Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A06
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: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2234201 characters in sequence are not A, C, G, or T
File 157 of 345
Found at i:53382070 original size:40 final size:39
Alignment explanation
Indices: 53381871--53382166 Score: 287
Period size: 39 Copynumber: 7.5 Consensus size: 39
53381861 AAATCACGTA
* * * **
53381871 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCAAATG
1 CCTTCGGGACTTAACCCGGATTTAG-TACTCGCACAAATG
* * * *
53381910 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATG
1 CCTTCGGGACTTAACCCGGATTTAGT-ACTCGCACAAATG
* *
53381949 CCTTCGGGACTTAACCCGGATTTAATACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGTACTCGCACAAATG
* *
53381988 CCTTCGGGACTTAACCCGGATTTAATACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGTACTCGCACAAATG
*
53382027 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTTAGTA-CTCGCACAAATG
* *
53382067 CCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCACAAATG
1 CCTTCGGGACTTAACCCGG-ATTTAGTA-CTCGCACAAATG
** * * *
53382107 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAA-G
1 CCTTCGGGA-CTTAACCCGGATTTAGT-AC-TCGCACAAATG
*
53382147 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
53382167 CAGCATTCAA
Statistics
Matches: 219, Mismatches: 28, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
38 7 0.03
39 111 0.51
40 86 0.39
41 15 0.07
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.26
Consensus pattern (39 bp):
CCTTCGGGACTTAACCCGGATTTAGTACTCGCACAAATG
Found at i:53382175 original size:41 final size:41
Alignment explanation
Indices: 53382098--53382175 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
53382088 CTTGTATCTC
* * *
53382098 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
53382139 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
53382176 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:53384654 original size:45 final size:45
Alignment explanation
Indices: 53384605--53384806 Score: 251
Period size: 45 Copynumber: 4.5 Consensus size: 45
53384595 ACCAGAAATA
* * *
53384605 AGTAAGACTATAGCTGAAAGACATTATGACATCAAAATTCTCTCG
1 AGTAAGACCATAGCTGAAAGACATTATGGCATCAAAATTCTATCG
** *
53384650 AGTAAGACCATAGCTGAAAGATGTTATGGCATCAAAATTATATCG
1 AGTAAGACCATAGCTGAAAGACATTATGGCATCAAAATTCTATCG
* * * ** *
53384695 ACTAAAACCATAGCTAAAAGACATTATGGCATCACGATTCTATTG
1 AGTAAGACCATAGCTGAAAGACATTATGGCATCAAAATTCTATCG
** **
53384740 AGTAAGACCATAGCTGAAAGATGTTATGGCATCATGATTCTATCG
1 AGTAAGACCATAGCTGAAAGACATTATGGCATCAAAATTCTATCG
*
53384785 AGTAAGAACATAGCTGAAAGAC
1 AGTAAGACCATAGCTGAAAGAC
53384807 GTTAAGGGAT
Statistics
Matches: 133, Mismatches: 24, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 133 1.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (45 bp):
AGTAAGACCATAGCTGAAAGACATTATGGCATCAAAATTCTATCG
Found at i:53384717 original size:90 final size:90
Alignment explanation
Indices: 53384614--53384806 Score: 280
Period size: 90 Copynumber: 2.1 Consensus size: 90
53384604 AAGTAAGACT
*
53384614 ATAGCTGAAAGACATTATGACATCAAAATTCTCTCGAGTAAGACCATAGCTGAAAGATGTTATGG
1 ATAGCTGAAAGACATTATGACATCAAAATTCTATCGAGTAAGACCATAGCTGAAAGATGTTATGG
53384679 CATCAAAATTATATCGACTAA-AACC
66 CATCAAAATTATATCGACTAAGAA-C
* * ** *
53384704 ATAGCTAAAAGACATTATGGCATCACGATTCTATTGAGTAAGACCATAGCTGAAAGATGTTATGG
1 ATAGCTGAAAGACATTATGACATCAAAATTCTATCGAGTAAGACCATAGCTGAAAGATGTTATGG
** * *
53384769 CATCATGATTCTATCGAGTAAGAAC
66 CATCAAAATTATATCGACTAAGAAC
53384794 ATAGCTGAAAGAC
1 ATAGCTGAAAGAC
53384807 GTTAAGGGAT
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
90 89 0.98
91 2 0.02
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (90 bp):
ATAGCTGAAAGACATTATGACATCAAAATTCTATCGAGTAAGACCATAGCTGAAAGATGTTATGG
CATCAAAATTATATCGACTAAGAAC
Found at i:53384840 original size:135 final size:135
Alignment explanation
Indices: 53384605--53384858 Score: 314
Period size: 135 Copynumber: 1.9 Consensus size: 135
53384595 ACCAGAAATA
* * *
53384605 AGTAAGACTATAGCTGAAAGACATTATGACATCAAAATTCTCTCGAGTAAGACCATAGCTGAAAG
1 AGTAAGACCATAGCTGAAAGACATTATGACATCAAAATTCTATCGAGTAAGAACATAGCTGAAAG
* * * * * *
53384670 ATGTTATGGCATCAAAATTATATCGACTAAAACCATAGCTAAAAGACATTATGGCATCACGATTC
66 ACGTTAAGGCATCAAAATCATATAGAATAAAACCATAGCTAAAAGACACTATGGCATCACGATTC
53384735 TATTG
131 TATTG
** * **
53384740 AGTAAGACCATAGCTGAAAGATGTTATGGCATCATGATTCTATCGAGTAAGAACATAGCTGAAAG
1 AGTAAGACCATAGCTGAAAGACATTATGACATCAAAATTCTATCGAGTAAGAACATAGCTGAAAG
* * * *
53384805 ACGTTAAGGGATCAATAATCA-A-AGAAATAAGACCATAGTTTAAAGACACTATGG
66 ACGTTAAGGCATCAA-AATCATATAG-AATAAAACCATAGCTAAAAGACACTATGG
53384859 GGACACAATG
Statistics
Matches: 99, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
134 1 0.01
135 94 0.95
136 4 0.04
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (135 bp):
AGTAAGACCATAGCTGAAAGACATTATGACATCAAAATTCTATCGAGTAAGAACATAGCTGAAAG
ACGTTAAGGCATCAAAATCATATAGAATAAAACCATAGCTAAAAGACACTATGGCATCACGATTC
TATTG
Found at i:53384850 original size:90 final size:90
Alignment explanation
Indices: 53384652--53384842 Score: 224
Period size: 90 Copynumber: 2.1 Consensus size: 90
53384642 TTCTCTCGAG
53384652 TAAGACCATAGCTGAAAGATGTTATGGCATCAAAATTATATCGACTAAAACCATAGCTAAAAGAC
1 TAAGACCATAGCTGAAAGATGTTATGGCATCAAAATTATATCGACTAAAACCATAGCTAAAAGAC
* * * ** *
53384717 ATTATGGCATCACGATTCTATTGAG
66 ATTAAGGCATCAAGAATCTAAAGAA
** * * *
53384742 TAAGACCATAGCTGAAAGATGTTATGGCATCATGATTCTATCGAGTAAGAA-CATAGCTGAAAGA
1 TAAGACCATAGCTGAAAGATGTTATGGCATCAAAATTATATCGACTAA-AACCATAGCTAAAAGA
* * *
53384806 CGTTAAGGGATCAATAATC-AAAGAAA
65 CATTAAGGCATCAAGAATCTAAAG-AA
53384832 TAAGACCATAG
1 TAAGACCATAG
53384843 TTTAAAGACA
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
89 2 0.02
90 81 0.95
91 2 0.02
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (90 bp):
TAAGACCATAGCTGAAAGATGTTATGGCATCAAAATTATATCGACTAAAACCATAGCTAAAAGAC
ATTAAGGCATCAAGAATCTAAAGAA
Found at i:53384996 original size:45 final size:45
Alignment explanation
Indices: 53384876--53384988 Score: 181
Period size: 45 Copynumber: 2.5 Consensus size: 45
53384866 ATGGAAAATG
*
53384876 AATAAGACCATGGTTGAAAGACATTATGGCATCAATACTAGAATA
1 AATAAGACCATGGTTGAAAGACATTATGGCATCAAGACTAGAATA
*
53384921 AATAAGACCATGGTTGAAAGATATTATGGCATCAAGACTAGAATA
1 AATAAGACCATGGTTGAAAGACATTATGGCATCAAGACTAGAATA
* * *
53384966 AGTAAGACAATAGTTGAAAGACA
1 AATAAGACCATGGTTGAAAGACA
53384989 CCATGGCACT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 62 1.00
ACGTcount: A:0.46, C:0.12, G:0.19, T:0.23
Consensus pattern (45 bp):
AATAAGACCATGGTTGAAAGACATTATGGCATCAAGACTAGAATA
Found at i:53387344 original size:70 final size:70
Alignment explanation
Indices: 53387218--53387360 Score: 200
Period size: 70 Copynumber: 2.0 Consensus size: 70
53387208 ACCTACAAAG
***
53387218 AATAACCAGACTTCCTTAGATCACTCCATTGGAAACTGTACCGCCTACACTGAACCATTACTAAT
1 AATAACCAGACTTCCTTAGATCACTCCATTGGAAACCACACCGCCTACACTGAACCATTACTAAT
53387283 ATGTA
66 ATGTA
* *
53387288 AATAACCAGACTTCCTTGGATCACTCCCTTGGAAACCACACCGTCC-ACACCT-AACCATTACTA
1 AATAACCAGACTTCCTTAGATCACTCCATTGGAAACCACACCG-CCTACA-CTGAACCATTACTA
*
53387351 ATCTGTA
64 ATATGTA
53387358 AAT
1 AAT
53387361 GTTGAAATGA
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
70 61 0.94
71 4 0.06
ACGTcount: A:0.34, C:0.30, G:0.10, T:0.26
Consensus pattern (70 bp):
AATAACCAGACTTCCTTAGATCACTCCATTGGAAACCACACCGCCTACACTGAACCATTACTAAT
ATGTA
Found at i:53387585 original size:5 final size:5
Alignment explanation
Indices: 53387575--53387601 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
53387565 ATACATTTAC
53387575 ATAAG ATAAG ATAAG ATAAG ATAAG AT
1 ATAAG ATAAG ATAAG ATAAG ATAAG AT
53387602 GGCACTTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.19, T:0.22
Consensus pattern (5 bp):
ATAAG
Found at i:53411886 original size:24 final size:25
Alignment explanation
Indices: 53411854--53411905 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 25
53411844 AGAACCCACA
53411854 TTTCAGCTTTTCA-CCTTTTCGAC-T
1 TTTCAGCTTTTCAGCCTTTT-GACGT
53411878 TTTCAGCTTTTCAGCCTTTTGACGT
1 TTTCAGCTTTTCAGCCTTTTGACGT
53411903 TTT
1 TTT
53411906 ACATCTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 16 0.62
25 10 0.38
ACGTcount: A:0.12, C:0.25, G:0.12, T:0.52
Consensus pattern (25 bp):
TTTCAGCTTTTCAGCCTTTTGACGT
Found at i:53413601 original size:40 final size:40
Alignment explanation
Indices: 53413546--53413697 Score: 216
Period size: 40 Copynumber: 3.8 Consensus size: 40
53413536 ATAACCACAA
* * * *
53413546 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
53413586 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
53413626 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC
* *
53413666 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
53413698 CATTCAAATG
Statistics
Matches: 102, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
39 1 0.01
40 97 0.95
41 4 0.04
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:53417048 original size:43 final size:43
Alignment explanation
Indices: 53416883--53417051 Score: 141
Period size: 43 Copynumber: 4.0 Consensus size: 43
53416873 ATATCGTACA
* * ** *
53416883 ATGCCAACGTCCCAAACGTGGTCTTACATGCTATCTCATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACATGAGATCACATATCG
* * * * * *
53416926 ATGTC-ACTATCCCAGATAGGGTCTTACACG-GATCAAATA-CG
1 ATGCCAAC-GTCCCAGACATGGTCTTACATGAGATCACATATCG
** *
53416967 ATGCGGATGTCCCAGACATGGTCTTCCACAT-A-ATCACATATCG
1 ATGCCAACGTCCCAGACATGGTCTT--ACATGAGATCACATATCG
*
53417010 ATGCCAACGTCCCAGACATGGTCTTACATGAGAACACATATC
1 ATGCCAACGTCCCAGACATGGTCTTACATGAGATCACATATC
53417052 AAAAACCCTA
Statistics
Matches: 96, Mismatches: 22, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
41 23 0.24
42 17 0.18
43 56 0.58
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACATGAGATCACATATCG
Found at i:53418196 original size:14 final size:15
Alignment explanation
Indices: 53418179--53418207 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
53418169 TCACGAAAAT
53418179 TTCACACAT-ATAAA
1 TTCACACATAATAAA
53418193 TTCACACATAATAAA
1 TTCACACATAATAAA
53418208 CATAGGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:53422853 original size:80 final size:82
Alignment explanation
Indices: 53422749--53422900 Score: 209
Period size: 80 Copynumber: 1.9 Consensus size: 82
53422739 GTATGAGTTA
* ** * * *
53422749 TCGTGTAAGACCATATCTGGGATATGGCGTTGATAT-GAT-CATGTAAGACCATGTCTGGGACAT
1 TCGTATAAGACCATATCTCAGATATGGCATCGATATAGATCCATGTAAGACCATGTCTAGGACAT
53422812 GGCGTCGAAATGAGAAT
66 GGCGTCGAAATGAGAAT
*
53422829 TCGTATAAGACCATATCTCAGATATGGCATCGATGTGAGATCCCATGTAAGACCATGTCTAGGAC
1 TCGTATAAGACCATATCTCAGATATGGCATCGATAT-AGAT-CCATGTAAGACCATGTCTAGGAC
53422894 ATGGCGT
64 ATGGCGT
53422901 TGGCATCTTA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
80 30 0.49
82 3 0.05
84 28 0.46
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (82 bp):
TCGTATAAGACCATATCTCAGATATGGCATCGATATAGATCCATGTAAGACCATGTCTAGGACAT
GGCGTCGAAATGAGAAT
