTAAATACATACATTTAATTACTCAATTCACAT
1 TTTCTCAAATCATATACATATAATCAATTCAATTAAATACATACATTTAATTACTCAATTCGCAT
17356451 AC
66 AC
* *
17356453 TTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAATTACTCAATTCGCGT
1 TTTCTCAAATCATATACATATAATCAATTCAATTAAATACATACATTTAATTACTCAATTCGCAT
17356518 AC
66 AC
*
17356520 TTTCTCAAATCATATACATATAATCAATTCAATTAAATACATACATTTAATTACTCAATTCACAT
1 TTTCTCAAATCATATACATATAATCAATTCAATTAAATACATACATTTAATTACTCAATTCGCAT
17356585 AC
66 AC
* * *
17356587 TTTCTCAAATTATATACAAATAATCAATTCAATTAAACACATACATTTAATTACT
1 TTTCTCAAATCATATACATATAATCAATTCAATTAAATACATACATTTAATTACT
17356642 ATTACAATTG
Statistics
Matches: 361, Mismatches: 27, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
66 61 0.17
67 300 0.83
ACGTcount: A:0.42, C:0.19, G:0.02, T:0.37
Consensus pattern (67 bp):
TTTCTCAAATCATATACATATAATCAATTCAATTAAATACATACATTTAATTACTCAATTCGCAT
AC
Found at i:17363233 original size:27 final size:27
Alignment explanation
Indices: 17363203--17363257 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
17363193 AATTGGAGTT
17363203 TGTCAATTCCGCAATTTAACTCAAAAC
1 TGTCAATTCCGCAATTTAACTCAAAAC
17363230 TGTCAATTCCGCAATTTAACTCAAAAC
1 TGTCAATTCCGCAATTTAACTCAAAAC
17363257 T
1 T
17363258 TCTCCTCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.31
Consensus pattern (27 bp):
TGTCAATTCCGCAATTTAACTCAAAAC
Found at i:17368633 original size:94 final size:94
Alignment explanation
Indices: 17368472--17368658 Score: 293
Period size: 94 Copynumber: 2.0 Consensus size: 94
17368462 CCTTTTATTG
* * * * *
17368472 TTCAATTTTGTTTTGAGAAAGGAAGTGAGATTTTGCATCATTAATCCCAAATAGTTCGAATCTTT
1 TTCAAGTTTATTTTGAGAAAGGAAGTGAGACTTCGCATCATGAATCCCAAATAGTTCGAATCTTT
*
17368537 GTATGAAAGTAAGGAAGACGAGAGGATTA
66 GTATGAAAGTAAGGAAGACAAGAGGATTA
* * *
17368566 TTCAAGTTTATTTTGAGAAAGGAAGTGAGACTTCGCATCATGGATTCCAAATAGTTCGAGTCTTT
1 TTCAAGTTTATTTTGAGAAAGGAAGTGAGACTTCGCATCATGAATCCCAAATAGTTCGAATCTTT
17368631 GTATGAAAGTAAGGAAGACAAGAGGATT
66 GTATGAAAGTAAGGAAGACAAGAGGATT
17368659 GAACTCAAGC
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
94 84 1.00
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.32
Consensus pattern (94 bp):
TTCAAGTTTATTTTGAGAAAGGAAGTGAGACTTCGCATCATGAATCCCAAATAGTTCGAATCTTT
GTATGAAAGTAAGGAAGACAAGAGGATTA
Found at i:17389771 original size:17 final size:17
Alignment explanation
Indices: 17389749--17389792 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
17389739 TCATGCTAAT
17389749 TTTTTTGAATTTT-TACA
1 TTTTTTGAATTTTATA-A
*
17389766 TTTTTTAAATTTTATAA
1 TTTTTTGAATTTTATAA
17389783 -TTTTTGAATT
1 TTTTTTGAATT
17389793 ATTTGTTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 9 0.38
17 13 0.54
18 2 0.08
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (17 bp):
TTTTTTGAATTTTATAA
Found at i:17391042 original size:31 final size:31
Alignment explanation
Indices: 17390993--17391051 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
17390983 TTCAAATATG
* *
17390993 TACAGTTGAATTAAAATTAAAGTTTCATTTA
1 TACACTTGAATTAAAATTAAAATTTCATTTA
**
17391024 TACACTTGAATTGTAATTAAAATTTCAT
1 TACACTTGAATTAAAATTAAAATTTCAT
17391052 GTGTATAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.42
Consensus pattern (31 bp):
TACACTTGAATTAAAATTAAAATTTCATTTA
Found at i:17414952 original size:86 final size:87
Alignment explanation
Indices: 17414834--17414997 Score: 276
Period size: 86 Copynumber: 1.9 Consensus size: 87
17414824 AAATTCTTAA
* * *
17414834 TAACATTTTAATTTGAGGACCAAGTTCATTTCATCCAATTTCAAATTCTCAATTTCATTTATACC
1 TAACATTTCAATTTGAGGACCAAGTTCATTTCATCCAATTTCAAATTCCCAATTCCATTTATACC
17414899 ATTTCGTCCAATGTTCTTTCAG
66 ATTTCGTCCAATGTTCTTTCAG
* *
17414921 TAACATTTCAATTTGA-GACCAAGTTCATTTCATCCAATTTCAAATTCCCGATTCCATTTATATC
1 TAACATTTCAATTTGAGGACCAAGTTCATTTCATCCAATTTCAAATTCCCAATTCCATTTATACC
17414985 ATTTCGTCCAATG
66 ATTTCGTCCAATG
17414998 GAACCTTAAT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
86 57 0.79
87 15 0.21
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (87 bp):
TAACATTTCAATTTGAGGACCAAGTTCATTTCATCCAATTTCAAATTCCCAATTCCATTTATACC
ATTTCGTCCAATGTTCTTTCAG
Found at i:17431129 original size:23 final size:25
Alignment explanation
Indices: 17431101--17431154 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 25
17431091 TTAAAAAAAG
*
17431101 AAATTAATA-ATTAAAATAA-A-TTT
1 AAATTAATACA-TAAAACAATATTTT
17431124 AAATTAATACATAAAACAATATTTT
1 AAATTAATACATAAAACAATATTTT
17431149 AAATTA
1 AAATTA
17431155 GTTTTAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 16 0.59
24 2 0.07
25 9 0.33
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (25 bp):
AAATTAATACATAAAACAATATTTT
Found at i:17436129 original size:24 final size:25
Alignment explanation
Indices: 17436096--17436147 Score: 88
Period size: 24 Copynumber: 2.1 Consensus size: 25
17436086 AACTCTAAAT
*
17436096 ACTGAAGAGTAGACCTGAACAATAA
1 ACTGAAGAGTAGACCTAAACAATAA
17436121 ACTG-AGAGTAGACCTAAACAATAA
1 ACTGAAGAGTAGACCTAAACAATAA
17436145 ACT
1 ACT
17436148 TAGTTTAGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.17
Consensus pattern (25 bp):
ACTGAAGAGTAGACCTAAACAATAA
Found at i:17439544 original size:13 final size:13
Alignment explanation
Indices: 17439526--17439553 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
17439516 GTATATTGGT
17439526 TATTATGCATGTC
1 TATTATGCATGTC
17439539 TATTATGCATGTC
1 TATTATGCATGTC
17439552 TA
1 TA
17439554 AGTTCAATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.46
Consensus pattern (13 bp):
TATTATGCATGTC
Found at i:17453661 original size:30 final size:30
Alignment explanation
Indices: 17453625--17453740 Score: 101
Period size: 30 Copynumber: 3.9 Consensus size: 30
17453615 TTTATTTTTC
*
17453625 AAAATTACATTTTAACCTCTGAACTTGCCT
1 AAAATTACATTTTAACCTCTGAACTTTCCT
* ** * * *
17453655 AAAATTATATTTGGACCCCTTAACTTTTC-
1 AAAATTACATTTTAACCTCTGAACTTTCCT
* * * *
17453684 AAAAGTACATTTTAACCTTTAAACTTTCTT
1 AAAATTACATTTTAACCTCTGAACTTTCCT
*
17453714 AAAATTTCATTTTAACC-CTTGAACTTT
1 AAAATTACATTTTAACCTC-TGAACTTT
17453741 TTGGAAATTA
Statistics
Matches: 64, Mismatches: 20, Indels: 4
0.73 0.23 0.05
Matches are distributed among these distances:
29 20 0.31
30 44 0.69
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.41
Consensus pattern (30 bp):
AAAATTACATTTTAACCTCTGAACTTTCCT
Found at i:17453739 original size:59 final size:59
Alignment explanation
Indices: 17453620--17453741 Score: 149
Period size: 59 Copynumber: 2.1 Consensus size: 59
17453610 AATTTTTTAT
* * *
17453620 TTTTCAAAATTACATTTTAACCTCTGAACTTGCCTAAAATTATATTTGGACCCCTTAAC
1 TTTTCAAAAGTACATTTTAACCTCTAAACTTGCCTAAAATTATATTTGGAACCCTTAAC
* * * *
17453679 TTTTCAAAAGTACATTTTAACCTTTAAACTTTCTTAAAATT-TCATTT-TAACCCTTGAAC
1 TTTTCAAAAGTACATTTTAACCTCTAAACTTGCCTAAAATTAT-ATTTGGAACCCTT-AAC
17453738 TTTT
1 TTTT
17453742 TGGAAATTAC
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
58 7 0.13
59 47 0.87
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (59 bp):
TTTTCAAAAGTACATTTTAACCTCTAAACTTGCCTAAAATTATATTTGGAACCCTTAAC
Found at i:17454112 original size:3 final size:3
Alignment explanation
Indices: 17454104--17454145 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
17454094 CTAGGCTTTT
* *
17454104 GAA GAA GAA GAA AAA GAA GAA GAA GAA GAA GAA GAA AAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
17454146 AGGAAAGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:17454122 original size:9 final size:9
Alignment explanation
Indices: 17454108--17454202 Score: 61
Period size: 9 Copynumber: 10.2 Consensus size: 9
17454098 GCTTTTGAAG
17454108 AAGAAGAAA
1 AAGAAGAAA
*
17454117 AAGAAGAAG
1 AAGAAGAAA
*
17454126 AAGAAGAAG
1 AAGAAGAAA
*
17454135 AAGAAAAAGA
1 AAGAAGAA-A
17454145 AAGGAAAGAAA
1 AA-G-AAGAAA
*
17454156 AA-AGGAAA
1 AAGAAGAAA
17454164 AAG--GAAA
1 AAGAAGAAA
17454171 AAGGAAGAAA
1 AA-GAAGAAA
*
17454181 AGAAAAGGAAA
1 A-AGAA-GAAA
*
17454192 AAGAATAAA
1 AAGAAGAAA
17454201 AA
1 AA
17454203 ATTTTAACAG
Statistics
Matches: 69, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
7 6 0.09
8 8 0.12
9 29 0.42
10 12 0.17
11 10 0.14
12 4 0.06
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.01
Consensus pattern (9 bp):
AAGAAGAAA
Found at i:17454122 original size:12 final size:12
Alignment explanation
Indices: 17454105--17454196 Score: 75
Period size: 12 Copynumber: 7.4 Consensus size: 12
17454095 TAGGCTTTTG
17454105 AAGAAGAAGAAA
1 AAGAAGAAGAAA
*
17454117 AAGAAGAAGAAG
1 AAGAAGAAGAAA
17454129 AAGAAGAAGAAA
1 AAGAAGAAGAAA
17454141 AAGAAAGGAAAGAAAA
1 AAG-AA-G-AAG-AAA
*
17454157 AAGGAAAAAGGAAA
1 AA-GAAGAA-GAAA
17454171 AAG--GAAG-AA
1 AAGAAGAAGAAA
17454180 AAGAA-AAGGAAA
1 AAGAAGAA-GAAA
17454192 AAGAA
1 AAGAA
17454197 TAAAAAATTT
Statistics
Matches: 66, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
9 5 0.08
10 3 0.05
11 3 0.05
12 32 0.48
13 3 0.05
14 8 0.12
15 4 0.06
16 7 0.11
17 1 0.02
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
AAGAAGAAGAAA
Found at i:17454124 original size:15 final size:15
Alignment explanation
Indices: 17454104--17454202 Score: 69
Period size: 15 Copynumber: 6.6 Consensus size: 15
17454094 CTAGGCTTTT
* *
17454104 GAAGAAGAAGAAAAA
1 GAAGAAAAAGAAGAA
*
17454119 GAAGAAGAAGAAGAA
1 GAAGAAAAAGAAGAA
*
17454134 GAAGAAAAAGAA-AG
1 GAAGAAAAAGAAGAA
*
17454148 GAAAGAAAAA-AGGAA
1 G-AAGAAAAAGAAGAA
*
17454163 AAAGGAAAAAGGAAGAA
1 GAA-GAAAAA-GAAGAA
* *
17454180 -AAGAAAAGGAAAAA
1 GAAGAAAAAGAAGAA
*
17454194 GAATAAAAA
1 GAAGAAAAA
17454203 ATTTTAACAG
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
14 10 0.15
15 51 0.76
16 2 0.03
17 4 0.06
ACGTcount: A:0.73, C:0.00, G:0.26, T:0.01
Consensus pattern (15 bp):
GAAGAAAAAGAAGAA
Found at i:17454146 original size:6 final size:6
Alignment explanation
Indices: 17454105--17454196 Score: 62
Period size: 6 Copynumber: 14.8 Consensus size: 6
17454095 TAGGCTTTTG
* * * * *
17454105 AAGAAG AAGAAA AAGAAG AAGAAG AAGAAG AAGAAA AAG-AA AGGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
* *
17454152 GAA-AAA AGGAAA AAGGAAA AAGGAAGAA AAGAAA AGGAAA AAGAA
1 -AAGAAA AAGAAA AA-GAAA AA-G-A-AA AAGAAA AAGAAA AAGAA
17454197 TAAAAAATTT
Statistics
