Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 131 of 240
Found at i:40677158 original size:12 final size:12
Alignment explanation
Indices: 40677128--40677202 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
40677118 CACCAATTTT
*
40677128 TTTTTAAAAAAA
1 TTTTTAAAAATA
40677140 GTATTTTAAAAATA
1 -T-TTTTAAAAATA
*
40677154 TTTTT-AAAATG
1 TTTTTAAAAATA
* * *
40677165 CTTATAAAAAAA
1 TTTTTAAAAATA
*
40677177 GCATTTTAAAAATA
1 --TTTTTAAAAATA
40677191 TTTTTAAAAATA
1 TTTTTAAAAATA
40677203 AAAAATAAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
11 8 0.17
12 19 0.40
13 2 0.04
14 19 0.40
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.41
Consensus pattern (12 bp):
TTTTTAAAAATA
Found at i:40677213 original size:37 final size:36
Alignment explanation
Indices: 40677133--40677214 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 36
40677123 ATTTTTTTTT
* ** *
40677133 AAAAAAAGTATTTTAAAAATATTTTTAAAATGCTTAT
1 AAAAAAAGCATTTTAAAAATATTTTTAAAAT-CAAAA
*
40677170 AAAAAAAGCATTTTAAAAATATTTTTAAAAATAAAAA
1 AAAAAAAGCATTTTAAAAATATTTTT-AAAATCAAAA
40677207 ATAAAAAA
1 A-AAAAAA
40677215 TATATTTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
37 27 0.71
38 11 0.29
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (36 bp):
AAAAAAAGCATTTTAAAAATATTTTTAAAATCAAAA
Found at i:40679838 original size:22 final size:22
Alignment explanation
Indices: 40679813--40679938 Score: 107
Period size: 22 Copynumber: 5.8 Consensus size: 22
40679803 GGCATTCCGA
*
40679813 TAGCCTTTATGGCATATTCTAT
1 TAGCCTTTGTGGCATATTCTAT
* *
40679835 TAGCCTTTGTAATGCAT-TT-TGT
1 TAGCCTTTGT--GGCATATTCTAT
* * *
40679857 TAGCCTTTTTGGCGTATTCTGT
1 TAGCCTTTGTGGCATATTCTAT
* * *
40679879 TAGCCTTTGTGGCACATTTTTT
1 TAGCCTTTGTGGCATATTCTAT
* *
40679901 TAGTCTTTGTGGC--ATTCTAC
1 TAGCCTTTGTGGCATATTCTAT
40679921 TAGCCTTTGTGGCATATT
1 TAGCCTTTGTGGCATATT
40679939 ATGTATGTCG
Statistics
Matches: 82, Mismatches: 16, Indels: 12
0.75 0.15 0.11
Matches are distributed among these distances:
20 19 0.23
21 2 0.02
22 55 0.67
23 2 0.02
24 4 0.05
ACGTcount: A:0.16, C:0.17, G:0.19, T:0.48
Consensus pattern (22 bp):
TAGCCTTTGTGGCATATTCTAT
Found at i:40679897 original size:44 final size:43
Alignment explanation
Indices: 40679813--40679934 Score: 129
Period size: 44 Copynumber: 2.8 Consensus size: 43
40679803 GGCATTCCGA
****
40679813 TAGCCTTTATGGCATATTCTATTAGCCTTTGTAATGCATTTTGT
1 TAGCCTTTATGGC-TATTCTATTAGCCTTTGTGGCACATTTTGT
* * *
40679857 TAGCCTTTTTGGCGTATTCTGTTAGCCTTTGTGGCACATTTTTT
1 TAGCCTTTATGGC-TATTCTATTAGCCTTTGTGGCACATTTTGT
* * *
40679901 TAGTCTTTGTGGC-ATTCTACTAGCCTTTGTGGCA
1 TAGCCTTTATGGCTATTCTATTAGCCTTTGTGGCA
40679935 TATTATGTAT
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 19 0.29
44 47 0.71
ACGTcount: A:0.16, C:0.18, G:0.20, T:0.47
Consensus pattern (43 bp):
TAGCCTTTATGGCTATTCTATTAGCCTTTGTGGCACATTTTGT
Found at i:40683157 original size:40 final size:40
Alignment explanation
Indices: 40683067--40683291 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
40683057 TTGAATGATG
* * * *
40683067 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
40683107 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
40683147 TCTGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40683186 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40683226 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
40683267 -ACGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40683292 AACGAGGAGC
Statistics
Matches: 162, Mismatches: 18, Indels: 10
0.85 0.09 0.05
Matches are distributed among these distances:
39 33 0.20
40 119 0.73
41 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:40683309 original size:80 final size:79
Alignment explanation
Indices: 40683154--40683324 Score: 204
Period size: 80 Copynumber: 2.2 Consensus size: 79
40683144 AATTCTGGGC
* * **
40683154 TAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAG
1 TAAGTCCCGAAGGCATTGGTGCGAGTTACTAAATACGGGCTAAGTCCCGAAGGCATTTGAACGAG
*
40683218 TTACTAAATCCGGGT
66 TGACTAAATCC-GGT
* *
40683233 TAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-ACGGGCTATGTCCCGAAGGCATTTGAACGA
1 TAAGTCCCGAAGGCATTGGTGCGAGTTACTA-AATACGGGCTAAGTCCCGAAGGCATTTGAACGA
*
40683297 G-GAGCTATATCCGGT
65 GTGA-CTAAATCCGGT
* *
40683312 TAAATTCCGAAGG
1 TAAGTCCCGAAGG
40683325 TACGTGATTT
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
79 19 0.24
80 58 0.73
81 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (79 bp):
TAAGTCCCGAAGGCATTGGTGCGAGTTACTAAATACGGGCTAAGTCCCGAAGGCATTTGAACGAG
TGACTAAATCCGGT
Found at i:40683313 original size:119 final size:119
Alignment explanation
Indices: 40683067--40683324 Score: 274
Period size: 119 Copynumber: 2.2 Consensus size: 119
40683057 TTGAATGATG
* *
40683067 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
** ** *
40683132 GTGCGAGATACTAATTCTGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGATACTAAAACTGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAA
* * * **
40683186 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
40683249 TTGTGCGAGTTACTATAAAC-GGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATA
64 TTGTGCGAGATACTA-AAACTGGGCTAAG-CCCGAAGGCATTGGAACGAGTGA-CTAAA
* *
40683306 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
40683325 TACGTGATTT
Statistics
Matches: 116, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
118 1 0.01
119 82 0.71
120 33 0.28
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAAAACTGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAA
Found at i:40691223 original size:40 final size:40
Alignment explanation
Indices: 40691076--40691299 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
40691066 TTGAATGATG
* * * *
40691076 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
40691116 TCCGGACTAAGAT--CGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40691155 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40691194 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
40691234 TCTGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
40691275 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40691300 AACGAGGAGC
Statistics
Matches: 161, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
39 55 0.34
40 103 0.64
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:40691270 original size:80 final size:79
Alignment explanation
Indices: 40691076--40691299 Score: 258
Period size: 79 Copynumber: 2.8 Consensus size: 79
40691066 TTGAATGATG
* * * * * *
40691076 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT--CGAAGGCAT
1 TCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTATAACCGGGCTAAG-TCCCGAAGGCAT
*
40691138 TTGTGCGAGATACTAAT
63 TTGTGCGAGATACTAAA
*
40691155 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTA-AATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTATAA-CCGGGCTAAGTCCCGAAGGCATTT
*
40691219 GTGCGAGTTACTAAA
65 GTGCGAGATACTAAA
* * * *
40691234 TCTGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
40691299 G
65 G
40691300 AACGAGGAGC
Statistics
Matches: 125, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
77 2 0.02
78 23 0.18
79 50 0.40
80 48 0.38
81 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATACTAAA
Found at i:40695157 original size:16 final size:17
Alignment explanation
Indices: 40695117--40695164 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
40695107 TTGCATATTG
*
40695117 CAACAACTCACACTTTA
1 CAACAACTCACACATTA
*
40695134 CCACAACTCACACATTA
1 CAACAACTCACACATTA
*
40695151 -AACAACTCGCACAT
1 CAACAACTCACACAT
40695165 ACTATGGATG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.42, C:0.38, G:0.02, T:0.19
Consensus pattern (17 bp):
CAACAACTCACACATTA
Found at i:40695400 original size:17 final size:17
Alignment explanation
Indices: 40695364--40695410 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
40695354 TTCTTTTGTT
* *
40695364 ACAACTTACACATGATC
1 ACAACTCACACATGAGC
*
40695381 ACAACTCACACATGGGC
1 ACAACTCACACATGAGC
*
40695398 ACAACTCGCACAT
1 ACAACTCACACAT
40695411 TTGGCATGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.38, C:0.34, G:0.11, T:0.17
Consensus pattern (17 bp):
ACAACTCACACATGAGC
Found at i:40695745 original size:14 final size:15
Alignment explanation
Indices: 40695709--40695748 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
40695699 CATAGAACTC
40695709 ACATATTACAGCTCG
1 ACATATTACAGCTCG
*
40695724 TACATATTACGGCTCG
1 -ACATATTACAGCTCG
40695740 -CATATTACA
1 ACATATTACA
40695749 TCTCACGCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 8 0.36
16 14 0.64
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (15 bp):
ACATATTACAGCTCG
Found at i:40695908 original size:52 final size:51
Alignment explanation
Indices: 40695852--40695987 Score: 191
Period size: 52 Copynumber: 2.6 Consensus size: 51
40695842 CATTTCATAT
* * *
40695852 ATTCGATGCAATGATAAGTCGCATATATATTCCATCACAAACTAGTTCATGC
1 ATTCGATGCAATGA-AAGTCGCATATACATTCCATCACAAAATAATTCATGC
*
40695904 ATTCGATGCAATGACAGTTCGCATATACATTCCATCACAAAATAATTCATGC
1 ATTCGATGCAATGAAAG-TCGCATATACATTCCATCACAAAATAATTCATGC
* *
40695956 ATTCGATACAATGACAACTCGCATATACATTC
1 ATTCGATGCAATGA-AAGTCGCATATACATTC
40695988 TATAGTAGCC
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
51 2 0.03
52 72 0.96
53 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (51 bp):
ATTCGATGCAATGAAAGTCGCATATACATTCCATCACAAAATAATTCATGC
Found at i:40709572 original size:66 final size:68
Alignment explanation
Indices: 40709461--40709599 Score: 194
Period size: 66 Copynumber: 2.1 Consensus size: 68
40709451 TAGGATTTTT
*
40709461 GGGTGTTTCTAAGCATGCATGAATATTTTTTTATCTAATATTGTAAAAAGAA-TAGGAAAAAAA-
1 GGGTGTTTCTAAGCATGCATGAATATTTTTTTATCTAATAATGTAAAAA-AATTAGGAAAAAAAT
*
40709524 TGAA
65 TAAA
* * * *
40709528 GGGTGTTTTTGAGCATGTATG-ATATTTTTTTTTCTAATAATGTAAAAAAATTAGGAAAAAAATT
1 GGGTGTTTCTAAGCATGCATGAATATTTTTTTATCTAATAATGTAAAAAAATTAGGAAAAAAATT
40709592 AAA
66 AAA
40709595 GGGTG
1 GGGTG
40709600 CGAGTTTCAG
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
65 2 0.03
66 36 0.56
67 26 0.41
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.37
Consensus pattern (68 bp):
GGGTGTTTCTAAGCATGCATGAATATTTTTTTATCTAATAATGTAAAAAAATTAGGAAAAAAATT
AAA
Found at i:40718530 original size:79 final size:77
Alignment explanation
Indices: 40718428--40718650 Score: 254
Period size: 79 Copynumber: 2.8 Consensus size: 77
40718418 GCTCCTCGTT
* *
40718428 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGT-ATTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
40718493 ATTTAGTAACTCGCA
63 AATTAGTAACTCGCA
*
40718508 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAT-TCGCACAAATGCCTTCGGGACTTAGCCCGGA
*
40718572 ATTAGTATCTCGCA
64 ATTAGTAACTCGCA
* * * * *
40718586 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCGCTTAGCAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGT--ATTCGCACAAATGCCTTCGGGACTTAGCCCG
40718649 GA
62 GA
40718651 CATCATTCAA
Statistics
Matches: 125, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
78 47 0.38
79 57 0.46
80 20 0.16
81 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (77 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTATTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT
TAGTAACTCGCA
Found at i:40718545 original size:39 final size:40
Alignment explanation
Indices: 40718428--40718650 Score: 264
Period size: 39 Copynumber: 5.7 Consensus size: 40
40718418 GCTCCTCGTT
* *
40718428 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
40718468 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
40718508 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
40718547 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* ** *
40718586 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCGCTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTATC-TCGCA
40718627 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40718651 CATCATTCAA
Statistics
Matches: 165, Mismatches: 11, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
38 2 0.01
39 89 0.54
40 64 0.39
41 10 0.06
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:40719746 original size:13 final size:13
Alignment explanation
Indices: 40719728--40719752 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40719718 AGGATGAGCA
40719728 TTTTTTTTCTTTG
1 TTTTTTTTCTTTG
40719741 TTTTTTTTCTTT
1 TTTTTTTTCTTT
40719753 CTAGTTTCGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.08, G:0.04, T:0.88
Consensus pattern (13 bp):
TTTTTTTTCTTTG
Found at i:40726460 original size:79 final size:79
Alignment explanation
Indices: 40726358--40726580 Score: 267
Period size: 79 Copynumber: 2.8 Consensus size: 79
40726348 GCTCCTCGTT
* * *
40726358 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGGATATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
40726423 ATTTAGTAACTCGCA
65 AATTAGTAACTCGCA
*
40726438 CAAATGCCTTCGGGCTTAGCCC-GAAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCG
1 CAAATGCCTTCGGGCTTAGCCCGGATA-TAGTAAT-TCGCACAAATGCCTTCGGGACTTAGCCCG
*
40726500 GAATTAGTATCTCGCA
64 GAATTAGTAACTCGCA
* * * * *
40726516 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGGATATAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCCG
40726579 GA
64 GA
40726581 CATCATTCAA
Statistics
Matches: 124, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
78 48 0.39
79 53 0.43
80 22 0.18
