Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 19 of 235
Found at i:5672852 original size:12 final size:12
Alignment explanation
Indices: 5672835--5672859 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5672825 TTCTGATCAT
5672835 AGCATCCTAATC
1 AGCATCCTAATC
5672847 AGCATCCTAATC
1 AGCATCCTAATC
5672859 A
1 A
5672860 TTTGGAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.32, G:0.08, T:0.24
Consensus pattern (12 bp):
AGCATCCTAATC
Found at i:5673241 original size:177 final size:178
Alignment explanation
Indices: 5672933--5673414 Score: 635
Period size: 177 Copynumber: 2.7 Consensus size: 178
5672923 GCAACATCAG
* * * * * *
5672933 TGAAAATCACAGATCTTATCTCCCTAAGCTGTAGAGGAGTAAATTGAAGACGGCGAATCTTATCT
1 TGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACGGTGAATCTTATCT
* * * *
5672998 CCATGTATCGAAAATGGAGTAGATTTTAGCCACCAGCCTCGTCTCCCTGAAGTTGCAGTGGAGCA
66 CCATGTATCGGAAATGGAGCAGATTTTAGCCACCAGCCTCATCTCCCTGAAGTAGCAGTGGAGCA
* *
5673063 GGTTCAAGATACAAGTCTTATC-TTCTTGAGGTAGTAAGGAAGTAGAC
131 GGTTCAAGATACAAGTCTTATCTTTCCTGAGGTAGCAAGGAAGTAGAC
*
5673110 TGAAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACGGTGAATCTTATCT
1 TGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACGGTGAATCTTATCT
* * * * * *
5673175 CCATGTATCGGCAATGGAGCAAATTTTAGCCACTAGCCTTATCTCTCTGAGGTAGCAG-GAGAGC
66 CCATGTATCGGAAATGGAGCAGATTTTAGCCACCAGCCTCATCTCCCTGAAGTAGCAGTG-GAGC
* *
5673239 AGGTTGAAGATACAAGTCTTATCTTTCCTGAGGTAGCAAGGGAGTAGAC
130 AGGTTCAAGATACAAGTCTTATCTTTCCTGAGGTAGCAAGGAAGTAGAC
* * *
5673288 TGAAAGTTATAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCAAAGACGGTGAATCTTATCT
1 TGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACGGTGAATCTTATCT
* * * * ** * * * *
5673353 CCATGTATCAGTAATGGAGCAGATTTAAGCTAGAAGTCTTATCTCCTTGAAGTTGCAGTGGA
66 CCATGTATCGGAAATGGAGCAGATTTTAGCCACCAGCCTCATCTCCCTGAAGTAGCAGTGGA
5673415 ACAGACTGAA
Statistics
Matches: 265, Mismatches: 37, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
176 1 0.00
177 132 0.50
178 131 0.49
179 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (178 bp):
TGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACGGTGAATCTTATCT
CCATGTATCGGAAATGGAGCAGATTTTAGCCACCAGCCTCATCTCCCTGAAGTAGCAGTGGAGCA
GGTTCAAGATACAAGTCTTATCTTTCCTGAGGTAGCAAGGAAGTAGAC
Found at i:5673427 original size:178 final size:176
Alignment explanation
Indices: 5672933--5673428 Score: 636
Period size: 178 Copynumber: 2.8 Consensus size: 176
5672923 GCAACATCAG
* * * * * *
5672933 TGAAAATCACAGATCTTATCTCCCTAAGCTGTAGAGGAGTAAATTGAAGACGGCGAATCTTATCT
1 TGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACGGTGAATCTTATCT
* * ** *
5672998 CCATGTATCGAAAATGGAGTAGATTTTAGCCACCAGCCTCGTCTCCCTGAAGTTGCAGTGGAGCA
66 CCATGTATCG-AAATGGAGCAGATTTTAGCCACAAGCCTTATCTCCTTGAAGTTGCAGTGGAGCA
* * *
5673063 GGTTCAAGATACAAGTCTTATCTTCTTGAGGTAGTAAGGAAGTAGAC
130 GGTTGAAGATACAAGTCTTATCTTCCTGAGGTAGCAAGGAAGTAGAC
*
