Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 126 of 356
Found at i:40077349 original size:81 final size:81
Alignment explanation
Indices: 40077234--40077431 Score: 306
Period size: 81 Copynumber: 2.4 Consensus size: 81
40077224 GTAATTTCAC
* * * *
40077234 AATCGAGGGTAAAATAGTAATTTTGTAAACTGAGGGTAAAATGGTAATTTTATAAATCGAGGGTA
1 AATCGAGGGTAAAATAGTAATTCTATAAATTGAGGGTAAAACGGTAATTTTATAAATCGAGGGTA
40077299 AAACGGTAATTCTATA
66 AAACGGTAATTCTATA
* * *
40077315 AATCGAGGGTAAAATGGTAATTCTATAAATTGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTG
1 AATCGAGGGTAAAATAGTAATTCTATAAATTGAGGGTAAAACGGTAATTTTATAAATCGAGGGTA
40077380 AAACGGTAATTCTATA
66 AAACGGTAATTCTATA
* * *
40077396 AATTGAGGGTAAAATAGTAATTCTACAAATCGAGGG
1 AATCGAGGGTAAAATAGTAATTCTATAAATTGAGGG
40077432 CATTTCAGTA
Statistics
Matches: 106, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 106 1.00
ACGTcount: A:0.40, C:0.07, G:0.24, T:0.29
Consensus pattern (81 bp):
AATCGAGGGTAAAATAGTAATTCTATAAATTGAGGGTAAAACGGTAATTTTATAAATCGAGGGTA
AAACGGTAATTCTATA
Found at i:40094724 original size:13 final size:13
Alignment explanation
Indices: 40094706--40094731 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40094696 TTGAATCCAT
40094706 ACCAAAACAATCA
1 ACCAAAACAATCA
40094719 ACCAAAACAATCA
1 ACCAAAACAATCA
40094732 TGAAACATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.31, G:0.00, T:0.08
Consensus pattern (13 bp):
ACCAAAACAATCA
Found at i:40099295 original size:18 final size:17
Alignment explanation
Indices: 40099258--40099296 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
40099248 TTATTTTCCC
40099258 TTTTTCTTACTTTCAAT
1 TTTTTCTTACTTTCAAT
* *
40099275 TTTTTCTTTCTTTCACT
1 TTTTTCTTACTTTCAAT
40099292 TTTTT
1 TTTTT
40099297 ATTAATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTCTTACTTTCAAT
Found at i:40100034 original size:23 final size:25
Alignment explanation
Indices: 40099992--40100037 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
40099982 TTTTTATTTT
*
40099992 AAAAAAAGTTATTTCTTAATATTGG
1 AAAAAAAGTTATGTCTTAATATTGG
40100017 AAAAAAA-TTATGTC-TAATATT
1 AAAAAAAGTTATGTCTTAATATT
40100038 TTTATCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 6 0.30
25 7 0.35
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (25 bp):
AAAAAAAGTTATGTCTTAATATTGG
Found at i:40100114 original size:8 final size:9
Alignment explanation
Indices: 40100096--40100152 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
40100086 TTACACTTAA
40100096 TTATAATTT
1 TTATAATTT
40100105 TTAT-ATTT
1 TTATAATTT
* **
40100113 TTCTAAAGT
1 TTATAATTT
*
40100122 TTATACTTTT
1 TTATA-ATTT
40100132 TTATAATTTT
1 TTATAA-TTT
40100142 TTATAATTT
1 TTATAATTT
40100151 TT
1 TT
40100153 TTAAAATTTC
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
8 7 0.19
9 15 0.41
10 15 0.41
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.67
Consensus pattern (9 bp):
TTATAATTT
Found at i:40100136 original size:10 final size:10
Alignment explanation
Indices: 40100121--40100153 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
40100111 TTTTCTAAAG
*
40100121 TTTATACTTT
1 TTTATAATTT
40100131 TTTATAATTT
1 TTTATAATTT
40100141 TTTATAATTT
1 TTTATAATTT
40100151 TTT
1 TTT
40100154 TAAAATTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTATAATTT
Found at i:40100151 original size:19 final size:19
Alignment explanation
Indices: 40100066--40100153 Score: 65
Period size: 20 Copynumber: 4.6 Consensus size: 19
40100056 TTCTAACTTA
*
40100066 TTATATATTTTTTAAAATTT
1 TTATA-ATTTTTTATAATTT
* * **
40100086 TTACACTTAATTATAATTT
1 TTATAATTTTTTATAATTT
*
40100105 TTAT-ATTTTTCTA-AA-GT
1 TTATAATTTTT-TATAATTT
*
40100122 TTATACTTTTTTATAATTTT
1 TTATAATTTTTTATAA-TTT
40100142 TTATAATTTTTT
1 TTATAATTTTTT
40100154 TAAAATTTCT
Statistics
Matches: 50, Mismatches: 13, Indels: 10
0.68 0.18 0.14
Matches are distributed among these distances:
17 7 0.14
18 12 0.24
19 15 0.30
20 16 0.32
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.64
Consensus pattern (19 bp):
TTATAATTTTTTATAATTT
Found at i:40100152 original size:11 final size:11
Alignment explanation
Indices: 40100128--40100161 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
40100118 AAGTTTATAC
40100128 TTTTTTATAA-
1 TTTTTTATAAT
40100138 TTTTTTATAAT
1 TTTTTTATAAT
*
40100149 TTTTTTAAAAT
1 TTTTTTATAAT
40100160 TT
1 TT
40100162 CTTAAATGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTTTATAAT
Found at i:40100173 original size:21 final size:21
Alignment explanation
Indices: 40100128--40100173 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
40100118 AAGTTTATAC
* *
40100128 TTTTTTATAATTTTTTATAAT
1 TTTTTTAAAATTTCTTATAAT
40100149 TTTTTTAAAATTTCTTA-AAT
1 TTTTTTAAAATTTCTTATAAT
*
40100169 GTTTT
1 TTTTT
40100174 AGATTATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTTTAAAATTTCTTATAAT
Found at i:40103189 original size:16 final size:16
Alignment explanation
Indices: 40103168--40103202 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
40103158 TATTATACCC
40103168 AACCATAAATCTCATG
1 AACCATAAATCTCATG
40103184 AACCATAAATCTCATG
1 AACCATAAATCTCATG
40103200 AAC
1 AAC
40103203 ATGTGTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.26, G:0.06, T:0.23
Consensus pattern (16 bp):
AACCATAAATCTCATG
Found at i:40107600 original size:38 final size:38
Alignment explanation
Indices: 40107558--40107633 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
40107548 TTCATCCTTT
40107558 TTCATTTCTTTTGGCCAAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCAAAAATTCTAAGGAAGGAGGAA
*
40107596 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCAAAAATTCTAAGGAAGGAGGAA
40107634 GGAGTTCTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.32
Consensus pattern (38 bp):
TTCATTTCTTTTGGCCAAAAATTCTAAGGAAGGAGGAA
Found at i:40108920 original size:40 final size:40
Alignment explanation
Indices: 40108826--40108970 Score: 200
Period size: 40 Copynumber: 3.6 Consensus size: 40
40108816 TACTCGAATG
* *
40108826 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCT-AGCGACT
* * *
40108867 ACATCCGGACTAAGATCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
* * *
40108907 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
*
40108947 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
40108971 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 64 0.70
41 28 0.30
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
Found at i:40110912 original size:50 final size:49
Alignment explanation
Indices: 40110843--40110992 Score: 203
Period size: 50 Copynumber: 3.0 Consensus size: 49
40110833 CACATAGTGG
* ** *
40110843 GATGCCAATGCCATATCCCAGGTATGGTCTTACATGGGTTGACACATATC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAT-ACACATATC
* *
40110893 GATTCCAATGTCATGTCCCAGACATGGTCTTACATGGGATCACACATATC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAT-ACACATATC
* *
40110943 GATGCCAATGCCATGTCCCCGACATGGTCTTTCATGGGAT-CACATATC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATACACATATC
40110991 GA
1 GA
40110993 AACTTTATCG
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
48 10 0.11
50 79 0.89
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (49 bp):
GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATACACATATC
Found at i:40114306 original size:47 final size:47
Alignment explanation
Indices: 40114212--40114429 Score: 227
Period size: 47 Copynumber: 4.7 Consensus size: 47
40114202 CCATCTGTGC
*
40114212 CGATGCCGTGTCCCAGACA-GGTCTTACACTA--ACACATGTCAAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATGTCAAGT
*
40114256 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCAAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATGTCAAGT
* *
40114303 CGATGCCATGTCCCAGACATGGTCTTACACT-G-ACTATCATCATCAAGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCAC-A-CAT-GTCAA-GT
* * * * **
40114352 CGATG-CGTGTCCTAGACA-CGTCTTACACTAGCACTCAACTCAA-T
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATGTCAAGT
*
40114396 ACCGATGCCATGTCTCAGACATGGTCTTACACTA
1 --CGATGCCATGTCCCAGACATGGTCTTACACTA
40114430 ACACGCATAT
Statistics
Matches: 145, Mismatches: 16, Indels: 22
0.79 0.09 0.12
Matches are distributed among these distances:
44 18 0.12
45 13 0.09
46 11 0.08
47 68 0.47
48 27 0.19
49 8 0.06
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATGTCAAGT
Found at i:40114402 original size:95 final size:92
Alignment explanation
Indices: 40114211--40114522 Score: 314
Period size: 95 Copynumber: 3.3 Consensus size: 92
40114201 TCCATCTGTG
* * * *
40114211 CCGATGCCGTGTCCCAGACA-GGTCTTACACTAACACATGTCAA-GTCGATGCCATGTCCCAGAC
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAACACATATCAAGGCCGATG-CATGTCCTAGAC
* * *
40114274 ATGGTCTTACACTAGCTCACATGTCAAGT-
65 A-CGTCTTACACTAGCTCTCATCTCAA-TA
* *
40114303 -CGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATCATCAAGGCCGATGCGTGTCCTAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAAC-A-CAT-ATCAAGGCCGATGCATGTCCTAG
* *
40114367 ACACGTCTTACACTAGCACTCAACTCAATA
63 ACACGTCTTACACTAGCTCTCATCTCAATA
* * *
40114397 CCGATGCCATGTCTCAGACATGGTCTTACACTAACACGCATATCTCGAGGCCGATGCATATCCTA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAACA--CATA--TCAAGGCCGATGCATGTCCTA
** * *
40114462 GACATTTCTTACACTGGCTCTCGTCTCAA-A
62 GACACGTCTTACACTAGCTCTCATCTCAATA
40114492 GCCGATG-CATGTCCCAGACAT-GTCTTACACT
1 -CCGATGCCATGTCCCAGACATGGTCTTACACT
40114523 GGCGCACATA
Statistics
Matches: 185, Mismatches: 24, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
91 18 0.10
92 13 0.07
93 2 0.01
94 35 0.19
95 64 0.35
96 53 0.29
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (92 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTAACACATATCAAGGCCGATGCATGTCCTAGACA
CGTCTTACACTAGCTCTCATCTCAATA
Found at i:40114496 original size:142 final size:139
Alignment explanation
Indices: 40114210--40114522 Score: 337
Period size: 142 Copynumber: 2.2 Consensus size: 139
40114200 ATCCATCTGT
* **
40114210 GCCGATGCCGTGTCCCAGACAGGTCTTACACTAACACATGTCAAGTCGATGCCATGTCCCAGACA
1 GCCGATG-CGTGTCCCAGACACGTCTTACACTAACACAACTCAAGTCGATGCCATGTCCCAGACA
* * * * *
40114275 TGGTCTTACACTAGCTCACATGTCAAGTCGATGCCATGTCCCAGACATGGTCTTACACTGACTAT
65 TGGTCTTACACTAACGCACATCTCAAGCCGATGCCATATCCCAGACATGGTCTTACACTGACTAT
*
40114340 CATCATCAAG
130 CATCATCAAA
* * *
40114350 GCCGATGCGTGTCCTAGACACGTCTTACACTAGCACTCAACTCAA-TACCGATGCCATGTCTCAG
1 GCCGATGCGTGTCCCAGACACGTCTTACACTA--ACACAACTCAAGT--CGATGCCATGTCCCAG
* * * *
40114414 ACATGGTCTTACACTAACACGCATATCTCGAGGCCGATG-CATATCCTAGACAT-TTCTTACACT
62 ACATGGTCTTACACT-A-ACGCACATCTC-AAGCCGATGCCATATCCCAGACATGGTCTTACACT
* * *
40114477 GGCTCTCGTC-TCAAA
124 GACTATCATCATCAAA
* *
40114492 GCCGATGCATGTCCCAGACATGTCTTACACT
1 GCCGATGCGTGTCCCAGACACGTCTTACACT
40114523 GGCGCACATA
Statistics
Matches: 144, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
139 23 0.16
140 8 0.06
141 8 0.06
142 62 0.43
143 17 0.12
144 19 0.13
145 7 0.05
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (139 bp):
GCCGATGCGTGTCCCAGACACGTCTTACACTAACACAACTCAAGTCGATGCCATGTCCCAGACAT
GGTCTTACACTAACGCACATCTCAAGCCGATGCCATATCCCAGACATGGTCTTACACTGACTATC
ATCATCAAA
Found at i:40117251 original size:50 final size:50
Alignment explanation
Indices: 40117174--40117317 Score: 225
Period size: 50 Copynumber: 2.9 Consensus size: 50
40117164 CACATAGTGA
* * * * *
40117174 GATGCCAATGTCATATCCTAGATATGGTCTTACATGGGTTCACACATACC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACACATACC
*
40117224 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACACATATC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACACATACC
*
40117274 GATGCCAATGCCATGTCCCCGACATGGTCTTACATGGGATCACA
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACA
40117318 TATCGAAACT
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 87 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (50 bp):
GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACACATACC
Found at i:40135872 original size:24 final size:24
Alignment explanation
Indices: 40135845--40135891 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
40135835 ATGTATGAAA
40135845 TGTGAGCTCAATATATGCTATATT
1 TGTGAGCTCAATATATGCTATATT
40135869 TGTGAGCTCAATATATGCTATAT
1 TGTGAGCTCAATATATGCTATAT
40135892 GAGGTGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (24 bp):
TGTGAGCTCAATATATGCTATATT
Found at i:40136633 original size:13 final size:13
Alignment explanation
Indices: 40136615--40136649 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
40136605 CCTAGCACAC
40136615 GGGCATGTGCCCT
1 GGGCATGTGCCCT
*
40136628 GGGCATGTGCCTT
1 GGGCATGTGCCCT
*
40136641 GGCCATGTG
1 GGGCATGTG
40136650 ACATTTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.09, C:0.26, G:0.40, T:0.26
Consensus pattern (13 bp):
GGGCATGTGCCCT
Found at i:40140547 original size:39 final size:39
Alignment explanation
Indices: 40140493--40140773 Score: 409
Period size: 39 Copynumber: 7.2 Consensus size: 39
40140483 GAAATGTGTA
40140493 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
* * *
40140532 TGGAAATATATCCGGGCCAAAGACCCACAGGCTTCGTGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
*
40140571 TGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTTGTGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
* * *
40140610 TGGAAATGTATCCGGGCTAAAGTCCCGTAGGCTTTGTGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
* * *
40140649 TGGAAATATATCTGGGCCAAAGACCCGCAGGCTTCGTGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
* * * *
40140688 TGGAAATGTATCCGGGCTAAAGACTCGCAAGCTTTGTAC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
* *
40140727 TGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTTGTGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
*
40140766 TGGTAATA
1 TGGAAATA
40140774 AAATTTTGGG
Statistics
Matches: 214, Mismatches: 28, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 214 1.00
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (39 bp):
TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
Found at i:40140699 original size:117 final size:117
Alignment explanation
Indices: 40140489--40140773 Score: 482
Period size: 117 Copynumber: 2.4 Consensus size: 117
40140479 AGACGAAATG
* *
40140489 TGTA-TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGCTGGAAATATATCCGGGCCAAA
1 TGTACTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTTGTGCTGGAAATATATCCGGGCCAAA
*
40140553 GACCCACAGGCTTCGTGCTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTT
66 GACCCACAGGCTTCGTGCTGGAAATGTATCCGGGCTAAAGACCCGCAAGCTT
* * *
40140605 TGTGCTGGAAATGTATCCGGGCTAAAGTCCCGTAGGCTTTGTGCTGGAAATATATCTGGGCCAAA
1 TGTACTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTTGTGCTGGAAATATATCCGGGCCAAA
* *
40140670 GACCCGCAGGCTTCGTGCTGGAAATGTATCCGGGCTAAAGACTCGCAAGCTT
66 GACCCACAGGCTTCGTGCTGGAAATGTATCCGGGCTAAAGACCCGCAAGCTT
*
40140722 TGTACTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTTGTGCTGGTAATA
1 TGTACTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTTGTGCTGGAAATA
40140774 AAATTTTGGG
Statistics
Matches: 157, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
116 3 0.02
117 154 0.98
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (117 bp):
TGTACTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTTGTGCTGGAAATATATCCGGGCCAAA
GACCCACAGGCTTCGTGCTGGAAATGTATCCGGGCTAAAGACCCGCAAGCTT
Found at i:40147365 original size:24 final size:24
Alignment explanation
Indices: 40147338--40147385 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
40147328 AAAATAAACA
40147338 AAGTAAGCTTTATAGCTTAGTAAG
1 AAGTAAGCTTTATAGCTTAGTAAG
40147362 AAGTAAGCTTTATAGCTTAGTAAG
1 AAGTAAGCTTTATAGCTTAGTAAG
40147386 CTCGTATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (24 bp):
AAGTAAGCTTTATAGCTTAGTAAG
Found at i:40147699 original size:40 final size:40
Alignment explanation
Indices: 40147655--40147794 Score: 167
Period size: 41 Copynumber: 3.5 Consensus size: 40
40147645 CAAATCGCAC
* *
40147655 ACTAAGTGCGATATATAGCCAAGCTCTCTCGATCTCACAA
1 ACTAAGTGCCATATATAGCCAAGCTATCTCGATCTCACAA
* * *
40147695 ACTAAGTGCCATATATAGCCAAAGCTATCTTGATCTCGCAC
1 ACTAAGTGCCATATATAGCC-AAGCTATCTCGATCTCACAA
* *
40147736 ACTAAGTGCCATATATAGCCAAAGCTATGTCGAATCGCAC--
1 ACTAAGTGCCATATATAGCC-AAGCTATCTCG-ATCTCACAA
*
40147776 ACTAAGTGCCACATATAGC
1 ACTAAGTGCCATATATAGC
40147795 TAATTTGTCG
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
40 37 0.42
41 46 0.52
42 5 0.06
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (40 bp):
ACTAAGTGCCATATATAGCCAAGCTATCTCGATCTCACAA
Found at i:40147740 original size:41 final size:41
Alignment explanation
Indices: 40147636--40147794 Score: 207
Period size: 40 Copynumber: 4.0 Consensus size: 41
40147626 TACATAGTCG
** *
40147636 AAGCTATCTC-AAATCGCACACTAAGTGCGATATATAGCC-
1 AAGCTATCTCGATCTCGCACACTAAGTGCCATATATAGCCA
* * *
40147675 AAGCTCTCTCGATCTCACAAACTAAGTGCCATATATAGCCA
1 AAGCTATCTCGATCTCGCACACTAAGTGCCATATATAGCCA
*
40147716 AAGCTATCTTGATCTCGCACACTAAGTGCCATATATAGCCA
1 AAGCTATCTCGATCTCGCACACTAAGTGCCATATATAGCCA
* * *
40147757 AAGCTATGTCGA-ATCGCACACTAAGTGCCACATATAGC
1 AAGCTATCTCGATCTCGCACACTAAGTGCCATATATAGC
40147795 TAATTTGTCG
Statistics
Matches: 104, Mismatches: 14, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
39 9 0.09
40 48 0.46
41 47 0.45
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (41 bp):
AAGCTATCTCGATCTCGCACACTAAGTGCCATATATAGCCA
Found at i:40151515 original size:48 final size:47
Alignment explanation
Indices: 40151353--40151584 Score: 175
Period size: 48 Copynumber: 4.9 Consensus size: 47
40151343 GTCGAGGCTG
* * * * * *
40151353 ATGCCATGTCCCAGACATGGTCTTACACCAGCTCTCAT-CTCAGTACCG
1 ATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATAC-AAG-ACCA
* * * * *
40151401 ATGCCATGTTCCAAACAAGGTCTTACACTGGCTCACGTATCGAGGCCA
1 ATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATA-CAAGACCA
* ** * * *
40151449 AAGCCGCG-TCCTAGACATGGCCTTACACTAGCTCTTGCATA-AATG-CCA
1 ATGCCATGTTCC-AAACATGGTCTTACACTAGCTC--ACATACAA-GACCA
* *
40151497 ATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCAAGACCG
1 ATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATA-CAAGACCA
* *
40151545 ATGCCATGTTCCAAACATGGTCTTACGCTGGCTCACATAC
1 ATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATAC
40151585 CCTAGTATCA
Statistics
Matches: 145, Mismatches: 29, Indels: 21
0.74 0.15 0.11
Matches are distributed among these distances:
46 4 0.03
47 5 0.03
48 126 0.87
49 6 0.04
50 4 0.03
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (47 bp):
ATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATACAAGACCA
Found at i:40156524 original size:46 final size:46
Alignment explanation
Indices: 40156471--40156641 Score: 197
Period size: 46 Copynumber: 3.7 Consensus size: 46
40156461 AGATTTGTGT
*
40156471 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGATA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGA
* * *
40156517 GCCAGTGTAGGACCATGTCTGGGACATGGCAT-TG--GCATTGA-GACGA
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCACATT-ATGA-GA
*
40156563 GGGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGA
1 --GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGA
* *
40156611 GCCAGTGTAAGACATGTTTGGGATATGCATC
1 GCCAGTGTAAGACATGTCTGGGACATGCATC
40156642 GGCCTCGAGA
Statistics
Matches: 104, Mismatches: 11, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
45 6 0.06
46 45 0.43
47 30 0.29
48 17 0.16
49 6 0.06
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.24
Consensus pattern (46 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGA
Found at i:40157362 original size:41 final size:41
Alignment explanation
Indices: 40157305--40157388 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
40157295 TCTGAGTATG
40157305 TAGGATTCAATTAAATAAAAATTATGGCTATCTTTCTCTTC
1 TAGGATTCAATTAAATAAAAATTATGGCTATCTTTCTCTTC
40157346 TAGGATTCAATTAAATAAAAATTATGGCTATCTTTCTCTTC
1 TAGGATTCAATTAAATAAAAATTATGGCTATCTTTCTCTTC
40157387 TA
1 TA
40157389 AGTATTCTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.42
Consensus pattern (41 bp):
TAGGATTCAATTAAATAAAAATTATGGCTATCTTTCTCTTC
Found at i:40159565 original size:80 final size:80
Alignment explanation
Indices: 40159432--40159635 Score: 295
Period size: 80 Copynumber: 2.5 Consensus size: 80
40159422 CGGATGATAA
* * * * *
40159432 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCTGGGTTAAGTCCCGAATAAATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCCCGAAGAAATTT
40159496 GTGCGAACTACTATAT
65 GTGCGAACTACTATAT
**
40159512 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGAAATTTG
40159577 TGCGAACTACTATAT
66 TGCGAACTACTATAT
* *
40159592 CCGGGCTAAGTCCCGAAGGCATTCGAGCGAG-TAGCTATATCCGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGG
40159636 TTAAATCCCG
Statistics
Matches: 113, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
79 2 0.02
80 110 0.97
81 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGAAATTTG
TGCGAACTACTATAT
Found at i:40159630 original size:40 final size:39
Alignment explanation
Indices: 40159432--40159635 Score: 257
Period size: 40 Copynumber: 5.1 Consensus size: 39
40159422 CGGATGATAA
*
40159432 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT-ACTATA-T
* * *** *
40159472 CTGGGTTAAGTCCCGAATAAATTTGTGCGAACTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTACTATAT
40159512 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT
*
40159552 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTACTATAT
* *
40159592 CCGGGCTAAGTCCCGAAGGCATTCGAGCGAGTAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTA-CTATAT
40159632 CCGG
1 CCGG
40159636 TTAAATCCCG
Statistics
Matches: 142, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
39 4 0.03
40 134 0.94
41 4 0.03
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATAT
Found at i:40167675 original size:40 final size:38
Alignment explanation
Indices: 40167620--40167835 Score: 226
Period size: 40 Copynumber: 5.5 Consensus size: 38
40167610 CGGATGATAA
40167620 CCGGGCT-AGATCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGC-AGT-ACTATA-T
*
40167660 CCGGGCTAAGTCCCGAAGG-AGTTTGTGCGAACTACTATAT
1 CCGGGCTAAGTCCCGAAGGCA-TTTGTGC--AGTACTATAT
40167700 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-AG-TACTATAT
*
40167740 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAGTACTATAT
* * *
40167777 ATCGGGCTAAGTCCCGAAGGCATTCGAGCGAGTAGCTATAT
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGC-AGTA-CTATAT
* *
40167818 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
40167836 TACTTGGTTT
Statistics
Matches: 154, Mismatches: 12, Indels: 21
0.82 0.06 0.11
Matches are distributed among these distances:
37 7 0.05
38 26 0.17
39 16 0.10
40 93 0.60
41 12 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAGTACTATAT
Found at i:40167753 original size:80 final size:79
Alignment explanation
Indices: 40167620--40167835 Score: 291
Period size: 80 Copynumber: 2.7 Consensus size: 79
40167610 CGGATGATAA
* *
40167620 CCGGGCT-AGATCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCCCGAAGG-AGT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCCCGAAGGCA-T
40167682 TTGTGCGAACTACTATAT
63 TTGTGCGAACTA-TATAT
40167700 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
40167765 TGCGAACTATATAT
66 TGCGAACTATATAT
* * * *
40167779 -CGGGCTAAGTCCCGAAGGCATTCGAGCGAG-TAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAAGTCCCGAAGG
40167836 TACTTGGTTT
Statistics
Matches: 126, Mismatches: 6, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
77 16 0.13
78 36 0.29
79 5 0.04
80 65 0.52
81 4 0.03
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAACTATATAT
Found at i:40182517 original size:27 final size:27
Alignment explanation
Indices: 40182487--40182664 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
