Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 191 of 444
Found at i:53319839 original size:29 final size:29
Alignment explanation
Indices: 53319822--53319937 Score: 214
Period size: 29 Copynumber: 4.0 Consensus size: 29
53319812 CCCAGTGTCG
*
53319822 TATATTTCCAGCATGCACACTTAGTGCCA
1 TATATTTGCAGCATGCACACTTAGTGCCA
53319851 TATATTTGCAGCATGCACACTTAGTGCCA
1 TATATTTGCAGCATGCACACTTAGTGCCA
53319880 TATATTTGCAGCATGCACACTTAGTGCCA
1 TATATTTGCAGCATGCACACTTAGTGCCA
*
53319909 TATATTTTCAGCATGCACACTTAGTGCCA
1 TATATTTGCAGCATGCACACTTAGTGCCA
53319938 ATCTCGTCAC
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 85 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.32
Consensus pattern (29 bp):
TATATTTGCAGCATGCACACTTAGTGCCA
Found at i:53319840 original size:58 final size:58
Alignment explanation
Indices: 53319778--53319937 Score: 171
Period size: 58 Copynumber: 2.8 Consensus size: 58
53319768 TTTTAAACCC
* * *
53319778 GCACACTTAGTGCCATACCCTTCG-AGC-TCGCACACCCAGTGTCGTATATTTCCAGCAT
1 GCACACTTAGTGCCATA-CATTCGCAGCAT-GCACACCCAGTGCCATATATTTCCAGCAT
* * ** *
53319836 GCACACTTAGTGCCATATATTTGCAGCATGCACACTTAGTGCCATATATTTGCAGCAT
1 GCACACTTAGTGCCATACATTCGCAGCATGCACACCCAGTGCCATATATTTCCAGCAT
* ** **
53319894 GCACACTTAGTGCCATATATTTTCAGCATGCACACTTAGTGCCA
1 GCACACTTAGTGCCATACATTCGCAGCATGCACACCCAGTGCCA
53319938 ATCTCGTCAC
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
57 3 0.03
58 87 0.96
59 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (58 bp):
GCACACTTAGTGCCATACATTCGCAGCATGCACACCCAGTGCCATATATTTCCAGCAT
Found at i:53319869 original size:87 final size:87
Alignment explanation
Indices: 53319778--53319937 Score: 216
Period size: 87 Copynumber: 1.8 Consensus size: 87
53319768 TTTTAAACCC
* * *
53319778 GCACACTTAGTGCCATACCCTTCG-AGC-TCGCACACCCAGTGTCGTATATTTCCAGCATGCACA
1 GCACACTTAGTGCCATA-CATTCGCAGCAT-GCACACCCAGTGCCATATATTTCCAGCATGCACA
53319841 CTTAGTGCCATATATTTGCAGCAT
64 CTTAGTGCCATATATTTGCAGCAT
* * ** *
53319865 GCACACTTAGTGCCATATATTTGCAGCATGCACACTTAGTGCCATATATTTTCAGCATGCACACT
1 GCACACTTAGTGCCATACATTCGCAGCATGCACACCCAGTGCCATATATTTCCAGCATGCACACT
53319930 TAGTGCCA
66 TAGTGCCA
53319938 ATCTCGTCAC
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
86 3 0.05
87 59 0.94
88 1 0.02
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (87 bp):
GCACACTTAGTGCCATACATTCGCAGCATGCACACCCAGTGCCATATATTTCCAGCATGCACACT
TAGTGCCATATATTTGCAGCAT
Found at i:53323907 original size:27 final size:28
Alignment explanation
Indices: 53323850--53323919 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
53323840 AAATTTGTAC
**
53323850 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
*
53323878 AGCACTATGTGTGCG-AGCTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
53323905 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
53323920 GACTTATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 24 0.63
28 14 0.37
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:53323928 original size:27 final size:27
Alignment explanation
Indices: 53323850--53323931 Score: 103
Period size: 27 Copynumber: 3.0 Consensus size: 27
53323840 AAATTTGTAC
* *
53323850 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGGACTT-ATTATAT
* *
53323878 AGCACTATGTGTGC-GAGCTGATTATAT
1 AGCACTAAGTGTGCGGA-CTTATTATAT
53323905 AGCACTAAGTGTGCGGACTTATTATAT
1 AGCACTAAGTGTGCGGACTTATTATAT
53323932 GCTTTTGCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
27 30 0.65
28 16 0.35
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.34
Consensus pattern (27 bp):
AGCACTAAGTGTGCGGACTTATTATAT
Found at i:53336365 original size:39 final size:39
Alignment explanation
Indices: 53336321--53336524 Score: 180
Period size: 39 Copynumber: 5.2 Consensus size: 39
53336311 TCGGGATTTA
* * * *
53336321 CCGGATATAACCACTCGCACAAGGCTTTCGGGTCTTAGC
1 CCGGATATAGCCACTAGCACAATGCCTTCGGGTCTTAGC
* * * *
53336360 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAGCCACTAGCA-CAATGCCTTCGGGTCTTAGC
***
53336400 CCGGATATA-ATGCTAGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAGCCACTAGCAC-AATGCCTTCGGGTCTTAGC
* * *
53336439 CCGGATATAGCAACTCGC-CAAATGCCTTCGGATCTTAG-
1 CCGGATATAGCCACTAGCAC-AATGCCTTCGGGTCTTAGC
* * * * *
53336477 TCGGATATAGTCACTAGCATAAAAGCCTTCGGGACTTAGC
1 CCGGATATAGCCACTAGCA-CAATGCCTTCGGGTCTTAGC
53336517 CCGGATAT
1 CCGGATAT
53336525 CATTCGAATA
Statistics
Matches: 131, Mismatches: 28, Indels: 11
0.77 0.16 0.06
Matches are distributed among these distances:
38 14 0.11
39 82 0.63
40 35 0.27
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (39 bp):
CCGGATATAGCCACTAGCACAATGCCTTCGGGTCTTAGC
Found at i:53336494 original size:78 final size:79
Alignment explanation
Indices: 53336309--53336524 Score: 221
Period size: 78 Copynumber: 2.8 Consensus size: 79
53336299 ACCCAAGTAT
* * * * * *
53336309 CTTCGGGATTTA--CCGGATATAACCACTCGCAC-AAGGCTTTCGGGTCTTAGCCCGGATATGGT
1 CTTCGGGACTTAGCCCGGATATAA-TACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATATAGT
*
53336371 CACTAGCATAAATGC
65 CACTAGCACAAATGC
* *
53336386 CTTCGGGACTTAGCCCGGATATAATGCTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAG-C
1 CTTCGGGACTTAGCCCGGATATAATACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATATAGTC
*
53336450 AACTCGC-CAAATGC
66 -ACTAGCACAAATGC
* * * *
53336464 CTTC-GGATCTTAG-TCGGATATAGTCACTAGCATAAAAGCCTTCGGGACTTAGCCCGGATAT
1 CTTCGGGA-CTTAGCCCGGATATAAT-ACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATAT
53336525 CATTCGAATA
Statistics
Matches: 118, Mismatches: 15, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
77 23 0.19
78 54 0.46
79 41 0.35
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25
Consensus pattern (79 bp):
CTTCGGGACTTAGCCCGGATATAATACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATATAGTC
ACTAGCACAAATGC
Found at i:53339564 original size:8 final size:9
Alignment explanation
Indices: 53339545--53339610 Score: 55
Period size: 9 Copynumber: 7.2 Consensus size: 9
53339535 AATTTCTCCT
53339545 TTTTCTTTC
1 TTTTCTTTC
53339554 TTTTC-TTC
1 TTTTCTTTC
53339562 -TTTCTTTC
1 TTTTCTTTC
*
53339570 TTTCTATTTC
1 TTT-TCTTTC
*
53339580 GTTTCTTCTC
1 TTTTCTT-TC
53339590 TGTTTCTTTC
1 T-TTTCTTTC
* *
53339600 TCTTGTTTC
1 TTTTCTTTC
53339609 TT
1 TT
53339611 GTTTTTATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
7 4 0.09
8 6 0.13
9 17 0.38
10 12 0.27
11 6 0.13
ACGTcount: A:0.02, C:0.23, G:0.05, T:0.71
Consensus pattern (9 bp):
TTTTCTTTC
Found at i:53339579 original size:26 final size:26
Alignment explanation
Indices: 53339550--53339600 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
53339540 CTCCTTTTTC
* *
53339550 TTTCTTTTCTTCTTTCTTTCTTTCTA
1 TTTCGTTTCTTCTCTCTTTCTTTCTA
*
53339576 TTTCGTTTCTTCTCTGTTTCTTTCT
1 TTTCGTTTCTTCTCTCTTTCTTTCT
53339601 CTTGTTTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.02, C:0.24, G:0.04, T:0.71
Consensus pattern (26 bp):
TTTCGTTTCTTCTCTCTTTCTTTCTA
Found at i:53339584 original size:15 final size:15
Alignment explanation
Indices: 53339546--53339600 Score: 58
Period size: 16 Copynumber: 3.6 Consensus size: 15
53339536 ATTTCTCCTT
* *
53339546 TTTCTTTCTTTTCTTC
1 TTTCTTTCTTCTC-TA
53339562 TTTCTTTCTT-TCTA
1 TTTCTTTCTTCTCTA
*
53339576 TTTCGTTTCTTCTCTG
1 TTTC-TTTCTTCTCTA
53339592 TTTCTTTCT
1 TTTCTTTCT
53339601 CTTGTTTCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
14 5 0.14
15 13 0.37
16 17 0.49
ACGTcount: A:0.02, C:0.24, G:0.04, T:0.71
Consensus pattern (15 bp):
TTTCTTTCTTCTCTA
Found at i:53339645 original size:18 final size:17
Alignment explanation
Indices: 53339613--53339650 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
53339603 TGTTTCTTGT
53339613 TTTTATTTATTCTTT-A
1 TTTTATTTATTCTTTCA
53339629 TTTTATTTTATTTCTTTCA
1 TTTTA-TTTA-TTCTTTCA
53339648 TTT
1 TTT
53339651 ACTAAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.26
17 4 0.21
18 6 0.32
19 4 0.21
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTATTTATTCTTTCA
Found at i:53339787 original size:3 final size:3
Alignment explanation
Indices: 53339775--53339867 Score: 165
Period size: 3 Copynumber: 32.0 Consensus size: 3
53339765 CAATTAATTG
53339775 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
53339821 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
53339868 GTAAGTAAAT
Statistics
Matches: 87, Mismatches: 0, Indels: 6
0.94 0.00 0.06
Matches are distributed among these distances:
2 6 0.07
3 81 0.93
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:53340322 original size:104 final size:104
Alignment explanation
Indices: 53340142--53340344 Score: 397
Period size: 104 Copynumber: 2.0 Consensus size: 104
53340132 ACTTTTTTCT
*
53340142 AAATATTTACGAACTCATTTTCCTAAGACGGAAGCCCTAAACTCACTTTTTCGGTGCCCGTGAAA
1 AAATATTTACGAACTCATTTTCCTAAGACGGAAGCCCTAAACTCACTTTTCCGGTGCCCGTGAAA
53340207 GATGGGTCGTTACATTGTCACTTTCAAGATTGCTGAAAA
66 GATGGGTCGTTACATTGTCACTTTCAAGATTGCTGAAAA
53340246 AAATATTTACGAACTCATTTTCCTAAGACGGAAGCCCTAAACTCACTTTTCCGGTGCCCGTGAAA
1 AAATATTTACGAACTCATTTTCCTAAGACGGAAGCCCTAAACTCACTTTTCCGGTGCCCGTGAAA
53340311 GATGGGTCGTTACATTGTCACTTTCAAGATTGCT
66 GATGGGTCGTTACATTGTCACTTTCAAGATTGCT
53340345 TGTAAGTGTA
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 98 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (104 bp):
AAATATTTACGAACTCATTTTCCTAAGACGGAAGCCCTAAACTCACTTTTCCGGTGCCCGTGAAA
GATGGGTCGTTACATTGTCACTTTCAAGATTGCTGAAAA
Found at i:53341127 original size:42 final size:42
Alignment explanation
Indices: 53341082--53341232 Score: 135
Period size: 42 Copynumber: 3.6 Consensus size: 42
53341072 ATGAGTTTAT
* * * *
53341082 GTGTAAGACTATATCTGGGATATGACATCGTTATGAGATTTT
1 GTGTAAGACCATATCTGGGATATGGCATCGATATGAGATTTC
* * * *
53341124 GTGTAAGACCATGTCTGGGACATGGCATCAATATGAGA-ATC
1 GTGTAAGACCATATCTGGGATATGGCATCGATATGAGATTTC
* * * **
53341165 GTGTAAGACCATAGCT-GGACTGTTGGCATTGATATGAGATCCC
1 GTGTAAGACCATATCTGGGA-T-ATGGCATCGATATGAGATTTC
* *
53341208 ATGTAAGACTATATCTGGGATATGG
1 GTGTAAGACCATATCTGGGATATGG
53341233 TATTGGTGTG
Statistics
Matches: 85, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