5673110 TGAAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACGGTGAATCTTATCT
1 TGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACGGTGAATCTTATCT
* * * * *
5673175 CCATGTATCGGCAATGGAGCAAATTTTAGCCACTAGCCTTATCT-CTCTGAGGTAGCAG-GAGAG
66 CCATGTATC-GAAATGGAGCAGATTTTAGCCACAAGCCTTATCTCCT-TGAAGTTGCAGTG-GAG
*
5673238 CAGGTTGAAGATACAAGTCTTATCTTTCCTGAGGTAGCAAGGGAGTAGAC
128 CAGGTTGAAGATACAAGTCTTATC-TTCCTGAGGTAGCAAGGAAGTAGAC
* * *
5673288 TGAAAGTTATAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCAAAGACGGTGAATCTTATCT
1 TGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACGGTGAATCTTATCT
* * * * * *
5673353 CCATGTATCAGTAATGGAGCAGATTTAAGCTAGAAGTCTTATCTCCTTGAAGTTGCAGTGGAACA
66 CCATGTATC-GAAATGGAGCAGATTTTAGCCACAAGCCTTATCTCCTTGAAGTTGCAGTGGAGCA
**
5673418 GACTGAAGATA
130 GGTTGAAGATA
5673429 GCGAATCTTA
Statistics
Matches: 276, Mismatches: 37, Indels: 11
0.85 0.11 0.03
Matches are distributed among these distances:
176 2 0.01
177 129 0.47
178 142 0.51
179 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.27
Consensus pattern (176 bp):
TGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACGGTGAATCTTATCT
CCATGTATCGAAATGGAGCAGATTTTAGCCACAAGCCTTATCTCCTTGAAGTTGCAGTGGAGCAG
GTTGAAGATACAAGTCTTATCTTCCTGAGGTAGCAAGGAAGTAGAC
Found at i:5674688 original size:21 final size:21
Alignment explanation
Indices: 5674657--5674697 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5674647 TCTTGATTTA
*
5674657 TTTATTTATTACTTTTTTTTGT
1 TTTATTTATTA-TTTATTTTGT
5674679 TTTA-TTATTATTTATTTTG
1 TTTATTTATTATTTATTTTG
5674698 AATTTCCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 6 0.33
22 4 0.22
ACGTcount: A:0.17, C:0.02, G:0.05, T:0.76
Consensus pattern (21 bp):
TTTATTTATTATTTATTTTGT
Found at i:5679563 original size:50 final size:50
Alignment explanation
Indices: 5679453--5679774 Score: 260
Period size: 50 Copynumber: 6.7 Consensus size: 50
5679443 AGGGTAAGAT
* * * * *
5679453 ACCGACGCCATATCCCAGACATGGTCTTACACTG--GCTCATACATC-AA
1 ACCGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATATCGAG
*
5679500 ACTCGATGCCATGTCCCAGGCATGGTCTTACACTGACTCTCATATATCGAG
1 AC-CGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATATCGAG
* * *
5679551 ACCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATCTGTC-AG
1 ACCGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATATCGAG
* * * * * *
5679600 TGCCGATGCCATATCCTAGACATGGTTTTACACTGA----CAAATATCAAG
1 -ACCGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATATCGAG
* * ** * *
5679647 -CCGATGCCATGTCCCAGATATGGTCTTACACT-AGCTTTCAGGTCTTGAG
1 ACCGATGCCATGTCCCAGACATGGTCTTACACTGA-CTCTCATATATCGAG
* * * * *
5679696 GCCGATGCCATGTCCCAAACATGGTCTTATACT-AGCCCTCATA-AT-GTG
1 ACCGATGCCATGTCCCAGACATGGTCTTACACTGA-CTCTCATATATCGAG
*
5679744 GCCGATG-CATGTCCCAGACAT-GTCTTACACT
1 ACCGATGCCATGTCCCAGACATGGTCTTACACT
5679775 AGCACACATA
Statistics
Matches: 225, Mismatches: 38, Indels: 25