40182477 ATATTGAGTC
* *
40182487 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
40182514 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
40182541 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
40182569 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* * **
40182596 TGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
40182623 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
40182650 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40182665 GTACAGTTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:40186013 original size:15 final size:15
Alignment explanation
Indices: 40185979--40186038 Score: 66
Period size: 15 Copynumber: 4.0 Consensus size: 15
40185969 TATAGATAAC
* * *
40185979 AAGAAAACCAGGATT
1 AAGAAATCCAAGATA
*
40185994 AAGAAGTCCAAGATA
1 AAGAAATCCAAGATA
* *
40186009 GAGAAATCAAAGATA
1 AAGAAATCCAAGATA
40186024 AAGAAATCCAAGATA
1 AAGAAATCCAAGATA
40186039 CAATATCATA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.57, C:0.12, G:0.18, T:0.13
Consensus pattern (15 bp):
AAGAAATCCAAGATA
Found at i:40186014 original size:30 final size:30
Alignment explanation
Indices: 40185980--40186038 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
40185970 ATAGATAACA
* * * *
40185980 AGAAAACCAGGATTAAGAAGTCCAAGATAG
1 AGAAAACAAAGATAAAGAAATCCAAGATAG
*
40186010 AGAAATCAAAGATAAAGAAATCCAAGATA
1 AGAAAACAAAGATAAAGAAATCCAAGATA
40186039 CAATATCATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.56, C:0.12, G:0.19, T:0.14
Consensus pattern (30 bp):
AGAAAACAAAGATAAAGAAATCCAAGATAG
Found at i:40190808 original size:47 final size:47
Alignment explanation
Indices: 40190756--40191067 Score: 464
Period size: 47 Copynumber: 6.6 Consensus size: 47
40190746 GATAATTGTG
* *
40190756 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
40190803 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
40190850 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
40190899 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
40190948 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * *
40190995 ATGTGAAAGTGTATATATGTGA-CAGAGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAG-GCCTAATGGCCGATGTGATGA
*
40191042 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
40191068 TCCCGAAGGG
Statistics
Matches: 246, Mismatches: 15, Indels: 7
0.92 0.06 0.03
Matches are distributed among these distances:
46 2 0.01
47 148 0.60
48 2 0.01
49 94 0.38
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:40190826 original size:96 final size:94
Alignment explanation
Indices: 40190756--40191067 Score: 439
Period size: 96 Copynumber: 3.3 Consensus size: 94
40190746 GATAATTGTG
40190756 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
40190821 GTGATAAGGCCG-AATGGCCAATGTGATGA
66 GTGATAAGG-CGTAATGGCCAATGTGATGA
40190850 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTG-AA-TGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TAT
* *
40190915 ATATGTGATAAGGCCTAATGGCCGATGTGATGA
62 ATATGTGATAAGGCGTAATGGCCAATGTGATGA
* * *
40190948 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
* * * * *
40191013 GTGACAGAGCCG-AGTGGCCAACGTGATGG
66 GTGATA-AGGCGTAATGGCCAATGTGATGA
* * *
40191042 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAATGTATATATATGTGATAAG
40191068 TCCCGAAGGG
Statistics
Matches: 198, Mismatches: 14, Indels: 12
0.88 0.06 0.05
Matches are distributed among these distances:
94 54 0.27
95 5 0.03
96 99 0.50
97 3 0.02
98 37 0.19
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (94 bp):
ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
GTGATAAGGCGTAATGGCCAATGTGATGA
Found at i:40194441 original size:101 final size:100
Alignment explanation
Indices: 40194230--40194468 Score: 273
Period size: 101 Copynumber: 2.4 Consensus size: 100
40194220 AACTGAAGCT
* * * * *
40194230 ATCTGGTACACATAGTATCCTGCACTTAGTACTGCACACATGACCTAACAATCTGGTACACGTAG
1 ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACATGACCGAACAATCGGGTACACATAG
* * * * * *
40194295 TAGTCTGCACTTAGTACTCCACACGTGTCCTAACC
66 TAGCCTACACTTAGTACTACACACGCGACCTAACA
* * * * **
40194330 ATC-GGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGCTATCGGGTATGCAT
1 ATCTGG-TACACATAGTAGCCTGCACTTAGTACTACACACATGACCGAA-CAATCGGGTACACAT
*
40194394 AGTAGCCTACACTTAGTACTACACATGCGACCTAACA
64 AGTAGCCTACACTTAGTACTACACACGCGACCTAACA
* *
40194431 ATCTAGTACACATAGTAGCCTGCACTTATTACTACACA
1 ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACA
40194469 TGTGTTCTCA
Statistics
Matches: 115, Mismatches: 21, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
99 2 0.02
100 39 0.34
101 73 0.63
102 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (100 bp):
ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACATGACCGAACAATCGGGTACACATAG
TAGCCTACACTTAGTACTACACACGCGACCTAACA
Found at i:40194469 original size:50 final size:50
Alignment explanation
Indices: 40194230--40194472 Score: 263
Period size: 50 Copynumber: 4.8 Consensus size: 50
40194220 AACTGAAGCT
* * **
40194230 ATCTGGTACACATAGTATCCTGCACTTAGTACTGCACACATGACCTAACA
1 ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACA
* * * * * *
40194280 ATCTGGTACACGTAGTAGTCTGCACTTAGTACTCCACACGTGTCCTAACC
1 ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACA
* * * * *
40194330 ATC-GGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGCT
1 ATCTGG-TACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAA-CA
* ** * *
40194381 ATCGGGTATGCATAGTAGCCTACACTTAGTACTACACATGCGACCTAACA
1 ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACA
* *
40194431 ATCTAGTACACATAGTAGCCTGCACTTATTACTACACATGTG
1 ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTG
40194473 TTCTCACAAC
Statistics
Matches: 161, Mismatches: 29, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
49 2 0.01
50 119 0.74
51 38 0.24
52 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (50 bp):
ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACA
Found at i:40208832 original size:40 final size:41
Alignment explanation
Indices: 40208770--40208921 Score: 193
Period size: 40 Copynumber: 3.8 Consensus size: 41
40208760 CATTTGAATG
* * * * *
40208770 ATATTCGGGCTAAGTCCTGAAGGCATTTATGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
*
40208810 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
*
40208850 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
* * *
40208890 ATACCCGGGTTAAGACCCGAAGGCAATTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC
40208922 TTGTGGTTAT
Statistics
Matches: 100, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
40 97 0.97
41 3 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (41 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
Found at i:40208933 original size:80 final size:80
Alignment explanation
Indices: 40208770--40208941 Score: 195
Period size: 80 Copynumber: 2.2 Consensus size: 80
40208760 CATTTGAATG
* * * * * * *
40208770 ATATTCGGGCTAAGTCCTGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGACTATACCCGGGCTAAGACCCGAAGGCA
* *
40208835 TTTGTGCGAGTTGAT
66 ATTGTGCGAGTGGAT
* *
40208850 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATACCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAG-TGACTATACCCGGGCTAAGACCCGAAGGC
** *
40208914 AATTGTGCTTGTGGTT
65 AATTGTGCGAGTGGAT
40208930 ATATCC-GGCTAA
1 ATATCCGGGCTAA
40208942 ACTCCAAAGA
Statistics
Matches: 77, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
79 6 0.08
80 69 0.90
81 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGACTATACCCGGGCTAAGACCCGAAGGCA
ATTGTGCGAGTGGAT
Found at i:40214124 original size:37 final size:37
Alignment explanation
Indices: 40214083--40214161 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
40214073 TTATTACGAA
* * *
40214083 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
40214120 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
40214157 GTCTT
1 GTCTT
40214162 TAGAGCTTGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:40214358 original size:47 final size:47
Alignment explanation
Indices: 40214280--40214705 Score: 708
Period size: 47 Copynumber: 8.9 Consensus size: 47
40214270 CCCTTCGGGA
* * * * * *
40214280 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40214327 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40214374 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40214421 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40214470 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40214519 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40214566 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40214613 CTTATCACATATATACACTTTGACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40214660 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTA
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTA
40214706 CGCCATACTA
Statistics
Matches: 361, Mismatches: 14, Indels: 6
0.95 0.04 0.02
Matches are distributed among these distances:
47 232 0.64
49 129 0.36
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:40214622 original size:22 final size:22
Alignment explanation
Indices: 40214594--40214669 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
40214584 TTTCACATTC
40214594 ATCACATCGGCCATTAGGCCTT
1 ATCACATCGGCCATTAGGCCTT
**** * * *
40214616 ATCACATATATACACTTTGACATT
1 ATCACAT-CGGCCA-TTAGGCCTT
40214640 CATCACATCGGCCATTAGGCCTT
1 -ATCACATCGGCCATTAGGCCTT
40214663 ATCACAT
1 ATCACAT
40214670 ATATATACAC
Statistics
Matches: 37, Mismatches: 14, Indels: 6
0.65 0.25 0.11
Matches are distributed among these distances:
22 14 0.38
23 8 0.22
24 8 0.22
25 7 0.19
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.30
Consensus pattern (22 bp):
ATCACATCGGCCATTAGGCCTT
Found at i:40226688 original size:39 final size:40
Alignment explanation
Indices: 40226644--40226736 Score: 134
Period size: 41 Copynumber: 2.3 Consensus size: 40
40226634 TTACAAAATA
* *
40226644 TTATCTAATTACACA-TTTTTGTACAAAATTGATAATATT
1 TTATCTAATTACACATTTTTTGTACAAAATTCATAACATT
* *
40226683 TTATCTAGTTACACATTTTTTTTTACAAAATTCATAACATT
1 TTATCTAATTACACA-TTTTTTGTACAAAATTCATAACATT
40226724 TTATCTAATTACA
1 TTATCTAATTACA
40226737 AAATATTTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 14 0.30
41 33 0.70
ACGTcount: A:0.37, C:0.13, G:0.03, T:0.47
Consensus pattern (40 bp):
TTATCTAATTACACATTTTTTGTACAAAATTCATAACATT
Found at i:40231270 original size:18 final size:18
Alignment explanation
Indices: 40231247--40231282 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
40231237 AAGTAAGTTC
40231247 GTTCGGTTTGTAATTTAA
1 GTTCGGTTTGTAATTTAA
40231265 GTTCGGTTTGTAATTTAA
1 GTTCGGTTTGTAATTTAA
40231283 TATCTATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.06, G:0.22, T:0.50
Consensus pattern (18 bp):
GTTCGGTTTGTAATTTAA
Found at i:40233704 original size:39 final size:39
Alignment explanation
Indices: 40233645--40233899 Score: 348
Period size: 39 Copynumber: 6.5 Consensus size: 39
40233635 TATAATTATA
*
40233645 CCCTGTTGTACTTCGATACCCCTGAATGCACATACGTGC
1 CCCTGTTGTACTTCGGTACCCCTGAATGCACATACGTGC
* * *
40233684 CCTTGTTGTACTTCGGTACCCCTAAACGCACATACGTGC
1 CCCTGTTGTACTTCGGTACCCCTGAATGCACATACGTGC
* * *
40233723 CCCTCTTGTACTTCAGTACCCATGAATGCACATACGTGC
1 CCCTGTTGTACTTCGGTACCCCTGAATGCACATACGTGC
* *
40233762 CCCTGTTGTAGTTTGGTACCCCTGAATGCACATACGTGC
1 CCCTGTTGTACTTCGGTACCCCTGAATGCACATACGTGC
** * * * *
40233801 CCCTGTTGTACTTTAGTACCCCTAAACGCAAATACGTTC
1 CCCTGTTGTACTTCGGTACCCCTGAATGCACATACGTGC
* * *
40233840 CCCTATTGTACTTTGGTACCCCTGAATGCACATATGTGC
1 CCCTGTTGTACTTCGGTACCCCTGAATGCACATACGTGC
40233879 CCCTGTTGTACTTCGGTACCC
1 CCCTGTTGTACTTCGGTACCC
40233900 ATGATTCACA
Statistics
Matches: 186, Mismatches: 30, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 186 1.00
ACGTcount: A:0.20, C:0.32, G:0.18, T:0.30
Consensus pattern (39 bp):
CCCTGTTGTACTTCGGTACCCCTGAATGCACATACGTGC
