Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 42 of 333
Found at i:11927636 original size:19 final size:19
Alignment explanation
Indices: 11927562--11927637 Score: 57
Period size: 19 Copynumber: 3.9 Consensus size: 19
11927552 TCTTTAATTT
* *
11927562 TTTTAAAAA-AATTTATAAT
1 TTTTAAAAATTATTT-TAAA
*
11927581 TTTTAAAAATATATATTGAAA
1 TTTTAAAAAT-TAT-TTTAAA
* *
11927602 TTTTTATAAAGT-TTTTAAA
1 -TTTTAAAAATTATTTTAAA
11927621 TTTTAAAAATTATTTTA
1 TTTTAAAAATTATTTTA
11927638 TTTTATTTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
18 9 0.20
19 19 0.43
20 1 0.02
21 5 0.11
22 10 0.23
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
TTTTAAAAATTATTTTAAA
Found at i:11928502 original size:13 final size:13
Alignment explanation
Indices: 11928486--11928551 Score: 87
Period size: 13 Copynumber: 5.1 Consensus size: 13
11928476 TTTAAATTAA
11928486 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
11928499 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
* * *
11928512 ACTTTTCTACAGT
1 ACTTTTCAAAAGC
11928525 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
11928538 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
11928551 A
1 A
11928552 TTGCCAAACT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 46 1.00
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:11935921 original size:24 final size:20
Alignment explanation
Indices: 11935876--11935916 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
11935866 ACCACACTAG
11935876 TCCTTTCAAAGACTTATGAC
1 TCCTTTCAAAGACTTATGAC
11935896 TCCTTTCAAAGACTTATGAC
1 TCCTTTCAAAGACTTATGAC
11935916 T
1 T
11935917 GACTCTCCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (20 bp):
TCCTTTCAAAGACTTATGAC
Found at i:11941016 original size:18 final size:18
Alignment explanation
Indices: 11940993--11941031 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
11940983 TAATTAACTT
11940993 TTAAAAAATTTTAAAAAA
1 TTAAAAAATTTTAAAAAA
* *
11941011 TTAAAAAGTTTTAATAAA
1 TTAAAAAATTTTAAAAAA
11941029 TTA
1 TTA
11941032 TTTAAAAAGT
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:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
TTAAAAAATTTTAAAAAA
Found at i:11941792 original size:21 final size:21
Alignment explanation
Indices: 11941750--11941793 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
11941740 TTTTAACGTT
* * *
11941750 TTTTTTAAAAAAGTTTACAAA
1 TTTTTTAAAAAAATTCAAAAA
11941771 TTTTTTAAAAAAATTCAAAAA
1 TTTTTTAAAAAAATTCAAAAA
11941792 TT
1 TT
11941794 ATGAAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (21 bp):
TTTTTTAAAAAAATTCAAAAA
Found at i:11948286 original size:23 final size:23
Alignment explanation
Indices: 11948259--11948302 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
11948249 CCTAAAAGGT
11948259 GTTTAATGTGAAATATGAAAAGC
1 GTTTAATGTGAAATATGAAAAGC
11948282 GTTTAATGTGAAATATGAAAA
1 GTTTAATGTGAAATATGAAAA
11948303 TGAATGTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.45, C:0.02, G:0.20, T:0.32
Consensus pattern (23 bp):
GTTTAATGTGAAATATGAAAAGC
Found at i:11949542 original size:21 final size:22
Alignment explanation
Indices: 11949518--11949564 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
11949508 CCAAATTCTC
11949518 TCAAA-TT-TCTCTCAATTTTTG
1 TCAAAGTTGTCTCT-AATTTTTG
11949539 TCAAAGTTGTCTCTAATTTTTG
1 TCAAAGTTGTCTCTAATTTTTG
11949561 -CAAA
1 TCAAA
11949565 AAAGCTCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.38
22 10 0.42
23 5 0.21
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.47
Consensus pattern (22 bp):
TCAAAGTTGTCTCTAATTTTTG
Found at i:11951373 original size:18 final size:18
Alignment explanation
Indices: 11951350--11951392 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
11951340 TACCAGGTGC
11951350 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
11951368 GTATCCTAACCCTTTTAT
1 GTATCCTAACCCTTATAT
*
11951386 GTTTCCT
1 GTATCCT
11951393 TTTCCCAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.28, G:0.07, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:11951671 original size:21 final size:21
Alignment explanation
Indices: 11951640--11951687 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
11951630 CTACAACCAG
* *
11951640 ATCCCATACCGGAGGAACTACA
1 ATCCC-TACCGGAGCAACCACA
11951662 ATCCCTACCGGAGCAACCACA
1 ATCCCTACCGGAGCAACCACA
11951683 A-CCCT
1 ATCCCT
11951688 CGCTGGAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.33, C:0.40, G:0.15, T:0.12
Consensus pattern (21 bp):
ATCCCTACCGGAGCAACCACA
Found at i:11952012 original size:129 final size:129
Alignment explanation
Indices: 11951799--11952035 Score: 379
Period size: 129 Copynumber: 1.8 Consensus size: 129
11951789 GTAGAAACTT
* ** *
11951799 TTTTTATATAGTTTCATATAATAAAATAAAAGTTTTTTTTAAATATTTTAATTGTACTCTACTTT
1 TTTTTATATAGTTTAATATAATAAAATAAAAGTTAGTTTTAAATATTATAATTGTACTCTACTTT
*
11951864 TTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATCTTTCTTATTTTTATATTTA
66 TTTTAATTTTAATAAAATAAATGTTCTTTTAAATTAGCCAATATCTTTCTTATTTTTATATTTA
*
11951928 TTTTTATATAGTTTTAAT-TAATAAAATAAAAGTTAGTTTT-AATATTATAATTGTACTTTACTT
1 TTTTTATATAG-TTTAATATAATAAAATAAAAGTTAGTTTTAAATATTATAATTGTACTCTAC-T
*
11951991 TTTTTTAATTTTAATACAATAAATGTTCTTTTAAATTAGCCAATA
64 TTTTTTAATTTTAATAAAATAAATGTTCTTTTAAATTAGCCAATA
11952036 ATTTTTATTA
Statistics
Matches: 99, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
128 19 0.19
129 75 0.76
130 5 0.05
ACGTcount: A:0.36, C:0.06, G:0.05, T:0.53
Consensus pattern (129 bp):
TTTTTATATAGTTTAATATAATAAAATAAAAGTTAGTTTTAAATATTATAATTGTACTCTACTTT
TTTTAATTTTAATAAAATAAATGTTCTTTTAAATTAGCCAATATCTTTCTTATTTTTATATTTA
Found at i:11955711 original size:24 final size:24
Alignment explanation
Indices: 11955684--11955733 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
11955674 TTTTTCTTAA
11955684 AAAAACACTAAA-ACATTAAACCCT
1 AAAAACACTAAATA-ATTAAACCCT
*
11955708 AAAAACCCTAAATAATTAAACCCT
1 AAAAACACTAAATAATTAAACCCT
11955732 AA
1 AA
11955734 CCCTAAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.58, C:0.24, G:0.00, T:0.18
Consensus pattern (24 bp):
AAAAACACTAAATAATTAAACCCT
Found at i:11957052 original size:28 final size:27
Alignment explanation
Indices: 11957021--11957080 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
11957011 ATATATATGA
*
11957021 TTTATTTCTCTTAATCTTTATTTTTTAC
1 TTTATTTCTCTTAATCATT-TTTTTTAC
* * *
11957049 TTTA-TTCTTTTTATCATTTTTTTTCC
1 TTTATTTCTCTTAATCATTTTTTTTAC
11957075 TTTATT
1 TTTATT
11957081 ATGCAGACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 11 0.41
27 12 0.44
28 4 0.15
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (27 bp):
TTTATTTCTCTTAATCATTTTTTTTAC
Found at i:11966183 original size:40 final size:40
Alignment explanation
Indices: 11966153--11966362 Score: 314
Period size: 40 Copynumber: 5.3 Consensus size: 40
11966143 GGATTATGAT
* * * *
11966153 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
11966193 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
11966233 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
* *
11966273 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
* * * * *
11966313 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
11966352 CCGAAGGCATT
1 CCGAAGGCATT
11966363 TGAACGAGGA
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 34 0.21
40 125 0.79
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
Found at i:11966199 original size:80 final size:80
Alignment explanation
Indices: 11966100--11966362 Score: 318
Period size: 80 Copynumber: 3.3 Consensus size: 80
11966090 TTGAATGCTG
* * * * *
11966100 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGATTATGAT-CCGAAGGCCT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTGATTAAATCCGGGTTATG-TCCCGAAGGCCT
*
11966163 TTGTGCGAGATACTAAA
64 TTGTGCGAGTTACTAAA
* * * * *
11966180 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTGATTAAATCCGGGTTATGTCCCGAAGGCCTTT
*
11966245 GTGCGAGTTATTAAA
66 GTGCGAGTTACTAAA
* *
11966260 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTG-TTAAATCCGGGTTATGTCCCGAAGG-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAG-TGATTAAATCCGGGTTATGTCCCGAAGGCCTT
*
11966323 TGTGTGAGTTACTAAA
65 TGTGCGAGTTACTAAA
* *
11966339 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
11966363 TGAACGAGGA
Statistics
Matches: 158, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
79 36 0.23
80 115 0.73
81 7 0.04
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTGATTAAATCCGGGTTATGTCCCGAAGGCCTTT
GTGCGAGTTACTAAA
Found at i:11966314 original size:120 final size:120
Alignment explanation
Indices: 11966100--11966362 Score: 325
Period size: 120 Copynumber: 2.2 Consensus size: 120
11966090 TTGAATGCTG
* * * *
11966100 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGATTATGATCCGAAGGCCTT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGATCCGAAGGCATT
* *
11966164 TGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
66 CGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
* * * * *
11966220 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGAT-CCGAAGGCAT
* ** * *
11966283 TCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
11966339 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
11966363 TGAACGAGGA
Statistics
Matches: 122, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
119 35 0.29
120 81 0.66
121 6 0.05
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGATCCGAAGGCATT
CGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:11974131 original size:40 final size:40
Alignment explanation
Indices: 11974101--11974310 Score: 314
Period size: 40 Copynumber: 5.3 Consensus size: 40
11974091 GGATTATGAT
* * * *
11974101 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
11974141 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
11974181 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
* *
11974221 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
* * * * *
11974261 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
11974300 CCGAAGGCATT
1 CCGAAGGCATT
11974311 TGAACGAGGA
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 34 0.21
40 125 0.79
