Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 111 of 222
Found at i:35540003 original size:23 final size:23
Alignment explanation
Indices: 35539972--35540016 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
35539962 TCCAAACCAA
*
35539972 TTCGCACCTAAACCTAAATCATT
1 TTCGAACCTAAACCTAAATCATT
35539995 TTCGAACCTAAACCTAAATCAT
1 TTCGAACCTAAACCTAAATCAT
35540017 AACCATTCCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.29, G:0.04, T:0.29
Consensus pattern (23 bp):
TTCGAACCTAAACCTAAATCATT
Found at i:35557745 original size:8 final size:8
Alignment explanation
Indices: 35557727--35557760 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
35557717 ACTTATATAT
35557727 ATAAT-AA
1 ATAATAAA
35557734 ATAATAAA
1 ATAATAAA
35557742 ATAATAAA
1 ATAATAAA
35557750 ATAATAAA
1 ATAATAAA
35557758 ATA
1 ATA
35557761 TCATTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.19
8 21 0.81
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
ATAATAAA
Found at i:35558690 original size:24 final size:24
Alignment explanation
Indices: 35558663--35558716 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
35558653 TTATGTTATG
*
35558663 TATGACTCATTTGTCTATGATTTT
1 TATGACTCATTTGTCTATGATTTC
* * *
35558687 TATGACTGATTTGTTTGTGATTTC
1 TATGACTCATTTGTCTATGATTTC
35558711 TATGAC
1 TATGAC
35558717 CGATTCTGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.52
Consensus pattern (24 bp):
TATGACTCATTTGTCTATGATTTC
Found at i:35558902 original size:32 final size:31
Alignment explanation
Indices: 35558857--35559051 Score: 214
Period size: 32 Copynumber: 6.1 Consensus size: 31
35558847 TAGCTTTGCT
35558857 GCTTTGTGCCGATCATATTATCGTTACTGATG
1 GCTTTGTGCCGATCATATTA-CGTTACTGATG
* *
35558889 GCTTTGTGTCGATCATATTACTGTTATTGATG
1 GCTTTGTGCCGATCATATTAC-GTTACTGATG
* *
35558921 GCTTTGTACCGATCATACTACCGTTACTGATG
1 GCTTTGTGCCGATCATATTA-CGTTACTGATG
*
35558953 GCTTTGTGCCGATCATATTACAGTTATTGATG
1 GCTTTGTGCCGATCATATTAC-GTTACTGATG
* *
35558985 GCTGTGTGCC-AGTCATATCAC-TACTACTGATG
1 GCTTTGTGCCGA-TCATATTACGT--TACTGATG
* * * *
35559017 GCTTTGTGCCAAACATATTACTTTACTTATG
1 GCTTTGTGCCGATCATATTACGTTACTGATG
35559048 GCTT
1 GCTT
35559052 GTAGCCATTC
Statistics
Matches: 139, Mismatches: 16, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
30 1 0.01
31 14 0.10
32 121 0.87
33 3 0.02
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.39
Consensus pattern (31 bp):
GCTTTGTGCCGATCATATTACGTTACTGATG
Found at i:35558934 original size:64 final size:63
Alignment explanation
Indices: 35558857--35559051 Score: 236
Period size: 64 Copynumber: 3.1 Consensus size: 63
35558847 TAGCTTTGCT
*
35558857 GCTTTGTGCCGATCATATTATCGTTACTGATGGCTTTGTGTCGATCATATTACTGTTATTGATG
1 GCTTTGTGCCGATCATATTA-CGTTACTGATGGCTTTGTGCCGATCATATTACTGTTATTGATG
* * *
35558921 GCTTTGTACCGATCATACTACCGTTACTGATGGCTTTGTGCCGATCATATTACAGTTATTGATG
1 GCTTTGTGCCGATCATATTA-CGTTACTGATGGCTTTGTGCCGATCATATTACTGTTATTGATG
* * * *
35558985 GCTGTGTGCC-AGTCATATCAC-TACTACTGATGGCTTTGTGCCAAACATATTACT-TTACTT-A
1 GCTTTGTGCCGA-TCATATTACGT--TACTGATGGCTTTGTGCCGATCATATTACTGTTA-TTGA
35559046 TG
62 TG
35559048 GCTT
1 GCTT
35559052 GTAGCCATTC
Statistics
Matches: 114, Mismatches: 13, Indels: 9
0.84 0.10 0.07
Matches are distributed among these distances:
62 1 0.01
63 11 0.10
64 102 0.89
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.39
Consensus pattern (63 bp):
GCTTTGTGCCGATCATATTACGTTACTGATGGCTTTGTGCCGATCATATTACTGTTATTGATG
Found at i:35559073 original size:22 final size:21
Alignment explanation
Indices: 35559043--35559107 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
35559033 ATTACTTTAC
35559043 TTATGGCTTGTAGCCATTCTGT
1 TTATGGCTT-TAGCCATTCTGT
* * * *
35559065 TTATAGCTTATAGCTATCCTAT
1 TTATGGCTT-TAGCCATTCTGT
35559087 TTATGGCTCTTAGCCATTCTG
1 TTATGGCT-TTAGCCATTCTG
35559108 ACTACTGGCA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
22 32 0.97
23 1 0.03
ACGTcount: A:0.18, C:0.20, G:0.17, T:0.45
Consensus pattern (21 bp):
TTATGGCTTTAGCCATTCTGT
Found at i:35570668 original size:28 final size:28
Alignment explanation
Indices: 35570634--35570698 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
35570624 TCCTTTTCAC
35570634 TCATTTTCTTTCCAATGTCATTTTC-TTT
1 TCATTTTCTTT-CAATGTCATTTTCATTT
* * *
35570662 TTATTTTCTTTCAATTTCTTTTTCATTT
1 TCATTTTCTTTCAATGTCATTTTCATTT
35570690 TCATTTTCT
1 TCATTTTCT
35570699 CGCTCGCCCT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 11 0.34
28 21 0.66
ACGTcount: A:0.14, C:0.18, G:0.02, T:0.66
Consensus pattern (28 bp):
TCATTTTCTTTCAATGTCATTTTCATTT
Found at i:35572524 original size:22 final size:20
Alignment explanation
Indices: 35572483--35572529 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
35572473 GGCATCTATG
*
35572483 TGTTCACACAATTATAAAAA
1 TGTTCACACAATCATAAAAA
*
35572503 TGTTCACACTAAATCATTAAAA
1 TGTTCACAC--AATCATAAAAA
35572525 T-TTCA
1 TGTTCA
35572530 GTTCATGCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 9 0.39
21 4 0.17
22 10 0.43
ACGTcount: A:0.45, C:0.17, G:0.04, T:0.34
Consensus pattern (20 bp):
TGTTCACACAATCATAAAAA
Found at i:35573233 original size:10 final size:10
Alignment explanation
Indices: 35573218--35573255 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
35573208 TTGGGTTAAG
35573218 ATTGAGCTGA
1 ATTGAGCTGA
35573228 ATTGAGCTCGA
1 ATTGAGCT-GA
35573239 A-TGAGCTGA
1 ATTGAGCTGA
*
35573248 CTTGAGCT
1 ATTGAGCT
35573256 CGAGTGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 20 0.80
11 3 0.12
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:35573268 original size:20 final size:20
Alignment explanation
Indices: 35573220--35573268 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
35573210 GGGTTAAGAT
*
35573220 TGAGCTGAATTGAGCTCGAA
1 TGAGCTGACTTGAGCTCGAA
*
35573240 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGACTTGAGCTCGAA
35573260 TGAGCTGAC
1 TGAGCTGAC
35573269 CTAAGTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.24
Consensus pattern (20 bp):
TGAGCTGACTTGAGCTCGAA
Found at i:35573804 original size:37 final size:39
Alignment explanation
Indices: 35573739--35573818 Score: 146
Period size: 37 Copynumber: 2.1 Consensus size: 39
35573729 CGATGGAGTA
35573739 AAGATAGGGTTTGGGATGGCAAGAACAAAATAAAGATTT
1 AAGATAGGGTTTGGGATGGCAAGAACAAAATAAAGATTT
35573778 AAGATAGGG-TTGGGAT-GCAAGAACAAAATAAAGATTT
1 AAGATAGGGTTTGGGATGGCAAGAACAAAATAAAGATTT
35573815 AAGA
1 AAGA
35573819 ATCAAAACGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 25 0.61
38 7 0.17
39 9 0.22
ACGTcount: A:0.46, C:0.05, G:0.28, T:0.21
Consensus pattern (39 bp):
AAGATAGGGTTTGGGATGGCAAGAACAAAATAAAGATTT
Found at i:35584696 original size:40 final size:40
Alignment explanation
Indices: 35584640--35584851 Score: 239
Period size: 40 Copynumber: 5.3 Consensus size: 40
35584630 ACTAACCGAA
**
35584640 GTATGTGTTTTCAGGGGTACCGAAGTACAAACAGGGGCAC
1 GTATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCAC
* * * *
35584680 GTGTGTGCATTTAGGGGTACCGAAGTACAAACAGAGGCAT
1 GTATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCAC
** * *
35584720 GTAAATGCATTCAGGGGTACCAAAGTACAAAACA-GGGCAT
1 GTATGTGCATTCAGGGGTACCGAAGTAC-AAACAGGGGCAC
* * * * *
35584760 GTATGTGCATTCAAGGATATCAAAGTACAAACAGGGGAAC
1 GTATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCAC
* *
35584800 GTAAGTGCATTCAGGGGTATCGAAGTACAAACA-GGGCAC
1 GTATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCAC
*
35584839 ATATGTGCATTCA
1 GTATGTGCATTCA
35584852 ACAATAATTA
Statistics
Matches: 144, Mismatches: 26, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
39 21 0.15
40 118 0.82
41 5 0.03
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (40 bp):
GTATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCAC
Found at i:35584786 original size:80 final size:79
Alignment explanation
Indices: 35584649--35584852 Score: 264
Period size: 80 Copynumber: 2.6 Consensus size: 79
35584639 AGTATGTGTT
* * * * *
35584649 TTCAGGGGTACCGAAGTACAAACAGGGGCACGTGTGTGCATTTAGGGGTACCGAAGTACAAACAG
1 TTCAGGGGTACCGAAGTACAAACA-GGGCACGTATGTGCATTCAAGGATACCAAAGTACAAACAG
* *
35584714 AGGCATGTAAATGCA
65 AGGAACGTAAATGCA
* * *
35584729 TTCAGGGGTACCAAAGTACAAAACAGGGCATGTATGTGCATTCAAGGATATCAAAGTACAAACAG
1 TTCAGGGGTACCGAAGTAC-AAACAGGGCACGTATGTGCATTCAAGGATACCAAAGTACAAACAG
* *
35584794 GGGAACGTAAGTGCA
65 AGGAACGTAAATGCA
* *
35584809 TTCAGGGGTATCGAAGTACAAACAGGGCACATATGTGCATTCAA
1 TTCAGGGGTACCGAAGTACAAACAGGGCACGTATGTGCATTCAA
35584853 CAATAATTAT
Statistics
Matches: 107, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
79 23 0.21
80 79 0.74
81 5 0.05
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.20
Consensus pattern (79 bp):
TTCAGGGGTACCGAAGTACAAACAGGGCACGTATGTGCATTCAAGGATACCAAAGTACAAACAGA
GGAACGTAAATGCA
Found at i:35584834 original size:20 final size:20
Alignment explanation
Indices: 35584777--35584835 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
35584767 CATTCAAGGA
*
35584777 TATCAAAGTACAAACAGGGG
1 TATCGAAGTACAAACAGGGG
* * **
35584797 -AACGTAAGTGCATTCAGGGG
1 TATCG-AAGTACAAACAGGGG
35584817 TATCGAAGTACAAACAGGG
1 TATCGAAGTACAAACAGGG
35584836 CACATATGTG
Statistics
Matches: 28, Mismatches: 9, Indels: 4
0.68 0.22 0.10
Matches are distributed among these distances:
19 2 0.07
20 23 0.82
21 3 0.11
ACGTcount: A:0.39, C:0.15, G:0.29, T:0.17
Consensus pattern (20 bp):
TATCGAAGTACAAACAGGGG
Found at i:35588015 original size:25 final size:25
Alignment explanation
Indices: 35587987--35588035 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
35587977 AGTTAATAAT
35587987 AATT-CTCATTGAGTTT-TTCTTAAAG
1 AATTGCTC-TTGAGTTTCTT-TTAAAG
35588012 AATTGCTCTTGAGTTTCTTTTAAA
1 AATTGCTCTTGAGTTTCTTTTAAA
35588036 AGCTGTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (25 bp):
AATTGCTCTTGAGTTTCTTTTAAAG
Found at i:35589274 original size:96 final size:96
Alignment explanation
Indices: 35589089--35589267 Score: 277
Period size: 96 Copynumber: 1.9 Consensus size: 96
35589079 ATAGGAGTAT
* * * * **
35589089 GATTGATCTCTCACCTGTTGTGAAATGTTATTGGTGTAGTTCAAAAGATCATGAGGTTTTCCGGT
1 GATTGAGCTATCACCTGTTGTGAAATGTTATTGGTGTAGTTCAAAAGATCATAAGGGTTTCCAAT
35589154 GTCCAATTAAATATCCAAATAGAGACAATAA
66 GTCCAATTAAATATCCAAATAGAGACAATAA
* * *