Found at i:40233851 original size:117 final size:117
Alignment explanation
Indices: 40233645--40233899 Score: 393
Period size: 117 Copynumber: 2.2 Consensus size: 117
40233635 TATAATTATA
* * *
40233645 CCCTGTTGTACTTCGATACCCCTGAATGCACATACGTGCCCTTGTTGTACTTCGGTACCCCTAAA
1 CCCTGTTGTACTTCGGTACCCCTGAATGCACATACGTGCCCCTGTTGTACTTCAGTACCCCTAAA
* *
40233710 CGCACATACGTGCCCCTCTTGTACTTCAGTACCCATGAATGCACATACGTGC
66 CGCAAATACGTGCCCCTATTGTACTTCAGTACCCATGAATGCACATACGTGC
* * *
40233762 CCCTGTTGTAGTTTGGTACCCCTGAATGCACATACGTGCCCCTGTTGTACTTTAGTACCCCTAAA
1 CCCTGTTGTACTTCGGTACCCCTGAATGCACATACGTGCCCCTGTTGTACTTCAGTACCCCTAAA
* ** * *
40233827 CGCAAATACGTTCCCCTATTGTACTTTGGTACCCCTGAATGCACATATGTGC
66 CGCAAATACGTGCCCCTATTGTACTTCAGTACCCATGAATGCACATACGTGC
40233879 CCCTGTTGTACTTCGGTACCC
1 CCCTGTTGTACTTCGGTACCC
40233900 ATGATTCACA
Statistics
Matches: 123, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
117 123 1.00
ACGTcount: A:0.20, C:0.32, G:0.18, T:0.30
Consensus pattern (117 bp):
CCCTGTTGTACTTCGGTACCCCTGAATGCACATACGTGCCCCTGTTGTACTTCAGTACCCCTAAA
CGCAAATACGTGCCCCTATTGTACTTCAGTACCCATGAATGCACATACGTGC
Found at i:40239037 original size:39 final size:39
Alignment explanation
Indices: 40238994--40239226 Score: 299
Period size: 39 Copynumber: 6.0 Consensus size: 39
40238984 GTGTGAGACA
*
40238994 TATATCCGGGCTAATTCCCGAAGGCATTTGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTGGTGT
* * *
40239033 TATATCCGGGCTAAGTCTCAAAGGCATTTGTGCTGGTGC
1 TATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTGGTGT
* *
40239072 TATATCCGAGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTGGTGT
* *
40239111 TATACCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTGGTGT
* * *
40239150 TATATCCGGGCTAAGTCCCGAAGGC-TTTATGTTGGTAT
1 TATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTGGTGT
* * * *
40239188 TATATCCAGGCTTAAAGTCCCGCATGC-TTTGTGGTGGTG
1 TATATCCGGGC-T-AAGTCCCGAAGGCATTTGTGCTGGTG
40239227 ATTGAATTTG
Statistics
Matches: 170, Mismatches: 22, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
38 19 0.11
39 131 0.77
40 20 0.12
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.31
Consensus pattern (39 bp):
TATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTGGTGT
Found at i:40243591 original size:20 final size:20
Alignment explanation
Indices: 40243566--40243603 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40243556 GTCACATATA
40243566 TCATGAACTCAGACCACAAC
1 TCATGAACTCAGACCACAAC
* *
40243586 TCATGAGCTCAGATCACA
1 TCATGAACTCAGACCACA
40243604 TAGTTCCTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.32, G:0.13, T:0.18
Consensus pattern (20 bp):
TCATGAACTCAGACCACAAC
Found at i:40257730 original size:21 final size:22
Alignment explanation
Indices: 40257681--40257736 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
40257671 GTGCAGGGCT
*
40257681 CACACGCCCGTGTAGTCCAAGG
1 CACACGCCCGTGTAGACCAAGG
* *
40257703 GACACGCCCGTGT-GACCATGG
1 CACACGCCCGTGTAGACCAAGG
40257724 CACACGCCCGTGT
1 CACACGCCCGTGT
40257737 TAGAGGTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 18 0.60
22 12 0.40
ACGTcount: A:0.20, C:0.38, G:0.29, T:0.14
Consensus pattern (22 bp):
CACACGCCCGTGTAGACCAAGG
Found at i:40261893 original size:43 final size:46
Alignment explanation
Indices: 40261838--40261955 Score: 156
Period size: 45 Copynumber: 2.7 Consensus size: 46
40261828 CGAGCTTCGG
* *
40261838 GCCTAGCAGGCTATAATGCCGGTGAAATGA-TA-TC-GGGCTTTGA
1 GCCTAGCAGGCTATAATGCCGGTGAAATGATTATTCAAGCCTTTGA
* *
40261881 GCTTA-CTAGGCTATGATGCCGGTGAAAT-ATTATTCAAGCCTTTGA
1 GCCTAGC-AGGCTATAATGCCGGTGAAATGATTATTCAAGCCTTTGA
40261926 GCCTAGCAGGCTATAATGCCGGTGAAATGA
1 GCCTAGCAGGCTATAATGCCGGTGAAATGA
40261956 AATGTTATAT
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
42 2 0.03
43 26 0.41
44 2 0.03
45 31 0.49
46 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (46 bp):
GCCTAGCAGGCTATAATGCCGGTGAAATGATTATTCAAGCCTTTGA
Found at i:40263058 original size:27 final size:27
Alignment explanation
Indices: 40263026--40263088 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
40263016 CTCGACTTGT
*
40263026 AAAATTACCAAAGTACTCTCGATTTAC
1 AAAATTACCAAAGTACCCTCGATTTAC
* ****
40263053 AGAATTACCGTTTTACCCTCGATTTAC
1 AAAATTACCAAAGTACCCTCGATTTAC
40263080 AAAATTACC
1 AAAATTACC
40263089 GTTTTACCCT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.37, C:0.24, G:0.08, T:0.32
Consensus pattern (27 bp):
AAAATTACCAAAGTACCCTCGATTTAC
Found at i:40263089 original size:27 final size:27
Alignment explanation
Indices: 40263043--40263314 Score: 361
Period size: 27 Copynumber: 10.1 Consensus size: 27
40263033 CCAAAGTACT
40263043 CTCGATTTACAGAATTACCGTTTTACC
1 CTCGATTTACAGAATTACCGTTTTACC
*
40263070 CTCGATTTACAAAATTACCGTTTTACC
1 CTCGATTTACAGAATTACCGTTTTACC
* *
40263097 CTCGATTTATAGAATTACTGTTTTACC
1 CTCGATTTACAGAATTACCGTTTTACC
*
40263124 CTC-AGTTTACAGAATTACTGTTTTACC
1 CTCGA-TTTACAGAATTACCGTTTTACC
* *
40263151 CTCGATTTATAGAATTACCGCTTTACC
1 CTCGATTTACAGAATTACCGTTTTACC
* ** *
40263178 CTCAATTTGTAAAATTACCGTTTTACC
1 CTCGATTTACAGAATTACCGTTTTACC
40263205 CTCGATTTACAGAATTACCGTTTTACC
1 CTCGATTTACAGAATTACCGTTTTACC
* **
40263232 CTC-AGTTTATAGAATTACTATTTTACC
1 CTCGA-TTTACAGAATTACCGTTTTACC
*
40263259 TTCGATTTACAGAATTACCGTTTTACC
1 CTCGATTTACAGAATTACCGTTTTACC
*
40263286 CTC-AGTTTACAGAATTACTGTTTTACC
1 CTCGA-TTTACAGAATTACCGTTTTACC
40263313 CT
1 CT
40263315 TAATTTGCAA
Statistics
Matches: 215, Mismatches: 25, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
26 3 0.01
27 210 0.98
28 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (27 bp):
CTCGATTTACAGAATTACCGTTTTACC
Found at i:40263342 original size:54 final size:54
Alignment explanation
Indices: 40263043--40263314 Score: 402
Period size: 54 Copynumber: 5.0 Consensus size: 54
40263033 CCAAAGTACT
* *
40263043 CTCGATTTACAGAATTACCGTTTTACCCTC-GATTTACAAAATTACCGTTTTACC
1 CTCGATTTACAGAATTACCGTTTTACCCTCAG-TTTACAGAATTACTGTTTTACC
* *
40263097 CTCGATTTATAGAATTACTGTTTTACCCTCAGTTTACAGAATTACTGTTTTACC
1 CTCGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACTGTTTTACC
* * * ** * *
40263151 CTCGATTTATAGAATTACCGCTTTACCCTCAATTTGTAAAATTACCGTTTTACC
1 CTCGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACTGTTTTACC
* *
40263205 CTCGATTTACAGAATTACCGTTTTACCCTCAGTTTATAGAATTACTATTTTACC
1 CTCGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACTGTTTTACC
*
40263259 TTCGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACTGTTTTACC
1 CTCGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACTGTTTTACC
40263313 CT
1 CT
40263315 TAATTTGCAA
Statistics
Matches: 195, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
54 194 0.99
55 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (54 bp):
CTCGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACTGTTTTACC
Found at i:40263345 original size:81 final size:81
Alignment explanation
Indices: 40263048--40263345 Score: 357
Period size: 81 Copynumber: 3.7 Consensus size: 81
40263038 GTACTCTCGA
* *
40263048 TTTACAGAATTACCGTTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTATAGAATT
1 TTTACAGAATTACCGTTTTACCCTCAATTTACAAAATTACCGATTTACCCTCGATTTATAGAATT
*
40263113 ACTGTTTTACCCTCAG
66 ACCGTTTTACCCTCAG
* * * * * * * *
40263129 TTTACAGAATTACTGTTTTACCCTCGATTTATAGAATTACCGCTTTACCCTCAATTTGTAAAATT
1 TTTACAGAATTACCGTTTTACCCTCAATTTACAAAATTACCGATTTACCCTCGATTTATAGAATT
40263194 ACCGTTTTACCCTC-G
66 ACCGTTTTACCCTCAG
* * * * * *
40263209 ATTTACAGAATTACCGTTTTACCCTCAGTTTATAGAATTA-CTATTTTACCTTCGATTTACAGAA
1 -TTTACAGAATTACCGTTTTACCCTCAATTTACAAAATTACCGA-TTTACCCTCGATTTATAGAA
40263273 TTACCGTTTTACCCTCAG
64 TTACCGTTTTACCCTCAG
* * * * **
40263291 TTTACAGAATTACTGTTTTACCCTTAATTTGCAAAATTACTGAAATACCCTCGAT
1 TTTACAGAATTACCGTTTTACCCTCAATTTACAAAATTACCGATTTACCCTCGAT
40263346 CAATAAAATT
Statistics
Matches: 184, Mismatches: 29, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
80 2 0.01
81 180 0.98
82 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.40
Consensus pattern (81 bp):
TTTACAGAATTACCGTTTTACCCTCAATTTACAAAATTACCGATTTACCCTCGATTTATAGAATT
ACCGTTTTACCCTCAG
Found at i:40263379 original size:27 final size:27
Alignment explanation
Indices: 40263348--40263424 Score: 100
Period size: 27 Copynumber: 2.9 Consensus size: 27
40263338 CCCTCGATCA
40263348 ATAAAATTACCAAAATACCCCTGGTTT
1 ATAAAATTACCAAAATACCCCTGGTTT
* *
40263375 GTAAAATTACCAAAATACCCTTGGTTT
1 ATAAAATTACCAAAATACCCCTGGTTT
* * * *
40263402 ACAAAATTATCGAAAGACCCCTG
1 ATAAAATTACCAAAATACCCCTG
40263425 TAGGGTAGAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.27
Consensus pattern (27 bp):
ATAAAATTACCAAAATACCCCTGGTTT
Found at i:40263436 original size:27 final size:27
Alignment explanation
Indices: 40263406--40263582 Score: 246
Period size: 27 Copynumber: 6.6 Consensus size: 27
40263396 TGGTTTACAA
*
40263406 AATTATCGAAAGACCCCTGTAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
40263433 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
*
40263460 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
* * *
40263487 AATTATAGCAATACCCCCGTAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
* *
40263514 AATTATCAAAATACCCTTGTAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
* * *
40263541 AAATACCGAAATACCCCTTTAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
* *
40263568 AATTACCGAGATACC
1 AATTATCGAAATACC
40263583 TTTGTGGGTT
Statistics
Matches: 132, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 132 1.00
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (27 bp):
AATTATCGAAATACCCCTGTAGGGTAG
Found at i:40263838 original size:27 final size:26
Alignment explanation
Indices: 40263800--40263882 Score: 103
Period size: 27 Copynumber: 3.1 Consensus size: 26
40263790 CGGAGGAAGC
40263800 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTATGCCAC-AATATCT
*
40263827 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTATGCCACAATATCT
* * **
40263853 GTATCTGGTGACTCTATCACAATATCT
1 GT-TCTGGTGGCTATGCCACAATATCT
40263880 GTT
1 GTT
40263883 GACCAATCGA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 10 0.20
27 41 0.80
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (26 bp):
GTTCTGGTGGCTATGCCACAATATCT
Found at i:40264215 original size:27 final size:27
Alignment explanation
Indices: 40264185--40264266 Score: 96
Period size: 27 Copynumber: 3.1 Consensus size: 27
40264175 TATTCTATTA
* *
40264185 GGTGGCTTTGCCACATTATCTG-ATTCT
1 GGTGGCTCTGCCACAATATCTGTA-TCT
40264212 GGTGGCTCTGCCACAATATCTGTATCT
1 GGTGGCTCTGCCACAATATCTGTATCT
* * *
40264239 GGTGACTCTGTCACGATATCTGT-TCT
1 GGTGGCTCTGCCACAATATCTGTATCT
40264265 GG
1 GG
40264267 CAGCCATGCT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
26 5 0.10
27 43 0.88
28 1 0.02
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.37
Consensus pattern (27 bp):
GGTGGCTCTGCCACAATATCTGTATCT
Found at i:40264393 original size:6 final size:6
Alignment explanation
Indices: 40264384--40264533 Score: 114
Period size: 6 Copynumber: 24.8 Consensus size: 6
40264374 TTGCATTCAC
* * * *
40264384 ATTCTG ATTCTA ATTCTG ATTCT- ATTACTA ATACTG ATTCTG ATTCTA
1 ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG ATTCTG
* * * *
40264432 ATTCTG -TTACTG ATTCTG ATTCTA ATTTTG -TCACCTA ATTCTG ATTCTG
1 ATTCTG ATT-CTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG
*
40264481 ATTCTG ATTCTG -TTACTA ATAT-TG ATTCTG ATTCTG ATTCTG -TTACTG
1 ATTCTG ATTCTG ATT-CTG AT-TCTG ATTCTG ATTCTG ATTCTG ATT-CTG
40264529 ATTCT
1 ATTCT
40264534 CATTTTGGTT
Statistics
Matches: 114, Mismatches: 17, Indels: 26
0.73 0.11 0.17
Matches are distributed among these distances:
5 11 0.10
6 93 0.82
7 8 0.07
8 2 0.02
ACGTcount: A:0.23, C:0.17, G:0.11, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:40264421 original size:30 final size:30
Alignment explanation
Indices: 40264387--40264527 Score: 159
Period size: 30 Copynumber: 4.9 Consensus size: 30
40264377 CATTCACATT