0.78 0.13 0.09
Matches are distributed among these distances:
44 1 0.00
45 28 0.12
46 14 0.06
47 17 0.08
48 38 0.17
49 9 0.04
50 115 0.51
51 3 0.01
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.27
Consensus pattern (50 bp):
ACCGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATATCGAG
Found at i:5679700 original size:95 final size:96
Alignment explanation
Indices: 5679543--5679720 Score: 245
Period size: 95 Copynumber: 1.9 Consensus size: 96
5679533 TGACTCTCAT
* *
5679543 ATATCGAGACCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATCTGTCAGTGCCGATG
1 ATATCAAGACCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTGTCAGTGCCGATG
* *
5679608 CCATATCCTAGACATGGTTTTACACTGACAA
66 CCATATCCCAAACATGGTTTTACACTGACAA
* * *
5679639 ATATCAAG-CCGATGCCATGTCCCAGATATGGTCTTACACTAGCTTTCAGGTCT-TGAG-GCCGA
1 ATATCAAGACCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCA--TCTGTCAGTGCCGA
*
5679701 TGCCATGTCCCAAACATGGT
64 TGCCATATCCCAAACATGGT
5679721 CTTATACTAG
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
95 59 0.82
96 10 0.14
97 3 0.04
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.27
Consensus pattern (96 bp):
ATATCAAGACCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTGTCAGTGCCGATG
CCATATCCCAAACATGGTTTTACACTGACAA
Found at i:5679737 original size:145 final size:148
Alignment explanation
Indices: 5679454--5679780 Score: 366
Period size: 145 Copynumber: 2.3 Consensus size: 148
5679444 GGGTAAGATA
* *
5679454 CCGACGCCATATCCCAGACATGGTCTTACACTGGCTCATACATCAAACTCGATGCCATGTCCCAG
1 CCGACGCCATATCCCAGACATGGTCTTACACTGGCACAAACATCAAACTCGATGCCATGTCCCAG
* * *
5679519 GCATGGTCTTACACTGACTCTCATATATCGAGACCGATGCCATGTCCCAGACATGGTCTTACACT
66 ACATGGTCTTACACTGACTCTCAGATATCGAGACCGATGCCATGTCCCAAACATGGTCTTACACT
* *
5679584 GGCTCTCATCTGTCAGTG
131 AGCCCTCATCTGTCAGTG
* * * * *
5679602 CCGATGCCATATCCTAGACATGGTTTTACACT-G-ACAAATATCAAGC-CGATGCCATGTCCCAG
1 CCGACGCCATATCCCAGACATGGTCTTACACTGGCACAAACATCAAACTCGATGCCATGTCCCAG
* * * * * * *
5679664 ATATGGTCTTACACT-AGCTTTCAGGTCTTGAGGCCGATGCCATGTCCCAAACATGGTCTTATAC
66 ACATGGTCTTACACTGA-CTCTCAGATATCGAGACCGATGCCATGTCCCAAACATGGTCTTACAC
*
5679728 TAGCCCTCATAATGT--G-G
130 TAGCCCTCAT-CTGTCAGTG
* * *
5679745 CCGATG-CATGTCCCAGACAT-GTCTTACACTAGCACA
1 CCGACGCCATATCCCAGACATGGTCTTACACTGGCACA
5679781 CATATCACCC
Statistics
Matches: 152, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
141 9 0.06
142 13 0.09
143 10 0.07
144 2 0.01
145 76 0.50
146 12 0.08
147 1 0.01
148 29 0.19
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (148 bp):
CCGACGCCATATCCCAGACATGGTCTTACACTGGCACAAACATCAAACTCGATGCCATGTCCCAG
ACATGGTCTTACACTGACTCTCAGATATCGAGACCGATGCCATGTCCCAAACATGGTCTTACACT
AGCCCTCATCTGTCAGTG
Found at i:5685434 original size:68 final size:66
Alignment explanation
Indices: 5685362--5685511 Score: 169
Period size: 67 Copynumber: 2.2 Consensus size: 66
5685352 CATCATGTGT
* * * *
