Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 260 of 356
Found at i:85401504 original size:55 final size:55
Alignment explanation
Indices: 85401278--85401483 Score: 349
Period size: 55 Copynumber: 3.7 Consensus size: 55
85401268 ATATTAAGTC
* * * *
85401278 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
*
85401333 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTACTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
*
85401388 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
*
85401443 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGC
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGC
85401484 GCACAATTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 144 1.00
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
Found at i:85417211 original size:40 final size:40
Alignment explanation
Indices: 85417167--85417318 Score: 162
Period size: 40 Copynumber: 3.8 Consensus size: 40
85417157 AAAGCCACAA
* * * *
85417167 GCACAATTGCCTTCGTGTCTTAACCTGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* *
85417207 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* * * * *
85417247 GCACAAATGCCTTCGGGTCTTAGCCAGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAACCCGGAT-ATAGCAACTC
* * *
85417287 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAT
85417319 CATTCAAATG
Statistics
Matches: 98, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
39 1 0.01
40 93 0.95
41 4 0.04
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
Found at i:85417252 original size:80 final size:80
Alignment explanation
Indices: 85417167--85417318 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 80
85417157 AAAGCCACAA
* * * * * * *
85417167 GCACAATTGCCTTCGTGTCTTAACCTGGGT-ATAGCAACTCGCACAAATGCCTTCGGGTCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCAGGATAAAAGC-ACTAGCACAAATGCCTTCGGGACTTAGC
85417231 CCGGATATATCAACTC
65 CCGGATATATCAACTC
* * *
85417247 GCACAAATGCCTTCGGGTCTTAGCCAGGATAAAATCACTAGCATAAATGCCTTCGGGACTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCAGGATAAAAGCACTAGCACAAATGCCTTCGGGACTTAGCC
85417312 CGGATAT
66 CGGATAT
85417319 CATTCAAATG
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
80 58 0.95
81 3 0.05
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCAGGATAAAAGCACTAGCACAAATGCCTTCGGGACTTAGCC
CGGATATATCAACTC
Found at i:85421283 original size:27 final size:27
Alignment explanation
Indices: 85421122--85421284 Score: 123
Period size: 27 Copynumber: 6.0 Consensus size: 27
85421112 TTTCACCCTG
* * * *
85421122 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
* *
85421149 CAAGGGTATTTTGATAATTCTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * **
85421176 CGATGGTATTTCT-GTAATTTTTGAAAGT
1 CAAGGGTATTT-TGGTAATTTTACAAA-T
* * **
85421204 CGAGGGTATTTTTGTAATTTTGTAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * *
85421231 CAGGGGTATTTCT-ATAATTTTCCAAAT
1 CAAGGGTATTT-TGGTAATTTTACAAAT
*
85421258 CAAGGATATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
85421285 TGAAGGTATT
Statistics
Matches: 109, Mismatches: 22, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
26 1 0.01
27 84 0.77
28 24 0.22
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.40
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAT
Found at i:85421380 original size:28 final size:27
Alignment explanation
Indices: 85421346--85421407 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 27
85421336 CGTATTTCAG
*
85421346 TAATTTTACAAATTAGGGATATTTTTGA
1 TAATTTTACAAACTAGGGATA-TTTTGA
* * * *
85421374 TAATTTTATAACCTAGGGGTATTTTGG
1 TAATTTTACAAACTAGGGATATTTTGA
85421401 TAATTTT
1 TAATTTT
85421408 GTAACCGAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 12 0.41
28 17 0.59
ACGTcount: A:0.31, C:0.05, G:0.16, T:0.48
Consensus pattern (27 bp):
TAATTTTACAAACTAGGGATATTTTGA
Found at i:85421406 original size:27 final size:27
Alignment explanation
Indices: 85421309--85421424 Score: 83
Period size: 27 Copynumber: 4.3 Consensus size: 27
85421299 TACAAGTTGA
**
85421309 GGTATTTTGGTAATTTTAT-AGGTCAAG
1 GGTATTTTGGTAATTTTATAACCT-AAG
* ** * * *
85421336 CGTATTTCAGTAATTTTACAA-ATTAG
1 GGTATTTTGGTAATTTTATAACCTAAG
* *
85421362 GGATATTTTTGATAATTTTATAACCTAGG
1 GG-TA-TTTTGGTAATTTTATAACCTAAG
* *
85421391 GGTATTTTGGTAATTTTGTAACCGAAG
1 GGTATTTTGGTAATTTTATAACCTAAG
85421418 GGTATTT
1 GGTATTT
85421425 CAGTAATTCT
Statistics
Matches: 67, Mismatches: 18, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
26 3 0.04
27 44 0.66
28 16 0.24
29 4 0.06
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.44
Consensus pattern (27 bp):
GGTATTTTGGTAATTTTATAACCTAAG
Found at i:85421430 original size:27 final size:27
Alignment explanation
Indices: 85421374--85421432 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
85421364 ATATTTTTGA
* * **
85421374 TAATTTTATAACCTAGGGGTATTTTGG
1 TAATTTTATAACCGAAGGGTATTTCAG
*
85421401 TAATTTTGTAACCGAAGGGTATTTCAG
1 TAATTTTATAACCGAAGGGTATTTCAG
85421428 TAATT
1 TAATT
85421433 CTATCCTACA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.42
Consensus pattern (27 bp):
TAATTTTATAACCGAAGGGTATTTCAG
Found at i:85421451 original size:27 final size:27
Alignment explanation
Indices: 85421421--85421497 Score: 100
Period size: 27 Copynumber: 2.9 Consensus size: 27
85421411 ACCGAAGGGT
*
85421421 ATTTCAGTAATTCTATCCTACAGGGGC
1 ATTTCAGTAATTCTACCCTACAGGGGC
* *
85421448 ATTTCAGTAATTCTACCCTTCAGGGGT
1 ATTTCAGTAATTCTACCCTACAGGGGC
* * *
85421475 ATTTCAATAATACTAGCCTACAG
1 ATTTCAGTAATTCTACCCTACAG
85421498 ATATGAGATT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.34
Consensus pattern (27 bp):
ATTTCAGTAATTCTACCCTACAGGGGC
Found at i:85424188 original size:66 final size:70
Alignment explanation
Indices: 85424058--85424188 Score: 153
Period size: 66 Copynumber: 1.9 Consensus size: 70
85424048 GGGATGTATC
* * *
85424058 CCATGTAGACAAGAGAGCTACGAGAGAGGATAAATGTAGCTAGGTCGCATGTGTGATTCCAAGTG
1 CCATGTAGACAAGAGAGCTA--AGAGAGGATAAATGTAGCTAGGTCACATGGGTGATACCAAGTG
85424123 AAGGACA
64 AAGGACA
* * * *
85424130 CCATGTAGACAAGAGAGCT-A-TGA-GATAAAT-TGGCTAGGTCACATGGGTGGTACTAAGTG
1 CCATGTAGACAAGAGAGCTAAGAGAGGATAAATGTAGCTAGGTCACATGGGTGATACCAAGTG
85424189 TTCACCATGT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
66 23 0.44
67 7 0.13
68 2 0.04
69 1 0.02
72 19 0.37
ACGTcount: A:0.34, C:0.15, G:0.31, T:0.21
Consensus pattern (70 bp):
CCATGTAGACAAGAGAGCTAAGAGAGGATAAATGTAGCTAGGTCACATGGGTGATACCAAGTGAA
GGACA
Found at i:85430963 original size:34 final size:35
Alignment explanation
Indices: 85430896--85430974 Score: 142
Period size: 35 Copynumber: 2.3 Consensus size: 35
85430886 CTTATTACAT
85430896 AAACAAATACCCAAATTAAATTACTTATAAATTAA
1 AAACAAATACCCAAATTAAATTACTTATAAATTAA
85430931 AAACAAATACCCAAATTAAATTA-TTATAAATTAA
1 AAACAAATACCCAAATTAAATTACTTATAAATTAA
85430965 AAATCAAATA
1 AAA-CAAATA
85430975 AGAAAGCAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
34 14 0.33
35 29 0.67
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28
Consensus pattern (35 bp):
AAACAAATACCCAAATTAAATTACTTATAAATTAA
Found at i:85431663 original size:54 final size:54
Alignment explanation
Indices: 85431573--85431842 Score: 324
Period size: 54 Copynumber: 5.0 Consensus size: 54
85431563 AAACATACAT
* * * * ** * *
85431573 CACATAGGGGTAAAACAGTCATCTTACCATAAAAGGGCATAACAGTCATTTTAC
1 CACATAAGGGCAAAACAATCATTTTACCCCATAAGGGCAAAACAGTCATTTTAC
* * * * *
85431627 CACATAAGGGCAAAATAGTCATTTTACCTCATAAGGGGCAAAACAGTTATCTTAC
1 CACATAAGGGCAAAACAATCATTTTACCCCATAA-GGGCAAAACAGTCATTTTAC
* * * *
85431682 CTCATAAGGGCAAAACAATTATTTTACCCCATAAGGGGAAAACAATCATTTTAC
1 CACATAAGGGCAAAACAATCATTTTACCCCATAAGGGCAAAACAGTCATTTTAC
* * * *
85431736 CTCATAAGGGCAAAACAATCATTTTATCCCATAAGGACAAAACAGTTATTTTAC
1 CACATAAGGGCAAAACAATCATTTTACCCCATAAGGGCAAAACAGTCATTTTAC
* *
85431790 CACATAAGGGCAAAACAATCATTTTACCCCATAAAGGCAAAAGAGTCATTTTA
1 CACATAAGGGCAAAACAATCATTTTACCCCATAAGGGCAAAACAGTCATTTTA
85431843 TCAATTAAGG
Statistics
Matches: 184, Mismatches: 31, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
54 138 0.75
55 46 0.25
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.25
Consensus pattern (54 bp):
CACATAAGGGCAAAACAATCATTTTACCCCATAAGGGCAAAACAGTCATTTTAC
Found at i:85431693 original size:82 final size:81
Alignment explanation
Indices: 85431575--85431838 Score: 334
Period size: 81 Copynumber: 3.2 Consensus size: 81
85431565 ACATACATCA
* * * * *
85431575 CATAGGGGTAAAACAGTCATCTTACCAT-AAAAGGGCATAACAGTCATTTTACCACATAAGGGCA
1 CATAAGGGCAAAACAGTCATCTTACC-TCATAAGGGCAAAACAGTTATTTTACCACATAAGGGCA
* *
85431639 AAATAGTCATTTTACCT
65 AAACAATCATTTTACCT
* * * *
85431656 CATAAGGGGCAAAACAGTTATCTTACCTCATAAGGGCAAAACAATTATTTTACCCCATAAGGGGA
1 CATAA-GGGCAAAACAGTCATCTTACCTCATAAGGGCAAAACAGTTATTTTACCACATAAGGGCA
85431721 AAACAATCATTTTACCT
65 AAACAATCATTTTACCT
* * *
85431738 CATAAGGGCAAAACAATCATTTTATCC-CATAAGGACAAAACAGTTATTTTACCACATAAGGGCA
1 CATAAGGGCAAAACAGTCATCTTA-CCTCATAAGGGCAAAACAGTTATTTTACCACATAAGGGCA
*
85431802 AAACAATCATTTTACCC
65 AAACAATCATTTTACCT
* *
85431819 CATAAAGGCAAAAGAGTCAT
1 CATAAGGGCAAAACAGTCAT
85431839 TTTATCAATT
Statistics
Matches: 158, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
81 87 0.55