* *
40264387 CTGATTCTAATTCTGATTCTATTACTAATA
1 CTGATTCTGATTCTGATTCTGTTACTAATA
*
40264417 CTGATTCTGATTCTAATTCTG----T--TA
1 CTGATTCTGATTCTGATTCTGTTACTAATA
* * * *
40264441 CTGATTCTGATTCTAATTTTGTCACCTAATT
1 CTGATTCTGATTCTGATTCTGTTA-CTAATA
40264472 CTGATTCTGATTCTGATTCTGTTACTAATA
1 CTGATTCTGATTCTGATTCTGTTACTAATA
*
40264502 TTGATTCTGATTCTGATTCTGTTACT
1 CTGATTCTGATTCTGATTCTGTTACT
40264528 GATTCTCATT
Statistics
Matches: 94, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
24 22 0.23
26 1 0.01
29 1 0.01
30 48 0.51
31 22 0.23
ACGTcount: A:0.23, C:0.17, G:0.11, T:0.49
Consensus pattern (30 bp):
CTGATTCTGATTCTGATTCTGTTACTAATA
Found at i:40265312 original size:38 final size:38
Alignment explanation
Indices: 40265269--40265504 Score: 296
Period size: 38 Copynumber: 6.2 Consensus size: 38
40265259 ATGATATTTG
* ** *
40265269 TATCCGGCTTAAAGACCGCAGGCTAT-ATGCTGGAATTA
1 TATCCGGGTTAAATCCCGCAGGCT-TCATGCTGGTATTA
*
40265307 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCATGCTGGTATTA
40265345 TATCCGGGTTAAATCCCGCAGGCTTCATGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCATGCTGGTATTA
* * * *
40265383 TATCTGGGTTAAATCTCGCAGGCTTCGTGCTGGTAATA
1 TATCCGGGTTAAATCCCGCAGGCTTCATGCTGGTATTA
* * * *
40265421 TATCCAGGTTAATTCCTGTAGGCTTCATGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCATGCTGGTATTA
* *
40265459 TATCTGGGTTAAATCCCGCAGGCCT-AGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCA-TGCTGGTATTA
*
40265497 TATTCGGG
1 TATCCGGG
40265505 CCTTTGAGCC
Statistics
Matches: 170, Mismatches: 26, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
37 2 0.01
38 168 0.99
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.33
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTCATGCTGGTATTA
Found at i:40265395 original size:76 final size:76
Alignment explanation
Indices: 40265269--40265504 Score: 330
Period size: 76 Copynumber: 3.1 Consensus size: 76
40265259 ATGATATTTG
* ** * *
40265269 TATCCGGCTTAAAGACCGCAGGCTAT-ATGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTC
1 TATCCGGGTTAAATCCCGCAGGCT-TCATGCTGGTATTATATCTGGGTTAAATCCCGCAGGCTTC
40265333 GTGCTGGTATTA
65 GTGCTGGTATTA
*
40265345 TATCCGGGTTAAATCCCGCAGGCTTCATGCTGGTATTATATCTGGGTTAAATCTCGCAGGCTTCG
1 TATCCGGGTTAAATCCCGCAGGCTTCATGCTGGTATTATATCTGGGTTAAATCCCGCAGGCTTCG
*
40265410 TGCTGGTAATA
66 TGCTGGTATTA
* * * * * *
40265421 TATCCAGGTTAATTCCTGTAGGCTTCATGCTGGTATTATATCTGGGTTAAATCCCGCAGGCCTAG
1 TATCCGGGTTAAATCCCGCAGGCTTCATGCTGGTATTATATCTGGGTTAAATCCCGCAGGCTTCG
40265486 TGCTGGTATTA
66 TGCTGGTATTA
*
40265497 TATTCGGG
1 TATCCGGG
40265505 CCTTTGAGCC
Statistics
Matches: 142, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
75 1 0.01
76 141 0.99
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.33
Consensus pattern (76 bp):
TATCCGGGTTAAATCCCGCAGGCTTCATGCTGGTATTATATCTGGGTTAAATCCCGCAGGCTTCG
TGCTGGTATTA
Found at i:40265547 original size:45 final size:45
Alignment explanation
Indices: 40265497--40265619 Score: 194
Period size: 45 Copynumber: 2.7 Consensus size: 45
40265487 GCTGGTATTA
*
40265497 TATTCGGGCCTTTGAGCCTAGCAGGCTATTATGCCGGTGAGACAC
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGACAC
* *
40265542 TATTCGGGCCTTTGGGCCTAGCAGGCTATAATGCCGGTGAGATAC
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGACAC
*
40265587 TAATCGGG-CTTTCGAGCCTAGCAGGCTATAATG
1 TATTCGGGCCTTT-GAGCCTAGCAGGCTATAATG
40265620 TCGATGAAAT
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
44 4 0.06
45 68 0.94
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (45 bp):
TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGACAC
Found at i:40284477 original size:30 final size:30
Alignment explanation
Indices: 40284441--40284509 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
40284431 TGTTACCAGA
*
40284441 CCGTGTGTTACACACGGTCTAGACATACGT
1 CCGTGTGTCACACACGGTCTAGACATACGT
40284471 CCGTGTGTCACACACGGTCTAGACATACGT
1 CCGTGTGTCACACACGGTCTAGACATACGT
*
40284501 CCTTGTGTC
1 CCGTGTGTC
40284510 TACCTGTGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.20, C:0.29, G:0.23, T:0.28
Consensus pattern (30 bp):
CCGTGTGTCACACACGGTCTAGACATACGT
Found at i:40287403 original size:40 final size:39
Alignment explanation
Indices: 40287319--40287463 Score: 150
Period size: 40 Copynumber: 3.6 Consensus size: 39
40287309 TCGAATGATG
* * * *
40287319 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAATGACTATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTCACTAAA
* * *
40287359 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTCACTAAA
*
40287399 TCCGGGCTAAG-CCTGAAGGCATTGGTGCGAGTCACTAAA
1 TCCGGGCTAAGTCC-GAAGGCATTTGTGCGAGTCACTAAA
*
40287438 TCCGGGTTAAGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
40287464 AACGAGTAGC
Statistics
Matches: 88, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
38 2 0.02
39 32 0.36
40 44 0.50
41 10 0.11
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTCACTAAA
Found at i:40287470 original size:40 final size:38
Alignment explanation
Indices: 40287319--40287486 Score: 124
Period size: 40 Copynumber: 4.3 Consensus size: 38
40287309 TCGAATGATG
* * * *
40287319 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAATGACTATA
1 TCCGGGTTAAG-CCCGAAGGCATTTGTGC-GAGT-ACTAAA
** * *
40287359 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGTTAAG-CCCGAAGGCATTTGTGCGAG-TACTAAA
* * *
40287399 TCCGGGCTAAGCCTGAAGGCATTGGTGCGAGTCACTAAA
1 TCCGGGTTAAGCCCGAAGGCATTTGTGCGAGT-ACTAAA
** *
40287438 TCCGGGTTAAGTCCCGAAGGCATTTGAACGAGTAGCTATA
1 TCCGGGTTAAG-CCCGAAGGCATTTGTGCGAGTA-CTAAA
40287478 TCC-GGTTAA
1 TCCGGGTTAA
40287487 ATTCTGAAGG
Statistics
Matches: 105, Mismatches: 18, Indels: 11
0.78 0.13 0.08
Matches are distributed among these distances:
38 1 0.01
39 39 0.37
40 57 0.54
41 8 0.08
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (38 bp):
TCCGGGTTAAGCCCGAAGGCATTTGTGCGAGTACTAAA
Found at i:40289823 original size:20 final size:20
Alignment explanation
Indices: 40289798--40289837 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
40289788 CTACATACTT
40289798 TTATTAATGGTCTAATTACC
1 TTATTAATGGTCTAATTACC
40289818 TTATTAATGGTCTAATTACC
1 TTATTAATGGTCTAATTACC
40289838 ATATGGGGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (20 bp):
TTATTAATGGTCTAATTACC
Found at i:40290723 original size:23 final size:23
Alignment explanation
Indices: 40290688--40290734 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
40290678 TTAATAATAG
* *
40290688 TGGTATAATTATTATATTAATCCT
1 TGGTATAAATATTAT-TTAACCCT
40290712 TGGT-TAAATATTATTTAACCCT
1 TGGTATAAATATTATTTAACCCT
40290734 T
1 T
40290735 TTAACTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 8 0.38
23 9 0.43
24 4 0.19
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.49
Consensus pattern (23 bp):
TGGTATAAATATTATTTAACCCT
Found at i:40293481 original size:15 final size:14
Alignment explanation
Indices: 40293449--40293490 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
40293439 TAGTCATGCA
*
40293449 TCTTTCTTCTCTTT
1 TCTTTCTTCTCTTC
40293463 TCTTTCTTACTCTTC
1 TCTTTCTT-CTCTTC
*
40293478 TCTTTCTTTTCTT
1 TCTTTCTTCTCTT
40293491 TCCTATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (14 bp):
TCTTTCTTCTCTTC
Found at i:40294725 original size:41 final size:41
Alignment explanation
Indices: 40294667--40294753 Score: 165
Period size: 41 Copynumber: 2.1 Consensus size: 41
40294657 ACTTGCAGAT
40294667 ACCACCATATTTAGATTGTATAAAAGTTGATTATTCACTCA
1 ACCACCATATTTAGATTGTATAAAAGTTGATTATTCACTCA
*
40294708 ACCACCATATTTTGATTGTATAAAAGTTGATTATTCACTCA
1 ACCACCATATTTAGATTGTATAAAAGTTGATTATTCACTCA
40294749 ACCAC
1 ACCAC
40294754 AGTGTTCGCG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.36
Consensus pattern (41 bp):
ACCACCATATTTAGATTGTATAAAAGTTGATTATTCACTCA
Found at i:40294950 original size:41 final size:41
Alignment explanation
Indices: 40294905--40295034 Score: 142
Period size: 41 Copynumber: 3.1 Consensus size: 41
40294895 CTTTTGTCCC
40294905 TTTCAAAGTCACACCATTGTTGTCCCTTTCTTCTTCATTTT
1 TTTCAAAGTCACACCATTGTTGTCCCTTTCTTCTTCATTTT
* * * * *
40294946 TTTC-AAGTTCAGCAGCC-CTGTTTTGCACCCTTCTT-TT-GTTCT
1 TTTCAAAG-TCA-CA-CCATTGTTGT-C-CCTTTCTTCTTCATTTT
40294988 TTTCAAAGTCACACCATTGTTGTCCCTTTCTTCTTCATTTT
1 TTTCAAAGTCACACCATTGTTGTCCCTTTCTTCTTCATTTT
40295029 TTTCAA
1 TTTCAA
40295035 GTTCAACAGC
Statistics
Matches: 70, Mismatches: 10, Indels: 18
0.71 0.10 0.18
Matches are distributed among these distances:
39 7 0.10
40 8 0.11
41 23 0.33
42 17 0.24
43 8 0.11
44 7 0.10
ACGTcount: A:0.16, C:0.27, G:0.09, T:0.48
Consensus pattern (41 bp):
TTTCAAAGTCACACCATTGTTGTCCCTTTCTTCTTCATTTT
Found at i:40295020 original size:83 final size:83
Alignment explanation
Indices: 40294881--40295052 Score: 299
Period size: 83 Copynumber: 2.1 Consensus size: 83
40294871 CCGTACAAAT
**
40294881 TGTTTTGCACTGTTCTTTTGTCCCTTTCAAAGTCACACCATTGTTGTCCCTTTCTTCTTCATTTT
1 TGTTTTGCACCCTTCTTTTGTCCCTTTCAAAGTCACACCATTGTTGTCCCTTTCTTCTTCATTTT
*
40294946 TTTCAAGTTCAGCAGCCC
66 TTTCAAGTTCAACAGCCC
* *
40294964 TGTTTTGCACCCTTCTTTTGTTCTTTTCAAAGTCACACCATTGTTGTCCCTTTCTTCTTCATTTT
1 TGTTTTGCACCCTTCTTTTGTCCCTTTCAAAGTCACACCATTGTTGTCCCTTTCTTCTTCATTTT
40295029 TTTCAAGTTCAACAGCCC
66 TTTCAAGTTCAACAGCCC
40295047 TGTTTT
1 TGTTTT
40295053 TGTAAGCCTT
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.15, C:0.27, G:0.11, T:0.48
Consensus pattern (83 bp):
TGTTTTGCACCCTTCTTTTGTCCCTTTCAAAGTCACACCATTGTTGTCCCTTTCTTCTTCATTTT
TTTCAAGTTCAACAGCCC
Found at i:40295021 original size:42 final size:42
Alignment explanation
Indices: 40294893--40295022 Score: 112
Period size: 42 Copynumber: 3.1 Consensus size: 42
40294883 TTTTGCACTG
* *
40294893 TTCTTTTGTCCCTTTCAAAGTCACACCATTGTTGTCCCTTTC
1 TTCTTTTGTTCTTTTCAAAGTCACACCATTGTTGTCCCTTTC
* * *
40294935 TTCTTCAT-TT-TTTTC-AAGTTCAGCAGCC-CTGTTTTGCACC---C
1 TTCTT-TTGTTCTTTTCAAAG-TCA-CA-CCATTGTTGT-C-CCTTTC
40294976 TTCTTTTGTTCTTTTCAAAGTCACACCATTGTTGTCCCTTTC
1 TTCTTTTGTTCTTTTCAAAGTCACACCATTGTTGTCCCTTTC
40295018 TTCTT
1 TTCTT
40295023 CATTTTTTTC
Statistics
Matches: 67, Mismatches: 8, Indels: 26
0.66 0.08 0.26
Matches are distributed among these distances:
39 2 0.03
40 7 0.10
41 22 0.33
42 27 0.40
43 7 0.10
44 2 0.03
ACGTcount: A:0.14, C:0.28, G:0.10, T:0.48
Consensus pattern (42 bp):
TTCTTTTGTTCTTTTCAAAGTCACACCATTGTTGTCCCTTTC
Found at i:40300163 original size:55 final size:55
Alignment explanation
Indices: 40300079--40300190 Score: 215
Period size: 55 Copynumber: 2.0 Consensus size: 55
40300069 CCCCAAAGGA
*
40300079 ATTAAATTAATTTCTTAGTCATCTTGAGAAAATACATTTACTGTGGATAGTATTC
1 ATTAAATTAATTTCTTAGTCATCTTGAGAAAATACATTTACTGTAGATAGTATTC
40300134 ATTAAATTAATTTCTTAGTCATCTTGAGAAAATACATTTACTGTAGATAGTATTC
1 ATTAAATTAATTTCTTAGTCATCTTGAGAAAATACATTTACTGTAGATAGTATTC
40300189 AT
1 AT
40300191 GCAATCTATT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.42
Consensus pattern (55 bp):
ATTAAATTAATTTCTTAGTCATCTTGAGAAAATACATTTACTGTAGATAGTATTC
Found at i:40300172 original size:26 final size:26
Alignment explanation
Indices: 40300088--40300172 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
40300078 AATTAAATTA
40300088 ATTTCTTAGTCATCTTGAGAAAATAC
1 ATTTCTTAGTCATCTTGAGAAAATAC
* * * * *
40300114 ATTTACTGTGGAT-AGTATTCATTAAATTA-
1 ATTT-CT-TAG-TCA-TCTTGA-GAAAATAC
40300143 ATTTCTTAGTCATCTTGAGAAAATAC
1 ATTTCTTAGTCATCTTGAGAAAATAC
40300169 ATTT
1 ATTT
40300173 ACTGTAGATA
Statistics
Matches: 42, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
25 5 0.12
26 13 0.31
27 5 0.12
28 5 0.12
29 9 0.21
30 5 0.12
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (26 bp):
ATTTCTTAGTCATCTTGAGAAAATAC
Found at i:40307479 original size:20 final size:21
Alignment explanation
Indices: 40307446--40307484 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
40307436 TTTTAACATT
40307446 AATAAGTATTTTAA-ATTTTA
1 AATAAGTATTTTAATATTTTA
40307466 AATAA-TATTCTTAATATTT
1 AATAAGTATT-TTAATATTT