5685362 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
5685425 TGTAG
62 TGTAG
** * *
5685430 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCATGT
5685495 AG
65 AG
5685497 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
5685512 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 24 0.34
65 3 0.04
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.21
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
G
Found at i:5685467 original size:64 final size:64
Alignment explanation
Indices: 5685386--5685569 Score: 203
Period size: 67 Copynumber: 2.8 Consensus size: 64
5685376 AGACATTATG
* * *
5685386 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
5685450 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
5685515 AA
63 AA
* * *
5685517 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAG-ACAAGAGAGC
5685570 CGAACTATAT
Statistics
Matches: 99, Mismatches: 16, Indels: 11
0.79 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 25 0.25
66 21 0.21
67 31 0.31
68 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:5692393 original size:19 final size:20
Alignment explanation
Indices: 5692371--5692408 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5692361 AAAGTATATC
5692371 TAACCTTTCCAAG-TGTACA
1 TAACCTTTCCAAGTTGTACA
*
5692390 TAACCTTTTCAAGTTGTAC
1 TAACCTTTCCAAGTTGTAC
5692409 CATTTGGGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (20 bp):
TAACCTTTCCAAGTTGTACA
Found at i:5695519 original size:41 final size:40
Alignment explanation
Indices: 5695426--5695535 Score: 132
Period size: 41 Copynumber: 2.7 Consensus size: 40
5695416 TGATATTCTG
* * *
5695426 ATCTGCATTCTGTATCTGATTGGGCTGAGGCCCTAATATAT
1 ATCTG-ATTCTGTATCTGAGTAGGCTAAGGCCCTAATATAT
* *
5695467 -TCCTGACTCTGTATCTGAGCTAGGCTAAGGCCCTAATTTAT
1 AT-CTGATTCTGTATCTGAG-TAGGCTAAGGCCCTAATATAT
*
5695508 ATCTGATTCTGTATCTAAGTAGGCTAAG
1 ATCTGATTCTGTATCTGAGTAGGCTAAG
5695536 ACCCACATTG
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
40 22 0.37
41 36 0.61
42 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (40 bp):
ATCTGATTCTGTATCTGAGTAGGCTAAGGCCCTAATATAT
Found at i:5698441 original size:44 final size:45
Alignment explanation
Indices: 5698376--5698537 Score: 161
Period size: 46 Copynumber: 3.5 Consensus size: 45
5698366 GCTGATGCCG
* *
5698376 TGTCCCAGATATGGTCTTACACTGA-TA-GATCTCGTA-GCCGATGCA
1 TGTCCCAGACAT-GTCTTACACTGACTACG-TCTC-AAGGCCGATGCA
5698421 TGTCCCAGACATGTCTTACACTGACTTACGTCTCAAGGCCGATGCA
1 TGTCCCAGACATGTCTTACACTGAC-TACGTCTCAAGGCCGATGCA
* * * *
5698467 TGTCCCAGACACGTCTTACACTAGCACT-TGTCCCAATGCCGATGCCA
1 TGTCCCAGACATGTCTTACACT-G-ACTACGTCTCAAGGCCGATG-CA
*
5698514 TGTCCCAAACATGGTCTTACACTG
1 TGTCCCAGACAT-GTCTTACACTG
5698538 GCTCTCATAG
Statistics
Matches: 101, Mismatches: 8, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
44 12 0.12
45 12 0.12
46 49 0.49
47 16 0.16
48 12 0.12