81 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGGCTTAGCCCGGATATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGA
ATTAGTAACTCGCA
Found at i:40726479 original size:39 final size:40
Alignment explanation
Indices: 40726358--40726580 Score: 257
Period size: 39 Copynumber: 5.7 Consensus size: 40
40726348 GCTCCTCGTT
* *
40726358 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
40726398 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
*
40726438 CAAATGCCTTCGGG-CTTAGCCCGAAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
40726477 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
40726516 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
40726557 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40726581 CATCATTCAA
Statistics
Matches: 164, Mismatches: 11, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
38 2 0.01
39 87 0.53
40 64 0.39
41 11 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:40726541 original size:118 final size:119
Alignment explanation
Indices: 40726358--40726578 Score: 285
Period size: 118 Copynumber: 1.9 Consensus size: 119
40726348 GCTCCTCGTT
*
40726358 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
*
40726423 AT-TTAGTAAC-TCGCACAAATGCCTTCGGG-CTTAGCCCGAAATTAGTATCTCGCA
66 ATATT-GTAACTTAGCAC-AA-GCCTTCGGGACTTAGCCCGAAATTAGTATCTCGCA
* **
40726477 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGT-ATCTCGCACAAATGCCTTC-GGATCTTAGTC
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAACC
*
40726538 CGGATATTGTCACTTAGCACAAGCCTTCGGGACTTAGCCCG
63 CGGATATTGTAACTTAGCACAAGCCTTCGGGACTTAGCCCG
40726579 GACATCATTC
Statistics
Matches: 90, Mismatches: 6, Indels: 13
0.83 0.06 0.12
Matches are distributed among these distances:
117 15 0.17
118 54 0.60
119 21 0.23
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (119 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATTGTAACTTAGCACAAGCCTTCGGGACTTAGCCCGAAATTAGTATCTCGCA
Found at i:40728624 original size:15 final size:17
Alignment explanation
Indices: 40728604--40728648 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
40728594 AGTTTTTCTA
40728604 CTATATAATATA-AT-G
1 CTATATAATATATATAG
40728619 CTATATAATATTATATAG
1 CTATATAATA-TATATAG
40728637 -TATATAATATAT
1 CTATATAATATAT
40728649 TAATAGTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 10 0.37
16 5 0.19
17 11 0.41
18 1 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (17 bp):
CTATATAATATATATAG
Found at i:40728663 original size:17 final size:18
Alignment explanation
Indices: 40728620--40728665 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
40728610 AATATAATGC
40728620 TATATA-ATATTATATAG
1 TATATATATATTATATAG
40728637 TATATAATATATTA-ATAG
1 TATAT-ATATATTATATAG
*
40728655 TTTATATATAT
1 TATATATATAT
40728666 GCATCAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 11 0.42
18 9 0.35
19 6 0.23
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (18 bp):
TATATATATATTATATAG
Found at i:40728903 original size:252 final size:252
Alignment explanation
Indices: 40728505--40728983 Score: 667
Period size: 252 Copynumber: 1.9 Consensus size: 252
40728495 CAATACATAA
* * * * * *
40728505 TATATAATTATTATCATATATTATTGTTTATTATTATATTGATTGCAATATGCTCTAAGTCTATG
1 TATATAATTATTATCATATACTATTGTTTATTATTATACTGACTGAAATATGCTCTAAGTCCATA
* * * * *
40728570 TAACTTTTAATACATTTGAAAATTAGTTTTTCTACTATATAATATAATGCTATATAATATTATAT
66 TAACTTTTAATAAATTTGAAAATTAGTTCTCCTACAATATAATATAATGCTATATAATATCATAT
* * *
40728635 AGTATATAATATATTAATAGTTTATATATATGCATCAATGATTAAAGATTATAATATCATGAAAT
131 AATATATAAGATATTAATAATTTATATATATGCATCAATGATTAAAGATTATAATATCATGAAAT
*
40728700 ACTATATCTTTTATTATAATTTATAATATAATAATTATTATAGATAATAGTAGTACAT
196 ACTATATCTTTTATTAT-ATTAATAATATAATAATTATTATAGATAATAGTAGTACAT
* * *
40728758 TATAT-ATTAATTATTATATACTATTGTTTATTATTATACTGGCTGAAATATGCTCTAAGTCCCT
1 TATATAATT-ATTATCATATACTATTGTTTATTATTATACTGACTGAAATATGCTCTAAGTCCAT
** * * *
40728822 AT-ACTTTTTGTAAATTTGAAAGTTAGTTCTCCTACAACT-TTATATAATGCTATATCATATCAT
65 ATAACTTTTAATAAATTTGAAAATTAGTTCTCCTACAA-TATAATATAATGCTATATAATATCAT
* * *
40728885 ATAATATATAAGATATTAATAATTTATATATATGCATCAATGATTAAATATTATAGTATCATGTA
129 ATAATATATAAGATATTAATAATTTATATATATGCATCAATGATTAAAGATTATAATATCATGAA
*
40728950 ATATTATATCTTTTATTATATTAATAATATAATA
194 ATACTATATCTTTTATTATATTAATAATATAATA
40728984 GTACTACATT
Statistics
Matches: 197, Mismatches: 27, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
251 14 0.07
252 129 0.65
253 54 0.27
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (252 bp):
TATATAATTATTATCATATACTATTGTTTATTATTATACTGACTGAAATATGCTCTAAGTCCATA
TAACTTTTAATAAATTTGAAAATTAGTTCTCCTACAATATAATATAATGCTATATAATATCATAT
AATATATAAGATATTAATAATTTATATATATGCATCAATGATTAAAGATTATAATATCATGAAAT
ACTATATCTTTTATTATATTAATAATATAATAATTATTATAGATAATAGTAGTACAT
Found at i:40728995 original size:235 final size:245
Alignment explanation
Indices: 40728505--40729127 Score: 659
Period size: 252 Copynumber: 2.6 Consensus size: 245
40728495 CAATACATAA
* * * * * **
40728505 TATATAATT-ATTATCATATATTATTGTTTATTATTATATTGATTGCAATATGCTCTAAGTCTAT
1 TATAT-ATTAATTATTATATACTATTGTTTATTATTATACTGGTTGAAATATGCTCTAAGTCCCT
* * * * * *
40728569 GTAACTTTTAATACATTTGAAAATTAGTTTTTCTACTATATAATATAATGCTATATAATATTATA
65 AT-ACTTTTAATAAATTTGAAAGTTAG-TTTCCTACTATATTATATAATGCTATATAATATCATA
* * *
40728634 TAGTATATAATATATTAATAGTTTATATATATGCATCAATGATTAAAGATTATAATATCATGAAA
128 TAATATATAAGATATTAATAATTTATATATATGCATCAATGATTAAAGATTATAATATCATGAAA
*
40728699 TACTATATCTTTTATTATAATTTATAATATAATAATTATTATAGATAATAGTAGTACAT
193 TACTATATC--TTATTATAA-TTATAATAT-ATAATTA-TATA-ATAATAGTACTACAT
*
40728758 TATATATTAATTATTATATACTATTGTTTATTATTATACTGGCTGAAATATGCTCTAAGTCCCTA
1 TATATATTAATTATTATATACTATTGTTTATTATTATACTGGTTGAAATATGCTCTAAGTCCCTA
** * *
40728823 TACTTTTTGTAAATTTGAAAGTTAGTTCTCCTACAACT-TTATATAATGCTATATCATATCATAT
66 TACTTTTAATAAATTTGAAAGTTAGTT-TCCTACTA-TATTATATAATGCTATATAATATCATAT
* * *
40728887 AATATATAAGATATTAATAATTTATATATATGCATCAATGATTAAATATTATAGTATCATGTAAT
129 AATATATAAGATATTAATAATTTATATATATGCATCAATGATTAAAGATTATAATATCATGAAAT
*
40728952 ATTATATC-T-TT-T-A-T-T-ATAT-TAA-TA-AT-ATAATAGTACTACAT
194 ACTATATCTTATTATAATTATAATATATAATTATATAATAATAGTACTACAT
* * * * * **
40728993 TATATATCAATTATTATCATAC-ATTATTAATTTTTATACTAGTTGAAATATATTCTAAGTCCCT
1 TATATATTAATTATTAT-ATACTATTGTTTATTATTATACTGGTTGAAATATGCTCTAAGTCCCT
* * * *
40729057 ATACTTTTCAT-ACTTTAAAAAGTTAGCTTTCCTACTATATTATATAATG--AGTATTATATCAT
65 ATACTTTTAATAAATTT-GAAAGTTAG-TTTCCTACTATATTATATAATGCTA-TATAATATCAT
40729119 ATAATATAT
127 ATAATATAT
40729128 TAATGGTATA
Statistics
Matches: 322, Mismatches: 40, Indels: 35
0.81 0.10 0.09
Matches are distributed among these distances:
233 1 0.00
234 24 0.07
235 99 0.31
236 6 0.02
237 2 0.01
239 2 0.01
240 3 0.01
242 4 0.01
243 1 0.00
244 1 0.00
246 1 0.00
247 1 0.00
248 2 0.01
249 1 0.00
251 2 0.01
252 118 0.37
253 54 0.17
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.46
Consensus pattern (245 bp):
TATATATTAATTATTATATACTATTGTTTATTATTATACTGGTTGAAATATGCTCTAAGTCCCTA
TACTTTTAATAAATTTGAAAGTTAGTTTCCTACTATATTATATAATGCTATATAATATCATATAA
TATATAAGATATTAATAATTTATATATATGCATCAATGATTAAAGATTATAATATCATGAAATAC
TATATCTTATTATAATTATAATATATAATTATATAATAATAGTACTACAT
Found at i:40729449 original size:15 final size:16
Alignment explanation
Indices: 40729423--40729454 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
40729413 TATAAGCATA
40729423 TTATTAAAATTATTTT
1 TTATTAAAATTATTTT
40729439 TTATT-AAATTATTTT
1 TTATTAAAATTATTTT
40729454 T
1 T
40729455 AAAAATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATTAAAATTATTTT
Found at i:40733977 original size:33 final size:33
Alignment explanation
Indices: 40733931--40734021 Score: 96
Period size: 33 Copynumber: 2.8 Consensus size: 33
40733921 CGGTGTTACA
* *
40733931 CTAT-GCATACTGATGATAAGACTATAGCTAGG
1 CTATGGCATACTGATGATAAGACCATAACTAGG
* *
40733963 CTATGGCATTCTGATGATAAGACCATAACTGGG
1 CTATGGCATACTGATGATAAGACCATAACTAGG
* **
40733996 TTATGGCACTA-TGAACATAAGACCAT
1 CTATGGCA-TACTGATGATAAGACCAT
40734022 GGTTGGACCA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
32 4 0.08
33 44 0.90
34 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (33 bp):
CTATGGCATACTGATGATAAGACCATAACTAGG
Found at i:40735281 original size:15 final size:15
Alignment explanation
Indices: 40735261--40735312 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
40735251 ACACACGACC
40735261 GTGTCACCAAGCCGT
1 GTGTCACCAAGCCGT
* *
40735276 GTGTCACACACGGC-T
1 GTGTCAC-CAAGCCGT
*
40735291 GTGTCACCAGGCCGT
1 GTGTCACCAAGCCGT
40735306 GTGTCAC
1 GTGTCAC
40735313 ACACGGCTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 4 0.13
15 23 0.74
16 4 0.13
ACGTcount: A:0.17, C:0.33, G:0.29, T:0.21
Consensus pattern (15 bp):
GTGTCACCAAGCCGT
Found at i:40735318 original size:30 final size:30
Alignment explanation
Indices: 40735251--40735321 Score: 115
Period size: 30 Copynumber: 2.4 Consensus size: 30
40735241 GCTACAGGGG
* *
40735251 ACACACGACCGTGTCACCAAGCCGTGTGTC
1 ACACACGGCTGTGTCACCAAGCCGTGTGTC
*
40735281 ACACACGGCTGTGTCACCAGGCCGTGTGTC
1 ACACACGGCTGTGTCACCAAGCCGTGTGTC
40735311 ACACACGGCTG
1 ACACACGGCTG
40735322 AGACACACGC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.21, C:0.35, G:0.27, T:0.17
Consensus pattern (30 bp):
ACACACGGCTGTGTCACCAAGCCGTGTGTC
Found at i:40735336 original size:30 final size:30
Alignment explanation
Indices: 40735272--40735337 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
40735262 TGTCACCAAG
* * *
40735272 CCGTGTGTCACACACGGCTGTGTCACCAGG
1 CCGTGTGTCACACACGGCTGAGACACCAGC
40735302 CCGTGTGTCACACACGGCTGAGACA-CACGC
1 CCGTGTGTCACACACGGCTGAGACACCA-GC
40735332 CCGTGT
1 CCGTGT
40735338 CTATGCTCGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 2 0.06
30 30 0.94
ACGTcount: A:0.18, C:0.35, G:0.29, T:0.18
Consensus pattern (30 bp):
CCGTGTGTCACACACGGCTGAGACACCAGC
Found at i:40738754 original size:20 final size:21
Alignment explanation
Indices: 40738726--40738768 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
40738716 AAAGTACGAA
*
40738726 AGAAAAAAAATACTTT-TTGGT
1 AGAAAAAAAGTA-TTTATTGGT
40738747 AGAAAAAAAGTATTTATTGGT
1 AGAAAAAAAGTATTTATTGGT
40738768 A
1 A
40738769 AAAGACCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.49, C:0.02, G:0.16, T:0.33
Consensus pattern (21 bp):
AGAAAAAAAGTATTTATTGGT
Found at i:40739865 original size:20 final size:20
Alignment explanation
Indices: 40739840--40739880 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
40739830 TTATTATGCG
*
40739840 AAGCAATAATATTGGATATT
1 AAGCAATAATATTGAATATT
*
40739860 AAGCAATAATGTTGAATATT
1 AAGCAATAATATTGAATATT
40739880 A
1 A
40739881 TAATAATAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.34
Consensus pattern (20 bp):
AAGCAATAATATTGAATATT
Found at i:40745440 original size:21 final size:21
Alignment explanation
Indices: 40745416--40745470 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
40745406 GTGCCTCAGT
***
40745416 CACACGACCATGTTTCTTAGC
1 CACACGACCATGTGAATTAGC
**
40745437 CACACGGGCATGTGAATTAGC
1 CACACGACCATGTGAATTAGC
40745458 CACACGACCATGT
1 CACACGACCATGT
40745471 CTACTCTGGT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (21 bp):
CACACGACCATGTGAATTAGC
Found at i:40754354 original size:27 final size:27
Alignment explanation
Indices: 40754281--40754347 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
40754271 AATTCGCCAT
*
40754281 AAGGCAATCCATTCATACTACACAAAA
1 AAGGCAATCCATTCATAGTACACAAAA
*
40754308 AAGGCAATCCATTCATAGTACACCAAA
1 AAGGCAATCCATTCATAGTACACAAAA
40754335 AAGGCAATCCATT
1 AAGGCAATCCATT
40754348 TAGAGTATGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.45, C:0.25, G:0.10, T:0.19
Consensus pattern (27 bp):
AAGGCAATCCATTCATAGTACACAAAA
Found at i:40769808 original size:20 final size:20
Alignment explanation
Indices: 40769776--40769829 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
40769766 GTCTCTTTCA
*
40769776 ATAAAAA-TACAAAATAGTTT
1 ATAAAAATTTCAAAATA-TTT
* *
40769796 -TCAAAATTTCAAATTATTT
1 ATAAAAATTTCAAAATATTT
40769815 ATAAAAATTTCAAAA
1 ATAAAAATTTCAAAA
40769830 AAAAATTCTA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 8 0.30
20 19 0.70
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (20 bp):
ATAAAAATTTCAAAATATTT
Found at i:40771629 original size:43 final size:43
Alignment explanation
Indices: 40771511--40771758 Score: 208
Period size: 43 Copynumber: 5.7 Consensus size: 43
40771501 TGTTGGTCTA
* **** *
40771511 TAGCGGCGCTTCTAGCACAAACGCCGCTAAAGATTAGGGTCTT
1 TAGCGGCGCTTCTACCACAAACGCCGCTAAAGACCCTGATCTT
* * * * *
40771554 TAGCGGTGCTTTTCCCACAAACGCCGCAAAAGACCCTGATCTC
1 TAGCGGCGCTTCTACCACAAACGCCGCTAAAGACCCTGATCTT
* ** * *
40771597 TAGCGGCGCTTCGACCACAAACGCCATTAAAGAACCTAATCTT
1 TAGCGGCGCTTCTACCACAAACGCCGCTAAAGACCCTGATCTT
* * * * *
40771640 TAGCGGCACTTTTCCCCACAAACGCTGCTAAAGACCATGATCTT
1 TAGCGGCGCTTCT-ACCACAAACGCCGCTAAAGACCCTGATCTT
* * * * * *
40771684 TAGTGGCGCTTTTTCCACAAACGCCGTTAAAGACCCTTATATT
1 TAGCGGCGCTTCTACCACAAACGCCGCTAAAGACCCTGATCTT
* * * *
40771727 TAGCGACGCTTTTACCAAAAACGCCACTAAAG
1 TAGCGGCGCTTCTACCACAAACGCCGCTAAAG
40771759 GCCAACACCT
Statistics
Matches: 159, Mismatches: 45, Indels: 2
0.77 0.22 0.01
Matches are distributed among these distances:
43 125 0.79
44 34 0.21
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (43 bp):
TAGCGGCGCTTCTACCACAAACGCCGCTAAAGACCCTGATCTT
Found at i:40771702 original size:87 final size:86
