Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 135 of 213
Found at i:39895736 original size:20 final size:20
Alignment explanation
Indices: 39895690--39895748 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
39895680 GTATAAACTG
* *
39895690 TAATTCATTCATATAACCAG
1 TAATTCATTCATATAAACAA
* * *
39895710 TAGTTCATTCGTATAAATAA
1 TAATTCATTCATATAAACAA
*
39895730 TAATTCATCCATATAAACA
1 TAATTCATTCATATAAACA
39895749 CATATCTTAT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (20 bp):
TAATTCATTCATATAAACAA
Found at i:39895958 original size:23 final size:22
Alignment explanation
Indices: 39895932--39896055 Score: 81
Period size: 23 Copynumber: 5.3 Consensus size: 22
39895922 AGGCTCTATT
39895932 GAGCTGAAATGGTAAGCTCTGAC
1 GAGCTGAAATGGTAAGCTCT-AC
* *
39895955 GAGCTTAGCA--GTAAGCTCATAC
1 GAGCTGA-AATGGTAAGCTC-TAC
* * *
39895977 GAGCTGAAACGGTAAACTCTAAT
1 GAGCTGAAATGGTAAGCTCT-AC
* *
39896000 GAGCTGAAAATAGTAGGCTCTTAC
1 GAGCTG-AAATGGTAAGCTC-TAC
39896024 GAGCTGAAATATCGGTAAGCTCATAC
1 GAGCTG-AA-AT-GGTAAGCTC-TAC
39896050 GAGCTG
1 GAGCTG
39896056 TGCTGAGTCC
Statistics
Matches: 78, Mismatches: 14, Indels: 15
0.73 0.13 0.14
Matches are distributed among these distances:
21 1 0.01
22 17 0.22
23 21 0.27
24 20 0.26
25 3 0.04
26 16 0.21
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (22 bp):
GAGCTGAAATGGTAAGCTCTAC
Found at i:39896027 original size:24 final size:26
Alignment explanation
Indices: 39896000--39896055 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
39895990 AAACTCTAAT
* *
39896000 GAGCTGAAA-AT-AGTAGGCTCTTAC
1 GAGCTGAAATATCAGTAAGCTCATAC
*
39896024 GAGCTGAAATATCGGTAAGCTCATAC
1 GAGCTGAAATATCAGTAAGCTCATAC
39896050 GAGCTG
1 GAGCTG
39896056 TGCTGAGTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 9 0.33
25 2 0.07
26 16 0.59
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (26 bp):
GAGCTGAAATATCAGTAAGCTCATAC
Found at i:39896279 original size:67 final size:67
Alignment explanation
Indices: 39896202--39896718 Score: 770
Period size: 67 Copynumber: 7.8 Consensus size: 67
39896192 AATAATTCAA
* * *
39896202 TTTCTCAAATCACATATATATAATCTATTCAATTAAATACATACATTTAAATACTCAATTTGCAT
1 TTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTCAATTCGCAT
39896267 AC
66 AC
* * ** *
39896269 CTTCTCAAATCACATATATATAATTGATTTAATTAAATACATACATTTAAATACTCAATTCGCAT
1 TTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTCAATTCGCAT
39896334 AC
66 AC
* * * *
39896336 TTTCTCAAATCATATACCTATAATCAATTCAATTAAATACATACATTTAATTACTAAATTCGCAT
1 TTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTCAATTCGCAT
39896401 AC
66 AC
* * * *
39896403 TTTCT-TAATCACATACATACAATCGATTTAATTAAATACATACATTTAAATACTCAATTCGCAT
1 TTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTCAATTCGCAT
39896467 AC
66 AC
* * *
39896469 TTTCTCAAATCATATACATATAATCAATTCAATTAAATACATACATTTAATTACTAAATTCGCAT
1 TTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTCAATTCGCAT
39896534 AC
66 AC
* * * *
39896536 TTTCTC-AATCACATACATACAATCGATTTAGTTAAATACATACATTTAAATACTCAATTCGCAT
1 TTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTCAATTCGCAT
39896600 AC
66 AC
* * *
39896602 TTTCTCAAATCATATACATATAATCAATTAAATTAAATACATACATTTAATTACTCAATTCGC-T
1 TTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTCAATTCGCAT
39896666 AC
66 AC
*
39896668 TTTCTCAAATCACATACATATAATCAATTGAATTAAATACATACATTTAAA
1 TTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAA
39896719 AACTATTGCA
Statistics
Matches: 403, Mismatches: 45, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
66 168 0.42
67 235 0.58
ACGTcount: A:0.42, C:0.19, G:0.02, T:0.37
Consensus pattern (67 bp):
TTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTCAATTCGCAT
AC
Found at i:39896466 original size:133 final size:134
Alignment explanation
Indices: 39896202--39896718 Score: 851
Period size: 133 Copynumber: 3.9 Consensus size: 134
39896192 AATAATTCAA
* * * * * *
39896202 TTTCTCAAATCACATATATATAATCTATTCAATTAAATACATACATTTAAATACTCAATTTGCAT
1 TTTCTCAAATCATATACATATAATCAATTCAATTAAATACATACATTTAATTACTAAATTCGCAT
* * * *
39896267 ACCTTCTCAAATCACATATATATAATTGATTTAATTAAATACATACATTTAAATACTCAATTCGC
66 ACTTTCTCAAATCACATACATACAATCGATTTAATTAAATACATACATTTAAATACTCAATTCGC
39896332 ATAC
131 ATAC
*
39896336 TTTCTCAAATCATATACCTATAATCAATTCAATTAAATACATACATTTAATTACTAAATTCGCAT
1 TTTCTCAAATCATATACATATAATCAATTCAATTAAATACATACATTTAATTACTAAATTCGCAT
*
39896401 ACTTTCT-TAATCACATACATACAATCGATTTAATTAAATACATACATTTAAATACTCAATTCGC
66 ACTTTCTCAAATCACATACATACAATCGATTTAATTAAATACATACATTTAAATACTCAATTCGC
39896465 ATAC
131 ATAC
39896469 TTTCTCAAATCATATACATATAATCAATTCAATTAAATACATACATTTAATTACTAAATTCGCAT
1 TTTCTCAAATCATATACATATAATCAATTCAATTAAATACATACATTTAATTACTAAATTCGCAT
*
39896534 ACTTTCTC-AATCACATACATACAATCGATTTAGTTAAATACATACATTTAAATACTCAATTCGC
66 ACTTTCTCAAATCACATACATACAATCGATTTAATTAAATACATACATTTAAATACTCAATTCGC
39896598 ATAC
131 ATAC
* *
39896602 TTTCTCAAATCATATACATATAATCAATTAAATTAAATACATACATTTAATTACTCAATTCGC-T
1 TTTCTCAAATCATATACATATAATCAATTCAATTAAATACATACATTTAATTACTAAATTCGCAT
* * *
39896666 ACTTTCTCAAATCACATACATATAATCAATTGAATTAAATACATACATTTAAA
66 ACTTTCTCAAATCACATACATACAATCGATTTAATTAAATACATACATTTAAA
39896719 AACTATTGCA
Statistics
Matches: 361, Mismatches: 20, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
132 9 0.02
133 288 0.80
134 64 0.18
ACGTcount: A:0.42, C:0.19, G:0.02, T:0.37
Consensus pattern (134 bp):
TTTCTCAAATCATATACATATAATCAATTCAATTAAATACATACATTTAATTACTAAATTCGCAT
ACTTTCTCAAATCACATACATACAATCGATTTAATTAAATACATACATTTAAATACTCAATTCGC
ATAC
Found at i:39896621 original size:200 final size:201
Alignment explanation
Indices: 39896202--39896723 Score: 771
Period size: 200 Copynumber: 2.6 Consensus size: 201
39896192 AATAATTCAA
* * * *
39896202 TTTCTCAAATCACATATATATAATCTATTCAATTAAATACATACATTTAAATACTCAATTTGCAT
1 TTTCTCAAATCACATACATATAATCAATTAAATTAAATACATACATTTAAATACTCAATTCGCAT
* * ** * *
39896267 ACCTTCTCAAATCACATATATATAATTGATTTAATTAAATACATACATTTAAATACTCAATTCGC
66 ACTTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTAAATTCGC
* * * *
39896332 ATACTTTCTCAAATCATATACCTATAATCAATTCAATTAAATACATACATTTAATTACTAAATTC
131 ATACTTTCTCAAATCACATACATACAATCAATTCAATTAAATACATACATTTAAATACTAAATTC
39896397 GCATAC
196 GCATAC
* * * *
39896403 TTTCT-TAATCACATACATACAATCGATTTAATTAAATACATACATTTAAATACTCAATTCGCAT
1 TTTCTCAAATCACATACATATAATCAATTAAATTAAATACATACATTTAAATACTCAATTCGCAT
* *
39896467 ACTTTCTCAAATCATATACATATAATCAATTCAATTAAATACATACATTTAATTACTAAATTCGC
66 ACTTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTAAATTCGC
* * * *
39896532 ATACTTTCTC-AATCACATACATACAATCGATTTAGTTAAATACATACATTTAAATACTCAATTC
131 ATACTTTCTCAAATCACATACATACAATCAATTCAATTAAATACATACATTTAAATACTAAATTC
39896596 GCATAC
196 GCATAC
* *
39896602 TTTCTCAAATCATATACATATAATCAATTAAATTAAATACATACATTTAATTACTCAATTCGC-T
1 TTTCTCAAATCACATACATATAATCAATTAAATTAAATACATACATTTAAATACTCAATTCGCAT
* *
39896666 ACTTTCTCAAATCACATACATATAATCAATTGAATTAAATACATACATTTAAAAACTA
66 ACTTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTA
39896724 TTGCAATTGT
Statistics
Matches: 288, Mismatches: 32, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
199 112 0.39
200 171 0.59
201 5 0.02
ACGTcount: A:0.42, C:0.19, G:0.02, T:0.37
Consensus pattern (201 bp):
TTTCTCAAATCACATACATATAATCAATTAAATTAAATACATACATTTAAATACTCAATTCGCAT
ACTTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTAAATTCGC
ATACTTTCTCAAATCACATACATACAATCAATTCAATTAAATACATACATTTAAATACTAAATTC
GCATAC
Found at i:39899640 original size:28 final size:28
Alignment explanation
Indices: 39899573--39899704 Score: 194
Period size: 28 Copynumber: 4.8 Consensus size: 28
39899563 AACAGTAGAG
*
39899573 TGTGGGCCTTAGCCCAATACAGT-ACAG
1 TGTGGGCCTTAGCCCAATACAGTAACAA
*
39899600 TGTGGGCCTTAGCCCAATACAATAACAA
1 TGTGGGCCTTAGCCCAATACAGTAACAA
* *
39899628 TGTGGGCCTTAGCCCAATGCAGTAATAA
1 TGTGGGCCTTAGCCCAATACAGTAACAA
**
39899656 TGTGGGTTTTAGCCCAATACAGTAACAA
1 TGTGGGCCTTAGCCCAATACAGTAACAA
*
39899684 TGTGGGCCTTCGCCCAATACA
1 TGTGGGCCTTAGCCCAATACA
39899705 ATATCGGTAC
Statistics
Matches: 92, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
27 22 0.24
28 70 0.76
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (28 bp):
TGTGGGCCTTAGCCCAATACAGTAACAA
Found at i:39899854 original size:26 final size:26
Alignment explanation
Indices: 39899815--39899915 Score: 148
Period size: 26 Copynumber: 3.9 Consensus size: 26
39899805 AACACACCAA
* * * *
39899815 TATCACAGAAAAGCTGCCAATAATAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
*
39899841 TATCGCAGCGAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
*
39899867 TATCTCAGCAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
39899893 TATCGCAGCAAAGCTGCCAGTAA
1 TATCGCAGCAAAGCTGCCAGTAA
39899916 TAGTGTACTT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 67 1.00
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.18
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTAACAG
Found at i:39900145 original size:27 final size:27
Alignment explanation
Indices: 39900085--39900362 Score: 185
Period size: 27 Copynumber: 10.3 Consensus size: 27
39900075 GGGTATAATA
*
39900085 GTCATATTACCCTATAGGGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGGTATTTCG
* * *
39900113 ATCATTTTACCCTATGGGAGTAATTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
39900140 GTCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
39900167 GTCATTTTACCTTATAGGTGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
39900194 ATCATTTTACTCTA--CGGG------G
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
39900213 GTCATTTTACCCTACGAGGCTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
**** **
39900240 GTCATTTACCCTAAACCCTACAAAGGTATTTTA
1 GTCATTT----T--ACCCTATGGGGGTATTTCG
*
39900273 GTCATTTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
39900300 GTTATTTTACACTACGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
39900327 GTCATTTTACCCTATGGGAGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
39900354 GTCATTTTA
1 GTCATTTTA
39900363 TTCTACAGGG
Statistics
Matches: 195, Mismatches: 41, Indels: 29
0.74 0.15 0.11
Matches are distributed among these distances:
19 13 0.07
21 2 0.01
25 2 0.01
27 141 0.72
28 13 0.07
29 1 0.01
31 1 0.01
33 22 0.11
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:39900174 original size:54 final size:53
Alignment explanation
Indices: 39900085--39900362 Score: 212
Period size: 54 Copynumber: 5.2 Consensus size: 53
39900075 GGGTATAATA
* * * * *
39900085 GTCATATTACCCTATAGGGGGTATTTCGATCATTTTACCCTATGGGAGTAATTCG
1 GTCATTTTACCCTA-CGGGGGTATTTTGGTCATTTTACCCTATGGG-GTATTTCG
* * *
39900140 GTCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCTTATAGGTGTATTTCG
1 GTCATTTTACCCTACGGGGGTATTTTGGTCATTTTACCCTAT-GGGGTATTTCG
* * * * *
39900194 ATCATTTTACTCTAC--GGG------GGTCATTTTACCCTACGAGGCTATTTTG
1 GTCATTTTACCCTACGGGGGTATTTTGGTCATTTTACCCTATG-GGGTATTTCG
*** *
39900240 GTCATTTACCCTAAACCCTACAAAGGTATTTTAGTCATTTTACCCTATAGGGGTATTTCG
1 GTCATTT----T--ACCCTACGGGGGTATTTTGGTCATTTTACCCTAT-GGGGTATTTCG
* * *
39900300 GTTATTTTACACTACGGGGGTATTTTGGTCATTTTACCCTATGGGAGTATTTCA
1 GTCATTTTACCCTACGGGGGTATTTTGGTCATTTTACCCTATGGG-GTATTTCG
39900354 GTCATTTTA
1 GTCATTTTA
39900363 TTCTACAGGG
Statistics
Matches: 175, Mismatches: 30, Indels: 37
0.72 0.12 0.15
Matches are distributed among these distances:
45 1 0.01
46 27 0.15
50 1 0.01
52 9 0.05
53 3 0.02
54 89 0.51
55 15 0.09
56 1 0.01
60 28 0.16
61 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.41
Consensus pattern (53 bp):
GTCATTTTACCCTACGGGGGTATTTTGGTCATTTTACCCTATGGGGTATTTCG
Found at i:39925008 original size:40 final size:40
Alignment explanation
Indices: 39924817--39925001 Score: 198
Period size: 40 Copynumber: 4.7 Consensus size: 40
39924807 TTGAATGATG