40307485 CAGTGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 9 0.53
21 4 0.24
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (21 bp):
AATAAGTATTTTAATATTTTA
Found at i:40312529 original size:20 final size:20
Alignment explanation
Indices: 40312502--40312564 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
40312492 AAATCATTCG
40312502 ATAACAGTAAC-TCATCCAT
1 ATAACAGTAACTTCATCCAT
*
40312521 TTAAACAGT-ACTTCATCCAT
1 AT-AACAGTAACTTCATCCAT
40312541 ATAACAGTAA-TTC-TCCAT
1 ATAACAGTAACTTCATCCAT
40312559 ATAACA
1 ATAACA
40312565 CATAGCTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
18 11 0.28
19 12 0.31
20 16 0.41
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.30
Consensus pattern (20 bp):
ATAACAGTAACTTCATCCAT
Found at i:40312799 original size:24 final size:23
Alignment explanation
Indices: 40312747--40312799 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
40312737 AGCTCTATTA
40312747 AGCTGAAACAGTAAGCTCTGACG
1 AGCTGAAACAGTAAGCTCTGACG
*
40312770 AACTGAGAACAGTAAGCTCTTG-CG
1 AGCTGA-AACAGTAAGCTC-TGACG
40312794 AGCTGA
1 AGCTGA
40312800 TATATCGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 5 0.19
24 19 0.73
25 2 0.08
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (23 bp):
AGCTGAAACAGTAAGCTCTGACG
Found at i:40323008 original size:14 final size:13
Alignment explanation
Indices: 40322985--40323015 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
40322975 GATGAACGAG
40322985 AAAGAAAAATTTC
1 AAAGAAAAATTTC
40322998 AAAGTAAAAATTTC
1 AAAG-AAAAATTTC
40323012 AAAG
1 AAAG
40323016 CACAAGGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.61, C:0.06, G:0.10, T:0.23
Consensus pattern (13 bp):
AAAGAAAAATTTC
Found at i:40327792 original size:15 final size:15
Alignment explanation
Indices: 40327772--40327802 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
40327762 TGGCATGACC
40327772 TCATGAGAAATTGAG
1 TCATGAGAAATTGAG
40327787 TCATGAGAAATTGAG
1 TCATGAGAAATTGAG
40327802 T
1 T
40327803 GGTCTGAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.29
Consensus pattern (15 bp):
TCATGAGAAATTGAG
Found at i:40329520 original size:19 final size:20
Alignment explanation
Indices: 40329480--40329528 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
40329470 TTTGATAATT
* *
40329480 GTAACTCATCCATTTAAACA
1 GTAATTCATCCATATAAACA
*
40329500 GTACTTCATCCATAT-AACA
1 GTAATTCATCCATATAAACA
40329519 GTAATTCATC
1 GTAATTCATC
40329529 TGTATAACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (20 bp):
GTAATTCATCCATATAAACA
Found at i:40329775 original size:24 final size:24
Alignment explanation
Indices: 40329706--40329800 Score: 86
Period size: 24 Copynumber: 3.9 Consensus size: 24
40329696 GAGTTGATGG
* *
40329706 ACAGTAAGCTC-TATTGAGCT-AAA
1 ACAGTAAGCTCTTA-CGAGCTGATA
* * *
40329729 ACAGTAAGCTCTGACAAGTTGATA
1 ACAGTAAGCTCTTACGAGCTGATA
40329753 ACAGTAAGCTCTTACGAGCTGATA
1 ACAGTAAGCTCTTACGAGCTGATA
* *
40329777 TATCGGTAAGCTCATACGAGCTGA
1 -A-CAGTAAGCTCTTACGAGCTGA
40329801 GGTGAGTCCG
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
23 14 0.24
24 24 0.41
25 1 0.02
26 19 0.33
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (24 bp):
ACAGTAAGCTCTTACGAGCTGATA
Found at i:40331741 original size:60 final size:60
Alignment explanation
Indices: 40331627--40331741 Score: 133
Period size: 60 Copynumber: 1.9 Consensus size: 60
40331617 TTGTACAAAC
** * ****
40331627 TATTTTTATATTGTTTTATTTAATAAAATAAAAGTTGTTTTGAATATTTTAATAGTAAAT
1 TATTTTTATATTGTCCTATTTAATAAAATAAAAGTTCTTTTGAATAAGGCAATAGTAAAT
**
40331687 TATTTTTATATTTGTCCTATTTAAT-AAATAGTAGTTCTTTTGAATAAGGCAATAG
1 TATTTTTATA-TTGTCCTATTTAATAAAATAAAAGTTCTTTTGAATAAGGCAATAG
40331742 GAATAATGCA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
60 33 0.73
61 12 0.27
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.50
Consensus pattern (60 bp):
TATTTTTATATTGTCCTATTTAATAAAATAAAAGTTCTTTTGAATAAGGCAATAGTAAAT
Found at i:40331747 original size:14 final size:14
Alignment explanation
Indices: 40331728--40331766 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
40331718 TAGTTCTTTT
*
40331728 GAATAAGGCAATAG
1 GAATAATGCAATAG
40331742 GAATAATGCAATAG
1 GAATAATGCAATAG
40331756 GAATAATGCAA
1 GAATAATGCAA
40331767 CATAGTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.51, C:0.08, G:0.23, T:0.18
Consensus pattern (14 bp):
GAATAATGCAATAG
Found at i:40333864 original size:40 final size:40
Alignment explanation
Indices: 40333820--40333995 Score: 230
Period size: 40 Copynumber: 4.4 Consensus size: 40
40333810 CACTCGAATA
*
40333820 CCTTCGGGACATAGCCCGAATA-TAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGAA-ACTAGTAACTCGCACAAATG
40333860 CCTTCGGGACTTAGCCCGAAACTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGAAACTAGTAACTCGCACAAATG
* * * *
40333900 CCTTCGGGACTTATCCCGGATA-TGGTAACTCGCAGAAATG
1 CCTTCGGGACTTAGCCC-GAAACTAGTAACTCGCACAAATG
* * * **
40333940 CCTTCGGGACATAGCCCGAAACTAGTCACTAGTGCAAATG
1 CCTTCGGGACTTAGCCCGAAACTAGTAACTCGCACAAATG
40333980 CCTTCGGGACTTAGCC
1 CCTTCGGGACTTAGCC
40333996 TGGTTATCAT
Statistics
Matches: 118, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
39 4 0.03
40 111 0.94
41 3 0.03
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGAAACTAGTAACTCGCACAAATG
Found at i:40333931 original size:80 final size:80
Alignment explanation
Indices: 40333820--40333995 Score: 262
Period size: 80 Copynumber: 2.2 Consensus size: 80
40333810 CACTCGAATA
* *
40333820 CCTTCGGGACATAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGAAACTAG
1 CCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGGACATAGCCCGAAACTAG
*
40333885 TAACTCGCACAAATG
66 TAACTAGCACAAATG
* * * *
40333900 CCTTCGGGACTTATCCCGGATATGGTAACTCGCAGAAATGCCTTCGGGACATAGCCCGAAACTAG
1 CCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGGACATAGCCCGAAACTAG
* **
40333965 TCACTAGTGCAAATG
66 TAACTAGCACAAATG
40333980 CCTTCGGGACTTAGCC
1 CCTTCGGGACTTAGCC
40333996 TGGTTATCAT
Statistics
Matches: 85, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 85 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGGACATAGCCCGAAACTAG
TAACTAGCACAAATG
Found at i:40342023 original size:40 final size:40
Alignment explanation
Indices: 40341953--40342166 Score: 242
Period size: 40 Copynumber: 5.4 Consensus size: 40
40341943 AAGCCAAGTA
* * * * *
40341953 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCACTCGAATA
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCACACAAATG
*
40341992 CCTTCGGGACATAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
*
40342032 CCTTCGGGACTTAGCCCGGA-ACTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCACACAAATG
* *
40342072 CCTTCGGGACTTAGCCCGGATATGGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
* *
40342112 CCTTCGGGACTTAG-CCGGA-ACTAGTCACT-AGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCA-CACAAATG
*
40342151 CCTTCGAGACTTAGCC
1 CCTTCGGGACTTAGCC
40342167 TGGTTATCAT
Statistics
Matches: 154, Mismatches: 14, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
38 1 0.01
39 44 0.29
40 108 0.70
41 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
Found at i:40342087 original size:80 final size:79
Alignment explanation
Indices: 40341992--40342166 Score: 278
Period size: 80 Copynumber: 2.2 Consensus size: 79
40341982 CACTCGAATA
*
40341992 CCTTCGGGACATAGCCCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAGCCCGGAACTAG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAG-CCGGAACTAG
*
40342057 TAACTCGCACAAATG
65 TAACTAGCACAAATG
* *
40342072 CCTTCGGGACTTAGCCCGGATATGGTAACTCGCACAAATGCCTTCGGGACTTAGCCGGAACTAGT
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAGCCGGAACTAGT
* *
40342137 CACTAGCGCAAATG
66 AACTAGCACAAATG
*
40342151 CCTTCGAGACTTAGCC
1 CCTTCGGGACTTAGCC
40342167 TGGTTATCAT
Statistics
Matches: 88, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
79 37 0.42
80 51 0.58
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.21
Consensus pattern (79 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAGCCGGAACTAGT
AACTAGCACAAATG
Found at i:40355953 original size:21 final size:21
Alignment explanation
Indices: 40355929--40355970 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40355919 TCATCATATC
*
40355929 TACACCTTGAGGCATCGGGGG
1 TACACCTTGAGGAATCGGGGG
**
40355950 TACAGGTTGAGGAATCGGGGG
1 TACACCTTGAGGAATCGGGGG
40355971 AGGTGGGGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.17, G:0.43, T:0.19
Consensus pattern (21 bp):
TACACCTTGAGGAATCGGGGG
Found at i:40368041 original size:11 final size:11
Alignment explanation
Indices: 40368025--40368050 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
40368015 ACTTGAACAG
40368025 AAATAAAAATA
1 AAATAAAAATA
40368036 AAATAAAAATA
1 AAATAAAAATA
40368047 AAAT
1 AAAT
40368051 TACATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:40370514 original size:604 final size:605
Alignment explanation
Indices: 40369313--40370514 Score: 1906
Period size: 605 Copynumber: 2.0 Consensus size: 605
40369303 ACACCCAATG
* *
40369313 GGAGTTTTCCACATACTAGATAATTAACCAAATCTACATACTAAAGGGTTGCATCTACAGTAAAT
1 GGAGTTTTCCACACACTAGATAATTAACCAAATCTACATACCAAAGGGTTGCATCTACAGTAAAT
* * ** *
40369378 AACTTCTCATCTGGGAATGCGTCGACAATTGGAAGTATGTTTCCATCTTCGTTGCCAACTTCCAA
66 AACTTCTCATCTGGGAATGCGTCAACAATTGGAAATACATTTCCATCTTCGCTGCCAACTTCCAA
* * * *
40369443 TTGAGACATATGGTTTGCAACTTGATTATTTGAACCCTTACGGTCTTTTATCTCGATGCCGAATT
131 TCGAGACAGATGGTCTGCAACTTGATTATCTGAACCCTTACGGTCTTTTATCTCGATGCCGAATT
* * * * *
40369508 CTTCCAACAGTAAGATCTAACGTATTAGTCTTGGTTTTGTATCCTTCTTCGTAAAAAGATATCTC
196 CTTCCAACAGTAAGATCCAACATATCAGTCTTGGTTTTGCATCCTTCTTCGCAAAAAGATATCTC
* * * * *
40369573 AACGCCGAGTGATTAGTAAATACAGTAACCTTTGCGCTGACAAGATCAGAATGAAACTTTTTGAA
261 AACGCCGAGTGATTAGTAAATACAGCAACCTTTGCACCGACAAGATAAGAATGAAACTTCTTGAA
*
40369638 AGCAAAGACTATAGCCAACAATTCTTTCTCAGTAGTGGTATAGTTGAGTTGAGCCTTTGTAAGAG
326 AGCAAAGACTATAGCCAACAATTCTTTCTCAGTAGTGGTATAGTTCAGTTGAGCCTTTGTAAGAG
* *
40369703 TTTTGCTAACATTATAGATGGCGTGAAATATTTTTCCCTTGCGTTGTCCTAGAACAGCACCCATA
391 TTTTGCTAACATAATAGATGGCGTGAAATATTTTTCCCTTGCGTTGTCCTAGAACAACACCCATA
* * *
40369768 GCAAAGTCGCTTGCATCGCACATAACTTCAAAAGGTTGAGACTAGTCTAGTGCAATGACAATGGG
456 GCAAAGTCGCTTGCATCGCACATAACTTCAAAAGGTTGAAACTAGTCTAGTGCAACGACAATGAG
* * * *
40369833 TGCAGTTACTAGTTGCATCTTTAATTGAATGAATGCCTTCAAACATGCATCATCATAGAAGAATT
521 TGCAGTTACTACTTACATCTTTAATTGAATGAATGCCTCCAAACATGCATCATCAAAGAAGAATT
*
40369898 TTCGATTCTGTTCTAGGAAT
586 TTCGACTCTGTTCTAGGAAT
* *
40369918 GGAGTTTTCCACACACTGGATAATTAACCAAATCTACATACCAAGGGGTTGCATCTACAGTAAAT
1 GGAGTTTTCCACACACTAGATAATTAACCAAATCTACATACCAAAGGGTTGCATCTACAGTAAAT
*
40369983 AACTTCTCATCTGGGAATGCGTCAACAATTTGAAATACATTTCCATCTTCGCTGCCAACTTCCAA
66 AACTTCTCATCTGGGAATGCGTCAACAATTGGAAATACATTTCCATCTTCGCTGCCAACTTCCAA
* * * * *
40370048 TCGTGACAGATGGTCTGTAACTTGATTCTCTGAACCCTTATGGTCTTTTATCTCGATGCCTAATT
131 TCGAGACAGATGGTCTGCAACTTGATTATCTGAACCCTTACGGTCTTTTATCTCGATGCCGAATT
*
40370113 CTTCCAACAGTATGATCCAACATATCAGTCTTGGTTTTGCATCCTTCTTCGCAAAAAGATATCTC
196 CTTCCAACAGTAAGATCCAACATATCAGTCTTGGTTTTGCATCCTTCTTCGCAAAAAGATATCTC
*
40370178 AACGCCGAGTGATTAGTAAATACTA-CAACCTTTGCACCGACAAGATAAG-GTGAAACTTCTTGA
261 AACGCCGAGTGATTAGTAAATAC-AGCAACCTTTGCACCGACAAGATAAGAATGAAACTTCTTGA
*
40370241 AAGCAAAGACTATAGCCAACAATTCTTTCTCTGTAGTGGTATAGTTCAGTTGAGCCTTTGTAAGA
325 AAGCAAAGACTATAGCCAACAATTCTTTCTCAGTAGTGGTATAGTTCAGTTGAGCCTTTGTAAGA
**
40370306 GTTTTGCTCGCATAATAGATGGCGTGAAATATTTTTCCCTTGCGTTGTCCTAGAACAACACCCAT
390 GTTTTGCTAACATAATAGATGGCGTGAAATATTTTTCCCTTGCGTTGTCCTAGAACAACACCCAT
40370371 AGCAAAGTCGCTTGCATCGCACATAACTTCAAAAGGTTGAAACTAGTCT-GATGCAACGACAATG
455 AGCAAAGTCGCTTGCATCGCACATAACTTCAAAAGGTTGAAACTAGTCTAG-TGCAACGACAATG
* * * * **
40370435 AGTGCATTTACTACTTACGTCTTTAATTGAATGAATGCGTCCAGACATGCATTGTCAAAGAAGAA
519 AGTGCAGTTACTACTTACATCTTTAATTGAATGAATGCCTCCAAACATGCATCATCAAAGAAGAA
40370500 TTTTCGACTCTGTTC
584 TTTTCGACTCTGTTC