Matches: 71, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
5 5 0.07
6 50 0.70
7 10 0.14
8 2 0.03
9 4 0.06
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:17454164 original size:7 final size:7
Alignment explanation
Indices: 17454149--17454194 Score: 58
Period size: 7 Copynumber: 6.6 Consensus size: 7
17454139 AAAAGAAAGG
*
17454149 AAAGAAA
1 AAAGGAA
17454156 AAAGGAA
1 AAAGGAA
17454163 AAAGGAA
1 AAAGGAA
17454170 AAAGGAA
1 AAAGGAA
*
17454177 GAAAAG-A
1 -AAAGGAA
17454184 AAAGGAA
1 AAAGGAA
17454191 AAAG
1 AAAG
17454195 AATAAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
6 4 0.12
7 26 0.76
8 4 0.12
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (7 bp):
AAAGGAA
Found at i:17454166 original size:14 final size:14
Alignment explanation
Indices: 17454149--17454201 Score: 63
Period size: 14 Copynumber: 3.7 Consensus size: 14
17454139 AAAAGAAAGG
17454149 AAAGAAAAAAGGAA
1 AAAGAAAAAAGGAA
*
17454163 AAAGGAAAAAGGAA
1 AAAGAAAAAAGGAA
*
17454177 GAAA-AGAAAAGGAA
1 -AAAGAAAAAAGGAA
17454191 AAAGAATAAAA
1 AAAGAA-AAAA
17454202 AATTTTAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
13 3 0.09
14 22 0.69
15 7 0.22
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (14 bp):
AAAGAAAAAAGGAA
Found at i:17454693 original size:17 final size:18
Alignment explanation
Indices: 17454667--17454701 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
17454657 CATTTTTTTG
17454667 TATTTATATTTTTAATTT
1 TATTTATATTTTTAATTT
17454685 TATTT-TATTTTTAATTT
1 TATTTATATTTTTAATTT
17454702 AAATAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TATTTATATTTTTAATTT
Found at i:17460166 original size:12 final size:11
Alignment explanation
Indices: 17460149--17460263 Score: 70
Period size: 11 Copynumber: 10.5 Consensus size: 11
17460139 AACTAAATCC
17460149 TTTCTCTCAAT
1 TTTCTCTCAAT
17460160 TTT-TCTCTAAT
1 TTTCTCTC-AAT
* *
17460171 ATTCTCTCAAA
1 TTTCTCTCAAT
* *
17460182 TTCCTCTCAAA
1 TTTCTCTCAAT
* *
17460193 TTCCTCTTAAT
1 TTTCTCTCAAT
* *
17460204 TTCCTCTCAAA
1 TTTCTCTCAAT
* *
17460215 TTCCTCTCAAA
1 TTTCTCTCAAT
* *
17460226 TTCCTCTTAAT
1 TTTCTCTCAAT
* *
17460237 TTCCTCTCAAA
1 TTTCTCTCAAT
* *
17460248 TTCCTCTCAAA
1 TTTCTCTCAAT
17460259 TTTCT
1 TTTCT
17460264 ATTTAAAAGA
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
10 4 0.04
11 81 0.91
12 4 0.04
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.46
Consensus pattern (11 bp):
TTTCTCTCAAT
Found at i:17460190 original size:11 final size:11
Alignment explanation
Indices: 17460174--17460260 Score: 138
Period size: 11 Copynumber: 7.9 Consensus size: 11
17460164 CTCTAATATT
17460174 CTCTCAAATTC
1 CTCTCAAATTC
17460185 CTCTCAAATTC
1 CTCTCAAATTC
* *
17460196 CTCTTAATTTC
1 CTCTCAAATTC
17460207 CTCTCAAATTC
1 CTCTCAAATTC
17460218 CTCTCAAATTC
1 CTCTCAAATTC
* *
17460229 CTCTTAATTTC
1 CTCTCAAATTC
17460240 CTCTCAAATTC
1 CTCTCAAATTC
17460251 CTCTCAAATT
1 CTCTCAAATT
17460261 TCTATTTAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 68 1.00
ACGTcount: A:0.25, C:0.33, G:0.00, T:0.41
Consensus pattern (11 bp):
CTCTCAAATTC
Found at i:17460190 original size:33 final size:33
Alignment explanation
Indices: 17460174--17460260 Score: 174
Period size: 33 Copynumber: 2.6 Consensus size: 33
17460164 CTCTAATATT
17460174 CTCTCAAATTCCTCTCAAATTCCTCTTAATTTC
1 CTCTCAAATTCCTCTCAAATTCCTCTTAATTTC
17460207 CTCTCAAATTCCTCTCAAATTCCTCTTAATTTC
1 CTCTCAAATTCCTCTCAAATTCCTCTTAATTTC
17460240 CTCTCAAATTCCTCTCAAATT
1 CTCTCAAATTCCTCTCAAATT
17460261 TCTATTTAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.25, C:0.33, G:0.00, T:0.41
Consensus pattern (33 bp):
CTCTCAAATTCCTCTCAAATTCCTCTTAATTTC
Found at i:17462128 original size:18 final size:18
Alignment explanation
Indices: 17462101--17462140 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
17462091 CAGGTGTGTA
*
17462101 TCCTAGCCCTTATATATG
1 TCCTAACCCTTATATATG
*
17462119 TCCTAACCCTTATATATT
1 TCCTAACCCTTATATATG
17462137 TCCT
1 TCCT
17462141 TTTTCTAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.30, G:0.05, T:0.42
Consensus pattern (18 bp):
TCCTAACCCTTATATATG
Found at i:17463820 original size:125 final size:125
Alignment explanation
Indices: 17463595--17463881 Score: 432
Period size: 125 Copynumber: 2.3 Consensus size: 125
17463585 CCAAACATGA
* * * * * * *
17463595 TACTGTAGCAAAAACGTGTCCACGTGGGAGCGATTTTAGTATTTCTTCTCATAAAGCATCCTGCT
1 TACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTAATAAAGCATCCTACT
17463660 TAAAGCATTTTACACACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACC
66 TAAAGCATTTTACACACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACC
*
17463720 TATTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTAATAAAGCATCCTACT
1 TACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTAATAAAGCATCCTACT
* ** * * *
17463785 TGAAGTGGTTTT-TATACTATTTGCTCAGAAACGTCAACTCGGAATTATTTTTTCAGGACC
66 TAAAG-CATTTTACACACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACC
17463845 TACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
1 TACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
17463882 CTTAATAAAT
Statistics
Matches: 146, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
125 142 0.97
126 4 0.03
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (125 bp):
TACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTAATAAAGCATCCTACT
TAAAGCATTTTACACACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACC
Found at i:17464085 original size:6 final size:6
Alignment explanation
Indices: 17464067--17464111 Score: 63
Period size: 6 Copynumber: 7.3 Consensus size: 6
17464057 AAATTTTAAA
* *
17464067 AACCCT AAACCCT AACCCT AACCGT AACTCT AACCCT AACCCT AA
1 AACCCT -AACCCT AACCCT AACCCT AACCCT AACCCT AACCCT AA
17464112 AAACCTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
6 28 0.82
7 6 0.18
ACGTcount: A:0.38, C:0.42, G:0.02, T:0.18
Consensus pattern (6 bp):
AACCCT
Found at i:17467310 original size:106 final size:106
Alignment explanation
Indices: 17467178--17467827 Score: 676
Period size: 107 Copynumber: 6.2 Consensus size: 106
17467168 TAGATATAAT
*
17467178 TTTTTTTTTACTTTTTT-GTATACTGATACCTGATACAGACATGAAAAAAAGTCAAAATTTTTTT
1 TTTTTTTTTACTTTTTTCGTATACTGATACCTGATACTGACATGAAAAAAAGTC-AAATTTTTTT
*
17467242 TACTGTACTGGGTGCCGGCCATTGACAGGCCAGCAACCTAAA
65 TACTGTACTGGGTGCCGGCCATTGACAGGCCAGCAACCCAAA
**
17467284 -TTTTTTTTACTTTTTTCGTATACTGATACCTGATACCAACATG-AAAAAAGTCAAATTTTTTTT
1 TTTTTTTTTACTTTTTTCGTATACTGATACCTGATACTGACATGAAAAAAAGTCAAATTTTTTTT
* * *
17467347 GCTGTATTGGGTGCCGGCCATTGACAGGCCCGC-ACCCAAAA
66 ACTGTACTGGGTGCCGGCCATTGACAGGCCAGCAACCC-AAA
** * ** * ** * ** * *
17467388 TTTTTTTTTTTTTTTTTTTCGTACT-CTGGTGTCGGCCATTGACAT-ACCAAAACTCGAATTTTT
1 --TTTTTTTTTACTTTTTTCGTA-TACTGATACCTGATACTGACATGAAAAAAAGTCAAATTTTT
* * *
17467451 TTTACTGTACTGGGTGTCGACCATTGACAGACCAGC-ACCCAAA
63 TTTACTGTACTGGGTGCCGGCCATTGACAGGCCAGCAACCCAAA
* * *
17467494 TTTTTTTTTTACTTTTTTTAGTATACTGATACCTGATACGGACATGAAAAAAAGTCAAATCTTTT
1 -TTTTTTTTTAC-TTTTTTCGTATACTGATACCTGATACTGACATGAAAAAAAGTCAAATTTTTT
*
17467559 TTACTGTACTGGGTGCCGGCCATTGACAGGTCAGC-ACCCAAA
64 TTACTGTACTGGGTGCCGGCCATTGACAGGCCAGCAACCCAAA
* *
17467601 TTTTTTTTTACTTTTTTTTCGTATACTGATACCTGATACTGATA-CAAAAAAAGTCAAAATTGTT
1 TTTTTTTTTAC--TTTTTTCGTATACTGATACCTGATACTGACATGAAAAAAAGTC-AAA-T-TT
17467665 TTTTTACTGTACTGGGT----G-C--TG---GGCCAGC-ACCCAAAA
61 TTTTTACTGTACTGGGTGCCGGCCATTGACAGGCCAGCAACCC-AAA
* * *
17467701 TTTTTTTTTTACTTTTTTTCGTATACTAATACCTGAT-GTGACACGAAAAAAAGTCAAAATTTTT
1 -TTTTTTTTTAC-TTTTTTCGTATACTGATACCTGATACTGACATGAAAAAAAGTC-AAA-TTTT
* * *
17467765 TTTTACTGTATTGGGTGCCGGCCATTGACAGGCCAGCACCCCAATT
62 TTTTACTGTACTGGGTGCCGGCCATTGACAGGCCAGCAACCCAA-A
17467811 TTTTTTTTTACTTTTTT
1 TTTTTTTTTACTTTTTT
17467828 TTGTACTGGG
Statistics
Matches: 455, Mismatches: 60, Indels: 56
0.80 0.11 0.10
Matches are distributed among these distances:
99 32 0.07
100 43 0.09
101 11 0.02
102 2 0.00
103 4 0.01
104 46 0.10
105 37 0.08
106 71 0.16
107 160 0.35
108 8 0.02
109 38 0.08
110 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (106 bp):
TTTTTTTTTACTTTTTTCGTATACTGATACCTGATACTGACATGAAAAAAAGTCAAATTTTTTTT
ACTGTACTGGGTGCCGGCCATTGACAGGCCAGCAACCCAAA
Found at i:17467496 original size:48 final size:48
Alignment explanation
Indices: 17467398--17467501 Score: 120
Period size: 48 Copynumber: 2.2 Consensus size: 48
17467388 TTTTTTTTTT
* * * * * *
17467398 TTTTTTTTTCGTACTCTGGTGTCGGCCATTGACATACCAAAACTCGAA
1 TTTTTTTTACGTACTCGGGTGTCGACCATTGACAGACCAAAACCCAAA
**
17467446 TTTTTTTTACTGTACT-GGGTGTCGACCATTGACAGACCAGCACCCAAA
1 TTTTTTTTAC-GTACTCGGGTGTCGACCATTGACAGACCAAAACCCAAA
17467494 TTTTTTTT
1 TTTTTTTT
17467502 TTACTTTTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
48 42 0.89
49 5 0.11
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39
Consensus pattern (48 bp):
TTTTTTTTACGTACTCGGGTGTCGACCATTGACAGACCAAAACCCAAA
Found at i:17467726 original size:100 final size:100
Alignment explanation
Indices: 17467482--17467828 Score: 364
Period size: 109 Copynumber: 3.3 Consensus size: 100
17467472 CATTGACAGA
* * *
17467482 CCAGCACCCAAATTTTTTTTTTACTTTTTTTAGTATACTGATACCTGATACGGACATGAAAAAAA
1 CCAGCACCCAAATTTTTTTTTTACTTTTTTTCGTATACTGATACCTGATACTGACA-CAAAAAAA
*
17467547 GTC-AAA-TCTTTTTTACTGTACTGGGTGCCGGCCATTGACAGG
65 GTCAAAATTTTTTTTTACTGTACTGGGT----G-CA-TG--AGG
* *
17467589 TCAGCACCCAAA-TTTTTTTTTACTTTTTTTTCGTATACTGATACCTGATACTGATACAAAAAAA
1 CCAGCACCCAAATTTTTTTTTTAC-TTTTTTTCGTATACTGATACCTGATACTGACACAAAAAAA
17467653 GTCAAAATTGTTTTTTTACTGTACTGGGTGC-TG-GG
65 GTCAAAATT-TTTTTTTACTGTACTGGGTGCATGAGG
* *
17467688 CCAGCACCCAAAATTTTTTTTTTACTTTTTTTCGTATACTAATACCTGAT-GTGACACGAAAAAA
1 CCAGCACCC-AAATTTTTTTTTTACTTTTTTTCGTATACTGATACCTGATACTGACAC-AAAAAA
*
17467752 AGTCAAAATTTTTTTTTACTGTATTGGGTGCCGGCCATTGACAGG
64 AGTCAAAATTTTTTTTTACTGTACTGGGT----G-CA-TG--AGG
*
17467797 CCAGCACCCCAATTTTTTTTTTTACTTTTTTT
1 CCAGCA-CCCAAATTTTTTTTTTACTTTTTTT
17467829 TGTACTGGGT
Statistics
Matches: 210, Mismatches: 12, Indels: 34
0.82 0.05 0.13
Matches are distributed among these distances:
99 33 0.16
100 43 0.20
101 11 0.05
102 2 0.01
103 1 0.00
104 2 0.01
105 1 0.00
106 23 0.11
107 43 0.20
108 1 0.00