82 71 0.45
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (81 bp):
CATAAGGGCAAAACAGTCATCTTACCTCATAAGGGCAAAACAGTTATTTTACCACATAAGGGCAA
AACAATCATTTTACCT
Found at i:85431839 original size:27 final size:27
Alignment explanation
Indices: 85431575--85431842 Score: 293
Period size: 27 Copynumber: 9.9 Consensus size: 27
85431565 ACATACATCA
* * * *
85431575 CATAGGGGTAAAACAGTCATCTTACCA
1 CATAAGGGCAAAACAGTCATTTTACCC
* * * *
85431602 TAAAAGGGCATAACAGTCATTTTACCA
1 CATAAGGGCAAAACAGTCATTTTACCC
* *
85431629 CATAAGGGCAAAATAGTCATTTTACCT
1 CATAAGGGCAAAACAGTCATTTTACCC
* * *
85431656 CATAAGGGGCAAAACAGTTATCTTACCT
1 CATAA-GGGCAAAACAGTCATTTTACCC
* *
85431684 CATAAGGGCAAAACAATTATTTTACCC
1 CATAAGGGCAAAACAGTCATTTTACCC
* * *
85431711 CATAAGGGGAAAACAATCATTTTACCT
1 CATAAGGGCAAAACAGTCATTTTACCC
* *
85431738 CATAAGGGCAAAACAATCATTTTATCC
1 CATAAGGGCAAAACAGTCATTTTACCC
* * *
85431765 CATAAGGACAAAACAGTTATTTTACCA
1 CATAAGGGCAAAACAGTCATTTTACCC
*
85431792 CATAAGGGCAAAACAATCATTTTACCC
1 CATAAGGGCAAAACAGTCATTTTACCC
* *
85431819 CATAAAGGCAAAAGAGTCATTTTA
1 CATAAGGGCAAAACAGTCATTTTA
85431843 TCAATTAAGG
Statistics
Matches: 205, Mismatches: 35, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
27 181 0.88
28 24 0.12
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.25
Consensus pattern (27 bp):
CATAAGGGCAAAACAGTCATTTTACCC
Found at i:85437514 original size:19 final size:20
Alignment explanation
Indices: 85437448--85437524 Score: 81
Period size: 19 Copynumber: 4.0 Consensus size: 20
85437438 CACTCTCAAT
*
85437448 CATATAAACAGTAATTCATT
1 CATATAAACAGTAATTCATC
*
85437468 C-GAT-AACAGTAACTT-ATC
1 CATATAAACAGTAA-TTCATC
* *
85437486 CATTTAAACAGTACTTCATC
1 CATATAAACAGTAATTCATC
85437506 CATAT-AACAGTAATTCATC
1 CATATAAACAGTAATTCATC
85437525 TGTGTAACAC
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
18 11 0.24
19 20 0.43
20 15 0.33
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.32
Consensus pattern (20 bp):
CATATAAACAGTAATTCATC
Found at i:85449478 original size:39 final size:40
Alignment explanation
Indices: 85449327--85449496 Score: 189
Period size: 40 Copynumber: 4.3 Consensus size: 40
85449317 GGACTAAGAT
* * * *
85449327 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGTGAGTTACTAAATCCGGGTTAAGTC
* * * *
85449367 TCGAGGGCATTCGTGTGAGTTATTAAAGCCGGGTTAAGTC
1 CCGAAGGCATTCGTGTGAGTTACTAAATCCGGGTTAAGTC
* ** *
85449407 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTACGTC
1 CCGAAGGCATTCGTGTGAGTTACTAAATCCGGGTTAAGTC
* * * *
85449447 CCGAAGGCA-TGGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGTGAGTTACTAAATCCGGGTTAAGTC
85449486 CCGAAGGCATT
1 CCGAAGGCATT
85449497 TGAACGAGGA
Statistics
Matches: 108, Mismatches: 21, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
39 32 0.30
40 76 0.70
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTCGTGTGAGTTACTAAATCCGGGTTAAGTC
Found at i:85449494 original size:79 final size:80
Alignment explanation
Indices: 85449327--85449496 Score: 216
Period size: 80 Copynumber: 2.1 Consensus size: 80
85449317 GGACTAAGAT
* * * * *
85449327 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCTCGAGGGCATTCGTGTGAGTTATTA
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGTGAGTTACTA
* *
85449392 AAGCCGGGTTAAGTC
66 AAACCGGGCTAAGTC
* ** * *
85449407 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTACGTCCCGAAGGCA-TGGTGTGAGTTACTA
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGTGAGTTACTA
*
85449471 AAACCGGGCTATGTC
66 AAACCGGGCTAAGTC
85449486 CCGAAGGCATT
1 CCGAAGGCATT
85449497 TGAACGAGGA
Statistics
Matches: 77, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
79 36 0.47
80 41 0.53
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.26
Consensus pattern (80 bp):
CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGTGAGTTACTA
AAACCGGGCTAAGTC
Found at i:85449516 original size:79 final size:80
Alignment explanation
Indices: 85449349--85449531 Score: 208
Period size: 79 Copynumber: 2.3 Consensus size: 80
85449339 GTGCGAGATA
* * * * *
85449349 CTAAATCCGGGTTAAGTCTCGAGGGCATTCGTGTGAGTTATTAAAGCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGTGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
85449414 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
85449429 TTAAATCCGGGTTACGTCCCGAAGGCA-TGGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGTGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
85449493 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
85449508 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
85449532 TACGTGATTT
Statistics
Matches: 85, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
78 14 0.16
79 48 0.56
80 23 0.27
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGTGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:85452878 original size:34 final size:34
Alignment explanation
Indices: 85452835--85452906 Score: 137
Period size: 34 Copynumber: 2.1 Consensus size: 34
85452825 ATCGAATTTC
85452835 CTTATCAATCTCAATCGGGTCATTTATCAACATA
1 CTTATCAATCTCAATCGGGTCATTTATCAACATA
85452869 CTTATCAATCTCAATCGGGTCATTTATCAACATA
1 CTTATCAATCTCAATCGGGTCATTTATCAACATA
85452903 -TTAT
1 CTTAT
85452907 TATTAAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 4 0.11
34 34 0.89
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (34 bp):
CTTATCAATCTCAATCGGGTCATTTATCAACATA
Found at i:85455221 original size:48 final size:48
Alignment explanation
Indices: 85455163--85455301 Score: 235
Period size: 48 Copynumber: 2.9 Consensus size: 48
85455153 AATATATATA
*
85455163 TTAGTTTGCAATTTACCGTGTTATGAAACGACATAAATCCAACGACGT
1 TTAGTATGCAATTTACCGTGTTATGAAACGACATAAATCCAACGACGT
* *
85455211 TTAGTATGCAACTTACCGTGTTATGAAACGACATAAATCCAATGACGT
1 TTAGTATGCAATTTACCGTGTTATGAAACGACATAAATCCAACGACGT
*
85455259 TTAGTATGCAATTTACTGTGTTAT-AAACGACATAAATCCAACG
1 TTAGTATGCAATTTACCGTGTTATGAAACGACATAAATCCAACG
85455302 GTGTACAACA
Statistics
Matches: 85, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
47 18 0.21
48 67 0.79
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (48 bp):
TTAGTATGCAATTTACCGTGTTATGAAACGACATAAATCCAACGACGT
Found at i:85455561 original size:23 final size:25
Alignment explanation
Indices: 85455511--85455562 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
85455501 GCCTATTTTC
*
85455511 ACAGCTCGCGTGAGCATATCAATTT
1 ACAGCTCGCGTGAGCATATCAATGT
* *
85455536 ACAGTTCGTGTGAGCATA-C-ATGT
1 ACAGCTCGCGTGAGCATATCAATGT
85455559 ACAG
1 ACAG
85455563 GAATTGACGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 7 0.29
24 1 0.04
25 16 0.67
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (25 bp):
ACAGCTCGCGTGAGCATATCAATGT
Found at i:85456678 original size:20 final size:20
Alignment explanation
Indices: 85456645--85456683 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
85456635 GCTATATGGT
85456645 TTGGCTTGTGTTATGGTATC
1 TTGGCTTGTGTTATGGTATC
85456665 TTGG-TTGTGATTATGGTAT
1 TTGGCTTGTG-TTATGGTAT
85456684 TTTGAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.13, C:0.05, G:0.31, T:0.51
Consensus pattern (20 bp):
TTGGCTTGTGTTATGGTATC
Found at i:85462407 original size:94 final size:94
Alignment explanation
Indices: 85462230--85462418 Score: 251
Period size: 94 Copynumber: 2.0 Consensus size: 94
85462220 AGCAAACGAG
* **
85462230 ATATGAAATACATTGTGATCACTCTCACTTCCACTATGGAATCATAGCTATAAAATCTCGATGGT
1 ATATGAAATACATCGTGATCACTCTCACTTCCACTATGGAAAAATAGCTATAAAATCTCGATGGT
*
85462295 ACCTGATGATCTGCTTTACCTGCTGAAAA
66 ACCTGATGATCTGCTTTACCTGCTAAAAA
* *
85462324 ATATGAAATTCATCGTGACTCACTTTCACTTCCACTATGGAAAAATAGGCTATAATAATC-CGAT
1 ATATGAAATACATCGTGA-TCACTCTCACTTCCACTATGGAAAAATA-GCTATAA-AATCTCGAT
*
85462388 -G-ACCTGATGCTC-GCTTTTACCTGCTAAAAA
63 GGTACCTGATGATCTGC-TTTACCTGCTAAAAA
85462418 A
1 A
85462419 CTCACAAATC
Statistics
Matches: 84, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
93 2 0.02
94 41 0.49
95 26 0.31
96 11 0.13
97 4 0.05
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (94 bp):
ATATGAAATACATCGTGATCACTCTCACTTCCACTATGGAAAAATAGCTATAAAATCTCGATGGT
ACCTGATGATCTGCTTTACCTGCTAAAAA
Found at i:85468467 original size:39 final size:39
Alignment explanation
Indices: 85468400--85468525 Score: 200
Period size: 39 Copynumber: 3.3 Consensus size: 39
85468390 CCAGCAATAT
*
85468400 GCCTGCTAGGTAT-AACCTGAACTTAACACCGGCACGAT
1 GCCTGCTAGGTATAAACCTGAACTTAACACCGGCACGAG
* ** *
85468438 GCCTGCTAGGTATAAACCTAAACTTAACACTAGCACTAG
1 GCCTGCTAGGTATAAACCTGAACTTAACACCGGCACGAG
85468477 GCCTGCTAGGTATAAACCTGAACTTAACACCGGCACGAG
1 GCCTGCTAGGTATAAACCTGAACTTAACACCGGCACGAG
85468516 GCCTGCTAGG
1 GCCTGCTAGG
85468526 CTCATGGCCC
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
38 13 0.17
39 65 0.83
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (39 bp):
GCCTGCTAGGTATAAACCTGAACTTAACACCGGCACGAG
Found at i:85470975 original size:29 final size:29
Alignment explanation
Indices: 85470943--85471010 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
85470933 AAGTCTACAT
* *
85470943 ACATGCATATGGCCCACTAGGCCCGAATC
1 ACATTCATATGGCCCACTAGGCCCAAATC
* *
85470972 ACATTCGTATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCACTAGGCCCAAATC
85471001 ACATTCATAT
1 ACATTCATAT