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
Found at i:11974147 original size:80 final size:80
Alignment explanation
Indices: 11974048--11974310 Score: 318
Period size: 80 Copynumber: 3.3 Consensus size: 80
11974038 TTGAATGCTG
* * * * *
11974048 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGATTATGAT-CCGAAGGCCT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTGATTAAATCCGGGTTATG-TCCCGAAGGCCT
*
11974111 TTGTGCGAGATACTAAA
64 TTGTGCGAGTTACTAAA
* * * * *
11974128 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTGATTAAATCCGGGTTATGTCCCGAAGGCCTTT
*
11974193 GTGCGAGTTATTAAA
66 GTGCGAGTTACTAAA
* *
11974208 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTG-TTAAATCCGGGTTATGTCCCGAAGG-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAG-TGATTAAATCCGGGTTATGTCCCGAAGGCCTT
*
11974271 TGTGTGAGTTACTAAA
65 TGTGCGAGTTACTAAA
* *
11974287 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
11974311 TGAACGAGGA
Statistics
Matches: 158, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
79 36 0.23
80 115 0.73
81 7 0.04
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTGATTAAATCCGGGTTATGTCCCGAAGGCCTTT
GTGCGAGTTACTAAA
Found at i:11974262 original size:120 final size:120
Alignment explanation
Indices: 11974048--11974310 Score: 325
Period size: 120 Copynumber: 2.2 Consensus size: 120
11974038 TTGAATGCTG
* * * *
11974048 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGATTATGATCCGAAGGCCTT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGATCCGAAGGCATT
* *
11974112 TGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
66 CGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
* * * * *
11974168 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGAT-CCGAAGGCAT
* ** * *
11974231 TCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
11974287 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
11974311 TGAACGAGGA
Statistics
Matches: 122, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
119 35 0.29
120 81 0.66
121 6 0.05
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGATCCGAAGGCATT
CGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:11977067 original size:35 final size:35
Alignment explanation
Indices: 11977019--11977294 Score: 254
Period size: 35 Copynumber: 7.9 Consensus size: 35
11977009 TTCACAAGTT
** * *
11977019 AGTATGGTTAATACCAAACCTAAGTTTCATAGCTC
1 AGTATGGACAATACCATACCTACGTTTCATAGCTC
* * *
11977054 AGTATGGACAATACCATACCTACGTTTCACAACTT
1 AGTATGGACAATACCATACCTACGTTTCATAGCTC
* * *
11977089 GGTATGGGA-AATACCATACCTACGGATT-ATAGCTT
1 AGTAT-GGACAATACCATACCTAC-GTTTCATAGCTC
* * * *
11977124 GGTATGAATAATACCATACCTATGTTTCATAGCTC
1 AGTATGGACAATACCATACCTACGTTTCATAGCTC
* * *
11977159 AGAATGGACAATACCATACCTACGTTTCACAACTC
1 AGTATGGACAATACCATACCTACGTTTCATAGCTC
* *
11977194 GGTATGGGA-AATATCATACCTACGTATT-ATAGCTC
1 AGTAT-GGACAATACCATACCTACGT-TTCATAGCTC
* * * * *
11977229 GGTATAGATAATACCATATCTACGTGTCATAGCTC
1 AGTATGGACAATACCATACCTACGTTTCATAGCTC
* *
11977264 AGTATGGCCAATACCATACCTACGTGTCATA
1 AGTATGGACAATACCATACCTACGTTTCATA
11977295 ACTTTTCCAT
Statistics
Matches: 197, Mismatches: 36, Indels: 16
0.79 0.14 0.06
Matches are distributed among these distances:
34 8 0.04
35 178 0.90
36 11 0.06
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (35 bp):
AGTATGGACAATACCATACCTACGTTTCATAGCTC
Found at i:11977202 original size:105 final size:105
Alignment explanation
Indices: 11977027--11977297 Score: 409
Period size: 105 Copynumber: 2.6 Consensus size: 105
11977017 TTAGTATGGT
* *
11977027 TAATACCAAACCTAAGTTTCATAGCTCAGTATGGACAATACCATACCTACGTTTCACAACTTGGT
1 TAATACCATACCTAAGTTTCATAGCTCAGTATGGACAATACCATACCTACGTTTCACAACTCGGT
*
11977092 ATGGGAAATACCATACCTACGGATTATAGCTTGGTAT-GAA
66 ATGGGAAATACCATACCTACGGATTATAGCTCGGTATAG-A
* *
11977132 TAATACCATACCTATGTTTCATAGCTCAGAATGGACAATACCATACCTACGTTTCACAACTCGGT
1 TAATACCATACCTAAGTTTCATAGCTCAGTATGGACAATACCATACCTACGTTTCACAACTCGGT
* *
11977197 ATGGGAAATATCATACCTACGTATTATAGCTCGGTATAGA
66 ATGGGAAATACCATACCTACGGATTATAGCTCGGTATAGA
* * * * * *
11977237 TAATACCATATCTACGTGTCATAGCTCAGTATGGCCAATACCATACCTACGTGTCATAACT
1 TAATACCATACCTAAGTTTCATAGCTCAGTATGGACAATACCATACCTACGTTTCACAACT
11977298 TTTCCATGGA
Statistics
Matches: 151, Mismatches: 14, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
105 150 0.99
106 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (105 bp):
TAATACCATACCTAAGTTTCATAGCTCAGTATGGACAATACCATACCTACGTTTCACAACTCGGT
ATGGGAAATACCATACCTACGGATTATAGCTCGGTATAGA
Found at i:11983692 original size:37 final size:36
Alignment explanation
Indices: 11983645--11983753 Score: 103
Period size: 37 Copynumber: 3.0 Consensus size: 36
11983635 CACGTTAGAA
* *
11983645 GCTCATAAGAGCTAATCCACCCGATAACACGCCAATT
1 GCTCAGAAGAGCTAATCCACCTGATAACACGCCAA-T
* * *
11983682 GCTCCGAAGAGCTAGTCCAACTG-TAAACACGCCAGAT
1 GCTCAGAAGAGCTAATCCACCTGAT-AACACGCCA-AT
* ** *
11983719 GCTTATTAGAGCTAATCAACCTGATAACACGCCAA
1 GCTCAGAAGAGCTAATCCACCTGATAACACGCCAA
11983754 AATAAGGAGT
Statistics
Matches: 57, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
36 2 0.04
37 53 0.93
38 2 0.04
ACGTcount: A:0.35, C:0.29, G:0.17, T:0.19
Consensus pattern (36 bp):
GCTCAGAAGAGCTAATCCACCTGATAACACGCCAAT
Found at i:11986371 original size:22 final size:22
Alignment explanation
Indices: 11986323--11986399 Score: 91
Period size: 23 Copynumber: 3.4 Consensus size: 22
11986313 GACATGGCCT
*
11986323 GTAAGCTCTTCATGAGCTATAACA
1 GTAAGCTC-TAATGAGCTA-AACA
*
11986347 GTAAGCTCTATTGAGCTAAACA
1 GTAAGCTCTAATGAGCTAAACA
* *
11986369 GTAAGCTCTAATGAGATAAAATA
1 GTAAGCTCTAATGAGCT-AAACA
11986392 GTAAGCTC
1 GTAAGCTC
11986400 ATACGAGCTA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
22 19 0.40
23 20 0.43
24 8 0.17
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (22 bp):
GTAAGCTCTAATGAGCTAAACA
Found at i:11986398 original size:23 final size:23
Alignment explanation
Indices: 11986323--11986399 Score: 93
Period size: 22 Copynumber: 3.3 Consensus size: 23
11986313 GACATGGCCT
* *
11986323 GTAAGCTCTTCATGAGCTATAACA
1 GTAAGCTC-TAATGAGCTAAAACA
*
11986347 GTAAGCTCTATTGAGCT-AAACA
1 GTAAGCTCTAATGAGCTAAAACA
* *
11986369 GTAAGCTCTAATGAGATAAAATA
1 GTAAGCTCTAATGAGCTAAAACA
11986392 GTAAGCTC
1 GTAAGCTC
11986400 ATACGAGCTA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
22 19 0.41
23 19 0.41
24 8 0.17
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (23 bp):
GTAAGCTCTAATGAGCTAAAACA
Found at i:11986408 original size:45 final size:46
Alignment explanation
Indices: 11986323--11986409 Score: 106
Period size: 45 Copynumber: 1.9 Consensus size: 46
11986313 GACATGGCCT
* * * *
11986323 GTAAGCTCTTCATGAGCTATAACAGTAAGCTCTATTGAGCTAAACA
1 GTAAGCTCTTAATGAGATAAAACAGTAAGCTCTATCGAGCTAAACA
*
11986369 GTAAGCTC-TAATGAGATAAAATAGTAAGCTC-ATACGAGCTA
1 GTAAGCTCTTAATGAGATAAAACAGTAAGCTCTAT-CGAGCTA
11986410 TGGTGAGTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
44 2 0.06
45 25 0.71
46 8 0.23
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.26
Consensus pattern (46 bp):
GTAAGCTCTTAATGAGATAAAACAGTAAGCTCTATCGAGCTAAACA
Found at i:12000148 original size:46 final size:46
Alignment explanation
Indices: 12000095--12000266 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 46
12000085 TGGGCATCCA
*
12000095 AACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAGCGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCG
* * * *
12000141 AACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATCC-
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCGTCCG
* *
12000187 AAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCG
1 AA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCG
* *
12000234 AGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
12000267 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 61 0.59
47 31 0.30
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.29
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCG
Found at i:12000246 original size:93 final size:93
Alignment explanation
Indices: 12000087--12000259 Score: 301
Period size: 93 Copynumber: 1.9 Consensus size: 93
12000077 GGGATATTTG
* * *
12000087 GGCATCCAAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
12000152 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* *
12000180 GGCATCCAAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
12000245 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
12000260 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:12004296 original size:15 final size:16
Alignment explanation
Indices: 12004267--12004298 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
12004257 AATCTTCTCA
12004267 TGATATGGTTAATATT
1 TGATATGGTTAATATT
12004283 TGATATGG-TAATATT
1 TGATATGGTTAATATT
12004298 T
1 T
12004299 ACGCTATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (16 bp):
TGATATGGTTAATATT
Found at i:12006015 original size:27 final size:26
Alignment explanation
Indices: 12005967--12006124 Score: 165
Period size: 27 Copynumber: 5.9 Consensus size: 26
12005957 GCGAGGCTGC
* * *
12005967 CAGATATTGTGACGGAGTCACCAGAT
1 CAGATATTGTGGCAGAGCCACCAGAT
*
12005993 ACAGATATTGTGGCAGAGCCACCAGAA
1 -CAGATATTGTGGCAGAGCCACCAGAT
*
12006020 CAAATATATGTGGCAGAGCCACCAGAT
1 CAGATAT-TGTGGCAGAGCCACCAGAT
* *
12006047 CAGATAATTATGGCATAGCCACCAGGAT
1 CAGAT-ATTGTGGCAGAGCCACCA-GAT
* *
12006075 -AGATATATGTGGTAGAGGCACCAGAT
1 CAGATAT-TGTGGCAGAGCCACCAGAT
*
12006101 CAGATAATTGTGGCATAGCCACCA
1 CAGAT-ATTGTGGCAGAGCCACCA
12006125 AGACGCTTCC
Statistics
Matches: 109, Mismatches: 16, Indels: 12
0.80 0.12 0.09
Matches are distributed among these distances:
26 11 0.10
27 91 0.83
28 7 0.06
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAT
Found at i:12006067 original size:54 final size:54
Alignment explanation
Indices: 12005985--12006124 Score: 201
Period size: 54 Copynumber: 2.6 Consensus size: 54
12005975 GTGACGGAGT
*
12005985 CACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAACAAATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAACAAATATATGTGGCAGAGC
* * * * * *
12006039 CACCAGATCAGATAATTATGGCATAGCCACCAGGATAGATATATGTGGTAGAGG