Found at i:53422898 original size:42 final size:42
Alignment explanation
Indices: 53422788--53422898 Score: 109
Period size: 42 Copynumber: 2.6 Consensus size: 42
53422778 TTGATATGAT
* * *
53422788 CATGTAAGACCATGTCTGGGACATGGCGTCGAAATGAGAATT
1 CATGTAAGACCATGTCTAGGACATGGCATCGAAATGAGAATC
* * * * **
53422830 CGTATAAGACCATATCTCA-GATATGGCATCGATGTGAG-ATCC
1 CATGTAAGACCATGTCT-AGGACATGGCATCGAAATGAGAAT-C
53422872 CATGTAAGACCATGTCTAGGACATGGC
1 CATGTAAGACCATGTCTAGGACATGGC
53422899 GTTGGCATCT
Statistics
Matches: 53, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
41 3 0.06
42 50 0.94
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (42 bp):
CATGTAAGACCATGTCTAGGACATGGCATCGAAATGAGAATC
Found at i:53426449 original size:22 final size:19
Alignment explanation
Indices: 53426405--53426451 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 19
53426395 AATGTGTTTG
*
53426405 GTTAATGATTTTCCATTAT
1 GTTAATGATTTTCCAGTAT
53426424 GTTAATGATTTTCCCTGAGTAT
1 GTTAATGATTTT-CC--AGTAT
53426446 GTTAAT
1 GTTAAT
53426452 TACATTGTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 12 0.50
20 2 0.08
22 10 0.42
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.49
Consensus pattern (19 bp):
GTTAATGATTTTCCAGTAT
Found at i:53433182 original size:27 final size:26
Alignment explanation
Indices: 53433152--53433204 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
53433142 GACCAAAATA
*
53433152 CCCCTAAAGGGTAAAATGACTGTTTTG
1 CCCCTAAAGGGT-AAATGACTGATTTG
**
53433179 CCCCTCGAGGGTAAATGACTGATTTG
1 CCCCTAAAGGGTAAATGACTGATTTG
53433205 TCTATGATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (26 bp):
CCCCTAAAGGGTAAATGACTGATTTG
Found at i:53433510 original size:32 final size:32
Alignment explanation
Indices: 53433463--53433550 Score: 113
Period size: 32 Copynumber: 2.8 Consensus size: 32
53433453 TGATATTGAA
** *
53433463 ATGGGCTAGTTCCAACTGATACTGGTTCTGAG
1 ATGGGCTAGGCCCAACTGATACTGATTCTGAG
*
53433495 ATGGGCTAGGCCCAACTGATATTGATTCTGAG
1 ATGGGCTAGGCCCAACTGATACTGATTCTGAG
* * *
53433527 ATGTGCTAGGCCCAATTGAGACTG
1 ATGGGCTAGGCCCAACTGATACTG
53433551 TGATGGGTTG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.28
Consensus pattern (32 bp):
ATGGGCTAGGCCCAACTGATACTGATTCTGAG
Found at i:53441971 original size:49 final size:49
Alignment explanation
Indices: 53441781--53441974 Score: 194
Period size: 50 Copynumber: 3.9 Consensus size: 49
53441771 TCTATTGTGA
* * *
53441781 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCAAAAACTG-T
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTA-CC--AGACTGTT
* * * * ** *
53441832 GATCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTATTAGA-TGGTGA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGACT-GT-T
* **
53441882 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGACTGTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGACTGTT
* *
53441931 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGA
53441975 TAGCTTCGGC
Statistics
Matches: 118, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
47 1 0.01
48 3 0.03
49 39 0.33
50 41 0.35
51 34 0.29
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGACTGTT
Found at i:53445002 original size:15 final size:15
Alignment explanation
Indices: 53444982--53445046 Score: 73
Period size: 15 Copynumber: 4.5 Consensus size: 15
53444972 GTATCTTGGG
53444982 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
53444997 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
*
53445012 TTT-TCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
53445026 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
53445040 TTTCTTT
1 TTTCTTT
53445047 TTATCTTTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
13 2 0.05
14 18 0.43
15 20 0.48
16 2 0.05
ACGTcount: A:0.09, C:0.14, G:0.14, T:0.63
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:53447348 original size:49 final size:49
Alignment explanation
Indices: 53447173--53447361 Score: 202
Period size: 50 Copynumber: 3.8 Consensus size: 49
53447163 TGTGAGGTTG
* * *
53447173 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCCGAAAACTG-TGATCA
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CC--AGACTGTTGGTCA
** * ** *
53447224 TGTGTGTAGTACTAAGTGCAGGCTACTACATGTATTAGA-TGGTGAGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACT-GT-TGGTCA
* *
53447274 CGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTTGGTCG
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTTGGTCA
* *
53447323 CATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA
53447362 TAGCTTCGGC
Statistics
Matches: 116, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
47 1 0.01
48 3 0.03
49 40 0.34
50 41 0.35
51 31 0.27
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.29
Consensus pattern (49 bp):
CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTTGGTCA
Found at i:53450533 original size:50 final size:50
Alignment explanation
Indices: 53450458--53450790 Score: 373
Period size: 50 Copynumber: 6.6 Consensus size: 50
53450448 ATGGTAAGCA
* *
53450458 TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGAACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCTGGAACACG
53450508 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCT-GATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCTGGA-ACACG
53450558 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCT-GATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCTGGA-ACACG
* *** * * * * *
53450608 TAGTAGCCTACACTTAGTACTACACATGTGATGGAAGCTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAA-CCATCTGGAACACG
* ** * * **
53450659 TAGTAGCCTGCACTTAGTACTGCACATACGACCTAACAATTTGGCGCACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCTGGAACACG
* * * ** *
53450709 TAGTAGCCTACACTTAATACTACACACGTGACCTAAAACCATCTTAAACACA
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCT--AACCATCTGGAACACG
* *
53450761 TAGTAACCTGCACATAGTACTACACATGTG
1 TAGTAGCCTGCACTTAGTACTACACATGTG
53450791 TTCTCACAAC
Statistics
Matches: 235, Mismatches: 43, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
49 2 0.01
50 162 0.69
51 36 0.15
52 35 0.15
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCTGGAACACG
Found at i:53450731 original size:151 final size:151
Alignment explanation
Indices: 53450456--53450790 Score: 411
Period size: 151 Copynumber: 2.2 Consensus size: 151
53450446 CTATGGTAAG
* * * *
53450456 CATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGAACACGTAGTAGCCTGCAC
1 CATAGTAGCCTGCACTTAGTACTACACATGTGACCGAACAATCGGGAACACATAGTAGCCTGCAC
** * * * * *
53450521 TTAGTACTACACATGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTACACATG
66 TTAGTACTACACATACGACCTAACAATCTGACACACGTAGTAGCCTACACTTAATACTACACACG
*
53450586 TGACCT-AACCATCTGATACA
131 TGACCTAAACCATCTGAAACA
* * ** * * *
53450606 CGTAGTAGCCTACACTTAGTACTACACATGTGATGGAAGCTATCGGGTACGCATAGTAGCCTGCA
1 CATAGTAGCCTGCACTTAGTACTACACATGTGACCGAA-CAATCGGGAACACATAGTAGCCTGCA
* * * *
53450671 CTTAGTACTGCACATACGACCTAACAATTTGGCGCACGTAGTAGCCTACACTTAATACTACACAC
65 CTTAGTACTACACATACGACCTAACAATCTGACACACGTAGTAGCCTACACTTAATACTACACAC
*
53450736 GTGACCTAAAACCATCTTAAACA
130 GTGACCT-AAACCATCTGAAACA
* *
53450759 CATAGTAACCTGCACATAGTACTACACATGTG
1 CATAGTAGCCTGCACTTAGTACTACACATGTG
53450791 TTCTCACAAC
Statistics
Matches: 154, Mismatches: 28, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
150 32 0.21
151 82 0.53
153 40 0.26
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (151 bp):
CATAGTAGCCTGCACTTAGTACTACACATGTGACCGAACAATCGGGAACACATAGTAGCCTGCAC
TTAGTACTACACATACGACCTAACAATCTGACACACGTAGTAGCCTACACTTAATACTACACACG
TGACCTAAACCATCTGAAACA
Found at i:53452982 original size:30 final size:30
Alignment explanation
Indices: 53452948--53453008 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
53452938 TCTTTAATAA
53452948 AAACTTTGGCAAAATTACA-TTTTTGCCCCT
1 AAACTTTGGCAAAATTACACTTTTT-CCCCT
* *
53452978 AAACTTTTGCATAATTACACTTTTTCCCCT
1 AAACTTTGGCAAAATTACACTTTTTCCCCT
53453008 A
1 A
53453009 GGCTCGGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 23 0.82
31 5 0.18
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACACTTTTTCCCCT
Found at i:53459365 original size:22 final size:22
Alignment explanation
Indices: 53459325--53459401 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
53459315 ACAGCTCGTA
*
53459325 AGAGCTTACTGTTTCAACTC-ATT
1 AGAGCTTACCG-TTCAACTCGA-T
*
53459348 GGAGCTTACCGTTCAACTCGAT
1 AGAGCTTACCGTTCAACTCGAT
53459370 AGAGCTTACCGTTCAACTCGAT
1 AGAGCTTACCGTTCAACTCGAT
53459392 AGAGCTTACC
1 AGAGCTTACC
53459402 ATTGTCAGCT
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
22 40 0.80
23 10 0.20
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (22 bp):
AGAGCTTACCGTTCAACTCGAT
Found at i:53469534 original size:13 final size:13
Alignment explanation
Indices: 53469516--53469541 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53469506 GATACTGTCT
53469516 GAAAATTCTATTC
1 GAAAATTCTATTC
53469529 GAAAATTCTATTC
1 GAAAATTCTATTC
53469542 ATCAAATCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
GAAAATTCTATTC
Found at i:53472844 original size:39 final size:40
Alignment explanation
Indices: 53472762--53472844 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 40
53472752 TTAATTCACT
* * *
53472762 AGCATTAAGCCTGCGGGACTTTAAACCCGGATACAATCCC
1 AGCATGAAGCCAGCGGGACTCTAAACCCGGATACAATCCC
* * *
53472802 AGCATGAAGCCAGCGGGTCTCT-AACCCGGATGCAATCTC
1 AGCATGAAGCCAGCGGGACTCTAAACCCGGATACAATCCC
53472841 AGCA
1 AGCA
53472845 CAATTCATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 19 0.51
40 18 0.49
ACGTcount: A:0.29, C:0.30, G:0.23, T:0.18
Consensus pattern (40 bp):
AGCATGAAGCCAGCGGGACTCTAAACCCGGATACAATCCC
Found at i:53478125 original size:47 final size:47
Alignment explanation
Indices: 53478056--53478392 Score: 512
Period size: 47 Copynumber: 7.1 Consensus size: 47
53478046 GAAATGATAG
*
53478056 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
53478103 TAAGGCCTAATGGCCGAAGTGATGAATGTGAAAGTGTATATATGAGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
53478150 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
53478199 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
53478248 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
53478295 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * *
53478342 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
53478389 TAAG
1 TAAG
53478393 TCCCGAAGGG
Statistics
Matches: 269, Mismatches: 19, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
47 175 0.65
49 94 0.35
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:53478567 original size:37 final size:37
Alignment explanation
Indices: 53478511--53478589 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
53478501 CCGAGCTCTA
* * *
53478511 AAGACCCGATGACTACGTGTGGGGATTTTGTCCAGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCAGGT
* *
53478548 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCAGGT
53478585 AAGAC
1 AAGAC
53478590 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCAGGT
Found at i:53495756 original size:27 final size:27
Alignment explanation
Indices: 53495694--53495756 Score: 92
Period size: 27 Copynumber: 2.3 Consensus size: 27
53495684 TTATATTAAT
*
53495694 ACATAGTTTTAATGTGTCTAGTTTAGG
1 ACATAATTTTAATGTGTCTAGTTTAGG
*
53495721 ACATCATTTTAATGTGTCTAGTTTAGGG
1 ACATAATTTTAATGTGTCTAGTTTA-GG
53495749 ACA-AATTT
1 ACATAATTT
53495757 ATTAGGTGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 27 0.84
28 5 0.16
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.43
Consensus pattern (27 bp):
ACATAATTTTAATGTGTCTAGTTTAGG
Found at i:53501639 original size:5 final size:5
Alignment explanation
Indices: 53501624--53501656 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
53501614 GGCTAAGGAG
53501624 AAATCA AAATA AAATA AAATA AAATA AAATA AA
1 AAAT-A AAATA AAATA AAATA AAATA AAATA AA
53501657 TGAGTATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:53521318 original size:89 final size:89
Alignment explanation
Indices: 53521167--53521350 Score: 332
Period size: 89 Copynumber: 2.1 Consensus size: 89
53521157 TAAATAAGAT
53521167 TAATTTGGCATTATAGATCAAGAGAAACGAGATTCAAGTCGCGATCGAGGGAAAAATAAAGTTTA
1 TAATTTGGCATTATAGATCAAGAGAAACGAGATTCAAGTCGCGATCGAGGGAAAAATAAAGTTTA
*
53521232 CGAAGAATAGGGCACGATTGCTAA
66 CGAAGAATAGGGCACAATTGCTAA
*
53521256 TAATTTGGCATTATAGATCAAGAGAAACGAGATTCAATTCGCGATCGAGGGAAAAATAAAGTTTA
1 TAATTTGGCATTATAGATCAAGAGAAACGAGATTCAAGTCGCGATCGAGGGAAAAATAAAGTTTA
* *
53521321 CGAAGAATAGGGCTCAATTGTTAA
66 CGAAGAATAGGGCACAATTGCTAA
53521345 TAATTT
1 TAATTT
53521351 TGTATCAAGG
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 91 1.00
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26
Consensus pattern (89 bp):
TAATTTGGCATTATAGATCAAGAGAAACGAGATTCAAGTCGCGATCGAGGGAAAAATAAAGTTTA
CGAAGAATAGGGCACAATTGCTAA
Found at i:53522476 original size:24 final size:24
Alignment explanation
Indices: 53522441--53522516 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
53522431 AGTCTGTCAA
*
53522441 GAGAGGATTTAGGAGTTGATAAGG
1 GAGAGGATTTAGGAGCTGATAAGG
*
53522465 GATAGGATTTAGGAGCTGATAAGG
1 GAGAGGATTTAGGAGCTGATAAGG
* *
53522489 AAGAGGATTTAGGAGCTGATTAGG
1 GAGAGGATTTAGGAGCTGATAAGG
53522513 GAGA
1 GAGA
53522517 ACAGTGTTGG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.34, C:0.03, G:0.39, T:0.24
Consensus pattern (24 bp):
GAGAGGATTTAGGAGCTGATAAGG
Found at i:53523922 original size:27 final size:27
Alignment explanation
Indices: 53523882--53523992 Score: 143
Period size: 27 Copynumber: 4.1 Consensus size: 27
53523872 AGGAAGCGTC
* **
53523882 CTGGTGGCTATGCCACATTTATCTAAT
1 CTGGTGGCTCTGCCACATTTATCTGTT
*
53523909 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACATTTATCTGTT
* *
53523936 CTGGTGGCTCTGCCACAATTAACTGTT
1 CTGGTGGCTCTGCCACATTTATCTGTT
* *
53523963 CTGGTGACTCTGTCACA-TTATCTGTT
1 CTGGTGGCTCTGCCACATTTATCTGTT
53523989 CTGG
1 CTGG
53523993 CAGCAATGCT
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
26 12 0.16
27 62 0.84
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACATTTATCTGTT
Found at i:53530364 original size:24 final size:24
Alignment explanation
Indices: 53530265--53530365 Score: 141
Period size: 24 Copynumber: 4.2 Consensus size: 24
53530255 AAGTCTATCA
*
53530265 GGAGAGGATTTAGGAGTTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
* *
53530289 GGATAGGATTTAGGAGTTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
*
53530313 GG-GTAGGATTTAGGATCTGATAAG
1 GGAG-AGGATTTAGGAGCTGATAAG
*
53530337 GGAGAGGATTTAGGAGCTGATTAG
1 GGAGAGGATTTAGGAGCTGATAAG
53530361 GGAGA
1 GGAGA
53530366 ATAGTGTTGG
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
24 68 0.99
25 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.41, T:0.26
Consensus pattern (24 bp):
GGAGAGGATTTAGGAGCTGATAAG
Found at i:53531209 original size:123 final size:123
Alignment explanation
Indices: 53530990--53531240 Score: 502
Period size: 123 Copynumber: 2.0 Consensus size: 123
53530980 GCTGAAACCC
53530990 CTAAAGGTTAGGGGGCTGTCGATTTGGGCATGTAGCTCTAAAGGGTGTTATAACTGTTTTATTTT
1 CTAAAGGTTAGGGGGCTGTCGATTTGGGCATGTAGCTCTAAAGGGTGTTATAACTGTTTTATTTT
53531055 GATAATAGTGGGATCTAAAGCTGCTGATCGAAGGCTTGGACAAGTGGAGTGACTGGAT
66 GATAATAGTGGGATCTAAAGCTGCTGATCGAAGGCTTGGACAAGTGGAGTGACTGGAT
53531113 CTAAAGGTTAGGGGGCTGTCGATTTGGGCATGTAGCTCTAAAGGGTGTTATAACTGTTTTATTTT
1 CTAAAGGTTAGGGGGCTGTCGATTTGGGCATGTAGCTCTAAAGGGTGTTATAACTGTTTTATTTT
53531178 GATAATAGTGGGATCTAAAGCTGCTGATCGAAGGCTTGGACAAGTGGAGTGACTGGAT
66 GATAATAGTGGGATCTAAAGCTGCTGATCGAAGGCTTGGACAAGTGGAGTGACTGGAT
53531236 CTAAA
1 CTAAA
53531241 CATAATCGCT
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
123 128 1.00
ACGTcount: A:0.26, C:0.12, G:0.31, T:0.31
Consensus pattern (123 bp):
CTAAAGGTTAGGGGGCTGTCGATTTGGGCATGTAGCTCTAAAGGGTGTTATAACTGTTTTATTTT
GATAATAGTGGGATCTAAAGCTGCTGATCGAAGGCTTGGACAAGTGGAGTGACTGGAT
Found at i:53531933 original size:27 final size:27
Alignment explanation
Indices: 53531894--53531997 Score: 113
Period size: 27 Copynumber: 3.9 Consensus size: 27
53531884 GGAAGCATCT
* *
53531894 TGGTGGCTATGCCATATTTATCTGATC
1 TGGTGGCTCTGCCACATTTATCTGATC
* *
53531921 TGGTGGCTCTGCCACATATATCTGTTC
1 TGGTGGCTCTGCCACATTTATCTGATC
*
53531948 TGGTGGCTCTGCCACAATTATCT-ATTC
1 TGGTGGCTCTGCCACATTTATCTGA-TC
* * *
53531975 TGGTGACTCAGTCACA-TTATCTG
1 TGGTGGCTCTGCCACATTTATCTG
53531998 TTCTAGCAGC
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
26 6 0.09
27 59 0.91
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.38
Consensus pattern (27 bp):
TGGTGGCTCTGCCACATTTATCTGATC
Found at i:53531977 original size:54 final size:53
Alignment explanation
Indices: 53531894--53532001 Score: 137
Period size: 54 Copynumber: 2.0 Consensus size: 53
53531884 GGAAGCATCT
* * * *
53531894 TGGTGGCTATGCCATATTTATCTGATCTGGTGGCTCTGCCACATATATCTGTTC
1 TGGTGGCTATGCCACAATTATCTGATCTGGTGACTCAGCCACAT-TATCTGTTC
* *
53531948 TGGTGGCTCTGCCACAATTATCT-ATTCTGGTGACTCAGTCACATTATCTGTTC
1 TGGTGGCTATGCCACAATTATCTGA-TCTGGTGACTCAGCCACATTATCTGTTC
53532001 T
1 T
53532002 AGCAGCAATG
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
53 11 0.23
54 36 0.77
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (53 bp):
TGGTGGCTATGCCACAATTATCTGATCTGGTGACTCAGCCACATTATCTGTTC
Found at i:53537739 original size:40 final size:40
Alignment explanation
Indices: 53537557--53537732 Score: 316
Period size: 40 Copynumber: 4.4 Consensus size: 40
53537547 ATAGCAACTC
* * * *
53537557 GCACGAATGCCTTTGGGACTTAGCCCGGACATAGTCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
53537597 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
53537637 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
53537677 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
53537717 GCACAAATGCCTTCGG
1 GCACAAATGCCTTCGG
53537733 ATCTTAGTCC
Statistics
Matches: 132, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 132 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
Found at i:53545563 original size:78 final size:79
Alignment explanation
Indices: 53545431--53545633 Score: 304
Period size: 78 Copynumber: 2.6 Consensus size: 79
53545421 AACCCAAGTA
* * * * * *
53545431 CCTTCGGAATTTAG-CCGGATATAGCAACTCGCACGAATGCCTT-GGGACTTAGCCCGGACATAG
1 CCTTCGGGACTTAGCCCGGATATATC-ACTAGCACAAATGCCTTCGGGACTTAGCCCGGACATAA
53545494 TCACTAGCA-AAATG
65 TCACTAGCACAAATG
*
53545508 CCTTCGGGACTTAGCCCGGATATATCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAAT
1 CCTTCGGGACTTAGCCCGGATATATCACTAGCACAAATGCCTTCGGGACTTAGCCCGGACATAAT
53545573 CACTAGCACAAATG
66 CACTAGCACAAATG
53545587 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATGCCTTCGG
1 CCTTCGGGACTTAGCCCGGATAT-ATCACTAGCACAAATGCCTTCGG
53545634 ATCTTAGTCC
Statistics
Matches: 115, Mismatches: 7, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
77 27 0.23
78 37 0.32
79 28 0.24
80 23 0.20
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.23
Consensus pattern (79 bp):
CCTTCGGGACTTAGCCCGGATATATCACTAGCACAAATGCCTTCGGGACTTAGCCCGGACATAAT
CACTAGCACAAATG
Found at i:53545640 original size:40 final size:40
Alignment explanation
Indices: 53545431--53545633 Score: 299
Period size: 40 Copynumber: 5.2 Consensus size: 40
53545421 AACCCAAGTA
* * * * *
53545431 CCTTCGGAATTTAG-CCGGATAT-AGCAACTCGCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAATC-ACTAGCACAAATG
* *
53545470 CCTT-GGGACTTAGCCCGGACATAGTCACTAGCA-AAATG
1 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATG
53545508 CCTTCGGGACTTAGCCCGGATAT-ATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATG
53545547 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATG
53545587 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATG
53545627 CCTTCGG
1 CCTTCGG
53545634 ATCTTAGTCC
Statistics
Matches: 150, Mismatches: 9, Indels: 9
0.89 0.05 0.05
Matches are distributed among these distances:
38 24 0.16
39 62 0.41
40 64 0.43
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATG
Found at i:53548296 original size:40 final size:40
Alignment explanation
Indices: 53548172--53548436 Score: 286
Period size: 40 Copynumber: 6.7 Consensus size: 40
53548162 TTGAATGCTG
* * * * *
53548172 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAA
** * * *
53548212 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATA-CAAGT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAA-A
* *
53548252 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
*
53548292 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
** *
53548332 TCCGGGTTAAGTCCCGAAGGCATTCATGCGAGTCATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
* *
53548372 TCCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
* * *
53548411 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
53548437 AACGAGGAGC
Statistics
Matches: 192, Mismatches: 27, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
39 32 0.17
40 150 0.78
41 10 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
Found at i:53553671 original size:30 final size:30
Alignment explanation
Indices: 53553635--53553692 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
53553625 CCGAGCCTAG
*
53553635 GGGCAAAAGTGTAATTATGCAAAAGTTTAA
1 GGGCAAAAATGTAATTATGCAAAAGTTTAA
* *
53553665 GGGCAAAAATGTAATTTTGCCAAAGTTT
1 GGGCAAAAATGTAATTATGCAAAAGTTT
53553693 GTTTTAAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (30 bp):
GGGCAAAAATGTAATTATGCAAAAGTTTAA
Found at i:53559649 original size:46 final size:45
Alignment explanation
Indices: 53559570--53559742 Score: 136
Period size: 46 Copynumber: 3.8 Consensus size: 45
53559560 TGTAACCCAC
* * **
53559570 CCATAAGCGTACTCGGACTCAACTCAATAAGTTCAGGCATTCGCAT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGTTC-GGCATTCGCAT
* *
53559616 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGG-ATGC-CTAGTT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGTTCGGCATTCGC-A--T
* * * * *
53559662 ACATCTCA-CGAACTCAGACTCAACTCAACGAGTTCGAACGTTTGCAT
1 CCA--TAAGCGAACTCAGACTCAACTCAACGAGTTCG-GCATTCGCAT
* * *
53559709 CCATAAGTGAACTCGGACTCAACTCAATGAGTTC