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (45 bp):
TGTCCCAGACATGTCTTACACTGACTACGTCTCAAGGCCGATGCA
Found at i:5698535 original size:48 final size:45
Alignment explanation
Indices: 5698412--5698537 Score: 164
Period size: 46 Copynumber: 2.7 Consensus size: 45
5698402 AGATCTCGTA
*
5698412 GCCGATGCATGTCCCAGACATGTCTTACACTGACTTACGTCTCAAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGACTTA-GTCCCAAG
* *
5698458 GCCGATGCATGTCCCAGACACGTCTTACACTAGCACTT-GTCCCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACT-G-ACTTAGTCCCAAG
*
5698504 GCCGATGCCATGTCCCAAACATGGTCTTACACTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTG
5698538 GCTCTCATAG
Statistics
Matches: 71, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
46 43 0.61
47 14 0.20
48 14 0.20
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.25
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGACTTAGTCCCAAG
Found at i:5700228 original size:24 final size:21
Alignment explanation
Indices: 5700201--5700245 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
5700191 TTAGTCTATT
5700201 TCTTCTCTTATAATGACATTTTCA
1 TCTT-TCTT-TAATG-CATTTTCA
*
5700225 TCTTTGTTTAATGCATTTTCA
1 TCTTTCTTTAATGCATTTTCA
5700246 GTTTCCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 5 0.25
23 3 0.15
24 4 0.20
ACGTcount: A:0.22, C:0.18, G:0.07, T:0.53
Consensus pattern (21 bp):
TCTTTCTTTAATGCATTTTCA
Found at i:5702886 original size:29 final size:29
Alignment explanation
Indices: 5702844--5702936 Score: 109
Period size: 29 Copynumber: 3.2 Consensus size: 29
5702834 TTCTTTTAAT
*
5702844 AGAGGTAGCCACAAAGGTATCCTTATAAC
1 AGAGATAGCCACAAAGGTATCCTTATAAC
*
5702873 AGAGATAGCCACAAA-TTCATCCTTATAAC
1 AGAGATAGCCACAAAGGT-ATCCTTATAAC
* * *
5702902 AAAGATAGCCACAAAGGAATCTTTATAGA-
1 AGAGATAGCCACAAAGGTATCCTTATA-AC
5702931 AGAGAT
1 AGAGAT
5702937 CACCATAAAG
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
28 1 0.02
29 52 0.96
30 1 0.02
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.22
Consensus pattern (29 bp):
AGAGATAGCCACAAAGGTATCCTTATAAC
Found at i:5702946 original size:29 final size:30
Alignment explanation
Indices: 5702890--5702999 Score: 88
Period size: 29 Copynumber: 3.8 Consensus size: 30
5702880 GCCACAAATT
* * *
5702890 CATCCTTATAACAAAGAT-AGCCACAAAGGA
1 CATCTTTATAACAGAGATCA-CCATAAAGGA
5702920 -ATCTTTATAGA-AGAGATCACCATAAA-GA
1 CATCTTTATA-ACAGAGATCACCATAAAGGA
* * *
5702948 CTTTTTTATAACAGAGATTACCATAAAGG-
1 CATCTTTATAACAGAGATCACCATAAAGGA
*
5702977 C-TTTCTTATAACAGAGATCACCA
1 CATCT-TTATAACAGAGATCACCA
5703000 CCGGGGATTT
Statistics
Matches: 67, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
28 6 0.09
29 58 0.87
30 3 0.04
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (30 bp):
CATCTTTATAACAGAGATCACCATAAAGGA
Found at i:5708090 original size:21 final size:21
Alignment explanation
Indices: 5708044--5708088 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