* * * * *
39924817 TCCGTGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* ** *
39924857 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGAAACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
39924897 TCCGGGCTAAG-CCCGATGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
39924936 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
39924977 -CCGGGCTATGTCCTGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
39925002 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
39 33 0.27
40 79 0.65
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:39925023 original size:79 final size:79
Alignment explanation
Indices: 39924870--39925034 Score: 183
Period size: 79 Copynumber: 2.1 Consensus size: 79
39924860 GGACTAAGAT
* * **
39924870 CCGAAGGCATTTGTGCGAGAAACTAATTCCGGGCTAAGCCCGATGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGAAACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
39924935 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
** * *
39924949 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCTGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGAAACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
39925012 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
39925028 CCGAAGG
1 CCGAAGG
39925035 TACGTGATTT
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.65
80 23 0.32
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGAAACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:39932918 original size:79 final size:81
Alignment explanation
Indices: 39932782--39932966 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
39932772 TTGAATGATG
*
39932782 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
39932846 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
39932861 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
39932923 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
39932941 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
39932967 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:39932980 original size:40 final size:40
Alignment explanation
Indices: 39932783--39932966 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
39932773 TGAATGATGT
* * * *
39932783 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
39932823 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
39932863 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
39932901 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
39932942 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
39932967 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:39932988 original size:79 final size:79
Alignment explanation
Indices: 39932835--39932999 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
39932825 GGACTAAGAT
* **
39932835 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
39932900 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
39932914 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
39932977 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
39932993 CCGAAGG
1 CCGAAGG
39933000 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:39947657 original size:11 final size:11
Alignment explanation
Indices: 39947641--39947670 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
39947631 GTATGATGAG
39947641 AAGAGAAACAC
1 AAGAGAAACAC
*
39947652 AAGAGAAATAC
1 AAGAGAAACAC
39947663 AAGAGAAA
1 AAGAGAAA
39947671 AGTAGTAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.67, C:0.10, G:0.20, T:0.03
Consensus pattern (11 bp):
AAGAGAAACAC
Found at i:39951871 original size:65 final size:65
Alignment explanation
Indices: 39951779--39951910 Score: 255
Period size: 65 Copynumber: 2.0 Consensus size: 65
39951769 AAGCTACATT
*
39951779 TTCTTTTAACTGAAACTTTTGACATAGAAATATTTATATTCGTCTATCTCATCCTACATTTAATC
1 TTCTTTTAACTGAAACTTTTGACATAGAAATATTTATATTCATCTATCTCATCCTACATTTAATC
39951844 TTCTTTTAACTGAAACTTTTGACATAGAAATATTTATATTCATCTATCTCATCCTACATTTAATC
1 TTCTTTTAACTGAAACTTTTGACATAGAAATATTTATATTCATCTATCTCATCCTACATTTAATC
39951909 TT
1 TT
39951911 TTTGCATGGA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.31, C:0.18, G:0.05, T:0.45
Consensus pattern (65 bp):
TTCTTTTAACTGAAACTTTTGACATAGAAATATTTATATTCATCTATCTCATCCTACATTTAATC
Found at i:39954906 original size:12 final size:12
Alignment explanation
Indices: 39954889--39954916 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
39954879 ATCCACATGA
39954889 TCAAAGACCGTT
1 TCAAAGACCGTT
39954901 TCAAAGACCGTT
1 TCAAAGACCGTT
39954913 TCAA
1 TCAA
39954917 CTATGTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (12 bp):
TCAAAGACCGTT
Found at i:39957218 original size:27 final size:27
Alignment explanation
Indices: 39957169--39957222 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 27
39957159 AAATCGTAGC
*
39957169 TTCGAAAAAAAAAAGTTAAAAAAAAGT
1 TTCGAAAAAAAAAAATTAAAAAAAAGT
39957196 TTCGAAAAAAAAAAATCTGAAAAAAAA
1 TTCGAAAAAAAAAAAT-T-AAAAAAAA
39957223 AGAAGAAGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 15 0.62
28 1 0.04
29 8 0.33
ACGTcount: A:0.69, C:0.06, G:0.09, T:0.17
Consensus pattern (27 bp):
TTCGAAAAAAAAAAATTAAAAAAAAGT
Found at i:39957251 original size:16 final size:16
Alignment explanation
Indices: 39957186--39957261 Score: 61
Period size: 16 Copynumber: 4.9 Consensus size: 16
39957176 AAAAAAAGTT
* * *
39957186 AAAAAAAAGTTTCGAA
1 AAAAAAAAATTGCAAA
39957202 AAAAAAAAATCTG-AAA
1 AAAAAAAAAT-TGCAAA
* *
39957218 AAAAAAGAA--G-AAGG
1 AAAAAAAAATTGCAA-A
39957232 AAAAAAAAATTGCAAA
1 AAAAAAAAATTGCAAA
39957248 AAAAAAAAATTGCA
1 AAAAAAAAATTGCA
39957262 TACGGTCTAG
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
13 3 0.06
14 8 0.17
16 34 0.71
17 3 0.06
ACGTcount: A:0.71, C:0.05, G:0.12, T:0.12
Consensus pattern (16 bp):
AAAAAAAAATTGCAAA
Found at i:39964522 original size:26 final size:26
Alignment explanation
Indices: 39964491--39964547 Score: 89
Period size: 25 Copynumber: 2.2 Consensus size: 26
39964481 TGGTTGAAAG
*
39964491 CCGAAAAACATCAAGGATCTGCTTAT
1 CCGAAAAACATCAAGGATCTACTTAT
*
39964517 CTG-AAAACATCAAGGATCTACTTAT
1 CCGAAAAACATCAAGGATCTACTTAT
39964542 CCGAAA
1 CCGAAA
39964548 GCACAAGTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 23 0.85
26 4 0.15
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (26 bp):
CCGAAAAACATCAAGGATCTACTTAT
Found at i:39967164 original size:157 final size:157
Alignment explanation
Indices: 39966878--39967192 Score: 558
Period size: 157 Copynumber: 2.0 Consensus size: 157
39966868 CAAGAAACAT
*
39966878 AATCATAGTGAGTTAGTCCAGTATGTTGTTCTCTAACACATACTCATGTATCAATTTTGACATCC
1 AATCATAGTGAGTTAGTCCAGTATGTTGTTCTCTAACACATACTCATGAATCAATTTTGACATCC
*
39966943 CTATGTCAATAAAAACACTTTGCCATCAATCAACTACACATTAGTCTCAATGCATTATCATTGTT
66 CTATGTCAATAAAAACACTTTGCCATCAATCAACTACACATTAGCCTCAATGCATTATCATTGTT
*
39967008 CAAGCCCACAATAATACTTGACTAAGG
131 CAAACCCACAATAATACTTGACTAAGG
* *
39967035 AATCATAGTGAGTTAGTCCAGTATGTTGTTCTCTAATACATACTCATGAATCGATTTTGACATCC
1 AATCATAGTGAGTTAGTCCAGTATGTTGTTCTCTAACACATACTCATGAATCAATTTTGACATCC
* * *
39967100 CTATGTCAATGAAAACACTTTGTCATCAATCAACTAGACATTAGCCTCAATGCATTATCATTGTT
66 CTATGTCAATAAAAACACTTTGCCATCAATCAACTACACATTAGCCTCAATGCATTATCATTGTT
39967165 CAAACCCACAATAATACTTGACTAAGG
131 CAAACCCACAATAATACTTGACTAAGG
39967192 A
1 A
39967193 CATTTTAAGA
Statistics
Matches: 150, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
157 150 1.00
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (157 bp):
AATCATAGTGAGTTAGTCCAGTATGTTGTTCTCTAACACATACTCATGAATCAATTTTGACATCC
CTATGTCAATAAAAACACTTTGCCATCAATCAACTACACATTAGCCTCAATGCATTATCATTGTT
CAAACCCACAATAATACTTGACTAAGG
Found at i:39968031 original size:14 final size:15
Alignment explanation
Indices: 39968007--39968035 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
39967997 CGTTTGTTTG
39968007 CTAATAAAATAATTT
1 CTAATAAAATAATTT
39968022 CTAA-AAAATAATTT
1 CTAATAAAATAATTT
39968036 ACTTTTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
CTAATAAAATAATTT
Found at i:39971306 original size:16 final size:16
Alignment explanation
Indices: 39971269--39971308 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
39971259 TTTTTATGCT
* *
39971269 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAC
39971285 TAAAATTAATTGTTAC
1 TAAAATTAATTGTTAC
39971301 TAAAATTA
1 TAAAATTA
39971309 TATCAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAC
Found at i:39972803 original size:25 final size:26
Alignment explanation
Indices: 39972775--39972834 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 26
39972765 TTTTAAACAG
39972775 AATACAGATTGAACATACAACCCA-A
1 AATACAGATTGAACATACAACCCAGA
* *
39972800 AATACAAATTGAACATACAATCCAGA
1 AATACAGATTGAACATACAACCCAGA
39972826 AA-ACAGATT
1 AATACAGATT
39972835 CCAAAATTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 28 0.90
26 3 0.10
ACGTcount: A:0.53, C:0.20, G:0.08, T:0.18
Consensus pattern (26 bp):
AATACAGATTGAACATACAACCCAGA
Found at i:39973319 original size:16 final size:16
Alignment explanation
Indices: 39973298--39973331 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
39973288 TTGGGGAAGA
*
39973298 GGGGAAACGGGAAATG
1 GGGGAAAAGGGAAATG
39973314 GGGGAAAAGGGAAATG
1 GGGGAAAAGGGAAATG
39973330 GG
1 GG
39973332 TGTTAAAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.53, T:0.06
Consensus pattern (16 bp):
GGGGAAAAGGGAAATG
Found at i:39974074 original size:28 final size:28
Alignment explanation
Indices: 39974038--39974095 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
39974028 ATAAAGAATG
* * **
39974038 AATATTTTAGGTATCAAAATTTAAATAA
1 AATAATTTAAGTATCAAAATAAAAATAA
*
39974066 AATAATTTAATTATCAAAATAAAAATAA
1 AATAATTTAAGTATCAAAATAAAAATAA
39974094 AA
1 AA
39974096 ATATTTCAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (28 bp):
AATAATTTAAGTATCAAAATAAAAATAA
Found at i:39974557 original size:24 final size:23
Alignment explanation
Indices: 39974530--39974607 Score: 70
Period size: 24 Copynumber: 3.3 Consensus size: 23
39974520 CTTTAGAAAC
*
39974530 TTAATAAATTTTTTTAATTTTTTA
1 TTAA-AAATTTTTATAATTTTTTA
* *
39974554 TTAAGAACTTTTTAT-CTTCTTTTA
1 TTAA-AAATTTTTATAATT-TTTTA
*
39974578 TT-AAAATTTCTTAAAATTTTTTA
1 TTAAAAATTT-TTATAATTTTTTA
39974601 TTAAAAA
1 TTAAAAA
39974608 ACATATTGAG
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
22 5 0.12
23 13 0.30
24 25 0.58
ACGTcount: A:0.36, C:0.05, G:0.01, T:0.58
Consensus pattern (23 bp):
TTAAAAATTTTTATAATTTTTTA
Found at i:39976451 original size:16 final size:17
Alignment explanation
Indices: 39976418--39976452 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
39976408 TGGCATTTCT
*
39976418 AAATTTAGTTTATTAAC
1 AAATTTAGCTTATTAAC
39976435 AAATTTAGCTT-TTAAC
1 AAATTTAGCTTATTAAC
39976451 AA
1 AA
39976453 TTATTCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.43
Consensus pattern (17 bp):
AAATTTAGCTTATTAAC
Found at i:39981116 original size:188 final size:187
Alignment explanation
Indices: 39980784--39981162 Score: 704
Period size: 188 Copynumber: 2.0 Consensus size: 187
39980774 CTATATGCTA
39980784 TTTTGCAGAAGAAACGGTGTCCATCGAGACTTGGATCCACCATAATATTAAGTAGTGCATTAATG
1 TTTTGCAGAAGAAACGGTGTCCATCGAGACTTGGATCCACCATAATATTAAGTAGTGCATTAATG
39980849 GTCAGAAAGTTAGGGTTTTCTTTCCCCACTCAGTGATAGCCTTGTGATAACTTTTGAAAAGAGTT
66 GTCAGAAAGTTAGGGTTTTCTTTCCCCACTCAGTGATAGCCTTGTGATAACTTTTGAAAAGAGTT
*
39980914 ATATTTAAGGCATCTAGATGGAATTAATTATTTGAAATTAAGTGAATACATCTGCAT
131 ATATTTAAGGCATCTAGATAGAATTAATTATTTGAAATTAAGTGAATACATCTGCAT
*
39980971 TTTTGCAGAAGAAACAGGTGTCCTTCGAGACTTGGATCCACCATAATATTAAGTAGTGCATTAAT
1 TTTTGCAGAAGAAAC-GGTGTCCATCGAGACTTGGATCCACCATAATATTAAGTAGTGCATTAAT
* *
39981036 GGTCAGAAAGTTAGGGTTTTCTTTCCCTACTTAGTGATAGCCTTGTGATAACTTTTGAAAAGAGT
65 GGTCAGAAAGTTAGGGTTTTCTTTCCCCACTCAGTGATAGCCTTGTGATAACTTTTGAAAAGAGT
