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 112 of 356
Found at i:35597118 original size:11 final size:11
Alignment explanation
Indices: 35597102--35597141 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
35597092 ATTAAATATT
35597102 AAAATATTTAA
1 AAAATATTTAA
35597113 AAAATATGTTTAA
1 AAAATA--TTTAA
*
35597126 AAAATATTAAA
1 AAAATATTTAA
35597137 AAAAT
1 AAAAT
35597142 CTAAACATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 15 0.58
13 11 0.42
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (11 bp):
AAAATATTTAA
Found at i:35597126 original size:13 final size:13
Alignment explanation
Indices: 35597108--35597132 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35597098 TATTAAAATA
35597108 TTTAAAAAATATG
1 TTTAAAAAATATG
35597121 TTTAAAAAATAT
1 TTTAAAAAATAT
35597133 TAAAAAAATC
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:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
TTTAAAAAATATG
Found at i:35599253 original size:64 final size:64
Alignment explanation
Indices: 35599172--35599355 Score: 221
Period size: 67 Copynumber: 2.8 Consensus size: 64
35599162 AGACATTATG
* * * *
35599172 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTAAGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * *
35599236 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAATGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTAAGTG--T-ACACCATGTAGACAAGAGAGCTACGAGAT
35599301 AA
63 AA
* *
35599303 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGGTACTAAGTGTACACCATGTAG-ACAAGAGAGC
35599356 CGAACTATAT
Statistics
Matches: 103, Mismatches: 12, Indels: 11
0.82 0.10 0.09
Matches are distributed among these distances:
62 1 0.01
63 18 0.17
64 28 0.27
66 24 0.23
67 30 0.29
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTAAGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:35599289 original size:67 final size:64
Alignment explanation
Indices: 35599148--35599355 Score: 197
Period size: 67 Copynumber: 3.2 Consensus size: 64
35599138 CATCATGTGT
* * * *
35599148 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATG
1 ACAAGAGAGCTAC--GAGA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAAGTGTACACCATG
35599213 TAG
62 TAG
* * *
35599216 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAATGACACCATGT
1 ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGCGTGATACCAAGTG--T-ACACCATGT
35599281 AG
63 AG
* * * * * *
35599283 ACAAGAGAGCTACGAGATAAACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-G
1 ACAAGAGAGCTACGAGATATA-TGTAGCTAGGTCGCATGCGTGATACCAAGTGTACACCATGTAG
35599345 TACAAGAGAGC
1 -ACAAGAGAGC
35599356 CGAACTATAT
Statistics
Matches: 121, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
62 1 0.01
63 18 0.15
64 28 0.23
65 3 0.02
66 26 0.21
67 30 0.25
68 15 0.12
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (64 bp):
ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGCGTGATACCAAGTGTACACCATGTAG
Found at i:35606436 original size:30 final size:31
Alignment explanation
Indices: 35606376--35606436 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
35606366 TTTTACGAGC
35606376 CTAGGGGCAAAATCGTAATTTTTGTAAAAGT
1 CTAGGGGCAAAATCGTAATTTTTGTAAAAGT
* * *
35606407 CTAGGGGCAAAATGGTCA-TTTTGTCAAAGT
1 CTAGGGGCAAAATCGTAATTTTTGTAAAAGT
35606437 ATGAATTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (31 bp):
CTAGGGGCAAAATCGTAATTTTTGTAAAAGT
Found at i:35606988 original size:45 final size:45
Alignment explanation
Indices: 35606937--35607337 Score: 543
Period size: 45 Copynumber: 8.8 Consensus size: 45
35606927 TGGGTGACAC
* *
35606937 GTGAGCCAGTGTAAGACCATGATGGACATGGCATCAGCGTTGATT
1 GTGAGCCAGTGTAAGACCATGTTGGACATGGCATCGGCGTTGATT
* * * *
35606982 GTGAGCCAGTGTAAGACCATGTTGAAAATGGCAACGGTGTTGATT
1 GTGAGCCAGTGTAAGACCATGTTGGACATGGCATCGGCGTTGATT
* * **
35607027 ATGAGCCAGTGTAAGACCATGTTGGACATGGCATTGGTATTGATT
1 GTGAGCCAGTGTAAGACCATGTTGGACATGGCATCGGCGTTGATT
*
35607072 GTGAGCCAGTGTAAGACCATGTTGGACATGGCATCGACGTTGATT
1 GTGAGCCAGTGTAAGACCATGTTGGACATGGCATCGGCGTTGATT
* * *
35607117 GTGAGCTAGTGTAAGACCATGTTAGACATGGCATCAGCGTTGATT
1 GTGAGCCAGTGTAAGACCATGTTGGACATGGCATCGGCGTTGATT
*
35607162 GTGAGCCAGTGTAAGACCATGTTGGACATGGCATCGAC-TTGGATT
1 GTGAGCCAGTGTAAGACCATGTTGGACATGGCATCGGCGTT-GATT
*
35607207 TTGAGCCAGTGTAAGACCATGTTGGACATGGCATCGGCGTTGATT
1 GTGAGCCAGTGTAAGACCATGTTGGACATGGCATCGGCGTTGATT
* * * *
35607252 GTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGACAT
1 GTGAGCCAGTGTAAGACCATGT-T-GGACATGGCATCGGCGTTGA-TT
* *
35607300 GTGAGCCAATGTAAGACCATGTCTGGGACATGACATCG
1 GTGAGCCAGTGTAAGACCATGT-T-GGACATGGCATCG
35607338 ACAATTCACC
Statistics
Matches: 316, Mismatches: 35, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
44 2 0.01
45 257 0.81
46 3 0.01
47 18 0.06
48 36 0.11
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.26
Consensus pattern (45 bp):
GTGAGCCAGTGTAAGACCATGTTGGACATGGCATCGGCGTTGATT
Found at i:35609100 original size:19 final size:18
Alignment explanation
Indices: 35609072--35609107 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
35609062 TATACGGCCT
35609072 AAGGACACGGGCGTGTCG
1 AAGGACACGGGCGTGTCG
*
35609090 AAGGCACACGGGTGTGTC
1 AAGG-ACACGGGCGTGTC
35609108 CCTGTGTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.22, C:0.22, G:0.42, T:0.14
Consensus pattern (18 bp):
AAGGACACGGGCGTGTCG
Found at i:35609137 original size:24 final size:22
Alignment explanation
Indices: 35609094--35609137 Score: 52
Period size: 24 Copynumber: 1.9 Consensus size: 22
35609084 GTGTCGAAGG
*
35609094 CACACGGGTGTGTCCCTGTGTC
1 CACACGGGTGTGACCCTGTGTC
*
35609116 CACACGGGCGTGTGACCTTGTG
1 CACAC-GG-GTGTGACCCTGTG
35609138 ACATGGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 2 0.11
24 11 0.61
ACGTcount: A:0.11, C:0.30, G:0.34, T:0.25
Consensus pattern (22 bp):
CACACGGGTGTGACCCTGTGTC
Found at i:35609510 original size:24 final size:24
Alignment explanation
Indices: 35609478--35609528 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
35609468 TACAAATCAC
*
35609478 TCATAGATGTTTAAAAAGAATTGG
1 TCATAGATGTTTAAAAAGAATTAG
35609502 TCATAGATGTTTAAAAAGAATTAG
1 TCATAGATGTTTAAAAAGAATTAG
35609526 TCA
1 TCA
35609529 ATCATTCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.33
Consensus pattern (24 bp):
TCATAGATGTTTAAAAAGAATTAG
Found at i:35610980 original size:34 final size:34
Alignment explanation
Indices: 35610937--35611003 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
35610927 GTTTCAGTTA
* *
35610937 GGGCTTTAGCCCAATAT-AGTAACAGTATCAGTAT
1 GGGCCTTAG-CCAATATCAGTAACAGTAACAGTAT
* *
35610971 GGGCCTTAGCCTATTTCAGTAACAGTAACAGTA
1 GGGCCTTAGCCAATATCAGTAACAGTAACAGTA
35611004 CAGATATGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 5 0.18
34 23 0.82
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (34 bp):
GGGCCTTAGCCAATATCAGTAACAGTAACAGTAT
Found at i:35622350 original size:39 final size:40
Alignment explanation
Indices: 35622146--35622368 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
35622136 TTGAATGCTG
* * * * * *
35622146 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
** * * *
35622186 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
35622226 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
**
35622266 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
35622306 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
35622345 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
35622369 TGAACGAGGA
Statistics
Matches: 161, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 35 0.22
40 118 0.73
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:35622388 original size:79 final size:80
Alignment explanation
Indices: 35622221--35622403 Score: 226
Period size: 79 Copynumber: 2.3 Consensus size: 80
35622211 GTGCGAGATA
* * *
35622221 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
35622286 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
35622301 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
35622365 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
35622380 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
35622404 TACGTGATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:35630629 original size:119 final size:119
Alignment explanation
Indices: 35630417--35630631 Score: 340
Period size: 119 Copynumber: 1.8 Consensus size: 119
35630407 TATATATATG
** * *
35630417 TAATGGCATGCTTGATTACAATCATACATCTCATAAGGGCATAATCGTCACTTTAGTACATAGGG
1 TAATGGCATGCTCAATTACAAACATACATCTCATAAGGGCATAATAGTCACTTTAGTACATAGGG
* * *
35630482 AACAACAGTCATTTGTCAGTTTGGGGGTCTACATATACTTATCGACCCAACATC
66 AACAACAATCATTTGTCACTTTGAGGGTCTACATATACTTATCGACCCAACATC
35630536 TAATGGCATGCTCAATTACAAACATACATCTCATAAGGGCATAATAGTCACTTTAGTACATAGGG
1 TAATGGCATGCTCAATTACAAACATACATCTCATAAGGGCATAATAGTCACTTTAGTACATAGGG
* * *
35630601 CATAACAATCATTTGTTACTTTGAGGGTCTA
66 AACAACAATCATTTGTCACTTTGAGGGTCTA
35630632 GGTATTCTTA
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
119 86 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Consensus pattern (119 bp):
TAATGGCATGCTCAATTACAAACATACATCTCATAAGGGCATAATAGTCACTTTAGTACATAGGG
AACAACAATCATTTGTCACTTTGAGGGTCTACATATACTTATCGACCCAACATC
Found at i:35633813 original size:18 final size:16
Alignment explanation
Indices: 35633785--35633818 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 16
35633775 GCCTTGTTCC
35633785 CAAAACAAAAACGAAAA
1 CAAAACAAAAAC-AAAA
35633802 CAAAATCAAAAACAAAA
1 CAAAA-CAAAAACAAAA
35633819 AACAATAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.76, C:0.18, G:0.03, T:0.03
Consensus pattern (16 bp):
CAAAACAAAAACAAAA
Found at i:35633819 original size:6 final size:6
Alignment explanation
Indices: 35633786--35633819 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
35633776 CCTTGTTCCC
* *
35633786 AAAACA AAAACG AAAACA AAATCA AAAACA AAAA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAA
35633820 ACAATAACAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.79, C:0.15, G:0.03, T:0.03
Consensus pattern (6 bp):
AAAACA
Found at i:35636598 original size:43 final size:42