Alignment explanation
Indices: 40771550--40771783 Score: 254
Period size: 87 Copynumber: 2.7 Consensus size: 86
40771540 AAGATTAGGG
* * * * * ***
40771550 TCTTTAGCGGTGCTTTTCCCACAAACGCCGCAAAAGACCCTGATCTCTAGCGGCGCTTCGACCAC
1 TCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGATCTTTAGTGGCGCTTTTTCCAC
40771615 AAACGCCATTAAAGAACCTAA
66 AAACGCCATTAAAGAACCTAA
* *
40771636 TCTTTAGCGGCACTTTTCCCCACAAACGCTGCTAAAGACCATGATCTTTAGTGGCGCTTTTTCCA
1 TCTTTAGCGGCGCTTTT-CCCACAAACGCCGCTAAAGACCATGATCTTTAGTGGCGCTTTTTCCA
* * *
40771701 CAAACGCCGTTAAAGACCCTTA
65 CAAACGCCATTAAAGAACCTAA
* * * * * * ** *
40771723 TATTTAGCGACGCTTTTACCAAAAACGCCACTAAAGGCCAACACCTTTAGTGGCG-TTTTTC
1 TCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGATCTTTAGTGGCGCTTTTTC
40771784 AAAAAAAACG
Statistics
Matches: 123, Mismatches: 24, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
85 6 0.05
86 45 0.37
87 72 0.59
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (86 bp):
TCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGATCTTTAGTGGCGCTTTTTCCAC
AAACGCCATTAAAGAACCTAA
Found at i:40771783 original size:130 final size:130
Alignment explanation
Indices: 40771526--40771772 Score: 289
Period size: 130 Copynumber: 1.9 Consensus size: 130
40771516 GCGCTTCTAG
** * *
40771526 CACAAACGCCGCTAAAGATTAGGGTCTTTAGCGGTGCTTTTCCCACAAACGCCGCAAAAGACCCT
1 CACAAACGCCGCTAAAGACCAGGATCTTTAGCGGCGCTTTTCCCACAAACGCCGCAAAAGACCCT
* * * * * *
40771591 GATCTCTAGCGGCGCTTCGACCACAAACGCCATTAAAGAACCTAATCTTTAGCGGCACTTTTCCC
66 GATATCTAGCGACGCTTCGACCAAAAACGCCACTAAAGAACCAAACCTTTAGCGGCACTTTTCCC
* * * * **
40771656 CACAAACGCTGCTAAAGACCATGATCTTTAGTGGCGCTTTTTCCACAAACGCCGTTAAAGACCCT
1 CACAAACGCCGCTAAAGACCAGGATCTTTAGCGGCGCTTTTCCCACAAACGCCGCAAAAGACCCT
* * ** *
40771721 TATATTTAGCGACGCTTTTACCAAAAACGCCACTAAAG-GCCAACACCTTTAG
66 GATATCTAGCGACGCTTCGACCAAAAACGCCACTAAAGAACCAA-ACCTTTAG
40771773 TGGCGTTTTT
Statistics
Matches: 95, Mismatches: 21, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
129 3 0.03
130 92 0.97
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (130 bp):
CACAAACGCCGCTAAAGACCAGGATCTTTAGCGGCGCTTTTCCCACAAACGCCGCAAAAGACCCT
GATATCTAGCGACGCTTCGACCAAAAACGCCACTAAAGAACCAAACCTTTAGCGGCACTTTTCCC
Found at i:40772195 original size:21 final size:21
Alignment explanation
Indices: 40772110--40772197 Score: 97
Period size: 21 Copynumber: 4.2 Consensus size: 21
40772100 TTTGACGCTG
40772110 CTCTCGCTGCAGCCTCTACTT
1 CTCTCGCTGCAGCCTCTACTT
* ** * *
40772131 CCCTCGCTATAGCCTTTGCTT
1 CTCTCGCTGCAGCCTCTACTT
* *
40772152 CCCTCGCTGCAGCCTGTACTT
1 CTCTCGCTGCAGCCTCTACTT
40772173 CTCTCGCTGCCA-CCTCTACTT
1 CTCTCGCTG-CAGCCTCTACTT
40772194 CTCT
1 CTCT
40772198 TTCTGCCGCA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
21 53 0.96
22 2 0.04
ACGTcount: A:0.09, C:0.43, G:0.14, T:0.34
Consensus pattern (21 bp):
CTCTCGCTGCAGCCTCTACTT
Found at i:40772275 original size:66 final size:65
Alignment explanation
Indices: 40772184--40772354 Score: 184
Period size: 66 Copynumber: 2.6 Consensus size: 65
40772174 TCTCGCTGCC
** * * *
40772184 ACCTCTACTTCTCTTTCTGCCGCATCTGCTTTAAGTTGCT-TCTGGAGTTCTTCATA-CTTTCGT
1 ACCTC-ACTTCTCTCGCTGCTGCATCTGCTTTAAGTTG-TAGCTAGAGTTCTTCATATCTTT-GT
40772247 TGA
63 TGA
*
40772250 ACCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTAGAGTTCTTCATATCTTTTTTG
1 ACCTCA-CTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTAGAGTTCTTCATATCTTTGTTG
40772315 A
65 A
* * * * *
40772316 ACCTCACTTTCTTTCGATGTTGCCTCCGCTTTAAGTTGT
1 ACCTCAC-TTCTCTCGCTGCTGCATCTGCTTTAAGTTGT
40772355 GTAATTTGCT
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
65 3 0.03
66 83 0.92
67 4 0.04
ACGTcount: A:0.15, C:0.26, G:0.16, T:0.43
Consensus pattern (65 bp):
ACCTCACTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTAGAGTTCTTCATATCTTTGTTGA
Found at i:40777790 original size:9 final size:9
Alignment explanation
Indices: 40777773--40779470 Score: 396
Period size: 9 Copynumber: 187.8 Consensus size: 9
40777763 TAAGTATAAT
*
40777773 TAAGCTATG
1 TAAGTTATG
40777782 TAAGTTATG
1 TAAGTTATG
40777791 T-A-TTATG
1 TAAGTTATG
40777798 TAAGTTAT-
1 TAAGTTATG
*
40777806 TTA-TTATG
1 TAAGTTATG
* *
40777814 AAAATTATG
1 TAAGTTATG
*
40777823 TAAGTTGTG
1 TAAGTTATG
40777832 T-A-TTATG
1 TAAGTTATG
*
40777839 -AA--AAT-
1 TAAGTTATG
* *
40777844 TATGCTATG
1 TAAGTTATG
40777853 TAAGTTATG
1 TAAGTTATG
* *
40777862 TAAGTCATA
1 TAAGTTATG
40777871 TAAGTTATG
1 TAAGTTATG
40777880 T-A-TTATG
1 TAAGTTATG
40777887 TAAGTTATG
1 TAAGTTATG
40777896 TAAGTTAT-
1 TAAGTTATG
*
40777904 TTA-TTATG
1 TAAGTTATG
* * *
40777912 AAAATTAAG
1 TAAGTTATG
40777921 TAAGTTATG
1 TAAGTTATG
*
40777930 TAATTTATG
1 TAAGTTATG
*
40777939 -AA-TAAT-
1 TAAGTTATG
***
40777945 TAAAAAAATG
1 T-AAGTTATG
40777955 TAAGTTATG
1 TAAGTTATG
40777964 TAAG-T-TG
1 TAAGTTATG
40777971 TAAG-T-TG
1 TAAGTTATG
40777978 TAAGTTATG
1 TAAGTTATG
40777987 TAAGTTATG
1 TAAGTTATG
* *
40777996 T-A-TAATA
1 TAAGTTATG
* **
40778003 TAAATTAAC
1 TAAGTTATG
40778012 TAAGTTATG
1 TAAGTTATG
*
40778021 TAATTTATG
1 TAAGTTATG
40778030 TATA-TTAAT-
1 TA-AGTT-ATG
40778039 TAAGTTATG
1 TAAGTTATG
*
40778048 TAATTTATG
1 TAAGTTATG
*
40778057 TATAATATTAATG
1 --TAA-GTT-ATG
40778070 TAAGTTATG
1 TAAGTTATG
40778079 TAAGTTAT-
1 TAAGTTATG
*
40778087 TTA-TTATG
1 TAAGTTATG
* * *
40778095 AAAATTAAG
1 TAAGTTATG
40778104 TAAGTTATG
1 TAAGTTATG
*
40778113 TAATTTATG
1 TAAGTTATG
*
40778122 -AA-TAAT-
1 TAAGTTATG
***
40778128 TAAACAAATG
1 T-AAGTTATG
40778138 TAAGTTATG
1 TAAGTTATG
40778147 TAAG-T-TG
1 TAAGTTATG
40778154 TAAGTTATG
1 TAAGTTATG
40778163 TAAGTTATG
1 TAAGTTATG
*
40778172 TATA-ATAT-
1 TA-AGTTATG
40778180 TAA-TTAAT-
1 TAAGTT-ATG
40778188 TAAGTTATG
1 TAAGTTATG
*
40778197 TAATTTATG
1 TAAGTTATG
*
40778206 TATTGCATTAATG
1 TA-AG--TT-ATG
40778219 TAAGTTATG
1 TAAGTTATG
*
40778228 TAACTTATG
1 TAAGTTATG
*
40778237 TATA-ATAT-
1 TA-AGTTATG
40778245 TAA-TTAAT-
1 TAAGTT-ATG
*
40778253 TAAGTCATG
1 TAAGTTATG
*
40778262 TAATTTATG
1 TAAGTTATG
*
40778271 TAAAATATTAATG
1 T--AA-GTT-ATG
*
40778284 CAAGTTATG
1 TAAGTTATG
*
40778293 TAATTTATG
1 TAAGTTATG
*
40778302 TATAATATTAATG
1 --TAA-GTT-ATG
40778315 TAAGTTATG
1 TAAGTTATG
*
40778324 TAATTTATG
1 TAAGTTATG
*
40778333 TATA-ATAT-
1 TA-AGTTATG
40778341 TAA-TTAAT-
1 TAAGTT-ATG
40778349 TAAGTTATG
1 TAAGTTATG
*
40778358 TAATTTATG
1 TAAGTTATG
*
40778367 TATTGCATTAATG
1 TA-AG--TT-ATG
40778380 TAAGTTATG
1 TAAGTTATG
*
40778389 TAATTTATG
1 TAAGTTATG
*
40778398 TATTGCATTAATG
1 TA-AG--TT-ATG
40778411 TAAGTTATG
1 TAAGTTATG
*
40778420 TAATTTATG
1 TAAGTTATG
40778429 AATAA-TTA--
1 --TAAGTTATG
* *** *
40778437 AAAAAAAAG
1 TAAGTTATG
40778446 TAAGTTATG
1 TAAGTTATG
40778455 TAAGTTATG
1 TAAGTTATG
*
40778464 TATA-ATAT-
1 TA-AGTTATG
40778472 TAA-TTAAT-
1 TAAGTT-ATG
40778480 TAAGTTATG
1 TAAGTTATG
*
40778489 TAATTTATG
1 TAAGTTATG
*
40778498 TATTGCATTAATG
1 TA-AG--TT-ATG
40778511 TAAGTTATG
1 TAAGTTATG
*
40778520 TAACTTATG
1 TAAGTTATG
*
40778529 TATA-ATAT-
1 TA-AGTTATG
40778537 TAA-TTAAT-
1 TAAGTT-ATG
*
40778545 TAAGTCATG
1 TAAGTTATG
*
40778554 TAATTTATG
1 TAAGTTATG
*
40778563 TATAATATTAATG
1 --TAA-GTT-ATG
*
40778576 CAAGTTATG
1 TAAGTTATG
*
40778585 TAATTTATG
1 TAAGTTATG
*
40778594 TATA-ATAT-
1 TA-AGTTATG
40778602 TAA-TTAAT-
1 TAAGTT-ATG
40778610 TAAGTTATG
1 TAAGTTATG
*
40778619 TAATTTATG
1 TAAGTTATG
*
40778628 TATAATATTAATG
1 --TAA-GTT-ATG
40778641 TAAGTTATG
1 TAAGTTATG
40778650 TAAGTTATG
1 TAAGTTATG
*
40778659 TATA-ATAT-
1 TA-AGTTATG
40778667 TAA-TTAAT-
1 TAAGTT-ATG
40778675 TAAGTTATG
1 TAAGTTATG
*
40778684 TAATTTATG
1 TAAGTTATG
*
40778693 TATTGCATTAATG
1 TA-AG--TT-ATG
40778706 TAAGTTATG
1 TAAGTTATG
*
40778715 TAATTTATG
1 TAAGTTATG
*
40778724 -AA-TAAT-
1 TAAGTTATG
*** *
40778730 TAAAAAAAAG
1 T-AAGTTATG
40778740 TAAGTTATG
1 TAAGTTATG
40778749 TAAG-T-TG
1 TAAGTTATG
40778756 TAAGTTATG
1 TAAGTTATG
40778765 TAAGTTATG
1 TAAGTTATG
40778774 TAAGTTATG
1 TAAGTTATG
*
40778783 TATA-ATAT-
1 TA-AGTTATG
40778791 TAA-TTAAT-
1 TAAGTT-ATG
40778799 TAAGTTATG
1 TAAGTTATG
*
40778808 TAATTTATG
1 TAAGTTATG
*
40778817 TATTGCATTAATG
1 TA-AG--TT-ATG
40778830 TAAGTTATG
1 TAAGTTATG
*
40778839 TAACTTATG
1 TAAGTTATG
*
40778848 TATA-ATAT-
1 TA-AGTTATG
40778856 TAA-TTAAT-
1 TAAGTT-ATG
*
40778864 TAAGTCATG
1 TAAGTTATG
*
40778873 TAATTTATG
1 TAAGTTATG
*
40778882 TATAATATTAATG
1 --TAA-GTT-ATG
*
40778895 CAAGTTATG
1 TAAGTTATG
*
40778904 TAATTTATG
1 TAAGTTATG
*
40778913 TTTAATATTAATG
1 --TAA-GTT-ATG
40778926 TAAGTTATG
1 TAAGTTATG
*
40778935 TAATTTATG
1 TAAGTTATG
*
40778944 TATA-ATAT-
1 TA-AGTTATG
40778952 TAA-TTAAT-
1 TAAGTT-ATG
40778960 TAAGTTATG
1 TAAGTTATG
*
40778969 TAATTTATG
1 TAAGTTATG
*
40778978 TATTGCATTAATG
1 TA-AG--TT-ATG
40778991 TAAGTTATG
1 TAAGTTATG
*
40779000 TAACTTATG
1 TAAGTTATG
*
40779009 TATA-ATAT-
1 TA-AGTTATG
40779017 TAA-TTAAT-
1 TAAGTT-ATG
*
40779025 TAAGTCATG
1 TAAGTTATG
*
40779034 TAATTTATG
1 TAAGTTATG
*
40779043 TATAATATTAATG
1 --TAA-GTT-ATG
*
40779056 CAAGTTATG
1 TAAGTTATG
*
40779065 TAATTTATG
1 TAAGTTATG
*
40779074 TATA-ATAT-
1 TA-AGTTATG
40779082 TAA-TTAAT-
1 TAAGTT-ATG
40779090 TAAGTTATG
1 TAAGTTATG
*
40779099 TAATTTATG
1 TAAGTTATG
*
40779108 TATAATATTAATG
1 --TAA-GTT-ATG
40779121 TAAGTTATG
1 TAAGTTATG
40779130 TAAGTTATG
1 TAAGTTATG
*
40779139 TATA-ATAT-
1 TA-AGTTATG
40779147 TAA-TTAAT-
1 TAAGTT-ATG
40779155 TAAGTTATG
1 TAAGTTATG
*
40779164 TAATTTATG
1 TAAGTTATG
*
40779173 TATTGCATTAATG
1 TA-AG--TT-ATG
40779186 TAAGTTATG
1 TAAGTTATG
*
40779195 TAATTTATG
1 TAAGTTATG
*
40779204 -AA-TAAT-
1 TAAGTTATG
*** *
40779210 TAAAAAAAG
1 TAAGTTATG
40779219 TAAGTTATG
1 TAAGTTATG
40779228 TAAG-T-TG
1 TAAGTTATG
40779235 TAAGTTATG
1 TAAGTTATG
40779244 TAAGTTATG
1 TAAGTTATG
40779253 TAAGTTATG
1 TAAGTTATG
*
40779262 TATA-ATAT-
1 TA-AGTTATG
40779270 TAA-TTAAT-
1 TAAGTT-ATG
40779278 TAAGTTATG
1 TAAGTTATG
*
40779287 TAATTTATG
1 TAAGTTATG
*
40779296 TATTGCATTAATG
1 TA-AG--TT-ATG
40779309 TAAGTTATG
1 TAAGTTATG
*
40779318 TAACTTATG
1 TAAGTTATG
*
40779327 TATA-ATAT-
1 TA-AGTTATG
40779335 TAA-TTAAT-
1 TAAGTT-ATG
*
40779343 TAAGTCATG
1 TAAGTTATG
*
40779352 TAATTTATG
1 TAAGTTATG
*
40779361 TATAATATTAATG
1 --TAA-GTT-ATG
*
40779374 CAAGTTATG
1 TAAGTTATG
*
40779383 TAATTTATG
1 TAAGTTATG
*
40779392 TTTAATATTAATG
1 --TAA-GTT-ATG
40779405 TAAGTTATG
1 TAAGTTATG
40779414 TAAG-T-TG
1 TAAGTTATG
40779421 TAAGTTATG
1 TAAGTTATG
*
40779430 TAAGTTATA
1 TAAGTTATG
*
40779439 TATA-ATAT-
1 TA-AGTTATG
40779447 TAA-TTAAT-
1 TAAGTT-ATG
40779455 TAAGTTATG
1 TAAGTTATG
40779464 TAAGTTA
1 TAAGTTA
40779471 ACTATTTTAA
Statistics
Matches: 1286, Mismatches: 208, Indels: 390
0.68 0.11 0.21
Matches are distributed among these distances:
6 5 0.00
7 117 0.09
8 191 0.15
9 718 0.56
10 65 0.05
11 63 0.05
12 49 0.04
13 78 0.06
ACGTcount: A:0.39, C:0.02, G:0.13, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:40777799 original size:16 final size:16
Alignment explanation
Indices: 40777778--40777897 Score: 96
Period size: 16 Copynumber: 7.9 Consensus size: 16
40777768 ATAATTAAGC
40777778 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
40777794 TATGTAAGTTATTTAT
1 TATGTAAGTTATGTAT
40777810 TATG-AA---A---AT
1 TATGTAAGTTATGTAT
*
40777819 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
* * *
40777835 TATGAAAATTATG--C
1 TATGTAAGTTATGTAT
40777849 TATGTAAGTTATGTAAGT
1 TATGTAAGTTATGT-A-T
* *
40777867 CATATAAGTTATGTAT
1 TATGTAAGTTATGTAT
40777883 TATGTAAGTTATGTA
1 TATGTAAGTTATGTA
40777898 AGTTATTTAT
Statistics
Matches: 80, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
9 6 0.08
10 2 0.03
12 1 0.01
14 11 0.14
15 2 0.03
16 45 0.56
17 1 0.01
18 12 0.15
ACGTcount: A:0.35, C:0.02, G:0.17, T:0.46
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:40777820 original size:25 final size:25
Alignment explanation
Indices: 40777792--40777946 Score: 129
Period size: 25 Copynumber: 6.2 Consensus size: 25
40777782 TAAGTTATGT
40777792 ATTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* *
40777817 ATTATGTAAGTTGTGTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* *
40777842 ATTATGCTATG-TA---AGTTATGTAA
1 ATTATG-TAAGTTATTTA-TTATGAAA
* * * * *
40777865 GTCATATAAGTTATGTATTATGTAA
1 ATTATGTAAGTTATTTATTATGAAA
*
40777890 GTTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* *
40777915 ATTAAGTAAGTTATGTAATTTATGAATA
1 ATTATGTAAGTTAT-TTA-TTATGAA-A
40777943 ATTA
1 ATTA
40777947 AAAAAATGTA
Statistics
Matches: 105, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
22 4 0.04
23 12 0.11
25 71 0.68
26 6 0.06
27 7 0.07
28 5 0.05
ACGTcount: A:0.38, C:0.01, G:0.15, T:0.45
Consensus pattern (25 bp):
ATTATGTAAGTTATTTATTATGAAA
Found at i:40777924 original size:34 final size:35
Alignment explanation
Indices: 40777818--40778784 Score: 216
Period size: 34 Copynumber: 28.2 Consensus size: 35
40777808 ATTATGAAAA
* *
40777818 TTATGTAAGTTGTGTATTATGAAAATTATGCTATGTAAG
1 TTATGTAAGTTATGAATTATGAAAATTA----ATGTAAG
*
40777857 TTATGTAAGTCATAT-AAGTTATG--TATT-ATGTAAG
1 TTATGTAAGT--TATGAA-TTATGAAAATTAATGTAAG
**
40777891 TTATGTAAGTTATTTATTATGAAAATTAA-GTAAG
1 TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
* * * *
40777925 TTATGTAATTTATGAATAATTAAAA-AAATGTAAG
1 TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
* * * *
40777959 TTATGTAAGTTGT-AAGT-TGTAAGTT-ATGTAAG
1 TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
* * *** * *
40777991 TTATGTATA-ATATAAATTAACTAAGTT-ATGTAAT
1 TTATGTA-AGTTATGAATTATGAAAATTAATGTAAG