5708034 GTATTTTGAT
5708044 GTTTGATGATAGATTATGAAA
1 GTTTGATGATAGATTATGAAA
5708065 GTTTGATGATAG-TTAT-ACAA
1 GTTTGATGATAGATTATGA-AA
5708085 GTTT
1 GTTT
5708089 TGTTAATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 1 0.04
20 10 0.43
21 12 0.52
ACGTcount: A:0.33, C:0.02, G:0.22, T:0.42
Consensus pattern (21 bp):
GTTTGATGATAGATTATGAAA
Found at i:5715750 original size:21 final size:20
Alignment explanation
Indices: 5715726--5715764 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
5715716 GAGTATTTTG
5715726 ATGTTTGATGATAGATTATGA
1 ATGTTTGATGATA-ATTATGA
5715747 ATGTTTGATGATAATTAT
1 ATGTTTGATGATAATTAT
5715765 ACAAGTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (20 bp):
ATGTTTGATGATAATTATGA
Found at i:5715774 original size:21 final size:21
Alignment explanation
Indices: 5715726--5715772 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
5715716 GAGTATTTTG
*
5715726 ATGTTTGATGATAGATTATGA
1 ATGTTTGATGATAGATTATCA
5715747 ATGTTTGATGATA-ATTATACA
1 ATGTTTGATGATAGATTAT-CA
5715768 A-GTTT
1 ATGTTT
5715773 TGTTAAGTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.34, C:0.02, G:0.19, T:0.45
Consensus pattern (21 bp):
ATGTTTGATGATAGATTATCA
Found at i:5716426 original size:47 final size:44
Alignment explanation
Indices: 5716317--5716442 Score: 141
Period size: 41 Copynumber: 2.8 Consensus size: 44
5716307 TTAGGGATAG
*
5716317 TTATCGAGATAGCTTCGGCTATG---ATTGGCACTTCGTGTGCA
1 TTATCGAGATAGCTTCGGCTATGTATATTGGCACTTCGGGTGCA
* *
5716358 TTATCGAGATGGCTTCAGCTATGTATATTGGCACTTCGGGTGCAAGA
1 TTATCGAGATAGCTTCGGCTATGTATATTGGCACTTCGGGTGC---A
* *
5716405 TTATTGAGATAGCTTCGGCTATATTATTATTGGCACTT
1 TTATCGAGATAGCTTCGGCTAT-GTA-TATTGGCACTT
5716443 ATTGTGTGAG
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
41 21 0.30
44 16 0.23
47 20 0.29
48 2 0.03
49 11 0.16
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.37
Consensus pattern (44 bp):
TTATCGAGATAGCTTCGGCTATGTATATTGGCACTTCGGGTGCA
Found at i:5718318 original size:24 final size:25
Alignment explanation
Indices: 5718291--5718338 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
5718281 GTAATCAACC
* *
5718291 TTTCACCTTTCATCTTCTT-TAACG
1 TTTCACATTTCATCTCCTTATAACG
5718315 TTTCACATTTCATCTCCTTATAAC
1 TTTCACATTTCATCTCCTTATAAC
5718339 CTGTTTACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.21, C:0.29, G:0.02, T:0.48
Consensus pattern (25 bp):
TTTCACATTTCATCTCCTTATAACG
Found at i:5721153 original size:40 final size:40
Alignment explanation
Indices: 5721098--5721179 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
5721088 GTGGCATTAG
5721098 GTGACTTGTTTTGGTAATAAAATAAAATAAAGAAAAAGTT
1 GTGACTTGTTTTGGTAATAAAATAAAATAAAGAAAAAGTT
5721138 GTGACTTGTTTTGGTAATAAAATAAAATAAAGAAAAAGTT
1 GTGACTTGTTTTGGTAATAAAATAAAATAAAGAAAAAGTT
5721178 GT
1 GT
5721180 AATCTTTTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.46, C:0.02, G:0.18, T:0.33
Consensus pattern (40 bp):