Alignment explanation
Indices: 35636551--35636632 Score: 94
Period size: 42 Copynumber: 1.9 Consensus size: 42
35636541 TCTCATATGT
35636551 AATCAAACATCGATGCC-ACTATCCCAAACAGGGTCTTACATGA
1 AATCAAACA-CGATGCCGA-TATCCCAAACAGGGTCTTACATGA
* * * * *
35636594 AATCAGATACGATTCCGATGTCCCAAACATGGTCTTACA
1 AATCAAACACGATGCCGATATCCCAAACAGGGTCTTACA
35636633 CTTAAAACAG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
42 25 0.76
43 8 0.24
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (42 bp):
AATCAAACACGATGCCGATATCCCAAACAGGGTCTTACATGA
Found at i:35643425 original size:27 final size:27
Alignment explanation
Indices: 35643394--35643699 Score: 326
Period size: 27 Copynumber: 11.3 Consensus size: 27
35643384 TTACTTTACC
35643394 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * *
35643421 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
35643448 AAATCACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* **
35643475 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
35643502 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
35643529 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * *
35643556 AAATTATCAAAACACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
35643583 AAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCCTGGTTTGTA
** * ***
35643610 AAATTACTGAAATACCCTTGACCTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
*** **
35643637 AAATTATTGAAATA-CCCTCGACTTGTA
1 AAATTACCAAAATACCCCT-GGTTTGTA
* * * *
35643664 AAATTACCAAAGTACCCTTGATTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
35643691 GAATTACCA
1 AAATTACCA
35643700 TTTTACCCTC
Statistics
Matches: 234, Mismatches: 43, Indels: 4
0.83 0.15 0.01
Matches are distributed among these distances:
26 3 0.01
27 228 0.97
28 3 0.01
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTGTA
Found at i:35643706 original size:27 final size:27
Alignment explanation
Indices: 35643676--35643928 Score: 299
Period size: 27 Copynumber: 9.4 Consensus size: 27
35643666 ATTACCAAAG
* *
35643676 TACCCTTGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCGTTT
* * * *
35643703 TACCCTCGATATACAAAATTACTGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
* * *
35643730 TACCCTTGATTTACAAAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
* *
35643757 TACACTCGATTTATAGAATTATCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
* **
35643784 TACCCTCGATTTACAGAATTACTATTT
1 TACCCTCGATTTATAGAATTACCGTTT
* * *
35643811 TACCCTCGATTTCTAAAATTATCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
*
35643838 TACCCTCGATTTATAGGATTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
* *
35643865 TACCCTCAATTTATAGAATTATCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
* * *
35643892 TACCCTCGATTTACAAAATTACTGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
35643919 TACCCTCGAT
1 TACCCTCGAT
35643929 CGACGGAGGC
Statistics
Matches: 189, Mismatches: 37, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 189 1.00
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.42
Consensus pattern (27 bp):
TACCCTCGATTTATAGAATTACCGTTT
Found at i:35646677 original size:43 final size:42
Alignment explanation
Indices: 35646630--35646775 Score: 102
Period size: 44 Copynumber: 3.4 Consensus size: 42
35646620 TCCTAGCTGT
** *
35646630 GGTCTTACATGAAATCAAAAATCGATGC-CACTGTCCTAGACAG
1 GGTCTTACACAAAATCAAAAA-CGATGCTCA-TGTCCCAGACAG
* * * *
35646673 GGTCTTAGACAAAATCAAATACGATGCTGATGTCCCAGACAT
1 GGTCTTACACAAAATCAAAAACGATGCTCATGTCCCAGACAG
** *
35646715 GGTCTTACACGTAAAA-CAGAAGTCGATGC-CAACGTCCCAGAC-G
1 GGTCTTACAC--AAAATCA-AAAACGATGCTC-ATGTCCCAGACAG
*
35646758 TCGTCTTACACAAAATCA
1 -GGTCTTACACAAAATCA
35646776 CATAACGAAA
Statistics
Matches: 82, Mismatches: 14, Indels: 14
0.75 0.13 0.13
Matches are distributed among these distances:
42 29 0.35
43 22 0.27
44 31 0.38
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (42 bp):
GGTCTTACACAAAATCAAAAACGATGCTCATGTCCCAGACAG
Found at i:35650481 original size:42 final size:42
Alignment explanation
Indices: 35650395--35650558 Score: 177
Period size: 42 Copynumber: 3.9 Consensus size: 42
35650385 TTAAGGTTAT
* * *
35650395 TGATATTACGTGTAAGACCATATCTGGGATATGGAATC-AGTA
1 TGATATTTCATGTAAGACCATATCTGGGATATGGCATCGA-TA
* * * *
35650437 TGAGACTTCGTGTAAGATCATATCTGGGATATGGCATCGATA
1 TGATATTTCATGTAAGACCATATCTGGGATATGGCATCGATA
* * * * *
35650479 TGATTTTTTATGTAAGACCATAGCTGGGCTATCAGCATCGATA
1 TGATATTTCATGTAAGACCATATCTGGGATAT-GGCATCGATA
* *
35650522 CGATATTTCATGTAAGACTATATCTGGGATATGGCAT
1 TGATATTTCATGTAAGACCATATCTGGGATATGGCAT
35650559 TGGTATGGTA
Statistics
Matches: 99, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
42 63 0.64
43 36 0.36
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (42 bp):
TGATATTTCATGTAAGACCATATCTGGGATATGGCATCGATA
Found at i:35652456 original size:34 final size:34
Alignment explanation
Indices: 35652390--35652458 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
35652380 TTTGTATGTT
* * *
35652390 TGCTTGTGTTTACCTCCGGTAATTCCTTGTACCC
1 TGCTTGTGTTTACATCCGATAATTCCTCGTACCC
*
35652424 TGCTTGTGTTTACATCTGATAATGT-CTCGTACCC
1 TGCTTGTGTTTACATCCGATAAT-TCCTCGTACCC
35652458 T
1 T
35652459 ATTCTGGCGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 29 0.97
35 1 0.03
ACGTcount: A:0.14, C:0.26, G:0.17, T:0.42
Consensus pattern (34 bp):
TGCTTGTGTTTACATCCGATAATTCCTCGTACCC
Found at i:35659567 original size:64 final size:64
Alignment explanation
Indices: 35659465--35659585 Score: 172
Period size: 64 Copynumber: 1.9 Consensus size: 64
35659455 TAAGCATCTA
* *
35659465 CGCCCAGAATAATCATTGTCCATGTGGACAATGCAGAAATTATTCTATTCGCCAATTTAGTTTG
1 CGCCCAGAACAATCATTGTCCATGTGGACAATGCAGAAATTATTCTATTCACCAATTTAGTTTG
* * * *
35659529 CGCCCTGAACAATCATTTTCC-TGGTGGACACTGTAGAAATTATTCTATTCACCAATT
1 CGCCCAGAACAATCATTGTCCAT-GTGGACAATGCAGAAATTATTCTATTCACCAATT
35659586 CAATTTGTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
63 1 0.02
64 49 0.98
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (64 bp):
CGCCCAGAACAATCATTGTCCATGTGGACAATGCAGAAATTATTCTATTCACCAATTTAGTTTG
Found at i:35662471 original size:29 final size:29
Alignment explanation
Indices: 35662408--35662475 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
35662398 TAATCAACCG
*
35662408 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
35662437 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
35662466 CGCACACTTA
1 CGCACACTTA
35662476 CCTTTTCCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:35662587 original size:174 final size:174
Alignment explanation
Indices: 35662297--35662624 Score: 638
Period size: 174 Copynumber: 1.9 Consensus size: 174
35662287 AACTCAAGGT
* *
35662297 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
35662362 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
35662427 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
35662471 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
35662536 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
35662601 ACTTTAAACTCACACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
35662625 TGTACAATTT
Statistics
Matches: 152, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
174 152 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:35662618 original size:29 final size:30
Alignment explanation
Indices: 35662584--35662655 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
35662574 ATCAACCGCG
*
35662584 CACACTTAGTGCCATGTAC-TTTAAACTCA
1 CACACTTAGTGCCATGTACATTTAAACCCA
*
35662613 CACACTTAGTG-C-TGTACAATTTAAACCCG
1 CACACTTAGTGCCATGTAC-ATTTAAACCCA
35662642 CACACTTAGTGCCA
1 CACACTTAGTGCCA
35662656 ATCTCATGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
27 5 0.14
28 1 0.03
29 30 0.81
30 1 0.03
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.28
Consensus pattern (30 bp):
CACACTTAGTGCCATGTACATTTAAACCCA
Found at i:35681071 original size:20 final size:18
Alignment explanation
Indices: 35681033--35681076 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 18
35681023 AAACCCTAAT
35681033 TTTCCC-TTTTCTTTTTC
1 TTTCCCTTTTTCTTTTTC
35681050 TTTCCCTTTTTCCTTCTTTC
1 TTTCCCTTTTT-CTT-TTTC
35681070 TTTCCCT
1 TTTCCCT
35681077 GCTAATCGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.25
18 4 0.17
19 3 0.12
20 11 0.46
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTCCCTTTTTCTTTTTC
Found at i:35681144 original size:12 final size:13
Alignment explanation
Indices: 35681122--35681168 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 13
35681112 TTATTTCTTT
*
35681122 TATTCTTTTATTA
1 TATTATTTTATTA
35681135 T-TTATTTTATTA
1 TATTATTTTATTA
*
35681147 TATTATTAACTATTA
1 TATTATT--TTATTA
35681162 TATTATT
1 TATTATT
35681169 ATAATCATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 11 0.38
13 6 0.21
15 12 0.41
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (13 bp):
TATTATTTTATTA
Found at i:35681152 original size:20 final size:20
Alignment explanation
Indices: 35681112--35681154 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
35681102 TTTTTATGTT
* * *
35681112 TTATTTCTTTTATTCTTTTA
1 TTATTTATTTTATTATATTA
35681132 TTATTTATTTTATTATATTA
1 TTATTTATTTTATTATATTA
35681152 TTA
1 TTA
35681155 ACTATTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (20 bp):
TTATTTATTTTATTATATTA
Found at i:35692069 original size:23 final size:24
Alignment explanation
Indices: 35692046--35692092 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
35692036 GAGGCGCATT
35692046 TTCACAACTCGGGTGAGCATATTTA
1 TTCACAACTCGGGTGAGCATA-TTA
* *
35692071 TTCACAGCTCGTGTGAGCATAT
1 TTCACAACTCGGGTGAGCATAT
35692093 ATGTAAAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 1 0.05
25 19 0.95
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (24 bp):
TTCACAACTCGGGTGAGCATATTA
Found at i:35694718 original size:26 final size:26
Alignment explanation
Indices: 35694689--35694798 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
35694679 TGGTACAAAT
35694689 TGATAATAGGTTAGGTAAATG-TTCAA
1 TGATAATAGGTTAGGTAAATGTTTC-A
*