109 47 0.22
110 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.40
Consensus pattern (100 bp):
CCAGCACCCAAATTTTTTTTTTACTTTTTTTCGTATACTGATACCTGATACTGACACAAAAAAAG
TCAAAATTTTTTTTTACTGTACTGGGTGCATGAGG
Found at i:17467874 original size:58 final size:57
Alignment explanation
Indices: 17467762--17467890 Score: 159
Period size: 58 Copynumber: 2.2 Consensus size: 57
17467752 AGTCAAAATT
* * ****
17467762 TTTTTTTACTGTATTGGGTGCCGGCCATTGACAGGCCAGCACCCCAATTTTTTTTTTTAC
1 TTTTTTT--TGTACTGGGTGCCGGCCATTGACAGGCCAACA-CCCAAAAAGTTTTTTTAC
*
17467822 TTTTTTTTGTACTGGGTGCCGGCCATTGACAGGCCAACACCCAAAAAGTTTTTTTCC
1 TTTTTTTTGTACTGGGTGCCGGCCATTGACAGGCCAACACCCAAAAAGTTTTTTTAC
17467879 TTCTTTTTTGTA
1 TT-TTTTTTGTA
17467891 TATTAGTATT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
57 15 0.25
58 39 0.64
60 7 0.11
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (57 bp):
TTTTTTTTGTACTGGGTGCCGGCCATTGACAGGCCAACACCCAAAAAGTTTTTTTAC
Found at i:17474869 original size:16 final size:16
Alignment explanation
Indices: 17474848--17474880 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
17474838 TCACAATACT
17474848 AGAGTAAATAAATTTG
1 AGAGTAAATAAATTTG
*
17474864 AGAGTATATAAATTTG
1 AGAGTAAATAAATTTG
17474880 A
1 A
17474881 AAATTTTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.33
Consensus pattern (16 bp):
AGAGTAAATAAATTTG
Found at i:17475660 original size:13 final size:15
Alignment explanation
Indices: 17475626--17475655 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17475616 AGCATGCCAT
*
17475626 CATATATATGTATAA
1 CATATTTATGTATAA
17475641 CATATTTATGTATAA
1 CATATTTATGTATAA
17475656 AATTTTTGAC
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:0.07, G:0.07, T:0.43
Consensus pattern (15 bp):
CATATTTATGTATAA
Found at i:17478870 original size:26 final size:26
Alignment explanation
Indices: 17478827--17478889 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
17478817 ATGAGATCTG
* * *
17478827 ATTTTTAAAAATATTTTCTATTTT-T
1 ATTTTCAAAAATAATTTCCATTTTCT
17478852 ATTTTCAAATAATAATTTCCATTTTCT
1 ATTTTCAAA-AATAATTTCCATTTTCT
*
17478879 ATTTTTAAAAA
1 ATTTTCAAAAA
17478890 ATTAAAAAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 8 0.25
26 15 0.47
27 9 0.28
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.56
Consensus pattern (26 bp):
ATTTTCAAAAATAATTTCCATTTTCT
Found at i:17481919 original size:2 final size:2
Alignment explanation
Indices: 17481914--17481950 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
17481904 TTTAATTACT
17481914 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17481951 TAAAAAAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17488285 original size:371 final size:371
Alignment explanation
Indices: 17487602--17488345 Score: 1371
Period size: 371 Copynumber: 2.0 Consensus size: 371
17487592 ATATAGCTGG
*
17487602 TGCTAATTTGGCCGATGAAAGTGGTGATGATTTCTTGTTAGTGTCAACAAGTGATAACTCCAAGC
1 TGCTAATTTGGCCGATGAAAGCGGTGATGATTTCTTGTTAGTGTCAACAAGTGATAACTCCAAGC
17487667 TTACATCCGAGTGGGTCCTACATTCGAGATGTTCTTTCCATATATGTCCCAATAGAGAATGGTTC
66 TTACATCCGAGTGGGTCCTACATTCGAGATGTTCTTTCCATATATGTCCCAATAGAGAATGGTTC
* *
17487732 TCCACATACAATTCGATTGAATATGGAGTTGTGCGCATGGGAAACGATTCATCCAATAAGGTATT
131 TCCACATACAATTCGATTGAATATGGAGTTGTGCGCATGAGAAACGATTCATCCAATAAGGTAAT
*
17487797 TGGTATTGGCAATGTTAAAATTAAAATACACGATGGGACAATTAGGACACTCTAAGATGTTAGGT
196 TGGTATTGGCAATGTTAAAATTAAAATACACGATGGAACAATTAGGACACTCTAAGATGTTAGGT
*
17487862 ATGTAGCTGATTTACAAAAAAATCTTATCTCATTGAGTATTTTAGACTTGAAATGATGCAAAATC
261 ATGTAGCTGATTTACAAAAAAATCTCATCTCATTGAGTATTTTAGACTTGAAATGATGCAAAATC
17487927 AACATCGAGTCGAGTGGCACTAAAGTATCTCGTGGAGCTCTCATTT
326 AACATCGAGTCGAGTGGCACTAAAGTATCTCGTGGAGCTCTCATTT
17487973 TGCTAATTTGGCCGATGAAAGCGGTGATGATTTCTTGTTAGTGTCAACAAGTGATAACTCCAAGC
1 TGCTAATTTGGCCGATGAAAGCGGTGATGATTTCTTGTTAGTGTCAACAAGTGATAACTCCAAGC
*
17488038 TTACATCCGAGTGGGTCCTGCATTCGAGATGTTCTTTCCATATATGTCCCAATAGAGAATGGTTC
66 TTACATCCGAGTGGGTCCTACATTCGAGATGTTCTTTCCATATATGTCCCAATAGAGAATGGTTC
* *
17488103 TCCACATACAATTCGGTTGAATGTGGAGTTGTGCGCATGAGAAACGATTCATCCAATAAGGTAAT
131 TCCACATACAATTCGATTGAATATGGAGTTGTGCGCATGAGAAACGATTCATCCAATAAGGTAAT
* *
17488168 TGGTATTGGTACTGTTAAAATTAAAATACACGATGGAACAATTAGGACACTCTAAGATGTTAGGT
196 TGGTATTGGCAATGTTAAAATTAAAATACACGATGGAACAATTAGGACACTCTAAGATGTTAGGT
* *
17488233 ATGTAGCTGATTTACGAAAAAATCTCATCTCATTGAGTATTTTAGACTTGAAATGATGCAGAATC
261 ATGTAGCTGATTTACAAAAAAATCTCATCTCATTGAGTATTTTAGACTTGAAATGATGCAAAATC
*
17488298 AACATCGAGTCGAGTGGCACTAAAGTATCTTGTGGAGCTCTCATTT
326 AACATCGAGTCGAGTGGCACTAAAGTATCTCGTGGAGCTCTCATTT
17488344 TG
1 TG
17488346 TTAAAAGGTA
Statistics
Matches: 360, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
371 360 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (371 bp):
TGCTAATTTGGCCGATGAAAGCGGTGATGATTTCTTGTTAGTGTCAACAAGTGATAACTCCAAGC
TTACATCCGAGTGGGTCCTACATTCGAGATGTTCTTTCCATATATGTCCCAATAGAGAATGGTTC
TCCACATACAATTCGATTGAATATGGAGTTGTGCGCATGAGAAACGATTCATCCAATAAGGTAAT
TGGTATTGGCAATGTTAAAATTAAAATACACGATGGAACAATTAGGACACTCTAAGATGTTAGGT
ATGTAGCTGATTTACAAAAAAATCTCATCTCATTGAGTATTTTAGACTTGAAATGATGCAAAATC
AACATCGAGTCGAGTGGCACTAAAGTATCTCGTGGAGCTCTCATTT
Found at i:17497500 original size:39 final size:39
Alignment explanation
Indices: 17497446--17497524 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
17497436 ACACACATGT
17497446 AAGCTTATAGAAAAGCTTAGTAAAGTTCATAGGCATAAA
1 AAGCTTATAGAAAAGCTTAGTAAAGTTCATAGGCATAAA
17497485 AAGCTTATAGAAAAGCTTAGTAAAGTTCATAGGCATAAA
1 AAGCTTATAGAAAAGCTTAGTAAAGTTCATAGGCATAAA
17497524 A
1 A
17497525 CATAAATCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.25
Consensus pattern (39 bp):
AAGCTTATAGAAAAGCTTAGTAAAGTTCATAGGCATAAA
Found at i:17497853 original size:36 final size:36
Alignment explanation
Indices: 17497806--17498094 Score: 443
Period size: 36 Copynumber: 8.0 Consensus size: 36
17497796 GCTAAGCTAC
17497806 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
17497842 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
* *
17497878 CACTTATCACTTTTTCACTTGATCAGATAAGTATAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
* *
17497914 CACTTATCACTTTTTCACTTGATCAGATAAGTATAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
* * *
17497950 CACTTATCATTTTGTCTCTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
* * *
17497986 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
* *
17498022 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
* * *
17498058 AACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
17498094 C
1 C
17498095 TAAAGCTACC
Statistics
Matches: 235, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 235 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
Found at i:17501076 original size:42 final size:42
Alignment explanation
Indices: 17500983--17501079 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 42
17500973 TTTGAGTTTT
* * * * * *
17500983 CGTTCAACCCTAATGGGTTTCCGTTCATCTCTTTTGAGCTTC
1 CGTTCAACCTTTATGGGATTCCGTTCAGCTCTTATGAACTTC
* *
17501025 TGTTTAACCTTTATGGGATTCCGTTCAGCTCTTATGAACTTC
1 CGTTCAACCTTTATGGGATTCCGTTCAGCTCTTATGAACTTC
17501067 CGTTCAACCTTTA
1 CGTTCAACCTTTA
17501080 CGGGTTTCTA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.18, C:0.26, G:0.15, T:0.41
Consensus pattern (42 bp):
CGTTCAACCTTTATGGGATTCCGTTCAGCTCTTATGAACTTC
Found at i:17502442 original size:51 final size:51
Alignment explanation
Indices: 17502383--17502599 Score: 286
Period size: 51 Copynumber: 4.4 Consensus size: 51
17502373 CTGATCACAT
*
17502383 TTATCACTTGTCACTCATCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
* * *
17502434 TTATCACTTGTCACTTGTAATTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
* *
17502485 TTATCACTTG-------TCACTGATCAGATAAATGTAGCTAAAGCTACCAG
1 TTATCACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
* * *
17502529 TTATCAATTGTCACTTGTCACTGATTAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
* *
17502580 TTATCACTTGTTACTGATCA
1 TTATCACTTGTCACTTATCA
17502600 GAAGTACTCA
Statistics
Matches: 143, Mismatches: 16, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
44 39 0.27
51 104 0.73
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
Found at i:17502486 original size:44 final size:44
Alignment explanation
Indices: 17502438--17502601 Score: 202
Period size: 44 Copynumber: 3.6 Consensus size: 44
17502428 TACCACTTAT
* * *
17502438 CACTTGTCACTTGTAATTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
*
17502482 CACTTATCACTTGTCACTGATCAGATAAATGTAGCTAAAGCTAC
1 CACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
* *
17502526 CAGTTATCAATTGTCACTTGTCACTGATTAGATAAGTGTAGCTAAAGCTAC
1 C----A-C--TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
*
17502577 CACTTATCACTTGTTACTGATCAGA
1 CACTTATCACTTGTCACTGATCAGA
17502602 AGTACTCAAA
Statistics
Matches: 103, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
44 60 0.58
46 1 0.01
47 1 0.01
48 1 0.01
49 1 0.01
51 39 0.38
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (44 bp):
CACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:17502527 original size:95 final size:95
Alignment explanation
Indices: 17502400--17502601 Score: 341
Period size: 95 Copynumber: 2.1 Consensus size: 95
17502390 TTGTCACTCA
* * *
17502400 TCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTGTAATTGATCAGATA
1 TCACTGATCAGATAAATGTAGCTAAAGCTACCACTTATCAATTGTCACTTGTAACTGATCAGATA
17502465 AGTGTAGCTAAAGCTACCACTTATCACTTG
66 AGTGTAGCTAAAGCTACCACTTATCACTTG
* * *
17502495 TCACTGATCAGATAAATGTAGCTAAAGCTACCAGTTATCAATTGTCACTTGTCACTGATTAGATA
1 TCACTGATCAGATAAATGTAGCTAAAGCTACCACTTATCAATTGTCACTTGTAACTGATCAGATA
17502560 AGTGTAGCTAAAGCTACCACTTATCACTTG
66 AGTGTAGCTAAAGCTACCACTTATCACTTG
*
17502590 TTACTGATCAGA
1 TCACTGATCAGA
17502602 AGTACTCAAA
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
95 100 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (95 bp):
TCACTGATCAGATAAATGTAGCTAAAGCTACCACTTATCAATTGTCACTTGTAACTGATCAGATA
AGTGTAGCTAAAGCTACCACTTATCACTTG
Found at i:17502695 original size:17 final size:17
Alignment explanation
Indices: 17502673--17502705 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