35589185 GATTGAGCTATCACCTTTTGTGAAATTTTATTTGTGTAGTTCAAAAGATCATAAGGGTTTCCAAT
1 GATTGAGCTATCACCTGTTGTGAAATGTTATTGGTGTAGTTCAAAAGATCATAAGGGTTTCCAAT
35589250 GTCCAATTAAATATCCAA
66 GTCCAATTAAATATCCAA
35589268 CAAGAGAAGA
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
96 74 1.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (96 bp):
GATTGAGCTATCACCTGTTGTGAAATGTTATTGGTGTAGTTCAAAAGATCATAAGGGTTTCCAAT
GTCCAATTAAATATCCAAATAGAGACAATAA
Found at i:35590320 original size:28 final size:28
Alignment explanation
Indices: 35590257--35590320 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
35590247 CTTGTGCTAA
** *
35590257 GCCGTGTGGTAGCTGTGTGTGACACATG
1 GCCGTGTGGTAGCCATGTGTGACACACG
* *
35590285 ACCATGTGGTAGCCATGTGTGACACACG
1 GCCGTGTGGTAGCCATGTGTGACACACG
35590313 GCCGTGTG
1 GCCGTGTG
35590321 ACAAGTCGTG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.17, C:0.22, G:0.36, T:0.25
Consensus pattern (28 bp):
GCCGTGTGGTAGCCATGTGTGACACACG
Found at i:35596804 original size:21 final size:23
Alignment explanation
Indices: 35596764--35596805 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
35596754 TATACAATAT
*
35596764 TAAAAATGCTAACTAAAATGTTC
1 TAAAAAAGCTAACTAAAATGTTC
35596787 TAAAAAAGC-AAC-AAAATGT
1 TAAAAAAGCTAACTAAAATGT
35596806 ACTTAAGTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 3 0.17
23 8 0.44
ACGTcount: A:0.55, C:0.12, G:0.10, T:0.24
Consensus pattern (23 bp):
TAAAAAAGCTAACTAAAATGTTC
Found at i:35601444 original size:19 final size:18
Alignment explanation
Indices: 35601403--35601446 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
35601393 AAACCTATAA
* *
35601403 AAAATAAATACATTAAGT
1 AAAATAAAAACACTAAGT
*
35601421 TAAATAAAAACTACTAAGT
1 AAAATAAAAAC-ACTAAGT
35601440 AAAATAA
1 AAAATAA
35601447 CCAAAACAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.25
Consensus pattern (18 bp):
AAAATAAAAACACTAAGT
Found at i:35601837 original size:165 final size:165
Alignment explanation
Indices: 35601565--35601888 Score: 567
Period size: 165 Copynumber: 2.0 Consensus size: 165
35601555 AAGTGATCAA
*
35601565 TATCATTCCCACGAGTATCGAGTTGAGGCAAAAAATTGGTCAAGTTATTATAATAAAATGTGATT
1 TATCATTCCCACGAGTATCGAATTGAGGCAAAAAATTGGTCAAGTTATTATAATAAAATGTGATT
** *
35601630 AATGCTATGGAAAAATTTGTGATAAATATGCAGTGGCAATTAGTGGAGTAGTGATGTAAGCAATA
66 AATGCTATGGAAAAATCAGTGATAAATATGCAGTGGCAATTAGTGGAGTAATGATGTAAGCAATA
* *
35601695 CGTGGAATTATTGAGTAACTGAAAATGCTGATGAG
131 CGTGGAATTAATGAGTAACTAAAAATGCTGATGAG
*
35601730 TATCATTCCCACGAGTATCGAATTGAGGCACAAAATTGGTCAAGTTATTATAATAAAATGTGATT
1 TATCATTCCCACGAGTATCGAATTGAGGCAAAAAATTGGTCAAGTTATTATAATAAAATGTGATT
* *
35601795 AATGCTATGGTAAAATCAGTGATAAATATGTAGTGGCAATTAGTGGAGTAATGATGTAAGCAATA
66 AATGCTATGGAAAAATCAGTGATAAATATGCAGTGGCAATTAGTGGAGTAATGATGTAAGCAATA
35601860 CGTGGAATTAATGAGTAACTAAAAATGCT
131 CGTGGAATTAATGAGTAACTAAAAATGCT
35601889 ACGGAAAAAG
Statistics
Matches: 150, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
165 150 1.00
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (165 bp):
TATCATTCCCACGAGTATCGAATTGAGGCAAAAAATTGGTCAAGTTATTATAATAAAATGTGATT
AATGCTATGGAAAAATCAGTGATAAATATGCAGTGGCAATTAGTGGAGTAATGATGTAAGCAATA
CGTGGAATTAATGAGTAACTAAAAATGCTGATGAG
Found at i:35604847 original size:29 final size:29
Alignment explanation
Indices: 35604786--35604970 Score: 108
Period size: 29 Copynumber: 6.3 Consensus size: 29
35604776 CAACGAATGG
* *
35604786 AAAGGGATAGCTTCGACTATCGAATA-CA
1 AAAGGGATAGCTTCGACTATCGATTATGA
35604814 GAAAGGGATAGCTTCGACTATCGATTATGA
1 -AAAGGGATAGCTTCGACTATCGATTATGA
* * * * **
35604844 AAAGGGAT-GGTGACGACCATCAACAATGA
1 AAAGGGATAGCT-TCGACTATCGATTATGA
* * * *
35604873 AAAGAGAT-GGTGAT-GACCATCGAACTATGA
1 AAAGGGATAGCT--TCGACTATCG-ATTATGA
* * * *
35604903 AAAAGGATGGCTTCGGCTATTGATCTATGA
1 AAAGGGATAGCTTCGACTATCGAT-TATGA
* * *
35604933 AAAAGGATAGCTTCGGCTATCAAATTATGA
1 AAAGGGATAGCTTCGACTATC-GATTATGA
35604963 AAAGGGAT
1 AAAGGGAT
35604971 GTGATGACCA
Statistics
Matches: 124, Mismatches: 24, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
28 2 0.02
29 64 0.52
30 54 0.44
31 4 0.03
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (29 bp):
AAAGGGATAGCTTCGACTATCGATTATGA
Found at i:35604962 original size:30 final size:30
Alignment explanation
Indices: 35604897--35604970 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
35604887 GACCATCGAA
* **
35604897 CTATGAAAAAGGATGGCTTCGGCTATTGAT
1 CTATGAAAAAGGATAGCTTCGGCTATAAAT
35604927 CTATGAAAAAGGATAGCTTCGGCTATCAAAT
1 CTATGAAAAAGGATAGCTTCGGCTAT-AAAT
*
35604958 -TATGAAAAGGGAT
1 CTATGAAAAAGGAT
35604971 GTGATGACCA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 37 0.95
31 2 0.05
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.27
Consensus pattern (30 bp):
CTATGAAAAAGGATAGCTTCGGCTATAAAT
Found at i:35604990 original size:119 final size:119
Alignment explanation
Indices: 35604790--35605089 Score: 347
Period size: 119 Copynumber: 2.5 Consensus size: 119
35604780 GAATGGAAAG
* * * *
35604790 GGATAGCTTCGACTATCGAA-TA-CAGAAAGGGATAGCTTCGACTATC-GATTATGAAAAGGGAT
1 GGATAGCTTCGACTATCGAACTATGA-AAAAGGATAGCTTCGGCTATCAAATTATGAAAAGGGAT
* * ** *
35604852 GGTGACGACCATCAACAATGAAAAGAGATGGTGATGACCATCGAACTATGAAAAA
65 GGTGACGACCATCAACAATGAAAAGAAATCGTGACAACCATCAAACTATGAAAAA
* * * *
35604907 GGATGGCTTCGGCTATTGATCTATGAAAAAGGATAGCTTCGGCTATCAAATTATGAAAAGGGAT-
1 GGATAGCTTCGACTATCGAACTATGAAAAAGGATAGCTTCGGCTATCAAATTATGAAAAGGGATG
* * *
35604971 GTGATGACCATCGAACAATGAAAAGAAATCGTGACAACCATCAAATTATGAAAAG
66 GTGACGACCATC-AACAATGAAAAGAAATCGTGACAACCATCAAACTATGAAAAA
* * * * * **
35605026 GGATAGCTTTGACTGTCGAACTATGAAAAGGGATAACTTCGGTTATCAAATTACAAAAAGGGAT
1 GGATAGCTTCGACTATCGAACTATGAAAAAGGATAGCTTCGGCTATCAAATTATGAAAAGGGAT
35605090 ACGTCAAGCA
Statistics
Matches: 152, Mismatches: 27, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
117 16 0.11
118 32 0.21
119 104 0.68
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (119 bp):
GGATAGCTTCGACTATCGAACTATGAAAAAGGATAGCTTCGGCTATCAAATTATGAAAAGGGATG
GTGACGACCATCAACAATGAAAAGAAATCGTGACAACCATCAAACTATGAAAAA
Found at i:35605022 original size:30 final size:29
Alignment explanation
Indices: 35604951--35605025 Score: 78
Period size: 30 Copynumber: 2.6 Consensus size: 29
35604941 AGCTTCGGCT
** **
35604951 ATCAAATTATGAAAAGGGATGTGATGACC
1 ATCAAATTATGAAAAGAAATGTGACAACC
* **
35604980 ATCGAACAATGAAAAGAAATCGTGACAACC
1 ATCAAATTATGAAAAGAAAT-GTGACAACC
35605010 ATCAAATTATGAAAAG
1 ATCAAATTATGAAAAG
35605026 GGATAGCTTT
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
29 15 0.43
30 20 0.57
ACGTcount: A:0.48, C:0.13, G:0.19, T:0.20
Consensus pattern (29 bp):
ATCAAATTATGAAAAGAAATGTGACAACC
Found at i:35606131 original size:12 final size:12
Alignment explanation
Indices: 35606114--35606139 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35606104 GCGGTTACAT
35606114 GGCCTAGCACAC
1 GGCCTAGCACAC
35606126 GGCCTAGCACAC
1 GGCCTAGCACAC
35606138 GG
1 GG
35606140 ACGTGTGAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.38, G:0.31, T:0.08
Consensus pattern (12 bp):
GGCCTAGCACAC
Found at i:35609291 original size:23 final size:23
Alignment explanation
Indices: 35609260--35609311 Score: 79
Period size: 24 Copynumber: 2.3 Consensus size: 23
35609250 TTGTTTTTGT
35609260 AAAAAAAATTC-AAAAAAAAAGA
1 AAAAAAAATTCGAAAAAAAAAGA
*
35609282 AAAATAAAATTCGAAAAGAAAAGA
1 AAAA-AAAATTCGAAAAAAAAAGA
35609306 AAAAAA
1 AAAAAA
35609312 TTGTATACGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 4 0.15
23 9 0.33
24 14 0.52
ACGTcount: A:0.79, C:0.04, G:0.08, T:0.10
Consensus pattern (23 bp):
AAAAAAAATTCGAAAAAAAAAGA
Found at i:35609380 original size:15 final size:15
Alignment explanation
Indices: 35609360--35609408 Score: 98
Period size: 15 Copynumber: 3.3 Consensus size: 15
35609350 AGTATCCGCA
35609360 AAAAAAATTTGACCC
1 AAAAAAATTTGACCC
35609375 AAAAAAATTTGACCC
1 AAAAAAATTTGACCC
35609390 AAAAAAATTTGACCC
1 AAAAAAATTTGACCC
35609405 AAAA
1 AAAA
35609409 GTCTGGAGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.57, C:0.18, G:0.06, T:0.18
Consensus pattern (15 bp):
AAAAAAATTTGACCC
Found at i:35614825 original size:22 final size:23
Alignment explanation
Indices: 35614777--35614825 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
35614767 TATTGGTATG
35614777 ATTAATGTGTCCTAATAAGTCGT
1 ATTAATGTGTCCTAATAAGTCGT
* *
35614800 -TTAATGTGTCTTAATAGGT-GT
1 ATTAATGTGTCCTAATAAGTCGT
35614821 ATTAA
1 ATTAA
35614826 AGAAGCTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (23 bp):
ATTAATGTGTCCTAATAAGTCGT
Found at i:35617312 original size:49 final size:51
Alignment explanation
Indices: 35617256--35617382 Score: 168
Period size: 49 Copynumber: 2.5 Consensus size: 51
35617246 TTGCATCTTT
*
35617256 TAATTATGACATGCATTATGTAACTCTCATGTTGGTT-AAGTTTACAT-AA
1 TAATTATGACATGCATTATGTAACTCTCATGTTAGTTAAAGTTTACATCAA
* * *
35617305 TAATTATGACATGCTTTATGTAACTCTCATGTTAGTTAAAGTTTGCATCAT
1 TAATTATGACATGCATTATGTAACTCTCATGTTAGTTAAAGTTTACATCAA
* * *
35617356 TAAATTAAGTCATGCATTAAGTAACTC
1 T-AATTATGACATGCATTATGTAACTC
35617383 ATTTGTTCAT
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
49 35 0.52
50 9 0.13
51 2 0.03
52 21 0.31
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (51 bp):
TAATTATGACATGCATTATGTAACTCTCATGTTAGTTAAAGTTTACATCAA
Found at i:35619544 original size:17 final size:19
Alignment explanation
Indices: 35619524--35619565 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
35619514 AAATGAGAGA
*
35619524 AAAAGAAATTG-AA-AAAG
1 AAAAGAAAGTGAAAGAAAG
*
35619541 AAAAGAGAGTGAAAGAAAG
1 AAAAGAAAGTGAAAGAAAG
35619560 AAAAGA
1 AAAAGA
35619566 GTGATTGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 9 0.43
18 2 0.10
19 10 0.48
ACGTcount: A:0.69, C:0.00, G:0.24, T:0.07
Consensus pattern (19 bp):
AAAAGAAAGTGAAAGAAAG
Found at i:35622888 original size:50 final size:52
Alignment explanation
Indices: 35622821--35622952 Score: 169
Period size: 50 Copynumber: 2.6 Consensus size: 52
35622811 ACGTGTTTTG
* * *
35622821 CATTAAATAAAGCCATGCATTATGTAACTCCCATGTTAGTT-AAGTTTACAT
1 CATTAAATTAAGACATGCATTAAGTAACTCCCATGTTAGTTAAAGTTTACAT
* * * * *
35622872 CA-TAAATTATGACATGCTTTACGTAACTCTCATGTTAGTTAAAGTTTGCAT
1 CATTAAATTAAGACATGCATTAAGTAACTCCCATGTTAGTTAAAGTTTACAT