GTGACTTGTTTTGGTAATAAAATAAAATAAAGAAAAAGTT
Found at i:5722358 original size:50 final size:50
Alignment explanation
Indices: 5722202--5722521 Score: 238
Period size: 50 Copynumber: 6.6 Consensus size: 50
5722192 TGACATGTGT
* * * * * *
5722202 GCTAGTGTAAGA-CATGCCTGGGACAT-GCATCGACCAC-A-TTATGAGA
1 GCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGAGATATGAAA
* * * * * * * *
5722248 GCCAGTGTAAGACCCTGTCTGGGACATGGCATCGGCAT-TA-AGACGAGA
1 GCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGAGATATGAAA
* * * *
5722296 GCTAATGTAAGACCATGTCTAAGATATGGCATCAGCCTCGAGATATGAAA
1 GCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGAGATATGAAA
* * *
5722346 GCTAGTGTAAGACTATGTCT-GAGACATGGCATCGG-CT--TGATATG--T
1 GCTAGTGTAAGACCATGTCTAG-GACATGGCATCGGCCTCGAGATATGAAA
* * * *
5722391 G-TCAATGTAAGACCATGTCTAGGACATGGCATCGGCATCGACAGATGAAA
1 GCT-AGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGAGATATGAAA
* * * *
5722441 GCCAGTGTAAGACCATGAT-TGGGACATGGCATCGGCCTCGATATATGAGA
1 GCTAGTGTAAGACCATG-TCTAGGACATGGCATCGGCCTCGAGATATGAAA
5722491 G-TCAGTGTAAGACCATGTCTAGGACATGGCA
1 GCT-AGTGTAAGACCATGTCTAGGACATGGCA
5722522 CCGACTTTGA
Statistics
Matches: 213, Mismatches: 44, Indels: 30
0.74 0.15 0.10
Matches are distributed among these distances:
44 1 0.00
45 29 0.14
46 13 0.06
47 18 0.08
48 47 0.22
49 4 0.02
50 100 0.47
51 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.23
Consensus pattern (50 bp):
GCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGAGATATGAAA
Found at i:5722441 original size:95 final size:98
Alignment explanation
Indices: 5722242--5722521 Score: 286
Period size: 95 Copynumber: 2.9 Consensus size: 98
5722232 CGACCACATT
* * * * * * *
5722242 ATGAGAGCCAGTGTAAGACCCTG-TCTGGGACATGGCATCGGCAT-TAAGACGAGAG-CTAATGT
1 ATGAAAGCCAGTGTAAGACCATGAT-TGAGACATGGCATCGGCCTCGAATA-TAGAGTC-AATGT
* * * * *
5722304 AAGACCATGTCTAAGATATGGCATCAGCCTCGAGAT
63 AAGACCATGTCTAGGACATGGCATCAGCATCGACAG
* * * *
5722340 ATGAAAGCTAGTGTAAGACTATG-TCTGAGACATGGCATCGG-CTTG-ATAT-GTGTCAATGTAA
1 ATGAAAGCCAGTGTAAGACCATGAT-TGAGACATGGCATCGGCCTCGAATATAGAGTCAATGTAA
*
5722401 GACCATGTCTAGGACATGGCATCGGCATCGACAG
65 GACCATGTCTAGGACATGGCATCAGCATCGACAG
* *
5722435 ATGAAAGCCAGTGTAAGACCATGATTGGGACATGGCATCGGCCTCGATATATGAGAGTCAGTGTA
1 ATGAAAGCCAGTGTAAGACCATGATTGAGACATGGCATCGGCCTCGA-ATAT-AGAGTCAATGTA
5722500 AGACCATGTCTAGGACATGGCA
64 AGACCATGTCTAGGACATGGCA
5722522 CCGACTTTGA
Statistics
Matches: 152, Mismatches: 22, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
95 73 0.48
96 5 0.03
97 3 0.02
98 40 0.26
100 31 0.20
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (98 bp):
ATGAAAGCCAGTGTAAGACCATGATTGAGACATGGCATCGGCCTCGAATATAGAGTCAATGTAAG
ACCATGTCTAGGACATGGCATCAGCATCGACAG
Found at i:5722479 original size:145 final size:146
Alignment explanation
Indices: 5722247--5722577 Score: 368
Period size: 145 Copynumber: 2.3 Consensus size: 146