40 3 0.04
41 15 0.18
42 49 0.58
43 15 0.18
44 3 0.04
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.30
Consensus pattern (42 bp):
GTGTAAGACCATATCTGGGATATGGCATCGATATGAGATTTC
Found at i:53343037 original size:26 final size:26
Alignment explanation
Indices: 53343001--53343053 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
53342991 TAACTACATG
53343001 TAAGACCATGTCTGGGACATGGGCAT
1 TAAGACCATGTCTGGGACATGGGCAT
*
53343027 TAAGACCATGTCTGGGACATTGGCAT
1 TAAGACCATGTCTGGGACATGGGCAT
53343053 T
1 T
53343054 GTCTTGTGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (26 bp):
TAAGACCATGTCTGGGACATGGGCAT
Found at i:53343075 original size:43 final size:42
Alignment explanation
Indices: 53343027--53343180 Score: 152
Period size: 43 Copynumber: 3.6 Consensus size: 42
53343017 ACATGGGCAT
*
53343027 TAAGACCATGTCTGGGACATTGGCATTGTCTTGTGATTATGTG
1 TAAGACCATGTCTGGGACATTGGCATCGT-TTGTGATTATGTG
* *
53343070 TAAGACCATGTCTGGGACATTGACATCGTATTATGATT-TCGTG
1 TAAGACCATGTCTGGGACATTGGCATCGT-TTGTGATTAT-GTG
* * * * **
53343113 TAAGACCCTGTCTGGGACAGTT-GCATCGATATGTGGTAACATG
1 TAAGACCATGTCTGGGACA-TTGGCATCG-TTTGTGATTATGTG
*
53343156 TAAGACCATATCTGGGACA-TGGCAT
1 TAAGACCATGTCTGGGACATTGGCAT
53343181 TGTAACAATT
Statistics
Matches: 92, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
41 1 0.01
42 5 0.05
43 83 0.90
44 3 0.03
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (42 bp):
TAAGACCATGTCTGGGACATTGGCATCGTTTGTGATTATGTG
Found at i:53344453 original size:2 final size:2
Alignment explanation
Indices: 53344446--53344489 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
53344436 CACATTCAGC
53344446 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53344488 TA
1 TA
53344490 AATGTATGCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53345076 original size:28 final size:28
Alignment explanation
Indices: 53345044--53345112 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
53345034 AATGAGATTG
*
53345044 GCACTAAGTGTGCGAGTTTAATT-GTATA
1 GCACTAAGTGTGCGAGTTTAATTATTA-A
*
53345072 GCACTAAGTGTGCGAGTTTGATTATTAA
1 GCACTAAGTGTGCGAGTTTAATTATTAA
53345100 GCACTAAGTGTGC
1 GCACTAAGTGTGC
53345113 AGACTTACTA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 36 0.95
29 2 0.05
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTATTAA
Found at i:53350916 original size:46 final size:46
Alignment explanation
Indices: 53350866--53351041 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
53350856 TGGTTGAGCA
53350866 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
53350912 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
53350957 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
53351005 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53351042 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:53351022 original size:93 final size:93
Alignment explanation
Indices: 53350863--53351034 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
53350853 GGATGGTTGA
* *
53350863 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
53350928 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
53350956 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
53351021 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
53351035 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:53358452 original size:46 final size:46
Alignment explanation
Indices: 53358402--53358577 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
53358392 TGGTTGAGCA
53358402 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
53358448 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
53358493 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
53358541 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53358578 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:53358558 original size:93 final size:93
Alignment explanation
Indices: 53358399--53358570 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
53358389 GGATGGTTGA
* *
53358399 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
53358464 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
53358492 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
53358557 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
53358571 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:53362453 original size:14 final size:15
Alignment explanation
Indices: 53362434--53362467 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
53362424 CACATCATCG
53362434 TTCTTCTC-TTCCTC
1 TTCTTCTCTTTCCTC
*
53362448 TTCTTCTCTTTCCTT
1 TTCTTCTCTTTCCTC
53362463 TTCTT
1 TTCTT
53362468 TAACTTGCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (15 bp):
TTCTTCTCTTTCCTC
Found at i:53363231 original size:23 final size:23
Alignment explanation
Indices: 53363192--53363246 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 23
53363182 ATCATAAATA
*
53363192 AAAAGATAGTAAAATATAGAAAAC
1 AAAAGA-ATTAAAATATAGAAAAC
53363216 AAAAGAATTAAAATATAGAAAAC
1 AAAAGAATTAAAATATAGAAAAC
53363239 AAAAGAAT
1 AAAAGAAT
53363247 CAACTTGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 24 0.80
24 6 0.20
ACGTcount: A:0.69, C:0.04, G:0.11, T:0.16
Consensus pattern (23 bp):
AAAAGAATTAAAATATAGAAAAC
Found at i:53372073 original size:26 final size:26
Alignment explanation
Indices: 53372022--53372073 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
53372012 AATGGTAATT
*
53372022 AAATGTTAAATTTATACACTGTTATG
1 AAATGTTAAATTTATACACTGCTATG
*
53372048 AAATGTTAGAATTTATATA-TGCTATG
1 AAATGTTA-AATTTATACACTGCTATG
53372074 GCCGAACATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.42
Consensus pattern (26 bp):
AAATGTTAAATTTATACACTGCTATG
Found at i:53378180 original size:18 final size:19
Alignment explanation
Indices: 53378140--53378181 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
53378130 TGCATGGAAA
** *
53378140 TATAAATTCATTAGGTATT
1 TATAAATTCATTAAATATG
53378159 TATAAATT-ATTAAATATG
1 TATAAATTCATTAAATATG
53378177 TATAA
1 TATAA
53378182 GTGAATTGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (19 bp):
TATAAATTCATTAAATATG
Found at i:53380679 original size:30 final size:30
Alignment explanation
Indices: 53380645--53380704 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
53380635 AGACCCTAGT
53380645 CATAATAGTGGTTTCGGGACCACAAAGCTG
1 CATAATAGTGGTTTCGGGACCACAAAGCTG
**
53380675 CATAATAGTGGTTTCGGGACCGTAAAGCTG
1 CATAATAGTGGTTTCGGGACCACAAAGCTG
53380705 AGTTAGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.25
Consensus pattern (30 bp):
CATAATAGTGGTTTCGGGACCACAAAGCTG
Found at i:53381862 original size:40 final size:40
Alignment explanation
Indices: 53381793--53381968 Score: 212
Period size: 40 Copynumber: 4.4 Consensus size: 40
53381783 GACTATGTTC
* * * *
53381793 GGCATTAAGTGTGTGATTTGAAATAGCTTCGGCTACAAGT
1 GGCACTAAGTGTGCGATTTGAAATAGCTTCAGCTATAAGT
*
53381833 GGCACTAAATGTGCGATTTGAAATAGCTTCAGCTATAAGT
1 GGCACTAAGTGTGCGATTTGAAATAGCTTCAGCTATAAGT
*
53381873 GGCACTAAGTGTGCGATTTG-AATAGCTTCGGCTATAAGT
1 GGCACTAAGTGTGCGATTTGAAATAGCTTCAGCTATAAGT
* * * * *
53381912 AGCACTAAGTGTGGGAATT-AGAATAGCTTCAGCTATATGA
1 GGCACTAAGTGTGCGATTTGA-AATAGCTTCAGCTATAAGT
* *
53381952 GGCACGAAGTATGCGAT
1 GGCACTAAGTGTGCGAT
53381969 ACCGAGATAG
Statistics
Matches: 116, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
39 34 0.29
40 82 0.71
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (40 bp):
GGCACTAAGTGTGCGATTTGAAATAGCTTCAGCTATAAGT
Found at i:53381937 original size:79 final size:80
Alignment explanation
Indices: 53381793--53381968 Score: 230
Period size: 79 Copynumber: 2.2 Consensus size: 80
53381783 GACTATGTTC
* * * *
53381793 GGCATTAAGTGTGTGATTTGAAATAGCTTCGGCTACAAGTGGCACTAAATGTGCGATTTGAAATA
1 GGCACTAAGTGTGCGATTTGAAATAGCTTCGGCTACAAGTAGCACTAAATGTGCGATTAGAAATA
*
53381858 GCTTCAGCTATAAGT
66 GCTTCAGCTATAAGA
* * *
53381873 GGCACTAAGTGTGCGATTTG-AATAGCTTCGGCTATAAGTAGCACTAAGTGTGGGAATTAG-AAT
1 GGCACTAAGTGTGCGATTTGAAATAGCTTCGGCTACAAGTAGCACTAAATGTGCG-ATTAGAAAT
*
53381936 AGCTTCAGCTATATGA
65 AGCTTCAGCTATAAGA
* *
53381952 GGCACGAAGTATGCGAT
1 GGCACTAAGTGTGCGAT
53381969 ACCGAGATAG
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
79 62 0.74
80 22 0.26
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (80 bp):
GGCACTAAGTGTGCGATTTGAAATAGCTTCGGCTACAAGTAGCACTAAATGTGCGATTAGAAATA
GCTTCAGCTATAAGA
Found at i:53385551 original size:43 final size:43
Alignment explanation
Indices: 53385489--53385711 Score: 324
Period size: 43 Copynumber: 5.2 Consensus size: 43
53385479 ACATTTTTGA
* *
53385489 GTTGGCATTGATATGTGATTACGTGTAAGACCACATCTGGGAC
1 GTTGGCATCGATATGTGATTACGTGTAAGACCACGTCTGGGAC
* **
53385532 GTTGGCATCGATATTTGATTACGTGTAAGACCACGTCTGGGTT
1 GTTGGCATCGATATGTGATTACGTGTAAGACCACGTCTGGGAC
*
53385575 GTTGGCATCGATATGTGATTACATGTAAGACCACGTCTGGGAC
1 GTTGGCATCGATATGTGATTACGTGTAAGACCACGTCTGGGAC
* *
53385618 GTTAGCATCGATATATGATTACGTGTAAGACC-CTGTCTGGGAC
1 GTTGGCATCGATATGTGATTACGTGTAAGACCAC-GTCTGGGAC
* *
53385661 AG-TGGCATCGATATGTGATTACATGTAAGACAACGTCTGGGAC
1 -GTTGGCATCGATATGTGATTACGTGTAAGACCACGTCTGGGAC
53385704 GTTGGCAT
1 GTTGGCAT
53385712 TATACAATAT
Statistics
Matches: 160, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
42 2 0.01
43 156 0.98
44 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (43 bp):
GTTGGCATCGATATGTGATTACGTGTAAGACCACGTCTGGGAC
Found at i:53386832 original size:2 final size:2
Alignment explanation
Indices: 53386825--53386858 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
53386815 TTGGTTAAAT
53386825 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53386859 AACTTGTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53388408 original size:38 final size:38
Alignment explanation
Indices: 53388349--53388456 Score: 189
Period size: 38 Copynumber: 2.8 Consensus size: 38
53388339 TCAATCATGC
*
53388349 ACTGGGCCGTAGCCCTTTTCATATTTCATATTTCATAAT
1 ACTGGGCCGAAG-CCTTTTCATATTTCATATTTCATAAT
*
53388388 ACTGGGCCGAAGCCTTTTCATGTTTCATATTTCATAAT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTCATAAT
53388426 ACTGGGCCGAAGCCTTTTCATATTTCATATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATT
53388457 ACTGGGCCGA
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
38 55 0.83
39 11 0.17
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.40
Consensus pattern (38 bp):
ACTGGGCCGAAGCCTTTTCATATTTCATATTTCATAAT
Found at i:53388414 original size:31 final size:31
Alignment explanation
Indices: 53388372--53388473 Score: 132
Period size: 31 Copynumber: 3.1 Consensus size: 31
53388362 CCTTTTCATA
53388372 TTTCATATTTCATAATACTGGGCCGAAGCCTTTTCAT
1 TTTCATATTTCATAATACTGGGCCGAAG-C----C-T
53388409 GTTTCATATTTCATAATACTGGGCCGAAGCCT
1 -TTTCATATTTCATAATACTGGGCCGAAGCCT
*
53388441 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
53388472 TT
1 TT
53388474 ACTGTAAACG
Statistics
Matches: 63, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
31 32 0.51
32 1 0.02
33 1 0.02
37 1 0.02
38 28 0.44
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAATACTGGGCCGAAGCCT
Found at i:53388765 original size:24 final size:24
Alignment explanation
Indices: 53388666--53388783 Score: 161
Period size: 23 Copynumber: 5.0 Consensus size: 24
53388656 GCTTTATCAT
* *
53388666 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTG
*
53388691 ATAACTGGGGCAAAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTG
53388714 ATAACTGGGGCATAAGCCC-TTTG
1 ATAACTGGGGCATAAGCCCTTTTG
*
53388737 ATAACTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
53388761 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
53388784 TCACTTCCTC
Statistics
Matches: 85, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
22 3 0.04
23 36 0.42
24 34 0.40
25 12 0.14
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTG
Found at i:53388781 original size:47 final size:46
Alignment explanation
Indices: 53388665--53388782 Score: 157
Period size: 47 Copynumber: 2.5 Consensus size: 46
53388655 TGCTTTATCA
* *
53388665 TATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTT
1 TATAACTGG-GGCATAAGCC-C-TTTGATAACTGGGGCAAAAGCCCTTT
**
53388713 TATAACTGGGGCATAAGCCCTTTGATAACTGGGGCGTAAGCCCTTT
1 TATAACTGGGGCATAAGCCCTTTGATAACTGGGGCAAAAGCCCTTT
53388759 TGATAACTGGGGCATAAGCCCTTT
1 T-ATAACTGGGGCATAAGCCCTTT
53388783 TTCACTTCCT
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
46 24 0.38
47 27 0.42
48 13 0.20
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (46 bp):
TATAACTGGGGCATAAGCCCTTTGATAACTGGGGCAAAAGCCCTTT
Found at i:53388854 original size:9 final size:9
Alignment explanation
Indices: 53388840--53388916 Score: 64
Period size: 9 Copynumber: 7.9 Consensus size: 9
53388830 ATCTCGTGTG
53388840 CATATCATA
1 CATATCATA
*
53388849 CATATCATGTG
1 CATATCA--TA
53388860 CATATCATA
1 CATATCATA
* *
53388869 CATGTCATGTG
1 CATATCA--TA
53388880 CATATCATA
1 CATATCATA
*
53388889 CATATCATGTG
1 CATATCA--TA
53388900 CATATCATA
1 CATATCATA
53388909 CATATCAT
1 CATATCAT
53388917 GTTTATCAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
9 31 0.57
11 23 0.43
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:53388859 original size:20 final size:20
Alignment explanation
Indices: 53388836--53388918 Score: 157
Period size: 20 Copynumber: 4.2 Consensus size: 20
53388826 GAACATCTCG
53388836 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
53388856 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
53388876 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
53388896 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
53388916 TGT
1 TGT
53388919 TTATCAAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:53388865 original size:11 final size:11
Alignment explanation
Indices: 53388836--53388907 Score: 66
Period size: 11 Copynumber: 7.1 Consensus size: 11
53388826 GAACATCTCG
53388836 TGTGCATATCA
1 TGTGCATATCA
*
53388847 --TACATATCA
1 TGTGCATATCA
53388856 TGTGCATATCA
1 TGTGCATATCA
* *
53388867 --TACATGTCA
1 TGTGCATATCA
53388876 TGTGCATATCA
1 TGTGCATATCA
*
53388887 --TACATATCA
1 TGTGCATATCA
53388896 TGTGCATATCA
1 TGTGCATATCA
53388907 T
1 T
53388908 ACATATCATG
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
9 23 0.49
11 24 0.51
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.36
Consensus pattern (11 bp):
TGTGCATATCA
Found at i:53396682 original size:25 final size:24
Alignment explanation
Indices: 53396563--53396681 Score: 147
Period size: 25 Copynumber: 5.0 Consensus size: 24
53396553 GCTTTATCAT
* *
53396563 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTG
*
53396588 ATAACTGGGGCAAAAGCCC-TTT-
1 ATAACTGGGGCATAAGCCCTTTTG
53396610 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
53396634 ATAAACT-GGGCATAAGCCCTTTTTG
1 AT-AACTGGGGCATAAGCCC-TTTTG
53396659 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
53396682 TCACTTCCTC
Statistics
Matches: 85, Mismatches: 3, Indels: 13
0.84 0.03 0.13
Matches are distributed among these distances:
22 18 0.21
23 6 0.07
24 26 0.31
25 35 0.41
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTG
Found at i:53396764 original size:11 final size:11
Alignment explanation
Indices: 53396748--53396806 Score: 63
Period size: 11 Copynumber: 5.7 Consensus size: 11
53396738 GTGCAACATA
53396748 CATATCATGTG
1 CATATCATGTG
*
53396759 CATATCA--TA
1 CATATCATGTG
*
53396768 CATGTCATGTG
1 CATATCATGTG
*
53396779 CATATCA--TA
1 CATATCATGTG
53396788 CATATCATGTG
1 CATATCATGTG
53396799 CATATCAT
1 CATATCAT
53396807 ACATATCATG
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 15 0.39
11 23 0.61
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
CATATCATGTG
Found at i:53396769 original size:20 final size:20
Alignment explanation
Indices: 53396744--53396817 Score: 139
Period size: 20 Copynumber: 3.7 Consensus size: 20
53396734 TCGTGTGCAA
53396744 CATACATATCATGTGCATAT
1 CATACATATCATGTGCATAT
*
53396764 CATACATGTCATGTGCATAT
1 CATACATATCATGTGCATAT
53396784 CATACATATCATGTGCATAT
1 CATACATATCATGTGCATAT
53396804 CATACATATCATGT
1 CATACATATCATGT
53396818 TTATCAAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (20 bp):
CATACATATCATGTGCATAT
Found at i:53396791 original size:9 final size:9
Alignment explanation
Indices: 53396744--53396815 Score: 54
Period size: 9 Copynumber: 7.3 Consensus size: 9
53396734 TCGTGTGCAA
53396744 CATACATAT
1 CATACATAT
*
53396753 CATGTGCATAT
1 CA--TACATAT
*
53396764 CATACATGT
1 CATACATAT
*
53396773 CATGTGCATAT
1 CA--TACATAT
53396784 CATACATAT
1 CATACATAT
*
53396793 CATGTGCATAT
1 CA--TACATAT
53396804 CATACATAT
1 CATACATAT
53396813 CAT
1 CAT
53396816 GTTTATCAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
9 26 0.53
11 23 0.47
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.35
Consensus pattern (9 bp):
CATACATAT
Found at i:53396879 original size:24 final size:24
Alignment explanation
Indices: 53396852--53396898 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
53396842 ATGTATAAAC
* * *
53396852 CCTAGGGGTATAATGGTCATTTTA
1 CCTAGGGGCAAAACGGTCATTTTA
*
53396876 CCTATGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
53396899 CATATTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (24 bp):
CCTAGGGGCAAAACGGTCATTTTA
Found at i:53401268 original size:24 final size:26
Alignment explanation
Indices: 53401231--53401280 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
53401221 TAATGAATGT
53401231 TTGAAATTG-TTTTTCATTAAAGTTA
1 TTGAAATTGTTTTTTCATTAAAGTTA
*
53401256 TTGAAA-TGTTTTTTCATTAAGGTTA
1 TTGAAATTGTTTTTTCATTAAAGTTA
53401281 AAATAGTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.52
Consensus pattern (26 bp):
TTGAAATTGTTTTTTCATTAAAGTTA
Found at i:53401793 original size:47 final size:48
Alignment explanation
Indices: 53401676--53401806 Score: 185
Period size: 47 Copynumber: 2.8 Consensus size: 48
53401666 GTGTGAGTTA
* * *
53401676 TACCTTGATTTGGCTACAGGACATGGTATAGGTATTTTGGAGAAGAGT
1 TACCTTGATTTGGCTACAGGCCATGGTATAGGTACTCTGGAGAAGAGT
*
53401724 TACCTTGATTTGGTTACAGGCCATGGTATAGGTACTCTGG-GATA-AGT
1 TACCTTGATTTGGCTACAGGCCATGGTATAGGTACTCTGGAGA-AGAGT
**
53401771 TACCTTGATTTGGCTATGGGCCATGGTATAGGTACT
1 TACCTTGATTTGGCTACAGGCCATGGTATAGGTACT
53401807 TATCGATTAA
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
47 38 0.51
48 37 0.49
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (48 bp):
TACCTTGATTTGGCTACAGGCCATGGTATAGGTACTCTGGAGAAGAGT
Found at i:53414026 original size:14 final size:15
Alignment explanation
Indices: 53413996--53414029 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
53413986 GTTAAAAAAT
*
53413996 ATATAAATATGATTC
1 ATATAAAAATGATTC
53414011 ATATAAAAAT-ATTC
1 ATATAAAAATGATTC
53414025 ATATA
1 ATATA
53414030 GTTTATCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (15 bp):
ATATAAAAATGATTC
Found at i:53416120 original size:41 final size:40
Alignment explanation
Indices: 53416066--53416250 Score: 135
Period size: 41 Copynumber: 4.6 Consensus size: 40
53416056 GGGTGTAAAT
** *
53416066 AGGGGCATGTATGTGCAATTCAGGAGTACCAAAGTACAAAT
1 AGGGGCACATATGTGCAATTCAGG-GTACCAAAGTACAAAC
* * * *
53416107 AAGGGCACATATGTGCAATTTAGCGGT----ATGAACAAAC
1 AGGGGCACATATGTGCAATTCAG-GGTACCAAAGTACAAAC
* * * * *
53416144 AGGGGCACGTACGTGCAATTTAGGGGTATCGAAGTACAAAC
1 AGGGGCACATATGTGCAATTCA-GGGTACCAAAGTACAAAC
* * *
53416185 AGGGGCACACATGTGCAATTCAAGGGTACCAAGGTACAAAT
1 AGGGGCACATATGTGCAATTC-AGGGTACCAAAGTACAAAC
* * * *
53416226 AGGGGCCCACATGTGAAATTAAGGG
1 AGGGGCACATATGTGCAATTCAGGG
53416251 AATAGTTAAC
Statistics
Matches: 114, Mismatches: 23, Indels: 15
0.75 0.15 0.10
Matches are distributed among these distances:
37 29 0.25
38 1 0.01
40 4 0.04
41 78 0.68
42 2 0.02
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.19
Consensus pattern (40 bp):
AGGGGCACATATGTGCAATTCAGGGTACCAAAGTACAAAC
Found at i:53416151 original size:37 final size:40
Alignment explanation
Indices: 53416109--53416204 Score: 126
Period size: 37 Copynumber: 2.5 Consensus size: 40
53416099 GTACAAATAA
53416109 GGGCACATATGTGCAATTTAGCGGTAT-G-A-ACAAACAG
1 GGGCACATATGTGCAATTTAGCGGTATCGAAGACAAACAG
* * *
53416146 GGGCACGTACGTGCAATTTAGGGGTATCGAAGTACAAACAG