40370515 CAGCAATGAG
Statistics
Matches: 544, Mismatches: 51, Indels: 5
0.91 0.09 0.01
Matches are distributed among these distances:
603 1 0.00
604 264 0.49
605 278 0.51
606 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (605 bp):
GGAGTTTTCCACACACTAGATAATTAACCAAATCTACATACCAAAGGGTTGCATCTACAGTAAAT
AACTTCTCATCTGGGAATGCGTCAACAATTGGAAATACATTTCCATCTTCGCTGCCAACTTCCAA
TCGAGACAGATGGTCTGCAACTTGATTATCTGAACCCTTACGGTCTTTTATCTCGATGCCGAATT
CTTCCAACAGTAAGATCCAACATATCAGTCTTGGTTTTGCATCCTTCTTCGCAAAAAGATATCTC
AACGCCGAGTGATTAGTAAATACAGCAACCTTTGCACCGACAAGATAAGAATGAAACTTCTTGAA
AGCAAAGACTATAGCCAACAATTCTTTCTCAGTAGTGGTATAGTTCAGTTGAGCCTTTGTAAGAG
TTTTGCTAACATAATAGATGGCGTGAAATATTTTTCCCTTGCGTTGTCCTAGAACAACACCCATA
GCAAAGTCGCTTGCATCGCACATAACTTCAAAAGGTTGAAACTAGTCTAGTGCAACGACAATGAG
TGCAGTTACTACTTACATCTTTAATTGAATGAATGCCTCCAAACATGCATCATCAAAGAAGAATT
TTCGACTCTGTTCTAGGAAT
Found at i:40374469 original size:56 final size:55
Alignment explanation
Indices: 40374396--40374565 Score: 254
Period size: 56 Copynumber: 3.1 Consensus size: 55
40374386 CCGAAGTAGA
*
40374396 ATTTTTTTTATCATTTTAAGGTCTATGGCATGATTGAATGATTGTGTGAAAATTT
1 ATTTTTTTTATCATTTTAAGGTCTATGGCATGATTGCATGATTGTGTGAAAATTT
* * *
40374451 ATTTATTTTTATCCTTTTAAGGTTTA-GGAAATGATTGCATGATTGTGTGAAAATTT
1 ATTT-TTTTTATCATTTTAAGGTCTATGG-CATGATTGCATGATTGTGTGAAAATTT
*
40374507 A-TTTTTTTATCATTTTAAGGTCTATGGCATGATTGCATGATTATGTGAAAATTT
1 ATTTTTTTTATCATTTTAAGGTCTATGGCATGATTGCATGATTGTGTGAAAATTT
40374561 CATTT
1 -ATTT
40374566 AGAAATTTTA
Statistics
Matches: 102, Mismatches: 8, Indels: 9
0.86 0.07 0.08
Matches are distributed among these distances:
54 44 0.43
55 11 0.11
56 47 0.46
ACGTcount: A:0.28, C:0.06, G:0.17, T:0.49
Consensus pattern (55 bp):
ATTTTTTTTATCATTTTAAGGTCTATGGCATGATTGCATGATTGTGTGAAAATTT
Found at i:40375813 original size:100 final size:100
Alignment explanation
Indices: 40375635--40375815 Score: 256
Period size: 100 Copynumber: 1.8 Consensus size: 100
40375625 ATTGTGAGAA
* *
40375635 CACATGTGTAGAACTATGGGCAGGCTACTATGTGTTAAGATGGTTTTAGGTCACGTGTGTAGTAC
1 CACATGTGTAGAACTAAGGGCAGGCCACTATGTGTTAAGATGG-TTTAGGTCACGTGTGTAGTAC
40375700 TAAGTGCAAGCTACTACATGTACTAGATAGTTAGGT
65 TAAGTGCAAGCTACTACATGTACTAGATAGTTAGGT
* * * * *
40375736 CACATGTGTAGTATTAAGTGCAGGCCACTATGTGTATCAGATGG-TTAGGTCATGTGTGTAGTAC
1 CACATGTGTAGAACTAAGGGCAGGCCACTATGTGT-TAAGATGGTTTAGGTCACGTGTGTAGTAC
* *
40375800 TAAGTGTAGGCTACTA
65 TAAGTGCAAGCTACTA
40375816 TGCGTACCAG
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
100 33 0.47
101 30 0.43
102 7 0.10
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (100 bp):
CACATGTGTAGAACTAAGGGCAGGCCACTATGTGTTAAGATGGTTTAGGTCACGTGTGTAGTACT
AAGTGCAAGCTACTACATGTACTAGATAGTTAGGT
Found at i:40375816 original size:50 final size:50
Alignment explanation
Indices: 40375639--40375827 Score: 202
Period size: 50 Copynumber: 3.8 Consensus size: 50
40375629 TGAGAACACA
* * * *
40375639 TGTGTAGAACTATGGGCAGGCTACTATGTGT-TAAGATGGTTTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGATGG--TTAGGTCACG
* ** * *
40375690 TGTGTAGTACTAAGTGCAAGCTACTACATGTA-CTAGATAGTTAGGTCACA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTATC-AGATGGTTAGGTCACG
* * *
40375740 TGTGTAGTATTAAGTGCAGGCCACTATGTGTATCAGATGGTTAGGTCATG
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGATGGTTAGGTCACG
* * *
40375790 TGTGTAGTACTAAGTGTAGGCTACTATGCGTACCAGAT
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGAT
40375828 AGCTTCGGTT
Statistics
Matches: 113, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
50 82 0.73
51 26 0.23
52 5 0.04
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGATGGTTAGGTCACG
Found at i:40376048 original size:16 final size:15
Alignment explanation
Indices: 40376027--40376056 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
40376017 GAATGGAGTA
40376027 AGTGAAATTATGTAAG
1 AGTGAAATT-TGTAAG
40376043 AGTGAAATTTGTAA
1 AGTGAAATTTGTAA
40376057 TAAAATTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (15 bp):
AGTGAAATTTGTAAG
Found at i:40380409 original size:122 final size:125
Alignment explanation
Indices: 40379965--40380466 Score: 620
Period size: 126 Copynumber: 4.0 Consensus size: 125
40379955 GCCAAGCAGG
* * * * * *
40379965 AACTACTGTAGAAAAAAAGCATCCACGTGGGAGCTTTTTTCAGTAATTTTGTTGACAATGCATCC
1 AACTACTGTAGAAAAAGAGCGTCCATGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCC
* ** * *
40380030 TCCTTGAAGCATTTTTAACACTACCTCTTCAGAA-CTGTCTTCTCAAAGTTAGTTTTTCAGA
66 TGCTTGAAGCATTTTTAACACTATTTTTTCAGAATC-GTCTTCTCAAA-TTATTTTTTCAGA
* * * **
40380091 AACTATTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATTA
1 AACTACTGTAGAAAAAGAGCGTCCATGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCC
* * * * * * *
40380156 TGCTTGAAGCATTTTTTACGCTATTTTTCCAGAACCATCTTCTCAAAATTATTTTTTTAGG
66 TGCTTGAAGCATTTTTAACACTATTTTTTCAGAATCGTCTTCTC-AAATTATTTTTTCAGA
* * *
40380217 AACTACCGTAGAAAAAGAGCGTCCATGTAGGAG-TTTTTTCAGTACTTTTGCTGACAGTGCATAC
1 AACTACTGTAGAAAAAGAGCGTCCATGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCC
* *
40380281 TACTTGAAGCATTTTTAACATTATTTTTTCAGAATCGTCTTCTC-AATTATTTTTTCAGA
66 TGCTTGAAGCATTTTTAACACTATTTTTTCAGAATCGTCTTCTCAAATTATTTTTTCAGA
** *
40380340 AACTACTGTATTAAAAGAGCGT-CATGTGGGATC-TTTTTCAGTACTTTTGCTGACAGTGCATCC
1 AACTACTGTAGAAAAAGAGCGTCCATGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCC
* * *
40380403 TGCTTGAAGCATTTTTATCACTATTTTTTCAAAATCGTCTTCTCAATATAATTTTTTCA-A
66 TGCTTGAAGCATTTTTAACACTATTTTTTCAGAATCGTCTTCTCAA-ATTATTTTTTCAGA
40380463 AACT
1 AACT
40380467 CAACCCTAAA
Statistics
Matches: 326, Mismatches: 45, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
122 77 0.24
123 38 0.12
124 11 0.03
125 66 0.20
126 130 0.40
127 4 0.01
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (125 bp):
AACTACTGTAGAAAAAGAGCGTCCATGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCC
TGCTTGAAGCATTTTTAACACTATTTTTTCAGAATCGTCTTCTCAAATTATTTTTTCAGA
Found at i:40380565 original size:34 final size:34
Alignment explanation
Indices: 40380518--40380636 Score: 115
Period size: 30 Copynumber: 3.6 Consensus size: 34
40380508 AATTATTTTA
*
40380518 AAAAAATCTTAAACCCTAATTTAATTAATTTTCTT
1 AAAAACTC-TAAACCCTAATTTAATTAATTTTCTT
*
40380553 AAAAACTCTAAACCC----TTAATTAATTTACTT
1 AAAAACTCTAAACCCTAATTTAATTAATTTTCTT
* * *
40380583 AAAACCCCTAAAACCTAATTTAATTAATTTT-TT
1 AAAAACTCTAAACCCTAATTTAATTAATTTTCTT
* * *
40380616 TAAAA-TTTAAACTCTAATTTA
1 AAAAACTCTAAACCCTAATTTA
40380637 TTTTTTAAAA
Statistics
Matches: 68, Mismatches: 12, Indels: 11
0.75 0.13 0.12
Matches are distributed among these distances:
30 26 0.38
32 12 0.18
33 5 0.07
34 18 0.26
35 7 0.10
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAAACTCTAAACCCTAATTTAATTAATTTTCTT
Found at i:40380608 original size:64 final size:60
Alignment explanation
Indices: 40380527--40380654 Score: 166
Period size: 64 Copynumber: 2.1 Consensus size: 60
40380517 AAAAAAATCT
*
40380527 TAAACCCTAATTTAATTAATTTTCTTAAAAACTCTAAACCCTTAATTAATTTACTTAAAACCCC
1 TAAAACCTAATTTAATTAATTTT-TTAAAAA-TCTAAACCC-TAATTAATTT-CTTAAAACCCC
* * * * *
40380591 TAAAACCTAATTTAATTAATTTTTTTAAAATTTAAACTCTAATTTATTTTTTAAAACCCC
1 TAAAACCTAATTTAATTAATTTTTTAAAAATCTAAACCCTAATTAATTTCTTAAAACCCC
40380651 TAAA
1 TAAA
40380655 CCTTAAAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
60 14 0.24
61 9 0.16
62 7 0.12
63 6 0.10
64 22 0.38
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (60 bp):
TAAAACCTAATTTAATTAATTTTTTAAAAATCTAAACCCTAATTAATTTCTTAAAACCCC
Found at i:40383468 original size:47 final size:47
Alignment explanation
Indices: 40383260--40383476 Score: 191
Period size: 46 Copynumber: 4.7 Consensus size: 47
40383250 TTTGTGGGCT
* *
40383260 AGTGTAAGA-CATGTCTGGGACAT-GCATCAAC--CACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAACTTGAGA-TAT--GAGCC
** * *
40383306 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGA-GAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAAC-TTGAGA-TATGAGCC
* * *
40383354 AGTGTAAGA-CATGTCTGGGACAT-GCATCGACTGCGAGATGAT-AGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAACT-TGAGAT-ATGAGCC
40383400 AGTGTAAGACC-TGTCTGGGACATGGCATCAACTTGAGATATGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAACTTGAGATATGAGCC
** * *
40383446 AGCATAAGACCATGTCTAGGACATGACATCA
1 AGTGTAAGACCATGTCTGGGACATGGCATCA
40383477 GCACCTTACC
Statistics
Matches: 140, Mismatches: 19, Indels: 23
0.77 0.10 0.13
Matches are distributed among these distances:
45 3 0.02
46 61 0.44
47 54 0.39
48 19 0.14
51 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCAACTTGAGATATGAGCC
Found at i:40392192 original size:30 final size:30
Alignment explanation
Indices: 40392156--40392215 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
40392146 GAGAGCCAGT
*
40392156 GTAAGACCATGTCTGGGACATGGCATCAGC
1 GTAAGACCATGTATGGGACATGGCATCAGC
40392186 GTAAGACCATGTATGGGACATGGCATCAGC
1 GTAAGACCATGTATGGGACATGGCATCAGC
40392216 ATTGAGACGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.22, G:0.30, T:0.20
Consensus pattern (30 bp):
GTAAGACCATGTATGGGACATGGCATCAGC
Found at i:40392259 original size:45 final size:46
Alignment explanation
Indices: 40392186--40392351 Score: 151
Period size: 46 Copynumber: 3.5 Consensus size: 46
40392176 TGGCATCAGC
* * *
40392186 GTAAGACCATGTATGGGACATGGCATCAGCATTGAGACG-AGAGCTAGT
1 GTAAGA-CATGTCTGGGACAT-GCATCAGCATCGAGACGTA-AGCCAGT
* *
40392234 GTAAGACAT-TCTGGGATATGCATCAGCCTCGAGACGTAAGCCAGT
1 GTAAGACATGTCTGGGACATGCATCAGCATCGAGACGTAAGCCAGT
* * * * *
40392279 GTAAGACATGTCTAGGACATGCATCGGC-TACGAGATG-ATAGTCAAT
1 GTAAGACATGTCTGGGACATGCATCAGCAT-CGAGACGTA-AGCCAGT
40392325 GTAAGACCATGTCTGGGACATGGCATC
1 GTAAGA-CATGTCTGGGACAT-GCATC
40392352 GACTTGAGAT
Statistics
Matches: 100, Mismatches: 12, Indels: 12
0.81 0.10 0.10
Matches are distributed among these distances:
45 32 0.32
46 41 0.41
47 16 0.16
48 11 0.11
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.22
Consensus pattern (46 bp):
GTAAGACATGTCTGGGACATGCATCAGCATCGAGACGTAAGCCAGT
Found at i:40392361 original size:47 final size:48
Alignment explanation
Indices: 40392186--40392394 Score: 159
Period size: 47 Copynumber: 4.5 Consensus size: 48
40392176 TGGCATCAGC
* * * * *
40392186 GTAAGACCATGTATGGGACATGGCATC-AGCATTGAGACGA-GAGCTAGT
1 GTAAGACCATGTCTGGGACATGGCATCGA-C-TCGAGACGATAAGCCAAT
* * *
40392234 GTAAGA-CAT-TCTGGGATAT-GCATCAGCCTCGAGACG-TAAGCCAGT
1 GTAAGACCATGTCTGGGACATGGCATC-GACTCGAGACGATAAGCCAAT
* * * *
40392279 GTAAGA-CATGTCTAGGACAT-GCATCGGCTACGAGATGAT-AGTCAAT
1 GTAAGACCATGTCTGGGACATGGCATCGACT-CGAGACGATAAGCCAAT
* * *
40392325 GTAAGACCATGTCTGGGACATGGCATCGACTTGAGA-TATGAGCCAAT
1 GTAAGACCATGTCTGGGACATGGCATCGACTCGAGACGATAAGCCAAT
* *
40392372 GTAAGACCATGTCTAGGATATGG
1 GTAAGACCATGTCTGGGACATGG
40392395 AATTGGTACC
Statistics
Matches: 133, Mismatches: 19, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
45 30 0.23
46 41 0.31
47 48 0.36
48 14 0.11
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.23
Consensus pattern (48 bp):
GTAAGACCATGTCTGGGACATGGCATCGACTCGAGACGATAAGCCAAT
Found at i:40400026 original size:16 final size:17
Alignment explanation
Indices: 40400001--40400041 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
40399991 GATCAAGCAC
*
40400001 AAAGAAGAGAAGCAA-AG
1 AAAGATGAGAAG-AAGAG
40400018 -AAGATGAGAAGAAGAG
1 AAAGATGAGAAGAAGAG
40400034 AAAGATGA
1 AAAGATGA
40400042 TTTTTAGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 2 0.10
16 12 0.57
17 7 0.33
ACGTcount: A:0.61, C:0.02, G:0.32, T:0.05
Consensus pattern (17 bp):
AAAGATGAGAAGAAGAG
Found at i:40404494 original size:39 final size:39
Alignment explanation
Indices: 40404440--40404604 Score: 276
Period size: 39 Copynumber: 4.2 Consensus size: 39
40404430 GATATTGATG
*
40404440 TATATCCAGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
*
40404479 TATATTCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
40404518 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