1 CCATAAGCGAACTCAGACTCAACTCAACGAGTTC
53559743 AGATGCTCAA
Statistics
Matches: 100, Mismatches: 18, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 4 0.04
46 56 0.56
47 30 0.30
48 2 0.02
49 2 0.02
50 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (45 bp):
CCATAAGCGAACTCAGACTCAACTCAACGAGTTCGGCATTCGCAT
Found at i:53559696 original size:93 final size:93
Alignment explanation
Indices: 53559580--53559748 Score: 241
Period size: 93 Copynumber: 1.8 Consensus size: 93
53559570 CCATAAGCGT
* * *
53559580 ACTCGGACTCAACTCAATAAGTTC-AGGCATTCGCATCCATAAGTGAACTCAGACTCAACTCAAC
1 ACTCAGACTCAACTCAACAAGTTCGA-ACATTCGCATCCATAAGTGAACTCAGACTCAACTCAAC
*
53559644 GAGTTCGGATGCCTAGTTACATCTCACGA
65 GAGTTCAGATGCCTAGTTACATCTCACGA
* * * * *
53559673 ACTCAGACTCAACTCAACGAGTTCGAACGTTTGCATCCATAAGTGAACTCGGACTCAACTCAATG
1 ACTCAGACTCAACTCAACAAGTTCGAACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACG
53559738 AGTTCAGATGC
66 AGTTCAGATGC
53559749 TCAAATATCT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
93 65 0.98
94 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (93 bp):
ACTCAGACTCAACTCAACAAGTTCGAACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACG
AGTTCAGATGCCTAGTTACATCTCACGA
Found at i:53581904 original size:13 final size:13
Alignment explanation
Indices: 53581886--53581910 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53581876 TCAATTTTTA
53581886 TTACTTTAGCCAT
1 TTACTTTAGCCAT
53581899 TTACTTTAGCCA
1 TTACTTTAGCCA
53581911 GGTTCTTATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.44
Consensus pattern (13 bp):
TTACTTTAGCCAT
Found at i:53587252 original size:24 final size:25
Alignment explanation
Indices: 53587169--53587263 Score: 120
Period size: 25 Copynumber: 3.8 Consensus size: 25
53587159 CTCTTTTAAT
* * *
53587169 AACTGGGGCAAAGCCCTTTTTGATG
1 AACTGGGGCAAAGCCCTTTTCGGTA
*
53587194 AACTGGGACAAAAGCCCTTTTCGGTA
1 AACTGGGGC-AAAGCCCTTTTCGGTA
53587220 AACTGGGGCAAAGCCCTTTTCGGT-
1 AACTGGGGCAAAGCCCTTTTCGGTA
* *
53587244 AACTAGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
53587264 GCACTTCCTT
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
24 18 0.29
25 23 0.37
26 21 0.34
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGGTA
Found at i:53598462 original size:40 final size:40
Alignment explanation
Indices: 53598364--53598626 Score: 307
Period size: 40 Copynumber: 6.6 Consensus size: 40
53598354 TCCTCGTTCA
* * * * *
53598364 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
53598403 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
53598443 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
53598483 AATGCCTTTGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * *
53598523 AATACCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
53598563 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
53598603 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
53598627 CAGCATTCAA
Statistics
Matches: 196, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
39 37 0.19
40 151 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:53605519 original size:33 final size:33
Alignment explanation
Indices: 53605470--53605533 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
53605460 GATCAACAAT
* *
53605470 AGTCTGGACCTGAGCCCTATTCAGTATTAGTAC
1 AGTCTGGACCTGAGCCCTATACAGTAATAGTAC
* *
53605503 AGTCTGGGCCTTAGCCCTATACAGTAATAGT
1 AGTCTGGACCTGAGCCCTATACAGTAATAGT
53605534 GTGGCCTAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (33 bp):
AGTCTGGACCTGAGCCCTATACAGTAATAGTAC
Found at i:53605746 original size:27 final size:27
Alignment explanation
Indices: 53605716--53605770 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
53605706 AGCTGCCAAA
*
53605716 AATAGTAAATGTGGCAAAGCCACCAGT
1 AATAGTAAATGTGACAAAGCCACCAGT
* * *
53605743 AATAGTGAATGTGACATAGTCACCAGT
1 AATAGTAAATGTGACAAAGCCACCAGT
53605770 A
1 A
53605771 CAGTACTTCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (27 bp):
AATAGTAAATGTGACAAAGCCACCAGT
Found at i:53605943 original size:27 final size:27
Alignment explanation
Indices: 53605912--53605976 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
53605902 GGGCATCATC
53605912 GTCATTTTACCAAACAAAGATATTACG
1 GTCATTTTACCAAACAAAGATATTACG
** * *
53605939 GTCATTTTACCCTACAAGGGTATTACG
1 GTCATTTTACCAAACAAAGATATTACG
53605966 GTCATTTTACC
1 GTCATTTTACC
53605977 CTATAAGGGC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.34
Consensus pattern (27 bp):
GTCATTTTACCAAACAAAGATATTACG
Found at i:53605977 original size:27 final size:27
Alignment explanation
Indices: 53605933--53606222 Score: 352
Period size: 27 Copynumber: 10.6 Consensus size: 27
53605923 AAACAAAGAT
*
53605933 ATTACGGTCATTTTACCCTACAAGGGT
1 ATTACGGTCATTTTACCCTACAAGGGC
*
53605960 ATTACGGTCATTTTACCCTATAAGGGC
1 ATTACGGTCATTTTACCCTACAAGGGC
* * *
53605987 ATTATGGTCTTTTTACCCTACAGGGGC
1 ATTACGGTCATTTTACCCTACAAGGGC
* *
53606014 ATTACGATCATTTTACCTTAC-AGGTGC
1 ATTACGGTCATTTTACCCTACAAGG-GC
*
53606041 ATTACGGTAATTTTACCCTACAAGGGC
1 ATTACGGTCATTTTACCCTACAAGGGC
*
53606068 ATTACGGTCATTTTACCGTACAAGGGC
1 ATTACGGTCATTTTACCCTACAAGGGC
* **
53606095 ATTACGGTCATTTTACCCTAC-ACGAT
1 ATTACGGTCATTTTACCCTACAAGGGC
*
53606121 ATTACGGTCATTTTACCTTACCCTACAGGGGC
1 ATTACGGTCA--TT---TTACCCTACAAGGGC
* * *
53606153 ATTACGATCATTTTACCCTAC-GGGGT
1 ATTACGGTCATTTTACCCTACAAGGGC
*
53606179 ATTATGGTCATTTTACCCTACAAGGGC
1 ATTACGGTCATTTTACCCTACAAGGGC
53606206 ATTACGGTCATTTTACC
1 ATTACGGTCATTTTACC
53606223 TATTTTGGGG
Statistics
Matches: 223, Mismatches: 31, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
26 37 0.17
27 160 0.72
28 5 0.02
30 2 0.01
31 9 0.04
32 10 0.04
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (27 bp):
ATTACGGTCATTTTACCCTACAAGGGC
Found at i:53612845 original size:35 final size:35
Alignment explanation
Indices: 53612805--53612941 Score: 175
Period size: 35 Copynumber: 3.9 Consensus size: 35
53612795 AGGAAAGTAT
*
53612805 ATGTGAGGTTATATTGAACTTGTATATTCGGCTGC
1 ATGTGAGGTTATATTGAACTTGTATATTCGGCTAC
* **
53612840 ATGTGAGGTTATATTGAACTTGTGTATTCGATTAC
1 ATGTGAGGTTATATTGAACTTGTATATTCGGCTAC
* * * *
53612875 ATGTGAGCTTATATTGCACTTGTATATTTGGTTAC
1 ATGTGAGGTTATATTGAACTTGTATATTCGGCTAC
* * *
53612910 ATATGAGGTTATATTGAATTTTTATATTCGGC
1 ATGTGAGGTTATATTGAACTTGTATATTCGGC
53612942 CATATGAGAT
Statistics
Matches: 86, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 86 1.00
ACGTcount: A:0.25, C:0.09, G:0.22, T:0.44
Consensus pattern (35 bp):
ATGTGAGGTTATATTGAACTTGTATATTCGGCTAC
Found at i:53612966 original size:70 final size:70
Alignment explanation
Indices: 53612803--53613018 Score: 195
Period size: 70 Copynumber: 3.1 Consensus size: 70
53612793 ATAGGAAAGT
* * * * * * *
53612803 ATATGTGAGGTTATATTGAACTTGTATATTCGGCTGCATGTGAGGTTATATTGAACTTGTGTATT
1 ATATGAGAGCTTATATTGAACTTGTATATTTGGTTACATGTGAGGTTATATTGAACTTATATATT
**
53612868 CGATT
66 CGACC
* * * * * *
53612873 ACATGTGAGCTTATATTGCACTTGTATATTTGGTTACATATGAGGTTATATTGAATTTTTATATT
1 ATATGAGAGCTTATATTGAACTTGTATATTTGGTTACATGTGAGGTTATATTGAACTTATATATT
*
53612938 CGGCC
66 CGACC
* * * * *
53612943 ATATGAGATGTTTAT-TTGAACTTGAACATTAT-GTTACATGTGATGATT-TATTGAACTTAAAT
1 ATATGAGA-GCTTATATTGAACTTGTATATT-TGGTTACATGTGA-GGTTATATTGAACTTATAT
53613005 ATTCGACC
63 ATTCGACC
53613013 ATATGA
1 ATATGA
53613019 AATAATATAA
Statistics
Matches: 118, Mismatches: 25, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
70 109 0.92
71 9 0.08
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.43
Consensus pattern (70 bp):
ATATGAGAGCTTATATTGAACTTGTATATTTGGTTACATGTGAGGTTATATTGAACTTATATATT
CGACC
Found at i:53617463 original size:13 final size:13
Alignment explanation
Indices: 53617447--53617471 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53617437 TTAAATCAGT
53617447 TAATTAGTTTAAA
1 TAATTAGTTTAAA
53617460 TAATTAGTTTAA
1 TAATTAGTTTAA
53617472 TAAACAAACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TAATTAGTTTAAA
Found at i:53622883 original size:30 final size:30
Alignment explanation
Indices: 53622847--53622908 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
53622837 AATCCTCCTA
*
53622847 TTTTTTTATTTAGTTTTATTTTTATTTT-AT
1 TTTTTTTATTTAGATTT-TTTTTATTTTCAT
*
53622877 TTTTTTTATTTTGATTTTTTTTATTTTCAT
1 TTTTTTTATTTAGATTTTTTTTATTTTCAT
53622907 TT
1 TT
53622909 CAATTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.15, C:0.02, G:0.03, T:0.81
Consensus pattern (30 bp):
TTTTTTTATTTAGATTTTTTTTATTTTCAT
Found at i:53622900 original size:35 final size:34
Alignment explanation
Indices: 53622845--53622928 Score: 96
Period size: 35 Copynumber: 2.4 Consensus size: 34
53622835 TGAATCCTCC
* * * * *
53622845 TATTTTTTTATTTAGTTTTATTTTTATTTTATTTT
1 TATTATTTTATTT-TTTTTATTTTCATTTCAATTT
*
53622880 TTTTATTTTGATTTTTTTTATTTTCATTTCAATTT
1 TATTATTTT-ATTTTTTTTATTTTCATTTCAATTT
53622915 TATTATTTTATTTT
1 TATTATTTTATTTT
53622929 GAAAGACATA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
34 5 0.12
35 32 0.78
36 4 0.10
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.77
Consensus pattern (34 bp):
TATTATTTTATTTTTTTTATTTTCATTTCAATTT
Found at i:53622908 original size:6 final size:5
Alignment explanation
Indices: 53622850--53622928 Score: 69
Period size: 5 Copynumber: 15.8 Consensus size: 5
53622840 CCTCCTATTT
53622850 TTTTA -TTTA GTTTTA TTTTTA TTTTA TTTT- TTTTA TTTTGA TTTT-
1 TTTTA TTTTA -TTTTA -TTTTA TTTTA TTTTA TTTTA TTTT-A TTTTA
*
53622895 TTTTA TTTTCA TTTCAA TTTTA --TTA TTTTA TTTT
1 TTTTA TTTT-A TTT-TA TTTTA TTTTA TTTTA TTTT
53622929 GAAAGACATA
Statistics
Matches: 62, Mismatches: 3, Indels: 18
0.75 0.04 0.22
Matches are distributed among these distances:
3 3 0.05
4 12 0.19
5 25 0.40
6 22 0.35
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:53633303 original size:49 final size:50
Alignment explanation
Indices: 53633183--53633305 Score: 133
Period size: 50 Copynumber: 2.5 Consensus size: 50
53633173 ATGACTTCGA
* * * *
53633183 TCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTATCAGGTGGTGAGG
1 TCACATGTGTAGTACTAAGTGCAGACAACTACGTGTATCAGGTGGTGAGG
* * * * *
53633233 TCACGTGTATAGTACTAAGTGCAGACAACTACGTGTA-CTGGATTGT-TGG
1 TCACATGTGTAGTACTAAGTGCAGACAACTACGTGTATCAGG-TGGTGAGG
*
53633282 TCGCATGTGTAGTACTAAGTGCAG
1 TCACATGTGTAGTACTAAGTGCAG
53633306 GCTACTATGC
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
49 26 0.42
50 36 0.58
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.30
Consensus pattern (50 bp):
TCACATGTGTAGTACTAAGTGCAGACAACTACGTGTATCAGGTGGTGAGG
Found at i:53633442 original size:27 final size:26
Alignment explanation
Indices: 53633412--53633463 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
53633402 GGGAAAATTG
53633412 ATAAAGTGGTAATATGTG-AAAGTTATT
1 ATAAAGTGG--ATATGTGCAAAGTTATT
* *
53633439 ATAAGGTGGATATGTGCAAATTTAT
1 ATAAAGTGGATATGTGCAAAGTTAT
53633464 GTTTATGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 7 0.32
26 7 0.32
27 8 0.36
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (26 bp):
ATAAAGTGGATATGTGCAAAGTTATT