1 GGGCACATATGTGCAATTTAGCGGTATCGAAG-ACAAACAG
*
53416187 GGGCACACATGTGCAATT
1 GGGCACATATGTGCAATT
53416205 CAAGGGTACC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
37 24 0.49
38 1 0.02
39 1 0.02
41 23 0.47
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (40 bp):
GGGCACATATGTGCAATTTAGCGGTATCGAAGACAAACAG
Found at i:53416777 original size:21 final size:21
Alignment explanation
Indices: 53416736--53416777 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
53416726 CTTATAAATT
* *
53416736 TACCATCAAAGACTCATAATC
1 TACCATCAAACACTCAGAATC
53416757 TACCATCAAACA-TCAAGAATC
1 TACCATCAAACACTC-AGAATC
53416778 ATGCAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.45, C:0.29, G:0.05, T:0.21
Consensus pattern (21 bp):
TACCATCAAACACTCAGAATC
Found at i:53422664 original size:29 final size:29
Alignment explanation
Indices: 53422621--53422703 Score: 139
Period size: 29 Copynumber: 2.9 Consensus size: 29
53422611 GCAAGAATAT
*
53422621 AATGTGACTTGGGCCTAATGGGCCACATA
1 AATGTGATTTGGGCCTAATGGGCCACATA
*
53422650 AATGTGATTTAGGCCTAATGGGCCACATA
1 AATGTGATTTGGGCCTAATGGGCCACATA
*
53422679 AATGTGATTTGGGCCTAAAGGGCCA
1 AATGTGATTTGGGCCTAATGGGCCA
53422704 TGTGAATATA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (29 bp):
AATGTGATTTGGGCCTAATGGGCCACATA
Found at i:53424417 original size:7 final size:7
Alignment explanation
Indices: 53424405--53424430 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
53424395 ACTAGATGAA
53424405 TTGGGCT
1 TTGGGCT
53424412 TTGGGCT
1 TTGGGCT
53424419 TTGGGCT
1 TTGGGCT
53424426 TTGGG
1 TTGGG
53424431 TTTCATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.46, T:0.42
Consensus pattern (7 bp):
TTGGGCT
Found at i:53426424 original size:40 final size:39
Alignment explanation
Indices: 53426380--53426455 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
53426370 TCACCACCAT
*
53426380 AAAGCATGCGAGACTTTAAGCCCAGATATAATACCAGTAC
1 AAAGCATGCGAGACTTT-AGCCCAGATATAACACCAGTAC
* * *
53426420 AAAGCCTGCGGGACTTTAGCCCGGATATAACACCAG
1 AAAGCATGCGAGACTTTAGCCCAGATATAACACCAG
53426456 CACGAATGCC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
39 17 0.53
40 15 0.47
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.18
Consensus pattern (39 bp):
AAAGCATGCGAGACTTTAGCCCAGATATAACACCAGTAC
Found at i:53426449 original size:39 final size:39
Alignment explanation
Indices: 53426398--53426688 Score: 397
Period size: 39 Copynumber: 7.5 Consensus size: 39
53426388 CGAGACTTTA
* * * * *
53426398 AGCCCAGATATAATACCAGTAC-AAAGCCTGCGGGACTTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGAC-TT
*
53426437 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGGCTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
*
53426476 AGCCCGGATATAACACCAGCACGAATGCCTTTGGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
***
53426515 AGCCCGGATATAACACCAGCACGAATGCCTAATGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
* * *
53426554 AGCTCGGATATAACACCAGTACGAATGCCTTTGGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
* *
53426593 AGCCCGGATATAACACCAGCATGAATGCCTTCAGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
53426632 AGCCCGGATATAACACCTA-CACGAATGCCTTCGGGACTT
1 AGCCCGGATATAACACC-AGCACGAATGCCTTCGGGACTT
* *
53426671 AGCTCAGATATAACACCA
1 AGCCCGGATATAACACCA
53426689 TTATAAAGTC
Statistics
Matches: 225, Mismatches: 25, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
38 1 0.00
39 212 0.94
40 12 0.05
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.20
Consensus pattern (39 bp):
AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
Found at i:53426794 original size:28 final size:28
Alignment explanation
Indices: 53426761--53426842 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
53426751 ATTTAATCAT
53426761 TCAATATTTTGCACACTAAGTGTCATTC
1 TCAATATTTTGCACACTAAGTGTCATTC
* * * *
53426789 TCAATATCTCGCACATTAAGTGCCATTC
1 TCAATATTTTGCACACTAAGTGTCATTC
* * *
53426817 TCAATATTTTGTACACTGAGTATCAT
1 TCAATATTTTGCACACTAAGTGTCAT
53426843 ATTTGATTGC
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (28 bp):
TCAATATTTTGCACACTAAGTGTCATTC
Found at i:53428624 original size:68 final size:68
Alignment explanation
Indices: 53428475--53428700 Score: 187
Period size: 68 Copynumber: 3.3 Consensus size: 68
53428465 CTAGCCGATT
* * * *
53428475 TATCTCGTAG-CTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACTCATGCGACCTAGCTAC
1 TATCTCGTAGCCT-TCTTGTCTACATGG-GTACATCAC--GGAATCACACATGTGACCTAGCTAC
*
53428539 -ATTTA-
62 TATATAG
* * *
53428544 TCTCTCACGTAG-CTCTCTTGTCTACATGGGATACATC-CCGTATCACACATGTGACCTAGCTAC
1 TATCT--CGTAGCCT-TCTTGTCTACATGGG-TACATCACGGAATCACACATGTGACCTAGCTAC
53428607 TATATAG
62 TATATAG
* * * * * *
53428614 TATCTCGTAGCCTTCTTGTAC-ACATGATGTGCA-CTCGGCACCATACATGTGACCTAGCTACTA
1 TATCTCGTAGCCTTCTTGT-CTACATG-GGTACATCACGGAATCACACATGTGACCTAGCTACTA
53428677 TATAG
64 TATAG
53428682 TATCTCGTAGCCTTCTTGT
1 TATCTCGTAGCCTTCTTGT
53428701 ACACATGATG
Statistics
Matches: 133, Mismatches: 15, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
67 1 0.01
68 88 0.66
69 12 0.09
70 6 0.05
71 26 0.20
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.34
Consensus pattern (68 bp):
TATCTCGTAGCCTTCTTGTCTACATGGGTACATCACGGAATCACACATGTGACCTAGCTACTATA
TAG
Found at i:53428701 original size:68 final size:68
Alignment explanation
Indices: 53428590--53428742 Score: 306
Period size: 68 Copynumber: 2.2 Consensus size: 68
53428580 CCCGTATCAC
53428590 ACATGTGACCTAGCTACTATATAGTATCTCGTAGCCTTCTTGTACACATGATGTGCACTCGGCAC
1 ACATGTGACCTAGCTACTATATAGTATCTCGTAGCCTTCTTGTACACATGATGTGCACTCGGCAC
53428655 CAT
66 CAT
53428658 ACATGTGACCTAGCTACTATATAGTATCTCGTAGCCTTCTTGTACACATGATGTGCACTCGGCAC
1 ACATGTGACCTAGCTACTATATAGTATCTCGTAGCCTTCTTGTACACATGATGTGCACTCGGCAC
53428723 CAT
66 CAT
53428726 ACATGTGACCTAGCTAC
1 ACATGTGACCTAGCTAC
53428743 GCTCCCTCTA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 85 1.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (68 bp):
ACATGTGACCTAGCTACTATATAGTATCTCGTAGCCTTCTTGTACACATGATGTGCACTCGGCAC
CAT
Found at i:53436215 original size:33 final size:33
Alignment explanation
Indices: 53436178--53436273 Score: 106
Period size: 34 Copynumber: 2.9 Consensus size: 33
53436168 CTATGGGCCA
* *
53436178 TACTGTTATCTGAAAAGGGGCTAAGGCCCAGT-T
1 TACTGTTATCTGAAAA-GGGCTTAGGCCCAGTAC
*
53436211 TACTG-TATTCTGAAAAGGGCTTCGGCCCAGTACC
1 TACTGTTA-TCTGAAAAGGGCTTAGGCCCAGTA-C
* *
53436245 TGCTGTTATCTGAATAGGGCTTAGGCCCA
1 TACTGTTATCTGAAAAGGGCTTAGGCCCA
53436274 ATGGGCTTGA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
32 15 0.28
33 13 0.25
34 23 0.43
35 2 0.04
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (33 bp):
TACTGTTATCTGAAAAGGGCTTAGGCCCAGTAC
Found at i:53436987 original size:16 final size:17
Alignment explanation
Indices: 53436955--53436987 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
53436945 CATCAAGAAG
53436955 GGTTTTCAATGAAAACAT
1 GGTTTTCAA-GAAAACAT
53436973 GGTTTTCAA-AAAACA
1 GGTTTTCAAGAAAACA
53436988 CTTCAATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (17 bp):
GGTTTTCAAGAAAACAT
Found at i:53438412 original size:40 final size:41
Alignment explanation
Indices: 53438327--53438422 Score: 110
Period size: 40 Copynumber: 2.4 Consensus size: 41
53438317 TAAGCCGATA
*
53438327 TCAGTAACAGT-GACAATATATGTTTGGGCTTTAGCCCATC
1 TCAGTAACAGTAAACAATATATGTTTGGGCTTTAGCCCATC
* * *
53438367 TCAGT-ACAG-AAACAATCATGTGTTTGGGCTTTGGCCTAT-
1 TCAGTAACAGTAAACAAT-ATATGTTTGGGCTTTAGCCCATC
53438406 TGCAGTAACAGTAAACA
1 T-CAGTAACAGTAAACA
53438423 GAGCAGTACT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
39 10 0.21
40 28 0.60
41 4 0.09
42 5 0.11
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (41 bp):
TCAGTAACAGTAAACAATATATGTTTGGGCTTTAGCCCATC
Found at i:53438430 original size:18 final size:18
Alignment explanation
Indices: 53438407--53438453 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
53438397 TTGGCCTATT
53438407 GCAGTAACAGTAAACAGA
1 GCAGTAACAGTAAACAGA
* *
53438425 GCAGT-ACTAGTAATCAGG
1 GCAGTAAC-AGTAAACAGA
53438443 GCAGTAACAGT
1 GCAGTAACAGT
53438454 TTAAACAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 2 0.08
18 21 0.84
19 2 0.08
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (18 bp):
GCAGTAACAGTAAACAGA
Found at i:53442555 original size:46 final size:46
Alignment explanation
Indices: 53442505--53442680 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
53442495 TGGTTGAGCA
53442505 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
53442551 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
53442596 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
53442644 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53442681 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:53442661 original size:93 final size:93
Alignment explanation
Indices: 53442502--53442673 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
53442492 GGATGGTTGA
* *
53442502 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
53442567 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
53442595 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
53442660 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
53442674 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:53445662 original size:15 final size:15
Alignment explanation
Indices: 53445623--53445701 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
53445613 GTATCTTGGG
*
53445623 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
53445638 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
53445653 TTTCTTTATTC-GGG
1 TTTCTTTATTCTGGA
*
53445667 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
53445682 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
53445696 TTTCTT
1 TTTCTT
53445702 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
13 2 0.04
14 17 0.32
15 32 0.60
16 2 0.04
ACGTcount: A:0.10, C:0.18, G:0.14, T:0.58
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:53445686 original size:29 final size:29
Alignment explanation