85471011 ACATGCTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (29 bp):
ACATTCATATGGCCCACTAGGCCCAAATC
Found at i:85475400 original size:38 final size:39
Alignment explanation
Indices: 85475255--85475434 Score: 181
Period size: 39 Copynumber: 4.6 Consensus size: 39
85475245 TATTCGAATG
*
85475255 ATATCCGGGCTAAG-TCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATAT-CGGGCTAAGAT-CCGAAGGCATTTGTGCTA-GTGACT
* * * *
85475296 ATAACCGGACTAAGATCCGAAGGCATTCGTGC-GGTTG-CT
1 AT-ATCGGGCTAAGATCCGAAGGCATTTGTGCTAG-TGACT
* *
85475335 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATAT-CGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
*
85475375 ATATCGGGCTAAG-TCCGAAGGCATTTATGCTAGTGAC-
1 ATATCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
* *
85475412 ATATCCGGCTAAGACCCGAAGGC
1 ATATCGGGCTAAGATCCGAAGGC
85475435 CTTGTGCAAG
Statistics
Matches: 116, Mismatches: 16, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
37 12 0.10
38 30 0.26
39 39 0.34
40 9 0.08
41 24 0.21
42 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (39 bp):
ATATCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
Found at i:85475454 original size:38 final size:38
Alignment explanation
Indices: 85475255--85475470 Score: 172
Period size: 38 Copynumber: 5.6 Consensus size: 38
85475245 TATTCGAATG
* * *
85475255 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCC-GGCTAAGACCCGAAGGCATTTGTGC-AAGTG-CT
* * * *
85475296 ATAACCGGACTAAGATCCGAAGGCATTCGTGC-GGTTGCT
1 ATATCCGG-CTAAGACCCGAAGGCATTTGTGCAAG-TGCT
* *
85475335 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCC-GGCTAAGACCCGAAGGCATTTGTGCAAGTG-CT
* * * *
85475375 ATATCGGGCTAAG-TCCGAAGGCATTTATGCTAGTGAC-
1 ATATCCGGCTAAGACCCGAAGGCATTTGTGCAAGTG-CT
* *
85475412 ATATCCGGCTAAGACCCGAAGGC-CTTGTGCAAGTAGTT
1 ATATCCGGCTAAGACCCGAAGGCATTTGTGCAAGT-GCT
85475450 ATATCCGGCTAA-ATCCCGAAG
1 ATATCCGGCTAAGA-CCCGAAG
85475471 ATTACTTGAG
Statistics
Matches: 146, Mismatches: 20, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
37 21 0.14
38 49 0.34
39 38 0.26
40 14 0.10
41 24 0.16
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (38 bp):
ATATCCGGCTAAGACCCGAAGGCATTTGTGCAAGTGCT
Found at i:85483280 original size:40 final size:40
Alignment explanation
Indices: 85483186--85483370 Score: 212
Period size: 40 Copynumber: 4.6 Consensus size: 40
85483176 TATTCAAATG
*
85483186 ATATCCGGGCTAAG-TCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTA-GTGACT
* * * * * *
85483227 ATAACCGGACTAAGATTCGAAGGCATTCGTGCCAGTTACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
* *
85483267 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
* * *
85483307 ATATCTGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGTGACT
*
85483347 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
85483371 CTTATGCAAG
Statistics
Matches: 119, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
40 92 0.77
41 26 0.22
42 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
Found at i:85483356 original size:80 final size:81
Alignment explanation
Indices: 85483186--85483370 Score: 239
Period size: 80 Copynumber: 2.3 Consensus size: 81
85483176 TATTCAAATG
* * * *
85483186 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGATTCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGATCCGAAGGC
* * *
85483251 ATTCGTGCCAGTTACT
66 ATTCATGCCAGTGACC
* * *
85483267 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTA-GCGACTATATCTGGGCTAAG-TCCCGAAGG
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGAT-CCGAAGG
* *
85483330 CATTTATGCTAGTGACC
65 CATTCATGCCAGTGACC
85483347 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
85483371 CTTATGCAAG
Statistics
Matches: 91, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
79 1 0.01
80 58 0.64
81 32 0.35
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.24
Consensus pattern (81 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGATCCGAAGGC
ATTCATGCCAGTGACC
Found at i:85486561 original size:29 final size:29
Alignment explanation
Indices: 85486448--85486563 Score: 187
Period size: 29 Copynumber: 4.0 Consensus size: 29
85486438 ATACATGTAC
* *
85486448 ATGGCCCACTAGGCCCAAATCACATTCGT
1 ATGGCCCATTAGGCCCAAATCACATTCAT
* **
85486477 ATGGCCCATTAGGCCCGAATCACATTTGT
1 ATGGCCCATTAGGCCCAAATCACATTCAT
85486506 ATGGCCCATTAGGCCCAAATCACATTCAT
1 ATGGCCCATTAGGCCCAAATCACATTCAT
85486535 ATGGCCCATTAGGCCCAAATCACATTCAT
1 ATGGCCCATTAGGCCCAAATCACATTCAT
85486564 CTACATGCTT
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 81 1.00
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.24
Consensus pattern (29 bp):
ATGGCCCATTAGGCCCAAATCACATTCAT
Found at i:85491238 original size:40 final size:40
Alignment explanation
Indices: 85491151--85491332 Score: 167
Period size: 40 Copynumber: 4.6 Consensus size: 40
85491141 AATGATGTCT
* * *
85491151 GGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT-TCC
* * *
85491191 GGACTAAGAT-CCGAAGGCATTTGTGCTAGTTACTAATTTC
1 GGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAATTCC
* *
85491231 GGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
* * * * *
85491270 GTGTTAAGTCCCGAAGGCATTTGTGCGAGTTTCT-ATAACT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCC
*
85491310 GGGCTATGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
85491333 AACGAGTAGC
Statistics
Matches: 116, Mismatches: 20, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
39 33 0.28
40 73 0.63
41 10 0.09
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
Found at i:85491355 original size:79 final size:79
Alignment explanation
Indices: 85491201--85491355 Score: 181
Period size: 79 Copynumber: 2.0 Consensus size: 79
85491191 GGACTAAGAT
* ** **
85491201 CCGAAGGCATTTGTGCTAGTTACTAATTTCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAAACTCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
85491266 ATCCGTGTTAAGTC
66 ATCCGTGTTAAGTC
* * *
85491280 CCGAAGGCATTTGTGCGAGTTTCTATAACT-GGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTA-AACTCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
*
85491343 TATATCCG-GTTAA
63 TAAATCCGTGTTAA
85491356 ATCTGAAGGT
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
79 37 0.58
80 27 0.42
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAAACTCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGTGTTAAGTC
Found at i:85499259 original size:40 final size:39
Alignment explanation
Indices: 85499175--85499359 Score: 146
Period size: 40 Copynumber: 4.6 Consensus size: 39
85499165 TCGAATGATG
* * * *
85499175 TCCGAGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA-
1 TCCG-GCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAAT
85499215 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACT-AAT
1 TCCGG-CTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAAT
* * *
85499255 TCCGGGCTAAGCCCAAAGGCATTGGTGCGAGTTACTAAAT
1 TCC-GGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAAT
* * *
85499295 TCAGGTTAAGTCCTGAAGGCATTTGTGCGAGTTAGTATAA-
1 TCCGGCTAAGTCC-GAAGGCATTTGTGCGAGTTACTA-AAT
*
85499335 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCC-GGCTAAGT-CCGAAGGCATTTG
85499360 AACGAGTAGC
Statistics
Matches: 119, Mismatches: 16, Indels: 20
0.77 0.10 0.13
Matches are distributed among these distances:
39 33 0.28
40 72 0.61
41 14 0.12
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAAT
Found at i:85499381 original size:79 final size:78
Alignment explanation
Indices: 85499212--85499382 Score: 177
Period size: 79 Copynumber: 2.2 Consensus size: 78
85499202 CTAAGTGACC
* *
85499212 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCAAAGGCAT
1 ATATCCGG-TTAAGATCCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCAAAGGCAT
**
85499277 TGGTGCGAGTTACT
65 TGGAACGAGTTACT
* * * * *
85499291 AAATTCAGGTTAAG-TCCTGAAGGCATTTGTGCGAGTTAGT-ATAACCGGGCTATGTCCCGAAGG
1 ATA-TCCGGTTAAGATCC-GAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCAAAGG
*
85499354 CATTTGAACGAG-TAGCT
62 CATTGGAACGAGTTA-CT
85499371 ATATCCGGTTAA
1 ATATCCGGTTAA
85499383 ATTTCGAAGG
Statistics
Matches: 75, Mismatches: 12, Indels: 10
0.77 0.12 0.10
Matches are distributed among these distances:
78 5 0.07
79 46 0.61
80 24 0.32
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.27
Consensus pattern (78 bp):
ATATCCGGTTAAGATCCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCAAAGGCATT
GGAACGAGTTACT
Found at i:85504818 original size:18 final size:18
Alignment explanation
Indices: 85504795--85504831 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
85504785 ATGGACATAT
*
85504795 TGATGCATACTTTAAAAA
1 TGATGCACACTTTAAAAA
*
85504813 TGATGCACATTTTAAAAA
1 TGATGCACACTTTAAAAA
85504831 T
1 T
85504832 TTTCCTACCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (18 bp):
TGATGCACACTTTAAAAA
Found at i:85504953 original size:22 final size:23
Alignment explanation
Indices: 85504912--85504986 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 23
85504902 TGGACTAGCC
* **
85504912 ACCACTGATTTGGAGTTAAACT-
1 ACCACTGATTTGTAAATAAACTA
* *
85504934 ATCATTGATTTGTAAATAAA-TA
1 ACCACTGATTTGTAAATAAACTA
*
85504956 ACCACTGATTTGTAGATAAACT-
1 ACCACTGATTTGTAAATAAACTA
*
85504978 GCCACTGAT
1 ACCACTGAT
85504987 AACACTGATG