* * * *
40778025 TTATGTATA-TTAATTAAGTTATG-TAATTTATGTATAATA
1 TTATGTA-AGTT-ATGAA-TTATGAAAATTAATG--TAA-G
40778064 TTAATGTAAGTTATGTAAGTTATTTATTATGAAAATTAA-GTAAG
1 TT-ATGTAAGTTA--T--G--A---ATTATGAAAATTAATGTAAG
* * *
40778108 TTATGTAATTTATGAATAATTAAACA--AATGTAAG
1 TTATGTAAGTTATGAATTATGAAA-ATTAATGTAAG
* * *
40778142 TTATGTAAGTTGT-AAGTTATGTAAGTT-ATGTATA-
1 TTATGTAAGTTATGAA-TTATGAAAATTAATGTA-AG
* * * * *
40778176 ATAT-TAA-TTAATTAAGTTATG-TAATTTATGTATTG
1 TTATGTAAGTT-ATGAA-TTATGAAAATTAATGTA-AG
*
40778211 CATTAATGTAAGTTATGTAACTTATGTATAA-T-AT-TAA-
1 --TT-ATGTAAGTTATG-AA-TTATG-AAAATTAATGTAAG
* *
40778248 TTAAT-TAAGTCATGTAATTTATGTAAAATATTAATGCAAG
1 TT-ATGTAAGTTATG-AA-TTATG--AAA-ATTAATGTAAG
* *
40778288 TTATGTAATTTATG---TAT-AATATTAATGTAAG
1 TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
* * * *
40778319 TTATGTAATTTATGTATAAT-ATTAATTAAT-TAAG
1 TTATGTAAGTTATGAATTATGA-AAATTAATGTAAG
* * *
40778353 TTATGTAATTTATGTA-T-TG--CATTAATGTAAG
1 TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
* * *
40778384 TTATGTAATTTATGTA-T-TG--CATTAATGTAAG
1 TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
* * * ** *
40778415 TTATGTAATTTATGAATAATTAAAAAAAAAGTAAG
1 TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
* * *
40778450 TTATGTAAGTTATGTATAAT-ATTAATTAAT-TAAG
1 TTATGTAAGTTATGAATTATGA-AAATTAATGTAAG
* * *
40778484 TTATGTAATTTATGTA-T-TG--CATTAATGTAAG
1 TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
* * * *
40778515 TTATGTAACTTATGTATAAT-ATTAATTAAT-TAAG
1 TTATGTAAGTTATGAATTATGA-AAATTAATGTAAG
* * * *
40778549 TCATGTAATTTATG---TAT-AATATTAATGCAAG
1 TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
* * * *
40778580 TTATGTAATTTATGTATAAT-ATTAATTAAT-TAAG
1 TTATGTAAGTTATGAATTATGA-AAATTAATGTAAG
* *
40778614 TTATGTAATTTATG---TAT-AATATTAATGTAAG
1 TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
* * *
40778645 TTATGTAAGTTATGTATAAT-ATTAATTAAT-TAAG
1 TTATGTAAGTTATGAATTATGA-AAATTAATGTAAG
* * *
40778679 TTATGTAATTTATGTA-T-TG--CATTAATGTAAG
1 TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
* * * * *
40778710 TTATGTAATTTATGAATAATTAAAA-AAAAGTAAG
1 TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
* * *
40778744 TTATGTAAGTTGT-AAGTTATGTAAGTT-ATGTAAG
1 TTATGTAAGTTATGAA-TTATGAAAATTAATGTAAG
40778778 TTATGTA
1 TTATGTA
40778785 TAATATTAAT
Statistics
Matches: 715, Mismatches: 122, Indels: 187
0.70 0.12 0.18
Matches are distributed among these distances:
30 30 0.04
31 151 0.21
32 34 0.05
33 25 0.03
34 286 0.40
35 75 0.10
36 7 0.01
37 3 0.00
38 7 0.01
39 29 0.04
40 28 0.04
41 10 0.01
42 3 0.00
43 9 0.01
44 2 0.00
45 4 0.01
47 6 0.01
48 6 0.01
ACGTcount: A:0.40, C:0.02, G:0.14, T:0.45
Consensus pattern (35 bp):
TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
Found at i:40778077 original size:31 final size:31
Alignment explanation
Indices: 40777976--40779416 Score: 1295
Period size: 31 Copynumber: 45.5 Consensus size: 31
40777966 AGTTGTAAGT
* *
40777976 TGTAAGTTATGTAAGTTATGTATAATATAAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
*
40778007 TTAACTAAGTTATGTAATTTATG--T-ATATTAA
1 -T--GTAAGTTATGTAATTTATGTATAATATTAA
40778038 T-TAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
*
40778068 TGTAAGTTATGTAAGTTATTTAT-TATGAAAATTAA
1 TGTAAGTTATGT-A---ATTTATGTAT-AATATTAA
* **
40778103 -GTAAGTTATGTAATTTATGAATAATTAAACAAA
1 TGTAAGTTATGTAATTTATGTATAA-T--ATTAA
* *
40778136 TGTAAGTTATGTAA-GT-TG--TAA-GTT-A
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* *
40778161 TGTAAGTTATGT-A--TA-ATATTA-ATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
***
40778187 T-TAAGTTATGTAATTTATGTATTGCATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
*
40778217 TGTAAGTTATGTAACTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* * *
40778248 TTAATTAAGTCATGTAATTTATGTAAAATATTAA
1 -T--GTAAGTTATGTAATTTATGTATAATATTAA
*
40778282 TGCAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
40778313 TGTAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* ***
40778344 TTAATTAAGTTATGTAATTTATGTATTGCATTAA
1 -T--GTAAGTTATGTAATTTATGTATAATATTAA
***
40778378 TGTAAGTTATGTAATTTATGTATTGCATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* **
40778409 TGTAAGTTATGTAATTTATGAATAATTAAAAAAAA
1 TGTAAGTTATGTAATTTATG--T-A-TAATATTAA
* *
40778444 AGTAAGTTATGTAAGTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* ***
40778475 TTAATTAAGTTATGTAATTTATGTATTGCATTAA
1 -T--GTAAGTTATGTAATTTATGTATAATATTAA
*
40778509 TGTAAGTTATGTAACTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* *
40778540 TTAATTAAGTCATGTAATTTATGTATAATATTAA
1 -T--GTAAGTTATGTAATTTATGTATAATATTAA
*
40778574 TGCAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
*
40778605 TTAATTAAGTTATGTAATTTATGTATAATATTAA
1 -T--GTAAGTTATGTAATTTATGTATAATATTAA
*
40778639 TGTAAGTTATGTAAGTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* ***
40778670 TTAATTAAGTTATGTAATTTATGTATTGCATTAA
1 -T--GTAAGTTATGTAATTTATGTATAATATTAA
* **
40778704 TGTAAGTTATGTAATTTATGAATAATTAAAAAAA
1 TGTAAGTTATGTAATTTATGTATAA-T--ATTAA
* * *
40778738 AGTAAGTTATGTAA-GT-TG--TAA-GTT-A
1 TGTAAGTTATGTAATTTATGTATAATATTAA
*
40778763 TGTAAGTTATGTAAGTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* ***
40778794 TTAATTAAGTTATGTAATTTATGTATTGCATTAA
1 -T--GTAAGTTATGTAATTTATGTATAATATTAA
*
40778828 TGTAAGTTATGTAACTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* *
40778859 TTAATTAAGTCATGTAATTTATGTATAATATTAA
1 -T--GTAAGTTATGTAATTTATGTATAATATTAA
* *
40778893 TGCAAGTTATGTAATTTATGTTTAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
40778924 TGTAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* ***
40778955 TTAATTAAGTTATGTAATTTATGTATTGCATTAA
1 -T--GTAAGTTATGTAATTTATGTATAATATTAA
*
40778989 TGTAAGTTATGTAACTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* *
40779020 TTAATTAAGTCATGTAATTTATGTATAATATTAA
1 -T--GTAAGTTATGTAATTTATGTATAATATTAA
*
40779054 TGCAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
*
40779085 TTAATTAAGTTATGTAATTTATGTATAATATTAA
1 -T--GTAAGTTATGTAATTTATGTATAATATTAA
*
40779119 TGTAAGTTATGTAAGTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* ***
40779150 TTAATTAAGTTATGTAATTTATGTATTGCATTAA
1 -T--GTAAGTTATGTAATTTATGTATAATATTAA
* **
40779184 TGTAAGTTATGTAATTTATGAATAATTAAAAAA
1 TGTAAGTTATGTAATTTATGTATAA-T-ATTAA
* * *
40779217 AGTAAGTTATGTAA-GT-TG--TAA-GTT-A
1 TGTAAGTTATGTAATTTATGTATAATATTAA
*
40779242 TGTAAGTTATGTAAGTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* ***
40779273 TTAATTAAGTTATGTAATTTATGTATTGCATTAA
1 -T--GTAAGTTATGTAATTTATGTATAATATTAA
*
40779307 TGTAAGTTATGTAACTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* *
40779338 TTAATTAAGTCATGTAATTTATGTATAATATTAA
1 -T--GTAAGTTATGTAATTTATGTATAATATTAA
* *
40779372 TGCAAGTTATGTAATTTATGTTTAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
40779403 TGTAAGTTATGTAA
1 TGTAAGTTATGTAA
40779417 GTTGTAAGTT
Statistics
Matches: 1158, Mismatches: 162, Indels: 179
0.77 0.11 0.12
Matches are distributed among these distances:
23 1 0.00
24 1 0.00
25 55 0.05
26 5 0.00
27 22 0.02
28 2 0.00
29 14 0.01
30 33 0.03
31 502 0.43
32 22 0.02
33 38 0.03
34 428 0.37
35 35 0.03
ACGTcount: A:0.39, C:0.02, G:0.13, T:0.46
Consensus pattern (31 bp):
TGTAAGTTATGTAATTTATGTATAATATTAA
Found at i:40778114 original size:65 final size:64
Alignment explanation
Indices: 40777880--40779419 Score: 999
Period size: 65 Copynumber: 24.4 Consensus size: 64
40777870 ATAAGTTATG
* *
40777880 TATT-ATGTAAGTTATGTAAGTTATTTATTATGAAAATTAAGTAAGTTATGTAATTTATGAAT-A
1 TATTAATGTAAGTTATGTAAGTTATGTATTAT-AAAATTAAGTAAGTTATGTAATTTATGTATAA
** * * *
40777943 -ATTAA---AA-AAATGTAAGTTATGTAAGTTGT-AAGTT--GTAAGTTATGTAAGTTATGTATA
1 TATTAATGTAAGTTATGTAAGTTATGT-A-TTATAAAATTAAGTAAGTTATGTAATTTATGTATA
40778000 A
64 A
* * * *
40778001 TATAAATTAACTAAGTTATGTAATTTATG---TAT---ATTAATTAAGTTATGTAATTTATGTAT
1 TATTAA-T--GTAAGTTATGTAAGTTATGTATTATAAAATTAAGTAAGTTATGTAATTTATGTAT
40778060 AA
63 AA
* *
40778062 TATTAATGTAAGTTATGTAAGTTATTTATTATGAAAATTAAGTAAGTTATGTAATTTATGAAT-A
1 TATTAATGTAAGTTATGTAAGTTATGTATTAT-AAAATTAAGTAAGTTATGTAATTTATGTATAA
** * * * * *
40778126 -ATTAA-ACAA---ATGTAAGTTATGTAAGTTGT-AAGTTATGTAAGTTATGT-A--TA-ATATT
1 TATTAATGTAAGTTATGTAAGTTATGT-A-TTATAAAATTAAGTAAGTTATGTAATTTATGTATA
40778181 A
64 A
* ** *
40778182 -ATTAAT-TAAGTTATGTAATTTATGTA-T-T-GCATTAATGTAAGTTATGTAACTTATGTATAA
1 TATTAATGTAAGTTATGTAAGTTATGTATTATAAAATTAA-GTAAGTTATGTAATTTATGTATAA
* * * * *
40778242 TATTAATTAATTAAGTCATGTAATTTATGTA--A-AATATTAATGCAAGTTATGTAATTTATGTA
1 TATTAA-T--GTAAGTTATGTAAGTTATGTATTATAAAATTAA-GTAAGTTATGTAATTTATGTA
40778304 TAA
62 TAA
* * * * **
40778307 TATTAATGTAAGTTATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTG
1 TATTAATGTAAGTTATGTAAGTTATGTATTATA-AAATTAAGTAAGTTATGTAATTTATGTATAA
* * **
40778372 CATTAATGTAAGTTATGTAATTTATGTA-T-T-GCATTAATGTAAGTTATGTAATTTATGAATAA
1 TATTAATGTAAGTTATGTAAGTTATGTATTATAAAATTAA-GTAAGTTATGTAATTTATG--T-A
40778434 TTAA
62 -TAA
* ** * * * * **
40778438 AAAAAAAGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTG
1 TATTAATGTAAGTTATGTAAGTTATGTATTATA-AAATTAAGTAAGTTATGTAATTTATGTATAA
* * * * * *
40778503 CATTAATGTAAGTTATGTAACTTATGTATAATATTAATTAATTAAGTCATGTAATTTATGTATAA
1 TATTAATGTAAGTTATGTAAGTTATGTATTATA-AAATTAAGTAAGTTATGTAATTTATGTATAA
* * * * *
40778568 TATTAATGCAAGTTATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAA
1 TATTAATGTAAGTTATGTAAGTTATGTATTATA-AAATTAAGTAAGTTATGTAATTTATGTATAA
* * * **
40778633 TATTAATGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTG
1 TATTAATGTAAGTTATGTAAGTTATGTATTATA-AAATTAAGTAAGTTATGTAATTTATGTATAA
* * * * ** *
40778698 CATTAATGTAAGTTATGTAATTTATGAATAATTAAAAAAAAGTAAGTTATGTAA-GT-TG--TAA
1 TATTAATGTAAGTTATGTAAGTTATGTATTA-TAAAATTAAGTAAGTTATGTAATTTATGTATAA
* * * * **
40778759 -GTT-ATGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTG
1 TATTAATGTAAGTTATGTAAGTTATGTATTATA-AAATTAAGTAAGTTATGTAATTTATGTATAA
* * * * * *
40778822 CATTAATGTAAGTTATGTAACTTATGTATAATATTAATTAATTAAGTCATGTAATTTATGTATAA
1 TATTAATGTAAGTTATGTAAGTTATGTATTATA-AAATTAAGTAAGTTATGTAATTTATGTATAA
* * *
40778887 TATTAATGCAAGTTATGTAATTTATG--TT-TAATATTAATGTAAGTTATGTAATTTATGTATAA
1 TATTAATGTAAGTTATGTAAGTTATGTATTATAAAATTAA-GTAAGTTATGTAATTTATGTATAA
* * ** *
40778949 TATTAATTAATTAAGTTATGTAATTTATGTA-T-T-GCATTAATGTAAGTTATGTAACTTATGTA
1 TATTAA-T--GTAAGTTATGTAAGTTATGTATTATAAAATTAA-GTAAGTTATGTAATTTATGTA
40779011 TAA
62 TAA
* * * * * *
40779014 TATTAAT-TAA-TTAAGTCATGTAATTTATGTATAATATTAATGCAAGTTATGTAATTTATGTAT
1 TATTAATGTAAGTTATGT-AAGTTATGTAT-TATAAAATTAA-GTAAGTTATGTAATTTATGTAT
40779077 AA
63 AA
* * * *
40779079 TATTAATTAATTAAGTTATGTAATTTATG---TATAATATTAATGTAAGTTATGTAAGTTATGTA
1 TATTAA-T--GTAAGTTATGTAAGTTATGTATTATAAAATTAA-GTAAGTTATGTAATTTATGTA
40779141 TAA
62 TAA
* * ** *
40779144 TATTAATTAATTAAGTTATGTAATTTATGTA-T-T-GCATTAATGTAAGTTATGTAATTTATGAA
1 TATTAA-T--GTAAGTTATGTAAGTTATGTATTATAAAATTAA-GTAAGTTATGTAATTTATGTA
40779206 T-A
62 TAA
* * * * * *
40779208 -ATTAA---AA--AAAGTAAGTTATGTAAGTTGT-AAGTTATGTAAGTTATGTAAGTTATGTATA
1 TATTAATGTAAGTTATGTAAGTTATGT-A-TTATAAAATTAAGTAAGTTATGTAATTTATGTATA
40779266 A
64 A
* * ** *
40779267 TATTAATTAATTAAGTTATGTAATTTATGTA-T-T-GCATTAATGTAAGTTATGTAACTTATGTA
1 TATTAA-T--GTAAGTTATGTAAGTTATGTATTATAAAATTAA-GTAAGTTATGTAATTTATGTA
40779329 TAA
62 TAA
* * * * * * *
40779332 TATTAAT-TAA-TTAAGTCATGTAATTTATGTATAATATTAATGCAAGTTATGTAATTTATGTTT
1 TATTAATGTAAGTTATGT-AAGTTATGTAT-TATAAAATTAA-GTAAGTTATGTAATTTATGTAT
40779395 AA
63 AA
40779397 TATTAATGTAAGTTATGTAAGTT
1 TATTAATGTAAGTTATGTAAGTT
40779420 GTAAGTTATG
Statistics
Matches: 1204, Mismatches: 172, Indels: 199
0.76 0.11 0.13
Matches are distributed among these distances:
55 17 0.01
56 23 0.02
57 23 0.02
58 42 0.03
59 109 0.09
60 27 0.02
61 74 0.06
62 73 0.06
63 19 0.02
64 16 0.01
65 671 0.56
66 55 0.05
67 8 0.01
68 12 0.01
69 25 0.02
70 10 0.01
ACGTcount: A:0.39, C:0.02, G:0.13, T:0.46
Consensus pattern (64 bp):
TATTAATGTAAGTTATGTAAGTTATGTATTATAAAATTAAGTAAGTTATGTAATTTATGTATAA
Found at i:40778171 original size:50 final size:50
Alignment explanation
Indices: 40778103--40778199 Score: 133
Period size: 50 Copynumber: 1.9 Consensus size: 50
40778093 TGAAAATTAA
*
40778103 GTAAGTTATGTAATTTATGAATAAT-TAAACAAATGTAAGTTATGTAAGTT
1 GTAAGTTATGTAAGTTATGAATAATATAAACAAAT-TAAGTTATGTAAGTT
* * **
40778153 GTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAA
1 GTAAGTTATGTAAGTTATGAATAATATAAACAAATTAAGTTATGTAA
40778200 TTTATGTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
50 35 0.85
51 6 0.15
ACGTcount: A:0.41, C:0.01, G:0.15, T:0.42
Consensus pattern (50 bp):
GTAAGTTATGTAAGTTATGAATAATATAAACAAATTAAGTTATGTAAGTT
Found at i:40778306 original size:130 final size:129
Alignment explanation
Indices: 40777978--40779403 Score: 1231
Period size: 130 Copynumber: 11.2 Consensus size: 129
40777968 TTGTAAGTTG
* * *
40777978 TAAGTTATGTAAGTTATGTATAATATAAATTAACTAAGTTATGTAATTTATG--T-ATATTAAT-
1 TAAGTTATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATG
* * *
40778039 TAAGTTATGTAATTTATGTATAATATTAA-T--GTAAGTTATGTAAGTTATTTATTATGAAAATT
66 TAAGTTATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATT-T---AATT
*
40778101 AAG
127 AAT
** * *
40778104 TAAGTTATGTAATTTATG----A-A-TAATTAAACAA---ATGTAAGTTATG--T-A-AGT--TG
1 TAAGTTATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATG
* **
40778154 TAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTGCATTAAT
66 TAAGTTATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTTAATTAAT
* * *
40778218 GTAAGTTATGTAACTTATGTATAATATTAATTAATTAAGTCATGTAATTTATGTAAAATATTAAT
1 -TAAGTTATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAAT
* *
40778283 GCAAGTTATGTAATTTATGTATAATATTAA-T--GTAAGTTATGTAATTTATGTATAATATTAAT
65 GTAAGTTATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATG--T-AT-TTAAT
40778345 TAAT
126 TAAT
** ***
40778349 TAAGTTATGTAATTTATG--T-AT-TGCATTAATGTAAGTTATGTAATTTATGTATTGCATTAAT
1 TAAGTTATGTAATTTATGTATAATATTAATTAAT-TAAGTTATGTAATTTATGTATAATATTAAT
* ** ** * *
40778410 GTAAGTTATGTAATTTATGAATAATTAAAAAAAAAGTAAGTTATGTAAGTTATGTATAATATTAA
65 GTAAGTTATGTAATTTATGTATAA-TATTAATTAATTAAGTTATGTAATTTATG--T-AT-TTAA
40778475 TTAAT
125 TTAAT
** *
40778480 TAAGTTATGTAATTTATG--T-AT-TGCATTAATGTAAGTTATGTAACTTATGTATAATATTAAT
1 TAAGTTATGTAATTTATGTATAATATTAATTAAT-TAAGTTATGTAATTTATGTATAATATTAA-
* * **
40778541 TAATTAAGTCATGTAATTTATGTATAATATTAA-T--GCAAGTTATGTAATTTATGTATAATATT
64 T--GTAAGTTATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATG--T-AT-TT
40778603 AATTAAT
123 AATTAAT
* *
40778610 TAAGTTATGTAATTTATGTATAATATTAA-T--GTAAGTTATGTAAGTTATGTATAATATTAATT
1 TAAGTTATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA-T
* ** *
40778672 AATTAAGTTATGTAATTTATG--T-AT-TGCATTAATGTAAGTTATGTAATTTATG-A-ATAATT
65 --GTAAGTTATGTAATTTATGTATAATATTAATTAAT-TAAGTTATGTAATTTATGTATTTAATT
40778731 AA-
127 AAT
** * * * *
40778733 -AA-AAAAGTAAGTTATGTA-AGT-TGTAAGTT-ATGTAAGTTATGTAAGTTATGTATAATATTA
1 TAAGTTATGTAATTTATGTATAATAT-TAA-TTAAT-TAAGTTATGTAATTTATGTATAATATTA
* ** *
40778793 ATTAATTAAGTTATGTAATTTATG--T-AT-TGCATTAATGTAAGTTATGTAACTTATGTATAAT
63 A-T--GTAAGTTATGTAATTTATGTATAATATTAATTAAT-TAAGTTATGTAATTTATG--T-AT
40778854 ATTAATTAAT
121 -TTAATTAAT
* ** *
40778864 TAAGTCATGTAATTTATGTATAATATTAA-T--GCAAGTTATGTAATTTATGTTTAATATTAATG
1 TAAGTTATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATG
**
40778926 TAAGTTATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTGCATTAAT
66 TAAGTTATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTTAATTAAT
* *
40778990 GTAAGTTATGTAACTTATGTATAATATTAATTAATTAAGTCATGTAATTTATGTATAATATTAAT
1 -TAAGTTATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAAT
* *
40779055 GCAAGTTATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTA-TAATATTAA
65 GTAAGTTATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTTA-ATTAA
40779119 T
129 T
* ***
40779120 GTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTGCATTAAT
1 -TAAGTTATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAAT
* * ** * * *
40779185 GTAAGTTATGTAATTTATGAATAAT-TAAAAAAAGTAAGTTATGTAA-GT-TGTA---AGTT-AT
65 GTAAGTTATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTTAATTAAT
* ***
40779243 GTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTGCATTAAT
1 -TAAGTTATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAAT
* * *
40779308 GTAAGTTATGTAACTTATGTATAATATTAATTAATTAAGTCATGTAATTTATGTA-TAATATTAA
65 GTAAGTTATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTTA-ATTAA
40779372 T
129 T
* *
40779373 GCAAGTTATGTAATTTATGTTTAATATTAAT
1 -TAAGTTATGTAATTTATGTATAATATTAAT
40779404 GTAAGTTATG
Statistics
Matches: 1111, Mismatches: 117, Indels: 140
0.81 0.09 0.10
Matches are distributed among these distances:
114 6 0.01
115 45 0.04
116 3 0.00
117 13 0.01
118 20 0.02
119 2 0.00
120 14 0.01
121 22 0.02
122 4 0.00
123 90 0.08
124 118 0.11
125 2 0.00
126 38 0.03
127 122 0.11
128 13 0.01
129 24 0.02
130 418 0.38
131 104 0.09
132 5 0.00
133 19 0.02
134 28 0.03
135 1 0.00
ACGTcount: A:0.39, C:0.02, G:0.13, T:0.46
Consensus pattern (129 bp):
TAAGTTATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATG
TAAGTTATGTAATTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTTAATTAAT
Found at i:40779431 original size:47 final size:49
Alignment explanation
Indices: 40779375--40779469 Score: 131
Period size: 47 Copynumber: 2.0 Consensus size: 49
40779365 ATATTAATGC
* * *
40779375 AAGTTATGTAATTTATGTTTAATATTAA-T-GTAAGTTATGTAAGTTGT
1 AAGTTATGTAAGTTATATATAATATTAATTAGTAAGTTATGTAAGTTGT
*
40779422 AAGTTATGTAAGTTATATATAATATTAATTAATTAAGTTATGTAAGTT
1 AAGTTATGTAAGTTATATATAATATTAATT-AGTAAGTTATGTAAGTT
40779470 AACTATTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
47 25 0.61
48 1 0.02
50 15 0.37
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (49 bp):
AAGTTATGTAAGTTATATATAATATTAATTAGTAAGTTATGTAAGTTGT
Found at i:40780482 original size:32 final size:33
Alignment explanation
Indices: 40780446--40780508 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
40780436 GAAAAATAAT
**
40780446 AATTAAACTATAC-AACTAAAATATAACCAAAA
1 AATTAAACTATACAAAAAAAAATATAACCAAAA
40780478 AATTAAACTATACAAAAAAAAATATAACCAA
1 AATTAAACTATACAAAAAAAAATATAACCAA
40780509 CTTAAAGATC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.65, C:0.14, G:0.00, T:0.21
Consensus pattern (33 bp):
AATTAAACTATACAAAAAAAAATATAACCAAAA
Found at i:40780489 original size:19 final size:17
Alignment explanation
Indices: 40780464--40780508 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
40780454 TATACAACTA
40780464 AAATATAACCAAAAAATT
1 AAATATAACCAAAAAA-T
40780482 AAACTAT-A-CAAAAAA-
1 AAA-TATAACCAAAAAAT
40780497 AAATATAACCAA
1 AAATATAACCAA
40780509 CTTAAAGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
14 3 0.12
15 4 0.17
16 3 0.12
17 7 0.29
18 4 0.17
19 3 0.12
ACGTcount: A:0.69, C:0.13, G:0.00, T:0.18
Consensus pattern (17 bp):
AAATATAACCAAAAAAT
Found at i:40781997 original size:22 final size:22
Alignment explanation
Indices: 40781956--40782009 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
40781946 TTGTATTTTC
* *
40781956 ATTAAAATTTTTAGTAAATAATT
1 ATTAAAGTTTTAAGTAAAT-ATT
40781979 ATTAAAGTTTTAAGT-AATATT
1 ATTAAAGTTTTAAGTAAATATT
*
40782000 -TAAAAGTTTT
1 ATTAAAGTTTT
40782010 TGATAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.32
21 3 0.11
22 3 0.11
23 13 0.46
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
ATTAAAGTTTTAAGTAAATATT
Found at i:40782024 original size:21 final size:21
Alignment explanation
Indices: 40781958--40782024 Score: 50
Period size: 20 Copynumber: 3.2 Consensus size: 21
40781948 GTATTTTCAT
*
40781958 TAAAA-TTTTTAGTAAATAATTA
1 TAAAAGTTTTAAGT-AA-AATTA
* *
40781980 TTAAAGTTTTAAGTAATATT-
1 TAAAAGTTTTAAGTAAAATTA
*
40782000 TAAAAGTTTT-TGATAAAATTA
1 TAAAAGTTTTAAG-TAAAATTA
40782021 TAAA
1 TAAA
40782025 TTTTAGTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
19 1 0.03
20 15 0.42
21 7 0.19
22 6 0.17
23 7 0.19
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (21 bp):
TAAAAGTTTTAAGTAAAATTA
Found at i:40782059 original size:22 final size:22
Alignment explanation
Indices: 40782031--40782076 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
40782021 TAAATTTTAG
40782031 TTTTTTATTTCCTTT-TTATATT
1 TTTTTTATTT-CTTTCTTATATT
*
40782053 TTTTTTATTTTTTTCTTATATT
1 TTTTTTATTTCTTTCTTATATT
40782075 TT
1 TT
40782077 GGTCTTGTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTTTATTTCTTTCTTATATT
Found at i:40782071 original size:11 final size:11
Alignment explanation
Indices: 40782043--40782076 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
40782033 TTTTATTTCC
40782043 TTTTTATATTT
1 TTTTTATATTT
40782054 TTTTTAT-TTT
1 TTTTTATATTT
40782064 TTTCTTATATTT
1 TTT-TTATATTT
40782076 T
1 T
40782077 GGTCTTGTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.29
11 11 0.52
12 4 0.19
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTATATTT
Found at i:40782842 original size:89 final size:84
Alignment explanation
Indices: 40782740--40783055 Score: 400
Period size: 89 Copynumber: 3.8 Consensus size: 84
40782730 CCAAACCCCT
*
40782740 ACCCCTAAACCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAA
1 ACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAA
40782805 CCCTAACTCGACCCCGAATCAC
66 CCCTAACTCGA-CCCGAAT--C
* *
40782827 TAACCCCTAACCCCTAAACATTATTTAATATATAAATTCAAAAACACTAATTAATCTAAATCTTA
1 --ACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTA
40782892 AACCCTAACTCGACCCGAATC
64 AACCCTAACTCGACCCGAATC
40782913 A---CTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAA
1 ACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAA
*
40782975 CCCT-A----ACCCTAA--
66 CCCTAACTCGACCCGAATC
* * * * * *
40782987 ATCCCTAACCCCTAAACATTATTTAATATTATATAATTTAAAATATATTAATTAGTCTAAACCCT
1 ACCCCTAACCCCTAAACATTATTTAATA-TATA-AA-TTAAAAAACACTAATTAATCTAAATCCT
40783052 AAAC
63 AAAC
40783056 TTTAACCTAA
Statistics
Matches: 210, Mismatches: 11, Indels: 21
0.87 0.05 0.09
Matches are distributed among these distances:
74 1 0.00
76 6 0.03
77 24 0.11
78 4 0.02
79 2 0.01
80 28 0.13
81 63 0.30
84 1 0.00
86 1 0.00
88 7 0.03
89 73 0.35
ACGTcount: A:0.45, C:0.24, G:0.02, T:0.29
Consensus pattern (84 bp):
ACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAA
CCCTAACTCGACCCGAATC
Found at i:40782988 original size:20 final size:21
Alignment explanation
Indices: 40782963--40783001 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40782953 ACTAATTAAT
40782963 CTAAAT-CCTAAACCCTAACC
1 CTAAATCCCTAAACCCTAACC
*
40782983 CTAAATCCCTAACCCCTAA
1 CTAAATCCCTAAACCCTAA
40783002 ACATTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.21
Consensus pattern (21 bp):
CTAAATCCCTAAACCCTAACC
Found at i:40783053 original size:80 final size:79
Alignment explanation
Indices: 40782831--40783055 Score: 301
Period size: 81 Copynumber: 2.8 Consensus size: 79
40782821 AATCACTAAC
* *
40782831 CCCTAACCCCTAAACATTATTTAATATATAAATTCAAAAACACTAATTAATCTAAATCTTAAACC
1 CCCTAACCCCTAAACATTATTTAATATATAAATTTAAAAACACTAATTAATCTAAATCCTAAACC
*
40782896 CTAACTCGACCCGAAT
66 CTAAC-C-ACCCAAAT
* *
40782912 CACTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAACC
1 CCCTAACCCCTAAACATTATTTAATATATAAATTTAAAAACACTAATTAATCTAAATCCTAAACC
*
40782977 CTAA-C-CCTAAAT
66 CTAACCACCCAAAT
* * * *
40782989 CCCTAACCCCTAAACATTATTTAATATTATATAATTTAAAATATATTAATTAGTCTAAACCCTAA
1 CCCTAACCCCTAAACATTATTTAATA-TATA-AATTTAAAA-ACACTAATTAATCTAAATCCTAA
40783054 AC
63 AC
40783056 TTTAACCTAA
Statistics
Matches: 130, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
77 30 0.23
78 4 0.03
79 9 0.07
80 21 0.16
81 66 0.51
ACGTcount: A:0.45, C:0.23, G:0.01, T:0.31
Consensus pattern (79 bp):
CCCTAACCCCTAAACATTATTTAATATATAAATTTAAAAACACTAATTAATCTAAATCCTAAACC
CTAACCACCCAAAT
Found at i:40783062 original size:80 final size:76
Alignment explanation
Indices: 40782831--40783062 Score: 252
Period size: 80 Copynumber: 2.9 Consensus size: 76
40782821 AATCACTAAC
*
40782831 CCCTAACCCCTAAACATTATTTAATATATAAATTCAAAAACACTAATTAATCTAAATCTTAAACC
1 CCCTAACCCCTAAACATTATTTAATATATAAATTTAAAAA-A-T-ATTAAT-T-AATC-TAAACC
** *
40782896 CT-AACTCGACCCGAAT
60 CTAAACTTAACCCAAAT
* * * *
40782912 CACTAACCCCTAAACATTATTTAATATATAAA-TTAAAAAACACTAATTAATCTAAATCCTAAAC
1 CCCTAACCCCTAAACATTATTTAATATATAAATTTAAAAAATATTAATTAATCTAAACCCTAAA-
*
40782976 CCTAACCCTAAAT
65 CTTAACCC-AAAT
* *
40782989 CCCTAACCCCTAAACATTATTTAATATTATATAATTTAAAATATATTAATTAGTCTAAACCCTAA
1 CCCTAACCCCTAAACATTATTTAATA-TATA-AATTTAAAAAATATTAATTAATCTAAACCCTAA
40783054 ACTTTAACC
64 AC-TTAACC
40783063 TAACACCGAA
Statistics
Matches: 128, Mismatches: 16, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
74 7 0.05
75 6 0.05
76 6 0.05
77 33 0.26
78 4 0.03
79 4 0.03
80 37 0.29
81 31 0.24
ACGTcount: A:0.44, C:0.23, G:0.01, T:0.31
Consensus pattern (76 bp):
CCCTAACCCCTAAACATTATTTAATATATAAATTTAAAAAATATTAATTAATCTAAACCCTAAAC
TTAACCCAAAT
Found at i:40783629 original size:41 final size:41
Alignment explanation
Indices: 40783575--40783838 Score: 338
Period size: 41 Copynumber: 6.5 Consensus size: 41
40783565 GTGCTTCCTT
40783575 AAAAACGCCGCTAAAGGTA-C-GAGCATTAGCGGCGCTTATTA
1 AAAAACGCCGCTAAA-G-ACCTGAGCATTAGCGGCGCTTATTA
*
40783616 AAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGGTTATTA
1 AAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTATTA
* *
40783657 AAAAATGCCGCT-AAGACCTGAGAATTAGCGGCGCTTATTA
1 AAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTATTA
* * * * * *
40783697 AAAAATGACACTAAAGACCTGAGCATTAGCGGCACTTAATC
1 AAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTATTA
* * * *
40783738 AAAAACGCCGCTAAAGACCGGAGCATTAGCGGCGCATGTTC
1 AAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTATTA
40783779 AAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTT-TTCA
1 AAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTATT-A
* *
40783820 GAAAATGCCGCTAAAGACC
1 AAAAACGCCGCTAAAGACC
40783839 CCAAAAACTA
Statistics
Matches: 196, Mismatches: 23, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
39 1 0.01
40 40 0.20
41 155 0.79
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTATTA
Found at i:40783995 original size:40 final size:39
Alignment explanation
Indices: 40783871--40784005 Score: 112
Period size: 40 Copynumber: 3.4 Consensus size: 39
40783861 GGGCTTAGGC
**
40783871 TTTTT-GCGGCGCTTTCCAAAAAACGCCGCTAATGCTT-A
1 TTTTTAGCGGCG-TTTTTAAAAAACGCCGCTAATGCTTGA
* ** * *
40783909 TTTTTAGCGGTGTTTTTTAAAAATTGCCGCTAATGATCGA
1 TTTTTAGCGGCG-TTTTTAAAAAACGCCGCTAATGCTTGA
** * * *
40783949 CCTTTAGCGGCGGTTTTACAAAAGCGCCGCTACTGCTTGA
1 TTTTTAGCGGCGTTTTTA-AAAAACGCCGCTAATGCTTGA
*
40783989 TTTTTAGTGGCGTTTTT
1 TTTTTAGCGGCGTTTTT
40784006 TGTCCAGACA
Statistics
Matches: 73, Mismatches: 21, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
38 5 0.07
39 29 0.40