Indices: 53445614--53445700 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
53445604 CATAGTATCG
* * * *
53445614 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTC-GGATTTCTC
*
53445644 TAT-TCTGGATTTCTTTATTCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCGGATTTCTC
*
53445673 TATCTTGGATTTCTTTATTCGGTTTTCT
1 TATCTTGGATTTCTTTATTCGGATTTCT
53445701 TGTTATCTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 32 0.65
30 17 0.35
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.56
Consensus pattern (29 bp):
TATCTTGGATTTCTTTATTCGGATTTCTC
Found at i:53448134 original size:46 final size:46
Alignment explanation
Indices: 53448084--53448259 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
53448074 TGGTTGAGCA
53448084 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
53448130 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
53448175 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
53448223 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53448260 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 64 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:53448240 original size:93 final size:93
Alignment explanation
Indices: 53448081--53448251 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
53448071 GGATGGTTGA
* *
53448081 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
53448146 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
53448174 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
53448239 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
53448252 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:53452476 original size:18 final size:19
Alignment explanation
Indices: 53452453--53452490 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
53452443 CCGAATGTAC
53452453 TTTTCATATACA-CATATA
1 TTTTCATATACATCATATA
*
53452471 TTTTCATTTACATCATATA
1 TTTTCATATACATCATATA
53452490 T
1 T
53452491 AATTTGTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTTCATATACATCATATA
Found at i:53452757 original size:41 final size:43
Alignment explanation
Indices: 53452679--53452798 Score: 172
Period size: 41 Copynumber: 2.8 Consensus size: 43
53452669 TCTCATACGT
* *
53452679 GGTCTTACATGCAATCACATATCGATGCCACTATCCCAGACAG
1 GGTCTTACATGCAATCACATATCGATGCCAATGTCCCAGACAG
* * *
53452722 GGTCTTACATG-AATCAAATA-CAATGCCAATGTCCCAGACAT
1 GGTCTTACATGCAATCACATATCGATGCCAATGTCCCAGACAG
*
53452763 GGTCTTACATGTAATCACATATCGATGCCAATGTCC
1 GGTCTTACATGCAATCACATATCGATGCCAATGTCC
53452799 TAGATGTGGT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
41 28 0.41
42 16 0.24
43 24 0.35
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.26
Consensus pattern (43 bp):
GGTCTTACATGCAATCACATATCGATGCCAATGTCCCAGACAG
Found at i:53452809 original size:43 final size:42
Alignment explanation
Indices: 53452677--53452828 Score: 166
Period size: 43 Copynumber: 3.6 Consensus size: 42
53452667 CATCTCATAC
* *
53452677 GTGGTCTTACATGCAATCACATATCGATGCCACTATCCCAGACA
1 GTGGTCTTACATG-AATCACATATCGATGCCAATGTCCCAGA-A
* *
53452721 G-GGTCTTACATGAATCAAATA-CAATGCCAATGTCCCAGACA
1 GTGGTCTTACATGAATCACATATCGATGCCAATGTCCCAGA-A
* *
53452762 -TGGTCTTACATGTAATCACATATCGATGCCAATGTCCTAGAT
1 GTGGTCTTACATG-AATCACATATCGATGCCAATGTCCCAGAA
* *
53452804 GTGGTCTTACACGAGAACACATATC
1 GTGGTCTTACATGA-ATCACATATC
53452829 AAAAATCCTA
Statistics
Matches: 93, Mismatches: 10, Indels: 11
0.82 0.09 0.10
Matches are distributed among these distances:
41 28 0.30
42 17 0.18
43 47 0.51
44 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (42 bp):
GTGGTCTTACATGAATCACATATCGATGCCAATGTCCCAGAA
Found at i:53457356 original size:40 final size:40
Alignment explanation
Indices: 53457311--53457518 Score: 220
Period size: 40 Copynumber: 5.2 Consensus size: 40
53457301 CGGAATACGA
*
53457311 CCGGATATAACCAC-ATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTA-GCACAAATGCCTTCGGGTCTTAGC
* * * *
53457351 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
53457391 CCGGATTTAACAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
* ** * * *
53457431 CCGGATGTAGTCACTAGCACAATTGCCTTTGGGTCTTAAC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * *
53457471 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
53457511 CCGGATAT
1 CCGGATAT
53457519 CATTCAATTG
Statistics
Matches: 138, Mismatches: 29, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
40 138 1.00
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:53459311 original size:22 final size:22
Alignment explanation
Indices: 53459286--53459329 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
53459276 TTAAATTGCC
53459286 ATGTATCATAAATTGGGGGTCT
1 ATGTATCATAAATTGGGGGTCT
53459308 ATGTATCATAAATTGGGGGTCT
1 ATGTATCATAAATTGGGGGTCT
53459330 TTAAATGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.09, G:0.27, T:0.36
Consensus pattern (22 bp):
ATGTATCATAAATTGGGGGTCT
Found at i:53476554 original size:70 final size:71
Alignment explanation
Indices: 53476471--53476633 Score: 310
Period size: 70 Copynumber: 2.3 Consensus size: 71
53476461 CGATTTGTCT
53476471 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACC-AGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
53476535 CTTTCA
66 CTTTCA
*
53476541 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
53476606 CTTTCA
66 CTTTCA
53476612 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
53476634 GATACATCTC
Statistics
Matches: 91, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
70 51 0.56
71 40 0.44
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.34
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:53476671 original size:71 final size:70
Alignment explanation
Indices: 53476471--53476667 Score: 249
Period size: 70 Copynumber: 2.8 Consensus size: 70
53476461 CGATTTGTCT
* * * *
53476471 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACC-AGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
53476535 CTTTCA
65 CTTTCA
* * * *
53476541 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
53476606 CTTTCA
65 CTTTCA
* *
53476612 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
53476668 TACAGGGTGT
Statistics
Matches: 118, Mismatches: 7, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
68 22 0.19
69 1 0.01
70 52 0.44
71 43 0.36
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.33
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:53484091 original size:71 final size:71
Alignment explanation
Indices: 53484007--53484170 Score: 310
Period size: 71 Copynumber: 2.3 Consensus size: 71
53483997 CGATTTGTCT
53484007 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
53484072 CTTTCA
66 CTTTCA
* *
53484078 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
53484143 CTTTCA
66 CTTTCA
53484149 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
53484171 GATACATCTC
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 91 1.00
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.34
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
CTTTCA
Found at i:53484208 original size:71 final size:70
Alignment explanation
Indices: 53484007--53484204 Score: 249
Period size: 71 Copynumber: 2.8 Consensus size: 70
53483997 CGATTTGTCT
* * * * *
53484007 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
53484072 CTTTCA
65 CTTTCA
* * * *
53484078 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
53484143 CTTTCA
65 CTTTCA
* *
53484149 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
53484205 TACAGGGTGT
Statistics
Matches: 118, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
68 22 0.19
69 1 0.01
70 1 0.01
71 94 0.80
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.33
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:53488268 original size:38 final size:37
Alignment explanation
Indices: 53488226--53488309 Score: 150
Period size: 38 Copynumber: 2.2 Consensus size: 37
53488216 AATTTGTCCA
53488226 TTTCCCAAATATTCCAAATCAACTGAATTTCGTTTTC
1 TTTCCCAAATATTCCAAATCAACTGAATTTCGTTTTC
*
53488263 TTTTCCCAAATATTCCAAATCAACTGAATTTTGTTTTC
1 -TTTCCCAAATATTCCAAATCAACTGAATTTCGTTTTC
53488301 TTTCCCAAA
1 TTTCCCAAA
53488310 CCATAAACAA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 9 0.20
38 36 0.80
ACGTcount: A:0.30, C:0.24, G:0.05, T:0.42
Consensus pattern (37 bp):
TTTCCCAAATATTCCAAATCAACTGAATTTCGTTTTC
Found at i:53489665 original size:5 final size:5
Alignment explanation
Indices: 53489651--53489709 Score: 50
Period size: 5 Copynumber: 11.4 Consensus size: 5
53489641 ACGAGAAAAC
* *
53489651 AAAGA GAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGAA AAAGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAG-A AAAGA AA-AGA
53489698 AAAGA AAAGA AA
1 AAAGA AAAGA AA
53489710 GGCAAAAGGC
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
4 4 0.09
5 24 0.55
6 16 0.36
ACGTcount: A:0.78, C:0.02, G:0.19, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:53489684 original size:21 final size:20
Alignment explanation
Indices: 53489646--53489709 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
53489636 TTGTAACGAG
53489646 AAAA-CAAAGAGAAGAAAAGA
1 AAAAGCAAA-AGAAGAAAAGA
53489666 AAAAGCAAAAGAAGAAAAAGA
1 AAAAGCAAAAGAAG-AAAAGA
* *
53489687 AAAAGAAATAAAAAGAAAAGA
1 AAAAGCAA-AAGAAGAAAAGA
53489708 AA
1 AA
53489710 GGCAAAAGGC
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
20 9 0.23
21 25 0.64
22 5 0.13
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.02
Consensus pattern (20 bp):
AAAAGCAAAAGAAGAAAAGA
Found at i:53489709 original size:15 final size:16
Alignment explanation
Indices: 53489661--53489710 Score: 68
Period size: 15 Copynumber: 3.2 Consensus size: 16
53489651 AAAGAGAAGA
*
53489661 AAAGAAAAAGCAAAAG
1 AAAGAAAAAGAAAAAG
53489677 -AAGAAAAAGAAAAAG
1 AAAGAAAAAGAAAAAG
*
53489692 AAATAAAAAG-AAAAG
1 AAAGAAAAAGAAAAAG
53489707 AAAG
1 AAAG
53489711 GCAAAAGGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
15 22 0.73
16 8 0.27
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (16 bp):
AAAGAAAAAGAAAAAG