*
35622923 CATTAAATTAAGTCATGCATTAAGTAACTC
1 CATTAAATTAAGACATGCATTAAGTAACTC
35622953 ATTTCATTTA
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
50 32 0.47
51 13 0.19
52 23 0.34
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (52 bp):
CATTAAATTAAGACATGCATTAAGTAACTCCCATGTTAGTTAAAGTTTACAT
Found at i:35625952 original size:19 final size:18
Alignment explanation
Indices: 35625928--35625963 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
35625918 ACGTATTAAA
35625928 CCGAGTTACAAAATTTCAT
1 CCGAGTTA-AAAATTTCAT
*
35625947 CCGAGTTAAAACTTTCA
1 CCGAGTTAAAAATTTCA
35625964 ACTTTTTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (18 bp):
CCGAGTTAAAAATTTCAT
Found at i:35629727 original size:50 final size:52
Alignment explanation
Indices: 35629627--35629814 Score: 204
Period size: 50 Copynumber: 3.6 Consensus size: 52
35629617 TTTTCTGTAC
* * * * * *
35629627 TGCCAATGCCATATCCTAGATACGGTCTTACATGGGA-GT-TCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCTCATCTCGG
* * *
35629677 TGCCCATGTCATGTCCCAGACATGGTCTTACA-GGGGCC-CTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCTCATCTCGG
* * *
35629727 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC-TCATCTC---GG
35629783 TGCCAATGCCATGTCCCAGACATGGTCTTACA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACA
35629815 CTGGCTCACA
Statistics
Matches: 114, Mismatches: 16, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
49 3 0.03
50 65 0.57
51 5 0.04
52 3 0.03
53 6 0.05
56 32 0.28
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.27
Consensus pattern (52 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCTCATCTCGG
Found at i:35629759 original size:100 final size:103
Alignment explanation
Indices: 35629627--35629814 Score: 238
Period size: 100 Copynumber: 1.8 Consensus size: 103
35629617 TTTTCTGTAC
* * * ** * * *
35629627 TGCCAATGCCATATCCTAGATACGGTCTTACATGGGAGTTCTCAT-A-TC-GGTGCCCATGTCAT
1 TGCCAACGCCATATCCCAGACACGGTCTTACATGGGACCTCTCATAACTCAGATGCCAATGCCAT
35629689 GTCCCAGACATGGTCTTACAGGGGCCCTCTCATCTCGG
66 GTCCCAGACATGGTCTTACAGGGGCCCTCTCATCTCGG
* *
35629727 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGC
1 TGCCAACGCCATATCCCAGACACGGTCTTACATGGGACCTCTCATAA-CTC-A-GATGCCAATGC
35629792 CATGTCCCAGACATGGTCTTACA
63 CATGTCCCAGACATGGTCTTACA
35629815 CTGGCTCACA
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
100 38 0.53
101 1 0.01
103 2 0.03
106 31 0.43
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.27
Consensus pattern (103 bp):
TGCCAACGCCATATCCCAGACACGGTCTTACATGGGACCTCTCATAACTCAGATGCCAATGCCAT
GTCCCAGACATGGTCTTACAGGGGCCCTCTCATCTCGG
Found at i:35630526 original size:19 final size:18
Alignment explanation
Indices: 35630502--35630537 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
35630492 ACGTATTAAA
35630502 CCGAGTTACAAAATTTCAT
1 CCGAGTTA-AAAATTTCAT
*
35630521 CCGAGTTAAAACTTTCA
1 CCGAGTTAAAAATTTCA
35630538 AATTTTAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (18 bp):
CCGAGTTAAAAATTTCAT
Found at i:35632155 original size:12 final size:12
Alignment explanation
Indices: 35632138--35632168 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
35632128 TTTCTTATAT
35632138 ATACTAAATAAA
1 ATACTAAATAAA
35632150 ATACT-AATAAA
1 ATACTAAATAAA
35632161 ATACTAAA
1 ATACTAAA
35632169 ATATCATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.26
Consensus pattern (12 bp):
ATACTAAATAAA
Found at i:35638055 original size:25 final size:25
Alignment explanation
Indices: 35637999--35638058 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
35637989 TAAACATACA
*
35637999 TGTTCTGTTCTGCTATGCTTCGTTC
1 TGTTCTGTTCTGCTATGCTCCGTTC
** * * *
35638024 TAATCTGTTCTTCTTTGCTCCGTTT
1 TGTTCTGTTCTGCTATGCTCCGTTC
35638049 TGTTCTGTTC
1 TGTTCTGTTC
35638059 AGTATTACTT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.05, C:0.23, G:0.17, T:0.55
Consensus pattern (25 bp):
TGTTCTGTTCTGCTATGCTCCGTTC
Found at i:35639000 original size:12 final size:12
Alignment explanation
Indices: 35638983--35639007 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35638973 CGAACAAGAG
35638983 TCATTTGCAAAT
1 TCATTTGCAAAT
35638995 TCATTTGCAAAT
1 TCATTTGCAAAT
35639007 T
1 T
35639008 ATGTCAAACA
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:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (12 bp):
TCATTTGCAAAT
Found at i:35641993 original size:17 final size:17
Alignment explanation
Indices: 35641950--35642000 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
35641940 TTGGTAGAGT
*
35641950 GGATAGGAAAATTGGAAA
1 GGATAGAAAAATT-GAAA
35641968 -GAT-GAAAAATTGAAA
1 GGATAGAAAAATTGAAA
*
35641983 GGATAGAAAAATAGAAA
1 GGATAGAAAAATTGAAA
35642000 G
1 G
35642001 AAGGAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 4 0.14
16 10 0.34
17 15 0.52
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.16
Consensus pattern (17 bp):
GGATAGAAAAATTGAAA
Found at i:35657808 original size:21 final size:21
Alignment explanation
Indices: 35657762--35657805 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
35657752 TATTAGAAAA
35657762 TAAA-TATCGATACCCAACTG
1 TAAATTATCGATACCCAACTG
*
35657782 TAAATTATCGATA-CCAACTT
1 TAAATTATCGATACCCAACTG
35657802 TAAA
1 TAAA
35657806 ATTTTGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (21 bp):
TAAATTATCGATACCCAACTG
Found at i:35659404 original size:131 final size:129
Alignment explanation
Indices: 35659170--35659722 Score: 581
Period size: 131 Copynumber: 4.3 Consensus size: 129
35659160 AGCGATTGGA
* * * *
35659170 AAATCAACTAACACAAATGAGATTGTTCATGATATTAAATCGAATGAACTTAAGTTGTGATATTA
1 AAATCAACTAACTCAAATAAGATTGTTCATGATATTAAATCAAATGAACTT-AGTTGTGATCTTA
*
35659235 AATCAGTGAACCTTAACGATATCAACTGTGATCTTAAATCAACGAGTTTTTTGGAGTAGCGATCT
65 AATCAGTGAACCTTAACGATATC-ACTGTGATCTTAAATCAACGAGTTGTTTGGAGTAGCGATCT
35659300 T
129 T
*
35659301 AAATCAACTAACTCAAATAAGATTGTTCATGATGTTAAATCAAATGAACTTAGTTTGTGATCTTA
1 AAATCAACTAACTCAAATAAGATTGTTCATGATATTAAATCAAATGAACTTAG-TTGTGATCTTA
** * * * *
35659366 AATTTGTGAACCTTAACGATATCACTTGTGATCTTAAATCATCGAGATGTTTGGAGTAGCGGTAT
65 AATCAGTGAACCTTAACGATATCAC-TGTGATCTTAAATCAACGAGTTGTTTGGAGTAGCGATCT
35659431 T
129 T
** ** *
35659432 AAATCAA-TGAACTCAAATAAGATTGTTCACAATATTAAATTGAATGAACTTAGGTTGTAATCTT
1 AAATCAACT-AACTCAAATAAGATTGTTCATGATATTAAATCAAATGAACTTA-GTTGTGATCTT
** ** ** * *
35659496 AAATCAACGAACCTTAACGATATTGGCTGCAATCTTAAATCAACAAATTGTTTGGAGTAGC-ACT
64 AAATCAGTGAACCTTAACGATA-TCACTGTGATCTTAAATCAACGAGTTGTTTGGAGTAGCGA-T
35659560 CTT
127 CTT
* * *
35659563 AAATCAACTAACTAAAATAAGATTGTTCATGATATTAAATC-AA-CAA---A----TGATATTAA
1 AAATCAACTAACTCAAATAAGATTGTTCATGATATTAAATCAAATGAACTTAGTTGTGATCTTAA
* * * * * * ** *
35659619 ATCAGCGAATCTCAA-TATATCAACTGTGATATTAAATCAGCGAACTATTTGGAGTAGCGATCTT
66 ATCAGTGAACCTTAACGATATC-ACTGTGATCTTAAATCAACGAGTTGTTTGGAGTAGCGATCTT
* *
35659683 AAATCAGCTAACTCAAATAAGATTTTTCATGATATATAAA
1 AAATCAACTAACTCAAATAAGATTGTTCATGATAT-TAAA
35659723 GTAAACAATA
Statistics
Matches: 357, Mismatches: 55, Indels: 30
0.81 0.12 0.07
Matches are distributed among these distances:
119 1 0.00
120 67 0.19
121 24 0.07
126 1 0.00
129 2 0.01
130 7 0.02
131 251 0.70
132 4 0.01
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (129 bp):
AAATCAACTAACTCAAATAAGATTGTTCATGATATTAAATCAAATGAACTTAGTTGTGATCTTAA
ATCAGTGAACCTTAACGATATCACTGTGATCTTAAATCAACGAGTTGTTTGGAGTAGCGATCTT
Found at i:35664920 original size:19 final size:20
Alignment explanation
Indices: 35664888--35664925 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
35664878 CAAGCTGATT
35664888 TTAGCTCAATTTCAGCTCCC
1 TTAGCTCAATTTCAGCTCCC
35664908 TTAGCTC-ATTTCAGCTCC
1 TTAGCTCAATTTCAGCTCC
35664926 AACCAGCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.18, C:0.34, G:0.11, T:0.37
Consensus pattern (20 bp):
TTAGCTCAATTTCAGCTCCC
Found at i:35671130 original size:72 final size:72
Alignment explanation
Indices: 35671013--35671202 Score: 283
Period size: 72 Copynumber: 2.6 Consensus size: 72
35671003 GTTGAATAAT
* * * *
35671013 CAGCTTAGAAAAATGCAACAGCAGCCTCCTCTCTT-AATGCCGTCCCAAATCCCATGCACACATT
1 CAGCTTGGAAAAATGCAGCAGCAACCTTCTCT-TTAAATGCCGTCCCAAATCCCATGCACACATT
35671077 AAATTCGG
65 AAATTCGG
* * *
35671085 CAGCTTGGAAAAAGGCAGCACCAACCTTCTCTTTAAATGCCGTCCCAAGTCCCATGCACACATTA
1 CAGCTTGGAAAAATGCAGCAGCAACCTTCTCTTTAAATGCCGTCCCAAATCCCATGCACACATTA
*
35671150 AATTTGG
66 AATTCGG
35671157 CAGCTTGGAAAAATGCAGCAGCAACCTTTCTCTTTAAATGCCGTCC
1 CAGCTTGGAAAAATGCAGCAGCAACC-TTCTCTTTAAATGCCGTCC
35671203 ATGTACCTGC
Statistics
Matches: 106, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
71 2 0.02
72 85 0.80
73 19 0.18
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.24
Consensus pattern (72 bp):
CAGCTTGGAAAAATGCAGCAGCAACCTTCTCTTTAAATGCCGTCCCAAATCCCATGCACACATTA
AATTCGG
Found at i:35674416 original size:30 final size:28
Alignment explanation
Indices: 35674382--35674437 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
35674372 GTGATTAAAT
35674382 AAAATCGACA-CAAGCAGAATTTAAAAGAAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAAA
*
35674412 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
35674438 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 8 0.33
29 2 0.08
30 10 0.42
31 4 0.17
ACGTcount: A:0.61, C:0.11, G:0.14, T:0.14
Consensus pattern (28 bp):
AAAATCGACAGCAAGAAATTAAAAGAAA
Found at i:35676435 original size:33 final size:33
Alignment explanation
Indices: 35676397--35676468 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
35676387 GATTACTCTC
35676397 TTCACTCG-TTTCTTTTACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTT-CAGACTCTCTTTCTTT
* *
35676430 TTCACTCGATTTCTTTTCAGGCTCTTTTTCTTT
1 TTCACTCGATTTCTTTTCAGACTCTCTTTCTTT
*
35676463 TCCACT
1 TTCACT
35676469 TTTGTTTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
33 27 0.77
34 8 0.23
ACGTcount: A:0.11, C:0.28, G:0.07, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAGACTCTCTTTCTTT
Found at i:35677658 original size:2 final size:2
Alignment explanation
Indices: 35677653--35677683 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
35677643 TTCCAAAATT
35677653 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