*
39981101 TATATTTAAGGCATCTAGATAGAATTAATTATTTGAAATTAAGTGAATTCATCTGCAT
130 TATATTTAAGGCATCTAGATAGAATTAATTATTTGAAATTAAGTGAATACATCTGCAT
39981159 TTTT
1 TTTT
39981163 AGGATAATTT
Statistics
Matches: 186, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
187 15 0.08
188 171 0.92
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (187 bp):
TTTTGCAGAAGAAACGGTGTCCATCGAGACTTGGATCCACCATAATATTAAGTAGTGCATTAATG
GTCAGAAAGTTAGGGTTTTCTTTCCCCACTCAGTGATAGCCTTGTGATAACTTTTGAAAAGAGTT
ATATTTAAGGCATCTAGATAGAATTAATTATTTGAAATTAAGTGAATACATCTGCAT
Found at i:39992963 original size:28 final size:28
Alignment explanation
Indices: 39992927--39993015 Score: 88
Period size: 28 Copynumber: 3.2 Consensus size: 28
39992917 CATGCAGTAG
* *
39992927 CAGTCTGGGCCTGAGCCCTATATAGCAA
1 CAGTATGGGCCTGAGCCCAATATAGCAA
* *
39992955 CAGTATGGGCCTTAGCCCAATATAGTAA
1 CAGTATGGGCCTGAGCCCAATATAGCAA
* * * * * *
39992983 CAATGTGAGCCTTAGCCCAATACAGTAA
1 CAGTATGGGCCTGAGCCCAATATAGCAA
39993011 CAGTA
1 CAGTA
39993016 CAATGCAGTA
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 51 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.22
Consensus pattern (28 bp):
CAGTATGGGCCTGAGCCCAATATAGCAA
Found at i:39993180 original size:26 final size:26
Alignment explanation
Indices: 39993121--39993196 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
39993111 CACCAATATT
* * * *
39993121 GCAGCAAGGCTGCCAGTAATAGTGAT
1 GCAGCAAAGCTGCCAGTAACAGTAAC
39993147 GCAGCAAAGCTGCCAGTAACAGTAAC
1 GCAGCAAAGCTGCCAGTAACAGTAAC
* * *
39993173 GCATCAAAGTTTCCAGTAACAGTA
1 GCAGCAAAGCTGCCAGTAACAGTA
39993197 TATGTGGCAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (26 bp):
GCAGCAAAGCTGCCAGTAACAGTAAC
Found at i:39993447 original size:27 final size:27
Alignment explanation
Indices: 39993363--39993450 Score: 95
Period size: 27 Copynumber: 3.3 Consensus size: 27
39993353 CAACTCCTAA
* * * *
39993363 GGGTATTACAGTCATTTTACTCTTCAG
1 GGGTATTTCGGTCATTTTACCCTTCGG
* * * *
39993390 GGGCATTTCGGTCAATTTACCCTTTGA
1 GGGTATTTCGGTCATTTTACCCTTCGG
*
39993417 GGGTATTTTGGTCATTTTACCCTTCGG
1 GGGTATTTCGGTCATTTTACCCTTCGG
39993444 GGGTATT
1 GGGTATT
39993451 GAGATGCATA
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.17, C:0.18, G:0.24, T:0.41
Consensus pattern (27 bp):
GGGTATTTCGGTCATTTTACCCTTCGG
Found at i:39993500 original size:23 final size:23
Alignment explanation
Indices: 39993462--39993512 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
39993452 AGATGCATAT
* *
39993462 TGTAATATCCCTAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
39993485 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
39993508 AGTAA
1 TGTAA
39993513 GAAAGTAGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.29
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:40004263 original size:6 final size:6
Alignment explanation
Indices: 40004252--40004276 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40004242 AAAAAATAAG
40004252 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
40004277 CTCCTCTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:40006258 original size:54 final size:56
Alignment explanation
Indices: 40006195--40006314 Score: 151
Period size: 56 Copynumber: 2.2 Consensus size: 56
40006185 ACACCCATCA
40006195 GTCTGGGACA-TGGCATTTTGGCAC-C-GA-GATGAGAGGGTTCCCATG-TAAGACCAT
1 GTCTGGGACATTGGCA-TTTGGCACTCGGAGGATGAGA-GG-TCCCATGTTAAGACCAT
* *
40006249 GTCTGGGACATTGGCATTTGGCACTCGGAGGGTGAGAGGTCCCATGTTAAGACTAT
1 GTCTGGGACATTGGCATTTGGCACTCGGAGGATGAGAGGTCCCATGTTAAGACCAT
*
40006305 GTCTAGGACA
1 GTCTGGGACA
40006315 NNNNNNNNNN
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
54 18 0.31
55 13 0.22
56 21 0.36
57 6 0.10
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (56 bp):
GTCTGGGACATTGGCATTTGGCACTCGGAGGATGAGAGGTCCCATGTTAAGACCAT
Found at i:40023356 original size:6 final size:6
Alignment explanation
Indices: 40023302--40023358 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
40023292 AAAAAATTCC
* * *
40023302 TATTAT TATTAT TATTATT TATTTT TACTATTT TA-TTT TATTTT CATTTT
1 TATTTT TATTTT TATT-TT TATTTT TA-T-TTT TATTTT TATTTT TATTTT
40023352 TATTTT T
1 TATTTT T
40023359 GCAGGAAAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
5 5 0.11
6 28 0.64
7 6 0.14
8 5 0.11
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.74
Consensus pattern (6 bp):
TATTTT
Found at i:40025835 original size:50 final size:50
Alignment explanation
Indices: 40025754--40026223 Score: 575
Period size: 50 Copynumber: 9.4 Consensus size: 50
40025744 ACACCCATCA
40025754 GTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCAT
1 GTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCAT
* * *
40025804 GTCTGGGACATGGCATTGGCACTGAGGTGAGAGGTCCCATGTAAGACTAT
1 GTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCAT
* *
40025854 GTCTAGGACATGGCCTTGGCACCGAGATGAGAGGTCCCATGTAAGACCAT
1 GTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCAT
* * *
40025904 GTCCGGGACATGGCGTTGGCATCGAGATGAGAGGTCCCATGTAAGACCAT
1 GTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCAT
* * *
40025954 GTCTGGGACATGGCATTTGCACCGAGATGAGCGGTCCAATGTAAGACCAT
1 GTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCAT
* * *
40026004 GTTTGGGACATGGCGTTGGCACCGAGATGAGAGGTTCCATGTAAGACCAT
1 GTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCAT
* * * * **
40026054 GTCTAGGACACGGCATTGGCACCGGGATGAGAGGCCCCCCGTAAGACCAT
1 GTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCAT
* * * ** * *
40026104 GTTTGGGACATGGCATGGGCACCGATATGAGAACTCTCATATAAGACCAT
1 GTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCAT
* * * * * * ** *
40026154 ATCTAGGATATGGCATTGGCA--GTACAGGAAACATCTCATGTAAGACCAT
1 GTCTGGGACATGGCATTGGCACCG-AGATGAGAGGTCCCATGTAAGACCAT
* *
40026203 GTTTGGGACATGGCTTTGGCA
1 GTCTGGGACATGGCATTGGCA
40026224 TGTTATTATC
Statistics
Matches: 357, Mismatches: 62, Indels: 3
0.85 0.15 0.01
Matches are distributed among these distances:
48 1 0.00
49 36 0.10
50 320 0.90
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (50 bp):
GTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCAT
Found at i:40027959 original size:30 final size:30
Alignment explanation
Indices: 40027898--40027961 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
40027888 TTGCCCAAGA
* **
40027898 GTAAATACTCAAAATTTGAGGGATTAAAGT
1 GTAAATACTCAAAATTTGAAGGACCAAAGT
*
40027928 GTAAATAC-GAAAATTTGAAGGACCAATAGT
1 GTAAATACTCAAAATTTGAAGGACCAA-AGT
40027958 GTAA
1 GTAA
40027962 CTATTTTAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 14 0.48
30 15 0.52
ACGTcount: A:0.45, C:0.08, G:0.20, T:0.27
Consensus pattern (30 bp):
GTAAATACTCAAAATTTGAAGGACCAAAGT
Found at i:40033252 original size:16 final size:17
Alignment explanation
Indices: 40033225--40033259 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
40033215 ATACCCCTTT
40033225 CACCTATTCATTCAACA
1 CACCTATTCATTCAACA
*
40033242 CACCT-TTCATTCCACA
1 CACCTATTCATTCAACA
40033258 CA
1 CA
40033260 TCTCTCTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.31, C:0.40, G:0.00, T:0.29
Consensus pattern (17 bp):
CACCTATTCATTCAACA
Found at i:40058091 original size:12 final size:13
Alignment explanation
Indices: 40058067--40058095 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
40058057 GGGCTATAAC
40058067 TATTGCATTTATT
1 TATTGCATTTATT
40058080 TATTGC-TTTATT
1 TATTGCATTTATT
40058092 TATT
1 TATT
40058096 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:40063674 original size:39 final size:38
Alignment explanation
Indices: 40063471--40063690 Score: 156
Period size: 40 Copynumber: 5.6 Consensus size: 38
40063461 TGAATGCTGT
* * * * *
40063471 CCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATAT
1 CCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTA-AA
** * * *
40063511 CCGGACTAAGAT-CTGAAGGCATTTGTGCGAGTTATTAATT
1 CCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* * *
40063551 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAA-A
* *
40063591 CCGGGTTAAGTCCCAAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACT-AAA
**
40063630 TCCGGGTTAAGTCCCGAAGGCATTGTATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTA-AA
* *
40063670 CCGGGCTATGTCCCGAAGGCA
1 CCGGGTTAAGTCCCGAAGGCA
40063691 CTTGAACGAG
Statistics
Matches: 147, Mismatches: 23, Indels: 21
0.77 0.12 0.11
Matches are distributed among these distances:
39 33 0.22
40 106 0.72
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:40070236 original size:22 final size:21
Alignment explanation
Indices: 40070211--40070254 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
40070201 TGATAAACTT
40070211 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
40070233 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
40070254 T
1 T
40070255 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:40074611 original size:50 final size:51
Alignment explanation
Indices: 40074548--40074724 Score: 205
Period size: 50 Copynumber: 3.4 Consensus size: 51
40074538 CAATGTCATA
* **
40074548 TCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGTCC-ATTCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGTCCAATTCCATG
** * *
40074598 TCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTG-CCAACTCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGTCCAATTCCATG
** *
40074648 TCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TCGGTG-T-CCAATTCCATG
40074704 TCCCAGACATGGTCTTACATG
1 TCCCAGACATGGTCTTACATG
40074725 AGATCTCTTT
Statistics
Matches: 106, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
49 2 0.02
50 70 0.66
53 4 0.04
56 30 0.28
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (51 bp):
TCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGTCCAATTCCATG
Found at i:40089886 original size:16 final size:16
Alignment explanation
Indices: 40089865--40089896 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
40089855 TTGATAAAAG
40089865 TTATACAGGAAATGAT
1 TTATACAGGAAATGAT
40089881 TTATACAGGAAATGAT
1 TTATACAGGAAATGAT
40089897 GAAGTCTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
TTATACAGGAAATGAT
Found at i:40112708 original size:32 final size:32
Alignment explanation
Indices: 40112667--40112783 Score: 157
Period size: 32 Copynumber: 3.7 Consensus size: 32
40112657 GCGATGCTAA
40112667 TGATGGCTTTGTGCC-AGTCATAGTACCGTTAC
1 TGATGGCTTTGTGCCGA-TCATAGTACCGTTAC
**
40112699 TGATGGCTTTGTGTTGATCATAGTACCGTTAC
1 TGATGGCTTTGTGCCGATCATAGTACCGTTAC
*
40112731 TGATGGCTTTGTGCCGATCATATTACCGTTAC
1 TGATGGCTTTGTGCCGATCATAGTACCGTTAC
* *
40112763 CGATGG-TTGTGTGTCGATCAT
1 TGATGGCTT-TGTGCCGATCAT
40112784 TTCACTATTA
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
31 2 0.03
32 73 0.96
33 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.38
Consensus pattern (32 bp):
TGATGGCTTTGTGCCGATCATAGTACCGTTAC
Found at i:40112845 original size:32 final size:31
Alignment explanation
Indices: 40112667--40112847 Score: 150
Period size: 32 Copynumber: 5.7 Consensus size: 31
40112657 GCGATGCTAA
40112667 TGATGGCTTTGTGCC-AGTCATAGTACCGTTAC
1 TGATGGCTTTGTGCCGA-TCATA-TACCGTTAC
**
40112699 TGATGGCTTTGTGTTGATCATAGTACCGTTAC
1 TGATGGCTTTGTGCCGATCATA-TACCGTTAC
40112731 TGATGGCTTTGTGCCGATCATATTACCGTTAC
1 TGATGGCTTTGTGCCGATCATA-TACCGTTAC
* * * **
40112763 CGATGG-TTGTGTGTCGATCATTTCACTATTAC
1 TGATGGCTT-TGTGCCGATCATAT-ACCGTTAC
* * * * * * *
40112795 AGATTGCTGTGTGTCGGTCATATCACTGCTAC
1 TGATGGCTTTGTGCCGATCATAT-ACCGTTAC
*
40112827 TGATGGCTTTGTGCCGGTCAT
1 TGATGGCTTTGTGCCGATCAT
40112848 GATTCCTAGC
Statistics
Matches: 124, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
31 3 0.02
32 119 0.96
33 2 0.02
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.38
Consensus pattern (31 bp):
TGATGGCTTTGTGCCGATCATATACCGTTAC