17502663 TATTCTCAAT
17502673 TCATCA-ACAAATATATC
1 TCATCATAC-AATATATC
17502690 TCATCATACAATATAT
1 TCATCATACAATATAT
17502706 AATTCATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
TCATCATACAATATATC
Found at i:17506575 original size:315 final size:315
Alignment explanation
Indices: 17506003--17506950 Score: 1700
Period size: 315 Copynumber: 3.0 Consensus size: 315
17505993 GGTCAAAGTA
17506003 AAGGTAGGTCTTTAGTGAGCCTCTGAACCTGACTTTTGCTTGTCATTTTATGTTGATTATGCTAT
1 AAGGTAGGTCTTTAGTGAGCCTCTGAACCTGACTTTTGCTTGTCATTTTATGTTGATTATGCTAT
* * *
17506068 GGCGTTTACCCTTAAATTACCTAGAGAACTATTCTGAGTGTGAAGGGATTAATAGAGAGGGGATC
66 GGTGTTTACCCTTAAATTACCTAGAGAACTATTTTGAGTGTCAAGGGATTAATAGAGAGGGGATC
17506133 TGGTTGGCAAATTGGTACAGGAGAAAGGGTGAACATCTAGAATGACTCGTGTATTCCTGAACTTA
131 TGGTTGGCAAATTGGTACAGGAGAAAGGGTGAACATCTAGAATGACTCGTGTATTCCTGAACTTA
* *
17506198 -AATATGAGAGAATTATACACCAGAATATTGATGTCGGATTTTTTGCTGTTGCACATTTGATCAA
196 GGA-ATGAGAGAATTATACACCAGAATATTGATGTCAGATTTTTTGCTGTTGCACATTTGATCAA
17506262 TTCAGACTCTTGTACTTGGAATGAAGGAAGAGTTAGATCCCTCTTTGATGCTGATC
260 TTCAGACTCTTGTACTTGGAATGAAGGAAGAGTTAGATCCCTCTTTGATGCTGATC
* * *
17506318 AAGGTAGGTCTTCAGTGAGCCTCTAAACCTGACTTTTGCTTGTCATTTTATGTTGATTATACTAT
1 AAGGTAGGTCTTTAGTGAGCCTCTGAACCTGACTTTTGCTTGTCATTTTATGTTGATTATGCTAT
* *
17506383 GGTGTTTACCCTTAAATTACCTAGAGAAGTATTTTGAGTGTCAAGGGATTAATAGATAGGGGATC
66 GGTGTTTACCCTTAAATTACCTAGAGAACTATTTTGAGTGTCAAGGGATTAATAGAGAGGGGATC
* *
17506448 TAGTTGGCAAATTGGTATAGGAGAAAGGGTGAACATCTAGAATGACTCGTGTATTCCTGAACTTA
131 TGGTTGGCAAATTGGTACAGGAGAAAGGGTGAACATCTAGAATGACTCGTGTATTCCTGAACTTA
*
17506513 GGAATGAGAGAATTATACACCAGAATATTGATGTCAGATTTTTTGATGTTGCACATTTGATCAAT
196 GGAATGAGAGAATTATACACCAGAATATTGATGTCAGATTTTTTGCTGTTGCACATTTGATCAAT
* * *
17506578 TCAGACTCTTGTACTTGGAATGAATGAAGAGTTAGATCACTTTTTGATGCTGATC
261 TCAGACTCTTGTACTTGGAATGAAGGAAGAGTTAGATCCCTCTTTGATGCTGATC
* *
17506633 AAGGTAGGTCTTTAGTGAGCCTCTGAACCTGACTTTTTCTTGTCATTTTATGTTGATTATGTTAT
1 AAGGTAGGTCTTTAGTGAGCCTCTGAACCTGACTTTTGCTTGTCATTTTATGTTGATTATGCTAT
*
17506698 GGTGTTTACCCTTAAATTACCTAGAGAACTATTTTAAGTGTCAAGGGATTAATAGAGAGGGGATC
66 GGTGTTTACCCTTAAATTACCTAGAGAACTATTTTGAGTGTCAAGGGATTAATAGAGAGGGGATC
17506763 TGGTTGGCAAATTGGTACAGGAGAAAGGGTGAACATCTAGAATGACTCGTGTATTCCTGAACTTA
131 TGGTTGGCAAATTGGTACAGGAGAAAGGGTGAACATCTAGAATGACTCGTGTATTCCTGAACTTA
*
17506828 GGAATGAGAGAATTATACACCAGAATATTGATGTTAGATTTTTTGCTGTTGCACATTTGATCAAT
196 GGAATGAGAGAATTATACACCAGAATATTGATGTCAGATTTTTTGCTGTTGCACATTTGATCAAT
17506893 TCAGACTCTTGTACTTGGAATGAAGGAAGAGTTAGATCCCTCTTTGATGCTGATC
261 TCAGACTCTTGTACTTGGAATGAAGGAAGAGTTAGATCCCTCTTTGATGCTGATC
17506948 AAG
1 AAG
17506951 CTGAGAAAGT
Statistics
Matches: 601, Mismatches: 31, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
315 600 1.00
316 1 0.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (315 bp):
AAGGTAGGTCTTTAGTGAGCCTCTGAACCTGACTTTTGCTTGTCATTTTATGTTGATTATGCTAT
GGTGTTTACCCTTAAATTACCTAGAGAACTATTTTGAGTGTCAAGGGATTAATAGAGAGGGGATC
TGGTTGGCAAATTGGTACAGGAGAAAGGGTGAACATCTAGAATGACTCGTGTATTCCTGAACTTA
GGAATGAGAGAATTATACACCAGAATATTGATGTCAGATTTTTTGCTGTTGCACATTTGATCAAT
TCAGACTCTTGTACTTGGAATGAAGGAAGAGTTAGATCCCTCTTTGATGCTGATC
Found at i:17522263 original size:27 final size:27
Alignment explanation
Indices: 17522233--17522297 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
17522223 CCTATCAGGT
17522233 AGGCGCCAATGAAGGTGCCTCATAAAG
1 AGGCGCCAATGAAGGTGCCTCATAAAG
** * **
17522260 AGGCGCCAATGAATTTGCCTCTTAGGG
1 AGGCGCCAATGAAGGTGCCTCATAAAG
17522287 AGGCGCCAATG
1 AGGCGCCAATG
17522298 GTGGCCTTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.28, C:0.23, G:0.31, T:0.18
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCATAAAG
Found at i:17522429 original size:3 final size:3
Alignment explanation
Indices: 17522423--17522457 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
17522413 GAGAGAAAGG
17522423 AGA AGA AGA A-A AGA AGA AGA AG- AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
17522458 AGAAAGAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:17522462 original size:4 final size:4
Alignment explanation
Indices: 17522453--17522478 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
17522443 AGAGAAGAAG
17522453 AAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AA
17522479 ATGTAATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:17522464 original size:11 final size:12
Alignment explanation
Indices: 17522411--17522477 Score: 68
Period size: 11 Copynumber: 5.4 Consensus size: 12
17522401 TGGGAAAAAA
17522411 AAGAGAGAAAGGAG
1 AAGA-AGAAA-GAG
17522425 AAGAAGAAA-AG
1 AAGAAGAAAGAG
17522436 AAGAAGAAGAGAAG
1 AAGAAGAA-AG-AG
17522450 AAGAAGAAAGA-
1 AAGAAGAAAGAG
17522461 AAGAAAGAAAGA-
1 AAG-AAGAAAGAG
17522473 AAGAA
1 AAGAA
17522478 AATGTAATGT
Statistics
Matches: 49, Mismatches: 0, Indels: 11
0.82 0.00 0.18
Matches are distributed among these distances:
11 15 0.31
12 13 0.27
13 7 0.14
14 14 0.29
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (12 bp):
AAGAAGAAAGAG
Found at i:17522464 original size:14 final size:14
Alignment explanation
Indices: 17522411--17522477 Score: 70
Period size: 14 Copynumber: 4.9 Consensus size: 14
17522401 TGGGAAAAAA
* *
17522411 AAGAGAGAAAGGAG
1 AAGAAAGAAAGAAG
17522425 AAG-AAGAAAAGAAG
1 AAGAAAG-AAAGAAG
17522439 AAG-AAGAGAAGAAG
1 AAGAAAGA-AAGAAG
17522453 AAGAAAGAAAG-A-
1 AAGAAAGAAAGAAG
17522465 AAGAAAGAAAGAA
1 AAGAAAGAAAGAA
17522478 AATGTAATGT
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
12 11 0.23
13 5 0.11
14 27 0.57
15 4 0.09
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (14 bp):
AAGAAAGAAAGAAG
Found at i:17522636 original size:19 final size:19
Alignment explanation
Indices: 17522608--17522730 Score: 83
Period size: 19 Copynumber: 6.2 Consensus size: 19
17522598 TTGGATTAGT
*
17522608 ATTTTATATGAATATTGTA
1 ATTTTGTATGAATATTGTA
17522627 ATTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTA
*
17522646 ATTATTTTAT-AATTAAATTTGT-
1 ATT-TTGTATGAA-T--A-TTGTA
* * *
17522668 ATTTATAGTTTTGGAT-TAGT-
1 ATTT-T-G-TATGAATATTGTA
17522688 ATTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTA
17522707 ATTTTTTGTATGAATATTGTA
1 A--TTTTGTATGAATATTGTA
17522728 ATT
1 ATT
17522731 ATTTTATAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
17 5 0.06
18 4 0.05
19 27 0.33
20 13 0.16
21 20 0.24
22 5 0.06
23 4 0.05
24 3 0.04
25 1 0.01
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (19 bp):
ATTTTGTATGAATATTGTA
Found at i:17522714 original size:21 final size:22
Alignment explanation
Indices: 17522687--17522735 Score: 91
Period size: 21 Copynumber: 2.3 Consensus size: 22
17522677 TTTGGATTAG
17522687 TATTTTGTATGAATATTGTAAT
1 TATTTTGTATGAATATTGTAAT
17522709 T-TTTTGTATGAATATTGTAAT
1 TATTTTGTATGAATATTGTAAT
17522730 TATTTT
1 TATTTT
17522736 ATAATTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (22 bp):
TATTTTGTATGAATATTGTAAT
Found at i:17522743 original size:82 final size:78
Alignment explanation
Indices: 17522590--17522748 Score: 273
Period size: 82 Copynumber: 2.0 Consensus size: 78
17522580 ATATTTAGTG
17522590 TTTATAGTTTGGATTAGTATTTTATATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTA
1 TTTATAGTTTGGATTAGTATTTTATATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTA
17522655 TAATTAAATTTGTA
66 TAATT-AATTTGTA
*
17522669 TTTATAGTTTTGGATTAGTATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATTATT
1 TTTATAG-TTTGGATTAGTATTTTATATGAATATTGTAA--TTTTGTATGAATATTGTAATTATT
17522734 TTATAATTAATTTGT
63 TTATAATTAATTTGT
17522749 TAGTAATTTA
Statistics
Matches: 76, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
79 7 0.09
80 30 0.39
81 7 0.09
82 32 0.42
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (78 bp):
TTTATAGTTTGGATTAGTATTTTATATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTA
TAATTAATTTGTA
Found at i:17522804 original size:60 final size:60
Alignment explanation
Indices: 17522723--17522844 Score: 174
Period size: 60 Copynumber: 2.0 Consensus size: 60
17522713 TGTATGAATA
* * * * *
17522723 TTGTAATTATTTTATAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
*
17522783 TTGTAATTA-TTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAGTTGTTGTGT
1 TTGTAATTATTTTAAAA-TTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
17522843 TT
1 TT
17522845 AGTTTAGTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 6 0.11
60 49 0.89
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54
Consensus pattern (60 bp):
TTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
Found at i:17528238 original size:27 final size:28
Alignment explanation
Indices: 17528165--17528239 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 28
17528155 GAAAAATCAG
* *
17528165 ACCATTGGCGCCTCTTA-ACATGACACC
1 ACCATTGGCGCCTCTCAGATATGACACC
* *
17528192 ACTATTGGCGCCTCTCAGATA-GGCACC
1 ACCATTGGCGCCTCTCAGATATGACACC
*
17528219 ACCATTGGCGCCTCTGAGATA
1 ACCATTGGCGCCTCTCAGATA
17528240 AGCGCCAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 39 0.95
28 2 0.05
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.23
Consensus pattern (28 bp):
ACCATTGGCGCCTCTCAGATATGACACC
Found at i:17528668 original size:6 final size:6
Alignment explanation
Indices: 17528657--17528697 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
17528647 TTCCTATACC
* *
17528657 CACGCT CACGCT CACGCT CACGCT CACGCC CACGCC CACGC
1 CACGCT CACGCT CACGCT CACGCT CACGCT CACGCT CACGC
17528698 GCCTTCTTGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.17, C:0.56, G:0.17, T:0.10
Consensus pattern (6 bp):
CACGCT
Found at i:17536872 original size:11 final size:11
Alignment explanation
Indices: 17536832--17536958 Score: 91
Period size: 11 Copynumber: 12.4 Consensus size: 11
17536822 ATAAATACCA
17536832 AAAAATTATTTT
1 AAAAA-TATTTT
*
17536844 -AAAA-A-TTA
1 AAAAATATTTT
17536852 AAAAAGTATTTT
1 AAAAA-TATTTT
17536864 AAAAATATTTT
1 AAAAATATTTT
17536875 --AAA-A--TT
1 AAAAATATTTT
*
17536881 AAAAA-A-TTA
1 AAAAATATTTT
17536890 AAAAAGTATTTT
1 AAAAA-TATTTT
17536902 AAAAATATTTT
1 AAAAATATTTT
17536913 AAAAATATTTT
1 AAAAATATTTT
**
17536924 --AAA-ATTAA
1 AAAAATATTTT