35694715 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
35694741 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
35694767 TGATAATTGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
35694793 TGATAA
1 TGATAA
35694799 GAATTTCATG
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
26 77 0.97
27 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:35698501 original size:26 final size:26
Alignment explanation
Indices: 35698472--35698581 Score: 179
Period size: 26 Copynumber: 4.2 Consensus size: 26
35698462 TGGTACAAAT
35698472 TGATAATAGGTTAGGTAAATG-TTCAA
1 TGATAATAGGTTAGGTAAATGTTTC-A
35698498 TGATAATAGGTTAGGTAAATG-TTCTA
1 TGATAATAGGTTAGGTAAATGTTTC-A
35698524 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
35698550 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
35698576 TGATAA
1 TGATAA
35698582 GAATTTCATG
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
26 78 0.96
27 3 0.04
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:35699782 original size:16 final size:15
Alignment explanation
Indices: 35699756--35699785 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
35699746 ACTAGATTGG
35699756 CAAAAGCCGAAAAGC
1 CAAAAGCCGAAAAGC
35699771 CAAAATGCCGAAAAG
1 CAAAA-GCCGAAAAG
35699786 TCAGTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.23, G:0.20, T:0.03
Consensus pattern (15 bp):
CAAAAGCCGAAAAGC
Found at i:35700241 original size:27 final size:27
Alignment explanation
Indices: 35700200--35700296 Score: 167
Period size: 27 Copynumber: 3.6 Consensus size: 27
35700190 GAGGAAGCGT
*
35700200 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
35700227 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
35700254 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
35700281 TCTGGTGGCTCTGCCA
1 TCTGGTGGCTCTGCCA
35700297 TGATATTCTG
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.32
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:35700306 original size:27 final size:27
Alignment explanation
Indices: 35700198--35700339 Score: 162
Period size: 27 Copynumber: 5.3 Consensus size: 27
35700188 TGGAGGAAGC
*
35700198 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCACAAATATCT
*
35700225 GATCTGGTGGCTCTGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCACAAATATCT
* *
35700252 GATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTCTGCCACAAATATCT
**
35700279 GTTCTGGTGGCTCTGCCA-TGATATTCT
1 GTTCTGGTGGCTCTGCCACAAATA-TCT
* * * *
35700306 GTATCTGGTGACTTTGTCAC-ATTATCT
1 GT-TCTGGTGGCTCTGCCACAAATATCT
35700333 GTTCTGG
1 GTTCTGG
35700340 CAGCCATGCT
Statistics
Matches: 101, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
26 8 0.08
27 78 0.77
28 15 0.15
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.37
Consensus pattern (27 bp):
GTTCTGGTGGCTCTGCCACAAATATCT
Found at i:35703255 original size:14 final size:14
Alignment explanation
Indices: 35703236--35703267 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
35703226 TAAAATGCTT
35703236 TTTAAATTTATTTA
1 TTTAAATTTATTTA
*
35703250 TTTAAATTTATTTC
1 TTTAAATTTATTTA
35703264 TTTA
1 TTTA
35703268 TATATAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTAAATTTATTTA
Found at i:35704342 original size:17 final size:17
Alignment explanation
Indices: 35704302--35704351 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
35704292 AGCTATGGGC
35704302 AATTTATATTACCTACT
1 AATTTATATTACCTACT
35704319 -A---ATATTACCTACT
1 AATTTATATTACCTACT
*
35704332 AATTTATATTATCTACT
1 AATTTATATTACCTACT
35704349 AAT
1 AAT
35704352 ATAATTTGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
13 12 0.43
14 1 0.04
16 1 0.04
17 14 0.50
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTTATATTACCTACT
Found at i:35704353 original size:13 final size:13
Alignment explanation
Indices: 35704307--35704334 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
35704297 TGGGCAATTT
35704307 ATATTACCTACTA
1 ATATTACCTACTA
35704320 ATATTACCTACTA
1 ATATTACCTACTA
35704333 AT
1 AT
35704335 TTATATTATC
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:0.21, G:0.00, T:0.39
Consensus pattern (13 bp):
ATATTACCTACTA
Found at i:35706813 original size:43 final size:43
Alignment explanation
Indices: 35706766--35707087 Score: 253
Period size: 43 Copynumber: 7.5 Consensus size: 43
35706756 AAATATAATG
*
35706766 GCACACATAGTGCATCATCGAGAAAGTTGAAGTAATTATACTA
1 GCACACATAGTGCATCATCGAGAAAGTCGAAGTAATTATACTA
* * * * *
35706809 GCACACGA-AGTGCATCATCGA-ATAGACTGAATTAATTATATTG
1 GCACAC-ATAGTGCATCATCGAGAAAGTC-GAAGTAATTATACTA
* * * *
35706852 GCACACATAATGCATCATCG-GATAAATCGAAGCAATCATACTA
1 GCACACATAGTGCATCATCGAGA-AAGTCGAAGTAATTATACTA
*
35706895 GCACACATAGTGCATCATCGAGAAAGTTGAAGTAATTATACTA
1 GCACACATAGTGCATCATCGAGAAAGTCGAAGTAATTATACTA
** * * * *
35706938 GCACATGGT-GTGCATCATCGA-ACAGACCGAAGTAATTATATTG
1 GCACA-CATAGTGCATCATCGAGAAAG-TCGAAGTAATTATACTA
* * * * *
35706981 GCACACATAATGCATCATC-AGATAAATCAAAGCAATCATACTA
1 GCACACATAGTGCATCATCGAGA-AAGTCGAAGTAATTATACTA
* * ** * * *
35707024 GCACATATAGTGTATCATC-AGATAAACCAAAGCAAATATACTA
1 GCACACATAGTGCATCATCGAGA-AAGTCGAAGTAATTATACTA
* *
35707067 GCACTCATAATGCATCATCGA
1 GCACACATAGTGCATCATCGA
35707088 CTAAACCAAA
Statistics
Matches: 219, Mismatches: 48, Indels: 23
0.76 0.17 0.08
Matches are distributed among these distances:
42 9 0.04
43 202 0.92
44 8 0.04
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (43 bp):
GCACACATAGTGCATCATCGAGAAAGTCGAAGTAATTATACTA
Found at i:35706974 original size:129 final size:129
Alignment explanation
Indices: 35706733--35707042 Score: 469
Period size: 129 Copynumber: 2.4 Consensus size: 129
35706723 AGTATATTAC
* * * * *
35706733 TGCATCATTGGATAAACCGAAGAAAAT-ATAATGGCACACATAGTGCATCATCGAGAAAGTTGAA
1 TGCATCATCGGATAAATCGAAG-CAATCATACTAGCACACATAGTGCATCATCGAGAAAGTTGAA
* * *
35706797 GTAATTATACTAGCACACGAAGTGCATCATCGAATAGACTGAATTAATTATATTGGCACACATAA
65 GTAATTATACTAGCACACGAAGTGCATCATCGAACAGACCGAAGTAATTATATTGGCACACATAA
35706862 TGCATCATCGGATAAATCGAAGCAATCATACTAGCACACATAGTGCATCATCGAGAAAGTTGAAG
1 TGCATCATCGGATAAATCGAAGCAATCATACTAGCACACATAGTGCATCATCGAGAAAGTTGAAG
* **
35706927 TAATTATACTAGCACATGGTGTGCATCATCGAACAGACCGAAGTAATTATATTGGCACACATAA
66 TAATTATACTAGCACACGAAGTGCATCATCGAACAGACCGAAGTAATTATATTGGCACACATAA
* * * *
35706991 TGCATCATCAGATAAATCAAAGCAATCATACTAGCACATATAGTGTATCATC
1 TGCATCATCGGATAAATCGAAGCAATCATACTAGCACACATAGTGCATCATC
35707043 AGATAAACCA
Statistics
Matches: 165, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
128 3 0.02
129 162 0.98
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (129 bp):
TGCATCATCGGATAAATCGAAGCAATCATACTAGCACACATAGTGCATCATCGAGAAAGTTGAAG
TAATTATACTAGCACACGAAGTGCATCATCGAACAGACCGAAGTAATTATATTGGCACACATAA
Found at i:35707064 original size:129 final size:129
Alignment explanation
Indices: 35706766--35707087 Score: 396
Period size: 129 Copynumber: 2.5 Consensus size: 129
35706756 AAATATAATG
**** * *
35706766 GCACACATAGTGCATCATCGAGAAAGTTGAAGTAATTATACTAGCACACGAAGTGCATCATCGAA
1 GCACACATAGTGCATCATCGAGAAAACCAAAGCAAATATACTAGCACACGAAGTGCATCATCGAA
* * * * *
35706831 TAGACTGAATTAATTATATTGGCACACATAATGCATCATCGGATAAATCGAAGCAATCATACTA
66 CAGACCGAAGTAATTATATTGGCACACATAATGCATCATCAGATAAATCAAAGCAATCATACTA
**** * * * **
35706895 GCACACATAGTGCATCATCGAGAAAGTTGAAGTAATTATACTAGCACATGGTGTGCATCATCGAA
1 GCACACATAGTGCATCATCGAGAAAACCAAAGCAAATATACTAGCACACGAAGTGCATCATCGAA
35706960 CAGACCGAAGTAATTATATTGGCACACATAATGCATCATCAGATAAATCAAAGCAATCATACTA
66 CAGACCGAAGTAATTATATTGGCACACATAATGCATCATCAGATAAATCAAAGCAATCATACTA
* * * *
35707024 GCACATATAGTGTATCATC-AGATAAACCAAAGCAAATATACTAGCACTC-ATAATGCATCATCG
1 GCACACATAGTGCATCATCGAGA-AAACCAAAGCAAATATACTAGCACACGA-AGTGCATCATCG
35707087 A
64 A
35707088 CTAAACCAAA
Statistics
Matches: 170, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
128 3 0.02
129 167 0.98
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (129 bp):
GCACACATAGTGCATCATCGAGAAAACCAAAGCAAATATACTAGCACACGAAGTGCATCATCGAA
CAGACCGAAGTAATTATATTGGCACACATAATGCATCATCAGATAAATCAAAGCAATCATACTA
Found at i:35711733 original size:26 final size:26
Alignment explanation
Indices: 35711698--35711747 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
35711688 GACACTTATA
*
35711698 TTTTGTAATTTATATAA-TTTATATTT
1 TTTTATAATTT-TATAATTTTATATTT
*
35711724 TTTTATAATTTTTTAATTTTATAT
1 TTTTATAATTTTATAATTTTATAT
35711748 AAGTGTCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (26 bp):
TTTTATAATTTTATAATTTTATATTT
Found at i:35712347 original size:27 final size:26
Alignment explanation
Indices: 35712266--35712352 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 26
35712256 AGTAACTAAC
* *
35712266 GTATTTTAGTAATTTTATAAACCGGGG
1 GTATTTTGGTAATTTTATAAA-CGAGG
* *
35712293 GTACTTTGGTAATTTTACTAATCGAGG
1 GTATTTTGGTAATTTTA-TAAACGAGG
* *
35712320 GTATTTTGGTAATTTTGTAAACTAAGG
1 GTATTTTGGTAATTTTATAAAC-GAGG
35712347 GTATTT
1 GTATTT
35712353 CAATAATTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
26 4 0.08
27 43 0.86
28 3 0.06
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.44
Consensus pattern (26 bp):
GTATTTTGGTAATTTTATAAACGAGG
Found at i:35712576 original size:27 final size:27
Alignment explanation
Indices: 35712364--35712565 Score: 305
Period size: 27 Copynumber: 7.5 Consensus size: 27
35712354 AATAATTTTT
* ** *
35712364 TAAATCGAGGATAAAACAATAATTCTG
1 TAAATCGAGGGTAAAACGGTAATTCTA
35712391 TAAATCGAGGGTAAAACGGTAATTCTA
1 TAAATCGAGGGTAAAACGGTAATTCTA
*
35712418 TAAATCGAGGGTAAAATGGTAATTCTA
1 TAAATCGAGGGTAAAACGGTAATTCTA
* *
35712445 TAAATCGAGGGTAAAACGATAATTCTG
1 TAAATCGAGGGTAAAACGGTAATTCTA
**
35712472 TAAATCGAGGGTAAAATAGTAATTCTA
1 TAAATCGAGGGTAAAACGGTAATTCTA
*
35712499 TAAATTGAGGGTAAAACGGTAATTCTA
1 TAAATCGAGGGTAAAACGGTAATTCTA
*
35712526 TAAATCGAGGGTAAAACGATAATTCTA
1 TAAATCGAGGGTAAAACGGTAATTCTA
35712553 TAAATCGAGGGTA
1 TAAATCGAGGGTA
35712566 CTTTGGTAAT
Statistics
Matches: 158, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 158 1.00
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.27
Consensus pattern (27 bp):
TAAATCGAGGGTAAAACGGTAATTCTA
Found at i:35712590 original size:81 final size:81