40 39 0.53
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTTAAAAAACGCCGCTAATGCTTGA
Found at i:40784186 original size:16 final size:17
Alignment explanation
Indices: 40784167--40784199 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
40784157 ATCTTGCAGA
*
40784167 TTTGAAGGAAAA-ATTT
1 TTTGAAAGAAAATATTT
40784183 TTTGAAAGAAAATATTT
1 TTTGAAAGAAAATATTT
40784200 CCTCTTTCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.39
Consensus pattern (17 bp):
TTTGAAAGAAAATATTT
Found at i:40784455 original size:7 final size:7
Alignment explanation
Indices: 40784445--40784471 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
40784435 GAATTTGATT
40784445 TTGAGAA
1 TTGAGAA
40784452 TTGAGAA
1 TTGAGAA
40784459 TTGAGAA
1 TTGAGAA
40784466 TTGAGA
1 TTGAGA
40784472 CCAAGAGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.30
Consensus pattern (7 bp):
TTGAGAA
Found at i:40796535 original size:16 final size:16
Alignment explanation
Indices: 40796493--40796527 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
40796483 TATATACACT
40796493 TTAAATA-AA-AATAA
1 TTAAATATAATAATAA
40796507 TTAAATATAATAATAA
1 TTAAATATAATAATAA
40796523 TTAAA
1 TTAAA
40796528 GTTTATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.37
15 2 0.11
16 10 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TTAAATATAATAATAA
Found at i:40808857 original size:234 final size:234
Alignment explanation
Indices: 40808448--40808915 Score: 936
Period size: 234 Copynumber: 2.0 Consensus size: 234
40808438 AAATGAATGG
40808448 GCCCTACTATCCATAGTTTTTTACTCATTGGGTTTTTCATGGCAATCTACCACATCACACTAATG
1 GCCCTACTATCCATAGTTTTTTACTCATTGGGTTTTTCATGGCAATCTACCACATCACACTAATG
40808513 GACAATGGGACCTCTCCTATAAATAGATTGACTAGCGATGAAGAAGGGATTAATTTCCAACACCC
66 GACAATGGGACCTCTCCTATAAATAGATTGACTAGCGATGAAGAAGGGATTAATTTCCAACACCC
40808578 TAAAGTTACTTTGAGCAATTATCCTCTCAATCAGTTTGTCCTCTTGTCCTTGTTCCAGCTCTTGG
131 TAAAGTTACTTTGAGCAATTATCCTCTCAATCAGTTTGTCCTCTTGTCCTTGTTCCAGCTCTTGG
40808643 CTTCTTTAGGTGAACTAGCCTCCACAACACCACCTTGAT
196 CTTCTTTAGGTGAACTAGCCTCCACAACACCACCTTGAT
40808682 GCCCTACTATCCATAGTTTTTTACTCATTGGGTTTTTCATGGCAATCTACCACATCACACTAATG
1 GCCCTACTATCCATAGTTTTTTACTCATTGGGTTTTTCATGGCAATCTACCACATCACACTAATG
40808747 GACAATGGGACCTCTCCTATAAATAGATTGACTAGCGATGAAGAAGGGATTAATTTCCAACACCC
66 GACAATGGGACCTCTCCTATAAATAGATTGACTAGCGATGAAGAAGGGATTAATTTCCAACACCC
40808812 TAAAGTTACTTTGAGCAATTATCCTCTCAATCAGTTTGTCCTCTTGTCCTTGTTCCAGCTCTTGG
131 TAAAGTTACTTTGAGCAATTATCCTCTCAATCAGTTTGTCCTCTTGTCCTTGTTCCAGCTCTTGG
40808877 CTTCTTTAGGTGAACTAGCCTCCACAACACCACCTTGAT
196 CTTCTTTAGGTGAACTAGCCTCCACAACACCACCTTGAT
40808916 CTCCTCTTTA
Statistics
Matches: 234, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
234 234 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (234 bp):
GCCCTACTATCCATAGTTTTTTACTCATTGGGTTTTTCATGGCAATCTACCACATCACACTAATG
GACAATGGGACCTCTCCTATAAATAGATTGACTAGCGATGAAGAAGGGATTAATTTCCAACACCC
TAAAGTTACTTTGAGCAATTATCCTCTCAATCAGTTTGTCCTCTTGTCCTTGTTCCAGCTCTTGG
CTTCTTTAGGTGAACTAGCCTCCACAACACCACCTTGAT
Found at i:40810465 original size:5 final size:5
Alignment explanation
Indices: 40810422--40810464 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
40810412 AACTATTAAT
* * *
40810422 ATATG ATATG ATATG ATATG ATATT ATAT- ATATA ATATA ATAT
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATAT
40810465 AGTGAGAGAG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
4 4 0.11
5 32 0.89
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (5 bp):
ATATG
Found at i:40810593 original size:256 final size:248
Alignment explanation
Indices: 40810322--40810814 Score: 647
Period size: 256 Copynumber: 1.9 Consensus size: 248
40810312 AGATTAATAC
*
40810322 ATATATAAATATTATTATAATATAGATTATAATAAAAGATAAAATATTACATGTGATATTATAAT
1 ATATATAAATATTATTATAATATAGATTACAATAAAAGATAAAATATTACA--TGATATTATAAT
* * *
40810387 GTTTAATCATCAG-TGC-ATATATATAAACTATTAATATATGATATGATA-TGATATGATATTAT
64 GCTTAATCAT-AGATGCAATATATATAAACTATTAACATAT--TAT-ATACT-ATATGATATGAT
*
40810449 ATATATAATATAATA-TAGTGAGAGAGCTAACTTTTAAATGTAAGAAAAATATA-GACTTAGAGC
124 ATA-A-AAT-T-ATAGTAG-GAG-G-GCTAACTTTCAAATGTAAGAAAAATATAGGACTTAGAGC
* * *
40810512 ATATTTCAACTAGTAGAATAATAAACGGTAATATA-TATAATAAGTAATATATAATGTATTGCTA
182 ATATTTCAACCAGTAGAATAATAAACAGTAATATATTATAATAAGTAACATATAATGTATTGCTA
40810576 TT
247 TT
* * *
40810578 ATATATAACTATTATTATAATATAGATTACAATAAAAGATATAGTATTACATGATATTATAATGC
1 ATATATAAATATTATTATAATATAGATTACAATAAAAGATAAAATATTACATGATATTATAATGC
* *
40810643 TTAATCATTGATGCATATATATATAAACTATTAACATATTATATACTATATGATATGATATAACA
66 TTAATCATAGATGCA-ATATATATAAACTATTAACATATTATATACTATATGATATGATATAAAA
* *
40810708 TTATAGTAGGAGGGCTAACTTTCAAATGTAAGAAAAATATAGGGACTTGGAGCATATTTTAACCA
130 TTATAGTAGGAGGGCTAACTTTCAAATGTAAGAAAAATATA-GGACTTAGAGCATATTTCAACCA
* *
40810773 GTATAATAATAAACAGTAATATATTATAATAATTAACATATA
194 GTAGAATAATAAACAGTAATATATTATAATAAGTAACATATA
40810815 GAGGTGCTCA
Statistics
Matches: 212, Mismatches: 17, Indels: 22
0.84 0.07 0.09
Matches are distributed among these distances:
247 27 0.13
248 1 0.00
249 46 0.22
250 20 0.09
251 2 0.01
252 1 0.00
253 18 0.08
254 28 0.13
256 69 0.33
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (248 bp):
ATATATAAATATTATTATAATATAGATTACAATAAAAGATAAAATATTACATGATATTATAATGC
TTAATCATAGATGCAATATATATAAACTATTAACATATTATATACTATATGATATGATATAAAAT
TATAGTAGGAGGGCTAACTTTCAAATGTAAGAAAAATATAGGACTTAGAGCATATTTCAACCAGT
AGAATAATAAACAGTAATATATTATAATAAGTAACATATAATGTATTGCTATT
Found at i:40810932 original size:16 final size:17
Alignment explanation
Indices: 40810907--40810938 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
40810897 TTAGATTAGT
40810907 TTTTTATTTAAAAATAA
1 TTTTTATTTAAAAATAA
40810924 TTTTT-TTTAAAAATA
1 TTTTTATTTAAAAATA
40810939 TAATACACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTTATTTAAAAATAA
Found at i:40830749 original size:226 final size:225
Alignment explanation
Indices: 40830356--40830802 Score: 867
Period size: 226 Copynumber: 2.0 Consensus size: 225
40830346 GCCTTTGTGA
40830356 CTCGTATCAAGCGTTCTCAACCTATAAATACCCCCTTGGCTTCTCACTTCAACATCATCTCAAAC
1 CTCGTATCAAGCGTTCTCAACCTATAAATACCCCCTTGGCTTCTCACTTCAACATCATCTCAAAC
40830421 CTATAAATCCCACCATTTAGAGCAGCATTTAAGTGTTCGTAGAAGCCTCGGTTCGACAAGAACAA
66 CTATAAATCCCACCATTTAGAGCAGCATTTAAGTGTTCGTAGAAGCCTCGGTTCGACAAGAACAA
40830486 GCGGAGAATGAGGAGTGGAGCAAACTAATCAAGCCACGGAGAAACACTGGATTTGATTCTTGTTC
131 GCGGAGAATGAGGAGTGGAGCAAACTAATCAAGCCACGGAGAAACACTGGATTTGATTCTTGTTC
40830551 CCCATCCTTTTAATTTTGTTGTTGTTTTGG
196 CCCATCCTTTTAATTTTGTTGTTGTTTTGG
40830581 CTCGTATCAAGCGTTCTCAACCTATAAATACCCCCCTTGGCTTCTCACTTCAACATCATCTCAAA
1 CTCGTATCAAGCGTTCTCAACCTATAAATA-CCCCCTTGGCTTCTCACTTCAACATCATCTCAAA
* *
40830646 CCTATAAATCCCACCATTTGGAGCAGCATTTCAGTGTTCGTAGAAGCCTCGGTTCGACAAGAACA
65 CCTATAAATCCCACCATTTAGAGCAGCATTTAAGTGTTCGTAGAAGCCTCGGTTCGACAAGAACA
40830711 AGCGGAGAATGAGGAGTGGAGCAAACTAATCAAGCCACGGAGAAACACTGGATTTGATTCTTGTT
130 AGCGGAGAATGAGGAGTGGAGCAAACTAATCAAGCCACGGAGAAACACTGGATTTGATTCTTGTT
40830776 CCCCATCCTTTTAATTTTGTTGTTGTT
195 CCCCATCCTTTTAATTTTGTTGTTGTT
40830803 ATGATGAACA
Statistics
Matches: 219, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
225 30 0.14
226 189 0.86
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (225 bp):
CTCGTATCAAGCGTTCTCAACCTATAAATACCCCCTTGGCTTCTCACTTCAACATCATCTCAAAC
CTATAAATCCCACCATTTAGAGCAGCATTTAAGTGTTCGTAGAAGCCTCGGTTCGACAAGAACAA
GCGGAGAATGAGGAGTGGAGCAAACTAATCAAGCCACGGAGAAACACTGGATTTGATTCTTGTTC
CCCATCCTTTTAATTTTGTTGTTGTTTTGG
Found at i:40831788 original size:29 final size:29
Alignment explanation
Indices: 40831756--40831812 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
40831746 TATTATTGTT
* * *
40831756 ATTATTTTATTGTATTAT-AAATTAAATTG
1 ATTATATTATTATATCATGAAA-TAAATTG
40831785 ATTATATTATTATATCATGAAATAAATT
1 ATTATATTATTATATCATGAAATAAATT
40831813 AGGAAAAGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (29 bp):
ATTATATTATTATATCATGAAATAAATTG
Found at i:40831913 original size:33 final size:31
Alignment explanation
Indices: 40831876--40831942 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 31
40831866 AGTACATATG
40831876 TATTATTTATATA-TAATTAGTAAAAAGATATTT
1 TATTATTTAT-TACTAATTAGT-AAAAGAT-TTT
40831909 TATTATTTATTACTAATTAGTAAAAGATTTT
1 TATTATTTATTACTAATTAGTAAAAGATTTT
40831940 TAT
1 TAT
40831943 ATGATAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
31 6 0.18
32 9 0.27
33 18 0.55
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.51
Consensus pattern (31 bp):
TATTATTTATTACTAATTAGTAAAAGATTTT
Found at i:40832051 original size:18 final size:19
Alignment explanation
Indices: 40832028--40832075 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
40832018 TGTAATATTT
*
40832028 ATATTTGTTATTA-AATAG
1 ATATTTATTATTATAATAG
40832046 ATATTTATTATTATAATA-
1 ATATTTATTATTATAATAG
*
40832064 ATAATTATTATT
1 ATATTTATTATT
40832076 GTTATTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (19 bp):
ATATTTATTATTATAATAG
Found at i:40833087 original size:18 final size:17
Alignment explanation
Indices: 40833060--40833113 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 17
40833050 AGTGAATGAA
*
40833060 AAAGTGAATTTGATATTG
1 AAAGTAAATTTGA-ATTG
*
40833078 AAAGTAAATTTTGAAATG
1 AAAGTAAA-TTTGAATTG
*
40833096 AAAGTCAATTTGAATTG
1 AAAGTAAATTTGAATTG
40833113 A
1 A
40833114 GAATTGGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 9 0.29
18 17 0.55
19 5 0.16
ACGTcount: A:0.44, C:0.02, G:0.19, T:0.35
Consensus pattern (17 bp):
AAAGTAAATTTGAATTG
Found at i:40833491 original size:20 final size:19
Alignment explanation
Indices: 40833463--40833508 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
40833453 GAAACGTGAT
* *
40833463 TGTGGATTATAATTTAAAAA
1 TGTGAATTA-AATATAAAAA
*
40833483 TGTGAATTAAATATGAAAA
1 TGTGAATTAAATATAAAAA
40833502 TGTGAAT
1 TGTGAAT
40833509 AGAAAGCATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (19 bp):
TGTGAATTAAATATAAAAA
Found at i:40838062 original size:25 final size:25
Alignment explanation
Indices: 40838023--40838107 Score: 109
Period size: 25 Copynumber: 3.4 Consensus size: 25
40838013 CTACGACTCT
40838023 TATGAGCATATCGATTCATAGCTCG
1 TATGAGCATATCGATTCATAGCTCG
* * * * *
40838048 TATGAGCTTACCGATTCACAACTCA
1 TATGAGCATATCGATTCATAGCTCG
40838073 TGA-GAGCATATCGATTCATAGCTCG
1 T-ATGAGCATATCGATTCATAGCTCG
40838098 TATGAGCATA
1 TATGAGCATA
40838108 CATGTATAGG
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
24 1 0.02
25 46 0.96
26 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (25 bp):
TATGAGCATATCGATTCATAGCTCG
Found at i:40843476 original size:29 final size:29
Alignment explanation
Indices: 40843434--40843846 Score: 249
Period size: 29 Copynumber: 14.3 Consensus size: 29
40843424 GTATACGTAA
*
40843434 GCCTTTGTGGCTATCTCAATTAAATGAAT
1 GCCTTTGTGGCTATCTCAGTTAAATGAAT
* * *
40843463 GCCTTTGTCGCTATCTC--TT-AATGGAC
1 GCCTTTGTGGCTATCTCAGTTAAATGAAT
* ** * *
40843489 ACCTTTACGGCTATCTCTGTTATAA-GAAA
1 GCCTTTGTGGCTATCTCAGTTA-AATGAAT
* * * *
40843518 GCATTTGTGGCGATCTTAGTTATAACGAA-
1 GCCTTTGTGGCTATCTCAGTTA-AATGAAT
*
40843547 GCCTTTGTGGC-AGTCTTAGTTAAATGAAT
1 GCCTTTGTGGCTA-TCTCAGTTAAATGAAT
40843576 GCCTTTGTGGCTATCTCAGTTAAATGAAT
1 GCCTTTGTGGCTATCTCAGTTAAATGAAT
* * *
40843605 GCCTTTATGG-TGATCTCTGTTATAAGGAA-
1 GCCTTTGTGGCT-ATCTCAGTTA-AATGAAT
* *
40843634 GCCTTTGTGGATATCTTAGTTAAATGAAT
1 GCCTTTGTGGCTATCTCAGTTAAATGAAT
* * * * *
40843663 GCCTTTTTTGCCGATCTCTGTTGAAA-GGAT
1 GCC-TTTGTGGCTATCTCAGTT-AAATGAAT
* * *
40843693 GCCTTTGTAG-TGATCTAAATTAAATGAAT
1 GCCTTTGTGGCT-ATCTCAGTTAAATGAAT
* * * ** * *
40843722 GACTTTTTGGCGATCTTTGTTAAAAGGAT
1 GCCTTTGTGGCTATCTCAGTTAAATGAAT
*
40843751 GCCTTTGTGGCTATCTCAATTAAATGAAT
1 GCCTTTGTGGCTATCTCAGTTAAATGAAT
* * * *
40843780 GTCTTTATGGCTATCT-ATGTTAAAAGGAT
1 GCCTTTGTGGCTATCTCA-GTTAAATGAAT
* * * *
40843809 GTCTTTATGGCCATCTCTA-TTAAAGGAAT
1 GCCTTTGTGGCTATCTC-AGTTAAATGAAT
*
40843838 ACC-TTGTGG
1 GCCTTTGTGG
40843847 AAAACTCTGT
Statistics
Matches: 295, Mismatches: 69, Indels: 41
0.73 0.17 0.10
Matches are distributed among these distances:
26 18 0.06
27 2 0.01
28 23 0.08
29 218 0.74
30 30 0.10
31 4 0.01
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (29 bp):
GCCTTTGTGGCTATCTCAGTTAAATGAAT
Found at i:40843638 original size:58 final size:58
Alignment explanation
Indices: 40843490--40843877 Score: 295
Period size: 58 Copynumber: 6.7 Consensus size: 58
40843480 TTAATGGACA
* * * * * * * *
40843490 CCTTTACGGCTATCTCTGTTATAAGAAAGCATTTGTGGCGATCTTAGTTATAACGAA-G
1 CCTTTATGGCGATCTCTGTTAAAAGGAAGCCTTTGTGGCTATCTCAGTTA-AATGAATG
* *
40843548 CCTTTGTGGC-AGTCT-TAGTT-AAATGAATGCCTTTGTGGCTATCTCAGTTAAATGAATG
1 CCTTTATGGCGA-TCTCT-GTTAAAAGGAA-GCCTTTGTGGCTATCTCAGTTAAATGAATG
* * * *
40843606 CCTTTATGGTGATCTCTGTTATAAGGAAGCCTTTGTGGATATCTTAGTTAAATGAATG
1 CCTTTATGGCGATCTCTGTTAAAAGGAAGCCTTTGTGGCTATCTCAGTTAAATGAATG
* * * * * * *
40843664 CCTTTTTTGCCGATCTCTGTTGAAAGGATGCCTTTGTAG-TGATCTAAATTAAATGAATG
1 CC-TTTATGGCGATCTCTGTTAAAAGGAAGCCTTTGTGGCT-ATCTCAGTTAAATGAATG
* * * * *
40843723 ACTTTTTGGCGATCTTTGTTAAAAGGATGCCTTTGTGGCTATCTCAATTAAATGAATG
1 CCTTTATGGCGATCTCTGTTAAAAGGAAGCCTTTGTGGCTATCTCAGTTAAATGAATG
* * * * * * * * *
40843781 TCTTTATGGCTATCTATGTTAAAAGGATGTCTTTATGGCCATCTCTA-TTAAAGGAATA
1 CCTTTATGGCGATCTCTGTTAAAAGGAAGCCTTTGTGGCTATCTC-AGTTAAATGAATG
* ** * *
40843839 CC-TTGTGGAAAACTCTGTTAAAAGGAATGCCTTCGTGGC
1 CCTTTATGGCGATCTCTGTTAAAAGGAA-GCCTTTGTGGC
40843878 AAAATCTTAA