Found at i:53640725 original size:49 final size:50
Alignment explanation
Indices: 53640607--53640736 Score: 147
Period size: 49 Copynumber: 2.6 Consensus size: 50
53640597 TACACGTGTG
* * *
53640607 TAGTACTAAGTGCAGGCTACTACATGTATCAGGTGGTGAGGTCACGTGTG
1 TAGTACTAAGTGCAGGCTACTACGTGTATCAGGTGGTGAGGTCACATGTA
* * * * *
53640657 TAGTACTAAGTTCAGGCTACTACGTGTA-CCGGATTGT-TGGTCGCATGTA
1 TAGTACTAAGTGCAGGCTACTACGTGTATCAGG-TGGTGAGGTCACATGTA
* *
53640706 TAGTACTAAGTGCAAGCTACTATGTGTATCA
1 TAGTACTAAGTGCAGGCTACTACGTGTATCA
53640737 AATAGCTTTG
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
49 36 0.55
50 30 0.45
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (50 bp):
TAGTACTAAGTGCAGGCTACTACGTGTATCAGGTGGTGAGGTCACATGTA
Found at i:53641150 original size:23 final size:23
Alignment explanation
Indices: 53641115--53641169 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
53641105 GGAAGCAAAA
53641115 GAATTCTAT-ATTGTGTGATATTT
1 GAATTCT-TGATTGTGTGATATTT
53641138 GAATTCTTGATTGTGTGATATTT
1 GAATTCTTGATTGTGTGATATTT
53641161 GAATTCTTG
1 GAATTCTTG
53641170 TGTAACAGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 1 0.03
23 30 0.97
ACGTcount: A:0.24, C:0.05, G:0.20, T:0.51
Consensus pattern (23 bp):
GAATTCTTGATTGTGTGATATTT
Found at i:53649609 original size:28 final size:29
Alignment explanation
Indices: 53649527--53649621 Score: 120
Period size: 29 Copynumber: 3.3 Consensus size: 29
53649517 AAAGCATGAC
*
53649527 TATGAATGTGATTTAGGTCTAATGGGCCA
1 TATGAATGTGATTTGGGTCTAATGGGCCA
* * *
53649556 TATGAATGTGATTTGGGCCAAATGGGTCA
1 TATGAATGTGATTTGGGTCTAATGGGCCA
* *
53649585 TATGAATGAGA-TTGGGTCTAGTGGGCCA
1 TATGAATGTGATTTGGGTCTAATGGGCCA
*
53649613 TATGCATGT
1 TATGAATGT
53649622 ATGTAGACTT
Statistics
Matches: 55, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
28 20 0.36
29 35 0.64
ACGTcount: A:0.26, C:0.11, G:0.31, T:0.33
Consensus pattern (29 bp):
TATGAATGTGATTTGGGTCTAATGGGCCA
Found at i:53651948 original size:249 final size:249
Alignment explanation
Indices: 53651510--53652008 Score: 980
Period size: 249 Copynumber: 2.0 Consensus size: 249
53651500 GCTTGAAAAT
53651510 GATTAGTGAACTTGGTTGGTTATTGATAGTTTAAAAATGTTAATAAATTATGTGTATGTTCGAAT
1 GATTAGTGAACTTGGTTGGTTATTGATAGTTTAAAAATGTTAATAAATTATGTGTATGTTCGAAT
*
53651575 ACGCATAGCTTTATTTGGTTCGGTTTGCATAGAAAGTGTATATCTACTTAAAGTGGTTAATTGTA
66 ACGCATAGCTTTATTTGGTTCGATTTGCATAGAAAGTGTATATCTACTTAAAGTGGTTAATTGTA
53651640 TAATGATATAGGTATGGTTAATAAAGTTAAATAAAGATTATTTATTGAGATTATTTGTTTAATAG
131 TAATGATATAGGTATGGTTAATAAAGTTAAATAAAGATTATTTATTGAGATTATTTGTTTAATAG
53651705 GGATTGTAAGTGAAACAAAGATAAATTACCAAATGAATAGTGATTTATGTAATA
196 GGATTGTAAGTGAAACAAAGATAAATTACCAAATGAATAGTGATTTATGTAATA
*
53651759 GATTAGTGAACTTGGTTGGTTATTGATAGTTTAAAAATGTTTATAAATTATGTGTATGTTCGAAT
1 GATTAGTGAACTTGGTTGGTTATTGATAGTTTAAAAATGTTAATAAATTATGTGTATGTTCGAAT
53651824 ACGCATAGCTTTATTTGGTTCGATTTGCATAGAAAGTGTATATCTACTTAAAGTGGTTAATTGTA
66 ACGCATAGCTTTATTTGGTTCGATTTGCATAGAAAGTGTATATCTACTTAAAGTGGTTAATTGTA
53651889 TAATGATATAGGTATGGTTAATAAAGTTAAATAAAGATTATTTATTGAGATTATTTGTTTAATAG
131 TAATGATATAGGTATGGTTAATAAAGTTAAATAAAGATTATTTATTGAGATTATTTGTTTAATAG
53651954 GGATTGTAAGTGAAACAAAGATAAATTACCAAATGAATAGTGATTTATGTAATA
196 GGATTGTAAGTGAAACAAAGATAAATTACCAAATGAATAGTGATTTATGTAATA
53652008 G
1 G
53652009 TATCTACGGG
Statistics
Matches: 248, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
249 248 1.00
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (249 bp):
GATTAGTGAACTTGGTTGGTTATTGATAGTTTAAAAATGTTAATAAATTATGTGTATGTTCGAAT
ACGCATAGCTTTATTTGGTTCGATTTGCATAGAAAGTGTATATCTACTTAAAGTGGTTAATTGTA
TAATGATATAGGTATGGTTAATAAAGTTAAATAAAGATTATTTATTGAGATTATTTGTTTAATAG
GGATTGTAAGTGAAACAAAGATAAATTACCAAATGAATAGTGATTTATGTAATA
Found at i:53656736 original size:42 final size:41
Alignment explanation
Indices: 53656635--53656797 Score: 139
Period size: 42 Copynumber: 3.8 Consensus size: 41
53656625 CATAAGCTCG
* * *
53656635 TACAATGCCAATGTCCCAGGCATGTCTTACATGTAATCAAA
1 TACAATGCCAATGTCCCAGACATGTCTTACACGAAATCAAA
* * * * *
53656676 TATCGATGCCACTATCCCAGACAGTGTCTTGCACGAAATCATA
1 TA-CAATGCCAATGTCCCAGACA-TGTCTTACACGAAATCAAA
*
53656719 TACAATACCAATGTCCCAGACATGGTCTTACACGTAAATCACAA
1 TACAATGCCAATGTCCCAGACAT-GTCTTACACG-AAATCA-AA
* * * *
53656763 -ATCGATGCCAACGTTCCAGACGTTGTCTTACACGA
1 TA-CAATGCCAATGTCCCAGAC-ATGTCTTACACGA
53656798 TAACATATAT
Statistics
Matches: 96, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
41 3 0.03
42 41 0.43
43 25 0.26
44 26 0.27
45 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (41 bp):
TACAATGCCAATGTCCCAGACATGTCTTACACGAAATCAAA
Found at i:53656782 original size:86 final size:84
Alignment explanation
Indices: 53656635--53656806 Score: 210
Period size: 86 Copynumber: 2.0 Consensus size: 84
53656625 CATAAGCTCG
* * *
53656635 TACAATGCCAATGTCCCAGGCATGTCTTACATGTAATCAAATATCGATGCCACTATCCCAGACAG
1 TACAATACCAATGTCCCAGACATGTCTTACACGTAATCAAATATCGATGCCACTATCCCAGAC-G
*
53656700 -TGTCTTGCACGA-AATCATA
65 TTGTCTTACACGATAA-CATA
53656719 TACAATACCAATGTCCCAGACATGGTCTTACACGTAAATCACAA-ATCGATGCCAACGT-T-CCA
1 TACAATACCAATGTCCCAGACAT-GTCTTACACGT-AATCA-AATATCGATGCC-AC-TATCCCA
53656781 GACGTTGTCTTACACGATAACATA
61 GACGTTGTCTTACACGATAACATA
53656805 TA
1 TA
53656807 TCGAATCCTA
Statistics
Matches: 77, Mismatches: 4, Indels: 12
0.83 0.04 0.13
Matches are distributed among these distances:
84 21 0.27
85 11 0.14
86 37 0.48
87 7 0.09
88 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.26
Consensus pattern (84 bp):
TACAATACCAATGTCCCAGACATGTCTTACACGTAATCAAATATCGATGCCACTATCCCAGACGT
TGTCTTACACGATAACATA
Found at i:53658784 original size:27 final size:27
Alignment explanation
Indices: 53658746--53658800 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
53658736 TGATTTGATA
53658746 AAAATATTTACATACAGCTAAATGCAC
1 AAAATATTTACATACAGCTAAATGCAC
53658773 AAAATATTTACATACAGCTAAATGCAC
1 AAAATATTTACATACAGCTAAATGCAC
53658800 A
1 A
53658801 CCTTATCATT
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:0.49, C:0.18, G:0.07, T:0.25
Consensus pattern (27 bp):
AAAATATTTACATACAGCTAAATGCAC
Found at i:53661942 original size:20 final size:20
Alignment explanation
Indices: 53661898--53661963 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
53661888 CATCCAAACA
*
53661898 CCAGAAAAGTAAATTA-TTT
1 CCAGAAAAGTAAATCATTTT
53661917 CCAGAAAAGTAAATCATTTT
1 CCAGAAAAGTAAATCATTTT
*
53661937 CTAGAAAAGTAAATCATTTT
1 CCAGAAAAGTAAATCATTTT
53661957 CCAGAAA
1 CCAGAAA
53661964 TCATTTTTCG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
19 15 0.35
20 28 0.65
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.29
Consensus pattern (20 bp):
CCAGAAAAGTAAATCATTTT
Found at i:53665103 original size:35 final size:35
Alignment explanation
Indices: 53665052--53665120 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
53665042 AAAAGTAGAG
*
53665052 GACTAAATCCGCACAAATCGATAAGTACAGGGACA
1 GACTAAATCCGCACAAATAGATAAGTACAGGGACA
53665087 GACTAAATCCAG-ACAAATAGATAAGTACAGGGAC
1 GACTAAATCC-GCACAAATAGATAAGTACAGGGAC
53665121 CATCCTCAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 31 0.97
36 1 0.03
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.14
Consensus pattern (35 bp):
GACTAAATCCGCACAAATAGATAAGTACAGGGACA
Found at i:53667171 original size:20 final size:20
Alignment explanation
Indices: 53667146--53667183 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
53667136 GGCAACAATC
53667146 TCAGTCCACCCCCAATCCTA
1 TCAGTCCACCCCCAATCCTA
53667166 TCAGTCCACCCCCAATCC
1 TCAGTCCACCCCCAATCC
53667184 CCTGGTGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.53, G:0.05, T:0.18
Consensus pattern (20 bp):
TCAGTCCACCCCCAATCCTA
Found at i:53669130 original size:22 final size:22
Alignment explanation
Indices: 53669102--53669146 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
53669092 AGGAATTTTG
53669102 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
53669124 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
53669146 T
1 T
53669147 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:53669131 original size:11 final size:12
Alignment explanation
Indices: 53669092--53669139 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
53669082 AATGTCCTAA
53669092 AGGAAT-TTTGT
1 AGGAATATTTGT
53669103 AGGAATATTCTGT
1 AGGAATATT-TGT
53669116 A--AATATTT-T
1 AGGAATATTTGT
53669125 AGGAATATTTTGT
1 AGGAATA-TTTGT
53669138 AG
1 AG
53669140 ATATTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
9 2 0.06
10 1 0.03
11 16 0.52
12 5 0.16
13 7 0.23
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.44
Consensus pattern (12 bp):
AGGAATATTTGT
Found at i:53674465 original size:22 final size:22
Alignment explanation
Indices: 53674437--53674481 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
53674427 AGGGGGAGTG
53674437 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
53674459 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
53674481 T
1 T
53674482 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:53674952 original size:21 final size:21
Alignment explanation
Indices: 53674928--53674967 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
53674918 TTAATATAAT
53674928 CTGTCAA-TAGGAGATTTGGGG
1 CTGTCAATTAGG-GATTTGGGG
53674949 CTGTCAATTAGGGATTTGG
1 CTGTCAATTAGGGATTTGG
53674968 AGATAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.23, C:0.10, G:0.35, T:0.33
Consensus pattern (21 bp):
CTGTCAATTAGGGATTTGGGG
Found at i:53679816 original size:18 final size:18
Alignment explanation
Indices: 53679793--53679828 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
53679783 AACTTCCACG
*
53679793 AATGAAAAAGATTAAAAT
1 AATGAAAAACATTAAAAT
53679811 AATGAAAAACATTAAAAT
1 AATGAAAAACATTAAAAT
53679829 TATTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.67, C:0.03, G:0.08, T:0.22
Consensus pattern (18 bp):
AATGAAAAACATTAAAAT
Found at i:53681725 original size:13 final size:13
Alignment explanation
Indices: 53681709--53681733 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53681699 TATAGTGAAA
53681709 AAGTATTTTTGAT
1 AAGTATTTTTGAT
53681722 AAGTATTTTTGA
1 AAGTATTTTTGA
53681734 AAATTGCTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (13 bp):
AAGTATTTTTGAT
Found at i:53682035 original size:14 final size:14
Alignment explanation
Indices: 53682016--53682042 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53682006 TTTAAATATA
53682016 ATAATTAGATATTT
1 ATAATTAGATATTT
53682030 ATAATTAGATATT
1 ATAATTAGATATT
53682043 GACACAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
ATAATTAGATATTT
Found at i:53682620 original size:32 final size:33
Alignment explanation
Indices: 53682584--53682646 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
53682574 ATTTTTTTAA
* * *
53682584 TATTATTTTCTTATTATTTTTCT-TTATTTTGC
1 TATTATTTTATTATTATATTACTATTATTTTGC
53682616 TATTATTTTATTATTATATTACTATTATTTT
1 TATTATTTTATTATTATATTACTATTATTTT
53682647 ATTGTTATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 20 0.74
33 7 0.26
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.70