Found at i:40118963 original size:54 final size:53
Alignment explanation
Indices: 40118904--40119024 Score: 138
Period size: 54 Copynumber: 2.2 Consensus size: 53
40118894 TGTCATCACC
* * * *
40118904 CGTGTAATTCACTGAGTTGCCCTAC-ATGCTCGTGTGCCAAGTCC-TGTGCTAGGT
1 CGTGTAACTCACTGAGTTG--CTACAATGCTCATGTG-CAAGGCCATGTGCCAGGT
* *
40118958 CGTGTAACTCTCTGAGTTGCTACATATGCTCATGTGCTAGGCCATGTGCCAGGT
1 CGTGTAACTCACTGAGTTGCTACA-ATGCTCATGTGCAAGGCCATGTGCCAGGT
40119012 CGTGTAACTCACT
1 CGTGTAACTCACT
40119025 AACTTGAAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
52 4 0.07
53 5 0.09
54 48 0.84
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.31
Consensus pattern (53 bp):
CGTGTAACTCACTGAGTTGCTACAATGCTCATGTGCAAGGCCATGTGCCAGGT
Found at i:40124906 original size:29 final size:29
Alignment explanation
Indices: 40124873--40125057 Score: 115
Period size: 29 Copynumber: 6.4 Consensus size: 29
40124863 TGGTCGACCA
* *
40124873 ATGAAAAGGGATAGCTTTGGTTATCGATT
1 ATGAAAAGGGATAGCTTCGATTATCGATT
**
40124902 ATGAAAACAGATAGCTTCGATTATCGATT
1 ATGAAAAGGGATAGCTTCGATTATCGATT
* * ** * *
40124931 ATGAAAAGGGAT-GGTGACGACCATCAACT
1 ATGAAAAGGGATAGCT-TCGATTATCGATT
* * ** ** *
40124960 ATGAAAATGGAT-GGTAAT-GACCATAAAAT
1 ATGAAAAGGGATAGCT--TCGATTATCGATT
*
40124989 ATGAAAAGGGATAGCTTCGATTATCAATT
1 ATGAAAAGGGATAGCTTCGATTATCGATT
* * ** *
40125018 ATGAAAAGGGATGGTTTCGACCATCGAAT
1 ATGAAAAGGGATAGCTTCGATTATCGATT
40125047 ATGAAAAGGGA
1 ATGAAAAGGGA
40125058 CAGTTACTAC
Statistics
Matches: 123, Mismatches: 29, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
28 3 0.02
29 118 0.96
30 2 0.02
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCGATTATCGATT
Found at i:40124992 original size:58 final size:58
Alignment explanation
Indices: 40124930--40125072 Score: 146
Period size: 58 Copynumber: 2.5 Consensus size: 58
40124920 GATTATCGAT
* *
40124930 TATGAAAAGGGAT-GGTGACGACCATCAACTATGAAAATGGATGGTAAT-GACCATAAAA
1 TATGAAAAGGGATAGCT-ACGACCATCAACTATGAAAAGGGATGGT-ATCGACCATAAAA
* ** * * **
40124988 TATGAAAAGGGATAGCTTCGATTATCAATTATGAAAAGGGATGGTTTCGACCATCGAA
1 TATGAAAAGGGATAGCTACGACCATCAACTATGAAAAGGGATGGTATCGACCATAAAA
* * *
40125046 TATGAAAAGGGACAGTTACTACCATCA
1 TATGAAAAGGGATAGCTACGACCATCA
40125073 TTTAGAACAC
Statistics
Matches: 68, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
57 1 0.01
58 65 0.96
59 2 0.03
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.24
Consensus pattern (58 bp):
TATGAAAAGGGATAGCTACGACCATCAACTATGAAAAGGGATGGTATCGACCATAAAA
Found at i:40142187 original size:23 final size:23
Alignment explanation
Indices: 40142157--40142202 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
40142147 GTGTACAAAG
**
40142157 AAAAAAAAAAAAATTATCAAAAA
1 AAAAAAAAAAAAAAGATCAAAAA
40142180 AAAAAAAAAAAAAAGATCAAAAA
1 AAAAAAAAAAAAAAGATCAAAAA
40142203 GGGAAAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.85, C:0.04, G:0.02, T:0.09
Consensus pattern (23 bp):
AAAAAAAAAAAAAAGATCAAAAA
Found at i:40142209 original size:24 final size:24
Alignment explanation
Indices: 40142157--40142202 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
40142147 GTGTACAAAG
*
40142157 AAAAAAAAAAAAATTATCAAAAAA
1 AAAAAAAAAAAAATGATCAAAAAA
40142181 AAAAAAAAAAAAA-GATCAAAAA
1 AAAAAAAAAAAAATGATCAAAAA
40142203 GGGAAAATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.85, C:0.04, G:0.02, T:0.09
Consensus pattern (24 bp):
AAAAAAAAAAAAATGATCAAAAAA
Found at i:40150001 original size:19 final size:19
Alignment explanation
Indices: 40149977--40150013 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
40149967 CAATTACTTA
40149977 GTTTTAACAACGAATTTAT
1 GTTTTAACAACGAATTTAT
40149996 GTTTTAACAACGAATTTA
1 GTTTTAACAACGAATTTA
40150014 AGTAAAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (19 bp):
GTTTTAACAACGAATTTAT
Found at i:40159758 original size:39 final size:39
Alignment explanation
Indices: 40159701--40159846 Score: 204
Period size: 39 Copynumber: 3.7 Consensus size: 39
40159691 ATGATATTTG
* * *
40159701 GAATTA-ATCTGGACTTAAGGTCCGCAGGCTATATGATG
1 GAATTATATCCGGACTTAAGGTCCGCAGGCTATATGCTA
*
40159739 GAATTATATCCAGACTTAAGGTCCGCAGGCTATATGCTA
1 GAATTATATCCGGACTTAAGGTCCGCAGGCTATATGCTA
* *
40159778 GAAATATATCCGGGCTTAAGGTCCGCAGGCTATATGCTA
1 GAATTATATCCGGACTTAAGGTCCGCAGGCTATATGCTA
* *
40159817 GAATTATAATTCGGACTTAAGGTTCGCAGG
1 GAATTAT-ATCCGGACTTAAGGTCCGCAGG
40159847 TTACGTGTAG
Statistics
Matches: 95, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
38 6 0.06
39 70 0.74
40 19 0.20
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (39 bp):
GAATTATATCCGGACTTAAGGTCCGCAGGCTATATGCTA
Found at i:40159874 original size:79 final size:78
Alignment explanation
Indices: 40159714--40159875 Score: 218
Period size: 79 Copynumber: 2.1 Consensus size: 78
40159704 TTAATCTGGA
* *
40159714 CTTAAGGTCCGCAGGCTATATGATGGAATTATATCCAGACTTAAGGTCCGCAGGCTATATGCTAG
1 CTTAAGGTCCGCAGGCTATATGATAGAATTATATCCAGACTTAAGGTCCGCAGGCTACATGCTAG
*
40159779 AAATATATCCGGG
66 AAATATATCCGAG
* * * * * *
40159792 CTTAAGGTCCGCAGGCTATATGCTAGAATTATAATTCGGACTTAAGGTTCGCAGGTTACGTG-TA
1 CTTAAGGTCCGCAGGCTATATGATAGAATTAT-ATCCAGACTTAAGGTCCGCAGGCTACATGCTA
40159856 GGAAATATATCCGAG
65 -GAAATATATCCGAG
40159871 CTTAA
1 CTTAA
40159876 AGTGTAGAAG
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
78 32 0.44
79 41 0.56
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (78 bp):
CTTAAGGTCCGCAGGCTATATGATAGAATTATATCCAGACTTAAGGTCCGCAGGCTACATGCTAG
AAATATATCCGAG
Found at i:40166408 original size:11 final size:12
Alignment explanation
Indices: 40166390--40166418 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
40166380 TGAGCATTCG
40166390 ACATTACTTATA
1 ACATTACTTATA
40166402 A-ATTACTTATA
1 ACATTACTTATA
40166413 ACATTA
1 ACATTA
40166419 GAAATGAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (12 bp):
ACATTACTTATA
Found at i:40167443 original size:39 final size:39
Alignment explanation
Indices: 40167383--40167598 Score: 254
Period size: 39 Copynumber: 5.5 Consensus size: 39
40167373 GCATGATATT
* *
40167383 TGGAATTA-ATCTGGACTTAAGGTCCGCAAGCTATATGC
1 TGGAATTATATCCGGACTTAAGGTCCGCAGGCTATATGC
* *
40167421 TGGAATTATATCCGAACTTAAGGTCCGCAGGCTATATGT
1 TGGAATTATATCCGGACTTAAGGTCCGCAGGCTATATGC
*
40167460 TGGAATTATATCCGGACTTAAGGTCCGTAGGCTATATGC
1 TGGAATTATATCCGGACTTAAGGTCCGCAGGCTATATGC
* * *
40167499 TGGAAATATATCTGGACTTAAGGTCCGCAGGCTATATGT
1 TGGAATTATATCCGGACTTAAGGTCCGCAGGCTATATGC
** ** * * **
40167538 TGGAATTATAATTTGGACTTAAGGTTTGTAGGTTACGTGC
1 TGGAATTAT-ATCCGGACTTAAGGTCCGCAGGCTATATGC
* *
40167578 TGGAAATATATCCGGGCTTAA
1 TGGAATTATATCCGGACTTAA
40167599 AGTTCCGAAG
Statistics
Matches: 152, Mismatches: 24, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
38 8 0.05
39 114 0.75
40 30 0.20
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (39 bp):
TGGAATTATATCCGGACTTAAGGTCCGCAGGCTATATGC
Found at i:40167510 original size:78 final size:78
Alignment explanation
Indices: 40167378--40167591 Score: 297
Period size: 78 Copynumber: 2.8 Consensus size: 78
40167368 AATATGCATG
* * *
40167378 ATAT-TTGGAATTA-ATCTGGACTTAAGGTCCGCAAGCTATATGCTGGAATTATATCCGAACTTA
1 ATATGTTGGAATTATATCTGGACTTAAGGTCCGTAGGCTATATGCTGGAAATATATCCGAACTTA
40167441 AGGTCCGCAGGCT
66 AGGTCCGCAGGCT
* * *
40167454 ATATGTTGGAATTATATCCGGACTTAAGGTCCGTAGGCTATATGCTGGAAATATATCTGGACTTA
1 ATATGTTGGAATTATATCTGGACTTAAGGTCCGTAGGCTATATGCTGGAAATATATCCGAACTTA
40167519 AGGTCCGCAGGCT
66 AGGTCCGCAGGCT
* ** * **
40167532 ATATGTTGGAATTATAATTTGGACTTAAGGTTTGTAGGTTACGTGCTGGAAATATATCCG
1 ATATGTTGGAATTAT-ATCTGGACTTAAGGTCCGTAGGCTATATGCTGGAAATATATCCG
40167592 GGCTTAAAGT
Statistics
Matches: 121, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
76 4 0.03
77 9 0.07
78 72 0.60
79 36 0.30
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (78 bp):
ATATGTTGGAATTATATCTGGACTTAAGGTCCGTAGGCTATATGCTGGAAATATATCCGAACTTA
AGGTCCGCAGGCT
Found at i:40171195 original size:81 final size:81
Alignment explanation
Indices: 40171060--40171222 Score: 267
Period size: 81 Copynumber: 2.0 Consensus size: 81
40171050 GTAACACCCT
40171060 TATCCGTATTCAACGTCAGAACAGAGTATAAGGCATTATCAGACTTATCACACAAACAAACATAC
1 TATCCGTATTCAACGTCAGAACAGAGTATAAGGCATTATCAGACTTATCACACAAACAAACATAC
40171125 AATTTCGGGCTATACA
66 AATTTCGGGCTATACA
* *
40171141 TATCCGTATTCAACGTCAGAATAG-GT-TACGAGGCATTATCGGACTTATCACACAAACAAACAT
1 TATCCGTATTCAACGTCAGAACAGAGTATA--AGGCATTATCAGACTTATCACACAAACAAACAT
*
40171204 ACAATTTCGGGTTATACA
64 ACAATTTCGGGCTATACA
40171222 T
1 T
40171223 TTGCGTCCAA
Statistics
Matches: 77, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
79 2 0.03
80 2 0.03
81 73 0.95
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.26
Consensus pattern (81 bp):
TATCCGTATTCAACGTCAGAACAGAGTATAAGGCATTATCAGACTTATCACACAAACAAACATAC
AATTTCGGGCTATACA
Found at i:40182030 original size:26 final size:27
Alignment explanation
Indices: 40181994--40182046 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
40181984 TGTCAGCTAG
* *
40181994 TGAAATTTTAA-TGTTCGAATGTATGC
1 TGAAATTTTAAGTGTCCGAATGCATGC
*
40182020 TGAATTTTTAAGTGTCCGAATGCATGC
1 TGAAATTTTAAGTGTCCGAATGCATGC
40182047 CAGAATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (27 bp):
TGAAATTTTAAGTGTCCGAATGCATGC
Found at i:40187517 original size:40 final size:40
Alignment explanation
Indices: 40187458--40187669 Score: 248
Period size: 40 Copynumber: 5.3 Consensus size: 40
40187448 CATTTGAATG
* *
40187458 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
40187498 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * *
40187538 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * * * * *
40187578 TTATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
40187618 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
40187658 ATATCC-GGCTAA
1 ATATCCGGGCTAA
40187670 ATTCCGAAGA
Statistics
Matches: 140, Mismatches: 30, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
39 8 0.06
40 130 0.93
41 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:40187598 original size:80 final size:79
Alignment explanation
Indices: 40187462--40187678 Score: 310
Period size: 80 Copynumber: 2.7 Consensus size: 79
40187452 TGAATGATAT
* *
40187462 CCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCC-GGCTAAGATCCGAAGGCATTTG
* *
40187527 TGCGAGTTGCTATAC
65 TGCGAGTTACTAAAC
*
40187542 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGACTAAGATCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGG-CTAAGATCCGAAGGCATTTG
*
40187607 TGCGAGTTACTAAAT
65 TGCGAGTTACTAAAC
* * * *
40187622 CCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTTATATCCGGCTAA-ATTCCGAAG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGCTAAGA-TCCGAAG
40187679 AAACTTGGGT
Statistics
Matches: 124, Mismatches: 11, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
78 1 0.01
79 13 0.10
80 110 0.89
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (79 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGCTAAGATCCGAAGGCATTTGT
GCGAGTTACTAAAC
Found at i:40195292 original size:1 final size:1
Alignment explanation
Indices: 40195286--40195347 Score: 124
Period size: 1 Copynumber: 62.0 Consensus size: 1
40195276 ATGTGCTAGA
40195286 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
40195348 GAAGCCATGA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:40197087 original size:55 final size:54
Alignment explanation
Indices: 40196992--40197141 Score: 149
Period size: 55 Copynumber: 2.8 Consensus size: 54
40196982 TTACTTTGTT
* ** * *
40196992 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAATGTGCGAGTTGACTAT-ATAGCACTAAGTGTGCGAATTGACCACGCG
* * * * ** *
40197046 GCACTAAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAATGTGCGAG-TTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
* *