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAAATATATGTGGCAGAGC
12006093 CACCAGATCAGATAATTGTGGCATAGCCACCA
1 CACCAGATCAGATAATTGTGGCATAGCCACCA
12006125 AGACGCTTCC
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
53 5 0.06
54 72 0.94
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAAATATATGTGGCAGAGC
Found at i:12007749 original size:26 final size:26
Alignment explanation
Indices: 12007719--12007826 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
12007709 TGAAATTCCC
12007719 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
12007745 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
12007771 ATCATGAAATATTTATCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
12007797 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
12007823 ATCA
1 ATCA
12007827 ATTTGTATCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:12014157 original size:29 final size:28
Alignment explanation
Indices: 12014115--12014181 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 28
12014105 GTTTGCATGT
*
12014115 AAAATATTTTTTGGAAAATGATTTCTGG
1 AAAATATTTCTTGGAAAATGATTTCTGG
12014143 AAAATAATTTCTTGGAAAATGATTTCTGG
1 AAAAT-ATTTCTTGGAAAATGATTTCTGG
12014172 AAAATGATTT
1 AAAAT-ATTT
12014182 ACTTTTTTGG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
28 5 0.14
29 31 0.86
ACGTcount: A:0.39, C:0.04, G:0.16, T:0.40
Consensus pattern (28 bp):
AAAATATTTCTTGGAAAATGATTTCTGG
Found at i:12014160 original size:15 final size:14
Alignment explanation
Indices: 12014126--12014181 Score: 94
Period size: 14 Copynumber: 3.9 Consensus size: 14
12014116 AAATATTTTT
12014126 TGGAAAATGATTTC
1 TGGAAAATGATTTC
*
12014140 TGGAAAATAATTTC
1 TGGAAAATGATTTC
12014154 TTGGAAAATGATTTC
1 -TGGAAAATGATTTC
12014169 TGGAAAATGATTT
1 TGGAAAATGATTT
12014182 ACTTTTTTGG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
14 26 0.67
15 13 0.33
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.38
Consensus pattern (14 bp):
TGGAAAATGATTTC
Found at i:12014664 original size:22 final size:22
Alignment explanation
Indices: 12014639--12014687 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
12014629 ATCCAAGTGC
12014639 ATAACTAATATTACACCACATG
1 ATAACTAATATTACACCACATG
12014661 ATAACTAATATTACACCACATG
1 ATAACTAATATTACACCACATG
12014683 ATAAC
1 ATAAC
12014688 AACAATATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.47, C:0.22, G:0.04, T:0.27
Consensus pattern (22 bp):
ATAACTAATATTACACCACATG
Found at i:12014685 original size:68 final size:68
Alignment explanation
Indices: 12014601--12014727 Score: 227
Period size: 68 Copynumber: 1.9 Consensus size: 68
12014591 GCATAATTAG
12014601 TATTACACCACATGATAACAACAACATTATCCAAGTGCATAACTAATATTACACCACATGATAAC
1 TATTACACCACATGATAACAACAACATTATCCAAGTGCATAACTAATATTACACCACATGATAAC
12014666 TAA
66 TAA
* * *
12014669 TATTACACCACATGATAACAACAATATTGTCCAAGTGCATAACTAATATTACACTACAT
1 TATTACACCACATGATAACAACAACATTATCCAAGTGCATAACTAATATTACACCACAT
12014728 TAAAAGTATC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 56 1.00
ACGTcount: A:0.44, C:0.23, G:0.06, T:0.27
Consensus pattern (68 bp):
TATTACACCACATGATAACAACAACATTATCCAAGTGCATAACTAATATTACACCACATGATAAC
TAA
Found at i:12015610 original size:15 final size:15
Alignment explanation
Indices: 12015569--12015623 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
12015559 CAAGGAAACC
12015569 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
*
12015584 -AGATAGAG-AATCCA
1 GA-ATAAAGAAATCCA
12015598 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
12015613 GAATAAAGAAA
1 GAATAAAGAAA
12015624 CCCAAAATAC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
14 12 0.34
15 23 0.66
ACGTcount: A:0.60, C:0.11, G:0.16, T:0.13
Consensus pattern (15 bp):
GAATAAAGAAATCCA
Found at i:12015632 original size:15 final size:15
Alignment explanation
Indices: 12015570--12015632 Score: 74
Period size: 15 Copynumber: 4.3 Consensus size: 15
12015560 AAGGAAACCG
12015570 AATAAAGAAATCCAA
1 AATAAAGAAATCCAA
* * *
12015585 GATAGAG-AATCCAG
1 AATAAAGAAATCCAA
*
12015599 AATAAAGAAATCCAG
1 AATAAAGAAATCCAA
*
12015614 AATAAAGAAACCCAA
1 AATAAAGAAATCCAA
12015629 AATA
1 AATA
12015633 CGATACTATG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
14 11 0.28
15 29 0.73
ACGTcount: A:0.60, C:0.14, G:0.13, T:0.13
Consensus pattern (15 bp):
AATAAAGAAATCCAA
Found at i:12018688 original size:93 final size:93
Alignment explanation
Indices: 12018576--12018745 Score: 286
Period size: 93 Copynumber: 1.8 Consensus size: 93
12018566 CCCATAAGTG
* *
12018576 AACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAAC
12018641 GAGCTCAGATGCCTAGTCACATCTCTCT
66 GAGCTCAGATGCCTAGTCACATCTCTCT
* *
12018669 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAAC
* *
12018734 GAGTTCGGATGC
66 GAGCTCAGATGC
12018746 TCAACCATCC
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (93 bp):
AACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAAC
GAGCTCAGATGCCTAGTCACATCTCTCT
Found at i:12018742 original size:46 final size:46
Alignment explanation
Indices: 12018567--12018742 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
12018557 TGTAACCCGC
* *
12018567 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* * * *
12018613 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCAGATGCCTAGTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-G--GAC-ATTCGCAT
* *
12018663 CTC-T--CT-AACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
12018706 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
12018743 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 1 0.01
43 8 0.07
44 2 0.02
45 1 0.01
46 62 0.57
47 24 0.22
48 1 0.01
49 2 0.02
50 7 0.06
51 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:12020401 original size:32 final size:32
Alignment explanation
Indices: 12020355--12020415 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
12020345 TGTCAATCAT
12020355 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATAAA
* *
12020387 TTCAATATCTAACAAGCTTGAAACATAAT
1 TTCAATATCCAACAAGCTTAAAACATAAT
12020416 CAATATCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.49, C:0.18, G:0.05, T:0.28
Consensus pattern (32 bp):
TTCAATATCCAACAAGCTTAAAACATAATAAA
Found at i:12020422 original size:27 final size:30
Alignment explanation
Indices: 12020355--12020428 Score: 91
Period size: 32 Copynumber: 2.5 Consensus size: 30
12020345 TGTCAATCAT
*
12020355 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCTAACAAGCTTAAAAC--AATAAA
*
12020387 TTCAATATCTAACAAGCTTGAAAC-AT-AA
1 TTCAATATCTAACAAGCTTAAAACAATAAA
12020415 -TCAATATCTAACAA
1 TTCAATATCTAACAA
12020429 AATCAAGACA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
27 14 0.35
28 2 0.05
29 2 0.05
32 22 0.55
ACGTcount: A:0.50, C:0.19, G:0.04, T:0.27
Consensus pattern (30 bp):
TTCAATATCTAACAAGCTTAAAACAATAAA
Found at i:12027817 original size:25 final size:23
Alignment explanation
Indices: 12027787--12027845 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 23
12027777 GAGACATGGC
12027787 CAGTAAGCTCTTCA-TGAGCTGATAA
1 CAGTAAGCTCTTCATTGAGC---TAA
12027812 CAGTAAGCTC-T-ATTGAGCTAA
1 CAGTAAGCTCTTCATTGAGCTAA
12027833 CAGTAAGCTCTTC
1 CAGTAAGCTCTTC
12027846 CAAGCTGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
21 13 0.42
22 1 0.03
23 1 0.03
24 6 0.19
25 10 0.32
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.29
Consensus pattern (23 bp):
CAGTAAGCTCTTCATTGAGCTAA
Found at i:12027851 original size:21 final size:21
Alignment explanation
Indices: 12027809--12027851 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
12027799 CATGAGCTGA
**
12027809 TAACAGTAAGCTCTATTGAGC
1 TAACAGTAAGCTCTATCAAGC
12027830 TAACAGTAAGCTCT-TCCAAGC
1 TAACAGTAAGCTCTAT-CAAGC
12027851 T
1 T
12027852 GAATCGATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (21 bp):
TAACAGTAAGCTCTATCAAGC
Found at i:12040894 original size:26 final size:26
Alignment explanation
Indices: 12040865--12040918 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
12040855 ATTGAACAAG
12040865 TAAATTTCTTAATTTAAAATTATCTA
1 TAAATTTCTTAATTTAAAATTATCTA
12040891 TAAATTTCTTAATTTAAAATTATCTA
1 TAAATTTCTTAATTTAAAATTATCTA
12040917 TA
1 TA
12040919 TATTATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (26 bp):
TAAATTTCTTAATTTAAAATTATCTA
Found at i:12041690 original size:13 final size:13
Alignment explanation
Indices: 12041674--12041699 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12041664 TTTTAATTCT
12041674 AAATATTTTTAAA
1 AAATATTTTTAAA
12041687 AAATATTTTTAAA
1 AAATATTTTTAAA
12041700 TTTTACTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATATTTTTAAA
Found at i:12042431 original size:3 final size:3
Alignment explanation
Indices: 12042408--12042593 Score: 127
Period size: 3 Copynumber: 62.3 Consensus size: 3
12042398 GGAGAGTGTG
* * *
12042408 TTA TTT TTA ATA TTG TTA TTA TTA TATA TTA TTA CTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA -TTA TTA TTA TTA
* * *
12042455 TTA -TA TTTA TTA -TA TTA -TA TT- TT- TTA TTA CTG TTA CTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
**
12042496 TTA -TA TATA TTTA TTA CCA TTA TTTA CTTA TTA TTA TTA TTA TTA TTA
1 TTA TTA T-TA -TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA
* ** * * *
12042544 GTA ACA -TA TTG TTA TTT TTA TTA TT- TTA TTA TTA TTA TTC TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12042590 TTA T
1 TTA T
12042594 CATGGTACTA
Statistics
Matches: 143, Mismatches: 27, Indels: 26
0.73 0.14 0.13
Matches are distributed among these distances:
2 15 0.10
3 109 0.76
4 18 0.13
5 1 0.01
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:12042452 original size:26 final size:26
Alignment explanation
Indices: 12042418--12042593 Score: 109
Period size: 23 Copynumber: 7.3 Consensus size: 26
12042408 TTATTTTTAA
*
12042418 TATTGTTATTATTATATATTATTACT
1 TATTATTATTATTATATATTATTACT
12042444 TATTATTATTATTATAT-TTATTA--
1 TATTATTATTATTATATATTATTACT
* *
12042467 TATTA-TATT-TT-T-TATTACT-GT
1 TATTATTATTATTATATATTATTACT
*
12042488 TACTATTATTA-TATATATTTATTAC-
1 TATTATTATTATTATATA-TTATTACT
*
12042513 CATTA-T-TTACTTAT-TATTATTA-T
1 TATTATTATTA-TTATATATTATTACT