Consensus pattern (33 bp):
TATTATTTTATTATTATATTACTATTATTTTGC
Found at i:53682654 original size:11 final size:11
Alignment explanation
Indices: 53682578--53682655 Score: 70
Period size: 11 Copynumber: 7.2 Consensus size: 11
53682568 TGACAAATTT
*
53682578 TTTTAATATTA
1 TTTTATTATTA
*
53682589 TTTTCTTATTA
1 TTTTATTATTA
53682600 TTTT-TCT-TTA
1 TTTTAT-TATTA
**
53682610 TTTTGCTATTA
1 TTTTATTATTA
53682621 TTTTATTATTA
1 TTTTATTATTA
* *
53682632 TATTACTATTA
1 TTTTATTATTA
*
53682643 TTTTATTGTTA
1 TTTTATTATTA
53682654 TT
1 TT
53682656 GTTTGGATAT
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
10 9 0.17
11 45 0.83
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:53682720 original size:30 final size:30
Alignment explanation
Indices: 53682684--53682745 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
53682674 ATTTATTTTA
53682684 TTATTAATTTTGTTATTATTTTAAAGATAT
1 TTATTAATTTTGTTATTATTTTAAAGATAT
* *
53682714 TTATTAATTTTGTTATTATTTTAGAGGTAT
1 TTATTAATTTTGTTATTATTTTAAAGATAT
53682744 TT
1 TT
53682746 GCTTGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (30 bp):
TTATTAATTTTGTTATTATTTTAAAGATAT
Found at i:53693793 original size:32 final size:32
Alignment explanation
Indices: 53693752--53693818 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
53693742 TCATGATCTG
53693752 TCAACCAATCCATACCCAATATAACATCAAAT
1 TCAACCAATCCATACCCAATATAACATCAAAT
53693784 TCAACCAATCCATACCCAATATAACATCAAAT
1 TCAACCAATCCATACCCAATATAACATCAAAT
53693816 TCA
1 TCA
53693819 TCAAACGGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.22
Consensus pattern (32 bp):
TCAACCAATCCATACCCAATATAACATCAAAT
Found at i:53697729 original size:21 final size:21
Alignment explanation
Indices: 53697702--53697756 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
53697692 TTGCGTGGCG
**
53697702 CAACACGTGATGTGTGTAGCA
1 CAACACGAAATGTGTGTAGCA
*
53697723 TAACACGAAATGTGTGTAGCA
1 CAACACGAAATGTGTGTAGCA
*
53697744 CAACACGCAATGT
1 CAACACGAAATGT
53697757 CTATGTTGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.22
Consensus pattern (21 bp):
CAACACGAAATGTGTGTAGCA
Found at i:53698837 original size:68 final size:67
Alignment explanation
Indices: 53698765--53698940 Score: 173
Period size: 68 Copynumber: 2.6 Consensus size: 67
53698755 CATCATGTGT
** * * *
53698765 ACAAGAGAGCTACGAGATACTATGTAGTAGCTAGGTCACATGTGTGAT-ACGGGATGTATC-CCA
1 ACAAGAGAGCTACGAGATA-TAAAT-GTAGCTAGGTCACATGTGTGATCAAGGGAAGGA-CACCA
53698828 TGTAG
63 TGTAG
* * *
53698833 ACAAGAGAGCTACGGGAGAGATAAATGTAGCTAGGTCGCATGTGTGATCCCAAGTGAAGGACACC
1 ACAAGAGAGCTAC--GAGATATAAATGTAGCTAGGTCACATGTGTGAT--CAAGGGAAGGACACC
53698898 ATGTAG
62 ATGTAG
*
53698904 ACAAGAGAGCTACGAG--ATAAAT-TGGCTAGGTCACATG
1 ACAAGAGAGCTACGAGATATAAATGTAGCTAGGTCACATG
53698941 GGTGGTACTA
Statistics
Matches: 92, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
66 13 0.14
67 6 0.07
68 34 0.37
69 6 0.07
70 6 0.07
71 27 0.29
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGAGATATAAATGTAGCTAGGTCACATGTGTGATCAAGGGAAGGACACCATGT
AG
Found at i:53700854 original size:14 final size:13
Alignment explanation
Indices: 53700830--53700869 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 13
53700820 AGGAAAGTCC
53700830 ATTAGGTTAATTTA
1 ATTA-GTTAATTTA
53700844 AGTTAGTTAATTTA
1 A-TTAGTTAATTTA
53700858 ATTAGTTTAATT
1 ATTAG-TTAATT
53700870 AAAATATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.17
14 17 0.71
15 3 0.12
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (13 bp):
ATTAGTTAATTTA
Found at i:53706085 original size:27 final size:27
Alignment explanation
Indices: 53706011--53706140 Score: 118
Period size: 27 Copynumber: 4.8 Consensus size: 27
53706001 ATTCAAAGTT
* *
53706011 CGCCACAAAGGCTATTCTTTCATATTA
1 CGCCATAAAGGCTTTTCTTTCATATTA
* * * * *
53706038 TGCCCATAGA-GATGTTCCTTTCAAATTA
1 CG-CCATAAAGGCT-TTTCTTTCATATTA
* * *
53706066 CACCATAAAGGCTTTTCTTTCCTTTTA
1 CGCCATAAAGGCTTTTCTTTCATATTA
*
53706093 TGCCATAAAGGCTTTTCTTTCATATTA
1 CGCCATAAAGGCTTTTCTTTCATATTA
* *
53706120 CGCCACAAAGGATTTTCTTTC
1 CGCCATAAAGGCTTTTCTTTC
53706141 CTGACGTATT
Statistics
Matches: 78, Mismatches: 22, Indels: 6
0.74 0.21 0.06
Matches are distributed among these distances:
27 60 0.77
28 18 0.23
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (27 bp):
CGCCATAAAGGCTTTTCTTTCATATTA
Found at i:53706130 original size:54 final size:55
Alignment explanation
Indices: 53706002--53706142 Score: 153
Period size: 54 Copynumber: 2.6 Consensus size: 55
53705992 AGGTGATCCA
* * *
53706002 TTCAAAGTT-CGCCACAAAGGCTATTCTTTCATATTATGCCCATAGAGATGTTCCT
1 TTCAAA-TTACGCCACAAAGGCTTTTCTTTCCTATTATGCCCATAAAGATGTTCCT
* * * * *
53706057 TTCAAATTACACCATAAAGGCTTTTCTTTCCTTTTATG-CCATAAAGGCT-TTTCT
1 TTCAAATTACGCCACAAAGGCTTTTCTTTCCTATTATGCCCATAAA-GATGTTCCT
* *
53706111 TTCATATTACGCCACAAAGGATTTTCTTTCCT
1 TTCAAATTACGCCACAAAGGCTTTTCTTTCCT
53706143 GACGTATTTA
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
54 40 0.56
55 32 0.44
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.39
Consensus pattern (55 bp):
TTCAAATTACGCCACAAAGGCTTTTCTTTCCTATTATGCCCATAAAGATGTTCCT
Found at i:53707228 original size:13 final size:13
Alignment explanation
Indices: 53707205--53707240 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
53707195 CTATTTCAAA
*
53707205 ATATTTTTTAAAG
1 ATATGTTTTAAAG
*
53707218 TTATGTTTTAAAG
1 ATATGTTTTAAAG
53707231 ATATGTTTTA
1 ATATGTTTTA
53707241 TGCGTTCTCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (13 bp):
ATATGTTTTAAAG
Found at i:53710124 original size:93 final size:93
Alignment explanation
Indices: 53710010--53710181 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
53710000 CGCCCATAAG
* *
53710010 CGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
53710075 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
53710103 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
53710168 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
53710182 TCAAACATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:53710178 original size:46 final size:46
Alignment explanation
Indices: 53710003--53710178 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
53709993 TGTAACCCGC
* * * *
53710003 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
53710049 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
53710099 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
53710142 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
53710179 TGCTCAAACA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 62 0.56
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:53711739 original size:48 final size:47
Alignment explanation
Indices: 53711593--53711853 Score: 185
Period size: 48 Copynumber: 5.4 Consensus size: 47
53711583 GGTGCTAGTG
* *
53711593 TAAGACATGTCTGGGACATGCATC-AGCCAT-A-G-TATGAGAGCTAGTA
1 TAAGACATGTCTGGGACATGCATCGA-CC-TCACGATAT-AAAGCCAGTA
* * *
53711639 TAAGACATGTCTGGGACATGCATCGACCTTGAC-ATATTTAAGCCA-AA
1 TAAGACATGTCTGGGACATGCATCGACC-TCACGATA-TAAAGCCAGTA
* *
53711686 GTAAGACATGTTTGGGACATGCATCGACCTCACGATATACAAGCTAGTA
1 -TAAGACATGTCTGGGACATGCATCGACCTCACGATATA-AAGCCAGTA
* * * * * * *
53711735 TAAGACCTGTCTAGGACATGGCATCGACACTGATAGAT-GAGAGCCAGTG
1 TAAGACATGTCTGGGACAT-GCATCGAC-CTCA-CGATATAAAGCCAGTA
* * * * *
53711784 TAAGACCTGTTTGGGACATGGCATCGGCCTCTCTATATGAAAGCCAGTA
1 TAAGACATGTCTGGGACAT-GCATCGACCTCACGATAT-AAAGCCAGTA
53711833 TAAGACCATGTCTGGGACATG
1 TAAGA-CATGTCTGGGACATG
53711854 GCGTCGGCAT
Statistics
Matches: 169, Mismatches: 31, Indels: 27
0.74 0.14 0.12
Matches are distributed among these distances:
46 27 0.16
47 9 0.05
48 59 0.35
49 55 0.33
50 16 0.09
51 3 0.02
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (47 bp):
TAAGACATGTCTGGGACATGCATCGACCTCACGATATAAAGCCAGTA
Found at i:53711788 original size:49 final size:49
Alignment explanation
Indices: 53711593--53711855 Score: 188
Period size: 49 Copynumber: 5.4 Consensus size: 49
53711583 GGTGCTAGTG
* * * *
53711593 TAAGACATGTCTGGGACAT-GCATC-AGC-C-ATAGTATGAGAGCTAGTA
1 TAAGACCTGTCTGGGACATGGCATCGACCTCGATAG-ATGAAAGCCAGTA
* * * * ** *
53711639 TAAGACATGTCTGGGACAT-GCATCGACCTTGACATATTTAAGCCA-AA
1 TAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAAAGCCAGTA
* * *
53711686 GTAAGACATGTTTGGGACAT-GCATCGACCTCACGAT--AT-ACAAGCTAGTA
1 -TAAGACCTGTCTGGGACATGGCATCGACCT--CGATAGATGA-AAGCCAGTA
* * *
53711735 TAAGACCTGTCTAGGACATGGCATCGACACT-GATAGATGAGAGCCAGTG
1 TAAGACCTGTCTGGGACATGGCATCGAC-CTCGATAGATGAAAGCCAGTA
* * ** *
53711784 TAAGACCTGTTTGGGACATGGCATCGGCCTCTCTATATGAAAGCCAGTA
1 TAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAAAGCCAGTA
53711833 TAAGACCATGTCTGGGACATGGC
1 TAAGACC-TGTCTGGGACATGGC
53711856 GTCGGCATCT
Statistics
Matches: 172, Mismatches: 30, Indels: 26
0.75 0.13 0.11
Matches are distributed among these distances:
46 24 0.14
47 6 0.03
48 59 0.34
49 64 0.37
50 19 0.11
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.24
Consensus pattern (49 bp):
TAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAAAGCCAGTA
Found at i:53711796 original size:97 final size:98
Alignment explanation
Indices: 53711592--53711855 Score: 278
Period size: 97 Copynumber: 2.7 Consensus size: 98
53711582 GGGTGCTAGT
* * *
53711592 GTAAGACATGTCTGGGACAT-GCATC-AGCCAT-A-G-TATGAGAGCTAGTATAAGACATGTCTG
1 GTAAGACATGTTTGGGACATGGCATCGA-CC-TCACGATATGAAAGCTAGTATAAGACCTGTCTG
* *
53711652 GGACAT-GCATCGACCTTGACATATTTAAGCCAAA
64 GGACATGGCATCGACCTTGACAGATTGAAGCCAAA
*
53711686 GTAAGACATGTTTGGGACAT-GCATCGACCTCACGATAT-ACAAGCTAGTATAAGACCTGTCTAG
1 GTAAGACATGTTTGGGACATGGCATCGACCTCACGATATGA-AAGCTAGTATAAGACCTGTCTGG
* **
53711749 GACATGGCATCGACAC-TGATAGA-TGAGAGCCAGT
65 GACATGGCATCGAC-CTTGACAGATTGA-AGCCAAA
* * * * *
53711783 GTAAGACCTGTTTGGGACATGGCATCGGCCTCTCTATATGAAAGCCAGTATAAGACCATGTCTGG
1 GTAAGACATGTTTGGGACATGGCATCGACCTCACGATATGAAAGCTAGTATAAGACC-TGTCTGG
53711848 GACATGGC
65 GACATGGC
53711856 GTCGGCATCT
Statistics
Matches: 144, Mismatches: 15, Indels: 17
0.82 0.09 0.10
Matches are distributed among these distances:
93 1 0.01
94 27 0.19
95 3 0.02
96 30 0.21
97 37 0.26
98 31 0.22
99 15 0.10
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (98 bp):
GTAAGACATGTTTGGGACATGGCATCGACCTCACGATATGAAAGCTAGTATAAGACCTGTCTGGG
ACATGGCATCGACCTTGACAGATTGAAGCCAAA
Found at i:53731361 original size:165 final size:165
Alignment explanation
Indices: 53731089--53731418 Score: 651
Period size: 165 Copynumber: 2.0 Consensus size: 165
53731079 TGGTATTTTT
53731089 TGACGATATACTTGTCTATTCCAACAGCTAGACTGAACATTTACAAGAGGTGTTGCAACTTTTGA
1 TGACGATATACTTGTCTATTCCAACAGCTAGACTGAACATTTACAAGAGGTGTTGCAACTTTTGA
*
53731154 GGGACAACCATTTGTTTGTCAAGCAAAGTATTTGGGGGATGTTATAGCTGCAGGAGAGGTGACGA
66 GGGAAAACCATTTGTTTGTCAAGCAAAGTATTTGGGGGATGTTATAGCTGCAGGAGAGGTGACGA
53731219 TGGATGCCGCAAAGGTAGAAAGGGTTTCAAATTGG
131 TGGATGCCGCAAAGGTAGAAAGGGTTTCAAATTGG
53731254 TGACGATATACTTGTCTATTCCAACAGCTAGACTGAACATTTACAAGAGGTGTTGCAACTTTTGA
1 TGACGATATACTTGTCTATTCCAACAGCTAGACTGAACATTTACAAGAGGTGTTGCAACTTTTGA