40197101 GCACTAAATGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCG
40197142 GGCTCAATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 37 0.47
55 42 0.53
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
Found at i:40197104 original size:27 final size:27
Alignment explanation
Indices: 40196965--40197141 Score: 153
Period size: 27 Copynumber: 6.6 Consensus size: 27
40196955 TTAATTGTAC
40196965 AGCACTAAGTGTGCGATTT-ACTT-TGT
1 AGCACTAAGTGTGCGATTTGA-TTATGT
* ** *
40196991 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGATTATGT
* ** *
40197017 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGATTATGT
* * *
40197045 GGCACTAAGTGTGCGGGTTTGACTATGT
1 AGCACTAAGTGTGC-GATTTGATTATGT
*
40197073 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGATTATGT
* * * *
40197100 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGATTATGT
*
40197127 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40197142 GGCTCAATAT
Statistics
Matches: 121, Mismatches: 25, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
26 17 0.14
27 82 0.68
28 22 0.18
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGATTATGT
Found at i:40197132 original size:82 final size:81
Alignment explanation
Indices: 40196962--40197143 Score: 197
Period size: 82 Copynumber: 2.2 Consensus size: 81
40196952 GGATTAATTG
* * * *
40196962 TACAGCACTAAGTGTGC-GATTTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGGGTTTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
*
40197026 GTGTGCGAATTGACCA
66 ATGTGCGAATTGACCA
* * ** *
40197042 TGCGGCACTAAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGGGTTT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
40197106 AAATGTGCGAGTTGATTA
64 AAATGTGCGAATTGACCA
* *
40197124 TATAGCACTGAGTGTGCGGG
1 TACAGCACTAAGTGTGCGGG
40197144 CTCAATATAC
Statistics
Matches: 82, Mismatches: 17, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
80 15 0.18
81 5 0.06
82 62 0.76
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGGGTTTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
ATGTGCGAATTGACCA
Found at i:40204999 original size:55 final size:54
Alignment explanation
Indices: 40204904--40205053 Score: 149
Period size: 55 Copynumber: 2.8 Consensus size: 54
40204894 CTACTTTGTT
* ** * *
40204904 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAATGTGCGAGTTGACTAT-ATAGCACTAAGTGTGCGAATTGACCACGCG
* * * * ** *
40204958 GCACTAAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAATGTGCGAG-TTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
* *
40205013 GCACTAAATGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCG
40205054 GGCTCAATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 37 0.47
55 42 0.53
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
Found at i:40205016 original size:27 final size:27
Alignment explanation
Indices: 40204876--40205053 Score: 146
Period size: 27 Copynumber: 6.6 Consensus size: 27
40204866 TAAATTGTAC
40204876 AGCACTAAGTGTGCGATTCT-ACTT-TGT
1 AGCACTAAGTGTGCGATT-TGA-TTATGT
* ** *
40204903 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGATTATGT
* ** *
40204929 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGATTATGT
* * *
40204957 GGCACTAAGTGTGCGGGTTTGACTATGT
1 AGCACTAAGTGTGC-GATTTGATTATGT
*
40204985 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGATTATGT
* * * *
40205012 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGATTATGT
*
40205039 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40205054 GGCTCAATAT
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 97 0.80
28 22 0.18
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGATTATGT
Found at i:40205017 original size:82 final size:81
Alignment explanation
Indices: 40204877--40205032 Score: 190
Period size: 82 Copynumber: 1.9 Consensus size: 81
40204867 AAATTGTACA
* * * *
40204877 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
40204942 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
40204958 GCACTAAGTGTGCGGGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAA
1 GCACTAAGTGTGC-GATTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAA
*
40205021 TGTGCGAGTTGA
63 TGTGCGAATTGA
40205033 TTATATAGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
81 15 0.24
82 48 0.76
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:40206973 original size:78 final size:79
Alignment explanation
Indices: 40206755--40207016 Score: 286
Period size: 79 Copynumber: 3.3 Consensus size: 79
40206745 TTGAATGATG
* * *
40206755 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGCTAAGACCCGAAGGCATTTGTGCGAGA-T-ACTAA-ATCCGGGCTAAG-TCCGAAGGCA
* *
40206816 TTTGTGTGAGATACTAAA
62 TTTGTGCGAGATACTAAT
* * * *
40206834 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTG
1 TCCGGGCTAAGACCCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGTCCGAAGGCATTTG
40206899 TGCGAGATACTAAT
66 TGCGAGATACTAAT
* * *
40206913 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCTGGGTTAAGTCCGAAGGCATTTG
1 TCCGGGCTAAGACCCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGTCCGAAGGCATTTG
40206977 TGCGA-ATTACT-AT
66 TGCGAGA-TACTAAT
* * *
40206990 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGACCCGAAGGCATTTG
40207017 AACGAGGAGC
Statistics
Matches: 158, Mismatches: 18, Indels: 14
0.83 0.09 0.07
Matches are distributed among these distances:
77 3 0.02
78 65 0.41
79 67 0.42
80 12 0.08
81 10 0.06
82 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
TCCGGGCTAAGACCCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGTCCGAAGGCATTTG
TGCGAGATACTAAT
Found at i:40206975 original size:39 final size:39
Alignment explanation
Indices: 40206755--40207016 Score: 293
Period size: 39 Copynumber: 6.6 Consensus size: 39
40206745 TTGAATGATG
*
40206755 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGA-T-ACTAA-A
* *
40206794 TCCGGACTAAGATCCGAAGGCATTTGTGTGAGATACTAAA
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGATACTAAA
* *
40206834 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGATACTAAA
* *
40206874 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAA
* *
40206913 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAA
* *
40206952 TCTGGGTTAAGTCCGAAGGCATTTGTGCGA-ATTACTATAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGA-TACTA-AA
*
40206992 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
40207017 AACGAGGAGC
Statistics
Matches: 199, Mismatches: 16, Indels: 15
0.87 0.07 0.07
Matches are distributed among these distances:
39 122 0.61
40 67 0.34
41 9 0.05
42 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:40207038 original size:78 final size:76
Alignment explanation
Indices: 40206756--40207049 Score: 258
Period size: 79 Copynumber: 3.7 Consensus size: 76
40206746 TGAATGATGT
* *
40206756 CCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAG-GACTATATCCGG-CTAAG-TCCGAAGGCATTT
*
40206819 GTGTGAGATACTAAA
62 GTGCGAGATACTAAA
* * *
40206834 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATTCCGGGCTAAGCCCGAAGGCATT
1 -CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAG-GACTATA-TCC-GGCTAAGTCCGAAGGCATT
*
40206897 TGTGCGAGATACTAATT
61 TGTGCGAGATACTAA-A
* * * *
40206914 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCTGGGTTAAGTCCGAAGGCATTTGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-GACTATATC-CGGCTAAGTCCGAAGGCATTTGT
40206978 GCGA-ATTACTATAA
64 GCGAGA-TACTA-AA
* ** * *
40206992 CCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTATATCCGGTTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGGA-CTATATCCGGCT-AAGTCCGAAGG
40207050 TACGTGATTT
Statistics
Matches: 180, Mismatches: 21, Indels: 28
0.79 0.09 0.12
Matches are distributed among these distances:
77 1 0.01
78 69 0.38
79 88 0.49
80 14 0.08
81 8 0.04
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (76 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGGACTATATCCGGCTAAGTCCGAAGGCATTTGTGC
GAGATACTAAA
Found at i:40213614 original size:13 final size:13
Alignment explanation
Indices: 40213596--40213620 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40213586 CCGAAACTAG
40213596 AAAGAAAAAAAAC
1 AAAGAAAAAAAAC
40213609 AAAGAAAAAAAA
1 AAAGAAAAAAAA
40213621 ATGCTCATCC
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:0.88, C:0.04, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAAAC
Found at i:40214756 original size:39 final size:39
Alignment explanation
Indices: 40214700--40214925 Score: 178
Period size: 39 Copynumber: 5.7 Consensus size: 39
40214690 TTGAATGATG
*
40214700 TCCGGGCTAAG-TCCCGAAGGC-TTGTGCTAAG-TGAC-AATA
1 TCCGGACTAAGAT-CCGAAGGCATTGTGC-AAGAT-ACTAA-A
*
40214739 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAA
1 TCCGGACTAAGATCCGAAGGCA-TTGTGCAAGATACTAAA
* *
40214779 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGACTAAGATCCGAAGGCA-TTGTGCAAGATACTAAA
* * * *
40214819 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGACTAAGATCCGAAGGCA-TTGTGCAAGATACTAAA
* * * *
40214858 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCA-TTGTGCAAGATACTAAA
* **
40214897 TCTGGGTTAAG-TCCCGAAGGCATTTGTGC
1 TCCGGACTAAGAT-CCGAAGGCA-TTGTGC
40214926 GAATTACTAT
Statistics
Matches: 171, Mismatches: 10, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
39 91 0.53
40 71 0.42
41 9 0.05
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (39 bp):
TCCGGACTAAGATCCGAAGGCATTGTGCAAGATACTAAA
Found at i:40214788 original size:40 final size:39
Alignment explanation
Indices: 40214700--40214962 Score: 286
Period size: 40 Copynumber: 6.6 Consensus size: 39
40214690 TTGAATGATG
*
40214700 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGA-T-ACTAA-A
*
40214739 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAA
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGATACTAAA
* *
40214779 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGATACTAAA
* *
40214819 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAA
* *
40214858 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAA
* *
40214897 TCTGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGA-TACTA-AA
* *
40214938 -CCTGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
40214963 AACGAGGAGC
Statistics
Matches: 201, Mismatches: 15, Indels: 15
0.87 0.06 0.06
Matches are distributed among these distances:
39 91 0.45
40 97 0.48
41 12 0.06
42 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:40214835 original size:79 final size:79
Alignment explanation
Indices: 40214738--40214962 Score: 280
Period size: 79 Copynumber: 2.8 Consensus size: 79
40214728 AAGTGACAAT
* *
40214738 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCAT
1 ATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAATCCGGACTAAG-CCCGAAGGCAT
40214802 TTGTGCGAGATACTAA
64 TTGTGCGAGATACTAA
* * *
40214818 TTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGCCCGAAGGCATTT
*
40214882 GTGCGAGTTACTAA
66 GTGCGAGATACTAA
* * *
40214896 ATCTGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACTATAA-CCTGG-CTATGTCCCGAAGGC
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTA-AATCC-GGACTAAG-CCCGAAGGC
40214958 ATTTG
62 ATTTG
40214963 AACGAGGAGC
Statistics
Matches: 128, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
78 35 0.27
79 66 0.52
80 27 0.21
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.25
Consensus pattern (79 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGCCCGAAGGCATTT
GTGCGAGATACTAA
Found at i:40214984 original size:79 final size:79
Alignment explanation
Indices: 40214752--40214995 Score: 216
Period size: 79 Copynumber: 3.1 Consensus size: 79
40214742 GGACTAAGAT
* * **
40214752 CCGAAGGCATTTGTGCGAGATACTAA-ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGAT-AC