* ** * *
12042536 TATTATTAGTAACATATTGTTATT-TT
1 TATTATTATTATTATA-TATTATTACT
12042562 TATTATT-TTATTAT-TATTATT-CT
1 TATTATTATTATTATATATTATTACT
12042585 TATTATTAT
1 TATTATTAT
12042594 CATGGTACTA
Statistics
Matches: 115, Mismatches: 17, Indels: 38
0.68 0.10 0.22
Matches are distributed among these distances:
19 1 0.01
20 5 0.04
21 6 0.05
22 9 0.08
23 33 0.29
24 9 0.08
25 22 0.19
26 30 0.26
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (26 bp):
TATTATTATTATTATATATTATTACT
Found at i:12042497 original size:32 final size:31
Alignment explanation
Indices: 12042411--12042507 Score: 99
Period size: 32 Copynumber: 3.1 Consensus size: 31
12042401 GAGTGTGTTA
* *
12042411 TTTTTAATATTGTTATTATTA-TATATTATTAC
1 TTTTTATTATTGTTA-TATTATTATATTA-TAT
* *
12042443 TTATTATTATTATTATATTTATTATATTATAT
1 TTTTTATTATTGTTATA-TTATTATATTATAT
*
12042475 TTTTTATTACTGTTACTATTATTATA-TATAT
1 TTTTTATTATTGTTA-TATTATTATATTATAT
12042506 TT
1 TT
12042508 ATTACCATTA
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
31 9 0.16
32 37 0.67
33 9 0.16
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (31 bp):
TTTTTATTATTGTTATATTATTATATTATAT
Found at i:12049622 original size:12 final size:12
Alignment explanation
Indices: 12049605--12049629 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12049595 TTCTGTTCAT
12049605 AGCATCCTAATC
1 AGCATCCTAATC
12049617 AGCATCCTAATC
1 AGCATCCTAATC
12049629 A
1 A
12049630 TTCGGCATAA
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:0.36, C:0.32, G:0.08, T:0.24
Consensus pattern (12 bp):
AGCATCCTAATC
Found at i:12049761 original size:46 final size:46
Alignment explanation
Indices: 12049701--12049926 Score: 283
Period size: 46 Copynumber: 4.9 Consensus size: 46
12049691 CATGAAATTA
* * *
12049701 CAGATCCTATACCCCTGAGACGTAGTGGGATGGATTGAAGAAAATG
1 CAGAACCTATACCCTTGAGACGCAGTGGGATGGATTGAAGAAAATG
* * *
12049747 CAGAACTTATACCCCTGAGACGCAGTGGGATGGATTAAAGAAAATG
1 CAGAACCTATACCCTTGAGACGCAGTGGGATGGATTGAAGAAAATG
* * * *
12049793 CA-AATCCTATATCCTTGAGACGCAATGGGATGGATTGAAGAGAATA
1 CAGAA-CCTATACCCTTGAGACGCAGTGGGATGGATTGAAGAAAATG
* ** *
12049839 CAGATCCTATACCCTTGAGACGTGGTGAGATGGATTGAAGAAAATG
1 CAGAACCTATACCCTTGAGACGCAGTGGGATGGATTGAAGAAAATG
* * *
12049885 TAGATCCTATACCCTTGAGACGCAGTGGAATGGATTGAAGAA
1 CAGAACCTATACCCTTGAGACGCAGTGGGATGGATTGAAGAA
12049927 GATTACAGAT
Statistics
Matches: 154, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
45 2 0.01
46 151 0.98
47 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.23
Consensus pattern (46 bp):
CAGAACCTATACCCTTGAGACGCAGTGGGATGGATTGAAGAAAATG
Found at i:12050135 original size:45 final size:44
Alignment explanation
Indices: 12050084--12050269 Score: 128
Period size: 44 Copynumber: 4.2 Consensus size: 44
12050074 AAGTAGTAAT
*
12050084 GGAGCAGATTGAAGACAGCGAATCTCATCTTCCCGAGGTAGTAG
1 GGAGCAGATTGAAGACAGCGAATCTTATCTTCCCGAGGTAGTAG
* * * ** * * * *
12050128 GGAAGCAGATTTAAGCCA-CTAGCCTTATCTTTCTGA-GCAGCAG
1 GG-AGCAGATTGAAGACAGCGAATCTTATCTTCCCGAGGTAGTAG
* * ** * * *
12050171 TGAGCAGGTTGAAGATTG-TAGATCTTATC-TCCCTAAGTAGTAG
1 GGAGCAGATTGAAGACAGCGA-ATCTTATCTTCCCGAGGTAGTAG
* * *
12050214 TGGAGTAGATCGAAGACGGCGAATCTTATCTTCCCGAGGTAGTAG
1 -GGAGCAGATTGAAGACAGCGAATCTTATCTTCCCGAGGTAGTAG
12050259 GGAAGCAGATT
1 GG-AGCAGATT
12050270 TAAGCCACCA
Statistics
Matches: 100, Mismatches: 34, Indels: 15
0.67 0.23 0.10
Matches are distributed among these distances:
42 15 0.15
43 17 0.17
44 36 0.36
45 32 0.32
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.25
Consensus pattern (44 bp):
GGAGCAGATTGAAGACAGCGAATCTTATCTTCCCGAGGTAGTAG
Found at i:12050245 original size:131 final size:132
Alignment explanation
Indices: 12049924--12050487 Score: 759
Period size: 132 Copynumber: 4.3 Consensus size: 132
12049914 ATGGATTGAA
12049924 GAAGATTACAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATC-AA-A----GAATCTTATCTT
1 GAAGATTACAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTT
** * * *
12049983 CTTGAGGTAGTAGGGAAGCTGATTTAAGCCACTAGCCTTATCTCACTGAGCAGCAGTGGAGCAGG
66 CCCGAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCTCTGAGCAGCAGTAGAGCAGG
12050048 CT
131 CT
*** * * * *
12050050 GAAGATTACAGATCTTATCTTTGTAAGTAGTAATGGAGCAGATTGAAGACAGCGAATCTCATCTT
1 GAAGATTACAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTT
*
12050115 CCCGAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTTTCTGAGCAGCAGT-GAGCAGG
66 CCCGAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCTCTGAGCAGCAGTAGAGCAGG
*
12050179 TT
131 CT
** *
12050181 GAAGATTGTAGATCTTATCTCCCTAAGTAGTAGTGGAGTAGATCGAAGACGGCGAATCTTATCTT
1 GAAGATTACAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTT
* * *
12050246 CCCGAGGTAGTAGGGAAGCAGATTTAAGCCACCAACCTTATCTCCCTGAGCAGCAGTAGAGCAGG
66 CCCGAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCTCTGAGCAGCAGTAGAGCAGG
12050311 CT
131 CT
* * *
12050313 GAAGATTACAGATCTTATCTCCTTAAGCT-GTAATGGAGCAGATCGAAGACGACGAATCTTATCT
1 GAAGATTACAGATCTTATCTCCCTAAG-TAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCT
* * *
12050377 TCCCGAGGTAGTAAGGAAGCAGACTTAAACCACTAGCCTTATCTCTCTGAGCAGCAGT-GAGCAG
65 TCCCGAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCTCTGAGCAGCAGTAGAGCAG
12050441 GCT
130 GCT
* ** * * * *
12050444 GAAGAATGTAGATCTTATCTCCTTAAGCAGTAGCGGAGTAGATC
1 GAAGATTACAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATC
12050488 TAAGCTACAA
Statistics
Matches: 383, Mismatches: 46, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
126 39 0.10
127 2 0.01
128 1 0.00
131 161 0.42
132 179 0.47
133 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.26
Consensus pattern (132 bp):
GAAGATTACAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTT
CCCGAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCTCTGAGCAGCAGTAGAGCAGG
CT
Found at i:12050385 original size:263 final size:257
Alignment explanation
Indices: 12049924--12050487 Score: 828
Period size: 263 Copynumber: 2.2 Consensus size: 257
12049914 ATGGATTGAA
** * **
12049924 GAAGATTACAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCAAAGAATCTTATCTTCTTGAG
1 GAAGATTGTAGATCTTATCTCCCTAAGTAGTAGTGGAGTAGATCAAAGAATCTTATCTTCCCGAG
* * * *
12049989 GTAGTAGGGAAGCTGATTTAAGCCACTAGCCTTATCTCACTGAGCAGCAGTGGAGCAGGCTGAAG
66 GTAGTAGGGAAGCAGATTTAAGCCACCAACCTTATCTCACTGAGCAGCAGTAGAGCAGGCTGAAG
* *
12050054 ATTACAGATCTTATCTTTGTAAGTAGTAATGGAGCAGATTGAAGACAGCGAATCTCATCTTCCCG
131 ATTACAGATCTTATCTCTGTAAGTAGTAATGGAGCAGATCGAAGACAGCGAATCTCATCTTCCCG
* * * * *
12050119 AGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTTTCTGAGCAGCAGTGAGCAGGTT
196 AGGTAGTAAGGAAGCAGACTTAAACCACTAGCCTTATCTCTCTGAGCAGCAGTGAGCAGGCT
12050181 GAAGATTGTAGATCTTATCTCCCTAAGTAGTAGTGGAGTAGATCGAAGACGGCGAATCTTATCTT
1 GAAGATTGTAGATCTTATCTCCCTAAGTAGTAGTGGAGTAGATC-AA-A----GAATCTTATCTT
*
12050246 CCCGAGGTAGTAGGGAAGCAGATTTAAGCCACCAACCTTATCTCCCTGAGCAGCAGTAGAGCAGG
60 CCCGAGGTAGTAGGGAAGCAGATTTAAGCCACCAACCTTATCTCACTGAGCAGCAGTAGAGCAGG
*
12050311 CTGAAGATTACAGATCTTATCTCCT-TAAGCT-GTAATGGAGCAGATCGAAGAC-GACGAATCTT
125 CTGAAGATTACAGATCTTATCT-CTGTAAG-TAGTAATGGAGCAGATCGAAGACAG-CGAATCTC
12050373 ATCTTCCCGAGGTAGTAAGGAAGCAGACTTAAACCACTAGCCTTATCTCTCTGAGCAGCAGTGAG
187 ATCTTCCCGAGGTAGTAAGGAAGCAGACTTAAACCACTAGCCTTATCTCTCTGAGCAGCAGTGAG
12050438 CAGGCT
252 CAGGCT
* * * *
12050444 GAAGAATGTAGATCTTATCTCCTTAAGCAGTAGCGGAGTAGATC
1 GAAGATTGTAGATCTTATCTCCCTAAGTAGTAGTGGAGTAGATC
12050488 TAAGCTACAA
Statistics
Matches: 276, Mismatches: 22, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
257 41 0.15
258 2 0.01
259 1 0.00
262 1 0.00
263 229 0.83
264 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.26
Consensus pattern (257 bp):
GAAGATTGTAGATCTTATCTCCCTAAGTAGTAGTGGAGTAGATCAAAGAATCTTATCTTCCCGAG
GTAGTAGGGAAGCAGATTTAAGCCACCAACCTTATCTCACTGAGCAGCAGTAGAGCAGGCTGAAG
ATTACAGATCTTATCTCTGTAAGTAGTAATGGAGCAGATCGAAGACAGCGAATCTCATCTTCCCG
AGGTAGTAAGGAAGCAGACTTAAACCACTAGCCTTATCTCTCTGAGCAGCAGTGAGCAGGCT
Found at i:12050759 original size:25 final size:25
Alignment explanation
Indices: 12050731--12050784 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
12050721 CAAGTAGAGC
12050731 CCAAAACACCAAATAAATTAACAAT
1 CCAAAACACCAAATAAATTAACAAT
* *
12050756 CCAAAACACCAAATGAATTAACAGT
1 CCAAAACACCAAATAAATTAACAAT
12050781 CCAA
1 CCAA
12050785 TTAACACTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.56, C:0.26, G:0.04, T:0.15
Consensus pattern (25 bp):
CCAAAACACCAAATAAATTAACAAT
Found at i:12051255 original size:3 final size:3
Alignment explanation
Indices: 12051232--12051413 Score: 101
Period size: 3 Copynumber: 60.3 Consensus size: 3
12051222 GGGGAGAGTG
* * *
12051232 TTA TTT TTA ATA TTG TTA TTA TTA TATA TTA TTA CTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA -TTA TTA TTA TTA
* * *
12051279 -TA TTTA TTA -TA TTA -TA TTTA TT- TTA TTA CTG TTA CTA TTA TT-
1 TTA -TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
** *
12051321 TTA -TA TATA TTTA TTA CCA TTA TTTA TTTA TTTA TTA TTA TTA GTA
1 TTA TTA T-TA -TTA TTA TTA TTA -TTA -TTA -TTA TTA TTA TTA TTA
** * * *
12051367 ACA -TA TTG TTA TTT TTA TTA TT- TTA TTA TTA TTA TTC TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12051413 T
1 T
12051414 CATGATACTA
Statistics
Matches: 138, Mismatches: 26, Indels: 30
0.71 0.13 0.15
Matches are distributed among these distances:
2 15 0.11
3 97 0.70
4 25 0.18
5 1 0.01
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:12051277 original size:23 final size:22
Alignment explanation
Indices: 12051242--12051413 Score: 113
Period size: 23 Copynumber: 7.7 Consensus size: 22
12051232 TTATTTTTAA
*
12051242 TATTGTTATTATTATATATTAT
1 TATTATTATTATTATATATTAT
12051264 TACTTATTATTATTATAT-TTAT
1 TA-TTATTATTATTATATATTAT
*
12051286 TA-TATTA-TATT-TATTTTAT
1 TATTATTATTATTATATATTAT
* *
12051305 TACTGTTACTATTATTTTATATATATT
1 TA---TTATTATTATTATATAT-TA-T
**
12051332 TATTACCATTATT-TAT-TTATT
1 TATTATTATTATTATATATTA-T
* * *
12051353 TATTATTATTAGTAACATATTGT
1 TATTATTATTA-TTATATATTAT
* *
12051376 TATTTTTATTATTTTATTATTAT
1 TATTATTATTATTATA-TATTAT
*
12051399 TATTCTTATTATTAT
1 TATTATTATTATTAT
12051414 CATGATACTA
Statistics
Matches: 120, Mismatches: 16, Indels: 27