53731319 GGGAAAACCATTTGTTTGTCAAGCAAAGTATTTGGGGGATGTTATAGCTGCAGGAGAGGTGACGA
66 GGGAAAACCATTTGTTTGTCAAGCAAAGTATTTGGGGGATGTTATAGCTGCAGGAGAGGTGACGA
53731384 TGGATGCCGCAAAGGTAGAAAGGGTTTCAAATTGG
131 TGGATGCCGCAAAGGTAGAAAGGGTTTCAAATTGG
53731419 CCCACCCCCA
Statistics
Matches: 164, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
165 164 1.00
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (165 bp):
TGACGATATACTTGTCTATTCCAACAGCTAGACTGAACATTTACAAGAGGTGTTGCAACTTTTGA
GGGAAAACCATTTGTTTGTCAAGCAAAGTATTTGGGGGATGTTATAGCTGCAGGAGAGGTGACGA
TGGATGCCGCAAAGGTAGAAAGGGTTTCAAATTGG
Found at i:53740562 original size:20 final size:19
Alignment explanation
Indices: 53740539--53740586 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
53740529 TCCAAAAAGA
53740539 ATCGATACC-TATCAATTTTT
1 ATCGATACCTTAT--ATTTTT
* *
53740559 ATCGATGCCTTATTTTTTT
1 ATCGATACCTTATATTTTT
53740578 ATCGATACC
1 ATCGATACC
53740587 CAAGTTGCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 13 0.54
20 8 0.33
21 3 0.12
ACGTcount: A:0.25, C:0.21, G:0.08, T:0.46
Consensus pattern (19 bp):
ATCGATACCTTATATTTTT
Found at i:53744558 original size:26 final size:27
Alignment explanation
Indices: 53744529--53744583 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 27
53744519 ATAACACATG
53744529 CCCATGG-GACACACACCCGTGTGTCA
1 CCCATGGCGACACACACCCGTGTGTCA
53744555 CCCATGGCCTAGACACACACCCGTGTGTC
1 CCCATGG-C--GACACACACCCGTGTGTC
53744584 TTACCCGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 7 0.28
30 18 0.72
ACGTcount: A:0.22, C:0.40, G:0.22, T:0.16
Consensus pattern (27 bp):
CCCATGGCGACACACACCCGTGTGTCA
Found at i:53745408 original size:47 final size:45
Alignment explanation
Indices: 53745304--53745613 Score: 198
Period size: 47 Copynumber: 6.7 Consensus size: 45
53745294 TACGCGTACT
* * *
53745304 GATGCATGTCCCAGACATGTCTTACACTAGCACAACTCTT-A-GCC
1 GATGCATGTCCCAGACATGTCTTACACTGGC-TATCTCTTGAGGCC
* *
53745348 GATGCGTGTCCCAGACACGTCTTACACTGGCTATCTCTTTCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCTATCTC-TT-GAGGCC
* * *
53745395 GATGCATGTCCCAGACATGTCTTACACTTGC-AGTCATCTCTG-TGTC
1 GATGCATGTCCCAGACATGTCTTACACTGGCTA-TC-TCT-TGAGGCC
* * * *
53745441 GATACCATGTCCCAGACATGCTCTTACACTGGCTATC-ATAGTATGGCT
1 GAT-GCATGTCCCAGACATG-TCTTACACTGGCTATCTCTTG-A-GGCC
* ** * ****
53745489 GATGCATGTCCCAGACATGTCTTACACTAGCCCTCGTCTGGATATT
1 GATGCATGTCCCAGACATGTCTTACACTGGCTATC-TCTTGAGGCC
* * * ** *
53745535 GATGCCATGCCCCAGACATAGTCTTACACTAGCTCTCATAATGTGGCC
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTATC-TCTTGAGGCC
* * *
53745583 GAAGCATGTCCCAAACACGTCTTACACTGGC
1 GATGCATGTCCCAGACATGTCTTACACTGGC
53745614 GCACAAATCA
Statistics
Matches: 207, Mismatches: 42, Indels: 32
0.74 0.15 0.11
Matches are distributed among these distances:
43 4 0.02
44 30 0.14
45 1 0.00
46 38 0.18
47 90 0.43
48 43 0.21
49 1 0.00
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.27
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTATCTCTTGAGGCC
Found at i:53745505 original size:94 final size:91
Alignment explanation
Indices: 53745253--53745610 Score: 314
Period size: 94 Copynumber: 3.8 Consensus size: 91
53745243 GATATATTGC
* * * * *
53745253 CGATGCCATGTCCCAGACATGGTCTTACACCGGCTCTTATATACGCGTACTGATGCATGTCCCAG
1 CGATGCCATGTCCCAGACAT-GTCTTACACTGGCTATCATATATG-G--CCGATGCATGTCCCAG
* *
53745318 ACATGTCTTACACTAGCA-CAACTCT-TAGC
62 ACATGTCTTACACTAGCATCATCTCTGT-GT
* * * *
53745347 CGATG-CGTGTCCCAGACACGTCTTACACTGGCTATC-TCTTTCGAGGCCGATGCATGTCCCAGA
1 CGATGCCATGTCCCAGACATGTCTTACACTGGCTATCATATAT---GGCCGATGCATGTCCCAGA
*
53745410 CATGTCTTACACTTGCAGTCATCTCTGTGT
63 CATGTCTTACACTAGCA-TCATCTCTGTGT
* *
53745440 CGATACCATGTCCCAGACATGCTCTTACACTGGCTATCATAGTATGGCTGATGCATGTCCCAGAC
1 CGATGCCATGTCCCAGACATG-TCTTACACTGGCTATCATA-TATGGCCGATGCATGTCCCAGAC
* *
53745505 ATGTCTTACACTAGC--CCTCGTCTGGATAT
64 ATGTCTTACACTAGCATCATC-TCT-G-TGT
* * * * * * *
53745534 TGATGCCATGCCCCAGACATAGTCTTACACTAGCTCTCATAATGTGGCCGAAGCATGTCCCAAAC
1 CGATGCCATGTCCCAGACAT-GTCTTACACTGGCTATCAT-ATATGGCCGATGCATGTCCCAGAC
*
53745599 ACGTCTTACACT
64 ATGTCTTACACT
53745611 GGCGCACAAA
Statistics
Matches: 218, Mismatches: 31, Indels: 30
0.78 0.11 0.11
Matches are distributed among these distances:
91 37 0.17
92 17 0.08
93 25 0.11
94 118 0.54
95 18 0.08
96 1 0.00
97 2 0.01
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (91 bp):
CGATGCCATGTCCCAGACATGTCTTACACTGGCTATCATATATGGCCGATGCATGTCCCAGACAT
GTCTTACACTAGCATCATCTCTGTGT
Found at i:53752479 original size:44 final size:45
Alignment explanation
Indices: 53752372--53752733 Score: 227
Period size: 47 Copynumber: 7.8 Consensus size: 45
53752362 GGGATATATT
* * * **
53752372 GCCGATGCCATGCCCCAGACATGGTCTTACACTGGCTCTCATATACGCA
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGC-ATCATCT-CTTA
* * *
53752421 TGCTGATGCATGTCCCAGACATGTCTTACACTAGCA-CAACTCTTA
1 -GCCGATGCATGTCCCAGACATGTCTTACACTGGCATCATCTCTTA
* * *
53752466 GCCGATGCGTGTCCCAGACACGTCTTACACTGGCTATC-TCTGTTGA
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGC-ATCATCTCTT-A
*
53752512 GGCCAATGCATGTCCCAGACATGTCTTACACTGGCACTCATCTCTGT-
1 -GCCGATGCATGTCCCAGACATGTCTTACACTGGCA-TCATCTCT-TA
* * *
53752559 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAGT-ATG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGC-ATCAT-CTCTTA
* * ** * * *
53752607 GCTGATGTATGTCCCAGACATGTCTTACACTATC-CCTTGTCTGGGT-
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCATCATCTCT---TA
* * * *
53752653 GCCGATCCATGCCCCAGACATAGTCTTACACTGG-ATC-TCATAATATG
1 GCCGATGCATGTCCCAGACAT-GTCTTACACTGGCATCATC-T-CT-TA
* *
53752700 GCCGAAGCATGTCCCAGACACGTCTTACACTGGC
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGC
53752734 GCACAAATCA
Statistics
Matches: 248, Mismatches: 42, Indels: 47
0.74 0.12 0.14
Matches are distributed among these distances:
43 2 0.01
44 32 0.13
45 7 0.03
46 54 0.22
47 91 0.37
48 40 0.16
49 16 0.06
50 6 0.02
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.27
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCATCATCTCTTA
Found at i:53752694 original size:93 final size:92
Alignment explanation
Indices: 53752371--53752730 Score: 342
Period size: 93 Copynumber: 3.9 Consensus size: 92
53752361 TGGGATATAT
* * *
53752371 TGCCGATGCCATGCCCCAGACATGGTCTTACACTGGCTCTCATA-TACGCATGCTGATGCATGTC
1 TGCCGATGCCATGCCCCAGACATGGTCTTACACTGGATCTCATAGTATG---GCCGATGCATGTC
53752435 CCAGACATGTCTTACACTAGCAC-AACTCT-
63 CCAGACATGTCTTACACTAGCACTAA-TCTG
* * * *
53752464 TAGCCGATG-CGTGTCCCAGACA-CGTCTTACACTGGCTATCTC-T-GT-TGAGGCCAATGCATG
1 T-GCCGATGCCATGCCCCAGACATGGTCTTACACTGG--ATCTCATAGTAT--GGCCGATGCATG
* *
53752524 TCCCAGACATGTCTTACACTGGCACTCATCTCTG
61 TCCCAGACATGTCTTACACTAGCACT-A-ATCTG
* * * * *
53752558 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAGTATGGCTGATGTATGTCCCA
1 TGCCGATGCCATGCCCCAGACATGGTCTTACACTGGATCTCATAGTATGGCCGATGCATGTCCCA
* * **
53752623 GACATGTCTTACACTATCCCTTGTCTGGG
66 GACATGTCTTACACTAGCACTAATCT--G
* * *
53752652 TGCCGAT-CCATGCCCCAGACATAGTCTTACACTGGATCTCATAATATGGCCGAAGCATGTCCCA
1 TGCCGATGCCATGCCCCAGACATGGTCTTACACTGGATCTCATAGTATGGCCGATGCATGTCCCA
*
53752716 GACACGTCTTACACT
66 GACATGTCTTACACT
53752731 GGCGCACAAA
Statistics
Matches: 220, Mismatches: 30, Indels: 34
0.77 0.11 0.12
Matches are distributed among these distances:
91 33 0.15
92 15 0.07
93 91 0.41
94 66 0.30
95 14 0.06
96 1 0.00
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (92 bp):
TGCCGATGCCATGCCCCAGACATGGTCTTACACTGGATCTCATAGTATGGCCGATGCATGTCCCA
GACATGTCTTACACTAGCACTAATCTG
Found at i:53752712 original size:187 final size:184
Alignment explanation
Indices: 53752371--53752733 Score: 448
Period size: 187 Copynumber: 1.9 Consensus size: 184
53752361 TGGGATATAT
*
53752371 TGCCGATGCCATGCCCCAGACATGGTCTTACACTGGCTCTCATATACGCATGCTGATGCATGTCC
1 TGCCGATGCCATGCCCCAGACATGGTCTTACACTGGCTATCATATACG-A-GCTGATGCATGTCC
* * * *
53752436 CAGACATGTCTTACACTAGCACAACTCTTAGCCGATGCGTGTCCCAGACACGTCTTACACTGGCT
64 CAGACATGTCTTACACTAGCACAACTCTTAGCCGATCCATGCCCCAGACAAGTCTTACACTGGC-
** *
53752501 ATCTCTGTTGAGGCCAATGCATGTCCCAGACATGTCTTACACTGGCACTCATCTCTG
128 ATCTCTAATGAGGCCAATGCATGTCCCAGACACGTCTTACACTGGCACTCATCTCTG
* * *
53752558 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAGTATG-GCTGATGTATGTCCC
1 TGCCGATGCCATGCCCCAGACATGGTCTTACACTGGCTATCATA-TACGAGCTGATGCATGTCCC
* * ***
53752622 AGACATGTCTTACACTATCCCTTGTCTGGGT-GCCGATCCATGCCCCAGACATAGTCTTACACTG
65 AGACATGTCTTACACTAGCACAACTCT---TAGCCGATCCATGCCCCAGACA-AGTCTTACACTG
53752686 G-ATCTCATAAT-ATGGCCGAA-GCATGTCCCAGACACGTCTTACACTGGC
126 GCATCTC-TAATGA-GGCC-AATGCATGTCCCAGACACGTCTTACACTGGC
53752734 GCACAAATCA
Statistics
Matches: 152, Mismatches: 16, Indels: 16
0.83 0.09 0.09
Matches are distributed among these distances:
185 36 0.24
186 6 0.04
187 92 0.61
188 18 0.12
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.27
Consensus pattern (184 bp):
TGCCGATGCCATGCCCCAGACATGGTCTTACACTGGCTATCATATACGAGCTGATGCATGTCCCA
GACATGTCTTACACTAGCACAACTCTTAGCCGATCCATGCCCCAGACAAGTCTTACACTGGCATC
TCTAATGAGGCCAATGCATGTCCCAGACACGTCTTACACTGGCACTCATCTCTG
Found at i:53755756 original size:13 final size:13
Alignment explanation
Indices: 53755720--53755756 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
53755710 TGATAGTTTG
*
53755720 GTATGAATTTATAT
1 GTATG-ATTTGTAT
53755734 GTATGATTTGTAT
1 GTATGATTTGTAT
53755747 GTATGATTTG
1 GTATGATTTG
53755757 CTAATTATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 17 0.77
14 5 0.23
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (13 bp):
GTATGATTTGTAT
Found at i:53758300 original size:28 final size:29
Alignment explanation
Indices: 53758268--53758322 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
53758258 CTAAAATATT
*
53758268 GATAT-CATGGCCCGAAGCGAAATCAGGC
1 GATATGCATGGCCCGAAGCCAAATCAGGC
53758296 GATATGCATGGCCCGAAGCCAAATCAG
1 GATATGCATGGCCCGAAGCCAAATCAG
53758323 TTTTTGTCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.33, C:0.25, G:0.27, T:0.15
Consensus pattern (29 bp):
GATATGCATGGCCCGAAGCCAAATCAGGC
Found at i:53761120 original size:53 final size:53
Alignment explanation
Indices: 53761063--53761199 Score: 204
Period size: 53 Copynumber: 2.6 Consensus size: 53
53761053 TGTATAACCA
*
53761063 TAACTGGTGGGTTATGGCATCATAT-TGAAAGAAGACCATATTGTGTAAGACCG
1 TAACTGGTGGGTTATGGCATCATATGGGAAA-AAGACCATATTGTGTAAGACCG
* * * *
53761116 TAACTAGTGGGTTATGGCATCATATGGGAAAAAGACTATATTGTGTCAGACTG
1 TAACTGGTGGGTTATGGCATCATATGGGAAAAAGACCATATTGTGTAAGACCG
*
53761169 TAACTGGTGGGTTATGGCATCATATAGGAAA
1 TAACTGGTGGGTTATGGCATCATATGGGAAA
53761200 TTTTAAGGAA
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
53 72 0.95
54 4 0.05
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (53 bp):
TAACTGGTGGGTTATGGCATCATATGGGAAAAAGACCATATTGTGTAAGACCG
Found at i:53762406 original size:16 final size:17
Alignment explanation
Indices: 53762377--53762442 Score: 55
Period size: 17 Copynumber: 3.6 Consensus size: 17
53762367 AACATTTAAG
53762377 CATAT-ATCACCATACT
1 CATATAATCACCATACT
53762393 CATATAATCA-CATAACATT