1 CCGAAGGCATTTGTGCGAGATACTAATA-CCGGGCTAAG-CCCGAAGGCATTTGAACGAG-TGAC
* *
40214815 TAATTC-CGGGCTAAG-C
63 TAAATCTC-GGTTAAGTC
* ** *
40214831 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
*
40214896 ATCTGGGTTAAGTC
66 ATCTCGGTTAAGTC
* *
40214910 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCTGGCTATGTCCCGAAGGCATTTGAACGAG-GAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-
* * *
40214972 CTATATC-CGGTTAAATT
62 CTAAATCTCGGTTAAGTC
40214989 CCGAAGG
1 CCGAAGG
40214996 TACGTGATTT
Statistics
Matches: 141, Mismatches: 16, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
77 1 0.01
78 35 0.25
79 81 0.57
80 24 0.17
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCTCGGTTAAGTC
Found at i:40228656 original size:50 final size:50
Alignment explanation
Indices: 40228585--40228748 Score: 229
Period size: 50 Copynumber: 3.3 Consensus size: 50
40228575 GGGAATGAGA
**
40228585 TCCCATGTAAGACCAACTCTGGGACATGGCGTAGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTAGGCACCGAGATGAGAGG
* *
40228635 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTAGGCACCGAGATGAGAGG
** * * * **
40228685 TCCCCCGTAAGACCATGTCTGGGACATGGCATAGGCTCCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTAGGCACCGAGATGAGAGG
40228735 TCCCATGTAAGACC
1 TCCCATGTAAGACC
40228749 TTATCTGGAA
Statistics
Matches: 99, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 99 1.00
ACGTcount: A:0.27, C:0.26, G:0.29, T:0.19
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCGTAGGCACCGAGATGAGAGG
Found at i:40228771 original size:100 final size:100
Alignment explanation
Indices: 40228591--40228771 Score: 236
Period size: 100 Copynumber: 1.8 Consensus size: 100
40228581 GAGATCCCAT
* ** *
40228591 GTAAGACCAACTCTGGGACATGGCGTAGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTG
1 GTAAGACCAACTCTGGGACATGGCATAGGCACCGAGATGAGAACTCCCATGTAAGACCATATCTG
* * **
40228656 GGACATGGCGTTGGCACCAAGATGAGAGGTCCCCC
66 GAACATCGCACTGGCACCAAGATGAGAGGTCCCCC
** * * *
40228691 GTAAGACCATGTCTGGGACATGGCATAGGCTCCGATATGAGAACTCCCATGTAAGACCTTATCTG
1 GTAAGACCAACTCTGGGACATGGCATAGGCACCGAGATGAGAACTCCCATGTAAGACCATATCTG
*
40228756 GAATATCGCACTGGCA
66 GAACATCGCACTGGCA
40228772 GTACAGAAAA
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
100 67 1.00
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (100 bp):
GTAAGACCAACTCTGGGACATGGCATAGGCACCGAGATGAGAACTCCCATGTAAGACCATATCTG
GAACATCGCACTGGCACCAAGATGAGAGGTCCCCC
Found at i:40230798 original size:50 final size:50
Alignment explanation
Indices: 40230648--40230930 Score: 293
Period size: 50 Copynumber: 5.7 Consensus size: 50
40230638 ATAATAAAAA
* * * ** *
40230648 GCCAAAGCCATGTGCCAGACATGGTCTTACATGGGA--TGTTTTCT-GTATT
1 GCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG--GT
* * * * * ** *
40230697 GCCAATGCCATATCCTAGATATGGTCTTACATAGGATTTCTCATATCGGT
1 GCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGT
* * * * ** *
40230747 GCCCATGCTATCTCCCAGACATGGTCTTACGGGGGACCTCTCATCTGGGT
1 GCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGT
* *
40230797 GCGAACACCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGT
1 GCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGT
* * *
40230847 GCCAATGCCATGTCCCAGACATGGTCCTACATGGGACCTCTCATCTTGGT
1 GCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGT
40230897 GCCAACGCCATGTCCCAGACATGGTCTTACATGG
1 GCCAACGCCATGTCCCAGACATGGTCTTACATGG
40230931 CTTACATATT
Statistics
Matches: 192, Mismatches: 39, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
49 30 0.16
50 157 0.82
51 4 0.02
52 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.28
Consensus pattern (50 bp):
GCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGT
Found at i:40235302 original size:50 final size:50
Alignment explanation
Indices: 40235238--40235803 Score: 789
Period size: 50 Copynumber: 11.4 Consensus size: 50
40235228 ATGCCATATT
* ** * * * *
40235238 CCAGATATGGTCTTACATGGGAGTTCTCATATCAGTGCCCATGCCATGTC
1 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
** * * *
40235288 AAAGACATGGTCTTAC-GGGGACCTCTCATCTCGGTGCCAATGCCACGTC
1 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
* * * *
40235337 CCAAACATAGTCTTACATGAGACCTCTCATCTCGGTGCCAATGCCATGTC
1 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
*
40235387 CCAGACATGGTCTTCCATGGGACCTCTCATCTCGGTGCC-ACGCCATGT-
1 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
* *
40235435 CCAGACATGGTCTTACA-GGGACCTCTCATCTCAGCGCCAACGCCATGTC
1 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
* *
40235484 CCAGACATGGTCTTACATGAGACCTCTCATCTCGGTGCCAATGCCATGTC
1 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
* * * **
40235534 CCAAACATGCTCTTACATGGGACCTCTCATCTCGATGCCAACGCTGTGTC
1 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
*
40235584 CCAAACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
1 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
* * * *
40235634 CCAAACATGGTCTTACGTGGGACCTCTCATCTCGGTGCCAACGCTATATC
1 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
* * *
40235684 GCAGACATGATCTTACATGGGACCTCTCATCTCGGTGCCAACGCCAAGTC
1 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
*
40235734 CCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGCCATGTC
1 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
40235784 CCAGACATGGTCTTACATGG
1 CCAGACATGGTCTTACATGG
40235804 CTCACATATT
Statistics
Matches: 458, Mismatches: 54, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
47 19 0.04
48 25 0.05
49 63 0.14
50 351 0.77
ACGTcount: A:0.22, C:0.32, G:0.21, T:0.25
Consensus pattern (50 bp):
CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
Found at i:40235594 original size:100 final size:100
Alignment explanation
Indices: 40235173--40235803 Score: 769
Period size: 100 Copynumber: 6.4 Consensus size: 100
40235163 TGATAATAAC
* * ** * * *
40235173 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA--TGTTTTCT-GTATTTCCAATGCCAT
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG--GTGCCAACGCCAT
* * * * ** *
40235235 ATTCCAGATATGGTCTTACATGGGAGTTCTCATATC-
64 GTCCCAAACATGGTCTTACATGGGACCTCTCATCTCG
* * ** * * *
40235271 AGTGCCCATGCCATGTCAAAGACATGGTCTTAC-GGGGACCTCTCATCTCGGTGCCAATGCCACG
1 A-TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
* *
40235335 TCCCAAACATAGTCTTACATGAGACCTCTCATCTCG
65 TCCCAAACATGGTCTTACATGGGACCTCTCATCTCG
* * *
40235371 GTGCCAATGCCATGTCCCAGACATGGTCTTCCATGGGACCTCTCATCTCGGTGCC-ACGCCATGT
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGT
*
40235435 -CCAGACATGGTCTTACA-GGGACCTCTCATCTC-
66 CCCAAACATGGTCTTACATGGGACCTCTCATCTCG
* * *
40235467 AGCGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGGTGCCAATGCCATG
1 A-TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
*
40235532 TCCCAAACATGCTCTTACATGGGACCTCTCATCTCG
65 TCCCAAACATGGTCTTACATGGGACCTCTCATCTCG
** *
40235568 ATGCCAACGCTGTGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGT
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGT
*
40235633 CCCAAACATGGTCTTACGTGGGACCTCTCATCTCG
66 CCCAAACATGGTCTTACATGGGACCTCTCATCTCG
* * * * * *
40235668 GTGCCAACGCTATATCGCAGACATGATCTTACATGGGACCTCTCATCTCGGTGCCAACGCCAAGT
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGT
*
40235733 CCCAGACATGGTCTTACATGGGACCTCTCATCTC-
66 CCCAAACATGGTCTTACATGGGACCTCTCATCTCG
40235767 AGTGCCAACGCCATGTCCCAGACATGGTCTTACATGG
1 A-TGCCAACGCCATGTCCCAGACATGGTCTTACATGG
40235804 CTCACATATT
Statistics
Matches: 460, Mismatches: 61, Indels: 22
0.85 0.11 0.04
Matches are distributed among these distances:
97 64 0.14
98 28 0.06
99 113 0.25
100 253 0.55
101 2 0.00
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (100 bp):
ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGT
CCCAAACATGGTCTTACATGGGACCTCTCATCTCG
Found at i:40238294 original size:8 final size:8
Alignment explanation
Indices: 40238281--40238305 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
40238271 ATATATACTA
40238281 AATAAAAT
1 AATAAAAT
40238289 AATAAAAT
1 AATAAAAT
40238297 AATAAAAT
1 AATAAAAT
40238305 A
1 A
40238306 TGTTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:40244930 original size:58 final size:53
Alignment explanation
Indices: 40244817--40245012 Score: 194
Period size: 50 Copynumber: 3.8 Consensus size: 53
40244807 GACATTAAGG
* *
40244817 GAATGAGA--TCCCATGTAAGACCATGTCTGGGACATGG-ATTGACATCACTATTGA
1 GAATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C-C-A-TGA
* *
40244871 GATTATGAGAGGTCCCATGTAAGACCATGTCTAGGATATGGCGTTGGCACC--GA
1 GA--ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCATGA
* *
40244924 G-ATGAGAGGTCCCATGTAAGACTATGTCTGGGACATGGCGTTGGAACC--GA
1 GAATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCATGA
** *
40244974 G-ATGAGAGGTCCCCCGTAAGACCATGTATGGGACATGGC
1 GAATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
40245013 ATGAGCACCG
Statistics
Matches: 125, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
50 80 0.64
53 3 0.02
54 2 0.02
56 6 0.05
57 1 0.01
58 28 0.22
59 5 0.04
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (53 bp):
GAATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCATGA
Found at i:40245056 original size:50 final size:50
Alignment explanation
Indices: 40244875--40245048 Score: 233
Period size: 50 Copynumber: 3.5 Consensus size: 50
40244865 TATTGAGATT
* *
40244875 ATGAGAGGTCCCATGTAAGACCATGTCTAGGATATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
* *
40244925 ATGAGAGGTCCCATGTAAGACTATGTCTGGGACATGGCGTTGGAACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
** * * *
40244975 ATGAGAGGTCCCCCGTAAGACCATGTATGGGACATGGC-ATGAGCACCGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTG-GCACCGAG
**
40245025 ATGAGAACTCCCATGTAAGACCAT
1 ATGAGAGGTCCCATGTAAGACCAT
40245049 ATTTGGGATA
Statistics
Matches: 108, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
49 2 0.02
50 106 0.98
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
Found at i:40245332 original size:12 final size:12
Alignment explanation
Indices: 40245315--40245353 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
40245305 ATGAGTTATT
40245315 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
40245327 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
40245339 TAAGTGAGTAAG
1 TAAGTAAGCAAG
40245351 TAA
1 TAA
40245354 AAAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:40253513 original size:20 final size:19
Alignment explanation
Indices: 40253484--40253521 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
40253474 AGTTAGTTAC
40253484 TAAATGCCTATATGGCATT
1 TAAATGCCTATATGGCATT
40253503 TAAAGTGCCTATATGGCAT
1 TAAA-TGCCTATATGGCAT
40253522 ATTGGTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (19 bp):
TAAATGCCTATATGGCATT
Found at i:40256461 original size:37 final size:37
Alignment explanation
Indices: 40256331--40256462 Score: 95
Period size: 37 Copynumber: 3.6 Consensus size: 37
40256321 AGCACAGTAA
* * * * *
40256331 TCCATCCAAAGACACGCCAAATGCTCAGAAGATCTCA-
1 TCCAACCAAAAACACGCCAAATGCTCCGAAAAGCT-AG
* * * ** *
40256368 TCCACCCGATAACATACCAATTGCTCCGAAAAGCTAG
1 TCCAACCAAAAACACGCCAAATGCTCCGAAAAGCTAG
* * *
40256405 TCCAACCAAAAACATGCCAAATGCTGCGAAGAGCTAG
1 TCCAACCAAAAACACGCCAAATGCTCCGAAAAGCTAG
* * *
40256442 TCCAATCGAAAGCACGCCAAA
1 TCCAACCAAAAACACGCCAAA
40256463 ATAGGGAGTA
Statistics
Matches: 73, Mismatches: 21, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
36 1 0.01
37 72 0.99
ACGTcount: A:0.39, C:0.31, G:0.15, T:0.15
Consensus pattern (37 bp):
TCCAACCAAAAACACGCCAAATGCTCCGAAAAGCTAG
Found at i:40258346 original size:16 final size:16
Alignment explanation
Indices: 40258325--40258355 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
40258315 TGAAGAAATA
40258325 TTTAAAATTATTATTT
1 TTTAAAATTATTATTT
40258341 TTTAAAATTATTATT
1 TTTAAAATTATTATT