Alignment explanation
Indices: 35712364--35712565 Score: 341
Period size: 81 Copynumber: 2.5 Consensus size: 81
35712354 AATAATTTTT
* * * *
35712364 TAAATCGAGGATAAAACAATAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGG
1 TAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATTGAGGG
*
35712429 TAAAATGGTAATTCTA
66 TAAAACGGTAATTCTA
*
35712445 TAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAATAGTAATTCTATAAATTGAGGG
1 TAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATTGAGGG
35712510 TAAAACGGTAATTCTA
66 TAAAACGGTAATTCTA
*
35712526 TAAATCGAGGGTAAAACGATAATTCTATAAATCGAGGGTA
1 TAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTA
35712566 CTTTGGTAAT
Statistics
Matches: 114, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 114 1.00
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.27
Consensus pattern (81 bp):
TAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATTGAGGG
TAAAACGGTAATTCTA
Found at i:35714099 original size:38 final size:38
Alignment explanation
Indices: 35714048--35714127 Score: 151
Period size: 38 Copynumber: 2.1 Consensus size: 38
35714038 CTAGAGATTG
*
35714048 TCAAACTTTGTGGATTTTTTTTCATATCTAAATACAAA
1 TCAAACTTTGTGGATTTGTTTTCATATCTAAATACAAA
35714086 TCAAACTTTGTGGATTTGTTTTCATATCTAAATACAAA
1 TCAAACTTTGTGGATTTGTTTTCATATCTAAATACAAA
35714124 TCAA
1 TCAA
35714128 GTGTTTTCTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (38 bp):
TCAAACTTTGTGGATTTGTTTTCATATCTAAATACAAA
Found at i:35721615 original size:13 final size:13
Alignment explanation
Indices: 35721597--35721621 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35721587 TAAAATAAAA
35721597 GAAATAAAGAAAT
1 GAAATAAAGAAAT
35721610 GAAATAAAGAAA
1 GAAATAAAGAAA
35721622 AAGGAAAAAG
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:0.16, T:0.12
Consensus pattern (13 bp):
GAAATAAAGAAAT
Found at i:35722650 original size:6 final size:6
Alignment explanation
Indices: 35722639--35722666 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
35722629 ACTCCGTACC
35722639 TTACTG TTACTG TTACTG TTACTG TTAC
1 TTACTG TTACTG TTACTG TTACTG TTAC
35722667 CCTTACGGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.14, T:0.50
Consensus pattern (6 bp):
TTACTG
Found at i:35722857 original size:18 final size:18
Alignment explanation
Indices: 35722798--35722857 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
35722788 GACTGTCTGC
*
35722798 TACTGAATAAATGACTGT
1 TACTGAATAAATGACTAT
* *
35722816 TACAGAATAAACGACTGA-
1 TACTGAATAAATGACT-AT
* *
35722834 TGCTGAATAAATGAATAT
1 TACTGAATAAATGACTAT
35722852 TACTGA
1 TACTGA
35722858 TTAACCGATT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
17 1 0.03
18 31 0.97
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (18 bp):
TACTGAATAAATGACTAT
Found at i:35728754 original size:27 final size:27
Alignment explanation
Indices: 35728723--35728900 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
35728713 TAAATTGTAC
35728723 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
35728750 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
35728776 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
35728804 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
35728832 AGCACTAAGTGTGCGATTTGATTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
35728859 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
35728886 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
35728901 GACTCGATAT
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 108 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:35728837 original size:82 final size:81
Alignment explanation
Indices: 35728724--35728879 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
35728714 AAATTGTACA
*
35728724 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTA-GCACTAAGTG
35728788 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
35728805 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTG
*
35728870 TGCGAGTTGA
65 TGCGAATTGA
35728880 TTATATAGCA
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 15 0.22
82 52 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:35728891 original size:82 final size:81
Alignment explanation
Indices: 35728720--35728900 Score: 238
Period size: 82 Copynumber: 2.2 Consensus size: 81
35728710 GATTAAATTG
*
35728720 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
35728785 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
35728801 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGAT-GCACT
* **
35728865 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
35728883 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
35728901 GACTCGATAT
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
81 18 0.21
82 67 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
GTGTGCGAATTGACCA
Found at i:35762430 original size:39 final size:39
Alignment explanation
Indices: 35762387--35762464 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
35762377 TTAAACGTTG
*
35762387 AGGTTAGCATTTGGGTTGTTGAATATGCCGAACTTGGAT
1 AGGTTAGCATTTGGGTTGTTCAATATGCCGAACTTGGAT
* *
35762426 AGGTTAGCATTTGGGTTGTTCAATGTGCCGAATTTGGAT
1 AGGTTAGCATTTGGGTTGTTCAATATGCCGAACTTGGAT
35762465 TTAGGGAGAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.22, C:0.10, G:0.31, T:0.37
Consensus pattern (39 bp):
AGGTTAGCATTTGGGTTGTTCAATATGCCGAACTTGGAT
Found at i:35764323 original size:47 final size:47
Alignment explanation
Indices: 35764242--35764974 Score: 1074
Period size: 47 Copynumber: 15.6 Consensus size: 47
35764232 TAATTGAATA
*
35764242 AATGTGAA-AGTGTATATGTGTGAATAGGGCCGAATGGCCAATGTGATG
1 AATGTGAACA-TGTATATGTGTG-ATAAGGCCGAATGGCCAATGTGATG
* * *
35764290 AATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
*
35764337 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* *
35764384 AAAGTGAACACGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* * *
35764431 AAAGTGAACATGTGTATGTGTGATAGGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* * *
35764478 AATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
*
35764525 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* *
35764572 AAAGTGAACACGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* * *
35764619 AAAGTGAACATGTGTATGTGTGATAGGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* * *
35764666 AATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
*
35764713 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* * *
35764760 AAAGTGAACACGTATATGTGTGATAACGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* *
35764807 AAAGTGAACATGTATATGTGTGATAAAGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* * * *
35764854 AAAGTGAACAGGTGTATGTGTGATAAGGCCGAGTGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* * * * *
35764901 AATGTGAGCATGTGTATGTGAGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
**
35764948 AATGTGAA-AGTGTATAAATGTGATAAG
1 AATGTGAACA-TGTATATGTGTGATAAG
35764975 TCCCGAAGGG
Statistics
Matches: 621, Mismatches: 62, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
46 1 0.00
47 602 0.97
48 17 0.03
49 1 0.00
ACGTcount: A:0.33, C:0.11, G:0.31, T:0.25
Consensus pattern (47 bp):
AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:35764582 original size:188 final size:188
Alignment explanation
Indices: 35764256--35764955 Score: 1247
Period size: 188 Copynumber: 3.7 Consensus size: 188
35764246 TGAAAGTGTA
35764256 TATGTGTGAATAGGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCG
1 TATGTGTG-ATAGGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCG
35764321 AATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAA
65 AATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAA
35764386 AGTGAACACGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACATGTG
130 AGTGAACACGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACATGTG
35764445 TATGTGTGATAGGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGA
1 TATGTGTGATAGGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGA
35764510 ATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAA
66 ATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAA
35764575 GTGAACACGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACATGTG
131 GTGAACACGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACATGTG
35764633 TATGTGTGATAGGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGA
1 TATGTGTGATAGGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGA
35764698 ATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAA
66 ATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAA
* *
35764763 GTGAACACGTATATGTGTGATAACGCCGAATGGCCAATGTGATGAAAGTGAACATGTA
131 GTGAACACGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACATGTG
** * * ** * *
35764821 TATGTGTGATAAAGCCGAATGGCCAATGTGATGAAAGTGAACAGGTGTATGTGTGATAAGGCCGA
1 TATGTGTGATAGGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGA
* * * * * *
35764886 GTGGCCAATGTGATGAATGTGAGCATGTGTATGTGAGATAAGGCCTAATGGCCGATGTGATGAAT
66 ATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAA
35764951 GTGAA
131 GTGAA
35764956 AGTGTATAAA
Statistics
Matches: 495, Mismatches: 16, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
188 487 0.98
189 8 0.02
ACGTcount: A:0.32, C:0.12, G:0.31, T:0.25
Consensus pattern (188 bp):
TATGTGTGATAGGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGA
ATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAA
GTGAACACGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACATGTG
Found at i:35765149 original size:37 final size:37
Alignment explanation
Indices: 35765093--35765172 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
35765083 CCGGGCTATA
* * *
35765093 AAGACCCGATGACTGCGTGTGG-GAATTTTGTCCGGGT
1 AAGACTCGATAACTGCGTGTGGAG-ATTATGTCCGGGT
*
35765130 AAGACTCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACTCGATAACTGCGTGTGGAGATTATGTCCGGGT
35765167 AAGACT
1 AAGACT
35765173 TCGTAATAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (37 bp):
AAGACTCGATAACTGCGTGTGGAGATTATGTCCGGGT
Found at i:35771569 original size:27 final size:27