Statistics
Matches: 269, Mismatches: 49, Indels: 24
0.79 0.14 0.07
Matches are distributed among these distances:
57 30 0.11
58 184 0.68
59 55 0.20
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.37
Consensus pattern (58 bp):
CCTTTATGGCGATCTCTGTTAAAAGGAAGCCTTTGTGGCTATCTCAGTTAAATGAATG
Found at i:40843890 original size:29 final size:29
Alignment explanation
Indices: 40843830--40843890 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
40843820 CATCTCTATT
*
40843830 AAAGGAATACCTTGTGGAAAACTCTGTTA
1 AAAGGAATACCTTGTGGAAAACTCTGTAA
*
40843859 AAAGGAATGCCTTCGTGGCAAAA-TCT-TAA
1 AAAGGAATACCTT-GTGG-AAAACTCTGTAA
40843888 AAA
1 AAA
40843891 TGGATCTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 17 0.61
30 7 0.25
31 4 0.14
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.25
Consensus pattern (29 bp):
AAAGGAATACCTTGTGGAAAACTCTGTAA
Found at i:40857790 original size:140 final size:136
Alignment explanation
Indices: 40857481--40857904 Score: 634
Period size: 140 Copynumber: 3.1 Consensus size: 136
40857471 TAGAAAAATG
* * * * *
40857481 AATTATATTATTTCTAAAAGAATATTAATTTCTATGTCTTTTATATTTTGACCAAACTTCATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTAAA-TTAATTAA
* *
40857546 TATAATTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTTTGAATCAAATT
65 TATAAATGTTTATATTAATAAATTT-GTAAAATATATACAATTAATATTTTGTATGAATCAAATT
40857611 CATATATT
129 CATATATT
40857619 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACT-AAATTAATTAA
*
40857684 TATAACTGTTTATATTAATAAATTTGATAAAATATATATACAATTAATATTTTGTATGAATCAAA
65 TATAAATGTTTATATTAATAAATTTG-T-AAA-ATATATACAATTAATATTTTGTATGAATCAAA
*
40857749 TTAATATATT
127 TTCATATATT
* * * **
40857759 GATTATATTCTTTCCAAAATAATATTTATTTCCATGTCTTTTGCATTTTGACATAAA-TAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGAC-TAAATTAATTAA
40857823 TATAAATGTTTATATTAATAAATTTTGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
65 TATAAATGTTTATATTAATAAA-TTTGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
40857888 CATATATT
129 CATATATT
*
40857896 CATTATATT
1 AATTATATT
40857905 TATGTTCTCT
Statistics
Matches: 264, Mismatches: 16, Indels: 13
0.90 0.05 0.04
Matches are distributed among these distances:
137 50 0.19
138 84 0.32
139 35 0.13
140 94 0.36
141 1 0.00
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.47
Consensus pattern (136 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTAAATTAATTAAT
ATAAATGTTTATATTAATAAATTTGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCA
TATATT
Found at i:40860266 original size:12 final size:12
Alignment explanation
Indices: 40860249--40860280 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
40860239 CCGATATAGC
40860249 TGATGGATAGTA
1 TGATGGATAGTA
*
40860261 TGATGGATAGTG
1 TGATGGATAGTA
40860273 TGATGGAT
1 TGATGGAT
40860281 CTCCGACAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.38, T:0.34
Consensus pattern (12 bp):
TGATGGATAGTA
Found at i:40860553 original size:23 final size:22
Alignment explanation
Indices: 40860504--40860554 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
40860494 AACTTAGCAA
40860504 ATTCATTACATAACATAATAGC
1 ATTCATTACATAACATAATAGC
* *
40860526 TTTCATGTACATAGCAT-ATAAGC
1 ATTCAT-TACATAACATAAT-AGC
40860549 ATTCAT
1 ATTCAT
40860555 ACTTTCATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (22 bp):
ATTCATTACATAACATAATAGC
Found at i:40861055 original size:15 final size:16
Alignment explanation
Indices: 40861029--40861059 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
40861019 TAATATGAAA
40861029 AAATAGCATTAAAATG
1 AAATAGCATTAAAATG
40861045 AAATA-CATTAAAATG
1 AAATAGCATTAAAATG
40861060 CTATTTAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.58, C:0.06, G:0.10, T:0.26
Consensus pattern (16 bp):
AAATAGCATTAAAATG
Found at i:40864358 original size:8 final size:8
Alignment explanation
Indices: 40864345--40864371 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
40864335 ACCTCCACCA
40864345 TTTAGAGG
1 TTTAGAGG
40864353 TTTAGAGG
1 TTTAGAGG
40864361 TTTAGAGG
1 TTTAGAGG
40864369 TTT
1 TTT
40864372 CATACCTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.44
Consensus pattern (8 bp):
TTTAGAGG
Found at i:40871076 original size:20 final size:20
Alignment explanation
Indices: 40871051--40871166 Score: 72
Period size: 20 Copynumber: 5.8 Consensus size: 20
40871041 GATTGTAAGG
* *
40871051 GTTTGCGCTTTGGTGCCTCT
1 GTTTGCACTTCGGTGCCTCT
*
40871071 GTTTGCACTTCGGTGTCTCT
1 GTTTGCACTTCGGTGCCTCT
** * *
40871091 GTTCACACTTCAGTGACTCT
1 GTTTGCACTTCGGTGCCTCT
* * *
40871111 GTATACAC-TCTAGTGCCTCT
1 GTTTGCACTTC-GGTGCCTCT
* ** *
40871131 GATTGCACAACCGTGCCTCT
1 GTTTGCACTTCGGTGCCTCT
* *
40871151 ATTTGCACTACGGTGC
1 GTTTGCACTTCGGTGC
40871167 ATATGTATAG
Statistics
Matches: 75, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
19 2 0.03
20 72 0.96
21 1 0.01
ACGTcount: A:0.14, C:0.28, G:0.22, T:0.36
Consensus pattern (20 bp):
GTTTGCACTTCGGTGCCTCT
Found at i:40872254 original size:15 final size:15
Alignment explanation
Indices: 40872226--40872279 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
40872216 TTAACCTAAT
*
40872226 TTAATTATA-ATTAA
1 TTAATTAAACATTAA
*
40872240 TTAATTAAACTTTAA
1 TTAATTAAACATTAA
*
40872255 TTAATCAAACATTAA
1 TTAATTAAACATTAA
40872270 GCTTAATTAA
1 --TTAATTAA
40872280 CTAAAATCTA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
14 8 0.25
15 17 0.53
17 7 0.22
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (15 bp):
TTAATTAAACATTAA
Found at i:40875594 original size:15 final size:15
Alignment explanation
Indices: 40875574--40875605 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
40875564 ACATGTTACA
40875574 CACTCATGTGGGGAG
1 CACTCATGTGGGGAG
40875589 CACTCATGTGGGGAG
1 CACTCATGTGGGGAG
40875604 CA
1 CA
40875606 TTTGAACTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.22, C:0.22, G:0.38, T:0.19
Consensus pattern (15 bp):
CACTCATGTGGGGAG
Found at i:40879708 original size:16 final size:17
Alignment explanation
Indices: 40879656--40879705 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
40879646 TCAACTTTGT
40879656 TTTTAAAGTATATAATAA
1 TTTTAAA-TATATAATAA
* *
40879674 TTTTAAAT-TATCATCA
1 TTTTAAATATATAATAA
*
40879690 TTTTAAATATAAAATA
1 TTTTAAATATATAATA
40879706 TTTATTTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 14 0.54
17 5 0.19
18 7 0.27
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (17 bp):
TTTTAAATATATAATAA
Found at i:40890606 original size:27 final size:27
Alignment explanation
Indices: 40890575--40890692 Score: 182
Period size: 27 Copynumber: 4.4 Consensus size: 27
40890565 CCTCAAAATA
*
40890575 GGTAAAATGATCGAAATACCCCCATAG
1 GGTAAAATGATCAAAATACCCCCATAG
*
40890602 GGTAAAATGATCAAAATACCTCCATAG
1 GGTAAAATGATCAAAATACCCCCATAG
* *
40890629 GGTAAAATGACCAAAATACCCCTATAG
1 GGTAAAATGATCAAAATACCCCCATAG
* *
40890656 GGTAAAATGATCGAAATACCCTCATAG
1 GGTAAAATGATCAAAATACCCCCATAG
40890683 GGTAAAATGA
1 GGTAAAATGA
40890693 CTGTTATACC
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 82 1.00
ACGTcount: A:0.43, C:0.19, G:0.18, T:0.20
Consensus pattern (27 bp):
GGTAAAATGATCAAAATACCCCCATAG
Found at i:40892127 original size:20 final size:21
Alignment explanation
Indices: 40892102--40892140 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
40892092 CAATTAGATA
40892102 TAACAT-TACAAC-ACAAAATT
1 TAACATATA-AACAACAAAATT
40892122 TAACATATAAACAACAAAA
1 TAACATATAAACAACAAAA
40892141 AAACATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.62, C:0.18, G:0.00, T:0.21
Consensus pattern (21 bp):
TAACATATAAACAACAAAATT
Found at i:40894012 original size:11 final size:11
Alignment explanation
Indices: 40893996--40894026 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
40893986 ATGAATACCC
40893996 ATAAAATTCAT
1 ATAAAATTCAT
40894007 ATAAAATTCAT
1 ATAAAATTCAT
40894018 ATAAAATTC
1 ATAAAATTC
40894027 TTTCAATGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAAAATTCAT
Found at i:40895484 original size:29 final size:29
Alignment explanation
Indices: 40895459--40895513 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
40895449 TAGAAAATAC
*
40895459 AGAAAAGAAA-AGAAAAAACAAAAAAACA
1 AGAAAAAAAATAGAAAAAACAAAAAAACA
* *
40895487 AGAAAAAAAATAGATAAAACAATAAAA
1 AGAAAAAAAATAGAAAAAACAAAAAAA
40895514 GGTTATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 9 0.39
29 14 0.61
ACGTcount: A:0.80, C:0.05, G:0.09, T:0.05
Consensus pattern (29 bp):
AGAAAAAAAATAGAAAAAACAAAAAAACA
Found at i:40895489 original size:18 final size:19
Alignment explanation
Indices: 40895450--40895494 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
40895440 ACCCAAATAT
*
40895450 AGAAAATACAGAAAAGAAA
1 AGAAAAAACAGAAAAGAAA
40895469 AGAAAAAACA-AAAA-AACA
1 AGAAAAAACAGAAAAGAA-A
40895487 AGAAAAAA
1 AGAAAAAA
40895495 AATAGATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 2 0.08
18 13 0.54
19 9 0.38
ACGTcount: A:0.80, C:0.07, G:0.11, T:0.02
Consensus pattern (19 bp):
AGAAAAAACAGAAAAGAAA
Found at i:40899518 original size:17 final size:17
Alignment explanation
Indices: 40899488--40899525 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
40899478 AGGGACTAAA
40899488 TTAAAATTGTAAAAAAGT
1 TTAAAATTGTAAAAAA-T
*
40899506 TTAAATTTG-AAAAAAT
1 TTAAAATTGTAAAAAAT
40899522 TTAA
1 TTAA
40899526 TATGTGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 6 0.32
18 8 0.42
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (17 bp):
TTAAAATTGTAAAAAAT
Found at i:40901438 original size:130 final size:131
Alignment explanation
Indices: 40901257--40901512 Score: 372
Period size: 132 Copynumber: 2.0 Consensus size: 131
40901247 TTAAACTATG
* * *
40901257 GTCTTCGCTTTTGTGTTATTTCAGTTCAATTAAAATGGGTTTGTTTGTTTTTAC-TTCTT-TTGT
1 GTCTTCGCTTTTGTGTTATTTCAGTTAAATTAAAATGGGTTTGTCTATTTTTACATTCTTCTTGT
* * *
40901320 ACTATTTGATTCTTATTGATTGCCCCTTTTGTTGATTTTGCTGTTCTTAGCTCTTTGCAAATTAT
66 ACTATTTGATTCTTATTGATTGCCCCTTTTGTTGATTTTACTGTTCTTAGCTATTGGCAAATTAT
40901385 A
131 A
* * * * * *
40901386 GTCTTTGCTTTTGTGTTCTTTTAGTTAAAATTTAAATGGGTTTGTCTATTTTTACATTTTTCTTT
1 GTCTTCGCTTTTGTGTTATTTCAGTT-AAATTAAAATGGGTTTGTCTATTTTTACATTCTTCTTG
*
40901451 TACTATTTGATTCTTATTGATTGCTCCTTTTGTTGATTTTACTGTTCTTAGCTATTGGCAAA
65 TACTATTTGATTCTTATTGATTGCCCCTTTTGTTGATTTTACTGTTCTTAGCTATTGGCAAA
40901513 CTGCATGTAA
Statistics
Matches: 111, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
129 23 0.21
130 24 0.22
131 4 0.04
132 60 0.54
ACGTcount: A:0.17, C:0.13, G:0.15, T:0.55
Consensus pattern (131 bp):
GTCTTCGCTTTTGTGTTATTTCAGTTAAATTAAAATGGGTTTGTCTATTTTTACATTCTTCTTGT
ACTATTTGATTCTTATTGATTGCCCCTTTTGTTGATTTTACTGTTCTTAGCTATTGGCAAATTAT
A
Found at i:40904478 original size:30 final size:30
Alignment explanation
Indices: 40904442--40904506 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
40904432 CGTTTCAAGT
*
40904442 TTTATATGAGCATGCTAAGAAAGGTATAGG
1 TTTATATAAGCATGCTAAGAAAGGTATAGG
* * ** *
40904472 TTTATATAATCATGTTGGGAAGGGTATAGG
1 TTTATATAAGCATGCTAAGAAAGGTATAGG
40904502 TTTAT
1 TTTAT
40904507 GTATTTAAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (30 bp):
TTTATATAAGCATGCTAAGAAAGGTATAGG
Found at i:40906942 original size:42 final size:42
Alignment explanation
Indices: 40906890--40907036 Score: 138
Period size: 42 Copynumber: 3.5 Consensus size: 42
40906880 CAGAAGCAGT
*
40906890 ATACAACACATAAAGTGCCTGAAACGACACACGTGGTGCCTA
1 ATACGACACATAAAGTGCCTGAAACGACACACGTGGTGCCTA
* * * * * * * ** *
40906932 ATACGACACATACAGTGCC-GGATCAATATATCAT-AAGCAGT-
1 ATACGACACATAAAGTGCCTGAAACGACACA-CGTGGTGC-CTA
40906973 ATACGACACATAAAGTGCCTGAAACGACACACGTGGTGCCTA
1 ATACGACACATAAAGTGCCTGAAACGACACACGTGGTGCCTA
* *
40907015 ATATGACACATATAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
40907037 TCGGAAAAGC
Statistics
Matches: 77, Mismatches: 23, Indels: 10
0.70 0.21 0.09
Matches are distributed among these distances:
41 29 0.38
42 48 0.62
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (42 bp):
ATACGACACATAAAGTGCCTGAAACGACACACGTGGTGCCTA
Found at i:40906949 original size:21 final size:22
Alignment explanation
Indices: 40906890--40906950 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 22
40906880 CAGAAGCAGT
*
40906890 ATACAACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
****
40906912 A-ACGACACACGTGGTGCCT-A
1 ATACGACACATAAAGTGCCTGA
*
40906932 ATACGACACATACAGTGCC
1 ATACGACACATAAAGTGCC
40906951 GGATCAATAT
Statistics
Matches: 29, Mismatches: 9, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
20 2 0.07
21 26 0.90
22 1 0.03
ACGTcount: A:0.38, C:0.28, G:0.18, T:0.16
Consensus pattern (22 bp):
ATACGACACATAAAGTGCCTGA
Found at i:40906970 original size:83 final size:83
Alignment explanation
Indices: 40906869--40907038 Score: 286
Period size: 83 Copynumber: 2.0 Consensus size: 83
40906859 CTCAATACCT
40906869 GATCAACATATCAGAAGCAGTATACAACACATAAAGTGCCTGAAACGACACACGTGGTGCCTAAT
1 GATCAACATATCAGAAGCAGTATACAACACATAAAGTGCCTGAAACGACACACGTGGTGCCTAAT
40906934 ACGACACATACAGTGCCG
66 ACGACACATACAGTGCCG
* * *
40906952 GATCAATATATCATAAGCAGTATACGACACATAAAGTGCCTGAAACGACACACGTGGTGCCTAAT
1 GATCAACATATCAGAAGCAGTATACAACACATAAAGTGCCTGAAACGACACACGTGGTGCCTAAT
* * *
40907017 ATGACACATATAGTGCCT
66 ACGACACATACAGTGCCG
40907035 GATC
1 GATC
40907039 GGAAAAGCCG
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.20
Consensus pattern (83 bp):
GATCAACATATCAGAAGCAGTATACAACACATAAAGTGCCTGAAACGACACACGTGGTGCCTAAT
ACGACACATACAGTGCCG