1 CATATAATCACCAT-AC--T
*
53762412 CAATCATATATCACCATAAT
1 C-AT-ATA-ATCACCATACT
53762432 CATATAATCAC
1 CATATAATCAC
53762443 ATAACACTCA
Statistics
Matches: 41, Mismatches: 1, Indels: 15
0.72 0.02 0.26
Matches are distributed among these distances:
16 8 0.20
17 11 0.27
18 3 0.07
19 4 0.10
20 4 0.10
21 3 0.07
22 5 0.12
23 3 0.07
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.30
Consensus pattern (17 bp):
CATATAATCACCATACT
Found at i:53762440 original size:8 final size:8
Alignment explanation
Indices: 53762354--53762486 Score: 57
Period size: 8 Copynumber: 17.0 Consensus size: 8
53762344 TCACATTACA
53762354 CATATAAT
1 CATATAAT
*
53762362 CACATAA-
1 CATATAAT
* *
53762369 CATTTAAG
1 CATATAAT
53762377 CATAT-AT
1 CATATAAT
* *
53762384 CACCATACT
1 CA-TATAAT
53762393 CATATAAT
1 CATATAAT
*
53762401 CACATAA-
1 CATATAAT
53762408 CAT-TCAAT
1 CATAT-AAT
53762416 CATAT-AT
1 CATATAAT
*
53762423 CACCATAAT
1 CA-TATAAT
53762432 CATATAAT
1 CATATAAT
*
53762440 CACATAA-
1 CATATAAT
* *
53762447 CACT-CAAG
1 CA-TATAAT
53762455 CATAT-AT
1 CATATAAT
*
53762462 CATAATACT
1 CAT-ATAAT
53762471 CATATAAT
1 CATATAAT
*
53762479 CACATAAT
1 CATATAAT
53762487 ATTCAAGCAT
Statistics
Matches: 91, Mismatches: 21, Indels: 26
0.66 0.15 0.19
Matches are distributed among these distances:
6 1 0.01
7 25 0.27
8 53 0.58
9 12 0.13
ACGTcount: A:0.46, C:0.23, G:0.02, T:0.30
Consensus pattern (8 bp):
CATATAAT
Found at i:53762471 original size:20 final size:20
Alignment explanation
Indices: 53762442--53762512 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
53762432 CATATAATCA
53762442 CATAACACTCAAGCATATAT
1 CATAACACTCAAGCATATAT
* *
53762462 CATAATACTC-A-TATA-AT
1 CATAACACTCAAGCATATAT
* *
53762479 CACATAATATTCAAGCATATAT
1 --CATAACACTCAAGCATATAT
*
53762501 CACAACACTCAA
1 CATAACACTCAA
53762513 AAACATGTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
17 2 0.05
18 3 0.08
19 10 0.26
20 19 0.49
21 3 0.08
22 2 0.05
ACGTcount: A:0.46, C:0.24, G:0.03, T:0.27
Consensus pattern (20 bp):
CATAACACTCAAGCATATAT
Found at i:53762511 original size:39 final size:39
Alignment explanation
Indices: 53762335--53762511 Score: 255
Period size: 39 Copynumber: 4.5 Consensus size: 39
53762325 ATTCACTCTT
* * *
53762335 AAGCATATATCACATTACACATATAATCACATAACATTT
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
*
53762374 AAGCATATATCACCATACTCATATAATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* * * *
53762413 AATCATATATCACCATAATCATATAATCACATAACACTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* *
53762452 AAGCATATATCATAATACTCATATAATCACATAATATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
*
53762491 AAGCATATATCACAACACTCA
1 AAGCATATATCACAATACTCA
53762512 AAAACATGTT
Statistics
Matches: 123, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 123 1.00
ACGTcount: A:0.46, C:0.23, G:0.02, T:0.29
Consensus pattern (39 bp):
AAGCATATATCACAATACTCATATAATCACATAACATTC
Found at i:53773919 original size:21 final size:20
Alignment explanation
Indices: 53773895--53773937 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
53773885 AAAATGATCA
* *
53773895 AAGAATAAAAGAAATTGAGAG
1 AAGAAAAAAAG-AATTGAAAG
53773916 AAGAAAAAAAGAATTGAAAG
1 AAGAAAAAAAGAATTGAAAG
53773936 AA
1 AA
53773938 AAGAGAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (20 bp):
AAGAAAAAAAGAATTGAAAG
Found at i:53773943 original size:29 final size:28
Alignment explanation
Indices: 53773894--53773951 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
53773884 GAAAATGATC
*
53773894 AAAGAATAAAAGAAATTGAGAGAAGAAAA
1 AAAGAATAAAAGAAATAGAGA-AAGAAAA
*
53773923 AAAGAATTGAAAGAAA-AGAGAAAGAAAA
1 AAAGAA-TAAAAGAAATAGAGAAAGAAAA
53773951 A
1 A
53773952 GAAAAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 8 0.31
29 10 0.38
30 8 0.31
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.09
Consensus pattern (28 bp):
AAAGAATAAAAGAAATAGAGAAAGAAAA
Found at i:53773996 original size:11 final size:11
Alignment explanation
Indices: 53773932--53773998 Score: 50
Period size: 12 Copynumber: 6.2 Consensus size: 11
53773922 AAAAGAATTG
*
53773932 AAAGAAAAGAG
1 AAAGAAAAGAA
53773943 AAAGAAAAAGAA
1 AAAG-AAAAGAA
*
53773955 AAAGAAATTGAA
1 AAAGAAA-AGAA
*
53773967 AAAG--AGGAA
1 AAAGAAAAGAA
* *
53773976 AATG-AGAGAA
1 AAAGAAAAGAA
53773986 AAAGAAAAGAA
1 AAAGAAAAGAA
53773997 AA
1 AA
53773999 TGTGAAAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
9 6 0.14
10 7 0.16
11 14 0.32
12 17 0.39
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.04
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:53775673 original size:40 final size:40
Alignment explanation
Indices: 53775619--53775794 Score: 316
Period size: 40 Copynumber: 4.4 Consensus size: 40
53775609 ATAGCAACTC
* * * *
53775619 GCACGAATGCCTTCGGGATTTAGCCCGGACATAGTCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
53775659 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
53775699 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
53775739 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
53775779 GCACAAATGCCTTCGG
1 GCACAAATGCCTTCGG
53775795 ATCGTAGTCC
Statistics
Matches: 132, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 132 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
Found at i:53791036 original size:40 final size:39
Alignment explanation
Indices: 53790952--53791136 Score: 203
Period size: 40 Copynumber: 4.6 Consensus size: 39
53790942 TTGAATGATG
* * * *
53790952 TCCGGGCTAAGTCTCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTC-CGAAGGCATTTGTGC-GAGTTACTAAA
* * *
53790992 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
53791032 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
* *
53791071 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
53791112 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
53791137 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
39 35 0.28
40 78 0.63
41 11 0.09
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:53791088 original size:79 final size:81
Alignment explanation
Indices: 53790952--53791136 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
53790942 TTGAATGATG
* * *
53790952 TCCGGGCTAAGTCTCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
53791016 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
53791031 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
53791093 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
53791111 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
53791137 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 56 0.62
80 33 0.37
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:53791158 original size:79 final size:79
Alignment explanation
Indices: 53791005--53791169 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
53790995 GGACTAAGAT
* * **
53791005 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
53791070 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
53791084 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
53791147 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
53791163 CCGAAGG
1 CCGAAGG
53791170 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:53796851 original size:50 final size:50
Alignment explanation
Indices: 53796751--53797021 Score: 328
Period size: 50 Copynumber: 5.6 Consensus size: 50
53796741 GAGTGCTAGC
* *
53796751 GTAAGACCATGTCTAGGACATGGCATCGA--T--AGA--TGAGAGCCAGT
1 GTAAGACCATGTCTGGGACATGGCATCGACCTCGATACGTGAGAGCCAGT
* *
53796795 GTAAGACCATGTATGGGACATGGCATCGACCTCGATATGTGAGAGCCAGT
1 GTAAGACCATGTCTGGGACATGGCATCGACCTCGATACGTGAGAGCCAGT
* * **
53796845 GTAAGACCATGTCTGGGACATGGCATCGGCCTTGATTTGTGAGAGCCAGT
1 GTAAGACCATGTCTGGGACATGGCATCGACCTCGATACGTGAGAGCCAGT
* *
53796895 GTAAGACCATGTCTGAGACATGGCATC-AGCCTCGATACGTGAGAGCTAGT
1 GTAAGACCATGTCTGGGACATGGCATCGA-CCTCGATACGTGAGAGCCAGT
* * * *
53796945 GTAAGACCATGTCTGGGACAAGGCATCG-GCTCGATACCTGAGAGTC-GAT
1 GTAAGACCATGTCTGGGACATGGCATCGACCTCGATACGTGAGAGCCAG-T
53796994 GTAAGACCATG-CTGGGACATGGCATCGA
1 GTAAGACCATGTCTGGGACATGGCATCGA
53797022 TATTAATGTA
Statistics
Matches: 197, Mismatches: 20, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
44 27 0.14
46 1 0.01
48 18 0.09
49 26 0.13
50 125 0.63
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGACATGGCATCGACCTCGATACGTGAGAGCCAGT
Found at i:53799386 original size:21 final size:21
Alignment explanation
Indices: 53799316--53799388 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
53799306 GATGGTATTT
**
53799316 TTGCTGATTAAGAGGACA-TTG
1 TTGCTGAAGAAGAGGA-AGTTG
53799337 TTGCTG-A-AA-AGGAAGTTG
1 TTGCTGAAGAAGAGGAAGTTG
* * *
53799355 CTACTGCAGAAGAGGAAGTTG
1 TTGCTGAAGAAGAGGAAGTTG
53799376 TTGCTGAAGAAGA
1 TTGCTGAAGAAGA
53799389 AGTTACTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
17 1 0.02
18 11 0.26
19 3 0.07
20 2 0.05
21 25 0.60
ACGTcount: A:0.33, C:0.10, G:0.32, T:0.26
Consensus pattern (21 bp):
TTGCTGAAGAAGAGGAAGTTG
Found at i:53799390 original size:18 final size:18
Alignment explanation
Indices: 53799334--53799392 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 18
53799324 TAAGAGGACA
53799334 TTGTTGCTGAA-AAGGAAG
1 TTGTTGCTGAAGAA-GAAG
* *
53799352 TTGCTACTGCAGAAGAGGAAG
1 TTG-T--TGCTGAAGAAGAAG
53799373 TTGTTGCTGAAGAAGAAG
1 TTGTTGCTGAAGAAGAAG
53799391 TT
1 TT
53799393 ACTAAAAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 17 0.52
19 1 0.03
20 1 0.03
21 13 0.39
22 1 0.03
ACGTcount: A:0.32, C:0.08, G:0.32, T:0.27
Consensus pattern (18 bp):
TTGTTGCTGAAGAAGAAG
Found at i:53799865 original size:17 final size:17
Alignment explanation
Indices: 53799843--53799876 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
53799833 AATAAGTATA
53799843 TATTGTCATTGCATTTT
1 TATTGTCATTGCATTTT
* *
53799860 TATTGTCCTTGCGTTTT
1 TATTGTCATTGCATTTT
53799877 CATGTTACTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.15, G:0.15, T:0.59
Consensus pattern (17 bp):
TATTGTCATTGCATTTT
Found at i:53803373 original size:28 final size:29
Alignment explanation
Indices: 53803319--53803373 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
53803309 ACAAGGGTTT
* *
53803319 TCACATGGCCAAGCACACGCTCGTGTCCC
1 TCACATGGCCAAGCACACGCCCATGTCCC
*
53803348 TCACATGGCCTAG-ACACGCCCATGTC
1 TCACATGGCCAAGCACACGCCCATGTC
53803374 ATTGCCCGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.22, C:0.40, G:0.20, T:0.18
Consensus pattern (29 bp):
TCACATGGCCAAGCACACGCCCATGTCCC
Found at i:53810512 original size:27 final size:28
Alignment explanation
Indices: 53810469--53810542 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 28
53810459 TGGCCCTTTT
* * *
53810469 AGGCCTAATCTCATTCATATGGCCTATC
1 AGGCCCAATCACATTCATATGGCCCATC
* *
53810497 -GGCCCAATCACTTTCATATGGCCCGTC
1 AGGCCCAATCACATTCATATGGCCCATC
53810524 AGGCCCAATCACATTCATA
1 AGGCCCAATCACATTCATA
53810543 GTCATGCAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 22 0.56
28 17 0.44
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.27
Consensus pattern (28 bp):
AGGCCCAATCACATTCATATGGCCCATC
Done.