40258356 AAAATAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTAAAATTATTATTT
Found at i:40258409 original size:59 final size:58
Alignment explanation
Indices: 40258346--40258462 Score: 159
Period size: 59 Copynumber: 2.0 Consensus size: 58
40258336 TATTTTTTAA
*
40258346 AATTATTATTAAA-A-TAA-AATTGAAATATTAAATACTTTATTAAAATTATAAATTATATT
1 AATTA-TATTAAATATTAATAATT-AAATAATAAATA-TTTATTAAAATTATAAA-TATATT
*
40258405 AATTATATTAAATATTAATAATTTAATAATAAATATTTATTAAAATTATAAATATATT
1 AATTATATTAAATATTAATAATTAAATAATAAATATTTATTAAAATTATAAATATATT
40258463 CAATATCAGA
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
58 13 0.25
59 23 0.43
60 13 0.25
61 4 0.08
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (58 bp):
AATTATATTAAATATTAATAATTAAATAATAAATATTTATTAAAATTATAAATATATT
Found at i:40258421 original size:21 final size:20
Alignment explanation
Indices: 40258370--40258447 Score: 58
Period size: 21 Copynumber: 3.9 Consensus size: 20
40258360 TAAAATTGAA
40258370 ATATTAAATACTTTATTAA--
1 ATATTAAATA-TTTATTAATT
40258389 A-ATTATAA-ATTATATTAATT
1 ATATTA-AATATT-TATTAATT
*
40258409 ATATTAAATA-TTAATAATTT
1 ATATTAAATATTTATTAA-TT
*
40258429 AATAATAAATATTTATTAA
1 -ATATTAAATATTTATTAA
40258448 AATTATAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
17 2 0.04
18 11 0.23
19 8 0.17
20 6 0.13
21 14 0.30
22 6 0.13
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATTAAATATTTATTAATT
Found at i:40258457 original size:19 final size:18
Alignment explanation
Indices: 40258374--40258459 Score: 57
Period size: 19 Copynumber: 4.4 Consensus size: 18
40258364 ATTGAAATAT
40258374 TAAATACTTTATTAAAATTA
1 TAAATA-TTTATT-AAATTA
* *
40258394 TAAAT-TATATTAATTATA
1 TAAATATTTATTAAAT-TA
* *
40258412 TTAAATATTAATAATTTAATAA
1 -TAAATATT--T-ATTAAATTA
40258434 TAAATATTTATTAAAATTA
1 TAAATATTTATT-AAATTA
40258453 TAAATAT
1 TAAATAT
40258460 ATTCAATATC
Statistics
Matches: 51, Mismatches: 8, Indels: 15
0.69 0.11 0.20
Matches are distributed among these distances:
17 3 0.06
18 10 0.20
19 17 0.33
20 6 0.12
21 8 0.16
22 2 0.04
23 5 0.10
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAATATTTATTAAATTA
Found at i:40260806 original size:51 final size:51
Alignment explanation
Indices: 40260751--40260853 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
40260741 TGTTCATATG
40260751 ATTGTTTCGTTACTTTCATATGAAAATAGATTCATCAAGGTTCGATTACAT
1 ATTGTTTCGTTACTTTCATATGAAAATAGATTCATCAAGGTTCGATTACAT
40260802 ATTGTTTCGTTACTTTCATATGAAAATAGATTCATCAAGGTTCGATTACAT
1 ATTGTTTCGTTACTTTCATATGAAAATAGATTCATCAAGGTTCGATTACAT
40260853 A
1 A
40260854 ATTTATTCAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (51 bp):
ATTGTTTCGTTACTTTCATATGAAAATAGATTCATCAAGGTTCGATTACAT
Found at i:40261735 original size:40 final size:40
Alignment explanation
Indices: 40261683--40261955 Score: 375
Period size: 40 Copynumber: 6.8 Consensus size: 40
40261673 ATTACCACAA
* * ** *
40261683 GCACAATTGCCTTCGGGTCTTAACCCGGGCATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* * *
40261723 GCACGAATGCCTTCGGGTCTTAGCCTGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
40261763 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGG--ATATATCAACTC
*
40261805 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
40261845 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACCC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
40261885 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* * *
40261925 GCACAATTGCCTTCGGGACTTAGCCCAGATA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATA
40261956 AAATTCAAAT
Statistics
Matches: 210, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
40 173 0.82
42 37 0.18
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:40261902 original size:122 final size:120
Alignment explanation
Indices: 40261683--40261955 Score: 384
Period size: 122 Copynumber: 2.3 Consensus size: 120
40261673 ATTACCACAA
* ** * *
40261683 GCACAATTGCCTTCGGGTCTTAACCCGGGCATAGCAACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGCCTGCGGGTCTTAGCC
* ** * *
40261748 TGGATATATCAACTTGCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTC
66 CGGATATATCAACCCGCACAAATGCCTGCGGGTCTTAGCCCGG--ATATATCAACTC
* * *
40261805 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCC
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGCCTGCGGGTCTTAGCC
*
40261870 CGGATATATCAACCCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTT
66 CGGATATATCAACCCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
* *
40261925 GCACAATTGCCTTCGGGACTTAGCCCAGATA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATA
40261956 AAATTCAAAT
Statistics
Matches: 133, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
120 38 0.29
122 95 0.71
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (120 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGCCTGCGGGTCTTAGCC
CGGATATATCAACCCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
Found at i:40270388 original size:40 final size:40
Alignment explanation
Indices: 40270336--40270608 Score: 411
Period size: 40 Copynumber: 6.8 Consensus size: 40
40270326 ATTACCACAA
* * ** *
40270336 GCACAATTGCCTTCGGGTCTTAACCCGGGCATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
40270376 GCACGAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
40270416 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGG--ATATATCAACTC
*
40270458 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
40270498 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
40270538 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
40270578 GCACAATTGCCTTCGGGACTTAGCCCGGATA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATA
40270609 AAATTCAAAT
Statistics
Matches: 215, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
40 178 0.83
42 37 0.17
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:40274355 original size:60 final size:60
Alignment explanation
Indices: 40274234--40274481 Score: 210
Period size: 60 Copynumber: 4.2 Consensus size: 60
40274224 ATGTGTAGTC
** * * * * ** * *
40274234 AGGGGCACCAAAGTGCGAACAGGGGCACGA-CATGCAAACAGGGATACTGAAGTTTATAT
1 AGGGGCACCAAAGTGCGAACAAAGGCACAATCGTGCAAATAGGGACACCAAAGTGTACAT
* * * * * *
40274293 AGGTGCGCCGAAGTGTGAACAAAGGCACAATCGTGCAAATAGGGACACTAAGGTGTACAT
1 AGGGGCACCAAAGTGCGAACAAAGGCACAATCGTGCAAATAGGGACACCAAAGTGTACAT
* *
40274353 AGGGGCACCAAAGTGCGAACAAGGGCACAATCGTGCAAATAGGGACACCAAAGTGTATAT
1 AGGGGCACCAAAGTGCGAACAAAGGCACAATCGTGCAAATAGGGACACCAAAGTGTACAT
* ** ** * * * ** * * *
40274413 AGGGGTACCAAAGTATGAACAGGGGCACAGTTGTGCAAACAATGACACCGAAGTGTATAC
1 AGGGGCACCAAAGTGCGAACAAAGGCACAATCGTGCAAATAGGGACACCAAAGTGTACAT
40274473 AGGGGCACC
1 AGGGGCACC
40274482 GAAGAGCAAA
Statistics
Matches: 154, Mismatches: 34, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
59 23 0.15
60 131 0.85
ACGTcount: A:0.36, C:0.19, G:0.30, T:0.15
Consensus pattern (60 bp):
AGGGGCACCAAAGTGCGAACAAAGGCACAATCGTGCAAATAGGGACACCAAAGTGTACAT
Found at i:40274460 original size:120 final size:119
Alignment explanation
Indices: 40274233--40274500 Score: 277
Period size: 120 Copynumber: 2.2 Consensus size: 119
40274223 TATGTGTAGT
* * ** * *
40274233 CAGGGGCACCAAAGTGCGAACAGGGGCACGACATGCAAACAGGGATACTGAAGTTTATATAGGTG
1 CAGGGGCACCAAAGTGCGAACAGGGGCACAACATGCAAACAGGGACACCAAAGTGTATATAGGGG
* * * * * *
40274298 CGCCGAAGTGTGAACAAAGGCACAATCGTGCAAATAGGGACA-CTAAGGTGTACA
66 CACCAAAGTATGAACAAAGGCACAATCGTGCAAACAAGGACACCGAA-GTGTACA
* * * *
40274352 TAGGGGCACCAAAGTGCGAACAAGGGCACAATCGTGCAAATAGGGACACCAAAGTGTATATAGGG
1 CAGGGGCACCAAAGTGCGAACAGGGGCACAA-CATGCAAACAGGGACACCAAAGTGTATATAGGG
* ** * * * *
40274417 GTACCAAAGTATGAACAGGGGCACAGTTGTGCAAACAATGACACCGAAGTGTATA
65 GCACCAAAGTATGAACAAAGGCACAATCGTGCAAACAAGGACACCGAAGTGTACA
* * *
40274472 CAGGGGCACCGAAGAGCAAACAGGGGCAC
1 CAGGGGCACCAAAGTGCGAACAGGGGCAC
40274501 TTCTTCATTT
Statistics
Matches: 119, Mismatches: 28, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
119 28 0.24
120 88 0.74
121 3 0.03
ACGTcount: A:0.36, C:0.20, G:0.30, T:0.14
Consensus pattern (119 bp):
CAGGGGCACCAAAGTGCGAACAGGGGCACAACATGCAAACAGGGACACCAAAGTGTATATAGGGG
CACCAAAGTATGAACAAAGGCACAATCGTGCAAACAAGGACACCGAAGTGTACA
Found at i:40274494 original size:60 final size:59
Alignment explanation
Indices: 40274316--40274500 Score: 165
Period size: 60 Copynumber: 3.1 Consensus size: 59
40274306 TGTGAACAAA
* * * * * * * * *
40274316 GGCACAATCGTGCAAATAGGGACACTAAGGTGTACATAGGGGCACCAAAGTGCGAACAAG
1 GGCACAATCGTGCAAACAAGGACACCAAAGTGTATACAGGGGCACC-AAGAGCAAACAGG
* * * * *
40274376 GGCACAATCGTGCAAATAGGGACACCAAAGTGTATATAGGGGTACCAA-AGTATGAACAGG
1 GGCACAATCGTGCAAACAAGGACACCAAAGTGTATACAGGGGCACCAAGAGCA--AACAGG
* * * *
40274436 GGCACAGTTGTGCAAACAATGACACCGAAGTGTATACAGGGGCACCGAAGAGCAAACAGG
1 GGCACAATCGTGCAAACAAGGACACCAAAGTGTATACAGGGGCACC-AAGAGCAAACAGG
40274496 GGCAC
1 GGCAC
40274501 TTCTTCATTT
Statistics
Matches: 104, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
58 1 0.01
59 2 0.02
60 96 0.92
61 2 0.02
62 3 0.03
ACGTcount: A:0.37, C:0.20, G:0.30, T:0.14
Consensus pattern (59 bp):
GGCACAATCGTGCAAACAAGGACACCAAAGTGTATACAGGGGCACCAAGAGCAAACAGG
Found at i:40278399 original size:15 final size:16
Alignment explanation
Indices: 40278370--40278399 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40278360 CAAACATGCT
40278370 TTAACACATTATCAAA
1 TTAACACATTATCAAA
40278386 TTAACACA-TATCAA
1 TTAACACATTATCAA
40278400 CAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:40279561 original size:25 final size:26
Alignment explanation
Indices: 40279533--40279587 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
40279523 GAATCAATAT
40279533 GCTCTG-ATGAGCT-ATAAATCGGTAA
1 GCTCTGTATGAGCTGA-AAATCGGTAA
*
40279558 GCTC-GTATGAGCTGAGAATCGGTAA
1 GCTCTGTATGAGCTGAAAATCGGTAA
40279583 GCTCT
1 GCTCT
40279588 CACGCGCTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
24 1 0.04
25 24 0.92
26 1 0.04
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (26 bp):
GCTCTGTATGAGCTGAAAATCGGTAA
Found at i:40279596 original size:25 final size:24
Alignment explanation
Indices: 40279549--40279609 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
40279539 ATGAGCTATA
* *
40279549 AATCGGTAAGCTCGTATGAGCTGAG
1 AATCGGTAAGCTCGTACGAGCTG-C
*
40279574 AATCGGTAAGCTC-TCACGCGCTGC
1 AATCGGTAAGCTCGT-ACGAGCTGC
*
40279598 AATCGATAAGCT
1 AATCGGTAAGCT
40279610 AATACAAGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 12 0.39
25 19 0.61
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (24 bp):
AATCGGTAAGCTCGTACGAGCTGC
Found at i:40282004 original size:27 final size:27
Alignment explanation
Indices: 40281966--40282025 Score: 104
Period size: 27 Copynumber: 2.2 Consensus size: 27
40281956 GTAATGGGCC
40281966 TAAAATGACCAAAATACCCTC-AAAGGG
1 TAAAATGACCAAAATACCCTCGAAA-GG
40281993 TAAAATGACCAAAATACCCTCGAAAGG
1 TAAAATGACCAAAATACCCTCGAAAGG
40282020 TAAAAT
1 TAAAAT
40282026 CACTATTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 29 0.91
28 3 0.09
ACGTcount: A:0.50, C:0.20, G:0.13, T:0.17
Consensus pattern (27 bp):
TAAAATGACCAAAATACCCTCGAAAGG
Found at i:40282398 original size:81 final size:81
Alignment explanation
Indices: 40282263--40282554 Score: 311
Period size: 81 Copynumber: 3.6 Consensus size: 81
40282253 AACAGCAAAA
* * * * * *
40282263 GCCCCTATAGGGTAAAATGACCGTATTACCCCAGTAGGGTAAAATGACTCTAATACCCCTATAGA
1 GCCCCTGTAGGGTAAAATAACCGTAATACCCCTGTAGGGTAAAATGACTATAATACCCCTGTAGA
*
40282328 GTAAAATAACTGTAAT
66 GTAAAATAACCGTAAT
* * * ** *
40282344 GCCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGGGTGAAATAACTATAATACCTTTGTAGG
1 GCCCCTGTAGGGTAAAATAACCGTAATACCCCTGTAGGGTAAAATGACTATAATACCCCTGTAGA
*
40282409 GTAAAATGACCGTAAT
66 GTAAAATAACCGTAAT
* * * ** * ** * **
40282425 GCCCCAGTATGGTAAAATAACCATAATGGCCCTGTAAGGTAAAATGACCGTAATACCCGTGTACT