0.74 0.10 0.17
Matches are distributed among these distances:
18 3 0.03
19 10 0.08
20 5 0.04
21 13 0.11
22 12 0.10
23 52 0.43
24 16 0.13
25 4 0.03
26 2 0.02
27 3 0.03
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.63
Consensus pattern (22 bp):
TATTATTATTATTATATATTAT
Found at i:12051355 original size:31 final size:31
Alignment explanation
Indices: 12051250--12051361 Score: 79
Period size: 35 Copynumber: 3.4 Consensus size: 31
12051240 AATATTGTTA
*
12051250 TTATTATATATTATTACTTATT--ATTATTATAT
1 TTATT-TATATTA-TATTTATTCCATTATT-TAT
**
12051282 TTA-TTATATTATATTTATTTTATTACTGTTACT
1 TTATTTATATTATATTTATTCCATTA-T-TTA-T
12051315 ATTATTT-TATATATATTTATTACCATTATTTAT
1 -TTATTTATAT-TATATTTATT-CCATTATTTAT
12051348 TTATTTATTATTAT
1 TTATTTA-TATTAT
12051362 TAGTAACATA
Statistics
Matches: 66, Mismatches: 3, Indels: 21
0.73 0.03 0.23
Matches are distributed among these distances:
29 7 0.11
30 7 0.11
31 5 0.08
32 12 0.18
33 6 0.09
34 12 0.18
35 13 0.20
36 4 0.06
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.63
Consensus pattern (31 bp):
TTATTTATATTATATTTATTCCATTATTTAT
Found at i:12053253 original size:63 final size:63
Alignment explanation
Indices: 12053154--12053278 Score: 214
Period size: 63 Copynumber: 2.0 Consensus size: 63
12053144 TCTCTCCCAC
* * *
12053154 AATTTAGGCCTCATTATGAGTCAGGTTATCTGTCCAGATTTGAATGTCCATTCGAAATGTGGA
1 AATTTAGGCCTCATCATGAGTCAGGTTATCTGTCCAGATTTGAATGTCCATTAGAAAAGTGGA
*
12053217 AATTTAGGCCTCATCATGAGTCGGGTTATCTGTCCAGATTTGAATGTCCATTAGAAAAGTGG
1 AATTTAGGCCTCATCATGAGTCAGGTTATCTGTCCAGATTTGAATGTCCATTAGAAAAGTGG
12053279 GAGGGTTTGG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (63 bp):
AATTTAGGCCTCATCATGAGTCAGGTTATCTGTCCAGATTTGAATGTCCATTAGAAAAGTGGA
Found at i:12053439 original size:11 final size:11
Alignment explanation
Indices: 12053423--12053470 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
12053413 TCTGTTGCTA
*
12053423 TTTGCTATTGT
1 TTTGCTATTAT
*
12053434 TTTGCTATCAT
1 TTTGCTATTAT
12053445 TTTGCTATTAT
1 TTTGCTATTAT
* * *
12053456 ATTGTTACTAT
1 TTTGCTATTAT
12053467 TTTG
1 TTTG
12053471 TTGTTATTAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.17, C:0.10, G:0.12, T:0.60
Consensus pattern (11 bp):
TTTGCTATTAT
Found at i:12056252 original size:20 final size:20
Alignment explanation
Indices: 12056227--12056265 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12056217 GTTTTTACAT
12056227 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
12056247 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
12056266 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:12060155 original size:17 final size:17
Alignment explanation
Indices: 12060133--12060165 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
12060123 GCATATTTTC
12060133 ACAGCTCACACATTACT
1 ACAGCTCACACATTACT
12060150 ACAGCTCACACATTAC
1 ACAGCTCACACATTAC
12060166 ATAGCTTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.36, G:0.06, T:0.21
Consensus pattern (17 bp):
ACAGCTCACACATTACT
Found at i:12060227 original size:33 final size:33
Alignment explanation
Indices: 12060135--12060264 Score: 95
Period size: 33 Copynumber: 3.9 Consensus size: 33
12060125 ATATTTTCAC
* * **
12060135 AGCTCACACATTACTACAGCTCACACATTA-CAT
1 AGCTCACAAATTAC-ACAGCTCACACATCATTGT
** * ** *
12060168 AGCTTGCATATTACACAATTCGCACATCATTGT
1 AGCTCACAAATTACACAGCTCACACATCATTGT
* *
12060201 AGCTTACAGATTACACAGCTCACACATCACTATG-
1 AGCTCACAAATTACACAGCTCACACATCA-T-TGT
*
12060235 A-CTCGCAAATTACACAGCTCACACATCATT
1 AGCTCACAAATTACACAGCTCACACATCATT
12060265 ACGACTCGCA
Statistics
Matches: 77, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
31 1 0.01
32 12 0.16
33 60 0.78
34 2 0.03
35 2 0.03
ACGTcount: A:0.35, C:0.30, G:0.09, T:0.26
Consensus pattern (33 bp):
AGCTCACAAATTACACAGCTCACACATCATTGT
Found at i:12060247 original size:66 final size:66
Alignment explanation
Indices: 12060135--12060264 Score: 156
Period size: 66 Copynumber: 2.0 Consensus size: 66
12060125 ATATTTTCAC
* * * * *
12060135 AGCTCACACATTACTACAGCTCACACATTACATAGCTTGCATATTACACAATTCGCACATCATTG
1 AGCTCACACATTACTACAGCTCACACATCACATAGCTCGCAAATTACACAACTCACACATCATTG
12060200 T
66 T
* * *
12060201 AGCTTACAGATTAC-ACAGCTCACACATCAC-TATGACTCGCAAATTACACAGCTCACACATCAT
1 AGCTCACACATTACTACAGCTCACACATCACATA-G-CTCGCAAATTACACAACTCACACATCAT
12060264 T
64 T
12060265 ACGACTCGCA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
64 2 0.04
65 16 0.30
66 36 0.67
ACGTcount: A:0.35, C:0.30, G:0.09, T:0.26
Consensus pattern (66 bp):
AGCTCACACATTACTACAGCTCACACATCACATAGCTCGCAAATTACACAACTCACACATCATTG
T
Found at i:12060271 original size:33 final size:33
Alignment explanation
Indices: 12060210--12060274 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
12060200 TAGCTTACAG
*
12060210 ATTACACAGCTCACACATCACTATGACTCGCAA
1 ATTACACAGCTCACACATCACTACGACTCGCAA
*
12060243 ATTACACAGCTCACACATCATTACGACTCGCA
1 ATTACACAGCTCACACATCACTACGACTCGCA
12060275 CATTGATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.35, C:0.34, G:0.09, T:0.22
Consensus pattern (33 bp):
ATTACACAGCTCACACATCACTACGACTCGCAA
Found at i:12079021 original size:17 final size:17
Alignment explanation
Indices: 12078989--12079030 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
12078979 AAAGTCCTAG
12078989 CTTTTTCTCCTTTCTTTCT
1 CTTTTTCT-CTTTC-TTCT
12079008 CTTTTTCT-TTTCTTCT
1 CTTTTTCTCTTTCTTCT
12079024 CTGTTTT
1 CT-TTTT
12079031 GTTTCTGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 6 0.27
17 8 0.36
19 8 0.36
ACGTcount: A:0.00, C:0.26, G:0.02, T:0.71
Consensus pattern (17 bp):
CTTTTTCTCTTTCTTCT
Found at i:12083866 original size:18 final size:18
Alignment explanation
Indices: 12083843--12083890 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
12083833 TTAACTCAAG
12083843 TACCCAACCCAACCCAAT
1 TACCCAACCCAACCCAAT
12083861 TACCCAACCCAACCCAAT
1 TACCCAACCCAACCCAAT
12083879 TACCCAACCCAA
1 TACCCAACCCAA
12083891 TCATAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.40, C:0.50, G:0.00, T:0.10
Consensus pattern (18 bp):
TACCCAACCCAACCCAAT
Found at i:12083867 original size:13 final size:13
Alignment explanation
Indices: 12083867--12083891 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12083857 CAATTACCCA
12083867 ACCCAACCCAATT
1 ACCCAACCCAATT
12083880 ACCCAACCCAAT
1 ACCCAACCCAAT
12083892 CATAAAAATT
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:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:12083932 original size:21 final size:20
Alignment explanation
Indices: 12083908--12083951 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
12083898 AATTACAAAT
12083908 AATTTAATAAATAAAAATAAA
1 AATTTAA-AAATAAAAATAAA
* *
12083929 AATTTAAAACTGAAAATAAA
1 AATTTAAAAATAAAAATAAA
12083949 AAT
1 AAT
12083952 AAAAAACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (20 bp):
AATTTAAAAATAAAAATAAA
Found at i:12083957 original size:20 final size:20
Alignment explanation
Indices: 12083921--12083958 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12083911 TTAATAAATA
**
12083921 AAAATAAAAATTTAAAACTG
1 AAAATAAAAATAAAAAACTG
12083941 AAAATAAAAATAAAAAAC
1 AAAATAAAAATAAAAAAC
12083959 ATATAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (20 bp):
AAAATAAAAATAAAAAACTG
Found at i:12083990 original size:9 final size:9
Alignment explanation
Indices: 12083976--12084044 Score: 68
Period size: 9 Copynumber: 7.7 Consensus size: 9
12083966 TTTATACAAA
*
12083976 TAATTTGAT
1 TAATTTGGT
12083985 TAATTTGGT
1 TAATTTGGT
*
12083994 TAATTCGGT
1 TAATTTGGT
12084003 TAATTTAGG-
1 TAATTT-GGT
* *
12084012 TAATTCGGG
1 TAATTTGGT
*
12084021 TAATTCGGT
1 TAATTTGGT
*
12084030 TAATTCGGT
1 TAATTTGGT
12084039 TAATTT
1 TAATTT
12084045 TATACTTATT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
8 2 0.04
9 48 0.92
10 2 0.04
ACGTcount: A:0.26, C:0.06, G:0.20, T:0.48
Consensus pattern (9 bp):
TAATTTGGT
Found at i:12084005 original size:18 final size:18
Alignment explanation
Indices: 12083984--12084044 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
12083974 AATAATTTGA
12083984 TTAATTTGGTTAATTCGG
1 TTAATTTGGTTAATTCGG
12084002 TTAATTTAGG-TAATTCGG
1 TTAATTT-GGTTAATTCGG
* *
12084020 GTAATTCGGTTAATTCGG
1 TTAATTTGGTTAATTCGG
12084038 TTAATTT
1 TTAATTT
12084045 TATACTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
17 2 0.05
18 33 0.89
19 2 0.05
ACGTcount: A:0.25, C:0.07, G:0.21, T:0.48
Consensus pattern (18 bp):
TTAATTTGGTTAATTCGG
Found at i:12085657 original size:4 final size:4
Alignment explanation
Indices: 12085648--12085686 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
12085638 GCTTTTTCTC
* *
12085648 CTTT CTTT CTTT CTTT TTTT CTTTT CTTT CTTT CCTT CT
1 CTTT CTTT CTTT CTTT CTTT C-TTT CTTT CTTT CTTT CT
12085687 CTGTTTCGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
CTTT
Found at i:12085664 original size:21 final size:21
Alignment explanation
Indices: 12085639--12085681 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
12085629 AAAATCCTAG
12085639 CTTTTTCTCCTTTCTTTCTTT
1 CTTTTTCTCCTTTCTTTCTTT
* *
12085660 CTTTTTTTCTTTTCTTTCTTT
1 CTTTTTCTCCTTTCTTTCTTT
12085681 C
1 C
12085682 CTTCTCTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (21 bp):
CTTTTTCTCCTTTCTTTCTTT
Found at i:12085686 original size:17 final size:17
Alignment explanation
Indices: 12085653--12085686 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12085643 TTCTCCTTTC
**
12085653 TTTCTTTCTTTTTTTCT
1 TTTCTTTCTTTCCTTCT
12085670 TTTCTTTCTTTCCTTCT
1 TTTCTTTCTTTCCTTCT
12085687 CTGTTTCGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTCTTTCTTTCCTTCT
Found at i:12085693 original size:25 final size:25
Alignment explanation
Indices: 12085648--12085699 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
12085638 GCTTTTTCTC
* * * *
12085648 CTTTCTTTCTTTCTTTTTTTCTTTT
1 CTTTCTTTCCTTCTCTGTTTCGTTT
12085673 CTTTCTTTCCTTCTCTGTTTCGTTT
1 CTTTCTTTCCTTCTCTGTTTCGTTT
12085698 CT
1 CT
12085700 GCTTTGGCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.00, C:0.25, G:0.04, T:0.71
Consensus pattern (25 bp):
CTTTCTTTCCTTCTCTGTTTCGTTT
Found at i:12085767 original size:5 final size:5