17536932 AAAAAGTATTTT
1 AAAAA-TATTTT
17536944 AAAAATATTTT
1 AAAAATATTTT
17536955 AAAA
1 AAAA
17536959 TTAAAAATAA
Statistics
Matches: 93, Mismatches: 8, Indels: 29
0.72 0.06 0.22
Matches are distributed among these distances:
6 2 0.02
8 10 0.11
9 17 0.18
10 3 0.03
11 39 0.42
12 22 0.24
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:17536942 original size:31 final size:30
Alignment explanation
Indices: 17536902--17536965 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 30
17536892 AAAGTATTTT
17536902 AAAAATATTTTAAAAATATTTTAAAATTAA
1 AAAAATATTTTAAAAATATTTTAAAATTAA
17536932 AAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAAA-TATTTTAAAAATATTTTAAAATTAA
17536963 AAA
1 AAA
17536966 TAAATATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 5 0.15
31 28 0.85
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (30 bp):
AAAAATATTTTAAAAATATTTTAAAATTAA
Found at i:17545793 original size:4 final size:4
Alignment explanation
Indices: 17545784--17545810 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
17545774 CATTTGAGTC
17545784 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
17545811 AGCAAAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:17547208 original size:43 final size:43
Alignment explanation
Indices: 17547101--17547228 Score: 138
Period size: 43 Copynumber: 3.0 Consensus size: 43
17547091 CTCGTACAAC
* * *
17547101 GCCAACGTCCCAGACGTGGTCTTACATGTAAACATATATCGAT
1 GCCAACGTCCCAGACGTGGTCTTACACGTAAACACAAATCGAT
*
17547144 GCC-ACTGTCCCAGATAG-GGTCTTACACGTAAACACAAA-CTGAT
1 GCCAAC-GTCCCAGA-CGTGGTCTTACACGTAAACACAAATC-GAT
* *
17547187 GCCAACGTCCCAGACGTGGTCTTTCACG-ATAACACATATCGA
1 GCCAACGTCCCAGACGTGGTCTTACACGTA-AACACAAATCGA
17547229 AAATCCTATG
Statistics
Matches: 71, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
42 5 0.07
43 62 0.87
44 4 0.06
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (43 bp):
GCCAACGTCCCAGACGTGGTCTTACACGTAAACACAAATCGAT
Found at i:17548100 original size:3 final size:3
Alignment explanation
Indices: 17548094--17548138 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
17548084 TTATAACATA
17548094 TAT TAT TA- TAT TAT TAT TAT T-T TAACT T-T TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-A-T TAT TAT TAT TAT TAT TAT
17548138 T
1 T
17548139 TATATATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
2 6 0.16
3 29 0.78
5 2 0.05
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:17550334 original size:34 final size:29
Alignment explanation
Indices: 17550306--17550360 Score: 103
Period size: 28 Copynumber: 1.9 Consensus size: 29
17550296 ATAATCAATT
17550306 TTCATTGAGAACAAGCAACATATG-ATAA
1 TTCATTGAGAACAAGCAACATATGAATAA
17550334 TTCATTGAGAACAAGCAACATATGAAT
1 TTCATTGAGAACAAGCAACATATGAAT
17550361 GGACCCATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 24 0.92
29 2 0.08
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (29 bp):
TTCATTGAGAACAAGCAACATATGAATAA
Found at i:17554257 original size:50 final size:50
Alignment explanation
Indices: 17554177--17554659 Score: 318
Period size: 50 Copynumber: 9.7 Consensus size: 50
17554167 TCCACTGAAC
* * * * * * *
17554177 GGGAAGTAAGATTCACTGTTTTAGCTTTAATATTTCTAACTGCAATATCG
1 GGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTTTCTAACTGCAATGTCG
* *
17554227 GGGAAGCAAGATTCGCCGTTGTGGCGTTAATCTGTTC-CACTGCACCACT-T--
1 GGGAAGCAAGATTCGCCGTTGTGGCTTTAATCT-TTCTAACTGCA--A-TGTCG
* * ** * * * *
17554277 GAGAAGTAAGATTCGTTGTTGTAGCTTTAATATTTTTAACTGCAATGGCG
1 GGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTTTCTAACTGCAATGTCG
* * * * ** *
17554327 GGGAAGCAAGGTTTGCCATTGTGGCTTTAATCTGTTC-CACTGCACCG-CTT
1 GGGAAGCAAGATTCGCCGTTGTGGCTTTAATCT-TTCTAACTGCAATGTC-G
* * *
17554377 GGGAAGTAGGATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCG
1 GGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTTTCTAACTGCAATGTCG
* * * * ** * *
17554427 GGGAAGCAAGATTCACCGATATGGGTTTAATCTGTTCT-ACTGCACCGCCA
1 GGGAAGCAAGATTCGCCGTTGTGGCTTTAATCT-TTCTAACTGCAATGTCG
* * * * *
17554477 GGGAAGTAGGATTCGCCGCTGTGGCTTTAATATTTTTAACTGCAATGTCG
1 GGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTTTCTAACTGCAATGTCG
* ** * * * *
17554527 GGGAAGCAAGATTCACCAATGTGGCTTTAAACTGTTC-CACTGC-ATCGCCT
1 GGGAAGCAAGATTCGCCGTTGTGGCTTTAATCT-TTCTAACTGCAAT-GTCG
* * * * * *
17554577 GGGAAGTAGGATTCACCGCTGTGGCTTTAATCTTTTTAACTGCAATGTCA
1 GGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTTTCTAACTGCAATGTCG
* * *
17554627 AGGAAGCAAGATTCACCGATGTGGCTTTAATCT
1 GGGAAGCAAGATTCGCCGTTGTGGCTTTAATCT
17554660 GTTCCACTGC
Statistics
Matches: 326, Mismatches: 89, Indels: 36
0.72 0.20 0.08
Matches are distributed among these distances:
47 1 0.00
48 1 0.00
49 12 0.04
50 296 0.91
51 13 0.04
52 2 0.01
53 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (50 bp):
GGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTTTCTAACTGCAATGTCG
Found at i:17554317 original size:100 final size:100
Alignment explanation
Indices: 17554177--17554684 Score: 667
Period size: 100 Copynumber: 5.1 Consensus size: 100
17554167 TCCACTGAAC
* * * * * * * *
17554177 GGGAAGTAAGATTCACTGTTTTAGCTTTAATATTTCTAACTGCAATATCGGGGAAGCAAGATTCG
1 GGGAAGTAGGATTCGCCGTTGTGGCTTTAATATTTTTAACTGCAATGTCGGGGAAGCAAGATTCA
* * * *
17554242 CCGTTGTGGCGTTAATCTGTTCCACTGCACCACTT
66 CCGATGTGGCTTTAATCTGTTCCACTGCACCGCCT
* * ** * * * **
17554277 GAGAAGTAAGATTCGTTGTTGTAGCTTTAATATTTTTAACTGCAATGGCGGGGAAGCAAGGTTTG
1 GGGAAGTAGGATTCGCCGTTGTGGCTTTAATATTTTTAACTGCAATGTCGGGGAAGCAAGATTCA
*
17554342 CC-ATTGTGGCTTTAATCTGTTCCACTGCACCGCTT
66 CCGA-TGTGGCTTTAATCTGTTCCACTGCACCGCCT
*
17554377 GGGAAGTAGGATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCA
1 GGGAAGTAGGATTCGCCGTTGTGGCTTTAATATTTTTAACTGCAATGTCGGGGAAGCAAGATTCA
* * * *
17554442 CCGATATGGGTTTAATCTGTTCTACTGCACCGCCA
66 CCGATGTGGCTTTAATCTGTTCCACTGCACCGCCT
*
17554477 GGGAAGTAGGATTCGCCGCTGTGGCTTTAATATTTTTAACTGCAATGTCGGGGAAGCAAGATTCA
1 GGGAAGTAGGATTCGCCGTTGTGGCTTTAATATTTTTAACTGCAATGTCGGGGAAGCAAGATTCA
* * *
17554542 CCAATGTGGCTTTAAACTGTTCCACTGCATCGCCT
66 CCGATGTGGCTTTAATCTGTTCCACTGCACCGCCT
* * * **
17554577 GGGAAGTAGGATTCACCGCTGTGGCTTTAATCTTTTTAACTGCAATGTCAAGGAAGCAAGATTCA
1 GGGAAGTAGGATTCGCCGTTGTGGCTTTAATATTTTTAACTGCAATGTCGGGGAAGCAAGATTCA
*
17554642 CCGATGTGGCTTTAATCTGTTCCACTGCATCGCCT
66 CCGATGTGGCTTTAATCTGTTCCACTGCACCGCCT
17554677 GGGAAGTA
1 GGGAAGTA
17554685 AAACTGGTAT
Statistics
Matches: 364, Mismatches: 42, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
100 363 1.00
101 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.32
Consensus pattern (100 bp):
GGGAAGTAGGATTCGCCGTTGTGGCTTTAATATTTTTAACTGCAATGTCGGGGAAGCAAGATTCA
CCGATGTGGCTTTAATCTGTTCCACTGCACCGCCT
Found at i:17555935 original size:15 final size:16
Alignment explanation
Indices: 17555915--17555944 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17555905 TCATTTTTCA
17555915 TTTTTCATTT-TCATT
1 TTTTTCATTTGTCATT
17555930 TTTTTCATTTGTCAT
1 TTTTTCATTTGTCAT
17555945 ATATTCTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.13, C:0.13, G:0.03, T:0.70
Consensus pattern (16 bp):
TTTTTCATTTGTCATT
Found at i:17555944 original size:7 final size:7
Alignment explanation
Indices: 17555892--17555932 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
17555882 TTAACCTCCC
17555892 CATTTTT
1 CATTTTT
*
17555899 -ACTTTCT
1 CA-TTTTT
17555906 CATTTTT
1 CATTTTT
17555913 CATTTTT
1 CATTTTT
17555920 CA-TTTT
1 CATTTTT
17555926 CATTTTT
1 CATTTTT
17555933 TTCATTTGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
6 7 0.24
7 21 0.72
8 1 0.03
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (7 bp):
CATTTTT
Found at i:17556840 original size:6 final size:6
Alignment explanation
Indices: 17556823--17556893 Score: 72
Period size: 6 Copynumber: 11.8 Consensus size: 6
17556813 CTCTTCTTTA
* * * *
17556823 ATTTTC ATTTTG ACTTTG ATTTTG ATTTTG ATTTTG ATTTTT CTTCTT-
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATT-TTG
* *
17556871 TTTTTG TTTTTG ATTTTG ATTTT
1 ATTTTG ATTTTG ATTTTG ATTTT
17556894 TTTTAATTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
5 2 0.04
6 52 0.93
7 2 0.04
ACGTcount: A:0.13, C:0.06, G:0.11, T:0.70
Consensus pattern (6 bp):
ATTTTG
Found at i:17556844 original size:18 final size:18
Alignment explanation
Indices: 17556818--17556863 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
17556808 CTTCTCTCTT
*
17556818 CTTTAATTTTCATTTTGA
1 CTTTGATTTTCATTTTGA
*
17556836 CTTTGATTTTGATTTTGA
1 CTTTGATTTTCATTTTGA
*
17556854 TTTTGATTTT
1 CTTTGATTTT
17556864 TCTTCTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.17, C:0.07, G:0.11, T:0.65
Consensus pattern (18 bp):
CTTTGATTTTCATTTTGA
Found at i:17556904 original size:30 final size:30
Alignment explanation
Indices: 17556842--17556904 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
17556832 TTGACTTTGA
**
17556842 TTTTGATTTTGATTTTGATTTTTCTTCTTT
1 TTTTGATTTTGATTTTGATTTTTCTTAATT
* *
17556872 TTTTGTTTTTGATTTTGATTTTTTTTAATT
1 TTTTGATTTTGATTTTGATTTTTCTTAATT
17556902 TTT
1 TTT
17556905 AATTTTTCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.11, C:0.03, G:0.10, T:0.76
Consensus pattern (30 bp):
TTTTGATTTTGATTTTGATTTTTCTTAATT
Found at i:17556911 original size:30 final size:30
Alignment explanation
Indices: 17556848--17556911 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
17556838 TTGATTTTGA
** **
17556848 TTTTGATTTTGATTTTTCTTCTTTTTTTGT
1 TTTTGATTTTGATTTTTCTTAATTTTTAAT
*
17556878 TTTTGATTTTGATTTTTTTTAATTTTTAAT
1 TTTTGATTTTGATTTTTCTTAATTTTTAAT
17556908 TTTT
1 TTTT
17556912 CTTTTTCCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.12, C:0.03, G:0.08, T:0.77
Consensus pattern (30 bp):
TTTTGATTTTGATTTTTCTTAATTTTTAAT
Found at i:17556963 original size:35 final size:35
Alignment explanation
Indices: 17556925--17556990 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
17556915 TTTCCTTTCT
*
17556925 TTTTTC-TTT-TTTTCATTGCTTTTTTTTATTTCAA
1 TTTTTCTTTTCTTTTCATT-CTTTTTATTATTTCAA
*
17556959 TTTTTCTTTTCTTTTTATTCTTTTTATTATTT
1 TTTTTCTTTTCTTTTCATTCTTTTTATTATTT
17556991 ATTTATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 6 0.21
35 15 0.54