Alignment explanation
Indices: 35771538--35771714 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
35771528 TAAATTGTAC
35771538 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
35771565 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
35771591 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
35771619 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
35771647 AGCACTAAGTGTGCGATTTGATTA-CT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
35771673 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
35771700 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
35771715 GACTCAATAT
Statistics
Matches: 128, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
26 24 0.19
27 81 0.63
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:35771684 original size:81 final size:81
Alignment explanation
Indices: 35771539--35771693 Score: 233
Period size: 81 Copynumber: 1.9 Consensus size: 81
35771529 AAATTGTACA
*
35771539 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
35771604 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
** *
35771620 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACT-A-GCACTAAGT
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATA-TGATGCACTAAGT
*
35771683 GTGCGAGTTGA
64 GTGCGAATTGA
35771694 TTATATAGCA
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
81 34 0.51
82 32 0.48
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:35771705 original size:81 final size:81
Alignment explanation
Indices: 35771535--35771714 Score: 229
Period size: 81 Copynumber: 2.2 Consensus size: 81
35771525 GATTAAATTG
*
35771535 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
35771600 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
35771616 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACT-A-GCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATA-TGATGCACT
* **
35771679 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
35771697 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
35771715 GACTCAATAT
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
81 51 0.61
82 32 0.38
83 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
GTGTGCGAATTGACCA
Found at i:35787260 original size:39 final size:39
Alignment explanation
Indices: 35787207--35787369 Score: 236
Period size: 39 Copynumber: 4.2 Consensus size: 39
35787197 GGACTTTAGC
* * * ** *
35787207 CCGGACATATTTCCAGCACGTAGCCTGTGGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTACGGACCCTAAGT
* *
35787246 CCGGTTATAATTCCAGCACATAGCCTACGGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTACGGACCCTAAGT
35787285 CCGGATATAATTCCAGCACATAGCCTACGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTACGGACCCTAAGT
**
35787324 CCGGATATAATTCCAGCACATAGCCTGTGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTACGGACCCTAAGT
35787363 CCGGATA
1 CCGGATA
35787370 AACATCACTG
Statistics
Matches: 114, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 114 1.00
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTACGGACCCTAAGT
Found at i:35795440 original size:38 final size:39
Alignment explanation
Indices: 35795328--35795475 Score: 217
Period size: 39 Copynumber: 3.8 Consensus size: 39
35795318 ACATATTTCT
* * * *
35795328 AGCACGTAGCATGCGGACCGTAAGTCCGGTTATAATTCC
1 AGCACATAGCCTGCGGACCCTAAGTCCGGATATAATTCC
* *
35795367 AGCACATAGCCTGCAGACCTTAAGTCCGGATATAATTCC
1 AGCACATAGCCTGCGGACCCTAAGTCCGGATATAATTCC
35795406 AGCACATAGCCTGCGGACCCT-AGTCCGGATATAATTCC
1 AGCACATAGCCTGCGGACCCTAAGTCCGGATATAATTCC
* *
35795444 AGCACATAACCTGCGGACCCTAAGTCCAGATA
1 AGCACATAGCCTGCGGACCCTAAGTCCGGATA
35795476 AACATCACTA
Statistics
Matches: 99, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
38 37 0.37
39 62 0.63
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (39 bp):
AGCACATAGCCTGCGGACCCTAAGTCCGGATATAATTCC
Found at i:35795447 original size:77 final size:78
Alignment explanation
Indices: 35795328--35795475 Score: 217
Period size: 77 Copynumber: 1.9 Consensus size: 78
35795318 ACATATTTCT
* * * * *
35795328 AGCACGTAGCATGCGGACCGTAAGTCCGGTTATAATTCCAGCACATAGCCTGCAGACCTTAAGTC
1 AGCACATAGCATGCGGACCCTAAGTCCGGATATAATTCCAGCACATAACCTGCAGACCCTAAGTC
*
35795393 CGGATATAATTCC
66 CAGATATAATTCC
* *
35795406 AGCACATAGCCTGCGGACCCT-AGTCCGGATATAATTCCAGCACATAACCTGCGGACCCTAAGTC
1 AGCACATAGCATGCGGACCCTAAGTCCGGATATAATTCCAGCACATAACCTGCAGACCCTAAGTC
35795470 CAGATA
66 CAGATA
35795476 AACATCACTA
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
77 44 0.71
78 18 0.29
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (78 bp):
AGCACATAGCATGCGGACCCTAAGTCCGGATATAATTCCAGCACATAACCTGCAGACCCTAAGTC
CAGATATAATTCC
Found at i:35802036 original size:40 final size:40
Alignment explanation
Indices: 35801986--35802175 Score: 294
Period size: 40 Copynumber: 4.8 Consensus size: 40
35801976 GATATAACTG
* * *
35801986 CTCGCTCAAATGCCTTCGAGACTTAGCCCGGTTATAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAA
35802026 CTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAA
*
35802066 CTTGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAA
* *
35802106 CTCGCACGAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTCA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAA
*
35802145 CTAGCACAAATGCCTTCGGGACTTAGCCCGG
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGG
35802176 TTATCGTCCG
Statistics
Matches: 139, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
38 1 0.01
39 34 0.24
40 104 0.75
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAA
Found at i:35807503 original size:13 final size:13
Alignment explanation
Indices: 35807485--35807511 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35807475 CATGTGAGCT
35807485 TACTAAGCATTTA
1 TACTAAGCATTTA
35807498 TACTAAGCATTTA
1 TACTAAGCATTTA
35807511 T
1 T
35807512 GCTTACTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
TACTAAGCATTTA
Found at i:35810158 original size:15 final size:15
Alignment explanation
Indices: 35810106--35810189 Score: 91
Period size: 15 Copynumber: 5.7 Consensus size: 15
35810096 ATATCTATCT
*
35810106 TGGGTTTCTTTATCC
1 TGGGTTTCTTTATTC
* *
35810121 TGGATCTCTTTATTC
1 TGGGTTTCTTTATTC
*
35810136 TGGATTTCTTTATTC
1 TGGGTTTCTTTATTC
*
35810151 TGGGTTTCTCTA-TC
1 TGGGTTTCTTTATTC
35810165 TTGGGTTTCTTTATTC
1 -TGGGTTTCTTTATTC
*
35810181 -GGTTTTCTT
1 TGGGTTTCTT
35810190 GTTATCTTTG
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
14 10 0.17
15 47 0.80
16 2 0.03
ACGTcount: A:0.08, C:0.17, G:0.18, T:0.57
Consensus pattern (15 bp):
TGGGTTTCTTTATTC
Found at i:35810174 original size:30 final size:30
Alignment explanation
Indices: 35810099--35810188 Score: 103
Period size: 30 Copynumber: 3.0 Consensus size: 30
35810089 CGGCATAATA
* *
35810099 TCTATCTTGGGTTTCTTTATCCTGGATCTC
1 TCTATCTTGGGTTTCTTTATTCTGGATTTC
* * *
35810129 TTTAT-TCTGGATTTCTTTATTCTGGGTTTC
1 TCTATCT-TGGGTTTCTTTATTCTGGATTTC
*
35810159 TCTATCTTGGGTTTCTTTATTC-GGTTTTC
1 TCTATCTTGGGTTTCTTTATTCTGGATTTC
35810188 T
1 T
35810189 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.09, C:0.18, G:0.17, T:0.57
Consensus pattern (30 bp):
TCTATCTTGGGTTTCTTTATTCTGGATTTC
Found at i:35810904 original size:94 final size:94
Alignment explanation
Indices: 35810738--35810935 Score: 378
Period size: 94 Copynumber: 2.1 Consensus size: 94
35810728 ACAGTGAGGT
35810738 AATGTGATAGTTTAGAGCATTCGATGTTACATAAAATCGGAGTTGTTAAAGGGGTTAAAGCCGAG
1 AATGTGATAGTTTAGAGCATTCGATGTTACATAAAATCGGAGTTGTTAAAGGGGTTAAAGCCGAG
35810803 CACTGGGATCTATCAAAATTATCCTTGTC
66 CACTGGGATCTATCAAAATTATCCTTGTC
35810832 AATGTGATAGTTTAGAGCATTCGATGTTACATAAAATCGGAGTTGTTAAAGGGGTTAAAGCCGAG
1 AATGTGATAGTTTAGAGCATTCGATGTTACATAAAATCGGAGTTGTTAAAGGGGTTAAAGCCGAG
*
35810897 CATTGGGATCTATCAAAATTATCCTTGTC
66 CACTGGGATCTATCAAAATTATCCTTGTC
35810926 AATGTTGATA
1 AATG-TGATA
35810936 TTGGGATGGA
Statistics
Matches: 102, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
94 97 0.95
95 5 0.05
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (94 bp):
AATGTGATAGTTTAGAGCATTCGATGTTACATAAAATCGGAGTTGTTAAAGGGGTTAAAGCCGAG
CACTGGGATCTATCAAAATTATCCTTGTC
Found at i:35817248 original size:45 final size:45
Alignment explanation
Indices: 35817047--35817258 Score: 210
Period size: 45 Copynumber: 4.7 Consensus size: 45
35817037 TACCGGAATT
* * * *
35817047 GAGTAAGGCCATAGTTGAAACACGTTATGGCATCACGATTCAGAC
1 GAGTAAGACCATAGCTGAAAGACGCTATGGCATCACGATTCAGAC
* * * *
35817092 GAGTAAGACCATAGCT-AACAGACACTATGGCCTTACGATTTAGAC
1 GAGTAAGACCATAGCTGAA-AGACGCTATGGCATCACGATTCAGAC
* * * * *
35817137 GAGTAAGACTATAGCTGAAAGATGCTATGGAATCACGATTCAAAT
1 GAGTAAGACCATAGCTGAAAGACGCTATGGCATCACGATTCAGAC
* * * * * *
35817182 GAGTAAGACCATAGCTAAAAGATGTTATCGCATCACGGTTCAGAT
1 GAGTAAGACCATAGCTGAAAGACGCTATGGCATCACGATTCAGAC
* * *
35817227 GTGTAAGACCATAGTTGAAAGACACTATGGCA
1 GAGTAAGACCATAGCTGAAAGACGCTATGGCA
35817259 ACATGACAGG
Statistics
Matches: 134, Mismatches: 31, Indels: 4
0.79 0.18 0.02
Matches are distributed among these distances:
44 2 0.01
45 130 0.97
46 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (45 bp):
GAGTAAGACCATAGCTGAAAGACGCTATGGCATCACGATTCAGAC
Found at i:35817290 original size:46 final size:46
Alignment explanation
Indices: 35817230--35817340 Score: 179
Period size: 46 Copynumber: 2.4 Consensus size: 46
35817220 TTCAGATGTG
*
35817230 TAAGACCATAGTTGAAAGACACTATGGCAACATGACAGG-AAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCAACATAAC-GGAAAATGAA
* *
35817276 TAAGACCATGGTTGAAAGACACTATGGCAATATAACGGAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCAACATAACGGAAAATGAA
35817322 TAAGACCATAGTTGAAAGA
1 TAAGACCATAGTTGAAAGA
35817341 TATGTCATCA
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
45 2 0.03
46 58 0.97
ACGTcount: A:0.46, C:0.14, G:0.22, T:0.19
Consensus pattern (46 bp):
TAAGACCATAGTTGAAAGACACTATGGCAACATAACGGAAAATGAA
Found at i:35817470 original size:26 final size:26
Alignment explanation
Indices: 35817440--35817504 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
35817430 ATGACGAATA
35817440 GTTATATG-AATTAATTATACA-AAATG