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
21 1 0.02
22 40 0.95
23 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (23 bp):
ACCACTGATTTGTAAATAAACTA
Found at i:85506771 original size:28 final size:27
Alignment explanation
Indices: 85506714--85506811 Score: 178
Period size: 27 Copynumber: 3.6 Consensus size: 27
85506704 TAAATTGTGC
85506714 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
85506741 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
85506769 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
85506796 AGCACTAAGTGTGCGA
1 AGCACTAAGTGTGCGA
85506812 GTTTGACTGT
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
27 42 0.62
28 26 0.38
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:85506778 original size:55 final size:55
Alignment explanation
Indices: 85506714--85506963 Score: 362
Period size: 55 Copynumber: 4.8 Consensus size: 55
85506704 TAAATTGTGC
85506714 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
85506769 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGA----G--T-T-T
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
85506816 -G-ACT--GTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* *
85506867 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * * *
85506922 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCG
85506964 GACTTAATAT
Statistics
Matches: 178, Mismatches: 5, Indels: 24
0.86 0.02 0.12
Matches are distributed among these distances:
43 35 0.20
45 3 0.02
46 1 0.01
47 2 0.01
48 1 0.01
49 2 0.01
50 1 0.01
51 2 0.01
52 1 0.01
53 3 0.02
55 127 0.71
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:85506838 original size:43 final size:43
Alignment explanation
Indices: 85506777--85506862 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
85506767 GTAGCACTAA
85506777 GTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACT
1 GTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACT
85506820 GTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACT
1 GTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACT
85506863 ATGTAGCACT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.23, C:0.14, G:0.30, T:0.33
Consensus pattern (43 bp):
GTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACT
Found at i:85506839 original size:98 final size:98
Alignment explanation
Indices: 85506722--85506915 Score: 379
Period size: 98 Copynumber: 2.0 Consensus size: 98
85506712 GCAGCACTAA
85506722 GTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAAT
1 GTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAAT
85506787 TGACTATGTAGCACTAAGTGTGCGAGTTTGACT
66 TGACTATGTAGCACTAAGTGTGCGAGTTTGACT
*
85506820 GTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGT
1 GTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAAT
85506885 TGACTATGTAGCACTAAGTGTGCGAGTTTGA
66 TGACTATGTAGCACTAAGTGTGCGAGTTTGA
85506916 TTATGTAGCA
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 95 1.00
ACGTcount: A:0.25, C:0.14, G:0.29, T:0.31
Consensus pattern (98 bp):
GTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAAT
TGACTATGTAGCACTAAGTGTGCGAGTTTGACT
Found at i:85506895 original size:27 final size:27
Alignment explanation
Indices: 85506820--85506963 Score: 225
Period size: 27 Copynumber: 5.3 Consensus size: 27
85506810 GAGTTTGACT
*
85506820 GTGTGCGAATTGACTATGTAGCACTAA
1 GTGTGCGAGTTGACTATGTAGCACTAA
85506847 GTGTGCGAGTTTGACTATGTAGCACTAA
1 GTGTGCGAG-TTGACTATGTAGCACTAA
85506875 GTGTGCGAGTTGACTATGTAGCACTAA
1 GTGTGCGAGTTGACTATGTAGCACTAA
*
85506902 GTGTGCGAGTTTGATTATGTAGCACTAA
1 GTGTGCGAG-TTGACTATGTAGCACTAA
* * *
85506930 GTGTGCGAGTTGATTATATAGCACTGA
1 GTGTGCGAGTTGACTATGTAGCACTAA
85506957 GTGTGCG
1 GTGTGCG
85506964 GACTTAATAT
Statistics
Matches: 111, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
27 58 0.52
28 53 0.48
ACGTcount: A:0.25, C:0.13, G:0.30, T:0.32
Consensus pattern (27 bp):
GTGTGCGAGTTGACTATGTAGCACTAA
Found at i:85513360 original size:47 final size:47
Alignment explanation
Indices: 85513279--85513482 Score: 286
Period size: 47 Copynumber: 4.3 Consensus size: 47
85513269 TAATTGAATA
* *
85513279 AATGTGAA-AGTGTATATGTGTGAATAGGGCCGAATGGCCAATGTGATG
1 AATGTGAACA-TGTGTATGTGTG-ATAAGGCCGAATGGCCAATGTGATG
** * *
85513327 AATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
85513374 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
* * *
85513421 AAAGTGAACAGGTGTATGTGTGATAAGG-CGAGTGGCCAATGTGATG
1 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
*
85513467 AATGTGAGCATGTGTA
1 AATGTGAACATGTGTA
85513483 NNNNNNNNNN
Statistics
Matches: 141, Mismatches: 14, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
46 30 0.21
47 93 0.66
48 17 0.12
49 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.32, T:0.26
Consensus pattern (47 bp):
AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:85524924 original size:33 final size:33
Alignment explanation
Indices: 85524886--85524948 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
85524876 GATTACTCAC
85524886 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
85524919 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
85524949 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:85524975 original size:21 final size:21
Alignment explanation
Indices: 85524946--85525001 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
85524936 CAAGCTCTCT
*
85524946 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
85524967 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
85524988 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
85525002 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:85524994 original size:14 final size:14
Alignment explanation
Indices: 85524945--85525001 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
85524935 TCAAGCTCTC
85524945 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
85524958 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
85524972 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
85524986 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
85525000 TT
1 TT
85525002 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:85525029 original size:18 final size:18
Alignment explanation
Indices: 85525008--85525066 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
85524998 TTTTCTCTCA
85525008 CTTTTTTGATTTCTTTTT
1 CTTTTTTGATTTCTTTTT
***
85525026 CTTTTGCAATTTCTTTTT
1 CTTTTTTGATTTCTTTTT
*
85525044 CTTTTTTGTTTTCTTTTT
1 CTTTTTTGATTTCTTTTT
*
85525062 GTTTT
1 CTTTT
85525067 CTTTCAATTT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.05, C:0.12, G:0.07, T:0.76
Consensus pattern (18 bp):
CTTTTTTGATTTCTTTTT
Found at i:85525055 original size:12 final size:12
Alignment explanation
Indices: 85525040--85525070 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
85525030 TGCAATTTCT
85525040 TTTTCTTTTTTG
1 TTTTCTTTTTTG
85525052 TTTTC-TTTTTG
1 TTTTCTTTTTTG
85525063 TTTTCTTT
1 TTTTCTTT
85525071 CAATTTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (12 bp):
TTTTCTTTTTTG
Found at i:85525083 original size:6 final size:6
Alignment explanation
Indices: 85524963--85525070 Score: 60
Period size: 6 Copynumber: 17.7 Consensus size: 6
85524953 TCTTTTTTCG
* * * **
85524963 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
* * **
85525014 -TGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT -TGTTTT CTTTTT
1 CT-TTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CT-TTTT CTTTTT
*
85525062 -GTTTT CTTT
1 CTTTTT CTTT
85525071 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 21, Indels: 14
0.68 0.19 0.13
Matches are distributed among these distances:
5 6 0.08
6 54 0.73
7 11 0.15
8 3 0.04
ACGTcount: A:0.06, C:0.17, G:0.04, T:0.73
Consensus pattern (6 bp):
CTTTTT
Found at i:85526148 original size:10 final size:11
Alignment explanation
Indices: 85526133--85526174 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
85526123 TGTCACTTCT
85526133 TTTTTTTTTC-
1 TTTTTTTTTCA
85526143 TTTTTTTTTCAA
1 TTTTTTTTTC-A
**
85526155 TTTTTTTTGAA
1 TTTTTTTTTCA
85526166 TTTTTTTTT
1 TTTTTTTTT
85526175 GAATTTCTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 10 0.37
11 9 0.33
12 8 0.30
ACGTcount: A:0.10, C:0.05, G:0.02, T:0.83
Consensus pattern (11 bp):
TTTTTTTTTCA
Found at i:85526158 original size:11 final size:11
Alignment explanation
Indices: 85526134--85526173 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
85526124 GTCACTTCTT
*
85526134 TTTTTTTTC-T
1 TTTTTTTTCAA
85526144 TTTTTTTTCAA
1 TTTTTTTTCAA
*
85526155 TTTTTTTTGAA
1 TTTTTTTTCAA
85526166 TTTTTTTT
1 TTTTTTTT
85526174 TGAATTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.10, C:0.05, G:0.03, T:0.82
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:85526158 original size:12 final size:12
Alignment explanation
Indices: 85526133--85526180 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
85526123 TGTCACTTCT
85526133 TTTTTTTTTC--
1 TTTTTTTTTCAA
85526143 TTTTTTTTTCAA
1 TTTTTTTTTCAA
*
85526155 -TTTTTTTTGAA
1 TTTTTTTTTCAA
*
85526166 TTTTTTTTTGAA
1 TTTTTTTTTCAA
85526178 TTT
1 TTT
85526181 CTTCTCTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
10 10 0.29