36 7 0.25
ACGTcount: A:0.11, C:0.11, G:0.02, T:0.77
Consensus pattern (35 bp):
TTTTTCTTTTCTTTTCATTCTTTTTATTATTTCAA
Found at i:17556968 original size:18 final size:16
Alignment explanation
Indices: 17556900--17556973 Score: 53
Period size: 18 Copynumber: 4.3 Consensus size: 16
17556890 TTTTTTTTAA
*
17556900 TTTTTAATTTTTCTTT
1 TTTTTCATTTTTCTTT
*
17556916 TTCCTTTCTTTTTTC-TT
1 TT--TTTCATTTTTCTTT
17556933 TTTTTCATTGCTTT-TTT
1 TTTTTCATT--TTTCTTT
17556950 TTATTTCAATTTTTCTTT
1 TT-TTTC-ATTTTTCTTT
17556968 TCTTTT
1 T-TTTT
17556974 TATTCTTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 16
0.71 0.05 0.25
Matches are distributed among these distances:
15 6 0.13
16 2 0.04
17 14 0.30
18 20 0.43
19 4 0.09
ACGTcount: A:0.08, C:0.14, G:0.01, T:0.77
Consensus pattern (16 bp):
TTTTTCATTTTTCTTT
Found at i:17566950 original size:6 final size:7
Alignment explanation
Indices: 17566929--17566958 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
17566919 TCTTTTAGGC
17566929 TTTCTTT
1 TTTCTTT
17566936 TTTCTTT
1 TTTCTTT
17566943 TTTC-TT
1 TTTCTTT
17566949 TTTCTTT
1 TTTCTTT
17566956 TTT
1 TTT
17566959 GTACATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTCTTT
Found at i:17566950 original size:13 final size:14
Alignment explanation
Indices: 17566929--17566958 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
17566919 TCTTTTAGGC
17566929 TTTCTTTTTTCTTT
1 TTTCTTTTTTCTTT
17566943 TTTC-TTTTTCTTT
1 TTTCTTTTTTCTTT
17566956 TTT
1 TTT
17566959 GTACATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTCTTTTTTCTTT
Found at i:17567049 original size:17 final size:18
Alignment explanation
Indices: 17567027--17567068 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
17567017 AGATTCGATC
*
17567027 TTTATACT-ACTTTATTT
1 TTTATACTAACTTGATTT
17567044 TTTATA-TAACTTGATTT
1 TTTATACTAACTTGATTT
*
17567061 TTTTTACT
1 TTTATACT
17567069 TTTATAATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 19 0.90
18 1 0.05
ACGTcount: A:0.24, C:0.10, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTATACTAACTTGATTT
Found at i:17569962 original size:7 final size:7
Alignment explanation
Indices: 17569947--17570005 Score: 73
Period size: 7 Copynumber: 8.3 Consensus size: 7
17569937 CGATTATGGT
*
17569947 GTTTTGG
1 GTTTAGG
17569954 GTTTAGG
1 GTTTAGG
17569961 GTTTAGG
1 GTTTAGG
*
17569968 AGTTTGGG
1 -GTTTAGG
*
17569976 GTTTAAG
1 GTTTAGG
17569983 GTTTAGG
1 GTTTAGG
*
17569990 GTTTGGG
1 GTTTAGG
17569997 GTTTAGG
1 GTTTAGG
17570004 GT
1 GT
17570006 GCTTAATTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
7 38 0.86
8 6 0.14
ACGTcount: A:0.12, C:0.00, G:0.44, T:0.44
Consensus pattern (7 bp):
GTTTAGG
Found at i:17569973 original size:21 final size:21
Alignment explanation
Indices: 17569947--17570005 Score: 91
Period size: 22 Copynumber: 2.8 Consensus size: 21
17569937 CGATTATGGT
*
17569947 GTTTTGGGTTTAGGGTTTAGG
1 GTTTGGGGTTTAGGGTTTAGG
*
17569968 AGTTTGGGGTTTAAGGTTTAGG
1 -GTTTGGGGTTTAGGGTTTAGG
17569990 GTTTGGGGTTTAGGGT
1 GTTTGGGGTTTAGGGT
17570006 GCTTAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 15 0.44
22 19 0.56
ACGTcount: A:0.12, C:0.00, G:0.44, T:0.44
Consensus pattern (21 bp):
GTTTGGGGTTTAGGGTTTAGG
Found at i:17571283 original size:45 final size:45
Alignment explanation
Indices: 17571201--17571288 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 45
17571191 TGTTGCGTCC
* **
17571201 TTCTTGCCCAATTTCTTGAATTCCCAAATCTGAAAATCGCCTCAT
1 TTCTTGCCCAATTTCTTGAAATCCCAAATCCCAAAATCGCCTCAT
* * *
17571246 TTCTTGCCTAATTTCTTGAAATCCGAAATCCCTAAATCGCCTC
1 TTCTTGCCCAATTTCTTGAAATCCCAAATCCCAAAATCGCCTC
17571289 CTTCCTCCTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.26, C:0.30, G:0.09, T:0.35
Consensus pattern (45 bp):
TTCTTGCCCAATTTCTTGAAATCCCAAATCCCAAAATCGCCTCAT
Found at i:17573027 original size:18 final size:17
Alignment explanation
Indices: 17572999--17573048 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
17572989 TTAAAGTTCA
*
17572999 AATTTCATATCTTACGT
1 AATTTCATATCTTACAT
17573016 AATTTACATATCTTACAT
1 AATTT-CATATCTTACAT
*
17573034 AA-TTCATAACTTACA
1 AATTTCATATCTTACA
17573049 CAACTTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 10 0.33
17 7 0.23
18 13 0.43
ACGTcount: A:0.38, C:0.18, G:0.02, T:0.42
Consensus pattern (17 bp):
AATTTCATATCTTACAT
Found at i:17573119 original size:23 final size:21
Alignment explanation
Indices: 17573109--17573149 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
17573099 TAGTTTATAT
17573109 ATATATATATATATATTTAAA
1 ATATATATATATATATTTAAA
*
17573130 AT-T-TATATATATTTTTAAA
1 ATATATATATATATATTTAAA
17573149 A
1 A
17573150 ATTGATACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.84
20 1 0.05
21 2 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATATATATATATATATTTAAA
Found at i:17573371 original size:21 final size:21
Alignment explanation
Indices: 17573346--17573422 Score: 68
Period size: 24 Copynumber: 3.6 Consensus size: 21
17573336 ATCATATCAC
17573346 AACTTACATAACCAACATAAT
1 AACTTACATAACCAACATAAT
* *
17573367 GACTTACATAATAACCTACATAAT
1 AACTTAC---ATAACCAACATAAT
**
17573391 AACTTACATAATAATACATAAT
1 AACTTACATAACCA-ACATAAT
17573413 AA--TACATAAC
1 AACTTACATAAC
17573423 ATCCATAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
20 7 0.16
21 10 0.22
22 9 0.20
24 19 0.42
ACGTcount: A:0.52, C:0.19, G:0.01, T:0.27
Consensus pattern (21 bp):
AACTTACATAACCAACATAAT
Found at i:17573377 original size:12 final size:12
Alignment explanation
Indices: 17573360--17573414 Score: 78
Period size: 12 Copynumber: 4.8 Consensus size: 12
17573350 TACATAACCA
*
17573360 ACATAATGACTT
1 ACATAATAACTT
*
17573372 ACATAATAACCT
1 ACATAATAACTT
17573384 ACATAATAACTT
1 ACATAATAACTT
17573396 ACATAATAA--T
1 ACATAATAACTT
17573406 ACATAATAA
1 ACATAATAA
17573415 TACATAACAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
10 10 0.25
12 30 0.75
ACGTcount: A:0.53, C:0.16, G:0.02, T:0.29
Consensus pattern (12 bp):
ACATAATAACTT
Found at i:17573387 original size:24 final size:24
Alignment explanation
Indices: 17573353--17573421 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
17573343 CACAACTTAC
* *
17573353 ATAACCAACATAATGACTTACATA
1 ATAACCTACATAATAACTTACATA
17573377 ATAACCTACATAATAACTTACATA
1 ATAACCTACATAATAACTTACATA
17573401 ATAA--TACATAATAA--TACATA
1 ATAACCTACATAATAACTTACATA
17573421 A
1 A
17573422 CATCCATAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.16
22 10 0.23
24 26 0.60
ACGTcount: A:0.54, C:0.17, G:0.01, T:0.28
Consensus pattern (24 bp):
ATAACCTACATAATAACTTACATA
Found at i:17573410 original size:10 final size:11
Alignment explanation
Indices: 17573360--17573421 Score: 74
Period size: 12 Copynumber: 5.5 Consensus size: 11
17573350 TACATAACCA
*
17573360 ACATAATGACTT
1 ACATAATAAC-T
17573372 ACATAATAACCT
1 ACATAATAA-CT
17573384 ACATAATAACTT
1 ACATAATAAC-T
17573396 ACATAATAA-T
1 ACATAATAACT
17573406 ACATAATAA-T
1 ACATAATAACT
17573416 ACATAA
1 ACATAA
17573422 CATCCATAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
10 17 0.36
11 1 0.02
12 28 0.60
13 1 0.02
ACGTcount: A:0.53, C:0.16, G:0.02, T:0.29
Consensus pattern (11 bp):
ACATAATAACT
Found at i:17573515 original size:9 final size:9
Alignment explanation
Indices: 17573488--17573595 Score: 86
Period size: 9 Copynumber: 12.6 Consensus size: 9
17573478 CTACATCCCT
17573488 ACTTACATA
1 ACTTACATA
17573497 A-TAATACATA
1 ACT--TACATA
17573507 ACTTACATA
1 ACTTACATA
*
17573516 A--GACATA
1 ACTTACATA
*
17573523 ACGTACATA
1 ACTTACATA
* *
17573532 AGTTTCATA
1 ACTTACATA
*
17573541 A--TACACA
1 ACTTACATA
*
17573548 ACTTACACA
1 ACTTACATA
*
17573557 ACTTACACA
1 ACTTACATA
17573566 ACTTACATA
1 ACTTACATA
17573575 ACTTACATA
1 ACTTACATA
17573584 A--TACATA
1 ACTTACATA
17573591 ACTTA
1 ACTTA
17573596 TTCCTAAATC
Statistics
Matches: 82, Mismatches: 8, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
7 18 0.22
8 1 0.01
9 55 0.67
10 7 0.09
11 1 0.01
ACGTcount: A:0.47, C:0.21, G:0.03, T:0.29
Consensus pattern (9 bp):
ACTTACATA
Found at i:17573531 original size:25 final size:25
Alignment explanation
Indices: 17573501--17573563 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
17573491 TACATAATAA
*
17573501 TACATAACTTACATAAGACATAACG
1 TACATAACTTACATAAGACACAACG
* * * *
17573526 TACATAAGTTTCATAATACACAACT
1 TACATAACTTACATAAGACACAACG
*
17573551 TACACAACTTACA
1 TACATAACTTACA
17573564 CAACTTACAT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.46, C:0.22, G:0.05, T:0.27
Consensus pattern (25 bp):
TACATAACTTACATAAGACACAACG
Found at i:17573563 original size:93 final size:94
Alignment explanation
Indices: 17573368--17573548 Score: 233
Period size: 96 Copynumber: 1.9 Consensus size: 94
17573358 CAACATAATG
*
17573368 ACTTACATAATAACCTACATAATAACTTACATAATAATACATAATAATACATAACATCCATAAAT
1 ACTTACATAATAACCTACATAATAACTTACATAATAATACATAAT-ATACATAACA-CCATAAAG
17573433 TAAATAAGTTACATAATACACAAAAACAAAA
64 TAAATAAGTTACATAATACACAAAAACAAAA
* ** * *
17573464 ACTTACATAATATCCTACATCCCT-ACTTACATAATAATACATAACT-TACATAAGA-CATAACG
1 ACTTACATAATAACCTACAT-AATAACTTACATAATAATACATAA-TATACATAACACCATAAAG
* *
17573526 TACATAAGTTTCATAATACACAA
64 TAAATAAGTTACATAATACACAA
17573549 CTTACACAAC
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
93 26 0.35
95 8 0.11
96 39 0.52
97 2 0.03
ACGTcount: A:0.51, C:0.19, G:0.02, T:0.28
Consensus pattern (94 bp):
ACTTACATAATAACCTACATAATAACTTACATAATAATACATAATATACATAACACCATAAAGTA
AATAAGTTACATAATACACAAAAACAAAA
Found at i:17573590 original size:16 final size:17
Alignment explanation
Indices: 17573488--17573595 Score: 89
Period size: 16 Copynumber: 6.3 Consensus size: 17
17573478 CTACATCCCT
17573488 ACTTACATAATAATACATA
1 ACTTACATAAT--TACATA
*
17573507 ACTTACATAA-GACATA
1 ACTTACATAATTACATA
* *
17573523 ACGTACATAAGTTTCATA
1 ACTTACATAA-TTACATA
* *
17573541 A--TACACAACTTACACA
1 ACTTACATAA-TTACATA
*
17573557 ACTTACACAACTTACATA
1 ACTTACATAA-TTACATA
17573575 ACTTACATAA-TACATA
1 ACTTACATAATTACATA
17573591 ACTTA
1 ACTTA
17573596 TTCCTAAATC
Statistics
Matches: 75, Mismatches: 10, Indels: 11
0.78 0.10 0.11
Matches are distributed among these distances:
16 37 0.49