Found at i:40907032 original size:21 final size:21
Alignment explanation
Indices: 40906975--40907036 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
40906965 TAAGCAGTAT
*
40906975 ACGACACATAAAGTGCCTGAA
1 ACGACACATATAGTGCCTGAA
** *
40906996 ACGACACACGTGGTGCCT-AA
1 ACGACACATATAGTGCCTGAA
*
40907016 TATGACACATATAGTGCCTGA
1 -ACGACACATATAGTGCCTGA
40907037 TCGGAAAAGC
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 2 0.06
21 28 0.90
22 1 0.03
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.19
Consensus pattern (21 bp):
ACGACACATATAGTGCCTGAA
Found at i:40907234 original size:29 final size:29
Alignment explanation
Indices: 40907200--40907257 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
40907190 CACTAATCAA
* *
40907200 CATTCAATTCAATATTAACATATATTTCT
1 CATTCAATTCAATACTAACACATATTTCT
40907229 CATTCAATTCAATACTAACACATATTTCT
1 CATTCAATTCAATACTAACACATATTTCT
40907258 GTAATATCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (29 bp):
CATTCAATTCAATACTAACACATATTTCT
Found at i:40908767 original size:11 final size:11
Alignment explanation
Indices: 40908738--40908780 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
40908728 ATCATTTAAC
*
40908738 AATAAAATAAT
1 AATAAAATATT
* *
40908749 ACTAAAAATCTT
1 AAT-AAAATATT
40908761 AATAAAATATT
1 AATAAAATATT
40908772 AATAAAATA
1 AATAAAATA
40908781 ACATTTATCT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 18 0.69
12 8 0.31
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:40911774 original size:309 final size:309
Alignment explanation
Indices: 40911215--40911808 Score: 974
Period size: 309 Copynumber: 1.9 Consensus size: 309
40911205 GGGTCGGTAT
*
40911215 GCTTACCTAGACCCCTAATTGACTGAAACAACTATATAGCTGATACGATTAAGCCTGATGATGTC
1 GCTTACCTAGACCCCTAATTGACTGAAACAACTATATAGCTGATACGATTAAGCCCGATGATGTC
* *
40911280 CCACTAATTTGATACTGTATGCCTTGTTTACATGCATGATATTATGTTATAGCATGTCATATCTG
66 CCACTAATTTGATACTGTATGCCTTATTTACATGCATGATATTATGTTATAGCATGTCATATATG
* * * * *
40911345 TATATTGCATTGCATTGCATTGGGGGATTATAATGTTTGAAGGAGGTGTACTGGAAGGCATTGAG
131 TATATTGCATTCCATTGCATTGGGCGATTATAATGTTTGAAGGAAGTGTACTGAAAGGCATCGAG
* *
40911410 CTTAATTTACTGGCAGCTTAGCTGCAAACTACTGTCTAATGCCGCATTCGGTACTACTTGGAGTG
196 CTTAATTTACTGGCAGCTCAGCTGCAAACTACTGTCTAATGCCCCATTCGGTACTACTTGGAGTG
40911475 TAGGGATGGGTGCGTTAATTATATCATGTCATATCTATAGGTTCAGTAA
261 TAGGGATGGGTGCGTTAATTATATCATGTCATATCTATAGGTTCAGTAA
* * *
40911524 GCTTACCTAGACCCCTAATTGACTGAAACGACTGTAT-GACTGATATGATTAAGCCCGATGATGT
1 GCTTACCTAGACCCCTAATTGACTGAAACAACTATATAG-CTGATACGATTAAGCCCGATGATGT
*
40911588 CCCACTGATTTGATACTGTATGCCTTATTTACATGCATGATATTATGTTATAGCATGTCATATAT
65 CCCACTAATTTGATACTGTATGCCTTATTTACATGCATGATATTATGTTATAGCATGTCATATAT
** * *
40911653 GTATATTGCATTCCATTGGGTTGGGCGATTATAATGTTTGGAGGAAGTGTACTGAAAGGCCTCGA
130 GTATATTGCATTCCATTGCATTGGGCGATTATAATGTTTGAAGGAAGTGTACTGAAAGGCATCGA
* *
40911718 GCTTAATTTACTGGCAGCTCAGCTGCAAACTACTGTCTAGTGCCCCATTCGGTACTACTTTGAGT
195 GCTTAATTTACTGGCAGCTCAGCTGCAAACTACTGTCTAATGCCCCATTCGGTACTACTTGGAGT
* *
40911783 GTAGGGATGTGTGGGTTAATTATATC
260 GTAGGGATGGGTGCGTTAATTATATC
40911809 CCCACGTGGA
Statistics
Matches: 262, Mismatches: 22, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
308 1 0.00
309 261 1.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.34
Consensus pattern (309 bp):
GCTTACCTAGACCCCTAATTGACTGAAACAACTATATAGCTGATACGATTAAGCCCGATGATGTC
CCACTAATTTGATACTGTATGCCTTATTTACATGCATGATATTATGTTATAGCATGTCATATATG
TATATTGCATTCCATTGCATTGGGCGATTATAATGTTTGAAGGAAGTGTACTGAAAGGCATCGAG
CTTAATTTACTGGCAGCTCAGCTGCAAACTACTGTCTAATGCCCCATTCGGTACTACTTGGAGTG
TAGGGATGGGTGCGTTAATTATATCATGTCATATCTATAGGTTCAGTAA
Found at i:40915141 original size:18 final size:19
Alignment explanation
Indices: 40915104--40915143 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
40915094 ATCATTTCTA
*
40915104 TTTACAAAAAACCTTAGTT
1 TTTACAAAAAACCGTAGTT
*
40915123 TTTAGAAAAAACCGT-GTT
1 TTTACAAAAAACCGTAGTT
40915141 TTT
1 TTT
40915144 TAGAGTTGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (19 bp):
TTTACAAAAAACCGTAGTT
Found at i:40920726 original size:62 final size:59
Alignment explanation
Indices: 40920566--40920729 Score: 169
Period size: 62 Copynumber: 2.7 Consensus size: 59
40920556 TATTATTTTT
* * *
40920566 TTAATATTATATATTATGATTTTTATT-AATTCATATTTTAATAAT-AATATTAAGAATGTTA
1 TTAA-ATTAT-TATTATTATTTTTATTAAATT-ATA-TTTAATAATAAATATTAAGAATATGA
* *
40920627 TTAAATTA-TA-TATTA-TTTTATTAACTTGTATTTAATAATAAATATGTTAA-AATATGA
1 TTAAATTATTATTATTATTTTTATTAAATTATATTTAATAATAAATA--TTAAGAATATGA
40920684 TTAAATTATTTATTATTATTTATTATTAAATTATATTTAATAATAA
1 TTAAATTA-TTATTATTATTT-TTATTAAATTATATTTAATAATAA
40920730 TCTTATTAAA
Statistics
Matches: 87, Mismatches: 7, Indels: 17
0.78 0.06 0.15
Matches are distributed among these distances:
55 9 0.10
56 13 0.15
57 20 0.23
58 6 0.07
59 2 0.02
60 9 0.10
61 6 0.07
62 22 0.25
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (59 bp):
TTAAATTATTATTATTATTTTTATTAAATTATATTTAATAATAAATATTAAGAATATGA
Found at i:40920905 original size:16 final size:15
Alignment explanation
Indices: 40920857--40920913 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 15
40920847 ACAACTGAAT
* *
40920857 TATTGATTACAACTC
1 TATTCATTACAGCTC
*
40920872 TATTCTATTAATAGCTC
1 TATTC-ATT-ACAGCTC
40920889 TATTACATTACAGCTC
1 TATT-CATTACAGCTC
40920905 TATTTCATT
1 TA-TTCATT
40920914 CCCCCCAACC
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
15 4 0.12
16 15 0.44
17 14 0.41
18 1 0.03
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.46
Consensus pattern (15 bp):
TATTCATTACAGCTC
Found at i:40921167 original size:25 final size:26
Alignment explanation
Indices: 40921133--40921183 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
40921123 GTAGGTAGTT
* *
40921133 GATTATTGTT-ATTAAATTTTAATAA
1 GATTATTGTTAAATAAAATTTAATAA
40921158 GATTATTGTTAAATAAAATTTAATAA
1 GATTATTGTTAAATAAAATTTAATAA
40921184 AATAATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (26 bp):
GATTATTGTTAAATAAAATTTAATAA
Found at i:40923306 original size:29 final size:32
Alignment explanation
Indices: 40923258--40923317 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 32
40923248 AATTTTGTGC
40923258 AGGAATACAATTTGGGGCTAAATAGAAGAAAA
1 AGGAATACAATTTGGGGCTAAATAGAAGAAAA
* *
40923290 AGGAA-ACAA-TT-GGGCTAGATTGAAGAAA
1 AGGAATACAATTTGGGGCTAAATAGAAGAAA
40923318 GAAGCAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 15 0.58
30 2 0.08
31 4 0.15
32 5 0.19
ACGTcount: A:0.48, C:0.07, G:0.27, T:0.18
Consensus pattern (32 bp):
AGGAATACAATTTGGGGCTAAATAGAAGAAAA
Found at i:40925838 original size:18 final size:18
Alignment explanation
Indices: 40925817--40925855 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
40925807 CCTTCTTCTC
40925817 CCCTTTCCCCTTTCCCTT
1 CCCTTTCCCCTTTCCCTT
*
40925835 CCCTTTCCCTTTTCCCTT
1 CCCTTTCCCCTTTCCCTT
40925853 CCC
1 CCC
40925856 CTTGGGTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (18 bp):
CCCTTTCCCCTTTCCCTT
Found at i:40925842 original size:6 final size:6
Alignment explanation
Indices: 40925817--40925858 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
40925807 CCTTCTTCTC
*
40925817 CCCTTT CCCCTTT CCC-TT CCCTTT CCCTTTT CCCTTC CCCTT
1 CCCTTT -CCCTTT CCCTTT CCCTTT CCC-TTT CCCTTT CCCTT
40925859 GGGTTGCAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
5 5 0.16
6 15 0.47
7 12 0.38
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (6 bp):
CCCTTT
Found at i:40925928 original size:3 final size:3
Alignment explanation
Indices: 40925920--40925987 Score: 59
Period size: 3 Copynumber: 22.0 Consensus size: 3
40925910 GGTAAGGCTC
*
40925920 CTT CTT CTT CTT CTT CTT CTT CCGTT CTT CATT CCTT TTT CTT CTT C-T
1 CTT CTT CTT CTT CTT CTT CTT -C-TT CTT C-TT -CTT CTT CTT CTT CTT
* *
40925968 GTT CTT CAT CTT C-T CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT
40925988 AGCATATTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
2 3 0.06
3 41 0.77
4 6 0.11
5 3 0.06
ACGTcount: A:0.03, C:0.32, G:0.03, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:40925963 original size:25 final size:24
Alignment explanation
Indices: 40925921--40925987 Score: 86
Period size: 25 Copynumber: 2.9 Consensus size: 24
40925911 GTAAGGCTCC
40925921 TTCTTC-TTCTTCTTCTTCTTCCG
1 TTCTTCATTCTTCTTCTTCTTCCG
* *
40925944 TTCTTCATTCCTTTTTCTTCTTCTG
1 TTCTTCATT-CTTCTTCTTCTTCCG
40925969 TTCTTCA-TCTTC-TCTTCTT
1 TTCTTCATTCTTCTTCTTCTT
40925988 AGCATATTCT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
22 7 0.18
23 9 0.23
24 3 0.08
25 20 0.51
ACGTcount: A:0.03, C:0.31, G:0.03, T:0.63
Consensus pattern (24 bp):
TTCTTCATTCTTCTTCTTCTTCCG
Found at i:40925981 original size:14 final size:14
Alignment explanation
Indices: 40925930--40925987 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 14
40925920 CTTCTTCTTC
* *
40925930 TTCTTCTTCTTCCG
1 TTCTTCATCTTCTG
*
40925944 TTCTTCAT-TCCT-
1 TTCTTCATCTTCTG
*
40925956 TT-TTCTTCTTCTG
1 TTCTTCATCTTCTG
*
40925969 TTCTTCATCTTCTC
1 TTCTTCATCTTCTG
40925983 TTCTT
1 TTCTT
40925988 AGCATATTCT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
11 4 0.12
12 5 0.15
13 4 0.12
14 21 0.62
ACGTcount: A:0.03, C:0.31, G:0.03, T:0.62
Consensus pattern (14 bp):
TTCTTCATCTTCTG
Found at i:40926235 original size:11 final size:11
Alignment explanation
Indices: 40926219--40926244 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
40926209 TTGCTGGATG
40926219 ATATTTTGGTT
1 ATATTTTGGTT
40926230 ATATTTTGGTT
1 ATATTTTGGTT
40926241 ATAT
1 ATAT
40926245 ACAAATGGTT
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:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (11 bp):
ATATTTTGGTT
Found at i:40928600 original size:22 final size:20
Alignment explanation
Indices: 40928557--40928595 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
40928547 TAATTTAAAA
40928557 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
40928577 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
40928596 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:40928719 original size:20 final size:20
Alignment explanation
Indices: 40928694--40928733 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40928684 AATAGTTTCC
*
40928694 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
40928714 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
40928734 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:40928740 original size:14 final size:14
Alignment explanation
Indices: 40928717--40928756 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
40928707 ACAGAAAAGT
*
40928717 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
40928731 AAATCATTTTACGG
1 AAAACATTTTACAG
40928745 AAAACATTTTAC
1 AAAACATTTTAC
40928757 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:40935533 original size:85 final size:85
Alignment explanation
Indices: 40935380--40935554 Score: 287
Period size: 85 Copynumber: 2.1 Consensus size: 85
40935370 CCAAACGAGT
* * * *
40935380 GATGGTTTGGAACCTAACTGAGCACTAAGAAACCTTGTATTAGGAAAGTATTTGGCCCTTAGAAT
1 GATGCTTTGAAACCTAACTAAGCACTAAGAAACCTTGTATTAGGAAAGTATTTGGCCATTAGAAT
*
40935445 ACGCACCATGAACGACGTAG
66 ACGCACCATCAACGACGTAG
*
40935465 GATGCTTTGAAACCTAACTAAGCACTAAGAAACCTTGTATTAGGAAAGTATTTGGCTATTAGAAT
1 GATGCTTTGAAACCTAACTAAGCACTAAGAAACCTTGTATTAGGAAAGTATTTGGCCATTAGAAT
40935530 ACGCACCATCAACGACGTAG
66 ACGCACCATCAACGACGTAG
*
40935550 TATGC
1 GATGC
40935555 ATTAAAATAA
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 83 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (85 bp):
GATGCTTTGAAACCTAACTAAGCACTAAGAAACCTTGTATTAGGAAAGTATTTGGCCATTAGAAT
ACGCACCATCAACGACGTAG
Found at i:40936024 original size:25 final size:25
Alignment explanation
Indices: 40935980--40936028 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
40935970 TAATTCCTTA
*
40935980 AATTAAAAAAAAAACCTATTTAACC
1 AATTAAAAAAAAAACATATTTAACC
**
40936005 AATTAAAAAAACGACATATTTAAC
1 AATTAAAAAAAAAACATATTTAAC
40936029 TTATTTAACC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.24
Consensus pattern (25 bp):
AATTAAAAAAAAAACATATTTAACC
Found at i:40936660 original size:29 final size:30
Alignment explanation
Indices: 40936593--40936654 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
40936583 TTAATTTGTG
* * *
40936593 AAAATTGGATCAAATCAAAATTTTATGTAT
1 AAAATTGCATAAAATCAAAAGTTTATGTAT
40936623 AAAATTGCATAAAAT-AAAAGTTTATGTAT
1 AAAATTGCATAAAATCAAAAGTTTATGTAT
40936652 AAA
1 AAA
40936655 TATGCACATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 16 0.55
30 13 0.45
ACGTcount: A:0.52, C:0.05, G:0.10, T:0.34
Consensus pattern (30 bp):
AAAATTGCATAAAATCAAAAGTTTATGTAT
Found at i:40937670 original size:16 final size:16
Alignment explanation
Indices: 40937645--40937677 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
40937635 TGATAAATTG
*
40937645 AAAAATTAAATGTTGA
1 AAAAAATAAATGTTGA
40937661 AAAAAATAAATGTTGA
1 AAAAAATAAATGTTGA
40937677 A
1 A
40937678 CATTTGAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (16 bp):
AAAAAATAAATGTTGA
Found at i:40938706 original size:16 final size:16
Alignment explanation
Indices: 40938675--40938711 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
40938665 GATTGAATAA
40938675 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
40938691 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
40938707 TATTA
1 TATTA
40938712 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Done.