11 10 0.29
12 14 0.41
ACGTcount: A:0.12, C:0.04, G:0.04, T:0.79
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:85526279 original size:12 final size:12
Alignment explanation
Indices: 85526264--85526295 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
85526254 CCAACTCAAA
85526264 TTTTTTTTTGA-
1 TTTTTTTTTGAC
85526275 TTTTTTTTTGAC
1 TTTTTTTTTGAC
85526287 TTTTTTTTT
1 TTTTTTTTT
85526296 CGTTACGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTGAC
Found at i:85530116 original size:23 final size:22
Alignment explanation
Indices: 85530065--85530116 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
85530055 CCTCGTCTTT
*
85530065 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
85530087 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
85530110 TTCTTTT
1 TTCTTTT
85530117 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:85530131 original size:18 final size:18
Alignment explanation
Indices: 85530110--85530148 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
85530100 TTTCTTCAAC
*
85530110 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTTCTT
*
85530128 TTCTGTTTCACATTTCTT
1 TTCTGTTTCAAATTTCTT
85530146 TTC
1 TTC
85530149 ACTCTCAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.13, C:0.21, G:0.03, T:0.64
Consensus pattern (18 bp):
TTCTGTTTCAAATTTCTT
Found at i:85533748 original size:11 final size:11
Alignment explanation
Indices: 85533710--85533748 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
85533700 TTAGTGAAAG
*
85533710 AAAAAATTCTA
1 AAAAAATTCAA
*
85533721 AAAAAATTCGA
1 AAAAAATTCAA
85533732 AAAAAATTCAA
1 AAAAAATTCAA
85533743 AAAAAA
1 AAAAAA
85533749 GTGTGTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.72, C:0.08, G:0.03, T:0.18
Consensus pattern (11 bp):
AAAAAATTCAA
Found at i:85534678 original size:15 final size:15
Alignment explanation
Indices: 85534631--85534672 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
85534621 ATCTTCTTGT
*
85534631 AAAAAGAAAACG-AG
1 AAAAAGAAAAAGAAG
*
85534645 -AAAAGCAAAAGAAG
1 AAAAAGAAAAAGAAG
85534659 AAAAAGAAAAAGAA
1 AAAAAGAAAAAGAA
85534673 ATAAAATAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 9 0.39
14 2 0.09
15 12 0.52
ACGTcount: A:0.76, C:0.05, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAGAAG
Found at i:85534788 original size:12 final size:12
Alignment explanation
Indices: 85534764--85534823 Score: 75
Period size: 12 Copynumber: 5.0 Consensus size: 12
85534754 AAAAAGAACG
*
85534764 AAAAGAGAGTGA
1 AAAAGAGATTGA
*
85534776 AAATGAGATTGA
1 AAAAGAGATTGA
*
85534788 AAAAGAAATTGA
1 AAAAGAGATTGA
*
85534800 AAAAGAGAATGA
1 AAAAGAGATTGA
*
85534812 AAAAGAGTTTGA
1 AAAAGAGATTGA
85534824 GAGAGAAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.58, C:0.00, G:0.25, T:0.17
Consensus pattern (12 bp):
AAAAGAGATTGA
Found at i:85539221 original size:13 final size:13
Alignment explanation
Indices: 85539203--85539227 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
85539193 TGGTCATCAT
85539203 GGTGTGAACACAA
1 GGTGTGAACACAA
85539216 GGTGTGAACACA
1 GGTGTGAACACA
85539228 TGATCAATAC
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:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:85543665 original size:13 final size:13
Alignment explanation
Indices: 85543647--85543671 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
85543637 GACATGAACA
85543647 CATTTAATCATAT
1 CATTTAATCATAT
85543660 CATTTAATCATA
1 CATTTAATCATA
85543672 ATTAAACAGC
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:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (13 bp):
CATTTAATCATAT
Found at i:85545754 original size:30 final size:30
Alignment explanation
Indices: 85545652--85545754 Score: 84
Period size: 30 Copynumber: 3.5 Consensus size: 30
85545642 TCAAGTTAAA
*
85545652 CTAAA-ATGAGCTAAGCTTTAGCTCGTGAG
1 CTAAATATGAGCTAAGATTTAGCTCGTGAG
* * * * * *
85545681 CTAAAGT-TAAGCTGAGATTAAACTCCTAAG
1 CTAAA-TATGAGCTAAGATTTAGCTCGTGAG
* ** *
85545711 CTGAAGCTGAGCTAAGGTTTAGCTCGTGAG
1 CTAAATATGAGCTAAGATTTAGCTCGTGAG
85545741 CTAAATATGAGCTA
1 CTAAATATGAGCTA
85545755 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 19, Indels: 5
0.68 0.25 0.07
Matches are distributed among these distances:
29 5 0.10
30 47 0.90
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (30 bp):
CTAAATATGAGCTAAGATTTAGCTCGTGAG
Found at i:85546391 original size:6 final size:5
Alignment explanation
Indices: 85546367--85546429 Score: 58
Period size: 5 Copynumber: 12.0 Consensus size: 5
85546357 AAGGGAAAAC
*
85546367 AAAGA AAAGA AAAGAA AAAGCA AAAGCA AAAGA AGA-A AAAGA AAATGA
1 AAAGA AAAGA AAAG-A AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA
85546415 AATA-A AAAGA AAAGA
1 AA-AGA AAAGA AAAGA
85546430 GAGGCAAGAG
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
4 4 0.08
5 25 0.50
6 20 0.40
7 1 0.02
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:85546397 original size:12 final size:10
Alignment explanation
Indices: 85546367--85546429 Score: 58
Period size: 11 Copynumber: 6.0 Consensus size: 10
85546357 AAGGGAAAAC
85546367 AAAGAAAAGA
1 AAAGAAAAGA
85546377 AAAGAAAAAGCA
1 AAAG-AAAAG-A
85546389 AAAGCAAAAGA
1 AAAG-AAAAGA
*
85546400 AGA-AAAAGA
1 AAAGAAAAGA
85546409 AAATGAAATA-A
1 AAA-GAAA-AGA
85546420 AAAGAAAAGA
1 AAAGAAAAGA
85546430 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
9 9 0.20
10 9 0.20
11 15 0.34
12 11 0.25
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.03
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:85546533 original size:30 final size:31
Alignment explanation
Indices: 85546497--85546578 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
85546487 TTTTGAAATC
* * *
85546497 AAAAAGAAAAAGAAAAAGAAA-ATGAGATTG
1 AAAAAGAGAATGAAAAAGAAATATGAGAGTG
*
85546527 AAAAAGAGAATG-AAAAGAAATTTGAGAGTG
1 AAAAAGAGAATGAAAAAGAAATATGAGAGTG
*
85546557 AAAAAGAGGATGAAAAAGAAAT
1 AAAAAGAGAATGAAAAAGAAAT
85546579 TGAAACAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 8 0.18
30 28 0.62
31 9 0.20
ACGTcount: A:0.65, C:0.00, G:0.23, T:0.12
Consensus pattern (31 bp):
AAAAAGAGAATGAAAAAGAAATATGAGAGTG
Found at i:85546551 original size:24 final size:24
Alignment explanation
Indices: 85546502--85546548 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
85546492 AAATCAAAAA
*
85546502 GAAAAAGAAAAAGAAAATGAGATT
1 GAAAAAGAAAAAGAAAATGAAATT
* *
85546526 GAAAAAGAGAATGAAAA-GAAATT
1 GAAAAAGAAAAAGAAAATGAAATT
85546549 TGAGAGTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.66, C:0.00, G:0.21, T:0.13
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAATGAAATT
Found at i:85549814 original size:23 final size:22
Alignment explanation
Indices: 85549762--85549814 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
85549752 TCCACGTCTT
*
85549762 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
85549784 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
85549807 TTTCTTTT
1 TTTCTTTT
85549815 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:85553448 original size:30 final size:30
Alignment explanation
Indices: 85553414--85553510 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
85553404 AGCTCACTCC
*
85553414 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAACCT
* * * * *
85553444 TAGCTCAACTTTAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
85553474 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
85553504 TAGCTCA
1 TAGCTCA
85553511 TTTTAATTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
30 47 0.90
31 5 0.10
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:85555876 original size:20 final size:20
Alignment explanation
Indices: 85555853--85555900 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
85555843 AGCTCCGTCT
85555853 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTG
*** *
85555873 AGCTCGTTTCAGCTCGTTTG
1 AGCTCAACTCAGCTCATTTG
85555893 AGCTCAAC
1 AGCTCAAC
85555901 CGAGCTTACT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:85561307 original size:30 final size:30
Alignment explanation
Indices: 85561273--85561369 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
85561263 TAAACTAAAA
* *
85561273 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* * * * * *
85561303 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* *
85561333 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGATTTAGCTCGTGAGCT-AAAGT
85561363 TGAGCTA
1 TGAGCTA
85561370 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 47 0.94
31 3 0.06
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
Found at i:85562223 original size:21 final size:21
Alignment explanation
Indices: 85562197--85562240 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
85562187 TTGGTATTTG
*
85562197 GGAATTGGTTCGAAATAGTAT
1 GGAATTGGTACGAAATAGTAT
*
85562218 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATAGTAT
85562239 GG
1 GG
85562241 TATTTGGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.05, G:0.34, T:0.30
Consensus pattern (21 bp):
GGAATTGGTACGAAATAGTAT
Found at i:85562252 original size:22 final size:22
Alignment explanation
Indices: 85562207--85562264 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