1 GTTATATGAAATT-ATTATA-AGAAATG
* *
35817466 GTTATGTGAAATTATTATAAGAATTG
1 GTTATATGAAATTATTATAAGAAATG
35817492 GTTATATGGAAAT
1 GTTATAT-GAAAT
35817505 AGATGTACGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
25 1 0.03
26 23 0.70
27 9 0.27
ACGTcount: A:0.42, C:0.02, G:0.17, T:0.40
Consensus pattern (26 bp):
GTTATATGAAATTATTATAAGAAATG
Found at i:35817563 original size:27 final size:28
Alignment explanation
Indices: 35817533--35817593 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
35817523 TATGAATTAG
35817533 TTATATGGAAACAGATAAACA-AAATAA
1 TTATATGGAAACAGATAAACAGAAATAA
* * * *
35817560 TTATAT-GAATCGGATATATAGAAATAA
1 TTATATGGAAACAGATAAACAGAAATAA
35817587 TTATATG
1 TTATATG
35817594 AAGTGTTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.51, C:0.05, G:0.13, T:0.31
Consensus pattern (28 bp):
TTATATGGAAACAGATAAACAGAAATAA
Found at i:35819131 original size:20 final size:21
Alignment explanation
Indices: 35819108--35819148 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
35819098 ATTTTTTTCT
35819108 TTACTTTTTTTATC-TCTTCC
1 TTACTTTTTTTATCATCTTCC
*
35819128 TTACTTTTTTTTTCATCTTCC
1 TTACTTTTTTTATCATCTTCC
35819149 CCTTTCTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.10, C:0.24, G:0.00, T:0.66
Consensus pattern (21 bp):
TTACTTTTTTTATCATCTTCC
Found at i:35819136 original size:21 final size:20
Alignment explanation
Indices: 35819108--35819148 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
35819098 ATTTTTTTCT
35819108 TTACTTTTTTTATC-TCTTCC
1 TTACTTTTTTT-TCATCTTCC
35819128 TTACTTTTTTTTTCATCTTCC
1 TTAC-TTTTTTTTCATCTTCC
35819149 CCTTTCTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.10, C:0.24, G:0.00, T:0.66
Consensus pattern (20 bp):
TTACTTTTTTTTCATCTTCC
Found at i:35820104 original size:20 final size:21
Alignment explanation
Indices: 35820061--35820121 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
35820051 TATCCATTAA
*
35820061 TAAAAATATAATTATATTATT
1 TAAAAATAAAATTATATTATT
35820082 TAAAAATAAAATT-TA-TATCT
1 TAAAAATAAAATTATATTAT-T
* *
35820102 TAAAATTAAAA-TATTTTATT
1 TAAAAATAAAATTATATTATT
35820122 ATTTATTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 4 0.12
20 15 0.44
21 15 0.44
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TAAAAATAAAATTATATTATT
Found at i:35823768 original size:22 final size:22
Alignment explanation
Indices: 35823743--35823789 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
35823733 GTTTCTAGTC
* *
35823743 CACACGGGCGTGTGCCTCTACT
1 CACACGGCCGTGTGCCCCTACT
*
35823765 CACACGGCCGTGTGCCCCTATT
1 CACACGGCCGTGTGCCCCTACT
35823787 CAC
1 CAC
35823790 GCAATTGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.15, C:0.40, G:0.23, T:0.21
Consensus pattern (22 bp):
CACACGGCCGTGTGCCCCTACT
Found at i:35826869 original size:18 final size:18
Alignment explanation
Indices: 35826846--35826881 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
35826836 GAGTTCGATG
35826846 TATGTTGTCAAATGCTAA
1 TATGTTGTCAAATGCTAA
35826864 TATGTTGTCAAATGCTAA
1 TATGTTGTCAAATGCTAA
35826882 CTTACCGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (18 bp):
TATGTTGTCAAATGCTAA
Found at i:35835739 original size:43 final size:43
Alignment explanation
Indices: 35835677--35835793 Score: 144
Period size: 43 Copynumber: 2.6 Consensus size: 43
35835667 GAGGGGGTGT
* * *
35835677 TAGGATTATTATCGGATATTAGCTTTTAACAATTTGATTCCTAA
1 TAGGA-TATTATAGGATATTATCTTTTAACAATTTGATTCCAAA
* * *
35835721 TAGGATATTATAGGATATTATCTCTTAGCAGTTTGATTCCAAA
1 TAGGATATTATAGGATATTATCTTTTAACAATTTGATTCCAAA
35835764 TAGGATATTATTAAGGATTATTATCTTTTA
1 TAGGATATTA-T-AGGA-TATTATCTTTTA
35835794 GTAATTTAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
43 42 0.67
44 6 0.10
45 4 0.06
46 11 0.17
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (43 bp):
TAGGATATTATAGGATATTATCTTTTAACAATTTGATTCCAAA
Found at i:35836837 original size:41 final size:41
Alignment explanation
Indices: 35836792--35836882 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 41
35836782 GTATATTATG
* *
35836792 TCAGGCCTTGAGCCTGGCAGGCTTTGTA-CCAATGTATTGAA
1 TCAGGCCTTAAGCCTGGCAAGCTTTG-AGCCAATGTATTGAA
* * *
35836833 TCAGGCGTTAAGCCTGGCAAGCTTTGAGTCAGTGTATTGAA
1 TCAGGCCTTAAGCCTGGCAAGCTTTGAGCCAATGTATTGAA
*
35836874 TCAAGCCTT
1 TCAGGCCTT
35836883 CATCGTAGCA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 1 0.02
41 41 0.98
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (41 bp):
TCAGGCCTTAAGCCTGGCAAGCTTTGAGCCAATGTATTGAA
Found at i:35840874 original size:38 final size:38
Alignment explanation
Indices: 35840831--35840906 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
35840821 GGTAAATGTA
*
35840831 CCAAAGTATGTGTTATGGGTTGGTTTGAATAATGTATG
1 CCAAAGTATGTGTTATGGGTCGGTTTGAATAATGTATG
*
35840869 CCAAAGTATGTGTTATGGGTCGGTTTGAATAATTTATG
1 CCAAAGTATGTGTTATGGGTCGGTTTGAATAATGTATG
35840907 TATTAAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.26, C:0.07, G:0.28, T:0.39
Consensus pattern (38 bp):
CCAAAGTATGTGTTATGGGTCGGTTTGAATAATGTATG
Found at i:35841267 original size:20 final size:20
Alignment explanation
Indices: 35841242--35841279 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
35841232 CTAGGAACTA
*
35841242 TGTGATCTGAGCTCATGAGT
1 TGTGATATGAGCTCATGAGT
*
35841262 TGTGATATGAGTTCATGA
1 TGTGATATGAGCTCATGA
35841280 TATATGTGAC
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:0.24, C:0.11, G:0.29, T:0.37
Consensus pattern (20 bp):
TGTGATATGAGCTCATGAGT
Found at i:35848511 original size:12 final size:12
Alignment explanation
Indices: 35848494--35848518 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35848484 TTTTGATCAA
35848494 AGATAATCACTT
1 AGATAATCACTT
35848506 AGATAATCACTT
1 AGATAATCACTT
35848518 A
1 A
35848519 TTGGAATGTT
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:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (12 bp):
AGATAATCACTT
Found at i:35856595 original size:36 final size:36
Alignment explanation
Indices: 35856543--35856613 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
35856533 AGTAAACTTT
* * *
35856543 ATTCAGTTCAGTAGCCTTTTGGATCTATTCTAACTG
1 ATTCAGTTCAGCAGCCTTTCGAATCTATTCTAACTG
35856579 ATTCAGTTCAGCAGCCTTTCGAATCTATTCTAACT
1 ATTCAGTTCAGCAGCCTTTCGAATCTATTCTAACT
35856614 AATGCGCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.39
Consensus pattern (36 bp):
ATTCAGTTCAGCAGCCTTTCGAATCTATTCTAACTG
Found at i:35861252 original size:12 final size:12
Alignment explanation
Indices: 35861235--35861261 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
35861225 ATTCTGAAGT
35861235 ATATATATATAC
1 ATATATATATAC
35861247 ATATATATATAC
1 ATATATATATAC
35861259 ATA
1 ATA
35861262 AGTATGCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATATATAC
Found at i:35861774 original size:27 final size:27
Alignment explanation
Indices: 35861743--35861920 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
35861733 TAAATTGTAC
35861743 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
35861770 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * * *
35861796 ATGAACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
35861824 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
35861852 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
35861879 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
35861906 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
35861921 GACTCAATAT
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 104 0.82
28 23 0.18
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:35861886 original size:82 final size:81
Alignment explanation
Indices: 35861744--35861899 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
35861734 AAATTGTACA
* *
35861744 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGAACTAAGTGT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGAACTAAGTGT
35861809 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
** * *
35861825 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACTAAGT
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GAACTAAGT
*
35861889 GTGCGAGTTGA
64 GTGCGAATTGA
35861900 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGAACTAAGTGT
GCGAATTGACCATGCG
Found at i:35861911 original size:82 final size:81
Alignment explanation
Indices: 35861740--35861920 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
35861730 GATTAAATTG
* *
35861740 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGAACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGAACTAA
35861805 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** * *
35861821 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GAACT
* **
35861885 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
35861903 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
35861921 GACTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGAACTAA
GTGTGCGAATTGACCA
Found at i:35869891 original size:27 final size:27
Alignment explanation
Indices: 35869860--35870037 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
35869850 TAAATTGTAC
35869860 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
35869887 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* *
35869913 ATGCACTAAGTGTGCGAATTGACCATGT
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
35869941 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
35869969 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
35869996 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
35870023 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
35870038 GACTCAATAT
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:35869974 original size:82 final size:81
Alignment explanation
Indices: 35869861--35870016 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
35869851 AAATTGTACA
* *
35869861 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
35869925 TGCGAATTGACCATGTG
65 TGCGAATTGACCATGTG
** *
35869942 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
35870007 TGCGAGTTGA
65 TGCGAATTGA
35870017 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGTG
Found at i:35870028 original size:82 final size:81
Alignment explanation
Indices: 35869860--35870037 Score: 232
Period size: 82 Copynumber: 2.2 Consensus size: 81
35869850 TAAATTGTAC
* *
35869860 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTG
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTG
*
35869925 TGCGAATTGACCATGT
66 TGCGAATTGACCATAT
* ** *
35869941 GGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACTAAG
1 AGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAG
* **
35870005 TGTGCGAGTTGATTATAT
64 TGTGCGAATTGACCATAT
*
35870023 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
35870038 GACTCAATAT
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
81 16 0.19
82 67 0.81
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTG
TGCGAATTGACCATAT
Found at i:35889102 original size:18 final size:18
Alignment explanation
Indices: 35889079--35889115 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
35889069 TTCAGAAGAG
35889079 ATACAGCATACATTACAC
1 ATACAGCATACATTACAC
35889097 ATACAGCATACATTACAC
1 ATACAGCATACATTACAC
35889115 A
1 A
35889116 CTTCTTAGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.27, G:0.05, T:0.22
Consensus pattern (18 bp):
ATACAGCATACATTACAC
Found at i:35891133 original size:39 final size:39
Alignment explanation
Indices: 35891016--35891239 Score: 238
Period size: 39 Copynumber: 5.6 Consensus size: 39
35891006 GCTACTCGTT
* * * *
35891016 CAAATGCCTTCAGGACATAGCCCGG-TTATAGTAACTCCCA
1 CAAATGCCTTC-GGGCTTAGCCCGGAAT-TAGTAACTCGCA
* *
35891056 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCA
*
35891096 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCA
* *
35891135 CAAATTCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCA
* * * * *
35891174 CAAATGCCTTCGGATCTTAGTCCGG-ATATGGTCACTTAGCA
1 CAAATGCCTTCGG-GCTTAGCCCGGAAT-TAGTAAC-TCGCA
35891215 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
35891240 CATCATTCAA
Statistics
Matches: 160, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
39 76 0.47
40 74 0.46
41 10 0.06
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCA
Found at i:35891183 original size:78 final size:79
Alignment explanation
Indices: 35891016--35891239 Score: 247
Period size: 79 Copynumber: 2.8 Consensus size: 79
35891006 GCTACTCGTT
*
35891016 CAAATGCCTTCAGGACATAGCCCGGTTATAGTAACTCCCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTC-GGACATAGCCCGGATATAGTAACTCCCACAAATGCCTTCGGGACTTAACCCGG
*
35891081 ATTTAGTAACTCGCA
65 AATTAGTAACTCGCA
* * * * * *
35891096 CAAATGCCTTCGGGCTTAGCCCGGA-ATTAGTATCTCGCACAAATTCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGACATAGCCCGGATA-TAGTAACTCCCACAAATGCCTTCGGGACTTAACCCGG
*
35891159 AATTAGTATCTCGCA
65 AATTAGTAACTCGCA
* * * * ** *
35891174 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGA-CATAGCCCGGATATAGTAAC-TCCCACAAATGCCTTCGGGACTTAACCCG
35891238 GA
64 GA
35891240 CATCATTCAA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
78 36 0.29
79 56 0.46
80 31 0.25
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGACATAGCCCGGATATAGTAACTCCCACAAATGCCTTCGGGACTTAACCCGGA
ATTAGTAACTCGCA
Found at i:35891239 original size:40 final size:40
Alignment explanation
Indices: 35891016--35891239 Score: 246
Period size: 40 Copynumber: 5.7 Consensus size: 40
35891006 GCTACTCGTT
* * * * *
35891016 CAAATGCCTTCAGGACATAGCCCGG-TTATAGTAACTCCCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTATCTCGCA
* * *
35891056 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
35891096 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
*
35891135 CAAATTCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* * *
35891174 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGT-ATC-TCGCA
35891215 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
35891240 CATCATTCAA
Statistics
Matches: 163, Mismatches: 13, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
38 2 0.01
39 72 0.44
40 75 0.46
41 14 0.09
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:35898988 original size:40 final size:40
Alignment explanation
Indices: 35898939--35899142 Score: 139
Period size: 40 Copynumber: 5.1 Consensus size: 40
35898929 CGGAATTTAA
** * *
35898939 CCGGATATAGCT-ACTCGTTCAAATGCCTTTGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACATAAC
* *
35898979 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACATAAC
* * * * * *
35899019 CCGGATTTAGTATCTCACACAAATTCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACATAAC
* * * **
35899058 CCGGA-ATTAGTATCTCGCACAAATGTCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CATAAC
* * * * *
35899098 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACATAAC
35899138 CCGGA
1 CCGGA
35899143 CATCATTCAA
Statistics
Matches: 134, Mismatches: 23, Indels: 14
0.78 0.13 0.08
Matches are distributed among these distances:
38 2 0.01
39 31 0.23
40 89 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACATAAC
Found at i:35899072 original size:39 final size:40
Alignment explanation
Indices: 35898986--35899089 Score: 140
Period size: 39 Copynumber: 2.6 Consensus size: 40
35898976 AGCCCGGTTA
* * *
35898986 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
1 TAGTATCTCGCACAAATTCCTTCGGGACTTAACCCGGAAT
* *
35899026 TAGTATCTCACACAAATTCCTTCGGG-CTTAGCCCGGAAT
1 TAGTATCTCGCACAAATTCCTTCGGGACTTAACCCGGAAT
35899065 TAGTATCTCGCACAAATGT-CTTCGG
1 TAGTATCTCGCACAAAT-TCCTTCGG
35899090 ATCTTAGTCC
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
39 33 0.58
40 24 0.42
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (40 bp):
TAGTATCTCGCACAAATTCCTTCGGGACTTAACCCGGAAT
Found at i:35899102 original size:79 final size:80
Alignment explanation
Indices: 35898925--35899142 Score: 191
Period size: 79 Copynumber: 2.8 Consensus size: 80
35898915 AAATCACGTA
* * ** * * *
35898925 CCTTCGGAATTTAA-CCGGATATAG-CTACTC-GTTCAAATGCCTTTGGGACATAGCCCGG-TTA
1 CCTTCGGGACTTAACCCGGATATAGTC-ACTCAGCACAAA-GCCTTCGGGACTTAGCCCGGAAT-
35898986 TAGTAACTCGCACAAATG
63 TAGTAACTCGCACAAATG
* *
35899004 CCTTCGGGACTTAACCCGGATTTAGT-ATCTCA-CACAAATTCCTTCGGG-CTTAGCCCGGAATT
1 CCTTCGGGACTTAACCCGGATATAGTCA-CTCAGCACAAA-GCCTTCGGGACTTAGCCCGGAATT
*
35899066 AGTATCTCGCACAAATG
64 AGTAACTCGCACAAATG
* ** * *
35899083 TCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 CCTTCGGGA-CTTAACCCGGATATAGTCACTCAGCACAAAGCCTTCGGGACTTAGCCCGGA
35899143 CATCATTCAA
Statistics
Matches: 113, Mismatches: 17, Indels: 17
0.77 0.12 0.12
Matches are distributed among these distances:
78 3 0.03
79 67 0.59
80 43 0.38
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (80 bp):
CCTTCGGGACTTAACCCGGATATAGTCACTCAGCACAAAGCCTTCGGGACTTAGCCCGGAATTAG
TAACTCGCACAAATG
Found at i:35904342 original size:19 final size:19
Alignment explanation
Indices: 35904318--35904360 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
35904308 AATGTTTGAA
*
35904318 TGTTGCATCACATACCCTG
1 TGTTGCAACACATACCCTG
35904337 TGTTGCAACACATACCCTG
1 TGTTGCAACACATACCCTG
35904356 TGTTG
1 TGTTG
35904361 ATCCATCACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.33
Consensus pattern (19 bp):
TGTTGCAACACATACCCTG
Found at i:35906330 original size:8 final size:8
Alignment explanation
Indices: 35906314--35906356 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
35906304 TTAGATTGGC
*
35906314 AAATCCCG
1 AAATACCG
35906322 AAATACCG
1 AAATACCG
*
35906330 AAATGCCG
1 AAATACCG
*
35906338 AAATGCCG
1 AAATACCG
*
35906346 AAATATCG
1 AAATACCG
35906354 AAA
1 AAA
35906357 AGCCAAAAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.47, C:0.23, G:0.16, T:0.14
Consensus pattern (8 bp):
AAATACCG
Found at i:35906633 original size:29 final size:29
Alignment explanation
Indices: 35906598--35906729 Score: 194
Period size: 29 Copynumber: 4.6 Consensus size: 29
35906588 TTCAGGCCGG
*
35906598 ATGGGCCATATGAACGTGATTTGGGCCTA
1 ATGGGCCATATGAATGTGATTTGGGCCTA
* *
35906627 ATAGGCCATACGAATGTGATTTGGGCCTA
1 ATGGGCCATATGAATGTGATTTGGGCCTA
35906656 ATGGGCCATATGAATGTGATTTGGGCCTA
1 ATGGGCCATATGAATGTGATTTGGGCCTA
**
35906685 ATGGGCCATATGAATAAGA-TTGGGCCTA
1 ATGGGCCATATGAATGTGATTTGGGCCTA
* *
35906713 GTGGGCCATATGCATGT
1 ATGGGCCATATGAATGT
35906730 ATGTAGACTT
Statistics
Matches: 92, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
28 22 0.24
29 70 0.76
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (29 bp):
ATGGGCCATATGAATGTGATTTGGGCCTA
Found at i:35910268 original size:11 final size:11
Alignment explanation
Indices: 35910252--35910277 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
35910242 ATTGCATGTA
35910252 TGATATTATTG
1 TGATATTATTG
35910263 TGATATTATTG
1 TGATATTATTG
35910274 TGAT
1 TGAT
35910278 GTGGGCTTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (11 bp):
TGATATTATTG
Found at i:35917752 original size:17 final size:19
Alignment explanation
Indices: 35917726--35917771 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
35917716 ATATTATGCG
35917726 AAAAACTAAA-T-AAAACA
1 AAAAACTAAATTAAAAACA
*
35917743 AAAAATTAAATTAAAAACA
1 AAAAACTAAATTAAAAACA
*
35917762 AATAACTAAA
1 AAAAACTAAA
35917772 CATATTGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 9 0.38
18 1 0.04
19 14 0.58
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (19 bp):
AAAAACTAAATTAAAAACA
Found at i:35919321 original size:16 final size:16
Alignment explanation
Indices: 35919300--35919340 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
35919290 CAATACATAC
*
35919300 ATTTAATATAATAATT
1 ATTTAATATAATAATA
*
35919316 ATTTAATATTATAATA
1 ATTTAATATAATAATA
*
35919332 ATTAAATAT
1 ATTTAATAT
35919341 TTAAATTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTTAATATAATAATA
Found at i:35924800 original size:20 final size:20
Alignment explanation
Indices: 35924775--35924820 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
35924765 TATATAAAAG
35924775 ATTTTTTTAAAAAAATTTA-A
1 ATTTTTTT-AAAAAATTTATA
*
35924795 ATTTTTTTATAAAATTTATA
1 ATTTTTTTAAAAAATTTATA
35924815 ATTTTT
1 ATTTTT
35924821 ATGATAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTTTTTAAAAAATTTATA
Found at i:35924801 original size:19 final size:20
Alignment explanation
Indices: 35924777--35924820 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
35924767 TATAAAAGAT
35924777 TTTTTTAAAAAAATTTA-AA
1 TTTTTTAAAAAAATTTATAA
* *
35924796 TTTTTTTATAAAATTTATAA
1 TTTTTTAAAAAAATTTATAA
35924816 TTTTT
1 TTTTT
35924821 ATGATAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTTTAAAAAAATTTATAA
Found at i:35924827 original size:21 final size:19
Alignment explanation
Indices: 35924786--35924829 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 19
35924776 TTTTTTTAAA
*
35924786 AAAATTTAAATTTTTTTAT
1 AAAATTTAAATTTTTTGAT
35924805 AAAATTTATAATTTTTATGAT
1 AAAATTTA-AATTTTT-TGAT
35924826 AAAA
1 AAAA
35924830 ATATCTCGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.36
20 7 0.32
21 7 0.32
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
AAAATTTAAATTTTTTGAT
Found at i:35927437 original size:17 final size:17
Alignment explanation
Indices: 35927415--35927475 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
35927405 ATTGAATCAA
35927415 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
35927432 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
35927452 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
35927469 TACATAA
1 TACATAA
35927476 GTCTTGAAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
17 20 0.61
20 13 0.39
ACGTcount: A:0.51, C:0.15, G:0.03, T:0.31
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:35927448 original size:37 final size:36
Alignment explanation
Indices: 35927406--35927497 Score: 139
Period size: 37 Copynumber: 2.5 Consensus size: 36
35927396 ATTAACCGAA
35927406 TTGAATCAATACATAATTAAAAACATTACATAAGTC
1 TTGAATCAATACATAATTAAAAACATTACATAAGTC
*
35927442 TTTGAATCACTACATAATTAAAAACATTACATAAGTC
1 -TTGAATCAATACATAATTAAAAACATTACATAAGTC
* *
35927479 TTGAAATTAACACATAATT
1 TTG-AATCAATACATAATT
35927498 GAAATGTAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
36 3 0.06
37 47 0.94
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (36 bp):
TTGAATCAATACATAATTAAAAACATTACATAAGTC
Found at i:35933073 original size:28 final size:30
Alignment explanation
Indices: 35933024--35933102 Score: 83
Period size: 28 Copynumber: 2.7 Consensus size: 30
35933014 AGAAACAAAC
* *
35933024 TATATACAT-AAATAGATTTAAAA-GAA-AA
1 TATATACATAAAATA-ATATAAAATCAATAA
*
35933052 TATTTACATAAAATAATATAAAATCAATAA
1 TATATACATAAAATAATATAAAATCAATAA
*
35933082 TATATACAAAAAAATAATATA
1 TATATAC-ATAAAATAATATA
35933103 CAACATAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
28 15 0.36
29 7 0.17
30 8 0.19
31 12 0.29
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (30 bp):
TATATACATAAAATAATATAAAATCAATAA
Found at i:35933112 original size:15 final size:15
Alignment explanation
Indices: 35933063--35933114 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
35933053 ATTTACATAA
*
35933063 AATAATATAAAATCAAT
1 AATAATATACAA-C-AT
* *
35933080 AAT-ATATACAAAAA
1 AATAATATACAACAT
35933094 AATAATATACAACAT
1 AATAATATACAACAT
35933109 AATAAT
1 AATAAT
35933115 GTGTAAAATC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
14 4 0.14
15 15 0.52
16 7 0.24
17 3 0.10
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (15 bp):
AATAATATACAACAT
Found at i:35935867 original size:33 final size:33
Alignment explanation
Indices: 35935830--35935912 Score: 139
Period size: 33 Copynumber: 2.5 Consensus size: 33
35935820 ACTACCACAA
*
35935830 CAATATTCCACTCCTCCTAGCCCATTACCACCG
1 CAATACTCCACTCCTCCTAGCCCATTACCACCG
* *
35935863 CAATACTCTACTCCTCCTAGCCCATTACCACTG
1 CAATACTCCACTCCTCCTAGCCCATTACCACCG
35935896 CAATACTCCACTCCTCC
1 CAATACTCCACTCCTCC
35935913 CGGCCTAAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.24, C:0.46, G:0.05, T:0.25
Consensus pattern (33 bp):
CAATACTCCACTCCTCCTAGCCCATTACCACCG
Found at i:35939426 original size:30 final size:30
Alignment explanation
Indices: 35939374--35939432 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
35939364 ATTTATCTTT
*
35939374 TTTCTTTCTTTTCTTTTCTTTTTCTTCTCA
1 TTTCTTTCTTTTCTTTTCTTTTTCCTCTCA
*
35939404 TTTCTTTC-TTTCTTTCTTTTTTTCCTCTC
1 TTTCTTTCTTTTCTTT-TCTTTTTCCTCTC
35939433 CTTCTCTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (30 bp):
TTTCTTTCTTTTCTTTTCTTTTTCCTCTCA
Found at i:35939443 original size:30 final size:29
Alignment explanation
Indices: 35939375--35939447 Score: 71
Period size: 30 Copynumber: 2.5 Consensus size: 29
35939365 TTTATCTTTT
*
35939375 TTCT-TTCTTTTCTTTTCTTTTTCTTCTCA
1 TTCTCTTC-TTTCTTTTCTTTTTCCTCTCA
* *
35939404 TT-TCTTTCTTTCTTTCTTTTTTTCCTCTCC
1 TTCTC-TTCTTTCTTT-TCTTTTTCCTCTCA
35939434 TTCTCTTC-TTCTTT
1 TTCTCTTCTTTCTTT
35939448 ACTGCTTTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
28 1 0.03
29 15 0.41
30 19 0.51
31 2 0.05
ACGTcount: A:0.01, C:0.27, G:0.00, T:0.71
Consensus pattern (29 bp):
TTCTCTTCTTTCTTTTCTTTTTCCTCTCA
Found at i:35939465 original size:25 final size:26
Alignment explanation
Indices: 35939433--35939490 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
35939423 TTTTCCTCTC
*
35939433 CTTC-TCTTCTTC-TTTACTGCTT-T
1 CTTCTTCTTCTTCTTTTACTACTTCT
35939456 CTTTCTTCTTCTTCTTTTACTACTTCT
1 C-TTCTTCTTCTTCTTTTACTACTTCT
35939483 CTTCTTCT
1 CTTCTTCT
35939491 CTACAAGGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 1 0.03
24 3 0.10
25 8 0.27
26 16 0.53
27 2 0.07
ACGTcount: A:0.05, C:0.31, G:0.02, T:0.62
Consensus pattern (26 bp):
CTTCTTCTTCTTCTTTTACTACTTCT
Found at i:35939470 original size:33 final size:35
Alignment explanation
Indices: 35939369--35939470 Score: 86
Period size: 33 Copynumber: 2.9 Consensus size: 35
35939359 AATAGATTTA
* *
35939369 TCTTT-TTTCTTTCTTTTCTTTTCTTTTTCTTCTCATT
1 TCTTTCTTTCTTGC-TTTC-TTTCTTCTTCTTCTCA-T
* * * *
35939406 TCTTTCTTTCTTTCTTTTTTTCCTCTCCTTCTC-T
1 TCTTTCTTTCTTGCTTTCTTTCTTCTTCTTCTCAT
35939440 TC-TTCTTTAC-TGCTTTCTTTCTTCTTCTTCT
1 TCTTTCTTT-CTTGCTTTCTTTCTTCTTCTTCT
35939471 TTTACTACTT
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
33 23 0.42
34 4 0.07
36 12 0.22
37 8 0.15
38 8 0.15
ACGTcount: A:0.02, C:0.27, G:0.01, T:0.70
Consensus pattern (35 bp):
TCTTTCTTTCTTGCTTTCTTTCTTCTTCTTCTCAT
Found at i:35940677 original size:41 final size:39
Alignment explanation
Indices: 35940546--35940684 Score: 140
Period size: 40 Copynumber: 3.5 Consensus size: 39
35940536 AACACACCAG
* * * *
35940546 TTTGACATCCAGTGCCTCATGGGATAATTCGAAGTAATAA
1 TTTGACACCCAGTGTCTCAT-CGATAATCCGAAGTAATAA
* * * *
35940586 TTTGATACCCAGTGTCTTATCTGCTAAACCGAAGT-A-AA
1 TTTGACACCCAGTGTCTCATC-GATAATCCGAAGTAATAA
*
35940624 -TTGGCACCCAGTGTCTCATCGAATTAATCCGAAGTAATAA
1 TTTGACACCCAGTGTCTCATCG-A-TAATCCGAAGTAATAA
35940664 TTTGACACCCAGTGTCTCATC
1 TTTGACACCCAGTGTCTCATC
35940685 AACTCGACGT
Statistics
Matches: 79, Mismatches: 14, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
36 1 0.01
37 17 0.22
38 12 0.15
39 2 0.03
40 28 0.35
41 19 0.24
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (39 bp):
TTTGACACCCAGTGTCTCATCGATAATCCGAAGTAATAA
Found at i:35942073 original size:16 final size:16
Alignment explanation
Indices: 35942019--35942073 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
35942009 CCATGGCCTC
35942019 TTAGTAAAATTTTAAT
1 TTAGTAAAATTTTAAT
***
35942035 TTAG-GCCATTTATAAT
1 TTAGTAAAATTT-TAAT
*
35942051 TTA-TAAAATTTTAAA
1 TTAGTAAAATTTTAAT
35942066 TTAGTAAA
1 TTAGTAAA
35942074 GATAATATTA
Statistics
Matches: 29, Mismatches: 7, Indels: 6
0.69 0.17 0.14
Matches are distributed among these distances:
15 10 0.34
16 19 0.66
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (16 bp):
TTAGTAAAATTTTAAT
Found at i:35949089 original size:26 final size:25
Alignment explanation
Indices: 35949042--35949091 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
35949032 TTAGTGTTAA
*
35949042 TTAATTTTAATTTATTTAATTAAGT
1 TTAATTTTAATTTATGTAATTAAGT
35949067 TTAATTGTTAATTT-TGTATATTAAG
1 TTAATT-TTAATTTATGTA-ATTAAG
35949092 GAATATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (25 bp):
TTAATTTTAATTTATGTAATTAAGT
Found at i:35957161 original size:41 final size:41
Alignment explanation
Indices: 35957100--35957198 Score: 155
Period size: 41 Copynumber: 2.4 Consensus size: 41
35957090 TTTAGATATA
*
35957100 TCCTTTTCAA-CTTTTCATGTGTTATCCCTTTCAGGTAATT
1 TCCTTTTCAACCTTTTCATGTGTTATCCCTTTCAGGTAACT
* * *
35957140 TCCTTTTCAACCTTTTCATGTGTTATTCTTTTCGGGTAACT
1 TCCTTTTCAACCTTTTCATGTGTTATCCCTTTCAGGTAACT
35957181 TCCTTTTCAACCTTTTCA
1 TCCTTTTCAACCTTTTCA
35957199 AGAATTTGGA
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
40 10 0.19
41 44 0.81
ACGTcount: A:0.16, C:0.24, G:0.09, T:0.51
Consensus pattern (41 bp):
TCCTTTTCAACCTTTTCATGTGTTATCCCTTTCAGGTAACT
Found at i:35959679 original size:55 final size:55
Alignment explanation
Indices: 35959613--35959724 Score: 206
Period size: 55 Copynumber: 2.0 Consensus size: 55
35959603 TACCCTTCAA
*
35959613 ATTGTCTATTAAATATATTGAATTTTAAATTACTCATATTCCAGTGCCCTATAGG
1 ATTGTCTATTAAATATATCGAATTTTAAATTACTCATATTCCAGTGCCCTATAGG
*
35959668 ATTGTCTATTAAATATATCGAATTTTAAATTACTTATATTCCAGTGCCCTATAGG
1 ATTGTCTATTAAATATATCGAATTTTAAATTACTCATATTCCAGTGCCCTATAGG
35959723 AT
1 AT
35959725 CTACTAGTCT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (55 bp):
ATTGTCTATTAAATATATCGAATTTTAAATTACTCATATTCCAGTGCCCTATAGG
Found at i:35965113 original size:15 final size:15
Alignment explanation
Indices: 35965093--35965123 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
35965083 GTCCTTCACG
35965093 ATTCTGATGTCCTTA
1 ATTCTGATGTCCTTA
35965108 ATTCTGATGTCCTTA
1 ATTCTGATGTCCTTA
35965123 A
1 A
35965124 CCGAAGAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (15 bp):
ATTCTGATGTCCTTA
Found at i:35968218 original size:15 final size:15
Alignment explanation
Indices: 35968200--35968231 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
35968190 TATAATCAAA
35968200 TCACATAAACAAGGG
1 TCACATAAACAAGGG
35968215 TCACATAAACAAGGG
1 TCACATAAACAAGGG
35968230 TC
1 TC
35968232 TAAGTAACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.16
Consensus pattern (15 bp):
TCACATAAACAAGGG
Done.