Found at i:53489782 original size:12 final size:13
Alignment explanation
Indices: 53489755--53489787 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
53489745 TTGAGGGAAC
53489755 TTGAAAAAGCCTT
1 TTGAAAAAGCCTT
53489768 TTGAAAAAGCC-T
1 TTGAAAAAGCCTT
53489780 TTGAAAAA
1 TTGAAAAA
53489788 CAAAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.27
Consensus pattern (13 bp):
TTGAAAAAGCCTT
Found at i:53489811 original size:12 final size:12
Alignment explanation
Indices: 53489789--53489813 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53489779 TTTGAAAAAC
53489789 AAAAAGAAAATG
1 AAAAAGAAAATG
53489801 AAAAAGAAAATG
1 AAAAAGAAAATG
53489813 A
1 A
53489814 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:53489820 original size:18 final size:18
Alignment explanation
Indices: 53489780--53489833 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
53489770 GAAAAAGCCT
* *
53489780 TTGAAAAACAAAAAGAAA
1 TTGAAAAAGAAAATGAAA
* *
53489798 ATGAAAAAGAAAATGAGA
1 TTGAAAAAGAAAATGAAA
*
53489816 TTGAAAAAGAGAATGAAA
1 TTGAAAAAGAAAATGAAA
53489834 AAGAGTTTGA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.67, C:0.02, G:0.19, T:0.13
Consensus pattern (18 bp):
TTGAAAAAGAAAATGAAA
Found at i:53489845 original size:30 final size:30
Alignment explanation
Indices: 53489789--53489887 Score: 83
Period size: 30 Copynumber: 3.3 Consensus size: 30
53489779 TTTGAAAAAC
**
53489789 AAAAAGAAAATGAAAAAGAAAATGAGATTG
1 AAAAAGAAAATGAAAAAGAAAATGAGAGAG
* ***
53489819 AAAAAGAGAATGAAAAAGAGTTTGAGAGAG
1 AAAAAGAAAATGAAAAAGAAAATGAGAGAG
** * * *
53489849 AAAAAGAATGTGAACAAGAAAA-AAGAGTGG
1 AAAAAGAAAATGAAAAAGAAAATGAGAG-AG
53489879 AAAAAGAAA
1 AAAAAGAAA
53489888 TTGAGATAAA
Statistics
Matches: 52, Mismatches: 16, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
29 4 0.08
30 48 0.92
ACGTcount: A:0.64, C:0.01, G:0.24, T:0.11
Consensus pattern (30 bp):
AAAAAGAAAATGAAAAAGAAAATGAGAGAG
Found at i:53489885 original size:18 final size:19
Alignment explanation
Indices: 53489849--53489887 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
53489839 TTTGAGAGAG
*
53489849 AAAAAGAATGTGAACAAGA
1 AAAAAGAATGTGAAAAAGA
*
53489868 AAAAAGAGTG-GAAAAAGA
1 AAAAAGAATGTGAAAAAGA
53489886 AA
1 AA
53489888 TTGAGATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.08
Consensus pattern (19 bp):
AAAAAGAATGTGAAAAAGA
Found at i:53500036 original size:20 final size:20
Alignment explanation
Indices: 53500011--53500050 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
53500001 TCTTCAGAGC
53500011 AAATACCACGGTAGCCAACT
1 AAATACCACGGTAGCCAACT
53500031 AAATACCACGGTAGCCAACT
1 AAATACCACGGTAGCCAACT
53500051 CCAAGTTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.30, G:0.15, T:0.15
Consensus pattern (20 bp):
AAATACCACGGTAGCCAACT
Found at i:53503074 original size:31 final size:27
Alignment explanation
Indices: 53503034--53503090 Score: 69
Period size: 31 Copynumber: 2.0 Consensus size: 27
53503024 AGGTTTCGGC
53503034 TAGAAGAAAAAGCAAAAAGGAAGAAAGAAAA
1 TAGAAGAAAAAG---AAAGGAAG-AAGAAAA
*
53503065 TAGAGGAAAAAGAAAGGAAGAAGAAA
1 TAGAAGAAAAAGAAAGGAAGAAGAAA
53503091 TCGGCACTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 6 0.24
28 8 0.32
31 11 0.44
ACGTcount: A:0.68, C:0.02, G:0.26, T:0.04
Consensus pattern (27 bp):
TAGAAGAAAAAGAAAGGAAGAAGAAAA
Found at i:53509858 original size:43 final size:43
Alignment explanation
Indices: 53509810--53509967 Score: 166
Period size: 43 Copynumber: 3.7 Consensus size: 43
53509800 AGATCGTACA
* * *
53509810 ATGCCAACGTCCTAGATGTGGTCTTACATGTAATCAAATATTG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATATCG
*
53509853 ATGCC-ACTGTCCCAGACAG-GGTCTTACATGGAATCAAATA-CG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGTAATCAAATATCG
* * *
53509895 ATGCCAATGT-CCAGACATGGTCTTACACT-TAAATACCAA-ATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACA-TGT-AAT-CAAATATCG
53509938 ATGCCAACGTCCCAGACGTGGTCTTACATG
1 ATGCCAACGTCCCAGACGTGGTCTTACATG
53509968 ATATCACATA
Statistics
Matches: 95, Mismatches: 10, Indels: 19
0.77 0.08 0.15
Matches are distributed among these distances:
41 15 0.16
42 15 0.16
43 48 0.51
44 17 0.18
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATATCG
Found at i:53513742 original size:40 final size:40
Alignment explanation
Indices: 53513694--53513849 Score: 269
Period size: 40 Copynumber: 3.9 Consensus size: 40
53513684 GGACTAAGAT
* *
53513694 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
53513734 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
53513774 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
**
53513814 CCGAAGGCATTTGTGCGAGTTGTTATATCC-GGCTAA
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAA
53513850 ATCGAAGGTA
Statistics
Matches: 112, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
39 6 0.05
40 106 0.95
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
Found at i:53521551 original size:40 final size:40
Alignment explanation
Indices: 53521503--53521668 Score: 228
Period size: 40 Copynumber: 4.2 Consensus size: 40
53521493 GGACTAAGAT
* *
53521503 CCGAAGGCATTTGTGCTAGTGACTATATCCAGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTC
*
53521543 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTC
* *
53521583 TCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTC
* * * *
53521623 CCGAAGGCATTTTTGCGAGTTG-TTATATCC-GGCTAAATG
1 CCGAAGGCATTTGTGCGAG-TGACTATATCCGGGCTAAGTC
53521662 CCGAAGG
1 CCGAAGG
53521669 TACTTGGATT
Statistics
Matches: 115, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 14 0.12
40 100 0.87
41 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTC
Found at i:53521629 original size:80 final size:80
Alignment explanation
Indices: 53521491--53521668 Score: 254
Period size: 80 Copynumber: 2.2 Consensus size: 80
53521481 CGGATGATAA
* *
53521491 CCGGACTAAGATCCGAAGGCATTTGTGCTAGTGACTATATCCAGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGATCCGAAGGCATTTGTGCGAGTGACTATATCCAGGCTAAGTCCCGAAGGCATTTG
53521556 TGCGAGTTACTATAT
66 TGCGAGTTACTATAT
* *
53521571 CCGGGCTAAG-TCTCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGATC-CGAAGGCATTTGTGCGAGTGACTATATCCAGGCTAAGTCCCGAAGGCATTT
* **
53521635 TTGCGAGTTGTTATAT
65 GTGCGAGTTACTATAT
53521651 CC-GGCTAA-ATGCCGAAGG
1 CCGGGCTAAGAT-CCGAAGG
53521669 TACTTGGATT
Statistics
Matches: 88, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
79 15 0.17
80 73 0.83
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (80 bp):
CCGGGCTAAGATCCGAAGGCATTTGTGCGAGTGACTATATCCAGGCTAAGTCCCGAAGGCATTTG
TGCGAGTTACTATAT
Found at i:53533254 original size:30 final size:29
Alignment explanation
Indices: 53533220--53533352 Score: 81
Period size: 29 Copynumber: 4.6 Consensus size: 29
53533210 TACTCGATTT
* *
53533220 CGCACACTTAGTGCCATGCGATTTAAGGCC
1 CGCACACTTAGTGCCATGCCATTCAA-GCC
** * * *
53533250 CGCACACACAGTGCCATGCCCTTCGAGCT
1 CGCACACTTAGTGCCATGCCATTCAAGCC
** * *
53533279 CGCACACTTAGTGCCAT-ATATTTCCAGCA
1 CGCACACTTAGTGCCATGCCA-TTCAAGCC
* ** * *
53533308 TGCACACTTAGTGCCAT-ATATTTCCAGCA
1 CGCACACTTAGTGCCATGCCA-TTCAAGCC
53533337 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
53533353 ATCTCGTCAC
Statistics
Matches: 86, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
29 66 0.77
30 20 0.23
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCCATTCAAGCC
Found at i:53533291 original size:29 final size:30
Alignment explanation
Indices: 53533219--53533295 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 30
53533209 ATACTCGATT
* *
53533219 TCGCACACTTAGTGCCATGCGATTTAAGGC
1 TCGCACACTTAGTGCCATGCCATTCAAGGC
* ** * *
53533249 CCGCACACACAGTGCCATGCCCTTCGA-GC
1 TCGCACACTTAGTGCCATGCCATTCAAGGC
53533278 TCGCACACTTAGTGCCAT
1 TCGCACACTTAGTGCCAT
53533296 ATATTTCCAG
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
29 17 0.46
30 20 0.54
ACGTcount: A:0.22, C:0.35, G:0.21, T:0.22
Consensus pattern (30 bp):
TCGCACACTTAGTGCCATGCCATTCAAGGC
Found at i:53533312 original size:29 final size:29
Alignment explanation
Indices: 53533279--53533352 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
53533269 CCTTCGAGCT
53533279 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
53533308 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
53533337 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
53533353 ATCTCGTCAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:53539335 original size:40 final size:40
Alignment explanation
Indices: 53539289--53539482 Score: 302
Period size: 40 Copynumber: 4.9 Consensus size: 40
53539279 ACTAAGATCA
*
53539289 GAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTCCC
1 GAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCC
* * *
53539329 GAAGGCATTTGTGTTAGTGATTATATCCGGGCTAAGTCTC
1 GAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCC
53539369 GAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCC
1 GAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCC
*
53539409 GAAGGCATTTGTGCTAGTGACTATGTCCGGGCTAAGTCCC
1 GAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCC
* *
53539449 GAAGGCATTCGTGCGAGTTG-CTATATCC-GGCTAA
1 GAAGGCATTTGTGCTAG-TGACTATATCCGGGCTAA
53539483 ATTCTGAAGG
Statistics
Matches: 144, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 6 0.04
40 136 0.94
41 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (40 bp):
GAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCC
Found at i:53544265 original size:29 final size:29
Alignment explanation
Indices: 53544231--53544333 Score: 154
Period size: 29 Copynumber: 3.6 Consensus size: 29
53544221 TAATCAGCCG
** *
53544231 CGCACACTTAGTGCCATATACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAGCT
53544260 CGCACACTTAGTGCCATGCATTTCAAGCT
1 CGCACACTTAGTGCCATGCATTTCAAGCT
53544289 CGCACACTTAGTGCCATGCATTTCAAGCT
1 CGCACACTTAGTGCCATGCATTTCAAGCT
*
53544318 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
53544334 ATCTCTCAAC
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
28 3 0.04
29 66 0.96
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAGCT
Found at i:53549353 original size:40 final size:40
Alignment explanation
Indices: 53549266--53549477 Score: 212
Period size: 40 Copynumber: 5.3 Consensus size: 40
53549256 CCTTCGGAAT
* * *
53549266 TTAA-CCGGATATAATGACTCGCTCAAATGCCTTCGGGAC
1 TTAACCCGGATATAATAACTCGCACAAATGCCTTCGGGTC
* * * * *
53549305 -GAAGCCCGGTTATAGTGACTCGCACAATTGCCTTCGGGTC
1 TTAA-CCCGGATATAATAACTCGCACAAATGCCTTCGGGTC
* ** *
53549345 TTAACCCGGATTTGGTAACTTGCACAAATGCCTTCGGGTC
1 TTAACCCGGATATAATAACTCGCACAAATGCCTTCGGGTC
* * *
53549385 TTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTC
1 TTAACCCGGATATAATAACTCGCACAAATGCCTTCGGGTC
* * * * *
53549425 TTAGCCCGGATATAATTACTAGCACAATTGCCTTCGGGAC
1 TTAACCCGGATATAATAACTCGCACAAATGCCTTCGGGTC
*
53549465 TTAGCCCGGATAT
1 TTAACCCGGATAT
53549478 CATTCCAATG
Statistics
Matches: 144, Mismatches: 26, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
38 2 0.01
40 140 0.97
41 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
TTAACCCGGATATAATAACTCGCACAAATGCCTTCGGGTC
Found at i:53549391 original size:80 final size:80
Alignment explanation
Indices: 53549266--53549477 Score: 248
Period size: 80 Copynumber: 2.7 Consensus size: 80
53549256 CCTTCGGAAT
* * * ** * ***
53549266 TTAA-CCGGATATAATGACTCGCTCAAATGCCTTCGGGACGAAGCCCGGTTATAGTGACTCGCAC
1 TTAACCCGGATATAATAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAACAACTCGCAC
53549330 -AATTGCCTTCGGGTC
66 GAA-TGCCTTCGGGTC
* ** * *
53549345 TTAACCCGGATTTGGTAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAACTCGCAC
1 TTAACCCGGATATAATAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAACAACTCGCAC
53549410 GAATGCCTTCGGGTC
66 GAATGCCTTCGGGTC
* * *
53549425 TTAGCCCGGATATAATTACTAGCACAATTGCCTTCGGGACTTAGCCCGGATAT
1 TTAACCCGGATATAATAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
53549478 CATTCCAATG
Statistics
Matches: 110, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
79 4 0.04
80 104 0.95
81 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (80 bp):
TTAACCCGGATATAATAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAACAACTCGCAC
GAATGCCTTCGGGTC
Found at i:53557185 original size:40 final size:40
Alignment explanation
Indices: 53557098--53557309 Score: 212
Period size: 40 Copynumber: 5.3 Consensus size: 40
53557088 CCTTCGGAAT
* * *
53557098 TTAA-CCGGATATAATGACTCGCTCAAATGCCTTCGGGAC
1 TTAACCCGGATATAATAACTCGCACAAATGCCTTCGGGTC
* * * * *
53557137 -GAAGCCCGGTTATAGTGACTCGCACAATTGCCTTCGGGTC
1 TTAA-CCCGGATATAATAACTCGCACAAATGCCTTCGGGTC
* ** *
53557177 TTAACCCGGATTTGGTAACTTGCACAAATGCCTTCGGGTC
1 TTAACCCGGATATAATAACTCGCACAAATGCCTTCGGGTC
* * *
53557217 TTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTC
1 TTAACCCGGATATAATAACTCGCACAAATGCCTTCGGGTC
* * * * *
53557257 TTAGCCCGGATATAATTACTAGCACAATTGCCTTCGGGAC
1 TTAACCCGGATATAATAACTCGCACAAATGCCTTCGGGTC
*
53557297 TTAGCCCGGATAT
1 TTAACCCGGATAT
53557310 CATTCCAATG
Statistics
Matches: 144, Mismatches: 26, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
38 2 0.01
40 140 0.97
41 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
TTAACCCGGATATAATAACTCGCACAAATGCCTTCGGGTC
Found at i:53557223 original size:80 final size:80
Alignment explanation
Indices: 53557098--53557309 Score: 248
Period size: 80 Copynumber: 2.7 Consensus size: 80
53557088 CCTTCGGAAT
* * * ** * ***
53557098 TTAA-CCGGATATAATGACTCGCTCAAATGCCTTCGGGACGAAGCCCGGTTATAGTGACTCGCAC
1 TTAACCCGGATATAATAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAACAACTCGCAC
53557162 -AATTGCCTTCGGGTC
66 GAA-TGCCTTCGGGTC
* ** * *
53557177 TTAACCCGGATTTGGTAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAACTCGCAC
1 TTAACCCGGATATAATAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAACAACTCGCAC
53557242 GAATGCCTTCGGGTC
66 GAATGCCTTCGGGTC
* * *
53557257 TTAGCCCGGATATAATTACTAGCACAATTGCCTTCGGGACTTAGCCCGGATAT
1 TTAACCCGGATATAATAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
53557310 CATTCCAATG
Statistics
Matches: 110, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
79 4 0.04
80 104 0.95
81 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (80 bp):
TTAACCCGGATATAATAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAACAACTCGCAC
GAATGCCTTCGGGTC
Found at i:53570167 original size:44 final size:42
Alignment explanation
Indices: 53570100--53570218 Score: 141
Period size: 44 Copynumber: 2.8 Consensus size: 42
53570090 TTATGATATG
* * *
53570100 TGATTTCGTGTAAGACCACGTCTGGGACGTTGGCATCG-ATT
1 TGATTTAGTGTAAGACCATGTCTGGGACGTTGGCATCGCATA
*
53570141 TGAGATTTAAGTGTAAGACCATGTCTGGGACATTGGCATCGCATA
1 T--GATTT-AGTGTAAGACCATGTCTGGGACGTTGGCATCGCATA
* *
53570186 TGATTTTGTGTAAGACCCTGTCTGGGACAGTTG
1 TGATTTAGTGTAAGACCATGTCTGGGAC-GTTG
53570219 AACCGATAGT
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
41 1 0.02
42 20 0.30
43 13 0.20
44 29 0.44
45 3 0.05
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.32
Consensus pattern (42 bp):
TGATTTAGTGTAAGACCATGTCTGGGACGTTGGCATCGCATA
Found at i:53570244 original size:43 final size:42
Alignment explanation
Indices: 53570152--53570245 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
53570142 GAGATTTAAG
* * * *
53570152 TGTAAGACCATGTCTGGGACATTGGCATCGCATATGATTTTG
1 TGTAAGACCATGTCTGGGACATTGGAACCGCATATGATTATA
*
53570194 TGTAAGACCCTGTCTGGGACAGTT-GAACCG-ATAGTTGATTATA
1 TGTAAGACCATGTCTGGGACA-TTGGAACCGCATA--TGATTATA
53570237 TGTAAGACC
1 TGTAAGACC
53570246 TCATCTAGGA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
41 3 0.07
42 24 0.55
43 17 0.39
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.31
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACATTGGAACCGCATATGATTATA
Found at i:53572625 original size:80 final size:80
Alignment explanation
Indices: 53572485--53572691 Score: 213
Period size: 80 Copynumber: 2.6 Consensus size: 80
53572475 CGGAATACAA
* *
53572485 CCAGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAAT-
1 CCAGATATAACAACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCAC-AATG
53572549 GCCTTCGGGTATTAGC
65 GCCTTCGGGTATTAGC
* * * * **
53572565 CCAGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCTGGATGTGGTC-ACTAGCACAATG
1 CCAGATATAACAACATGCACGAATGCCTTCGGGTCTTAGCCCGGAT-AGAACGACTAGCACAATG
* *
53572629 GCCTTCGGGTCTTAAC
65 GCCTTCGGGTATTAGC
* ** ** * *
53572645 CCGGATATAATTAC-TAGCATAAATGTCTTCGGGACTTAGCCCGGATA
1 CCAGATATAACAACAT-GCACGAATGCCTTCGGGTCTTAGCCCGGATA
53572692 TCATTCAATT
Statistics
Matches: 104, Mismatches: 20, Indels: 7
0.79 0.15 0.05
Matches are distributed among these distances:
79 4 0.04
80 98 0.94
81 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (80 bp):
CCAGATATAACAACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAATGG
CCTTCGGGTATTAGC
Found at i:53572692 original size:40 final size:40
Alignment explanation
Indices: 53572488--53572692 Score: 182
Period size: 40 Copynumber: 5.1 Consensus size: 40
53572478 AATACAACCA
* *
53572488 GATATAACCAC-ATGCACGAATGCCTTCGGGTCTTAGCCCG
1 GATATAACAACTA-GCACAAATGCCTTCGGGTCTTAGCCCG
* * * * *
53572528 GATAGAACGACTTGCACAAATGCCTTCGGGTATTAGCCCA
1 GATATAACAACTAGCACAAATGCCTTCGGGTCTTAGCCCG
* * * *
53572568 GATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCTG
1 GATATAACAACTAGCACAAATGCCTTCGGGTCTTAGCCCG
* ** *
53572608 GATGTGGTC-ACTAGCAC-AATGGCCTTCGGGTCTTAACCCG
1 GATAT-AACAACTAGCACAAAT-GCCTTCGGGTCTTAGCCCG
** * * *
53572648 GATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCG
1 GATATAACAACTAGCACAAATGCCTTCGGGTCTTAGCCCG
53572688 GATAT
1 GATAT
53572693 CATTCAATTG
Statistics
Matches: 133, Mismatches: 27, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
39 3 0.02
40 126 0.95
41 4 0.03
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (40 bp):
GATATAACAACTAGCACAAATGCCTTCGGGTCTTAGCCCG
Found at i:53576393 original size:40 final size:40
Alignment explanation
Indices: 53576344--53576438 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 40
53576334 CGGTTATTTG
** *
53576344 TGGCACTTAGTGTGTGATACGACATAGCTTC-GACTATATA
1 TGGCACTTAGTGTGCAATACGACATAGCTTCAG-CAATATA
* * * *
53576384 TGGTACTTAGTGTGCAATTCGAGATAGCTTCAGCAATGTA
1 TGGCACTTAGTGTGCAATACGACATAGCTTCAGCAATATA
53576424 TGGCACTTAGTGTGC
1 TGGCACTTAGTGTGC
53576439 GAGATACCAA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 45 0.98
41 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (40 bp):
TGGCACTTAGTGTGCAATACGACATAGCTTCAGCAATATA
Found at i:53576461 original size:28 final size:28
Alignment explanation
Indices: 53576421--53576494 Score: 112
Period size: 28 Copynumber: 2.6 Consensus size: 28
53576411 CTTCAGCAAT
53576421 GTATGGCACTTAGTGTGCGAGATACCAA
1 GTATGGCACTTAGTGTGCGAGATACCAA
* * *
53576449 GTATGGCACTTAGTGTGCTAGATATCGA
1 GTATGGCACTTAGTGTGCGAGATACCAA
*
53576477 GTATGACACTTAGTGTGC
1 GTATGGCACTTAGTGTGC
53576495 AAGGCATTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (28 bp):
GTATGGCACTTAGTGTGCGAGATACCAA
Found at i:53576985 original size:33 final size:33
Alignment explanation
Indices: 53576943--53577009 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
53576933 CATAAGATGA
53576943 TGAACTTGATGATGTTTATATATGTACAAATGG
1 TGAACTTGATGATGTTTATATATGTACAAATGG
* *
53576976 TGAACTTGATGTTGTTTATATATGTGCAAATGG
1 TGAACTTGATGATGTTTATATATGTACAAATGG
53577009 T
1 T
53577010 TCTAATATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.30, C:0.06, G:0.22, T:0.42
Consensus pattern (33 bp):
TGAACTTGATGATGTTTATATATGTACAAATGG
Found at i:53583114 original size:76 final size:78
Alignment explanation
Indices: 53583023--53583203 Score: 303
Period size: 76 Copynumber: 2.3 Consensus size: 78
53583013 GAATGTTCGA
*
53583023 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGC-AAGCCCGAAGG-
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTATGATATCCGGGCTAAGCCCGAAGGC
53583086 AATTGTGCAAATT
66 AATTGTGCAAATT
* *
53583099 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGC
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTATGATATCCGGGCTAAGCCCGAAGGC
53583164 AATTGTGCAAATT
66 AATTGTGCAAATT
*
53583177 GTGATATCCGGGTTAAGTCCCGAAGGC