85562197 GGAATTGGTT
* *
85562207 CGAAATAGTATGG-AATTGGTA
1 CGAAATGGTATGGTAATTGGAA
*
85562228 CGAAATGGTATGGTATTTGGAA
1 CGAAATGGTATGGTAATTGGAA
*
85562250 CGAATTGGTAATGGT
1 CGAAATGGT-ATGGT
85562265 TCAAAAGGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 12 0.39
22 14 0.45
23 5 0.16
ACGTcount: A:0.33, C:0.05, G:0.31, T:0.31
Consensus pattern (22 bp):
CGAAATGGTATGGTAATTGGAA
Found at i:85565179 original size:12 final size:12
Alignment explanation
Indices: 85565164--85565194 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
85565154 TTCTTTTTGC
85565164 TTTTCAAAGGCT
1 TTTTCAAAGGCT
85565176 TTTTCAAAGGCT
1 TTTTCAAAGGCT
85565188 TTTTCAA
1 TTTTCAA
85565195 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:85565252 original size:5 final size:5
Alignment explanation
Indices: 85565242--85565298 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
85565232 CTCTTGCCTC
*
85565242 TCTTT TCTTT T-TATT TCTTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
85565289 TCTTT TCTTT
1 TCTTT TCTTT
85565299 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:85565262 original size:15 final size:14
Alignment explanation
Indices: 85565242--85565305 Score: 65
Period size: 16 Copynumber: 4.2 Consensus size: 14
85565232 CTCTTGCCTC
85565242 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-TT
*
85565257 TCTTTTTCTTTTTCT
1 TC-TTTTCTTTTTTT
85565272 TCTTTTGCTTTTTCTTT
1 TCTTTT-C-TTTT-TTT
*
85565289 TCTTTTCTTTGTTT
1 TCTTTTCTTTTTTT
85565303 TCT
1 TCT
85565306 CTTTACAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
14 10 0.24
15 9 0.21
16 15 0.36
17 8 0.19
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.78
Consensus pattern (14 bp):
TCTTTTCTTTTTTT
Found at i:85565274 original size:25 final size:25
Alignment explanation
Indices: 85565246--85565294 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
85565236 TGCCTCTCTT
85565246 TTCTTTT-TATTTCTTTTTCTTTTTC
1 TTCTTTTCTATTTC-TTTTCTTTTTC
*
85565271 TTCTTTTGCTTTTTCTTTTCTTTT
1 TTCTTTT-CTATTTCTTTTCTTTT
85565295 CTTTGTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 9 0.43
27 5 0.24
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (25 bp):
TTCTTTTCTATTTCTTTTCTTTTTC
Found at i:85565299 original size:21 final size:21
Alignment explanation
Indices: 85565242--85565309 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
85565232 CTCTTGCCTC
*
85565242 TCTTTTCTTTT-TATTTCTTTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
85565263 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
85565284 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
85565304 CTCTTT
1 -TCTTT
85565310 ACAAAAATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 7 0.17
21 28 0.70
22 5 0.12
ACGTcount: A:0.01, C:0.18, G:0.03, T:0.78
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:85567867 original size:30 final size:30
Alignment explanation
Indices: 85567833--85567929 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
85567823 TAAACTAAAA
* *
85567833 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* * * * * *
85567863 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* *
85567893 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGATTTAGCTCGTGAGCT-AAAGT
85567923 TGAGCTA
1 TGAGCTA
85567930 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 47 0.94
31 3 0.06
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
Found at i:85569502 original size:15 final size:15
Alignment explanation
Indices: 85569482--85569532 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
85569472 CGTATCTTGA
85569482 GTTTCTTTATTCTGG
1 GTTTCTTTATTCTGG
*
85569497 GTTTCTCTA-TCTTGG
1 GTTTCTTTATTC-TGG
*
85569512 ATTTCTTTATTC-GG
1 GTTTCTTTATTCTGG
*
85569526 TTTTCTT
1 GTTTCTT
85569533 GTTATCTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 10 0.33
15 18 0.60
16 2 0.07
ACGTcount: A:0.08, C:0.16, G:0.16, T:0.61
Consensus pattern (15 bp):
GTTTCTTTATTCTGG
Found at i:85569510 original size:30 final size:29
Alignment explanation
Indices: 85569474--85569531 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
85569464 TATAGTATCG
85569474 TATCTT-GAGTTTCTTTATTCTGGGTTTCTC
1 TATCTTGGA-TTTCTTTATTC-GGGTTTCTC
*
85569504 TATCTTGGATTTCTTTATTCGGTTTTCT
1 TATCTTGGATTTCTTTATTCGGGTTTCT
85569532 TGTTATCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 7 0.27
30 17 0.65
31 2 0.08
ACGTcount: A:0.10, C:0.16, G:0.16, T:0.59
Consensus pattern (29 bp):
TATCTTGGATTTCTTTATTCGGGTTTCTC
Found at i:85572817 original size:10 final size:10
Alignment explanation
Indices: 85572801--85572863 Score: 67
Period size: 11 Copynumber: 6.0 Consensus size: 10
85572791 GTAAGTTTCA
85572801 AAAAAAAATT
1 AAAAAAAATT
85572811 GAAAAAAAA-T
1 -AAAAAAAATT
85572821 AAAAAAAAGTT
1 AAAAAAAA-TT
85572832 -AAAAAAATT
1 AAAAAAAATT
85572841 AGAAAAAAACCTT
1 A-AAAAAAA--TT
85572854 AAAAAAAATT
1 AAAAAAAATT
85572864 TTTGACCATT
Statistics
Matches: 46, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
9 10 0.22
10 10 0.22
11 16 0.35
12 7 0.15
13 3 0.07
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.17
Consensus pattern (10 bp):
AAAAAAAATT
Found at i:85574154 original size:30 final size:29
Alignment explanation
Indices: 85574114--85574205 Score: 85
Period size: 30 Copynumber: 3.1 Consensus size: 29
85574104 TCGAGTTAAA
* *
85574114 CTAAAATGAGCTAAGCTTTAGCTCGTGAG
1 CTAAACTGAGCTAAGATTTAGCTCGTGAG
* * * * * *
85574143 CTAAAGTTGAGCTGAGATTAAACTCCTAAG
1 CTAAA-CTGAGCTAAGATTTAGCTCGTGAG
*
85574173 CTGAAACTGAGCTAAGGTTTAGCTCGTGAG
1 CT-AAACTGAGCTAAGATTTAGCTCGTGAG
85574203 CTA
1 CTA
85574206 GGAGTGAGCT
Statistics
Matches: 47, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
29 6 0.13
30 38 0.81
31 3 0.06
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (29 bp):
CTAAACTGAGCTAAGATTTAGCTCGTGAG
Found at i:85574565 original size:14 final size:15
Alignment explanation
Indices: 85574523--85574567 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 15
85574513 TTTTATTGCT
*
85574523 TCTCTTTTCTTTTGA
1 TCTCTTTTCTTTTCA
85574538 TCTCCTTTTGCTTTTCA
1 TCT-CTTTT-CTTTTCA
85574555 TCT-TTTTCTTTTC
1 TCTCTTTTCTTTTC
85574568 TCGTCTTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.22
15 7 0.26
16 5 0.19
17 9 0.33
ACGTcount: A:0.04, C:0.24, G:0.04, T:0.67
Consensus pattern (15 bp):
TCTCTTTTCTTTTCA
Found at i:85577869 original size:21 final size:21
Alignment explanation
Indices: 85577840--85577895 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
85577830 CAAGCTCTCT
*
85577840 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
85577861 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
85577882 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
85577896 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:85577888 original size:14 final size:14
Alignment explanation
Indices: 85577839--85577895 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
85577829 TCAAGCTCTC
85577839 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
85577852 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
85577866 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
85577880 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
85577894 TT
1 TT
85577896 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:85577955 original size:18 final size:18
Alignment explanation
Indices: 85577857--85577994 Score: 86
Period size: 18 Copynumber: 7.6 Consensus size: 18
85577847 TCTTTTTTCG
85577857 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
85577876 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* **
85577896 CTCTCACTTTTTCGA-TTT
1 CTTTTTCTTTTTC-ATTTT
* *
85577914 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
*
85577932 CTTTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCATTTT
*
85577950 CTTTTT-GTTTTC--TTT
1 CTTTTTCTTTTTCATTTT
** * *
85577965 CAATTTCTTTTTCAATCT
1 CTTTTTCTTTTTCATTTT
85577983 CTTTCTTCTTTT
1 CTTT-TTCTTTT
85577995 CTCGCTCAAT
Statistics
Matches: 90, Mismatches: 21, Indels: 16
0.71 0.17 0.13
Matches are distributed among these distances:
15 7 0.08
16 5 0.06
17 6 0.07
18 46 0.51
19 10 0.11
20 8 0.09
21 8 0.09
ACGTcount: A:0.08, C:0.20, G:0.03, T:0.70
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:85577977 original size:6 final size:6
Alignment explanation
Indices: 85577857--85577964 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
85577847 TCTTTTTTCG
* * * **
85577857 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
85577908 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
85577956 -GTTTT CTTT
1 CTTTTT CTTT
85577965 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 25, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
5 4 0.05
6 58 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:85579029 original size:26 final size:26
Alignment explanation
Indices: 85579000--85579061 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
85578990 TTAAACTTGA
*
85579000 TTTTTTTTTGCTC-ACCTTTTTTTTC-T
1 TTTTTTTTTGCTCGA--TTTTTTTTCAC
85579026 TTTTTTTTTGCTCGATTTTTTTTCAC
1 TTTTTTTTTGCTCGATTTTTTTTCAC
85579052 TTTTTTTTTG
1 TTTTTTTTTG
85579062 AATTTTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
25 9 0.27
26 23 0.70