Alignment explanation
Indices: 12085757--12085809 Score: 97
Period size: 5 Copynumber: 10.6 Consensus size: 5
12085747 TTTTTATTAT
*
12085757 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ACATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
12085807 ATA
1 ATA
12085810 CATATTTATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:12085862 original size:15 final size:15
Alignment explanation
Indices: 12085751--12085862 Score: 72
Period size: 15 Copynumber: 7.4 Consensus size: 15
12085741 TTTATTTTTT
12085751 TATTATATATAATATA
1 TATTA-ATATAATATA
12085767 -ATATAATATAATATA
1 TAT-TAATATAATATA
12085782 -ATATAATATAATATA
1 TAT-TAATATAATATA
* *
12085797 -ATATAACATAATACA
1 TAT-TAATATAATATA
*
12085812 TATT--TATACTTATA
1 TATTAATATA-ATATA
* * *
12085826 TGTTAAGTAAAAGATA
1 TATTAA-TATAATATA
*
12085842 TTTTAATATAATATA
1 TATTAATATAATATA
12085857 TATTAA
1 TATTAA
12085863 ATTCAAAGAA
Statistics
Matches: 77, Mismatches: 13, Indels: 13
0.75 0.13 0.13
Matches are distributed among these distances:
13 3 0.04
14 6 0.08
15 53 0.69
16 12 0.16
17 3 0.04
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.43
Consensus pattern (15 bp):
TATTAATATAATATA
Found at i:12088415 original size:22 final size:22
Alignment explanation
Indices: 12088389--12088437 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
12088379 GTCCAAGTGC
*
12088389 ATAACTAATATTACACCATATG
1 ATAACTAATATTACACCACATG
12088411 ATAACTAATATTACACCACATG
1 ATAACTAATATTACACCACATG
12088433 ATAAC
1 ATAAC
12088438 AACAACATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.47, C:0.20, G:0.04, T:0.29
Consensus pattern (22 bp):
ATAACTAATATTACACCACATG
Found at i:12090683 original size:17 final size:17
Alignment explanation
Indices: 12090660--12090703 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
12090650 GAGATTGAAT
*
12090660 TGAAAAATTACT-TAAC
1 TGAAAAATTACTAAAAC
12090676 TAGAAAAA-TACTAAAAC
1 T-GAAAAATTACTAAAAC
12090693 TGAAAAATTAC
1 TGAAAAATTAC
12090704 ATTCCTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.57, C:0.11, G:0.07, T:0.25
Consensus pattern (17 bp):
TGAAAAATTACTAAAAC
Found at i:12092378 original size:13 final size:13
Alignment explanation
Indices: 12092360--12092388 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
12092350 TTTAGTTTAA
12092360 TTAGTTAATTAGT
1 TTAGTTAATTAGT
12092373 TTAGTTAATTAGT
1 TTAGTTAATTAGT
12092386 TTA
1 TTA
12092389 ATAAACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:12097740 original size:6 final size:6
Alignment explanation
Indices: 12097729--12097761 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
12097719 TCCTTCTATC
*
12097729 TTTTTA TTTTTA TTTTTA TTTTTA TTTTCA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT
12097762 CAATTGTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTA
Found at i:12100314 original size:23 final size:23
Alignment explanation
Indices: 12100288--12100363 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
12100278 ATAAGTGCCA
12100288 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
12100311 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
12100334 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
12100357 CACTGAT
1 CACTGAT
12100364 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:12100615 original size:18 final size:17
Alignment explanation
Indices: 12100589--12100627 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
12100579 ATTTTCCTTC
12100589 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
12100606 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
12100624 CACA
1 CACA
12100628 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:12120792 original size:17 final size:18
Alignment explanation
Indices: 12120745--12120804 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 18
12120735 TTTCTTTTCT
*
12120745 TTTCTTTTATTATTATTA
1 TTTCATTTATTATTATTA
* *
12120763 TTTCCTTTTTTATT-TTA
1 TTTCATTTATTATTATTA
* *
12120780 TTTTATTTATTATTACTA
1 TTTCATTTATTATTATTA
12120798 TTT-ATTT
1 TTTCATTT
12120805 TTTAATATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
17 18 0.51
18 17 0.49
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTCATTTATTATTATTA
Found at i:12124551 original size:39 final size:39
Alignment explanation
Indices: 12124503--12124616 Score: 186
Period size: 39 Copynumber: 3.1 Consensus size: 39
12124493 TTCCGACTCT
12124503 TCACAACACTTCACCCTGATTGATACCACCACATCTTCC
1 TCACAACACTTCACCCTGATTGATACCACCACATCTTCC
12124542 TCACAACACTTCACCCTGATTGATACCACCACATCTTCC
1 TCACAACACTTCACCCTGATTGATACCACCACATCTTCC
12124581 TCACAACAC-T-----TGATTGATACCACCACATCTTCC
1 TCACAACACTTCACCCTGATTGATACCACCACATCTTCC
12124614 TCA
1 TCA
12124617 GTACTCTTTC
Statistics
Matches: 75, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
33 26 0.35
38 1 0.01
39 48 0.64
ACGTcount: A:0.29, C:0.39, G:0.05, T:0.26
Consensus pattern (39 bp):
TCACAACACTTCACCCTGATTGATACCACCACATCTTCC
Found at i:12126787 original size:23 final size:23
Alignment explanation
Indices: 12126761--12126806 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
12126751 AAAGGCAAAC
* *
12126761 AAAACCGTAACTAATAGTAAAAA
1 AAAACCATAACTAAAAGTAAAAA
*
12126784 AAAACCATATCTAAAAGTAAAAA
1 AAAACCATAACTAAAAGTAAAAA
12126807 GTAAATTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.63, C:0.13, G:0.07, T:0.17
Consensus pattern (23 bp):
AAAACCATAACTAAAAGTAAAAA
Found at i:12130393 original size:23 final size:23
Alignment explanation
Indices: 12130367--12130442 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
12130357 ATAAGTGCCA
12130367 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
12130390 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
12130413 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
12130436 CACTGAT
1 CACTGAT
12130443 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:12130694 original size:18 final size:17
Alignment explanation
Indices: 12130668--12130706 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
12130658 ATTTTCCTTC
12130668 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
12130685 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
12130703 CACA
1 CACA
12130707 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:12133390 original size:13 final size:13
Alignment explanation
Indices: 12133372--12133400 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
12133362 TTTAGTTTAA
12133372 TTAGTTAATTAGT
1 TTAGTTAATTAGT
12133385 TTAGTTAATTAGT
1 TTAGTTAATTAGT
12133398 TTA
1 TTA
12133401 ATAAACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:12136821 original size:3 final size:3
Alignment explanation
Indices: 12136813--12136839 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12136803 TTGGCTTTAA
12136813 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
12136840 TTCTCATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:12149671 original size:47 final size:46
Alignment explanation
Indices: 12149471--12149832 Score: 201
Period size: 47 Copynumber: 7.7 Consensus size: 46
12149461 TGAGATATAT
* * * *
12149471 TGTCGATTCCATGTCCCAGACATGGTCTTACACGGGCTCTCATATAC-G
1 TGTCGA-TGCATGTCCCAGACAT-GTCTTACACTGGCACTCATCT-CTG
* * *
12149519 CGTGCTGATGCATGTCCCAGACATGTCTTACACTTGCA--CAACTCT-
1 TGT-C-GATGCATGTCCCAGACATGTCTTACACTGGCACTCATCTCTG
* * * * *
12149564 TAGGCAATGCGTGTCCCAAACACGTCTTACACTGG--CT-ATCTCTG
1 T-GTCGATGCATGTCCCAGACATGTCTTACACTGGCACTCATCTCTG
* * *
12149608 TCGAGGCCGACGCATGTCCCAAACATGTCTTACACTGGCACTCATCTCTG
1 T----GTCGATGCATGTCCCAGACATGTCTTACACTGGCACTCATCTCTG
* * * *
12149658 TGTCGATGCCATGTCCCAGACATGGTTTTACACTGGCTA-TTATAGTATG
1 TGTCGATG-CATGTCCCAGACAT-GTCTTACACTGGC-ACTCAT-CTCTG
* * * *
12149707 -G-CGATGCATGTCCCAGACATGTCTTACACTAGCCCTCGTCT-GG
1 TGTCGATGCATGTCCCAGACATGTCTTACACTGGCACTCATCTCTG
* * *
12149750 ATG-CAGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATATG
1 -TGTC-GATG-CATGTCCCAGACAT-GTCTTACACTGGCACTCAT-CTCTG
* * *
12149800 -GCCGAAGGATGTCCCAGACATGTCTTACACTGG
1 TGTCGATGCATGTCCCAGACATGTCTTACACTGG
12149833 AGTACAAATC
Statistics
Matches: 246, Mismatches: 42, Indels: 54
0.72 0.12 0.16
Matches are distributed among these distances:
43 6 0.02
44 27 0.11
45 17 0.07
46 39 0.16
47 73 0.30
48 49 0.20
49 24 0.10
50 11 0.04
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (46 bp):
TGTCGATGCATGTCCCAGACATGTCTTACACTGGCACTCATCTCTG
Found at i:12149727 original size:93 final size:94
Alignment explanation
Indices: 12149471--12149832 Score: 341
Period size: 93 Copynumber: 3.9 Consensus size: 94
12149461 TGAGATATAT
* * * * *
12149471 TGTCGATTCCATGTCCCAGACATGGTCTTACACGGGCTCTCATA-TACGCGTGCTGATGCATGTC
1 TGTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAGTA--TG-GCCGATGCATGTC
* *
12149535 CCAGACATGTCTTACACTTGCA--CAACTCT-
63 CCAGACATGTCTTACACTGGCACTCATCTCTG
* * * * * * *
12149564 TAGGCAATG-CGTGTCCCAAACA-CGTCTTACACTGGCTATC-TCTGTCGA-GGCCGACGCATGT
1 T-GTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCAT-AGT--ATGGCCGATGCATGT
*
12149625 CCCAAACATGTCTTACACTGGCACTCATCTCTG
62 CCCAGACATGTCTTACACTGGCACTCATCTCTG
* *
12149658 TGTCGATGCCATGTCCCAGACATGGTTTTACACTGGCTATTATAGTATGG-CGATGCATGTCCCA
1 TGTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAGTATGGCCGATGCATGTCCCA
* * * *
12149722 GACATGTCTTACACTAGCCCTCGTCT-GG
66 GACATGTCTTACACTGGCACTCATCTCTG
* * * *
12149750 ATG-CAGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATATGGCCGAAGGATGTCC
1 -TGTC-GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAGTATGGCCGATGCATGTCC
12149814 CAGACATGTCTTACACTGG
64 CAGACATGTCTTACACTGG
12149833 AGTACAAATC
Statistics
Matches: 219, Mismatches: 35, Indels: 29
0.77 0.12 0.10
Matches are distributed among these distances:
91 32 0.15
92 18 0.08
93 104 0.47
94 46 0.21
95 18 0.08
96 1 0.00
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (94 bp):
TGTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAGTATGGCCGATGCATGTCCCA
GACATGTCTTACACTGGCACTCATCTCTG
Found at i:12149814 original size:187 final size:184
Alignment explanation
Indices: 12149471--12149832 Score: 412
Period size: 187 Copynumber: 1.9 Consensus size: 184
12149461 TGAGATATAT
* *