18 28 0.37
19 10 0.13
ACGTcount: A:0.47, C:0.21, G:0.03, T:0.29
Consensus pattern (17 bp):
ACTTACATAATTACATA
Found at i:17579066 original size:21 final size:21
Alignment explanation
Indices: 17579042--17579110 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
17579032 CAGCAACTTA
*
17579042 AAGCAGAGGCGACAGCGAGGG
1 AAGCAGAGGCGACAGCGAGAG
* *
17579063 AAGCAAAGGCTACAGCGAGAG
1 AAGCAGAGGCGACAGCGAGAG
17579084 AAGCAGAGGCTG-CAGCGAGAG
1 AAGCAGAGGC-GACAGCGAGAG
17579105 AAGCAG
1 AAGCAG
17579111 CAAGAGAAGC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.38, C:0.19, G:0.41, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCGACAGCGAGAG
Found at i:17579116 original size:12 final size:12
Alignment explanation
Indices: 17579095--17579134 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
17579085 AGCAGAGGCT
*
17579095 GCAGCGAGAGAA
1 GCAGCAAGAGAA
17579107 GCAGCAAGAGAA
1 GCAGCAAGAGAA
*
17579119 GCAGCAATAGAA
1 GCAGCAAGAGAA
17579131 GCAG
1 GCAG
17579135 AGGTTCAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.45, C:0.17, G:0.35, T:0.03
Consensus pattern (12 bp):
GCAGCAAGAGAA
Found at i:17579663 original size:42 final size:42
Alignment explanation
Indices: 17579554--17579865 Score: 373
Period size: 43 Copynumber: 7.4 Consensus size: 42
17579544 GTTTGTGAAA
* * * * *
17579554 TAAGCGCCGCTATAGAACATTA-CTTTTAGAGGCGTTTCCTTCC
1 TAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTT-TTTTC
* *
17579597 AAAGCGCCGCTAAAAGAACATGATCTTTAGCGGCGTTTTTTCC
1 TAAGCGCCGCT-AAAGAACATGATCTTTAGCGGCGTTTTTTTC
*
17579640 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTA
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
* *
17579682 TAAGCGCCGCTAAAGAGCATGATCTTTAGGGGCG---TTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
* *
17579721 TAAGCGCCGCTAAAGAGCGTGATCTTTAG-GTGCGTTTGTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCG-GCGTTT-TTTTC
* *
17579764 TAAGCGCCGCTAAAGAGCATGATCTTTAGCGGCGTTTGTTTTT
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-TTTTC
17579807 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTAC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT-C
* *
17579850 GTAAGCACCGCAAAAG
1 -TAAGCGCCGCTAAAG
17579866 TTAGTGACGT
Statistics
Matches: 241, Mismatches: 18, Indels: 19
0.87 0.06 0.07
Matches are distributed among these distances:
38 1 0.00
39 35 0.15
42 65 0.27
43 104 0.43
44 35 0.15
45 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
Found at i:17579774 original size:124 final size:125
Alignment explanation
Indices: 17579553--17579844 Score: 394
Period size: 124 Copynumber: 2.3 Consensus size: 125
17579543 CGTTTGTGAA
* * * *
17579553 ATAAGCGCCGCTATAGAACATTA-CTTTTAGAGGCGTTTCCTTCCAAAGCGCCGCTAAAAGAACA
1 ATAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCG-TT--TT-CTAAGCGCCGCTAAAAGAACA
17579617 TGATCTTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-TTTT
61 TGATCTTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTGTTTT
* * * *
17579681 ATAAGCGCCGCTAAAGAGCATGATCTTTAGGGGCGTTTTCTAAGCGCCGCT-AAAGAGCGTGATC
1 ATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCTAAGCGCCGCTAAAAGAACATGATC
* *
17579745 TTTAG-GTGCGTTTGTTTTCTAAGCGCCGCTAAAGAGCATGATCTTTAGCGGCGTTTGTTTT
66 TTTAGCG-GCGTTT-TTTCCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTGTTTT
*
17579806 TTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTT
1 ATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTT
17579845 TTTACGTAAG
Statistics
Matches: 148, Mismatches: 12, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
122 1 0.01
123 22 0.15
124 51 0.34
125 42 0.28
127 2 0.01
128 29 0.20
129 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (125 bp):
ATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCTAAGCGCCGCTAAAAGAACATGATC
TTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTGTTTT
Found at i:17579968 original size:22 final size:22
Alignment explanation
Indices: 17579937--17579979 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
17579927 TAGTGGCGTT
* *
17579937 AAAAAGCGCCGCTAAAGACCTA
1 AAAAAACGCCGCTAAAAACCTA
17579959 AAAAAACGCCGCTAAAAACCT
1 AAAAAACGCCGCTAAAAACCT
17579980 GTTCTGCTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.28, G:0.14, T:0.09
Consensus pattern (22 bp):
AAAAAACGCCGCTAAAAACCTA
Found at i:17580562 original size:29 final size:30
Alignment explanation
Indices: 17580521--17580577 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
17580511 TGATTCAATG
17580521 TGTAATATAATACAT-AAACTTTGATTTTA
1 TGTAATATAATACATGAAACTTTGATTTTA
* * *
17580550 TGTAATTTTATACATGAAATTTTGATTT
1 TGTAATATAATACATGAAACTTTGATTT
17580578 GATTCAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (30 bp):
TGTAATATAATACATGAAACTTTGATTTTA
Found at i:17580587 original size:30 final size:29
Alignment explanation
Indices: 17580521--17580588 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
17580511 TGATTCAATG
* * *
17580521 TGTAATATAATACATAAACTTTGATTTTA
1 TGTAATTTTATACATAAACTTTGATTTGA
*
17580550 TGTAATTTTATACATGAAATTTTGATTTGA
1 TGTAATTTTATACAT-AAACTTTGATTTGA
17580580 T-TCAATTTT
1 TGT-AATTTT
17580589 TATAAATTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 14 0.42
30 19 0.58
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (29 bp):
TGTAATTTTATACATAAACTTTGATTTGA
Found at i:17580716 original size:6 final size:6
Alignment explanation
Indices: 17580707--17580733 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
17580697 TATACAATTG
17580707 AATCAA AATCAA AATCAA AATCAA AAT
1 AATCAA AATCAA AATCAA AATCAA AAT
17580734 TTTATGTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.19
Consensus pattern (6 bp):
AATCAA
Found at i:17582622 original size:8 final size:8
Alignment explanation
Indices: 17582609--17582644 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
17582599 AATATTTTTA
17582609 AAATATAT
1 AAATATAT
*
17582617 AAATATTT
1 AAATATAT
17582625 ATAATATAT
1 A-AATATAT
17582634 AAATATAT
1 AAATATAT
17582642 AAA
1 AAA
17582645 AGAACTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 18 0.72
9 7 0.28
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
AAATATAT
Found at i:17582623 original size:19 final size:18
Alignment explanation
Indices: 17582599--17582639 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
17582589 AATAACTTAC
17582599 AATATTTTTAAAATATATA
1 AATA-TTTTAAAATATATA
*
17582618 AATA-TTTATAATATATA
1 AATATTTTAAAATATATA
17582635 AATAT
1 AATAT
17582640 ATAAAAGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 16 0.80
19 4 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATATTTTAAAATATATA
Found at i:17582630 original size:17 final size:17
Alignment explanation
Indices: 17582605--17582680 Score: 73
Period size: 17 Copynumber: 4.4 Consensus size: 17
17582595 TTACAATATT
17582605 TTTAAAATATATAAATA
1 TTTAAAATATATAAATA
*
17582622 TTTATAATATATAAATA
1 TTTAAAATATATAAATA
* * *
17582639 TATAAAAGA-ACTAAAAA
1 TTTAAAATATA-TAAATA
* *
17582656 TTTATAATATATAGAAGA
1 TTTAAAATATATA-AATA
17582674 TTTAAAA
1 TTTAAAA
17582681 AACACATCTA
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
16 1 0.02
17 35 0.76
18 10 0.22
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (17 bp):
TTTAAAATATATAAATA
Found at i:17582641 original size:19 final size:18
Alignment explanation
Indices: 17582599--17582645 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
17582589 AATAACTTAC
*
17582599 AATATTTTTAAAATATAT
1 AATATATTTAAAATATAT
*
17582617 AA-ATATTTATAATATAT
1 AATATATTTAAAATATAT
*
17582634 AA-ATATATAAAA
1 AATATATTTAAAA
17582646 GAACTAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 23 0.92
18 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATATATTTAAAATATAT
Found at i:17583526 original size:29 final size:28
Alignment explanation
Indices: 17583475--17583529 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
17583465 TCTTTGTAAA
* **
17583475 TTTAGAATTTAATCTTTGTACTTTTATT
1 TTTAGAATTTAATCCTTCCACTTTTATT
17583503 TTTAGAAATTTAATCCTTCCACTTTTA
1 TTTAG-AATTTAATCCTTCCACTTTTA
17583530 AATTTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.27, C:0.13, G:0.05, T:0.55
Consensus pattern (28 bp):
TTTAGAATTTAATCCTTCCACTTTTATT
Found at i:17591482 original size:25 final size:25
Alignment explanation
Indices: 17591438--17591486 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
17591428 TATAGTCTAT
*
17591438 CTATAGTAGTCTTAGTATATACTAC
1 CTATAGTAGTCTTAGGATATACTAC
17591463 CTATAGTAGT-TTCAGGATATACTA
1 CTATAGTAGTCTT-AGGATATACTA
17591487 TCAAAGATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (25 bp):
CTATAGTAGTCTTAGGATATACTAC
Found at i:17598481 original size:24 final size:24
Alignment explanation
Indices: 17598436--17598492 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
17598426 TATACATTTC
*
17598436 TTTTATTTTAAATTTAACATGTAT
1 TTTTATTTAAAATTTAACATGTAT
*
17598460 TATTTATTTAAAATTT-ATATGTAT
1 T-TTTATTTAAAATTTAACATGTAT
*
17598484 TTTAATTTA
1 TTTTATTTA
17598493 CTTCTTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.24
24 9 0.31
25 13 0.45
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (24 bp):
TTTTATTTAAAATTTAACATGTAT
Found at i:17602605 original size:20 final size:20
Alignment explanation
Indices: 17602582--17602645 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
17602572 ATGTACGTAT
* *
17602582 ATATATTATACTTTCTATAC
1 ATATATTATAATTTATATAC
* *
17602602 ATATTTTATAATTTATATAT
1 ATATATTATAATTTATATAC
* *
17602622 ATATA-TAT-ATATATACAC
1 ATATATTATAATTTATATAC
17602640 ATATAT
1 ATATAT
17602646 GCAATCATTA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
18 12 0.34
19 3 0.09
20 20 0.57
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATTATAATTTATATAC
Found at i:17603389 original size:98 final size:98
Alignment explanation
Indices: 17603269--17603465 Score: 331
Period size: 98 Copynumber: 2.0 Consensus size: 98
17603259 TTTAAAATCA
* * *
17603269 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAATGTATTGGGTGTGACTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGACTTC
* *
17603334 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGCGGATATTCTTTTAAAG
* *