35677684 TTTTAATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:35678866 original size:72 final size:73
Alignment explanation
Indices: 35678783--35678937 Score: 222
Period size: 72 Copynumber: 2.1 Consensus size: 73
35678773 CTCCTCCCTT
* * * * *
35678783 AATGCCATCCCAAATCCCATGCACACATTAAATTTGGCAGCTTGGAAAAAGGCAACATCAAC-CT
1 AATGCCGTCCCAAATCCCATCCACACATTAAATTCGGCAGCTTGAAAAAAGGCAACAGCAACTCT
35678847 TCTCTTTA
66 TCTCTTTA
* * *
35678855 AATGCCGTCCCAAGTCCCATCCACACATTAAATTCGGCAGCTTGAAAAAATGCAACAGCAACTTT
1 AATGCCGTCCCAAATCCCATCCACACATTAAATTCGGCAGCTTGAAAAAAGGCAACAGCAACTCT
35678920 TCTCTTTA
66 TCTCTTTA
*
35678928 AATGCTGTCC
1 AATGCCGTCC
35678938 ATGTACCTGC
Statistics
Matches: 73, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
72 55 0.75
73 18 0.25
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (73 bp):
AATGCCGTCCCAAATCCCATCCACACATTAAATTCGGCAGCTTGAAAAAAGGCAACAGCAACTCT
TCTCTTTA
Found at i:35682325 original size:41 final size:40
Alignment explanation
Indices: 35682229--35682328 Score: 100
Period size: 41 Copynumber: 2.5 Consensus size: 40
35682219 CTTATTAAAC
* *
35682229 AAAGAT-A-AAAAATAGAAATGAAACAACAGTAAATAATT
1 AAAGATAACAAAAATAAAAATGAAACAACAGTAAACAATT
*
35682267 AATGATAACAAATAATAAAAATGAAATCAA-AGTAAAGCAATT
1 AAAGATAACAAA-AATAAAAATGAAA-CAACAGTAAA-CAATT
*
35682309 AAAGA-AAGGAAAAATAAAAA
1 AAAGATAA-CAAAAATAAAAA
35682329 CAAAAATACT
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
38 5 0.10
39 1 0.02
40 3 0.06
41 28 0.55
42 14 0.27
ACGTcount: A:0.67, C:0.05, G:0.11, T:0.17
Consensus pattern (40 bp):
AAAGATAACAAAAATAAAAATGAAACAACAGTAAACAATT
Found at i:35686525 original size:58 final size:58
Alignment explanation
Indices: 35686455--35686565 Score: 195
Period size: 58 Copynumber: 1.9 Consensus size: 58
35686445 AAGTGTGGCG
* * *
35686455 TTTGCTATACCTTTGGTTCTTATCTCGTTAGATAGTGGGTCAAGGTTTATTTGTTGAT
1 TTTGCTATACCTTTGGTTCCTATCTCGTTAAATAGTGAGTCAAGGTTTATTTGTTGAT
35686513 TTTGCTATACCTTTGGTTCCTATCTCGTTAAATAGTGAGTCAAGGTTTATTTG
1 TTTGCTATACCTTTGGTTCCTATCTCGTTAAATAGTGAGTCAAGGTTTATTTG
35686566 ATAATTTCAC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.19, C:0.14, G:0.21, T:0.47
Consensus pattern (58 bp):
TTTGCTATACCTTTGGTTCCTATCTCGTTAAATAGTGAGTCAAGGTTTATTTGTTGAT
Found at i:35690156 original size:21 final size:21
Alignment explanation
Indices: 35690132--35690173 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
35690122 TAAATTTAAC
35690132 TCAATTCAATACAATTCACAT
1 TCAATTCAATACAATTCACAT
* *
35690153 TCAATTTAATCCAATTCACAT
1 TCAATTCAATACAATTCACAT
35690174 CTTAGGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (21 bp):
TCAATTCAATACAATTCACAT
Found at i:35693522 original size:19 final size:18
Alignment explanation
Indices: 35693486--35693525 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
35693476 TTTCCACTCG
*
35693486 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
35693504 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
35693523 TTT
1 TTT
35693526 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:35694605 original size:14 final size:15
Alignment explanation
Indices: 35694585--35694623 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
35694575 AGCTTCTTCT
35694585 TTTTTTTTCACGAAA
1 TTTTTTTTCACGAAA
*
35694600 TTTTTTTTCACG-AT
1 TTTTTTTTCACGAAA
35694614 TTTTTTTTCA
1 TTTTTTTTCA
35694624 ACTTGATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.18, C:0.13, G:0.05, T:0.64
Consensus pattern (15 bp):
TTTTTTTTCACGAAA
Found at i:35694680 original size:13 final size:13
Alignment explanation
Indices: 35694660--35694718 Score: 95
Period size: 13 Copynumber: 4.7 Consensus size: 13
35694650 AATGGAAACT
35694660 AATTTTTTTTTG-
1 AATTTTTTTTTGA
*
35694672 AATTTTTTTTTCA
1 AATTTTTTTTTGA
35694685 AATTTTTTTTTGA
1 AATTTTTTTTTGA
35694698 AATTTTTTTTTG-
1 AATTTTTTTTTGA
35694710 AATTTTTTT
1 AATTTTTTT
35694719 CGAAGATGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
12 20 0.45
13 24 0.55
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (13 bp):
AATTTTTTTTTGA
Found at i:35694694 original size:25 final size:25
Alignment explanation
Indices: 35694660--35694718 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
35694650 AATGGAAACT
35694660 AATTTTTTTTTG-AATTTTTTTTTCA
1 AATTTTTTTTTGAAATTTTTTTTT-A
*
35694685 AATTTTTTTTTGAAATTTTTTTTTG
1 AATTTTTTTTTGAAATTTTTTTTTA
35694710 AATTTTTTT
1 AATTTTTTT
35694719 CGAAGATGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 21 0.66
26 11 0.34
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (25 bp):
AATTTTTTTTTGAAATTTTTTTTTA
Found at i:35697857 original size:21 final size:21
Alignment explanation
Indices: 35697833--35697890 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 21
35697823 TCGATTTTAC
35697833 CTCACTTTTTCTTTTTGTTTT
1 CTCACTTTTTCTTTTTGTTTT
* *
35697854 CTCACTCTTT-TTTCT-TTTT
1 CTCACTTTTTCTTTTTGTTTT
35697873 CT-A-TCTTTTCTTTTTGTT
1 CTCACT-TTTTCTTTTTGTT
35697891 CTTTTGCTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
17 1 0.03
18 4 0.13
19 10 0.33
20 6 0.20
21 9 0.30
ACGTcount: A:0.05, C:0.21, G:0.03, T:0.71
Consensus pattern (21 bp):
CTCACTTTTTCTTTTTGTTTT
Found at i:35698984 original size:22 final size:22
Alignment explanation
Indices: 35698954--35698997 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
35698944 TTTGGTATTT
*
35698954 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAAAGGTAA
*
35698976 GGGATTTGGTACGAAAAGGTAA
1 GGGAATTGGTACGAAAAGGTAA
35698998 TGGTTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.36, T:0.23
Consensus pattern (22 bp):
GGGAATTGGTACGAAAAGGTAA
Found at i:35699834 original size:31 final size:32
Alignment explanation
Indices: 35699789--35699855 Score: 77
Period size: 31 Copynumber: 2.1 Consensus size: 32
35699779 ACATGCATGC
*
35699789 ACCTTGCTAAAATGAATCTCCA-A-ATTCGGCTA
1 ACCTTGCTAAAATG-ATC-CCACACATTCGGCCA
*
35699821 ACCTTG-TTAAATGATCCCACACATTCGGCCA
1 ACCTTGCTAAAATGATCCCACACATTCGGCCA
35699852 ACCT
1 ACCT
35699856 ATATAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 3 0.10
30 4 0.13
31 18 0.58
32 6 0.19
ACGTcount: A:0.31, C:0.30, G:0.12, T:0.27
Consensus pattern (32 bp):
ACCTTGCTAAAATGATCCCACACATTCGGCCA
Found at i:35700187 original size:30 final size:30
Alignment explanation
Indices: 35700129--35700187 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
35700119 TTGAAAATGT
* *
35700129 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
35700159 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
35700188 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:35708522 original size:18 final size:20
Alignment explanation
Indices: 35708485--35708527 Score: 72
Period size: 18 Copynumber: 2.2 Consensus size: 20
35708475 ACATGTATAA
35708485 GTATGTGTATTAATTAAAAT
1 GTATGTGTATTAATTAAAAT
35708505 GTATGTGTATT-A-TAAAAT
1 GTATGTGTATTAATTAAAAT
35708523 GTATG
1 GTATG
35708528 CATGTATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 11 0.48
19 1 0.04
20 11 0.48
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (20 bp):
GTATGTGTATTAATTAAAAT
Found at i:35710027 original size:41 final size:43
Alignment explanation
Indices: 35709965--35710081 Score: 157
Period size: 41 Copynumber: 2.7 Consensus size: 43
35709955 TGGTAAATTT
* * *
35709965 AATCCGCTCCACTGCAACTTCAGGGAGATAGGATT-T-GCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTAGATTC
*
35710006 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATATTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GTAGATTC
* *
35710050 AAGCTGCTCCACAGCAACTTCAGGGAGATAAG
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAG
35710082 GTTTGATATG
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
41 33 0.49
43 1 0.01
44 33 0.49
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (43 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTAGATTC
Found at i:35710067 original size:44 final size:41
Alignment explanation
Indices: 35709970--35710088 Score: 157
Period size: 44 Copynumber: 2.8 Consensus size: 41
35709960 AATTTAATCC
* * *
35709970 GCTCCACTGCAACTTCAGGGAGATAGGATTTGCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTTGATTCAAGCT
*
35710011 GCTCCACTGCAACTTCAGGGAGATAAGATTGGTATATTCAAGCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATT--T-GATTCAAGCT
* *
35710055 GCTCCACAGCAACTTCAGGGAGATAAGGTTTGAT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTTGAT
35710089 ATGGTGTGAT
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
41 31 0.46
42 1 0.01
43 1 0.01
44 35 0.51
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.27
Consensus pattern (41 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATTTGATTCAAGCT
Found at i:35710224 original size:50 final size:50
Alignment explanation
Indices: 35710170--35710920 Score: 353
Period size: 50 Copynumber: 15.1 Consensus size: 50
35710160 TGCGATGTCG
* * * * *
35710170 GGGAAGCAAGATTCGCTGTTGTAGCTTTAATCTGCTTCACTGCACTACCA
1 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTTCACTGCAATGCCA
* * * * * * * *
35710220 GGGAAGTAAGATTCGCTGTTGTGGCTTCAATCT-TTTAAATTGCAATGTCA
1 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTT-CACTGCAATGCCA
* * *
35710270 GGGAA-CAAGATTCACCGTTGTACCTTCAATCTGATCCACTGC-ATCGCCA
1 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTTCACTGCAAT-GCCA
* * ** * * * *
35710319 GGAAAGTAAGATTCACCGTTGCGGCTTCAATCTTCTT-ATTGCAATGTCG
1 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTTCACTGCAATGCCA
* * ***
35710368 GGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTGTGCTGCCA
1 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTTCACTGCAATGCCA
* * * * * * * *
35710418 GGGAAGTAAGATTCGCTGTTGTGGCTTTAATCT--TTAACTGCGATGTC-
1 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTTCACTGCAATGCCA
* *** * * **
35710465 GAGGAA-TAAGATTTTTCATTGTAGCTTTAATCTG-TTCCACTGCACCGCCA
1 G-GGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTT-CACTGCAATGCCA
* ** ** * * *
35710515 GGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTC-
1 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTTCACTGCAATGCCA
* * * * * *
35710564 GGGGAGACAAGATTCACTGTTATGGCTTCAATCTGCTCCACTGCACTGCCA
1 GGGAAG-CAAGATTCACCGTTGTAGCTTCAATCTGCTTCACTGCAATGCCA
* ** ** * * * *