1 GCCCCTGTAGGGTAAAATAACCGTAATACCCCTGTAGGGTAAAATGACTATAATACCCCTGTAGA
*
40282490 GTAAAATTACCGTAAT
66 GTAAAATAACCGTAAT
*
40282506 GCCCCTGTAGGGTAAAATAACCGTAAT-GCCCTGGT-GGGT-AAATGACTAT
1 GCCCCTGTAGGGTAAAATAACCGTAATACCCCT-GTAGGGTAAAATGACTAT
40282555 TTTTGCCCTT
Statistics
Matches: 176, Mismatches: 34, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
79 8 0.05
80 8 0.05
81 160 0.91
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (81 bp):
GCCCCTGTAGGGTAAAATAACCGTAATACCCCTGTAGGGTAAAATGACTATAATACCCCTGTAGA
GTAAAATAACCGTAAT
Found at i:40282533 original size:27 final size:27
Alignment explanation
Indices: 40282263--40282551 Score: 271
Period size: 27 Copynumber: 10.8 Consensus size: 27
40282253 AACAGCAAAA
* *
40282263 GCCCCTATAGGGTAAAATGACCGTATT
1 GCCCCTGTAGGGTAAAATGACCGTAAT
* *
40282290 ACCCCAGTAGGGTAAAATGACTC-TAAT
1 GCCCCTGTAGGGTAAAATGAC-CGTAAT
* * * * *
40282317 ACCCCTATAGAGTAAAATAACTGTAAT
1 GCCCCTGTAGGGTAAAATGACCGTAAT
40282344 GCCCCTGTAGGGTAAAATGACCGTAAT
1 GCCCCTGTAGGGTAAAATGACCGTAAT
* * * **
40282371 ACCCCTGTAGGGTGAAATAACTATAAT
1 GCCCCTGTAGGGTAAAATGACCGTAAT
* **
40282398 ACCTTTGTAGGGTAAAATGACCGTAAT
1 GCCCCTGTAGGGTAAAATGACCGTAAT
* * * *
40282425 GCCCCAGTATGGTAAAATAACCATAAT
1 GCCCCTGTAGGGTAAAATGACCGTAAT
* *
40282452 GGCCCTGTAAGGTAAAATGACCGTAAT
1 GCCCCTGTAGGGTAAAATGACCGTAAT
* * ** *
40282479 ACCCGTGTACTGTAAAATTACCGTAAT
1 GCCCCTGTAGGGTAAAATGACCGTAAT
*
40282506 GCCCCTGTAGGGTAAAATAACCGTAAT
1 GCCCCTGTAGGGTAAAATGACCGTAAT
40282533 G-CCCTGGT-GGGT-AAATGAC
1 GCCCCT-GTAGGGTAAAATGAC
40282552 TATTTTTGCC
Statistics
Matches: 210, Mismatches: 49, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
25 6 0.03
26 8 0.04
27 195 0.93
28 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (27 bp):
GCCCCTGTAGGGTAAAATGACCGTAAT
Found at i:40282629 original size:24 final size:24
Alignment explanation
Indices: 40282596--40282654 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
40282586 TCTGTGGTTA
*
40282596 AATGACTGATTTGTCTGTG-TTTG
1 AATGACTGATTTGTCTATGATTTG
*
40282619 CTATGACTGATTTGTCTATGATTTG
1 -AATGACTGATTTGTCTATGATTTG
40282644 AATGACTGATT
1 AATGACTGATT
40282655 CTAAACATGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 27 0.87
25 4 0.13
ACGTcount: A:0.22, C:0.10, G:0.22, T:0.46
Consensus pattern (24 bp):
AATGACTGATTTGTCTATGATTTG
Found at i:40282787 original size:26 final size:26
Alignment explanation
Indices: 40282758--40282826 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 26
40282748 TACTACTGGA
40282758 AGCTTTGCTTCGATACTGTTGCTCGC
1 AGCTTTGCTTCGATACTGTTGCTCGC
* *
40282784 AGCTTTGCTGT-GATATTGTTGCTGGC
1 AGCTTTGCT-TCGATACTGTTGCTCGC
*
40282810 AGCTTTGCTGCGATACT
1 AGCTTTGCTTCGATACT
40282827 ACTGATGGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 36 0.97
27 1 0.03
ACGTcount: A:0.13, C:0.22, G:0.26, T:0.39
Consensus pattern (26 bp):
AGCTTTGCTTCGATACTGTTGCTCGC
Found at i:40282835 original size:26 final size:26
Alignment explanation
Indices: 40282744--40282835 Score: 69
Period size: 26 Copynumber: 3.5 Consensus size: 26
40282734 TTGGCCACAT
* *
40282744 ATACTACT-ACTGGAAGCTTTGCTTCG
1 ATACTACTGA-TGGCAGCTTTGCTGCG
** * * *
40282770 ATACTGTTGCTCGCAGCTTTGCTGTG
1 ATACTACTGATGGCAGCTTTGCTGCG
* ** *
40282796 ATATTGTTGCTGGCAGCTTTGCTGCG
1 ATACTACTGATGGCAGCTTTGCTGCG
40282822 ATACTACTGATGGC
1 ATACTACTGATGGC
40282836 TTTGTACCGA
Statistics
Matches: 51, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
26 51 1.00
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.36
Consensus pattern (26 bp):
ATACTACTGATGGCAGCTTTGCTGCG
Found at i:40282924 original size:32 final size:32
Alignment explanation
Indices: 40282826--40282914 Score: 151
Period size: 32 Copynumber: 2.8 Consensus size: 32
40282816 GCTGCGATAC
*
40282826 TACTGATGGCTTTGTACCGATCACAGTACCGT
1 TACTGATGGCTTTGTACCGATCATAGTACCGT
*
40282858 TACTGATGGCTTTGTGCCGATCATAGTACCGT
1 TACTGATGGCTTTGTACCGATCATAGTACCGT
*
40282890 TACTGATGGCTTTGTACTGATCATA
1 TACTGATGGCTTTGTACCGATCATA
40282915 TTATTGTTAC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.35
Consensus pattern (32 bp):
TACTGATGGCTTTGTACCGATCATAGTACCGT
Found at i:40282938 original size:64 final size:64
Alignment explanation
Indices: 40282826--40282979 Score: 159
Period size: 64 Copynumber: 2.4 Consensus size: 64
40282816 GCTGCGATAC
* * * * * * *
40282826 TACTGATGGCTTTGTACCGATCACAGTACCGTTACTGATGGCTTTGTGCCGATCATAGT-ACCGT
1 TACTGATGGCTTTGTACCGATCATATTACCGTTACCGAAGGATGTGTGCCAATCAT-GTCACCGT
* ** * *
40282890 TACTGATGGCTTTGTACTGATCATATTATTGTTACCGAAGGATGTGTGCCAATCATTTCACTGT
1 TACTGATGGCTTTGTACCGATCATATTACCGTTACCGAAGGATGTGTGCCAATCATGTCACCGT
*
40282954 TACTGATGG-TTGTGTGCCGATCATAT
1 TACTGATGGCTT-TGTACCGATCATAT
40282980 CACTACTACT
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
63 3 0.04
64 71 0.96
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (64 bp):
TACTGATGGCTTTGTACCGATCATATTACCGTTACCGAAGGATGTGTGCCAATCATGTCACCGT
Found at i:40282945 original size:32 final size:33
Alignment explanation
Indices: 40282909--40282983 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 33
40282899 CTTTGTACTG
*
40282909 ATCATATT-ATTGTTACCGAAGGATGTGTGCCA
1 ATCATATTCACTGTTACCGAAGGATGTGTGCCA
* * * *
40282941 ATCAT-TTCACTGTTACTGATGGTTGTGTGCCG
1 ATCATATTCACTGTTACCGAAGGATGTGTGCCA
40282973 ATCATA-TCACT
1 ATCATATTCACT
40282984 ACTACTGATG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 2 0.06
32 34 0.94
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (33 bp):
ATCATATTCACTGTTACCGAAGGATGTGTGCCA
Found at i:40282990 original size:32 final size:32
Alignment explanation
Indices: 40282932--40283067 Score: 143
Period size: 32 Copynumber: 4.2 Consensus size: 32
40282922 TACCGAAGGA
* * **
40282932 TGTGTGCCAATCATTTCACTGTTACTGATGGT
1 TGTGTGCCGATCATATCACTACTACTGATGGT
40282964 TGTGTGCCGATCATATCACTACTACTGATGGT
1 TGTGTGCCGATCATATCACTACTACTGATGGT
* * * * *
40282996 TTTGTGTCGATAATGTTA-T-CGTTACTGATGGT
1 TGTGTGCCGATCATATCACTAC--TACTGATGGT
40283028 TGTGTGCCGATCATATCACTACTACTGATGGCT
1 TGTGTGCCGATCATATCACTACTACTGATGG-T
40283061 T-TGTGCC
1 TGTGTGCC
40283068 ACTCAGATTA
Statistics
Matches: 85, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
30 1 0.01
31 1 0.01
32 79 0.93
33 3 0.04
34 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (32 bp):
TGTGTGCCGATCATATCACTACTACTGATGGT
Found at i:40283020 original size:96 final size:96
Alignment explanation
Indices: 40282856--40283067 Score: 241
Period size: 96 Copynumber: 2.2 Consensus size: 96
40282846 TCACAGTACC
** * *
40282856 GTTACTGATGGCTTTGTGCCGATCATAGTACCGTTACTGATGGCTTTGTACTGATCATATTATTG
1 GTTACTGATGGCTTTGTGCCGATCATAGTACCACTACTGATGGCTTTGTACTGATAATATTATCG
*
40282921 TTACCGAAGGATGTGTGCCAATCATTTCACT
66 TTACCGAAGGATGTGTGCCAATCATATCACT
* * * *
40282952 GTTACTGATGG-TTGTGTGCCGATCATA-TCACTACTACTGATGGTTTTGT-GTCGATAATGTTA
1 GTTACTGATGGCTT-TGTGCCGATCATAGT-ACCACTACTGATGGCTTTGTACT-GATAATATTA
* * * *
40283014 TCGTTACTGATGGTTGTGTGCCGATCATATCACT
63 TCGTTACCGAAGGATGTGTGCCAATCATATCACT
**
40283048 ACTACTGATGGCTTTGTGCC
1 GTTACTGATGGCTTTGTGCC
40283068 ACTCAGATTA
Statistics
Matches: 97, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
95 4 0.04
96 91 0.94
97 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.38
Consensus pattern (96 bp):
GTTACTGATGGCTTTGTGCCGATCATAGTACCACTACTGATGGCTTTGTACTGATAATATTATCG
TTACCGAAGGATGTGTGCCAATCATATCACT
Found at i:40283171 original size:26 final size:26
Alignment explanation
Indices: 40283142--40283194 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
40283132 AGCTCTTAGC
* *
40283142 CATTCTGACTACTGGCAGCTCTGCTG
1 CATTATGACTACTGGCAGCTATGCTG
*
40283168 CATTATTACTACTGGCAGCTATGCTG
1 CATTATGACTACTGGCAGCTATGCTG
40283194 C
1 C
40283195 GATATTAGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.19, C:0.28, G:0.21, T:0.32
Consensus pattern (26 bp):
CATTATGACTACTGGCAGCTATGCTG
Found at i:40286472 original size:24 final size:27
Alignment explanation
Indices: 40286429--40286479 Score: 81
Period size: 24 Copynumber: 2.0 Consensus size: 27
40286419 TACATCGATC
40286429 CATTCACATTATAAATAACA-TAATAA
1 CATTCACATTATAAATAACATTAATAA
40286455 CATTCA-ATT-TAAATAACATTAATAA
1 CATTCACATTATAAATAACATTAATAA
40286480 GATAACCGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 9 0.38
25 9 0.38
26 6 0.25
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (27 bp):
CATTCACATTATAAATAACATTAATAA
Found at i:40299274 original size:73 final size:75
Alignment explanation
Indices: 40299130--40299275 Score: 233
Period size: 74 Copynumber: 2.0 Consensus size: 75
40299120 AAGGAAAACA
40299130 AGGATTATTCCCTTACTAATAGAGAAGGCAAATGAAAAATTAGAAAAATGAATTATATTCTTTCC
1 AGGATTATTCCCTTACTAATAGAGAAGGCAAATGAAAAATTAGAAAAATGAATTATATTCTTTCC
40299195 AAAAGAATCT
66 AAAAGAATCT
* * * * *
40299205 AGGATTATTCCTTTATTAAT-GAGAAGGCAAATGGAAAGTTAGAAAAA-GAATTATATTTTTTCC
1 AGGATTATTCCCTTACTAATAGAGAAGGCAAATGAAAAATTAGAAAAATGAATTATATTCTTTCC
40299268 AAAAGAAT
66 AAAAGAAT
40299276 ATTAATTTCC
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
73 23 0.35
74 25 0.38
75 18 0.27
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.31
Consensus pattern (75 bp):
AGGATTATTCCCTTACTAATAGAGAAGGCAAATGAAAAATTAGAAAAATGAATTATATTCTTTCC
AAAAGAATCT
Found at i:40299433 original size:138 final size:138
Alignment explanation
Indices: 40299253--40299525 Score: 417
Period size: 138 Copynumber: 2.0 Consensus size: 138
40299243 TTAGAAAAAG
* * **
40299253 AATTATATTTTTTCCAAAAGAATATTAATTTCCATATTTTTTATATTTT-ACCTA-AAGTTAATT
1 AATTATATTATTTCCAAAAGAATATAAATTTCCATACCTTTTATATTTTGACC-AGAA-TTAATT
* *
40299316 AATATAACTATTTATATTAATAAATTCGGTAGAATATATACACTTAATATTTTGTATGAATCAAA
64 AATATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAA
40299381 TTCATATATT
129 TTCATATATT
*
40299391 AATTATATTATTTCCAAAAGAATATAAATTTTCA-AGCCTTTTATATTTTGACCAGAATTAATTA
1 AATTATATTATTTCCAAAAGAATATAAATTTCCATA-CCTTTTATATTTTGACCAGAATTAATTA
* *
40299455 ATATAACTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
65 ATATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
40299520 TCATAT
130 TCATAT
40299526 TTGCATTGTA
Statistics
Matches: 123, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
137 1 0.01
138 117 0.95
139 5 0.04
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (138 bp):
AATTATATTATTTCCAAAAGAATATAAATTTCCATACCTTTTATATTTTGACCAGAATTAATTAA
TATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:40299617 original size:25 final size:25
Alignment explanation
Indices: 40299588--40299636 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
40299578 GTGTTTAATA
40299588 TTTAACTATCAAATTAAATTAATTG
1 TTTAACTATCAAATTAAATTAATTG
40299613 TTTAACTATCAAATTAAATTAATT
1 TTTAACTATCAAATTAAATTAATT
40299637 AATGTGACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (25 bp):
TTTAACTATCAAATTAAATTAATTG
Found at i:40303821 original size:15 final size:15
Alignment explanation
Indices: 40303801--40303830 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
40303791 AAGAAGATCA
40303801 ACATGACTCATCATT
1 ACATGACTCATCATT
40303816 ACATGACTCATCATT
1 ACATGACTCATCATT
40303831 GATCGAACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (15 bp):
ACATGACTCATCATT
Found at i:40309551 original size:20 final size:20
Alignment explanation
Indices: 40309521--40309589 Score: 111
Period size: 20 Copynumber: 3.4 Consensus size: 20
40309511 AAAAGTTAAA
*
40309521 AAAAGGAATTACATACTTTTT
1 AAAA-GAATTATATACTTTTT
40309542 AAAAGAATTATATACTTTTT
1 AAAAGAATTATATACTTTTT
*
40309562 AAAAGAATTATATTCTTTTT
1 AAAAGAATTATATACTTTTT
40309582 AAAAGAAT
1 AAAAGAAT
40309590 ATAGGATTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
20 42 0.91
21 4 0.09
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (20 bp):
AAAAGAATTATATACTTTTT
Done.