27 1 0.03
ACGTcount: A:0.05, C:0.15, G:0.06, T:0.74
Consensus pattern (26 bp):
TTTTTTTTTGCTCGATTTTTTTTCAC
Found at i:85579069 original size:14 final size:14
Alignment explanation
Indices: 85579052--85579103 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
85579042 TTTTTTTCAC
85579052 TTTTTTTTT-GAAT
1 TTTTTTTTTCGAAT
*
85579065 TTTTTTTTCAATCAAAT
1 TTTTTTTT---TCGAAT
85579082 TTTTTTTTTCGAAT
1 TTTTTTTTTCGAAT
85579096 TTTTTTTT
1 TTTTTTTT
85579104 GATTTTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
13 8 0.24
14 13 0.39
16 1 0.03
17 11 0.33
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.73
Consensus pattern (14 bp):
TTTTTTTTTCGAAT
Found at i:85579108 original size:11 final size:13
Alignment explanation
Indices: 85579041--85579112 Score: 53
Period size: 13 Copynumber: 5.5 Consensus size: 13
85579031 TTTTGCTCGA
*
85579041 TTTTTTTTC-ACT
1 TTTTTTTTCGAAT
85579053 TTTTTTTT-GAATT
1 TTTTTTTTCGAA-T
*
85579066 TTTTTTTCAATCAAATT
1 TTTTTTT---TCGAA-T
85579083 TTTTTTTTCGAAT
1 TTTTTTTTCGAAT
85579096 TTTTTTTT-G-AT
1 TTTTTTTTCGAAT
85579107 TTTTTT
1 TTTTTT
85579113 GTTACTCCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
11 8 0.16
12 10 0.20
13 17 0.33
14 4 0.08
16 1 0.02
17 11 0.22
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.74
Consensus pattern (13 bp):
TTTTTTTTCGAAT
Found at i:85580619 original size:20 final size:20
Alignment explanation
Indices: 85580596--85580639 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
85580586 AGCTCAAACG
*
85580596 AGCTAAAGTAAGCTAAATTA
1 AGCTAAAGTAAGCTAAATCA
* * *
85580616 AGCTCATGTGAGCTAAATCA
1 AGCTAAAGTAAGCTAAATCA
85580636 AGCT
1 AGCT
85580640 GGGAAAAACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (20 bp):
AGCTAAAGTAAGCTAAATCA
Found at i:85583366 original size:30 final size:30
Alignment explanation
Indices: 85583280--85583377 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 30
85583270 TTAAACTAAA
* *
85583280 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * * * * *
85583310 TTGAGCTGAGATTAAACTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * *
85583340 GTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
85583370 ATGAGCTA
1 ATGAGCTA
85583378 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
Found at i:85587701 original size:13 final size:13
Alignment explanation
Indices: 85587683--85587707 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
85587673 TGGTCATCAT
85587683 GGTGTGAACACAA
1 GGTGTGAACACAA
85587696 GGTGTGAACACA
1 GGTGTGAACACA
85587708 TGATCAATAC
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:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:85589609 original size:17 final size:18
Alignment explanation
Indices: 85589587--85589620 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
85589577 ACAACACTCC
*
85589587 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
85589604 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
85589621 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:85590811 original size:13 final size:14
Alignment explanation
Indices: 85590793--85590843 Score: 77
Period size: 14 Copynumber: 3.6 Consensus size: 14
85590783 CCGTATGCAA
85590793 TTTTTTTTTC-AAT
1 TTTTTTTTTCAAAT
85590806 TTTTTTTTTCAAAT
1 TTTTTTTTTCAAAT
*
85590820 TTTTTTTTTCGAACT
1 TTTTTTTTTC-AAAT
85590835 TTTTTTTTT
1 TTTTTTTTT
85590844 ACGCACCTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
13 10 0.29
14 13 0.37
15 12 0.34
ACGTcount: A:0.14, C:0.08, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTTTTTTTCAAAT
Found at i:85591822 original size:13 final size:13
Alignment explanation
Indices: 85591804--85591828 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
85591794 TGGTCATCAT
85591804 GGTGTGAACACAA
1 GGTGTGAACACAA
85591817 GGTGTGAACACA
1 GGTGTGAACACA
85591829 TGATCAATAC
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:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:85592853 original size:4 final size:4
Alignment explanation
Indices: 85592844--85592870 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
85592834 TTGTAAAGTT
85592844 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
85592871 TACTTAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:85595238 original size:27 final size:27
Alignment explanation
Indices: 85595206--85595257 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
85595196 ACAAGTGAGG
85595206 AAAAAGAAAAAGAGAATGAAAAAGAGC
1 AAAAAGAAAAAGAGAATGAAAAAGAGC
* ** *
85595233 AAAAAGAGATTGAGAGTGAAAAAGA
1 AAAAAGAAAAAGAGAATGAAAAAGA
85595258 AATTGAAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.25, T:0.08
Consensus pattern (27 bp):
AAAAAGAAAAAGAGAATGAAAAAGAGC
Found at i:85603685 original size:10 final size:10
Alignment explanation
Indices: 85603670--85603731 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
85603660 TTTGAACCAT
85603670 TACCAATTCA
1 TACCAATTCA
*
85603680 TACCAAATACCA
1 TACC-AAT-TCA
*
85603692 TACCATTTCA
1 TACCAATTCA
*
85603702 TACCAAGTCCA
1 TACCAA-TTCA
* *
85603713 TACCATTTCG
1 TACCAATTCA
85603723 TACCAATTC
1 TACCAATTC
85603732 CCAAATACCA
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
10 21 0.52
11 13 0.32
12 6 0.15
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.29
Consensus pattern (10 bp):
TACCAATTCA
Found at i:85603715 original size:21 final size:22
Alignment explanation
Indices: 85603665--85603728 Score: 85
Period size: 21 Copynumber: 2.9 Consensus size: 22
85603655 ACCTCTTTGA
*
85603665 ACCATTACCAATTCATACCAAAT
1 ACCA-TACCATTTCATACCAAAT
*
85603688 ACCATACCATTTCATACCAAGT
1 ACCATACCATTTCATACCAAAT
*
85603710 -CCATACCATTTCGTACCAA
1 ACCATACCATTTCATACCAA
85603729 TTCCCAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 18 0.47
22 16 0.42
23 4 0.11
ACGTcount: A:0.38, C:0.33, G:0.03, T:0.27
Consensus pattern (22 bp):
ACCATACCATTTCATACCAAAT
Found at i:85608431 original size:34 final size:33
Alignment explanation
Indices: 85608362--85608435 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
85608352 TTTAATTAAA
* *
85608362 TGCATTTTTAGTTAATGTCATGCATTATTGATC
1 TGCATTTTTAATTAATGACATGCATTATTGATC
*
85608395 TGCATATTTTAATT-ATGACATGCATTATATGTTC
1 TGCAT-TTTTAATTAATGACATGCATTAT-TGATC
85608429 TGCATTT
1 TGCATTT
85608436 AATAAAGCCA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 20 0.56
34 16 0.44
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.49
Consensus pattern (33 bp):
TGCATTTTTAATTAATGACATGCATTATTGATC
Found at i:85611224 original size:26 final size:26
Alignment explanation
Indices: 85611195--85611302 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
85611185 TGGTACAAAT
85611195 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
85611221 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
85611247 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
85611273 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
85611299 TGAT
1 TGAT
85611303 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:85613910 original size:20 final size:20
Alignment explanation
Indices: 85613887--85613934 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
85613877 AGCTCCGTCC
85613887 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTG
*** *
85613907 AGCTCGTTTCAGCTCGTTTG
1 AGCTCAACTCAGCTCATTTG
85613927 AGCTCAAC
1 AGCTCAAC
85613935 CGAGCTTACT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:85616366 original size:21 final size:21
Alignment explanation
Indices: 85616342--85616409 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
85616332 GATTTTGAAT
85616342 GAAATCGAGAGAAGAAACAAA
1 GAAATCGAGAGAAGAAACAAA
***** *
85616363 GAAAAT-GAGAGAATCTTGAAT
1 G-AAATCGAGAGAAGAAACAAA
*
85616384 GAAATCGAGAAAAGAAACAAA
1 GAAATCGAGAGAAGAAACAAA
85616405 GAAAT
1 GAAAT
85616410 GAAAGAAAAA
Statistics
Matches: 32, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
20 4 0.12
21 24 0.75
22 4 0.12
ACGTcount: A:0.59, C:0.07, G:0.22, T:0.12
Consensus pattern (21 bp):
GAAATCGAGAGAAGAAACAAA
Found at i:85616382 original size:42 final size:42
Alignment explanation
Indices: 85616320--85616416 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
85616310 AGATTATGAG
* * *
85616320 AGAAAATGAGAGGATTTTGAATGAAATCGAGAGAAGAAACAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
85616362 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
*
85616404 AG-AAATGAAAGAA
1 AGAAAATGAGAGAA
85616417 AAAGAAAAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 10 0.20
42 41 0.80
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (42 bp):
AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
Found at i:85616443 original size:18 final size:18
Alignment explanation
Indices: 85616420--85616469 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
85616410 GAAAGAAAAA
*
85616420 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGAATGAGAGT
* *
85616438 GAAAAAGAAAATGAGATT
1 GAAAAAGAGAATGAGAGT
85616456 GAAAAAGAGAATGA
1 GAAAAAGAGAATGA
85616470 AAAAAAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.28, T:0.14
Consensus pattern (18 bp):
GAAAAAGAGAATGAGAGT
Found at i:85616446 original size:24 final size:24
Alignment explanation