35710615 GGGAAGTAAGATTTGCCGTTGCGGCTTCAATCT-TTTCAATTGCAATGTCG
1 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTTC-ACTGCAATGCCA
* *
35710665 GGGAAACAAGATTCACCGTTGTAGCTTCAATCTGGC-CCACTGC-ATCGCCTA
1 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCT-GCTTCACTGCAAT-GCC-A
* * * * ** * * * * *
35710716 -GAAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGTAATGTCG
1 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTTCACTGCAATGCCA
* * ** * * ** *
35710765 GGGAAACAAAATTCGTCGTCGTAACTTCAATCTAATCCACTGC-ATCGCCA
1 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTTCACTGCAAT-GCCA
* * * ** ** * * *
35710815 GGAAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCA
1 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTTCACTGCAATGCCA
* * * * *
35710865 GGGAAGCAAGATTCACCGTCGTAACTTTAATCTGCTCCACTGCACTGCCA
1 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTTCACTGCAATGCCA
*
35710915 AGGAAG
1 GGGAAG
35710921 GTAACTTCAT
Statistics
Matches: 503, Mismatches: 174, Indels: 48
0.69 0.24 0.07
Matches are distributed among these distances:
47 22 0.04
48 17 0.03
49 93 0.18
50 359 0.71
51 12 0.02
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (50 bp):
GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTTCACTGCAATGCCA
Found at i:35710618 original size:100 final size:99
Alignment explanation
Indices: 35710142--35710920 Score: 890
Period size: 100 Copynumber: 7.8 Consensus size: 99
35710132 GTGATTTATA
* * * * * * *
35710142 GCTTCAAACTTTTTAAACTGCGATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTTAATCTGCTT
1 GCTTCAATCTTTTT-AATTGCAATGTCGGGGAA-CAAGATTCACCGTTGTAGCTTCAATCTGCTC
* * *
35710207 CACTGCACTACCAGGGAAGTAAGATTCGCTGTTGTG
64 CACTGCACTGCCAGGGAAGTAAGATTCGCCGTTGCG
* * * *
35710243 GCTTCAATCTTTTAAATTGCAATGTCAGGGAACAAGATTCACCGTTGTACCTTCAATCTGATCCA
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGAACAAGATTCACCGTTGTAGCTTCAATCTGCTCCA
* *
35710308 CTGCA-TCGCCAGGAAAGTAAGATTCACCGTTGCG
66 CTGCACT-GCCAGGGAAGTAAGATTCGCCGTTGCG
* *
35710342 GCTTCAATCTTCTT-ATTGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGCTCC
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGAA-CAAGATTCACCGTTGTAGCTTCAATCTGCTCC
** * *
35710406 ACTGTGCTGCCAGGGAAGTAAGATTCGCTGTTGTG
65 ACTGCACTGCCAGGGAAGTAAGATTCGCCGTTGCG
* * * * * *** * * *
35710441 GCTTTAATC--TTTAACTGCGATGTCGAGGAATAAGATTTTTCATTGTAGCTTTAATCTGTTCCA
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGAACAAGATTCACCGTTGTAGCTTCAATCTGCTCCA
* *
35710504 CTGCACCGCCAGGGAAGTAAGATTCACCGTTGCG
66 CTGCACTGCCAGGGAAGTAAGATTCGCCGTTGCG
* * *
35710538 GCTTCAATCTTTTTAATTGCAATGTCGGGGAGACAAGATTCACTGTTATGGCTTCAATCTGCTCC
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGA-ACAAGATTCACCGTTGTAGCTTCAATCTGCTCC
*
35710603 ACTGCACTGCCAGGGAAGTAAGATTTGCCGTTGCG
65 ACTGCACTGCCAGGGAAGTAAGATTCGCCGTTGCG
*
35710638 GCTTCAATCTTTTCAATTGCAATGTCGGGGAAACAAGATTCACCGTTGTAGCTTCAATCTGGC-C
1 GCTTCAATCTTTTTAATTGCAATGTCGGGG-AACAAGATTCACCGTTGTAGCTTCAATCT-GCTC
* *
35710702 CACTGCA-TCGCCTA-GAAAGTAAGATTCGCCGTTGTG
64 CACTGCACT-GCC-AGGGAAGTAAGATTCGCCGTTGCG
* * ** * * **
35710738 GCTTCAATCTTTTTAATTGTAATGTCGGGGAAACAAAATTCGTCGTCGTAACTTCAATCTAATCC
1 GCTTCAATCTTTTTAATTGCAATGTCGGGG-AACAAGATTCACCGTTGTAGCTTCAATCTGCTCC
*
35710803 ACTGCA-TCGCCAGGAAAGTAAGATTCGCCGTTGCG
65 ACTGCACT-GCCAGGGAAGTAAGATTCGCCGTTGCG
* * * *
35710838 GCTTCAATCTTTTTAATTGCAATGTCAGGGAAGCAAGATTCACCGTCGTAACTTTAATCTGCTCC
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGAA-CAAGATTCACCGTTGTAGCTTCAATCTGCTCC
*
35710903 ACTGCACTGCCAAGGAAG
65 ACTGCACTGCCAGGGAAG
35710921 GTAACTTCAT
Statistics
Matches: 572, Mismatches: 91, Indels: 31
0.82 0.13 0.04
Matches are distributed among these distances:
97 63 0.11
98 31 0.05
99 151 0.26
100 310 0.54
101 17 0.03
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.30
Consensus pattern (99 bp):
GCTTCAATCTTTTTAATTGCAATGTCGGGGAACAAGATTCACCGTTGTAGCTTCAATCTGCTCCA
CTGCACTGCCAGGGAAGTAAGATTCGCCGTTGCG
Found at i:35712190 original size:5 final size:5
Alignment explanation
Indices: 35712167--35712213 Score: 51
Period size: 5 Copynumber: 9.0 Consensus size: 5
35712157 GGCCTCTCCT
*
35712167 TTTTC TTTTTC GTTCTTC TTTTC TTTTC TTTTC TTTTG TTTT- TTTTC
1 TTTTC -TTTTC -TT-TTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
35712214 AAGTTAAGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
4 4 0.11
5 21 0.57
6 9 0.24
7 3 0.08
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:35715436 original size:19 final size:20
Alignment explanation
Indices: 35715402--35715458 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
35715392 AGGGTCACTT
* *
35715402 CATGAAAATCTAATGCATATG
1 CATG-AAATGTAATGCAAATG
*
35715423 -ATGCAATGTAATGCAAATG
1 CATGAAATGTAATGCAAATG
35715442 CATGAAATG-AATGCAAA
1 CATGAAATGTAATGCAAA
35715459 AAGAGACGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 21 0.68
20 10 0.32
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.25
Consensus pattern (20 bp):
CATGAAATGTAATGCAAATG
Found at i:35717794 original size:18 final size:20
Alignment explanation
Indices: 35717757--35717799 Score: 72
Period size: 18 Copynumber: 2.2 Consensus size: 20
35717747 ACATGTATAA
35717757 GTATGTGTATTAATTAAAAT
1 GTATGTGTATTAATTAAAAT
35717777 GTATGTGTATT-A-TAAAAT
1 GTATGTGTATTAATTAAAAT
35717795 GTATG
1 GTATG
35717800 CATGTATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 11 0.48
19 1 0.04
20 11 0.48
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (20 bp):
GTATGTGTATTAATTAAAAT
Found at i:35729071 original size:14 final size:13
Alignment explanation
Indices: 35729049--35729082 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
35729039 AGTCATTGTG
*
35729049 AAAAAAAATTGGA
1 AAAAAAAATTCGA
35729062 AAAAACAAATTCGA
1 AAAAA-AAATTCGA
35729076 AAAAAAA
1 AAAAAAA
35729083 TTCAAGGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.74, C:0.06, G:0.09, T:0.12
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:35729171 original size:15 final size:16
Alignment explanation
Indices: 35729159--35729188 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
35729149 AAACAAAAGA
35729159 AATTCGAAA-AAAAAT
1 AATTCGAAAGAAAAAT
35729174 AATTCGAAAGAAAAA
1 AATTCGAAAGAAAAA
35729189 AAAGAGAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.67, C:0.07, G:0.10, T:0.17
Consensus pattern (16 bp):
AATTCGAAAGAAAAAT
Found at i:35729172 original size:16 final size:15
Alignment explanation
Indices: 35729148--35729191 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
35729138 AAAAATTGAA
35729148 AAAACAAAAGAAATTCG
1 AAAA-AAAA-AAATTCG
*
35729165 AAAAAAAATAATTCG
1 AAAAAAAAAAATTCG
35729180 AAAGAAAAAAAA
1 AAA-AAAAAAAA
35729192 GAGAGGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 9 0.38
16 11 0.46
17 4 0.17
ACGTcount: A:0.73, C:0.07, G:0.09, T:0.11
Consensus pattern (15 bp):
AAAAAAAAAAATTCG
Found at i:35732775 original size:47 final size:47
Alignment explanation
Indices: 35732630--35733182 Score: 901
Period size: 47 Copynumber: 11.8 Consensus size: 47
35732620 CCCTTCGGGA
* * * * * * *
35732630 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
35732677 CCTGTCACATATATACACTTTCACATTCA-CACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35732723 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35732770 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
35732817 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
35732864 CTTATCACCTATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
35732911 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
35732958 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTTGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
35733005 CTTATCACACATATACACTTTCACATTCATCACATCGACCATTTGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
35733052 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
35733099 CTTATCACACATATACACTTTCACATTCATCACGTCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35733146 CTTATCACATATATACACTTTCACATTCATCACATCG
1 CTTATCACATATATACACTTTCACATTCATCACATCG
35733183 CAAGATTTAG
Statistics
Matches: 481, Mismatches: 24, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
46 40 0.08
47 441 0.92
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:35737122 original size:102 final size:102
Alignment explanation
Indices: 35736946--35737153 Score: 398
Period size: 102 Copynumber: 2.0 Consensus size: 102
35736936 CATCATCTAT
35736946 TGTGTGCAAATACTTGCTATTGTTTTGATACTTAGTTTTTGAATAAGGTAATGAAATTTGCCAAA
1 TGTGTGCAAATACTTGCTATTGTTTTGATACTTAGTTTTTGAATAAGGTAATGAAATTTGCCAAA
35737011 ATTTTTTTCAATTTATATTCGTGCCTTAAACAGTTCC
66 ATTTTTTTCAATTTATATTCGTGCCTTAAACAGTTCC
*
35737048 TGTGTGCAAATACTTTCTATTGTTTTGATACTTAGTTTTTGAATAAGGTAATGAAATTTGCCAAA
1 TGTGTGCAAATACTTGCTATTGTTTTGATACTTAGTTTTTGAATAAGGTAATGAAATTTGCCAAA
*
35737113 TTTTTTTTCAATTTATATTCGTGCCTTAAACAGTTCC
66 ATTTTTTTCAATTTATATTCGTGCCTTAAACAGTTCC
35737150 TGTG
1 TGTG
35737154 GTTGTACTTG
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 104 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.45
Consensus pattern (102 bp):
TGTGTGCAAATACTTGCTATTGTTTTGATACTTAGTTTTTGAATAAGGTAATGAAATTTGCCAAA
ATTTTTTTCAATTTATATTCGTGCCTTAAACAGTTCC
Found at i:35746181 original size:33 final size:33
Alignment explanation
Indices: 35746099--35746184 Score: 93
Period size: 33 Copynumber: 2.5 Consensus size: 33
35746089 GAAAGAAAAC
* *
35746099 GAAAAGAAAACGAAAGTGGAAAAGAAAAAGAGCCT
1 GAAAAGAAATCG--AGTGAAAAAGAAAAAGAGCCT
* **
35746134 GAAAAGAAATCGAGTGAAAAAGAAAGAGAGTTT
1 GAAAAGAAATCGAGTGAAAAAGAAAAAGAGCCT
35746167 GTAAAAGAAA-CGAGTGAA
1 G-AAAAGAAATCGAGTGAA
35746185 GAGAGTAATC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
33 26 0.58
34 8 0.18
35 11 0.24
ACGTcount: A:0.57, C:0.06, G:0.27, T:0.10
Consensus pattern (33 bp):
GAAAAGAAATCGAGTGAAAAAGAAAAAGAGCCT
Found at i:35761519 original size:45 final size:45
Alignment explanation
Indices: 35761434--35761519 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 45
35761424 TCTTCTTTCT
** *
35761434 TCAATTTCTTTTTCGATTTTCTCTTTTTCACATCCTTTTTCAATC
1 TCAATTTCTTTTTCGATTTTCTCACTTTCACATCCATTTTCAATC
*
35761479 TCAATTTCCTTTTTC-TTTTTCTCACTTTCAC-TCTCATTTTC