17603367 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGACTTC
17603432 TTAAATCTTGGATAAGCGGATATTCTTTTAAAG
66 TTAAATCTTGGATAAGCGGATATTCTTTTAAAG
17603465 T
1 T
17603466 TTTATTGTAC
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGACTTC
TTAAATCTTGGATAAGCGGATATTCTTTTAAAG
Found at i:17608290 original size:29 final size:27
Alignment explanation
Indices: 17608245--17608304 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 27
17608235 GTTCAGATAT
17608245 AAAAAACAAAAACAAAAAATAAAAAAAG
1 AAAAAACAAAAACAAAAAA-AAAAAAAG
** *
17608273 CAAAAAACAAAATGAAAAAAAGAAAAAG
1 -AAAAAACAAAAACAAAAAAAAAAAAAG
17608301 AAAA
1 AAAA
17608305 GCAAGAGGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 4 0.14
28 7 0.25
29 17 0.61
ACGTcount: A:0.83, C:0.07, G:0.07, T:0.03
Consensus pattern (27 bp):
AAAAAACAAAAACAAAAAAAAAAAAAG
Found at i:17609660 original size:44 final size:44
Alignment explanation
Indices: 17609612--17610039 Score: 132
Period size: 44 Copynumber: 9.7 Consensus size: 44
17609602 AAAATTGTAG
*
17609612 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGACAA
* * *
17609656 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGA-CAA
** * * * * ** * * * * *
17609700 GCCTTGTCTCCTTGAGCAGCACCGGAGAAGGTTGAAGATTG-TAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-CGACAA
* * * *
17609744 ATCTTATCTCCCTAAGCAGTAGTAGAGCCGATCGAAGAC-AGTAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGA-CAA
* * *
17609788 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGA-CAA
** * * ** * * * * * *
17609832 GCCTTGTCTCCCTGAGCAGCGGCGGAGAAGGTTGAAGATTG-TAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-CGACAA
* *
17609876 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGACAA
* * *
17609920 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGA-CAA
** * * * * * * * *
17609964 GCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTG-TAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-CGACAA
*
17610008 ATCTTATCTCCCTAAGCAGTAGTTGAGCAGAT
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
17610040 CAAAGGCGGT
Statistics
Matches: 257, Mismatches: 97, Indels: 60
0.62 0.23 0.14
Matches are distributed among these distances:
42 12 0.05
43 21 0.08
44 202 0.79
45 18 0.07
46 4 0.02
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGACAA
Found at i:17610263 original size:132 final size:132
Alignment explanation
Indices: 17609569--17610222 Score: 1065
Period size: 132 Copynumber: 5.0 Consensus size: 132
17609559 AAGACATCAA
* * * *
17609569 CCTTGCCTCCTTGAGCAGCAGTGGAGAAGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAG
1 CCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAG
**
17609634 TGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCA
66 TGGAGCAGATCGAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCA
17609699 AG
131 AG
* *
17609701 CCTTGTCTCCTTGAGCAGCACCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAG
1 CCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAG
* * *
17609766 TAGAGCCGATCGAAGACAGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCA
66 TGGAGCAGATCGAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCA
17609831 AG
131 AG
*
17609833 CCTTGTCTCCCTGAGCAGCGGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAG
1 CCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAG
*
17609898 TGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCA
66 TGGAGCAGATCGAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCA
17609963 AG
131 AG
*
17609965 CCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAAATCTTATCTCCCTAAGCAGTAG
1 CCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAG
* * *
17610030 TTGAGCAGATCAAAGGCGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCA
66 TGGAGCAGATCGAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCA
*
17610095 AA
131 AG
* * * *
17610097 CCCTGTCTCCCTGAGCAGCAGCGGAGTAGGTTAAAGATTGTAGATCTTATCCCCCTAAGCAGTAG
1 CCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAG
* * * * *
17610162 TGGGGCAGATCGAAAACGGTAAATCATATATTTCCAAGATAGTGGGAAGCAGATTAAAGCC
66 TGGAGCAGATCGAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCC
17610223 GACAATTCTA
Statistics
Matches: 486, Mismatches: 36, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 486 1.00
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (132 bp):
CCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAG
TGGAGCAGATCGAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCA
AG
Found at i:17610279 original size:44 final size:44
Alignment explanation
Indices: 17610231--17610563 Score: 172
Period size: 44 Copynumber: 7.7 Consensus size: 44
17610221 CCGACAATTC
* *
17610231 TATCTCCTTGAAGTTGTAGTGGAGCGGATTAAAATCACAGATCT
1 TATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCT
* * *
17610275 TATCT-CTCTGAAGTTGCAG-AGAGCAGATT-ACATC-TAG-TCT
1 TATCTCCT-TGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCT
* * * * *
17610315 TATCTCCCTGAAGTTGCACTGGAACAGACT-AAATAAGCA-AGTCT
1 TATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAATCA-CAGA-TCT
* * * * *
17610359 TATCCTCC-TAAAGTTGTAGTGGGGCAGACTGAAGATGGCA-AG-TCT
1 TAT-CTCCTTGAAGTTGCAGTGGAGCAGA-TTAAAAT--CACAGATCT
* * * * * *
17610404 TATCTCCCTAAAGTTGCAGTAGAGCAGATTAAAGCTGATA-ATCT
1 TATCTCCTTGAAGTTGCAGTGGAGCAGATTAAA-ATCACAGATCT
* * ** * *
17610448 TATTTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATA-ATCC
1 TATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAATC-ACAGATCT
* * * ** *
17610492 TATCTCATTGAAGTTGCATTGGAGCGGATTAAAGCCTCAGATCT
1 TATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCT
*
17610536 TATCT-CTCTGAAGTTGCAG-AGAGCAGAT
1 TATCTCCT-TGAAGTTGCAGTGGAGCAGAT
17610564 CGCAGCTAGT
Statistics
Matches: 221, Mismatches: 48, Indels: 41
0.71 0.15 0.13
Matches are distributed among these distances:
40 18 0.08
41 13 0.06
42 4 0.02
43 21 0.10
44 132 0.60
45 28 0.13
46 4 0.02
48 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (44 bp):
TATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCT
Found at i:17610869 original size:45 final size:44
Alignment explanation
Indices: 17610755--17610876 Score: 156
Period size: 45 Copynumber: 2.8 Consensus size: 44
17610745 GATCGCAGCT
*
17610755 AGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCTTCCTGAAGTTACAGTGGAGCAGACTAAGTAAGCA
* * * *
17610799 AGTCTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAG-ATGGCA
1 AGTCTTATCTTCCTGAAGTTACAGTGGAGCAGACT-AAGTA-AGCA
* *
17610844 AGTCTTATCTTCCTAAAATTACAGTGGAGCAGA
1 AGTCTTATCTTCCTGAAGTTACAGTGGAGCAGA
17610877 TTAAAACCGA
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
44 32 0.48
45 34 0.52
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.26
Consensus pattern (44 bp):
AGTCTTATCTTCCTGAAGTTACAGTGGAGCAGACTAAGTAAGCA
Found at i:17610916 original size:44 final size:43
Alignment explanation
Indices: 17610862--17610964 Score: 118
Period size: 44 Copynumber: 2.3 Consensus size: 43
17610852 CTTCCTAAAA
17610862 TTACAGTGGAGCAGATTAAAACCGATA-ATCCTATCTCCCTGAAG
1 TTACA-TGGAGCAGATTAAAACC-ATAGATCCTATCTCCCTGAAG
* * * * *
17610906 TTGCATTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAG
1 TTACA-TGGAGCAGATTAAAACCATAGATCCTATCTCCCTGAAG
*
17610950 TTACATAGAGCAGAT
1 TTACATGGAGCAGAT
17610965 CGCATCTAGT
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
43 10 0.20
44 39 0.80
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (43 bp):
TTACATGGAGCAGATTAAAACCATAGATCCTATCTCCCTGAAG
Found at i:17611191 original size:132 final size:131
Alignment explanation
Indices: 17610997--17611644 Score: 967
Period size: 132 Copynumber: 4.9 Consensus size: 131
17610987 GCAGCAGCGA
* * * *
17610997 AGCAAATCGAAGATGACAGATTTTACCTCCCTGTGGTTATAGTGGAGTACCTTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
* *
17611062 TCTACTTCCCTGTGCAGCAGTGGAATAGATTGAAGATTTCAGATATTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTG-GCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
17611127 GG
130 GG
17611129 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
17611194 TCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCT-GGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
17611259 GG
130 GG
* * *
17611261 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAATAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
* * *
17611326 TCTACTTTCCTGGGCAACAGTAGAATAGATTGAAAATTTCAGATCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCT-GGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
17611391 GG
130 GG
* * * * **
17611393 AGCAGATTGAAGATTGTGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGATAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
*
17611458 TCTACTTCCCTAGGCAATAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCT-GGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
17611523 GG
130 GG
* * * * *
17611525 AGTAAATCGAAGATGGTGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGTCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
* * * *
17611590 CCTA-TCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTTTA-AGTCTTATCTCCCT
66 TCTACT-TCCCTGG-CAACAGTGGAATAGATTGAAGATTTCAGA-TCTTATCTCCCT
17611645 GCAGTTGCAG
Statistics
Matches: 475, Mismatches: 37, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
131 4 0.01
132 470 0.99
133 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.30
Consensus pattern (131 bp):
AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
TCTACTTCCCTGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
G
Found at i:17612133 original size:20 final size:20
Alignment explanation
Indices: 17612108--17612177 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
17612098 TAATGGAAAG
17612108 AAATCAAAAGATTGAGAATC
1 AAATCAAAAGATTGAGAATC
* **
17612128 AAATCAAAGCAAAATATG-GAAGG
1 AAATC-AA--AAGAT-TGAGAATC
*
17612151 AAATCAAGAGATTGAGAATC
1 AAATCAAAAGATTGAGAATC
17612171 AAATCAA
1 AAATCAA
17612178 TGTAAACATG
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
19 2 0.05
20 18 0.47
21 2 0.05
22 2 0.05
23 12 0.32
24 2 0.05
ACGTcount: A:0.56, C:0.10, G:0.17, T:0.17
Consensus pattern (20 bp):
AAATCAAAAGATTGAGAATC
Done.