* * *
40404557 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
*
40404596 TATGTCCGG
1 TATATCCGG
40404605 GCTAAAGTCC
Statistics
Matches: 119, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 119 1.00
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.28
Consensus pattern (39 bp):
TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
Found at i:40404618 original size:39 final size:39
Alignment explanation
Indices: 40404440--40404642 Score: 248
Period size: 39 Copynumber: 5.2 Consensus size: 39
40404430 GATATTGATG
* * *
40404440 TATATCCAGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAT
* * *
40404479 TATATTCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAT
* *
40404518 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAT
*
40404557 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAT
* * * * * *
40404596 TATGTCCGGGC-TAAAGTCCCGCAGGCTTCGAGCTGGTAT
1 TATATCCGGACTTAAGGT-CCGCAGGCTACGTGCTGGAAT
40404635 TATA-CCGG
1 TATATCCGG
40404643 GTTTAAATTC
Statistics
Matches: 149, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
38 9 0.06
39 140 0.94
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.27
Consensus pattern (39 bp):
TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAT
Found at i:40404657 original size:117 final size:117
Alignment explanation
Indices: 40404440--40404674 Score: 253
Period size: 117 Copynumber: 2.0 Consensus size: 117
40404430 GATATTGATG
* * * * **
40404440 TATATCCAGACTTAGGGTCCGCAGGCTATGTGCTGGAATTATATTCGGACTTAGGGTCCGCAGGC
1 TATATCCAGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCCGGACTTAAAGTCCGCAGGC
* **
40404505 TATGTGCTGGAATTATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGG-AAT
66 TATGAGCTGGAATTATATCCGGACTTAAAGTCCGCAGGCT-TGTGCTGGTAAT
* * *
40404557 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATGTCCGGGC-TAAAGTCCCGCAGG
1 TATATCCAGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCCGGACTTAAAGT-CCGCAGG
* ** * *
40404621 CT-TCGAGCTGGTATTATA-CCGGGTTTAAATTCCCGCAGGCTTGTGTTGGTAAT
65 CTAT-GAGCTGGAATTATATCCGGACTTAAAGT-CCGCAGGCTTGTGCTGGTAAT
40404674 T
1 T
40404675 GGTTTCAAGT
Statistics
Matches: 97, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
116 20 0.21
117 77 0.79
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (117 bp):
TATATCCAGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCCGGACTTAAAGTCCGCAGGC
TATGAGCTGGAATTATATCCGGACTTAAAGTCCGCAGGCTTGTGCTGGTAAT
Found at i:40408606 original size:34 final size:33
Alignment explanation
Indices: 40408555--40408627 Score: 101
Period size: 34 Copynumber: 2.2 Consensus size: 33
40408545 TCAGTCTAAA
*
40408555 TATCAGTGTGGGACTTAGCCCAATTTCGTAACAG
1 TATCAGTGTGGGACTTAGCCCAATTTAG-AACAG
* * *
40408589 TATCGGTGTGGGGCTTAGCCCATTTTAGAACAG
1 TATCAGTGTGGGACTTAGCCCAATTTAGAACAG
40408622 TATCAG
1 TATCAG
40408628 AAATGCATAC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 10 0.29
34 24 0.71
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (33 bp):
TATCAGTGTGGGACTTAGCCCAATTTAGAACAG
Found at i:40419581 original size:21 final size:20
Alignment explanation
Indices: 40419539--40419627 Score: 58
Period size: 21 Copynumber: 4.4 Consensus size: 20
40419529 ATTTTTGATA
**
40419539 AGGAAGTTACTGCTGCAAAAG
1 AGGAAGTTGTTGCTG-AAAAG
40419560 AGGAAGTTGTTGCTGAAGAAG
1 AGGAAGTTGTTGCTGAA-AAG
* * *
40419581 AAGAA--T-TTACTGAAAATA
1 AGGAAGTTGTTGCTGAAAA-G
*
40419599 AGAAAGTTGTTGCTGAAGAAG
1 AGGAAGTTGTTGCTGAA-AAG
*
40419620 AAGAAGTT
1 AGGAAGTT
40419628 ACTGAAAATA
Statistics
Matches: 51, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
17 2 0.04
18 10 0.20
19 1 0.02
20 3 0.06
21 33 0.65
22 2 0.04
ACGTcount: A:0.42, C:0.07, G:0.28, T:0.24
Consensus pattern (20 bp):
AGGAAGTTGTTGCTGAAAAG
Found at i:40419583 original size:18 final size:18
Alignment explanation
Indices: 40419557--40419622 Score: 53
Period size: 18 Copynumber: 3.5 Consensus size: 18
40419547 ACTGCTGCAA
*
40419557 AAGAGGAAGTTGTTGCTG
1 AAGAAGAAGTTGTTGCTG
* *
40419575 AAGAAGAAGAAT-TTACTG
1 AAGAAGAAG-TTGTTGCTG
*
40419593 AAAATAAGAAAGTTGTTGCTG
1 --AAGAAG-AAGTTGTTGCTG
40419614 AAGAAGAAG
1 AAGAAGAAG
40419623 AAGTTACTGA
Statistics
Matches: 36, Mismatches: 7, Indels: 10
0.68 0.13 0.19
Matches are distributed among these distances:
18 16 0.44
19 6 0.17
20 6 0.17
21 8 0.22
ACGTcount: A:0.44, C:0.05, G:0.29, T:0.23
Consensus pattern (18 bp):
AAGAAGAAGTTGTTGCTG
Found at i:40419607 original size:39 final size:39
Alignment explanation
Indices: 40419563--40419643 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
40419553 GCAAAAGAGG
*
40419563 AAGTTGTTGCTGAAGAAGAAGAATTTACTGAAAATAAGA
1 AAGTTGTTGCTGAAGAAGAAGAAGTTACTGAAAATAAGA
40419602 AAGTTGTTGCTGAAGAAGAAGAAGTTACTGAAAATAAGA
1 AAGTTGTTGCTGAAGAAGAAGAAGTTACTGAAAATAAGA
40419641 AAG
1 AAG
40419644 AAAAAGAAGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.47, C:0.05, G:0.25, T:0.23
Consensus pattern (39 bp):
AAGTTGTTGCTGAAGAAGAAGAAGTTACTGAAAATAAGA
Found at i:40419644 original size:21 final size:21
Alignment explanation
Indices: 40419581--40419645 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
40419571 GCTGAAGAAG
*
40419581 AAGAATTTACTGAAAATAAGA
1 AAGAAGTTACTGAAAATAAGA
** * *
40419602 AAGTTGTTGCTG--AAGAAG-
1 AAGAAGTTACTGAAAATAAGA
40419620 AAGAAGTTACTGAAAATAAGA
1 AAGAAGTTACTGAAAATAAGA
40419641 AAGAA
1 AAGAA
40419646 AAAGAAGAAG
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
18 9 0.28
19 5 0.16
20 5 0.16
21 13 0.41
ACGTcount: A:0.52, C:0.05, G:0.22, T:0.22
Consensus pattern (21 bp):
AAGAAGTTACTGAAAATAAGA
Found at i:40419656 original size:39 final size:39
Alignment explanation
Indices: 40419574--40419659 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 39
40419564 AGTTGTTGCT
* ***** **
40419574 GAAGAAGAAGAATTTACTGAAAATAAGAAAGTTGTTGCT
1 GAAGAAGAAGAAGTTACTGAAAATAAGAAAGAAAAAGAA
40419613 GAAGAAGAAGAAGTTACTGAAAATAAGAAAGAAAAAGAA
1 GAAGAAGAAGAAGTTACTGAAAATAAGAAAGAAAAAGAA
40419652 GAAGAAGA
1 GAAGAAGA
40419660 TTATGTTGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.56, C:0.03, G:0.24, T:0.16
Consensus pattern (39 bp):
GAAGAAGAAGAAGTTACTGAAAATAAGAAAGAAAAAGAA
Found at i:40425313 original size:36 final size:36
Alignment explanation
Indices: 40425226--40425336 Score: 136
Period size: 36 Copynumber: 3.1 Consensus size: 36
40425216 ATTTTGATTA
*
40425226 GACTAGCTCTT-TAGAGCCAT-TGGTGTGTTATCGGGTG
1 GACTAGCTCTTAT-GAG-CATCTGGTGTGTT-TCGGTTG
* *
40425263 GACCAACTCTTATGAGCATCTGGTGTGTTTCGGTTG
1 GACTAGCTCTTATGAGCATCTGGTGTGTTTCGGTTG
* *
40425299 GATTAGCTCTTATGAGCATCTAGTGTGTTTCGGTTG
1 GACTAGCTCTTATGAGCATCTGGTGTGTTTCGGTTG
40425335 GA
1 GA
40425337 ATATCAATGT
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
36 43 0.66
37 21 0.32
38 1 0.02
ACGTcount: A:0.17, C:0.16, G:0.30, T:0.37
Consensus pattern (36 bp):
GACTAGCTCTTATGAGCATCTGGTGTGTTTCGGTTG
Found at i:40428593 original size:46 final size:46
Alignment explanation
Indices: 40428378--40428593 Score: 197
Period size: 46 Copynumber: 4.6 Consensus size: 46
40428368 AAGTCGACTC
* * *
40428378 CATGTCCCATACATGGTCTTACACT-GACTATCATCTCGTAGCCGATG
1 CATGTCCCAGACAT-GTCTTACACTAG-CTCTCATCTCGTGGCCGATG
* * * * *
40428425 CATGTCCCAAACATGTCTTACACTGGCT-TACATCTCGAGCCCGTTG
1 CATGTCCCAGACATGTCTTACACTAGCTCT-CATCTCGTGGCCGATG
* * * * *
40428471 CATGTCCCAGACATGTCTTACACTAGCCCTCGTCTCCAT-ACTGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTCATCT-CGTGGCCGATG
* * *
40428517 CCATGTCCCAGATATGGTCTTACACCAGCTCTCATAAT-GTGGCCGATG
1 -CATGTCCCAGACAT-GTCTTACACTAGCTCTCAT-CTCGTGGCCGATG
40428565 CATGTCCCAGACATGTCTTACACTAGCTC
1 CATGTCCCAGACATGTCTTACACTAGCTC
40428594 ACACACGAAT
Statistics
Matches: 137, Mismatches: 24, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
45 1 0.01
46 71 0.52
47 43 0.31
48 21 0.15
49 1 0.01
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTAGCTCTCATCTCGTGGCCGATG
Found at i:40428987 original size:29 final size:30
Alignment explanation
Indices: 40428927--40428992 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
40428917 ATTCACTTCT
* *
40428927 TTGGTAAAATGACCATTTTGCCCCTAGACC
1 TTGGAAAAATGACCATTTTACCCCTAGACC
* *
40428957 TTGGAAAAATGACTATTTTACCCTTAG-CC
1 TTGGAAAAATGACCATTTTACCCCTAGACC
40428986 TT-GAAAA
1 TTGGAAAA
40428993 TCGATTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 5 0.16
29 4 0.12
30 23 0.72
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (30 bp):
TTGGAAAAATGACCATTTTACCCCTAGACC
Found at i:40432120 original size:27 final size:27
Alignment explanation
Indices: 40432090--40432162 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
40432080 TACTGAAATG
* *
40432090 CCCTCGATTTGTAGAATTACCATTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
*
40432117 CCCTCAATTTATAAAATTACCATTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
* *
40432144 CCCTTGA-TTATGAAATTAC
1 CCCTCGATTTATAAAATTAC
40432163 TAAAATACCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
26 11 0.28
27 29 0.73
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.40
Consensus pattern (27 bp):
CCCTCGATTTATAAAATTACCATTTTA
Found at i:40432225 original size:54 final size:54
Alignment explanation
Indices: 40432156--40432336 Score: 206
Period size: 54 Copynumber: 3.4 Consensus size: 54
40432146 CTTGATTATG
* ** *
40432156 AAATTACTAAAATACCCCT-GTAGGATAGAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTG-TAGAATTACCGAAATACCCCTAGTTTGTA
* * * *
40432210 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCGAAATACCACTGGTTTGTG
1 AAATTACCAAAATACCCCTAGTTTGTAGAATTACCGAAATACCCCTAGTTTGTA
* * * *
40432264 AAATTACCGAAATACCACTGGTTTGT-GAAATTACCGAAATA-CCCTCAATTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTAG-AATTACCGAAATACCCCT-AGTTTGTA
40432318 AAATTACCAAAATACCCCT
1 AAATTACCAAAATACCCCT
40432337 GATTTACAAA
Statistics
Matches: 106, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
53 3 0.03
54 100 0.94
55 3 0.03
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28
Consensus pattern (54 bp):
AAATTACCAAAATACCCCTAGTTTGTAGAATTACCGAAATACCCCTAGTTTGTA
Found at i:40432271 original size:81 final size:81
Alignment explanation
Indices: 40432184--40432333 Score: 221
Period size: 81 Copynumber: 1.9 Consensus size: 81
40432174 TGTAGGATAG
* * *
40432184 AATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCC-CTAGTTTGTAAAATTACCGAA
1 AATTACCAAAATACCACTAGTTTGTAAAATTACCAAAATACCCTC-AATTTGTAAAATTACCAAA
40432248 ATACCACTGGTTTGTGA
65 ATACCACTGGTTTGTGA
* * * *
40432265 AATTACCGAAATACCACTGGTTTGTGAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAA
1 AATTACCAAAATACCACTAGTTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAA
40432330 TACC
66 TACC
40432334 CCTGATTTAC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
81 60 0.98
82 1 0.02
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (81 bp):
AATTACCAAAATACCACTAGTTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAA
TACCACTGGTTTGTGA
Found at i:40432341 original size:27 final size:27
Alignment explanation
Indices: 40432156--40432350 Score: 182
Period size: 27 Copynumber: 7.2 Consensus size: 27
40432146 CTTGATTATG
* **
40432156 AAATTACTAAAATACCCCTG-TAGGATA
1 AAATTACCAAAATACCCCTGATTTG-TA
*
40432183 GAATTACCAAAATACCCCT-AGTTTGTA
1 AAATTACCAAAATACCCCTGA-TTTGTA
40432210 AAATTACCAAAATACCCCT-AGTTTGTA
1 AAATTACCAAAATACCCCTGA-TTTGTA
* * * *
40432237 AAATTACCGAAATACCACTGGTTTGTG
1 AAATTACCAAAATACCCCTGATTTGTA
* * * *
40432264 AAATTACCGAAATACCACTGGTTTGTG
1 AAATTACCAAAATACCCCTGATTTGTA
* *
40432291 AAATTACCGAAATA-CCCTCAATTTGTA
1 AAATTACCAAAATACCCCT-GATTTGTA
**
40432318 AAATTACCAAAATACCCCTGATTTACA
1 AAATTACCAAAATACCCCTGATTTGTA
40432345 AAATTA
1 AAATTA
40432351 TAGAAATATC
Statistics
Matches: 146, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
26 3 0.02
27 137 0.94
28 6 0.04
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.29
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGATTTGTA
Done.