1 TCAATTT-CTTTTTCGATTTTCTCACTTTCACATC-CATTTTC
35761520 TTTTTTGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
44 2 0.06
45 26 0.74
46 7 0.20
ACGTcount: A:0.14, C:0.27, G:0.01, T:0.58
Consensus pattern (45 bp):
TCAATTTCTTTTTCGATTTTCTCACTTTCACATCCATTTTCAATC
Found at i:35761560 original size:12 final size:12
Alignment explanation
Indices: 35761512--35761586 Score: 55
Period size: 12 Copynumber: 6.2 Consensus size: 12
35761502 ACTTTCACTC
35761512 TCATTTTCTTTTT
1 TCATTTTC-TTTT
* *
35761525 TGA-TTTCTTGT
1 TCATTTTCTTTT
*
35761536 TC-TCTTTCATTT
1 TCAT-TTTCTTTT
*
35761548 TCATTTTATTTT
1 TCATTTTCTTTT
*
35761560 TCAATTTCTTTT
1 TCATTTTCTTTT
**
35761572 TGTTTTTCTTTT
1 TCATTTTCTTTT
35761584 TCA
1 TCA
35761587 CATGCTGTTT
Statistics
Matches: 45, Mismatches: 14, Indels: 7
0.68 0.21 0.11
Matches are distributed among these distances:
11 4 0.09
12 38 0.84
13 3 0.07
ACGTcount: A:0.11, C:0.15, G:0.04, T:0.71
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:35761561 original size:18 final size:18
Alignment explanation
Indices: 35761540--35761586 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
35761530 TCTTGTTCTC
35761540 TTTCATTTTCATTTTATT
1 TTTCATTTTCATTTTATT
* * *
35761558 TTTCAATTTCTTTTTGTT
1 TTTCATTTTCATTTTATT
*
35761576 TTTCTTTTTCA
1 TTTCATTTTCA
35761587 CATGCTGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.13, C:0.13, G:0.02, T:0.72
Consensus pattern (18 bp):
TTTCATTTTCATTTTATT
Found at i:35762543 original size:19 final size:19
Alignment explanation
Indices: 35762501--35762548 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
35762491 TACTTCACCT
*
35762501 TTTTTTTTAAATATACTCAA
1 TTTTTTTT-AATATACACAA
* *
35762521 TTTTTTTTAATATTCACAC
1 TTTTTTTTAATATACACAA
35762540 TTTTTTTTA
1 TTTTTTTTA
35762549 TACTCTCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTTTTTAATATACACAA
Found at i:35769719 original size:79 final size:81
Alignment explanation
Indices: 35769579--35769763 Score: 209
Period size: 79 Copynumber: 2.3 Consensus size: 81
35769569 TTGAATGATG
* *
35769579 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
35769643 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * * **
35769658 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCTGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
35769720 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* * *
35769738 ACTGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
35769764 AACGAGTAGC
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
78 1 0.01
79 55 0.62
80 33 0.37
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:35769770 original size:40 final size:40
Alignment explanation
Indices: 35769582--35769763 Score: 201
Period size: 40 Copynumber: 4.6 Consensus size: 40
35769572 AATGATGTCC
* * * * *
35769582 GGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCT
* * * *
35769622 GGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTCC
1 GGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCT
35769662 GGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCT
* *
35769701 GGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA-CT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCT
*
35769741 GGGCTATGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
35769764 AACGAGTAGC
Statistics
Matches: 121, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
39 34 0.28
40 77 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCT
Found at i:35769785 original size:79 final size:79
Alignment explanation
Indices: 35769632--35769796 Score: 183
Period size: 79 Copynumber: 2.1 Consensus size: 79
35769622 GGACTAAGAT
* * **
35769632 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
* *
35769697 ATCTGGGTTAAGTC
66 ATCTCGGTTAAATC
* * *
35769711 CCGAAGGCAATTGTGCGAGTTACT-ATAACTGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
35769774 TATATC-CGGTTAAATT
63 TAAATCTCGGTTAAATC
35769790 CCGAAGG
1 CCGAAGG
35769797 TACGTGATTT
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
78 2 0.03
79 46 0.64
80 24 0.33
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCTCGGTTAAATC
Found at i:35777672 original size:39 final size:39
Alignment explanation
Indices: 35777610--35777705 Score: 131
Period size: 39 Copynumber: 2.4 Consensus size: 39
35777600 TACTAATTCA
* *
35777610 GGCTAAGCCCGAAGGCATTTGTGCGAGTTACTA-AATCCG
1 GGCTAAGTCCGAAGGCAATTGTGCGAGTTACTATAA-CCG
*
35777649 GGTTAAGTCCGAAGGCAATTGTGCGAGTTACTATAACCG
1 GGCTAAGTCCGAAGGCAATTGTGCGAGTTACTATAACCG
*
35777688 GGCTATGTCCCGAAGGCA
1 GGCTAAGT-CCGAAGGCA
35777706 TTTGAACAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
39 39 0.78
40 11 0.22
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (39 bp):
GGCTAAGTCCGAAGGCAATTGTGCGAGTTACTATAACCG
Found at i:35794942 original size:27 final size:27
Alignment explanation
Indices: 35794911--35795088 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
35794901 TAAATTGTAC
35794911 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
35794938 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * * *
35794964 ATGCACTAAGTGTGTGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
35794992 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
35795020 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
35795047 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
35795074 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
35795089 GACTCAATAT
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 104 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:35795079 original size:82 final size:81
Alignment explanation
Indices: 35794908--35795088 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
35794898 GATTAAATTG
* *
35794908 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
*
35794973 GTGTGTGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
35794989 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
35795053 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
35795071 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
35795089 GACTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:35797008 original size:29 final size:29
Alignment explanation
Indices: 35796972--35797136 Score: 215
Period size: 29 Copynumber: 5.7 Consensus size: 29
35796962 AGATAACCAT
*
35796972 AAAGGCATCCTTTTAACAGATATAGCCAC
1 AAAGGCATCCTTTTAACAGAAATAGCCAC
* * *
35797001 AAAAGCATCCTTTTAATAGAGATAGACC-C
1 AAAGGCATCCTTTTAACAGAAATAG-CCAC
*
35797030 AAAGGCATCCTTTTAACAGAAATCGCCAC
1 AAAGGCATCCTTTTAACAGAAATAGCCAC
* * * *
35797059 AAAGGCTTCCTTTTAATAGAGATAGACAC
1 AAAGGCATCCTTTTAACAGAAATAGCCAC
*
35797088 AAAGGCATCCTTTTAACAGAAATCGCCAC
1 AAAGGCATCCTTTTAACAGAAATAGCCAC
*
35797117 AAAGGCTTCCTTTTAACAGA
1 AAAGGCATCCTTTTAACAGA
35797137 GATCACCGTA
Statistics
Matches: 116, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
28 2 0.02
29 112 0.97
30 2 0.02
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (29 bp):
AAAGGCATCCTTTTAACAGAAATAGCCAC
Found at i:35797016 original size:58 final size:59
Alignment explanation
Indices: 35796954--35797139 Score: 281
Period size: 58 Copynumber: 3.2 Consensus size: 59
35796944 AAAACATTTA
* * * * *
35796954 TTTAACTA-AGATA-ACCATAAAGGCATCCTTTTAACAGATATAGCCACAAAAGCATCCT
1 TTTAA-TAGAGATAGACCACAAAGGCATCCTTTTAACAGAAATCGCCACAAAGGCTTCCT
35797012 TTTAATAGAGATAGACC-CAAAGGCATCCTTTTAACAGAAATCGCCACAAAGGCTTCCT
1 TTTAATAGAGATAGACCACAAAGGCATCCTTTTAACAGAAATCGCCACAAAGGCTTCCT
35797070 TTTAATAGAGATAGA-CACAAAGGCATCCTTTTAACAGAAATCGCCACAAAGGCTTCCT
1 TTTAATAGAGATAGACCACAAAGGCATCCTTTTAACAGAAATCGCCACAAAGGCTTCCT
*
35797128 TTTAACAGAGAT
1 TTTAATAGAGAT
35797140 CACCGTAAAA
Statistics
Matches: 119, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
57 3 0.03
58 113 0.95
59 3 0.03
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (59 bp):
TTTAATAGAGATAGACCACAAAGGCATCCTTTTAACAGAAATCGCCACAAAGGCTTCCT
Found at i:35797154 original size:87 final size:87
Alignment explanation
Indices: 35796979--35797158 Score: 227
Period size: 87 Copynumber: 2.1 Consensus size: 87
35796969 CATAAAGGCA
* * * *
35796979 TCCTTTTAACAGATATAGCCACAAAAGCATCCTTTTAATAGAGATAGACCCAAAGGCATCCTTTT
1 TCCTTTTAACAGAGATAGACACAAAAGCATCCTTTTAACAGAAATAGACCCAAAGGCATCCTTTT
* *
35797044 AACAGAAATCGCCACAAAGGCT
66 AACAGAAATCACCACAAAAGCT
* * * *
35797066 TCCTTTTAATAGAGATAGACACAAAGGCATCCTTTTAACAGAAATCG-CCACAAAGGCTTCCTTT
1 TCCTTTTAACAGAGATAGACACAAAAGCATCCTTTTAACAGAAATAGACC-CAAAGGCATCCTTT
* **
35797130 TAACAGAGATCACCGTAAAAGCT
65 TAACAGAAATCACCACAAAAGCT
35797153 TCCTTT
1 TCCTTT
35797159 ATTAGACATT
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
86 2 0.03
87 77 0.97
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (87 bp):
TCCTTTTAACAGAGATAGACACAAAAGCATCCTTTTAACAGAAATAGACCCAAAGGCATCCTTTT
AACAGAAATCACCACAAAAGCT
Found at i:35797158 original size:29 final size:29
Alignment explanation
Indices: 35796954--35797143 Score: 190
Period size: 29 Copynumber: 6.6 Consensus size: 29
35796944 AAAACATTTA
* *
35796954 TTTAACTA-AGATAACCATAAAGGCATCCT
1 TTTAAC-AGAGATCACCACAAAGGCATCCT
* *
35796983 TTTAACAGATAT-AGCCACAAAAGCATCCT
1 TTTAACAGAGATCA-CCACAAAGGCATCCT
* *
35797012 TTTAATAGAGATAGACC-CAAAGGCATCCT
1 TTTAACAGAGAT-CACCACAAAGGCATCCT
* * *
35797041 TTTAACAGAAATCGCCACAAAGGCTTCCT
1 TTTAACAGAGATCACCACAAAGGCATCCT
* *
35797070 TTTAATAGAGAT-AGACACAAAGGCATCCT
1 TTTAACAGAGATCA-CCACAAAGGCATCCT
* * *
35797099 TTTAACAGAAATCGCCACAAAGGCTTCCT
1 TTTAACAGAGATCACCACAAAGGCATCCT
35797128 TTTAACAGAGATCACC
1 TTTAACAGAGATCACC
35797144 GTAAAAGCTT
Statistics
Matches: 131, Mismatches: 23, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
28 4 0.03
29 124 0.95
30 2 0.02
31 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (29 bp):
TTTAACAGAGATCACCACAAAGGCATCCT
Found at i:35801478 original size:42 final size:42
Alignment explanation
Indices: 35801431--35801572 Score: 167
Period size: 44 Copynumber: 3.3 Consensus size: 42
35801421 TTTTTCACAT
** * *
35801431 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTAGCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCAC
* *
35801473 AAACGCCACTAAAGAACATGATCTTTAGCGGCGCTTTTTACCAT
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGC--TTTACCAC