Indices: 85616413--85616494 Score: 92
Period size: 24 Copynumber: 3.4 Consensus size: 24
85616403 AAGAAATGAA
85616413 AGAAAAAGAAAAAGAGATTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
* * * *
85616437 TGAAAAAGAAAATGAGATTGAAAA
1 AGAAAAAGAAAAAGAGATTGAGAG
* * * *
85616461 AGAGAATGAAAAAAAGTTTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
85616485 AGAAAAAGAA
1 AGAAAAAGAA
85616495 TGTGAACAAG
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.12
Consensus pattern (24 bp):
AGAAAAAGAAAAAGAGATTGAGAG
Found at i:85616523 original size:18 final size:19
Alignment explanation
Indices: 85616487--85616525 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
85616477 TTTGAGAGAG
*
85616487 AAAAAGAATGTGAACAAGA
1 AAAAAGAATGTGAAAAAGA
*
85616506 AAAAAGAGTG-GAAAAAGA
1 AAAAAGAATGTGAAAAAGA
85616524 AA
1 AA
85616526 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:85619951 original size:23 final size:22
Alignment explanation
Indices: 85619900--85619952 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
85619890 CCTCGTCTTT
*
85619900 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
85619922 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
85619945 TTCTTTTC
1 TTCTTTTC
85619953 AATTTTCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.19
23 14 0.54
24 5 0.19
ACGTcount: A:0.09, C:0.25, G:0.02, T:0.64
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:85637394 original size:20 final size:19
Alignment explanation
Indices: 85637371--85637435 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
85637361 AAGCTCAAAC
85637371 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
85637391 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * *
85637411 AAGCTCATGTGAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
85637431 GAGCT
1 GAGCT
85637436 GGGAAAAACT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 31 0.84
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:85637395 original size:10 final size:10
Alignment explanation
Indices: 85637371--85637435 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
85637361 AAGCTCAAAC
*
85637371 GAGCTAAAGT
1 GAGCTAAATT
*
85637381 AAGCTAAATT
1 GAGCTAAATT
*
85637391 GAGCTCAAA-C
1 GAGCT-AAATT
85637401 GAGCTAAATT
1 GAGCTAAATT
* *
85637411 AAGCT-CATGT
1 GAGCTAAAT-T
85637421 GAGCTAAATT
1 GAGCTAAATT
85637431 GAGCT
1 GAGCT
85637436 GGGAAAAACT
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
9 5 0.12
10 32 0.76
11 5 0.12
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (10 bp):
GAGCTAAATT
Found at i:85638553 original size:30 final size:30
Alignment explanation
Indices: 85638468--85638555 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
85638458 TAAACTAAAA
* * *
85638468 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* ** * * *
85638498 TGAGCTGAGATCAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
85638528 TGAGCTAAGGTTTAGCTCGTGAGCTGAA
1 TGAGCTAAGATTTAGCTCGTGAGCTGAA
85638556 TATGAGCAAG
Statistics
Matches: 42, Mismatches: 16, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:85639144 original size:13 final size:13
Alignment explanation
Indices: 85639126--85639153 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
85639116 GAATGGTCAT
85639126 CAAGGTGTGAACA
1 CAAGGTGTGAACA
85639139 CAAGGTGTGAACA
1 CAAGGTGTGAACA
85639152 CA
1 CA
85639154 TGATCAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.29, T:0.14
Consensus pattern (13 bp):
CAAGGTGTGAACA
Found at i:85642501 original size:12 final size:12
Alignment explanation
Indices: 85642484--85642527 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
85642474 CTCTCTCAAA
85642484 CTCTTTTTCATT
1 CTCTTTTTCATT
*
85642496 CTCTTTTTCAAT
1 CTCTTTTTCATT
*
85642508 CTCATTTTCACTT
1 CTCTTTTTCA-TT
85642521 -TCTTTTT
1 CTCTTTTT
85642528 GTTCTTTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 26 0.96
13 1 0.04
ACGTcount: A:0.11, C:0.25, G:0.00, T:0.64
Consensus pattern (12 bp):
CTCTTTTTCATT
Found at i:85642515 original size:13 final size:12
Alignment explanation
Indices: 85642479--85642527 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
85642469 TTTTTCTCTC
*
85642479 TCAAACTCTTTT
1 TCAATCTCTTTT
*
85642491 TCATTCTCTTTT
1 TCAATCTCTTTT
*
85642503 TCAATCTCATTT
1 TCAATCTCTTTT
* *
85642515 TCACTTTCTTTT
1 TCAATCTCTTTT
85642527 T
1 T
85642528 GTTCTTTTTC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.59
Consensus pattern (12 bp):
TCAATCTCTTTT
Found at i:85642515 original size:24 final size:24
Alignment explanation
Indices: 85642479--85642527 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
85642469 TTTTTCTCTC
*
85642479 TCAAACTCTTTTTCA-TTCTCTTTT
1 TCAAACTCATTTTCACTT-TCTTTT
*
85642503 TCAATCTCATTTTCACTTTCTTTT
1 TCAAACTCATTTTCACTTTCTTTT
85642527 T
1 T
85642528 GTTCTTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.59
Consensus pattern (24 bp):
TCAAACTCATTTTCACTTTCTTTT
Found at i:85642637 original size:15 final size:15
Alignment explanation
Indices: 85642625--85642666 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
85642615 TCTCTTTTAT
85642625 TTCTTTTTCTTTTTC
1 TTCTTTTTCTTTTTC
*
85642640 TTCTTTTGC-TTTTC
1 TTCTTTTTCTTTTTC
*
85642654 -TCGTTTTCTTTTT
1 TTCTTTTTCTTTTT
85642667 ACAAGAAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.00, C:0.19, G:0.05, T:0.76
Consensus pattern (15 bp):
TTCTTTTTCTTTTTC
Found at i:85643562 original size:9 final size:9
Alignment explanation
Indices: 85643548--85643581 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
85643538 TACCAAGCTT
85643548 TTTTTTTAA
1 TTTTTTTAA
*
85643557 TTTTTTTGA
1 TTTTTTTAA
85643566 TTTTTTTGAA
1 TTTTTTT-AA
85643576 TTTTTT
1 TTTTTT
85643582 CTTATGAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 15 0.68
10 7 0.32
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:85646868 original size:34 final size:34
Alignment explanation
Indices: 85646825--85646908 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
85646815 TGGACCAGAG
*
85646825 CCCTT-TTCAGATTACAATAAACTAGGCCTTATC
1 CCCTTATTCAGATAACAATAAACTAGGCCTTATC
85646858 CCCTTATTCAGATAACAATAAACTAGGCCTTATC
1 CCCTTATTCAGATAACAATAAACTAGGCCTTATC
85646892 CCCTTATTCAGATAACA
1 CCCTTATTCAGATAACA
85646909 GTATGGCCCA
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 5 0.10
34 44 0.90
ACGTcount: A:0.33, C:0.27, G:0.08, T:0.31
Consensus pattern (34 bp):
CCCTTATTCAGATAACAATAAACTAGGCCTTATC
Found at i:85651342 original size:11 final size:13
Alignment explanation
Indices: 85651326--85651358 Score: 52
Period size: 11 Copynumber: 2.7 Consensus size: 13
85651316 ATTGTAGATT
85651326 AAAAAAAATC-A-
1 AAAAAAAATCGAG
85651337 AAAAAAAATCGAG
1 AAAAAAAATCGAG
85651350 AAAAAAAAT
1 AAAAAAAAT
85651359 TGCATACAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
12 1 0.05
13 9 0.45
ACGTcount: A:0.79, C:0.06, G:0.06, T:0.09
Consensus pattern (13 bp):
AAAAAAAATCGAG
Found at i:85653245 original size:177 final size:177
Alignment explanation
Indices: 85652949--85653309 Score: 713
Period size: 177 Copynumber: 2.0 Consensus size: 177
85652939 CGAAGAGATT
85652949 TCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCAAATCTTGCA
1 TCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCAAATCTTGCA
*
85653014 GCCAAAATGCATTGGATCTCCATTACGAGCATCAACGACCCAATTTTGGTAGGAGATGGATCACG
66 GCCAAAACGCATTGGATCTCCATTACGAGCATCAACGACCCAATTTTGGTAGGAGATGGATCACG
85653079 AGCCCAAATTCTTGAAGGCGAGGCCCAATAACCAAAATCCAGCCCAA
131 AGCCCAAATTCTTGAAGGCGAGGCCCAATAACCAAAATCCAGCCCAA
85653126 TCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCAAATCTTGCA
1 TCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCAAATCTTGCA
85653191 GCCAAAACGCATTGGATCTCCATTACGAGCATCAACGACCCAATTTTGGTAGGAGATGGATCACG
66 GCCAAAACGCATTGGATCTCCATTACGAGCATCAACGACCCAATTTTGGTAGGAGATGGATCACG
85653256 AGCCCAAATTCTTGAAGGCGAGGCCCAATAACCAAAATCCAGCCCAA
131 AGCCCAAATTCTTGAAGGCGAGGCCCAATAACCAAAATCCAGCCCAA
85653303 TCAAGAA
1 TCAAGAA
85653310 ATTTCTTCAT
Statistics
Matches: 183, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
177 183 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (177 bp):
TCAAGAATCAAGAAAATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACCAAATCTTGCA
GCCAAAACGCATTGGATCTCCATTACGAGCATCAACGACCCAATTTTGGTAGGAGATGGATCACG
AGCCCAAATTCTTGAAGGCGAGGCCCAATAACCAAAATCCAGCCCAA
Found at i:85660556 original size:21 final size:21
Alignment explanation
Indices: 85660521--85660573 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
85660511 TACGAATTCG
*
85660521 TACCAAATACCATACCATTTCA
1 TACC-AATTCCATACCATTTCA
*
85660543 TACCAATTCCATACCATTTCG
1 TACCAATTCCATACCATTTCA
85660564 TACCAATTCC
1 TACCAATTCC
85660574 CAAATACCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.34, C:0.34, G:0.02, T:0.30
Consensus pattern (21 bp):
TACCAATTCCATACCATTTCA
Found at i:85660912 original size:13 final size:13
Alignment explanation
Indices: 85660896--85660920 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
85660886 AAAAAAAAAA
85660896 GAAAAAAAAATTT
1 GAAAAAAAAATTT
85660909 GAAAAAAAAATT
1 GAAAAAAAAATT
85660921 GCATACGGTT
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:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (13 bp):
GAAAAAAAAATTT
Done.