12149471 TGTCGATTCCATGTCCCAGACATGGTCTTACACGGGCTCTCATATACGCGTGCTGATGCATGTCC
1 TGTCGATGCCATGTCCCAGACATGGTCTTACACGGGCTATCATATAC-CGTGCTGATGCATGTCC
* * *
12149536 CAGACATGTCTTACACTTGCACAACTCTTAGGCAATGCGTGTCCCAAACACGTCTTACACTGGCT
65 CAGACATGTCTTACACTAGCACAACTCTGAGGCAATGCATGTCCCAAACACGTCTTACACTGGC-
* *
12149601 ATCTCTGTCGAGGCCGACGCATGTCCCAAACATGTCTTACACTGGCACTCATCTCTG
129 ATCTCTATC-AGGCCGAAGCATGTCCCAAACATGTCTTACACTGGCACTCATCTCTG
* * * *
12149658 TGTCGATGCCATGTCCCAGACATGGTTTTACACTGGCTATTATAGTA-TG-GC-GATGCATGTCC
1 TGTCGATGCCATGTCCCAGACATGGTCTTACACGGGCTATCATA-TACCGTGCTGATGCATGTCC
** * * *
12149720 CAGACATGTCTTACACTAGC-CCTCGTCTGGATGCAGATGCCATGTCCCAGACATGGTCTTACAC
65 CAGACATGTCTTACACTAGCACAAC-TCT-GAGGCA-ATG-CATGTCCCAAACA-CGTCTTACAC
* *
12149784 TGGC-TCTCATAAT-ATGGCCGAAGGATGTCCCAGACATGTCTTACACTGG
125 TGGCATCTC-T-ATCA-GGCCGAAGCATGTCCCAAACATGTCTTACACTGG
12149833 AGTACAAATC
Statistics
Matches: 148, Mismatches: 18, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
183 2 0.01
184 33 0.22
185 6 0.04
186 9 0.06
187 82 0.55
188 16 0.11
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (184 bp):
TGTCGATGCCATGTCCCAGACATGGTCTTACACGGGCTATCATATACCGTGCTGATGCATGTCCC
AGACATGTCTTACACTAGCACAACTCTGAGGCAATGCATGTCCCAAACACGTCTTACACTGGCAT
CTCTATCAGGCCGAAGCATGTCCCAAACATGTCTTACACTGGCACTCATCTCTG
Found at i:12152650 original size:12 final size:13
Alignment explanation
Indices: 12152622--12152653 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
12152612 AATTTAAAAC
12152622 TTTTAAGATAGAT
1 TTTTAAGATAGAT
12152635 TTTTAAGATAGAT
1 TTTTAAGATAGAT
12152648 TTTTAA
1 TTTTAA
12152654 TTATTATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (13 bp):
TTTTAAGATAGAT
Found at i:12152733 original size:20 final size:20
Alignment explanation
Indices: 12152669--12152732 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
12152659 ATAATGTTTG
12152669 AACAAGGGCA-CAAATGTGCA
1 AACAAGGGCACCAAA-GTGCA
* *
12152689 TACAAGGGCACCATAGTGCA
1 AACAAGGGCACCAAAGTGCA
*
12152709 AACAGGGGCACCAAAGTGCA
1 AACAAGGGCACCAAAGTGCA
12152729 AACA
1 AACA
12152733 GAATAAGCGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
20 35 0.92
21 3 0.08
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.09
Consensus pattern (20 bp):
AACAAGGGCACCAAAGTGCA
Found at i:12155306 original size:31 final size:31
Alignment explanation
Indices: 12155271--12155353 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
12155261 CTTCCTGCAT
* *
12155271 TAAAATCCAACCAAATACAACAAATATAGTA
1 TAAAATCCAACCAAAAACAACAAATATAGCA
* * * *
12155302 TAAAATGCAGCCAAAAACAGCAAATTTAGCA
1 TAAAATCCAACCAAAAACAACAAATATAGCA
*
12155333 TAAAAAATACAACCAAAAACA
1 T--AAAATCCAACCAAAAACA
12155354 TTAATTCTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 26 0.62
33 16 0.38
ACGTcount: A:0.59, C:0.19, G:0.06, T:0.16
Consensus pattern (31 bp):
TAAAATCCAACCAAAAACAACAAATATAGCA
Found at i:12155598 original size:21 final size:21
Alignment explanation
Indices: 12155585--12155681 Score: 135
Period size: 21 Copynumber: 4.6 Consensus size: 21
12155575 TCTGCTGCCA
12155585 TCGCTGCTGCCTCTGCCTCCC
1 TCGCTGCTGCCTCTGCCTCCC
12155606 TCGCT-CGTGCCTCTGCCTCCC
1 TCGCTGC-TGCCTCTGCCTCCC
* *
12155627 TCGCTACTGCCACTGCCTCCC
1 TCGCTGCTGCCTCTGCCTCCC
12155648 TCGCTGCTG-CTACTGCCTCCC
1 TCGCTGCTGCCT-CTGCCTCCC
*
12155669 TCTCTGCTGCCTC
1 TCGCTGCTGCCTC
12155682 CGCTCTAAGT
Statistics
Matches: 68, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.03
21 63 0.93
22 3 0.04
ACGTcount: A:0.03, C:0.51, G:0.18, T:0.29
Consensus pattern (21 bp):
TCGCTGCTGCCTCTGCCTCCC
Found at i:12161240 original size:9 final size:9
Alignment explanation
Indices: 12161219--12161339 Score: 63
Period size: 9 Copynumber: 13.6 Consensus size: 9
12161209 TATATATTAC
*
12161219 GTAAGTTAA
1 GTAAGTTAT
12161228 GTAAGCTT-T
1 GTAAG-TTAT
12161237 GTAAGTTAT
1 GTAAGTTAT
12161246 GTAAGTTAT
1 GTAAGTTAT
* *
12161255 GTTA-TGAT
1 GTAAGTTAT
* *
12161263 ATACATTTAT
1 GTA-AGTTAT
**
12161273 GTAAGGCAT
1 GTAAGTTAT
12161282 GTAAGTTAT
1 GTAAGTTAT
* *
12161291 GATATGATAT
1 G-TAAGTTAT
* *
12161301 AT-ATTTAT
1 GTAAGTTAT
12161309 GT-A-TTAT
1 GTAAGTTAT
*
12161316 GTAAGTTGT
1 GTAAGTTAT
12161325 GTAAGTTAT
1 GTAAGTTAT
12161334 GATAAG
1 G-TAAG
12161340 ATATATATTT
Statistics
Matches: 83, Mismatches: 21, Indels: 15
0.70 0.18 0.13
Matches are distributed among these distances:
7 6 0.07
8 12 0.14
9 48 0.58
10 17 0.20
ACGTcount: A:0.34, C:0.02, G:0.21, T:0.43
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:12161422 original size:113 final size:112
Alignment explanation
Indices: 12161293--12161503 Score: 361
Period size: 113 Copynumber: 1.9 Consensus size: 112
12161283 TAAGTTATGA
*
12161293 TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATTTATGATATA
1 TATGAAATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATTTATGATATA
12161358 TATTTGGA-GTATTATGTAAGTTGTGTAAGTTATGATATGATACATATT
66 TATTT--ATGTATTATGTAAGTTGTGTAAGTTATGATATGATACATATT
* *
12161406 TATGAAATATATTTATGTATTATGTTAGTTGTGTAAGTTATGATATGATATATATTTATGATATA
1 TATGAAATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATTTATGATATA
*
12161471 TATTTATGTATTATGTAAGTTTTGTAAGTTATG
66 TATTTATGTATTATGTAAGTTGTGTAAGTTATG
12161504 TAAGTTTTGT
Statistics
Matches: 93, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
111 1 0.01
112 25 0.27
113 67 0.72
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (112 bp):
TATGAAATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATTTATGATATA
TATTTATGTATTATGTAAGTTGTGTAAGTTATGATATGATACATATT
Found at i:12161467 original size:13 final size:13
Alignment explanation
Indices: 12161449--12161478 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
12161439 TAAGTTATGA
12161449 TATGATATATATT
1 TATGATATATATT
12161462 TATGATATATATT
1 TATGATATATATT
12161475 TATG
1 TATG
12161479 TATTATGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (13 bp):
TATGATATATATT
Found at i:12161498 original size:9 final size:9
Alignment explanation
Indices: 12161481--12161529 Score: 80
Period size: 9 Copynumber: 5.4 Consensus size: 9
12161471 TATTTATGTA
12161481 TTATGTAAG
1 TTATGTAAG
*
12161490 TTTTGTAAG
1 TTATGTAAG
12161499 TTATGTAAG
1 TTATGTAAG
*
12161508 TTTTGTAAG
1 TTATGTAAG
12161517 TTATGTAAG
1 TTATGTAAG
12161526 TTAT
1 TTAT
12161530 TATATGATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (9 bp):
TTATGTAAG
Found at i:12161504 original size:18 final size:18
Alignment explanation
Indices: 12161481--12161527 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
12161471 TATTTATGTA
12161481 TTATGTAAGTTTTGTAAG
1 TTATGTAAGTTTTGTAAG
12161499 TTATGTAAGTTTTGTAAG
1 TTATGTAAGTTTTGTAAG
12161517 TTATGTAAGTT
1 TTATGTAAGTT
12161528 ATTATATGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (18 bp):
TTATGTAAGTTTTGTAAG
Found at i:12161521 original size:56 final size:56
Alignment explanation
Indices: 12161293--12161507 Score: 344
Period size: 56 Copynumber: 3.8 Consensus size: 56
12161283 TAAGTTATGA
12161293 TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATT
1 TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATT
* *
12161349 TATGATATATATTTGGA-GTATTATGTAAGTTGTGTAAGTTATGATATGATACATATT
1 TATGATATATATTT--ATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATT
* * *
12161406 TATGAAATATATTTATGTATTATGTTAGTTGTGTAAGTTATGATATGATATATATT
1 TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATT
*
12161462 TATGATATATATTTATGTATTATGTAAGTTTTGTAAGTTATG-TAAG
1 TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAG
12161508 TTTTGTAAGT
Statistics
Matches: 147, Mismatches: 9, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
55 4 0.03
56 91 0.62
57 51 0.35
58 1 0.01
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.48
Consensus pattern (56 bp):
TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATT
Found at i:12161980 original size:37 final size:37
Alignment explanation
Indices: 12161936--12162026 Score: 104
Period size: 36 Copynumber: 2.5 Consensus size: 37
12161926 AAATTATATT
*
12161936 AATTGATAAATATTGAAATAT-TG-AAAT-ATATTTAA
1 AATTGATAAATATTGAAATATAAGCAAATCAT-TTTAA
12161971 AATGTTGAT-AA-A-TGAAATATAAGCAAATCATTTTAA
1 AA--TTGATAAATATTGAAATATAAGCAAATCATTTTAA
12162007 AATTGATAAATATTGAAATA
1 AATTGATAAATATTGAAATA
12162027 CATTAAAGAA
Statistics
Matches: 47, Mismatches: 1, Indels: 14
0.76 0.02 0.23
Matches are distributed among these distances:
34 13 0.28
35 6 0.13
36 14 0.30
37 14 0.30
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (37 bp):
AATTGATAAATATTGAAATATAAGCAAATCATTTTAA
Found at i:12165694 original size:26 final size:26
Alignment explanation
Indices: 12165664--12165771 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
12165654 TGAAATGCCC
12165664 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
12165690 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
12165716 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
12165742 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
12165768 ATCA
1 ATCA
12165772 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:12167213 original size:19 final size:18
Alignment explanation
Indices: 12167189--12167237 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
12167179 TTCTCTTCAG
12167189 TTTATTTAAAAATATTTTA
1 TTTA-TTAAAAATATTTTA
*
12167208 TTTATTAAAATTATTTT-
1 TTTATTAAAAATATTTTA
*
12167225 TATTATTATAAAT
1 T-TTATTAAAAAT
12167238 TTTAATTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 1 0.04
18 21 0.81
19 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTATTAAAAATATTTTA
Found at i:12168770 original size:60 final size:59
Alignment explanation
Indices: 12168671--12168801 Score: 181
Period size: 60 Copynumber: 2.2 Consensus size: 59
12168661 TTTCGAATTG
* * * ** * *
12168671 GGGAAAAGGGGGTAATTATTTTAGGGTTTTGAATTAGGGAAAATGGGGGGAAATAAACTA
1 GGGAGAAGGGGGTAATTATTTTAGGGATTCGAAGAAGGGAAAAT-AGGGGAAATAAACCA
*
12168731 GGGAGAAGGGGGTGATTATTTTAGGGATTCGAAGAAGGGAAAATAGGGGAAATAAACCA
1 GGGAGAAGGGGGTAATTATTTTAGGGATTCGAAGAAGGGAAAATAGGGGAAATAAACCA
12168790 GGGAGAAGGGGG
1 GGGAGAAGGGGG
12168802 AAAATGAATA
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
59 25 0.40