* **
35801517 AAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTTGATTAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTT-ACCAC
*
35801560 AAACACCGCTAAA
1 AAACGCCGCTAAA
35801573 AGTACCGTTC
Statistics
Matches: 85, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.39
43 14 0.16
44 38 0.45
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCAC
Found at i:35801533 original size:44 final size:44
Alignment explanation
Indices: 35801409--35801553 Score: 179
Period size: 44 Copynumber: 3.3 Consensus size: 44
35801399 ACGTCGCTAA
* * ** *
35801409 CTTTTGCGGCG-TTTTTTCACATAAACGCCGCTAAAGGTCATGTT
1 CTTTAGCGGCGCTTTTTAC-CATAAACGCCGCTAAAGAACATGAT
* * *
35801453 CTTTAGCGGCGC--TTTAGCACAAACGCCACTAAAGAACATGAT
1 CTTTAGCGGCGCTTTTTACCATAAACGCCGCTAAAGAACATGAT
35801495 CTTTAGCGGCGCTTTTTACCATAAACGCCGCTAAAGAACATGAT
1 CTTTAGCGGCGCTTTTTACCATAAACGCCGCTAAAGAACATGAT
*
35801539 CTTTAGCGACGCTTT
1 CTTTAGCGGCGCTTT
35801554 GATTACAAAC
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
42 32 0.37
43 3 0.03
44 51 0.59
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (44 bp):
CTTTAGCGGCGCTTTTTACCATAAACGCCGCTAAAGAACATGAT
Found at i:35801660 original size:16 final size:16
Alignment explanation
Indices: 35801641--35801674 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
35801631 AAATATTAAA
*
35801641 TATTAAAATCAAACAT
1 TATTAAAATCAAAAAT
*
35801657 TATTAATATCAAAAAT
1 TATTAAAATCAAAAAT
35801673 TA
1 TA
35801675 ATTAGTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (16 bp):
TATTAAAATCAAAAAT
Found at i:35804221 original size:13 final size:13
Alignment explanation
Indices: 35804203--35804235 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
35804193 ATAAACGAAT
35804203 CCACTTCATGCAC
1 CCACTTCATGCAC
*
35804216 CCACTTCATGTAC
1 CCACTTCATGCAC
35804229 CCACTTC
1 CCACTTC
35804236 TGTACAAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.21, C:0.45, G:0.06, T:0.27
Consensus pattern (13 bp):
CCACTTCATGCAC
Found at i:35806171 original size:16 final size:16
Alignment explanation
Indices: 35806146--35806177 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
35806136 ACACTTAACC
*
35806146 ATTTTTAAAATTTGGG
1 ATTTTGAAAATTTGGG
35806162 ATTTTGAAAATTTGGG
1 ATTTTGAAAATTTGGG
35806178 GATAATATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (16 bp):
ATTTTGAAAATTTGGG
Found at i:35806911 original size:15 final size:14
Alignment explanation
Indices: 35806873--35806919 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
35806863 CCTTAAATCG
*
35806873 TAAATCATAAACCA
1 TAAATCATAAACCC
35806887 TAAATCATAAACCC
1 TAAATCATAAACCC
*
35806901 TAAACTCATAATCCC
1 TAAA-TCATAAACCC
35806916 TAAA
1 TAAA
35806920 CCCATAATCC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 17 0.57
15 13 0.43
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAATCATAAACCC
Found at i:35806920 original size:15 final size:15
Alignment explanation
Indices: 35806873--35806935 Score: 67
Period size: 15 Copynumber: 4.3 Consensus size: 15
35806863 CCTTAAATCG
35806873 TAAA-TCATAAACCA
1 TAAACTCATAAACCA
*
35806887 TAAA-TCATAAACCC
1 TAAACTCATAAACCA
* *
35806901 TAAACTCATAATCCC
1 TAAACTCATAAACCA
* *
35806916 TAAACCCATAATCCA
1 TAAACTCATAAACCA
35806931 TAAAC
1 TAAAC
35806936 CTTAAAATAG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
14 17 0.39
15 27 0.61
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (15 bp):
TAAACTCATAAACCA
Found at i:35806941 original size:22 final size:22
Alignment explanation
Indices: 35806878--35806941 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
35806868 AATCGTAAAT
*
35806878 CATAAACCATAAATCATAAACC
1 CATAAACCATAAACCATAAACC
* *
35806900 C-TAAACTCATAATCCCTAAACC
1 CATAAAC-CATAAACCATAAACC
* *
35806922 CATAATCCATAAACCTTAAA
1 CATAAACCATAAACCATAAA
35806942 ATAGTATCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 5 0.15
22 25 0.74
23 4 0.12
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (22 bp):
CATAAACCATAAACCATAAACC
Found at i:35807153 original size:14 final size:14
Alignment explanation
Indices: 35807134--35807183 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
35807124 AACCCTAAAT
35807134 CCCTAACTCTTAAC
1 CCCTAACTCTTAAC
35807148 CCCTAACATC-TAAC
1 CCCTAAC-TCTTAAC
*
35807162 CCCTAAACCCTTAAC
1 CCCT-AACTCTTAAC
*
35807177 CTCTAAC
1 CCCTAAC
35807184 CCCTAAACCT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.32, C:0.44, G:0.00, T:0.24
Consensus pattern (14 bp):
CCCTAACTCTTAAC
Found at i:35807170 original size:22 final size:22
Alignment explanation
Indices: 35807145--35807192 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
35807135 CCTAACTCTT
35807145 AACCCCTAACATCTAACCCCTA
1 AACCCCTAACATCTAACCCCTA
* *
35807167 AACCCTTAACCTCTAACCCCTA
1 AACCCCTAACATCTAACCCCTA
35807189 AACC
1 AACC
35807193 TTAAATCCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.46, G:0.00, T:0.19
Consensus pattern (22 bp):
AACCCCTAACATCTAACCCCTA
Found at i:35807184 original size:14 final size:14
Alignment explanation
Indices: 35807124--35807185 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
35807114 TAAATCCTTA
* *
35807124 AACCCTAAATCCCT
1 AACCCTTAACCCCT
*
35807138 AACTCTTAACCCCT
1 AACCCTTAACCCCT
*
35807152 AA-CATCTAACCCCT
1 AACCCT-TAACCCCT
*
35807166 AAACCCTTAACCTCT
1 -AACCCTTAACCCCT
35807181 AACCC
1 AACCC
35807186 CTAAACCTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
13 1 0.03
14 26 0.68
15 9 0.24
16 2 0.05
ACGTcount: A:0.34, C:0.44, G:0.00, T:0.23
Consensus pattern (14 bp):
AACCCTTAACCCCT
Found at i:35807634 original size:41 final size:41
Alignment explanation
Indices: 35807589--35807833 Score: 269
Period size: 41 Copynumber: 5.8 Consensus size: 41
35807579 TAAAATGTTT
* * *
35807589 TTAGCGGCGCTTTTTCAAAAATGCCGCTAAA-ACACAAAGCA
1 TTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGA-ACCAAGCA
*
35807630 TTAGCGGCACTTTCTCAAAAACGCCGCTAATGCGTTAAAGAACCAAGCA
1 TTAGCGGCGCTTTCTCAAAAACG-C-C----GC--TAAAGAACCAAGCA
* ** *
35807679 TTAGCGGCGCTTTCTCAAAAATGCCATTAAAGAACCAACCA
1 TTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGAACCAAGCA
*
35807720 TTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGAACCAACCA
1 TTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGAACCAAGCA
* *
35807761 TTAGCGGCGCTTT-TGCAAAAATGCCGCTAAAGAACCCAGCA
1 TTAGCGGCGCTTTCT-CAAAAACGCCGCTAAAGAACCAAGCA
* *
35807802 TTAGCGGCACTTTTTCAAAAACGCCGCTAAAG
1 TTAGCGGCGCTTTCTCAAAAACGCCGCTAAAG
35807834 CCTCGAGCAT
Statistics
Matches: 176, Mismatches: 17, Indels: 22
0.82 0.08 0.10
Matches are distributed among these distances:
40 1 0.01
41 135 0.77
42 2 0.01
43 1 0.01
47 3 0.02
48 1 0.01
49 32 0.18
50 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (41 bp):
TTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGAACCAAGCA
Found at i:35807843 original size:41 final size:40
Alignment explanation
Indices: 35807665--35807878 Score: 178
Period size: 41 Copynumber: 5.2 Consensus size: 40
35807655 GCTAATGCGT
* * * * **
35807665 TAAAGAACCAAGCATTAGCGGCGCTTTCTCAAAAATGCCAT
1 TAAAG-ACCCAGCATTAGCGGCACTTTTTCAAAAACGCCGC
* * * *
35807706 TAAAGAACCAACCATTAGCGGCGCTTTCTCAAAAACGCCGC
1 TAAAG-ACCCAGCATTAGCGGCACTTTTTCAAAAACGCCGC
* * * * *
35807747 TAAAGAACCAACCATTAGCGGCGCTTTTGCAAAAATGCCGC
1 TAAAG-ACCCAGCATTAGCGGCACTTTTTCAAAAACGCCGC
35807788 TAAAGAACCCAGCATTAGCGGCACTTTTTCAAAAACGCCGC
1 TAAAG-ACCCAGCATTAGCGGCACTTTTTCAAAAACGCCGC
* * ** **
35807829 TAAAG-CCTCGAGCATTAGTGACACTTTTTTGAAAACGCTAC
1 TAAAGACC-C-AGCATTAGCGGCACTTTTTCAAAAACGCCGC
35807870 TAAAGACCC
1 TAAAGACCC
35807879 GAAAGGTAAG
Statistics
Matches: 152, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
39 2 0.01
40 1 0.01
41 147 0.97
42 2 0.01
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (40 bp):
TAAAGACCCAGCATTAGCGGCACTTTTTCAAAAACGCCGC
Found at i:35812835 original size:28 final size:28
Alignment explanation
Indices: 35812804--35812866 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
35812794 CTATTCAGTA
**
35812804 ACAGTAACAGTGTGGGTGTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
35812832 ACAGTAACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
35812860 ACAGTAA
1 ACAGTAA
35812867 TAGTACAGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.22
Consensus pattern (28 bp):
ACAGTAACAGTGTGGGCCTTAGCCCAAT
Found at i:35813002 original size:26 final size:26
Alignment explanation
Indices: 35812972--35813052 Score: 117
Period size: 26 Copynumber: 3.1 Consensus size: 26
35812962 AACACACCAA
* * *
35812972 TATCGCAGCAAAGCTACCAATAATAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
*
35812998 TATCGCAGCAAAGCTGCCAGTACCAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
*
35813024 TATCACAGCAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
35813050 TAT
1 TAT
35813053 ATGTGGCAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.19
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTAACAG
Found at i:35820722 original size:28 final size:28
Alignment explanation
Indices: 35820683--35820772 Score: 146
Period size: 28 Copynumber: 3.2 Consensus size: 28
35820673 CTATTCAGTA
35820683 ACAGT-ACAGTGTGGGCCATAGCCCAAT
1 ACAGTAACAGTGTGGGCCATAGCCCAAT
*
35820710 ACAGTAACAGTGTGGGCCATAGCCTAAT
1 ACAGTAACAGTGTGGGCCATAGCCCAAT
* *
35820738 ATAGTAACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCATAGCCCAAT
35820766 ACAGTAA
1 ACAGTAA
35820773 TACTACAGTG
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 5 0.09
28 52 0.91
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.21
Consensus pattern (28 bp):
ACAGTAACAGTGTGGGCCATAGCCCAAT
Found at i:35822432 original size:27 final size:26
Alignment explanation
Indices: 35822366--35822432 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 26
35822356 AACACACCAA
* * *
35822366 TATTGTAGCAAAGCTGCCATTAATAG
1 TATTGTAGCAAAGCTACCAGTAACAG
35822392 TATTGTAGCAAAGCTACCAGTAACAG
1 TATTGTAGCAAAGCTACCAGTAACAG
*
35822418 TATATGTGGCAAAGC
1 TAT-TGTAGCAAAGC
35822433 CATTAGTACA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 26 0.72
27 10 0.28
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (26 bp):
TATTGTAGCAAAGCTACCAGTAACAG
Found at i:35822960 original size:20 final size:20
Alignment explanation