1 GTGATATCCGGGCTAAG-CCCGAAGGC
53583204 CTTTGTGCGG
Statistics
Matches: 98, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
76 49 0.50
77 11 0.11
78 29 0.30
79 9 0.09
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (78 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTATGATATCCGGGCTAAGCCCGAAGGC
AATTGTGCAAATT
Found at i:53583143 original size:39 final size:39
Alignment explanation
Indices: 53583023--53583203 Score: 303
Period size: 39 Copynumber: 4.7 Consensus size: 39
53583013 GAATGTTCGA
53583023 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
53583062 GTGATATCCGGGC-AAGCCCGAAGG-AATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
* *
53583099 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
53583138 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
53583177 GTGATATCCGGGTTAAGTCCCGAAGGC
1 GTGATATCCGGGCTAAG-CCCGAAGGC
53583204 CTTTGTGCGG
Statistics
Matches: 132, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
37 26 0.20
38 22 0.17
39 75 0.57
40 9 0.07
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
Found at i:53591141 original size:39 final size:39
Alignment explanation
Indices: 53591087--53591230 Score: 243
Period size: 39 Copynumber: 3.7 Consensus size: 39
53591077 GAATGTTCGA
53591087 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
* *
53591126 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
53591165 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
53591204 GTGATATCCGGGTTAAGTCCCGAAGGC
1 GTGATATCCGGGCTAAG-CCCGAAGGC
53591231 CTTTGTGCGG
Statistics
Matches: 97, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 88 0.91
40 9 0.09
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
Found at i:53591177 original size:78 final size:79
Alignment explanation
Indices: 53591088--53591270 Score: 278
Period size: 78 Copynumber: 2.3 Consensus size: 79
53591078 AATGTTCGAG
53591088 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAG-CCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
53591152 AATTGTGCGAGTTA
66 AATTGTGCGAGTTA
*
53591166 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGTTAAGTCCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
** *
53591231 CTTTGTGCGGGTTA
66 AATTGTGCGAGTTA
** * *
53591245 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
53591271 GTTTGAACGA
Statistics
Matches: 95, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
78 54 0.57
79 32 0.34
80 9 0.09
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (79 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
AATTGTGCGAGTTA
Found at i:53596268 original size:53 final size:53
Alignment explanation
Indices: 53596188--53596288 Score: 202
Period size: 53 Copynumber: 1.9 Consensus size: 53
53596178 GAATAAAGGA
53596188 TATACAATATAGATTTGGAAGGTTAGGATTAGTAAGAATCTACCCTTATTGCT
1 TATACAATATAGATTTGGAAGGTTAGGATTAGTAAGAATCTACCCTTATTGCT
53596241 TATACAATATAGATTTGGAAGGTTAGGATTAGTAAGAATCTACCCTTA
1 TATACAATATAGATTTGGAAGGTTAGGATTAGTAAGAATCTACCCTTA
53596289 CTGCCATTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.35
Consensus pattern (53 bp):
TATACAATATAGATTTGGAAGGTTAGGATTAGTAAGAATCTACCCTTATTGCT
Found at i:53597970 original size:49 final size:50
Alignment explanation
Indices: 53597903--53598135 Score: 254
Period size: 49 Copynumber: 4.7 Consensus size: 50
53597893 AGCTATTGTG
* * *
53597903 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATTGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTT
* * * * * *
53597953 -GGTCGCATGTGTAGTACTAAGTGCAGGCTAATATGCGTACCTGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT-AGTT
* * * * * *
53598003 CGATCACGTGTGTAGTACTGAGTGCAGGCTACTACGTGTATCAGATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTT
* * * *
53598053 AGGTCACGTGTGTAGTACTAAGTGCATGCTACTACGTGTACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTT
* *
53598103 -GGTCGCATGTGTACTACTAAGTGCAGGCTACTA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTA
53598136 TGCATACTAC
Statistics
Matches: 149, Mismatches: 32, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
49 67 0.45
50 46 0.31
51 36 0.24
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTT
Found at i:53598039 original size:28 final size:28
Alignment explanation
Indices: 53598008--53598091 Score: 74
Period size: 28 Copynumber: 3.2 Consensus size: 28
53597998 AACTTCGATC
53598008 ACGTGTGTAGTACTGAGTGCAGGCTACT
1 ACGTGTGTAGTACTGAGTGCAGGCTACT
* *
53598036 ACGTGTATCAG-A-TG-GT-TAGG-T-C-
1 ACGTGTGT-AGTACTGAGTGCAGGCTACT
* *
53598058 ACGTGTGTAGTACTAAGTGCATGCTACT
1 ACGTGTGTAGTACTGAGTGCAGGCTACT
53598086 ACGTGT
1 ACGTGT
53598092 ACCGGATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
21 2 0.05
22 8 0.19
23 2 0.05
24 3 0.07
25 5 0.12
26 3 0.07
27 3 0.07
28 14 0.33
29 2 0.05
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.31
Consensus pattern (28 bp):
ACGTGTGTAGTACTGAGTGCAGGCTACT
Found at i:53601066 original size:28 final size:28
Alignment explanation
Indices: 53601021--53601089 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
53601011 TTTAAAACCC
*
53601021 TAGGGGT-ATATCGGTAATTATGCTCTT
1 TAGGGGTAATTTCGGTAATTATGCTCTT
*
53601048 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTATGCTCTT
53601076 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
53601090 TGATCTACGC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 7 0.18
28 32 0.82
ACGTcount: A:0.20, C:0.10, G:0.28, T:0.42
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTATGCTCTT
Found at i:53604584 original size:24 final size:24
Alignment explanation
Indices: 53604552--53604696 Score: 272
Period size: 24 Copynumber: 6.0 Consensus size: 24
53604542 GGGTAGAAAG
53604552 TTTACTATGGCACTGTGTGTGCGA
1 TTTACTATGGCACTGTGTGTGCGA
*
53604576 TTTATTATGGCACTGTGTGTGCGA
1 TTTACTATGGCACTGTGTGTGCGA
53604600 TTTACTATGGCACTGTGTGTGCGA
1 TTTACTATGGCACTGTGTGTGCGA
53604624 TTTACTATGGCACTGTGTGTGCGA
1 TTTACTATGGCACTGTGTGTGCGA
53604648 TTTACTATGGCACTGTGTGTGCGA
1 TTTACTATGGCACTGTGTGTGCGA
*
53604672 TTTACTATGGCACTATGTGTGCGA
1 TTTACTATGGCACTGTGTGTGCGA
53604696 T
1 T
53604697 CATAATAAGC
Statistics
Matches: 118, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 118 1.00
ACGTcount: A:0.17, C:0.16, G:0.28, T:0.39
Consensus pattern (24 bp):
TTTACTATGGCACTGTGTGTGCGA
Found at i:53604709 original size:72 final size:72
Alignment explanation
Indices: 53604561--53604717 Score: 244
Period size: 72 Copynumber: 2.2 Consensus size: 72
53604551 GTTTACTATG
* * *
53604561 GCACTGTGTGTGCGATTTATTATGGCACTGTGTGTGCGATTTACTATGGCACTGTGTGTGCGATT
1 GCACTGTGTGTGCGATTTACTATGGCACTGTGTGTGCGATTTACTATGGCACTATGTGTGCGATA
* *
53604626 TACTATG
66 TAATATA
53604633 GCACTGTGTGTGCGATTTACTATGGCACTGTGTGTGCGATTTACTATGGCACTATGTGTGCGATC
1 GCACTGTGTGTGCGATTTACTATGGCACTGTGTGTGCGATTTACTATGGCACTATGTGTGCGAT-
53604698 ATAATA-A
65 ATAATATA
*
53604705 GCACTATGTGTGC
1 GCACTGTGTGTGC
53604718 CACATTCGGT
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
72 74 0.95
73 4 0.05
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.36
Consensus pattern (72 bp):
GCACTGTGTGTGCGATTTACTATGGCACTGTGTGTGCGATTTACTATGGCACTATGTGTGCGATA
TAATATA
Found at i:53612431 original size:24 final size:24
Alignment explanation
Indices: 53612400--53612567 Score: 320
Period size: 24 Copynumber: 7.0 Consensus size: 24
53612390 AAGGTAAAAG
53612400 TTTA-TATGGCACTGTGTGTGCGA
1 TTTACTATGGCACTGTGTGTGCGA
53612423 TTTACTATGGCACTGTGTGTGCGA
1 TTTACTATGGCACTGTGTGTGCGA
53612447 TTTACTATGGCACTGTGTGTGCGA
1 TTTACTATGGCACTGTGTGTGCGA
53612471 TTTACTATGGCACTGTGTGTGCGA
1 TTTACTATGGCACTGTGTGTGCGA
53612495 TTTACTATGGCACTGTGTGTGCGA
1 TTTACTATGGCACTGTGTGTGCGA
53612519 TTTACTATGGCACTGTGTGTGCGA
1 TTTACTATGGCACTGTGTGTGCGA
*
53612543 TTTACTATGGCACTATGTGTGCGA
1 TTTACTATGGCACTGTGTGTGCGA
53612567 T
1 T
53612568 CATAATAAGC
Statistics
Matches: 143, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
23 4 0.03
24 139 0.97
ACGTcount: A:0.17, C:0.16, G:0.29, T:0.38
Consensus pattern (24 bp):
TTTACTATGGCACTGTGTGTGCGA
Found at i:53618670 original size:16 final size:17
Alignment explanation
Indices: 53618649--53618682 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53618639 TCACATTGAA
53618649 GTGTTTT-TTGAAAACC
1 GTGTTTTATTGAAAACC
53618665 GTGTTTTCATTGAAAACC
1 GTGTTTT-ATTGAAAACC
53618683 ATTCTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (17 bp):
GTGTTTTATTGAAAACC
Found at i:53621606 original size:39 final size:39
Alignment explanation
Indices: 53621552--53621738 Score: 338
Period size: 39 Copynumber: 4.8 Consensus size: 39
53621542 TATCAGTACA
*
53621552 AAGCCTGCGGGACTTTAACCCGGATACATTTCCAGCACG
1 AAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACG
* *
53621591 AAGCCTGCGGGACTTTGGCCCGGATATATTTCCAGCACG
1 AAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACG
*
53621630 AAGCCTGCGGGACTTTAGCCCGGATATATTTCCAGCACG
1 AAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACG
53621669 AAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACG
1 AAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACG
53621708 AAGCCTGCGGGACTTTAGCCCGGATACATTT
1 AAGCCTGCGGGACTTTAGCCCGGATACATTT
53621739 TCAGTGTCTT
Statistics
Matches: 143, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 143 1.00
ACGTcount: A:0.23, C:0.29, G:0.26, T:0.22
Consensus pattern (39 bp):
AAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACG
Found at i:53623642 original size:30 final size:29
Alignment explanation
Indices: 53623548--53623649 Score: 109
Period size: 28 Copynumber: 3.5 Consensus size: 29
53623538 TATAGTGAAT
* * *
53623548 CCGCACACTTAGTGCTATATATTTTCAGC
1 CCGCACACTTAGTGCTATAAATTTTAAAC
* *
53623577 TCGCACACTTAGTGCTATAGAA--TCAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
* *
53623605 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
53623635 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
53623650 CAATCTTGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 23 0.38
29 18 0.30
30 20 0.33
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATAAATTTTAAAC
Done.