60 38 0.60
ACGTcount: A:0.37, C:0.03, G:0.40, T:0.21
Consensus pattern (59 bp):
GGGAGAAGGGGGTAATTATTTTAGGGATTCGAAGAAGGGAAAATAGGGGAAATAAACCA
Found at i:12169110 original size:114 final size:113
Alignment explanation
Indices: 12168869--12169416 Score: 545
Period size: 114 Copynumber: 4.8 Consensus size: 113
12168859 CAAAATAAAT
* * * * *
12168869 TAACATTT-GCGGCGTTTTCCCCTAGCGCCGCTAAAGGCAAACCAATTGCGACGTTTTAACAT-A
1 TAACATTTAGTGGCGTTTT-CCCTAGCGCCGCTAAATGCAAACCTATTGCGGCGTTTTAACCTAA
* * *
12168932 AACGCCACTAAAAA-ACAAACAAAACGACACCGTTTTGATATAAATAGAA
65 AACGCCACTAAAAATCCAAA-AAAACGACACCGTTTTGATATAAACAAAA
* * * *
12168981 TAA-ACTTTAGTGGCGTTTTCCCATAGCGCCGCTAAATGCAAATCAATTGCGGCGTTTCACCCTA
1 TAACA-TTTAGTGGCGTTTTCCC-TAGCGCCGCTAAATGCAAACCTATTGCGGCGTTTTAACCTA
** * * *
12169045 AAACGCCACTAAAAATCCAAAAAAACGACGTCGTTTTCATATGAACAGAA
64 AAACGCCACTAAAAATCCAAAAAAACGACACCGTTTTGATATAAACAAAA
* * * *
12169095 TAACATTTAGTGGCGTTTTATCTCCAAGCGCCGCTAAAGGCGAAA-CTATTGCGGCATTTTACCC
1 TAACATTTAGTGGCG-TTT-TC-CCTAGCGCCGCTAAATGC-AAACCTATTGCGGCGTTTTAACC
* * ** * **
12169159 TAAAACGCCACTAAGAATCGATCAAAACAACATTGTTTTGATATAAACAAAA
62 TAAAACGCCACTAAAAATCCAAAAAAACGACACCGTTTTGATATAAACAAAA
* * * *
12169211 TAACCA-TTAGTGGCGTTTATACCCTAGCACCGCTAAAT-CAAACCTATTGTGGCGTTTAAACCA
1 TAA-CATTTAGTGGCGTTT-T-CCCTAGCGCCGCTAAATGCAAACCTATTGCGGCGTTTTAACCT
* * *
12169274 AAAACGCCACTAAAAATCCATAAAAACTACACCGTTTTGATCTAAACAAAA
63 AAAACGCCACTAAAAATCCAAAAAAACGACACCGTTTTGATATAAACAAAA
** * * * *
12169325 TAACCCTTAGTGGCGTTTATTCCCTTGCACCGCTAAAT-CAACCCTATTGTGGCGTTTTAACCTA
1 TAACATTTAGTGGCG-TT-TTCCCTAGCGCCGCTAAATGCAAACCTATTGCGGCGTTTTAACCTA
12169389 AAACGCCACTAAAAATCCAAAGAAAACG
64 AAACGCCACTAAAAATCCAAA-AAAACG
12169417 GTGTCGTCTT
Statistics
Matches: 369, Mismatches: 50, Indels: 31
0.82 0.11 0.07
Matches are distributed among these distances:
111 1 0.00
112 9 0.02
113 47 0.13
114 183 0.50
115 34 0.09
116 88 0.24
117 7 0.02
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.25
Consensus pattern (113 bp):
TAACATTTAGTGGCGTTTTCCCTAGCGCCGCTAAATGCAAACCTATTGCGGCGTTTTAACCTAAA
ACGCCACTAAAAATCCAAAAAAACGACACCGTTTTGATATAAACAAAA
Found at i:12169267 original size:230 final size:229
Alignment explanation
Indices: 12168892--12169342 Score: 548
Period size: 230 Copynumber: 2.0 Consensus size: 229
12168882 GTTTTCCCCT
*
12168892 AGCGCCGCTAAAGGCAAACCAATTGCGACGTTTTAACATAAACGCCACTAAAAAACAAACAAAAC
1 AGCGCCGCTAAAGGCAAACCAATTGCGACATTTTAACATAAACGCCACTAAAAAACAAACAAAAC
* * * * *
12168957 GACACCGTTTTGATATAAATAGAATAAACTTTAGTGGCGTTTTCCCATAGCGCCGCTAAATGCAA
66 AACACCGTTTTGATATAAACAAAATAAACATTAGTGGCGTTTTCCCATAGCACCGCTAAATGCAA
* * * * **
12169022 ATCAATTGCGGCGTTTCACCCTAAAACGCCACTAAAAATCCAAAAAAACGACGTCGTTTTCATAT
131 ACCAATTGCGGCGTTTAAACCAAAAACGCCACTAAAAATCCAAAAAAACGACACCGTTTTCATAT
* * *
12169087 GAACAGAATAACATTTAGTGGCGTTTTATCTCCA
196 AAACAAAATAACACTTAGTGGCGTTTTATCTCCA
* * * * * * * *
12169121 AGCGCCGCTAAAGGCGAAA-CTATTGCGGCATTTTACCCTAAAACGCCACTAAGAATCGATCAAA
1 AGCGCCGCTAAAGGC-AAACCAATTGCGACATTTTAACAT-AAACGCCACTAAAAAACAAACAAA
** *
12169185 ACAACATTGTTTTGATATAAACAAAATAACCATTAGTGGCGTTTATACCC-TAGCACCGCTAAAT
64 ACAACACCGTTTTGATATAAACAAAATAAACATTAGTGGCGTTT-T-CCCATAGCACCGCTAAAT
* * * * *
12169249 -CAAACCTATTGTGGCGTTTAAACCAAAAACGCCACTAAAAATCCATAAAAACTACACCGTTTTG
127 GCAAACCAATTGCGGCGTTTAAACCAAAAACGCCACTAAAAATCCAAAAAAACGACACCGTTTTC
* *
12169313 ATCTAAACAAAATAACCCTTAGTGGCGTTT
192 ATATAAACAAAATAACACTTAGTGGCGTTT
12169343 ATTCCCTTGC
Statistics
Matches: 185, Mismatches: 33, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
229 30 0.16
230 138 0.75
231 14 0.08
232 3 0.02
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (229 bp):
AGCGCCGCTAAAGGCAAACCAATTGCGACATTTTAACATAAACGCCACTAAAAAACAAACAAAAC
AACACCGTTTTGATATAAACAAAATAAACATTAGTGGCGTTTTCCCATAGCACCGCTAAATGCAA
ACCAATTGCGGCGTTTAAACCAAAAACGCCACTAAAAATCCAAAAAAACGACACCGTTTTCATAT
AAACAAAATAACACTTAGTGGCGTTTTATCTCCA
Found at i:12170311 original size:16 final size:17
Alignment explanation
Indices: 12170290--12170322 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12170280 ATAGTTTAGT
12170290 GTTTAG-GGTTTAGGGG
1 GTTTAGTGGTTTAGGGG
*
12170306 GTTTAGTGTTTTAGGGG
1 GTTTAGTGGTTTAGGGG
12170323 TTATAGATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.12, C:0.00, G:0.45, T:0.42
Consensus pattern (17 bp):
GTTTAGTGGTTTAGGGG
Found at i:12170325 original size:45 final size:45
Alignment explanation
Indices: 12170263--12170372 Score: 141
Period size: 45 Copynumber: 2.4 Consensus size: 45
12170253 TGGGGTTTAA
** *
12170263 TTAAGGTTTTAAAGGTTATAGTTTAGTGTTTAGGGTTTAGGGGGT
1 TTAAGGTTTTAGGGGTTATAGATTAGTGTTTAGGGTTTAGGGGGT
* * **
12170308 TT-AGTGTTTTAGGGGTTATAGATTAGTGTTTATGTTTTTTGGGGT
1 TTAAG-GTTTTAGGGGTTATAGATTAGTGTTTAGGGTTTAGGGGGT
12170353 TTAAGGTTTTAGGGGTTATA
1 TTAAGGTTTTAGGGGTTATA
12170373 TGACTTTTAG
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
44 2 0.04
45 52 0.93
46 2 0.04
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.48
Consensus pattern (45 bp):
TTAAGGTTTTAGGGGTTATAGATTAGTGTTTAGGGTTTAGGGGGT
Found at i:12170458 original size:41 final size:40
Alignment explanation
Indices: 12170377--12170512 Score: 150
Period size: 41 Copynumber: 3.4 Consensus size: 40
12170367 GTTATATGAC
* * *
12170377 TTTTAGCGGCGCTTTACCGAAA-TGCCGCTAATGCTCTGG
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG
* *
12170416 TTTCTAGCGGCGTTTTA-CATAAAGCGCCGCTAATTCTTTGG
1 TTT-TAGCGGCGTTTTACCA-AAAGCGCCGCTAATGCTCTGG
* * *
12170457 TTTTTAGTGGCGTTTTACCAAAAGCGCCACAAATGCTCTGG
1 -TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG
12170498 CTTTTAGCGGCGTTT
1 -TTTTAGCGGCGTTT
12170513 CTATTGCTCT
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
39 4 0.05
40 15 0.19
41 56 0.70
42 5 0.06
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.35
Consensus pattern (40 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG
Found at i:12172570 original size:20 final size:20
Alignment explanation
Indices: 12172506--12172570 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
12172496 TTTTTGAAAT
12172506 TTTTTTAATAATAAATTTAAAAA
1 TTTTTTAA-AATAAA-TT-AAAA
* * *
12172529 ATCTTTAAAATAAATTAGAA
1 TTTTTTAAAATAAATTAAAA
* *
12172549 TTTTTTAAAATTATTTAAAA
1 TTTTTTAAAATAAATTAAAA
12172569 TT
1 TT
12172571 CTAAAATTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
20 20 0.59
21 2 0.06
22 6 0.18
23 6 0.18
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
TTTTTTAAAATAAATTAAAA
Found at i:12177762 original size:17 final size:17
Alignment explanation
Indices: 12177742--12177802 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 17
12177732 GTGAACTGCA
12177742 AGCTCACCAAAACTACG
1 AGCTCACCAAAACTACG
* *
12177759 AGCTCACCAAAATTGCG
1 AGCTCACCAAAACTACG
* * * *
12177776 AGCTTACTAAGACCACG
1 AGCTCACCAAAACTACG
12177793 AGCTCACCAA
1 AGCTCACCAA
12177803 GCTTGAGAGC
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.38, C:0.33, G:0.15, T:0.15
Consensus pattern (17 bp):
AGCTCACCAAAACTACG
Found at i:12182148 original size:19 final size:19
Alignment explanation
Indices: 12182124--12182161 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12182114 AAGTTAAGAA
*
12182124 CAAATTTGATTACGGTGGG
1 CAAATTTAATTACGGTGGG
*
12182143 CAAATTTAATTATGGTGGG
1 CAAATTTAATTACGGTGGG
12182162 TGGCAGTGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.08, G:0.29, T:0.34
Consensus pattern (19 bp):
CAAATTTAATTACGGTGGG
Found at i:12182913 original size:16 final size:17
Alignment explanation
Indices: 12182889--12182931 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
12182879 TAGTTCAATT
*
12182889 TTCATAGAT-CAACTCA
1 TTCAGAGATACAACTCA
*
12182905 TTCAGAGATAGCAGCTCA
1 TTCAGAGATA-CAACTCA
12182923 TTCAGAGAT
1 TTCAGAGAT
12182932 GGCAACAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 8 0.35
18 15 0.65
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (17 bp):
TTCAGAGATACAACTCA
Found at i:12185000 original size:25 final size:25
Alignment explanation
Indices: 12184972--12185023 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
12184962 ATTTTTCTAC
12184972 CTTTAATATCATATGGTTGGGTGTT
1 CTTTAATATCATATGGTTGGGTGTT
12184997 CTTTAATATCATATGGTTGGGTGTT
1 CTTTAATATCATATGGTTGGGTGTT
12185022 CT
1 CT
12185024 CATCTAACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.10, G:0.23, T:0.48
Consensus pattern (25 bp):
CTTTAATATCATATGGTTGGGTGTT
Found at i:12186808 original size:14 final size:14
Alignment explanation
Indices: 12186789--12186818 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12186779 GACATGACAC
12186789 AAAAATAATGGACT
1 AAAAATAATGGACT
*
12186803 AAAAATGATGGACT
1 AAAAATAATGGACT
12186817 AA
1 AA
12186819 CAATCAAGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.07, G:0.17, T:0.20
Consensus pattern (14 bp):
AAAAATAATGGACT
Found at i:12189096 original size:22 final size:22
Alignment explanation
Indices: 12189071--12189116 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
12189061 TCAATGTTAG
*
12189071 TTAAAAAACTTAATTGTTGCAT
1 TTAAAAAACTTAATAGTTGCAT
12189093 TTAAAAAACTTAATAGTTGCAT
1 TTAAAAAACTTAATAGTTGCAT
12189115 TT
1 TT
12189117 TTACGATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (22 bp):
TTAAAAAACTTAATAGTTGCAT
Found at i:12203411 original size:19 final size:17
Alignment explanation
Indices: 12203376--12203408 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
12203366 TACTTTTAGA
12203376 ATTCTCTCTTTGTAAAC
1 ATTCTCTCTTTGTAAAC
12203393 ATTCTCTCTTTGTAAA
1 ATTCTCTCTTTGTAAA
12203409 AACCATCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.06, T:0.48
Consensus pattern (17 bp):
ATTCTCTCTTTGTAAAC
Found at i:12207080 original size:25 final size:25
Alignment explanation
Indices: 12207005--12207082 Score: 102
Period size: 25 Copynumber: 3.1 Consensus size: 25
12206995 GTTTTTATAA
*
12207005 ACTTTAAATTAAGAATTCTATTAGA
1 ACTTTAAATTAAGAATTCTATTAGG
*
12207030 ACTTTAAATTAAGAATTCTATCAGG
1 ACTTTAAATTAAGAATTCTATTAGG
* * **
12207055 ACTTCAAATTAGGAATTAGATTAGG
1 ACTTTAAATTAAGAATTCTATTAGG
12207080 ACT
1 ACT
12207083 CTCCCTTTGT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (25 bp):
ACTTTAAATTAAGAATTCTATTAGG
Done.