Indices: 35822914--35822961 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
35822904 TGGCTCATCT
*
35822914 CGGCCCAACATGGCCTATTA
1 CGGCCCAACATGGCCAATTA
*
35822934 CGACCCAACATGGCCAATTA
1 CGGCCCAACATGGCCAATTA
*
35822954 TGGCCCAA
1 CGGCCCAA
35822962 GCCCATGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.19, T:0.17
Consensus pattern (20 bp):
CGGCCCAACATGGCCAATTA
Found at i:35831473 original size:27 final size:27
Alignment explanation
Indices: 35831443--35831497 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
35831433 ACGGGCAATA
*
35831443 TATGTTAATTTAATATTTCTAAAATTG
1 TATGCTAATTTAATATTTCTAAAATTG
*
35831470 TATGCTAATTTAATATTTCTATAATTG
1 TATGCTAATTTAATATTTCTAAAATTG
35831497 T
1 T
35831498 GTCTTAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (27 bp):
TATGCTAATTTAATATTTCTAAAATTG
Found at i:35842716 original size:40 final size:40
Alignment explanation
Indices: 35842661--35842932 Score: 463
Period size: 40 Copynumber: 6.8 Consensus size: 40
35842651 AACATTGGAT
35842661 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
35842701 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
35842741 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* *
35842781 CATATCCGGGCTAAGACCCGAAGGCAATTATGCGAATTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* * *
35842821 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
*
35842861 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTCA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* * *
35842901 TATGTCCGGGTTAAGACCCGAAGGCAAATATG
1 TATATCCGGGCTAAGACCCGAAGGCAATTATG
35842933 TTTGCGGCTG
Statistics
Matches: 218, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 218 1.00
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
Found at i:35846809 original size:25 final size:25
Alignment explanation
Indices: 35846776--35846855 Score: 117
Period size: 25 Copynumber: 3.2 Consensus size: 25
35846766 GAGCTGTAAT
*
35846776 TGGTAAGCTCCTCTAAGCTGAATAA
1 TGGTAAGCTCCTCTAAGCTAAATAA
35846801 TGGTAAGCTCCTCTAAGCTAAATAA
1 TGGTAAGCTCCTCTAAGCTAAATAA
* * *
35846826 CGGTAAGCTCCTCTGAGCTAAA-AT
1 TGGTAAGCTCCTCTAAGCTAAATAA
35846850 TGGTAA
1 TGGTAA
35846856 CCCTAATGAC
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
24 6 0.12
25 44 0.88
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (25 bp):
TGGTAAGCTCCTCTAAGCTAAATAA
Found at i:35849623 original size:19 final size:19
Alignment explanation
Indices: 35849595--35849635 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
35849585 TCTTAGAAAC
35849595 AAAGAGAGCAGAAGAAAAG
1 AAAGAGAGCAGAAGAAAAG
*
35849614 AAAGATAGCAGAAGAAAAG
1 AAAGAGAGCAGAAGAAAAG
35849633 AAA
1 AAA
35849636 CAAAGGGGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.66, C:0.05, G:0.27, T:0.02
Consensus pattern (19 bp):
AAAGAGAGCAGAAGAAAAG
Found at i:35854285 original size:13 final size:13
Alignment explanation
Indices: 35854267--35854294 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
35854257 TATATAAAAG
35854267 AATATAACAGCAA
1 AATATAACAGCAA
35854280 AATATAACAGCAA
1 AATATAACAGCAA
35854293 AA
1 AA
35854295 AGAAAATAAA
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:0.64, C:0.14, G:0.07, T:0.14
Consensus pattern (13 bp):
AATATAACAGCAA
Found at i:35857021 original size:56 final size:56
Alignment explanation
Indices: 35856949--35857067 Score: 229
Period size: 56 Copynumber: 2.1 Consensus size: 56
35856939 ACGACACTGT
*
35856949 AAAGAAATTCTAACTAAGATAGCATTGAAGCGTCCTTCAAATTGGATCAAGGCTTG
1 AAAGCAATTCTAACTAAGATAGCATTGAAGCGTCCTTCAAATTGGATCAAGGCTTG
35857005 AAAGCAATTCTAACTAAGATAGCATTGAAGCGTCCTTCAAATTGGATCAAGGCTTG
1 AAAGCAATTCTAACTAAGATAGCATTGAAGCGTCCTTCAAATTGGATCAAGGCTTG
35857061 AAAGCAA
1 AAAGCAA
35857068 ATCAAAGTTT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (56 bp):
AAAGCAATTCTAACTAAGATAGCATTGAAGCGTCCTTCAAATTGGATCAAGGCTTG
Found at i:35864350 original size:21 final size:22
Alignment explanation
Indices: 35864299--35864350 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
35864289 TAAAAATAAG
*
35864299 AAATTAAAATAAAAACAATTTT
1 AAATTAAAATAAAAACAATTTC
** *
35864321 ACCTT-AAATAAAATCAA-TTC
1 AAATTAAAATAAAAACAATTTC
35864341 AAATTAAAAT
1 AAATTAAAAT
35864351 TCATCTGGTC
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
20 5 0.22
21 15 0.65
22 3 0.13
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATTAAAATAAAAACAATTTC
Found at i:35867977 original size:26 final size:26
Alignment explanation
Indices: 35867900--35867982 Score: 107
Period size: 26 Copynumber: 3.2 Consensus size: 26
35867890 CGTACAAAGG
35867900 CTTTCATATTACGCCACAAACT-CTTT
1 CTTTCATATTACGCCACAAA-TGCTTT
*
35867926 ATTTCATATTACGCCACAAA-GACTTT
1 CTTTCATATTACGCCACAAATG-CTTT
* *
35867952 CTTTCATATTATGCCATAAATGCTTT
1 CTTTCATATTACGCCACAAATGCTTT
35867978 CTTTC
1 CTTTC
35867983 CTGACGTGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
26 49 0.98
27 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.41
Consensus pattern (26 bp):
CTTTCATATTACGCCACAAATGCTTT
Found at i:35868552 original size:41 final size:41
Alignment explanation
Indices: 35868490--35868571 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
35868480 TGTAAGAGTT
* **
35868490 AGTTTAGGGACTTACTTGACAACCATTGATATCAGCTAGGA
1 AGTTTAGGGACTCACCCGACAACCATTGATATCAGCTAGGA
35868531 AGTTTAGGGACTCACCCGACAACCATTGATATCAGCTAGGA
1 AGTTTAGGGACTCACCCGACAACCATTGATATCAGCTAGGA
35868572 CTTTAGATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.26
Consensus pattern (41 bp):
AGTTTAGGGACTCACCCGACAACCATTGATATCAGCTAGGA
Found at i:35876575 original size:14 final size:14
Alignment explanation
Indices: 35876531--35876584 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
35876521 ACTCTCCTCA
*
35876531 TTCTTTTCTTTCTTT
1 TTCTTTT-TCTCTTT
*
35876546 TTC-TTTTCACTCTT
1 TTCTTTTTCTCT-TT
*
35876560 TTGTTTTTCTCTTT
1 TTCTTTTTCTCTTT
35876574 TTCTTTTTCTC
1 TTCTTTTTCTC
35876585 GCTCAATAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
13 3 0.09
14 19 0.59
15 10 0.31
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.74
Consensus pattern (14 bp):
TTCTTTTTCTCTTT
Found at i:35892994 original size:48 final size:49
Alignment explanation
Indices: 35892930--35893024 Score: 131
Period size: 49 Copynumber: 2.0 Consensus size: 49
35892920 AAGGTGGAAG
* *
35892930 TATGTGACAGTTTATCTGC-ATTAAT-GTGACACTGTTCACAATTTTGAT
1 TATGTGACAGTATATCTGCGATT-ATGGTGACACTGTTCACAAATTTGAT
* *
35892978 TATGTGGCAGTATATCTGCGATTTTGGTGACACTGTTCACAAATTTG
1 TATGTGACAGTATATCTGCGATTATGGTGACACTGTTCACAAATTTG
35893025 GTGTGTTGGA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
48 18 0.44
49 23 0.56
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (49 bp):
TATGTGACAGTATATCTGCGATTATGGTGACACTGTTCACAAATTTGAT
Found at i:35895040 original size:27 final size:27
Alignment explanation
Indices: 35894981--35895042 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
35894971 CCTAAACTGA
**
35894981 TATAAAATGGCTGTTATGCCCCCACGT
1 TATAAAATAACTGTTATGCCCCCACGT
** * *
35895008 GGTAAAATAACTGTTATGCCCCTATGT
1 TATAAAATAACTGTTATGCCCCCACGT
35895035 TATAAAAT
1 TATAAAAT
35895043 GACTACATGC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (27 bp):
TATAAAATAACTGTTATGCCCCCACGT
Found at i:35897187 original size:3 final size:3
Alignment explanation
Indices: 35897179--35897226 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
35897169 AAGGGCTCAA
* * * *
35897179 ATT ATT ATT ATC ATT ATC ATT ACT ATT ATT ATT AAAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT
35897225 AT
1 AT
35897227 CTTTTTTTAC
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
3 34 0.94
4 2 0.06
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:35897711 original size:147 final size:146
Alignment explanation
Indices: 35897552--35897831 Score: 406
Period size: 147 Copynumber: 1.9 Consensus size: 146
35897542 TCTTGAGAAT
*
35897552 TTTTTTTAAAAAAAGGGAAAGTTTAGATT-TTAAAAATAAAAAAAATAT-TTTTTTAGTCATTTC
1 TTTTTTTAAAAAAAGAGAAAGTTTAGATTGTT-AAAAT---AAAAATATGTTTTTTAGTCATTTC
* * *
35897615 AAAGG-AAATTTTAAA-ATTTTAAAACAAAGTTATGATTTTTTTTAACTATTTCGAAATAAAAGC
62 AAAGGAAAAATTTAAATATTTTAAAACAAAGTTATGATCTTTTTCAACTATTTCGAAATAAAA-C
35897678 TTTGATTTAAAAAAAATAATA
126 TTTGATTTAAAAAAAATAATA
* **
35897699 TTTTTTTAAAAAAAGAGAAAGTTTAGATTGTTGAAATAAAAATATGTTTTTTAGTCATTTTTAAG
1 TTTTTTTAAAAAAAGAGAAAGTTTAGATTGTTAAAATAAAAATATGTTTTTTAGTCATTTCAAAG
* *
35897764 GAAAAATTTAAATTTTTTAAAACAAAGTTTTGATCTTTTTCAACTATTTCGAAATAAAACTTTGA
66 GAAAAATTTAAATATTTTAAAACAAAGTTATGATCTTTTTCAACTATTTCGAAATAAAACTTTGA
35897829 TTT
131 TTT
35897832 TTAAAGAAAG
Statistics
Matches: 120, Mismatches: 9, Indels: 9
0.87 0.07 0.07
Matches are distributed among these distances:
144 8 0.07
145 18 0.15
146 18 0.15
147 74 0.62
148 2 0.02
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.42
Consensus pattern (146 bp):
TTTTTTTAAAAAAAGAGAAAGTTTAGATTGTTAAAATAAAAATATGTTTTTTAGTCATTTCAAAG
GAAAAATTTAAATATTTTAAAACAAAGTTATGATCTTTTTCAACTATTTCGAAATAAAACTTTGA
TTTAAAAAAAATAATA
Found at i:35897869 original size:21 final size:21
Alignment explanation
Indices: 35897819--35897870 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
35897809 ATTTCGAAAT
35897819 AAAACTTTGA--TTTTTAAAG
1 AAAACTTTGATTTTTTTAAAG
* *
35897838 -AAAGTAGTGATTTTTTTAAAG
1 AAAACT-TTGATTTTTTTAAAG
35897859 AAAACTTTGATT
1 AAAACTTTGATT
35897871 CCACAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
18 4 0.16
19 3 0.12
21 14 0.56
22 4 0.16
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.42
Consensus pattern (21 bp):
AAAACTTTGATTTTTTTAAAG
Found at i:35907780 original size:20 final size:20
Alignment explanation
Indices: 35907755--35907827 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
35907745 GCAAGTTAAG
35907755 ATAAGCTGAAGTTGAGCTGA
1 ATAAGCTGAAGTTGAGCTGA
*** *
35907775 ATAAGCT-AAGGACAAGCTCA
1 ATAAGCTGAA-GTTGAGCTGA
* *
35907795 ATGAGCTAAAGTTGAGCTGA
1 ATAAGCTGAAGTTGAGCTGA
*
35907815 ATGAGCTTGAAGT
1 ATAAGC-TGAAGT
35907828 AGAGTGCACG
Statistics
Matches: 40, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
19 2 0.05
20 31 0.77
21 7 0.17
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.23
Consensus pattern (20 bp):
ATAAGCTGAAGTTGAGCTGA
Done.