5722237 ACATTATGAG
* * * * * *
5722247 AGCCAGTGTAAGACCCTGTCTGGGACATGGCATCGGCAT-TAAGACGAGAGCTAATGTAAGACCA
1 AGCCAATGTAAGACCATGTCTAGGACATGGCATCGGCATCGAAGACGAAAGCCAATGTAAGACCA
* *
5722311 TGTCTAAGATATGGCATCAGCCTCGAGATATGAAAG-CTAGTGTAAGACTATGTCT-GAGACATG
66 TGTCTAAGACATGGCATCAGCCTCGAGATATGAAAGTC-AGTGTAAGACCATGTCTAG-GACATG
* *
5722374 GCATCGGC-TTGATATGT
129 GCACCGACTTTGATATGT
* * *
5722391 -GTCAATGTAAGACCATGTCTAGGACATGGCATCGGCATCGACAGATGAAAGCCAGTGTAAGACC
1 AGCCAATGTAAGACCATGTCTAGGACATGGCATCGGCATCGA-AGACGAAAGCCAATGTAAGACC
** * * *
5722455 ATGAT-TGGGACATGGCATCGGCCTCGATATATGAGAGTCAGTGTAAGACCATGTCTAGGACATG
65 ATG-TCTAAGACATGGCATCAGCCTCGAGATATGAAAGTCAGTGTAAGACCATGTCTAGGACATG
*
5722519 GCACCGACTTTGATGTGT
129 GCACCGACTTTGATATGT
* * * *
5722537 GAGCCAGTGTAAGACCATGTCCAAGACATGGCGTCGGCATC
1 -AGCCAATGTAAGACCATGTCTAGGACATGGCATCGGCATC
5722578 TTACCCTATG
Statistics
Matches: 155, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
143 34 0.22
144 1 0.01
145 75 0.48
146 11 0.07
148 34 0.22
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (146 bp):
AGCCAATGTAAGACCATGTCTAGGACATGGCATCGGCATCGAAGACGAAAGCCAATGTAAGACCA
TGTCTAAGACATGGCATCAGCCTCGAGATATGAAAGTCAGTGTAAGACCATGTCTAGGACATGGC
ACCGACTTTGATATGT
Found at i:5722565 original size:98 final size:96
Alignment explanation
Indices: 5722242--5722574 Score: 280
Period size: 98 Copynumber: 3.4 Consensus size: 96
5722232 CGACCACATT
* * * * ** * * *
5722242 ATGAGAGCCAGTGTAAGACCCTGTCTGGGACATGGCATCGGCATTAAGACGAGAGCTAATGTAAG
1 ATGAAAGCCAGTGTAAGACCATGTCTGAGACATGGCATCGGCCTCGATATGAG-TC-AATGTAAG
* * * * * *
5722307 ACCATGTCTAAGATATGGCATC-AGCCTCGAGAT
64 ACCATGTCTAGGACATGGCACCGA-CATCGACAG
* * * *
5722340 ATGAAAGCTAGTGTAAGACTATGTCTGAGACATGGCATCGG-CTTGATATGTGTCAATGTAAGAC
1 ATGAAAGCCAGTGTAAGACCATGTCTGAGACATGGCATCGGCCTCGATATGAGTCAATGTAAGAC
* *
5722404 CATGTCTAGGACATGGCATCGGCATCGACAG
66 CATGTCTAGGACATGGCACCGACATCGACAG
* *
5722435 ATGAAAGCCAGTGTAAGACCATGAT-TGGGACATGGCATCGGCCTCGATATATGAGAGTCAGTGT
1 ATGAAAGCCAGTGTAAGACCATG-TCTGAGACATGGCATCGGCCTCG--ATAT--GAGTCAATGT
* * *
5722499 AAGACCATGTCTAGGACATGGCACCGACTTTGA-TG
61 AAGACCATGTCTAGGACATGGCACCGACATCGACAG
** ** *
5722534 -TGTGAGCCAGTGTAAGACCATGTCCAAGACATGGCGTCGGC
1 ATGAAAGCCAGTGTAAGACCATGTCTGAGACATGGCATCGGC
5722575 ATCTTACCCT
Statistics
Matches: 193, Mismatches: 34, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
95 70 0.36
96 5 0.03
97 7 0.04
98 73 0.38
99 1 0.01
100 37 0.19
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (96 bp):
ATGAAAGCCAGTGTAAGACCATGTCTGAGACATGGCATCGGCCTCGATATGAGTCAATGTAAGAC
CATGTCTAGGACATGGCACCGACATCGACAG
Found at i:5724947 original size:27 final size:27
Alignment explanation
Indices: 5724914--5724974 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
5724904 TCATGTGTTA
*
5724914 ATATTACTTAGTTTCAAACCATGCTTTT
1 ATATTACTTAGTTTCAAA-CATACTTTT
* *
5724942 -TATTACTTATTTTTAAACATACTTTT
1 ATATTACTTAGTTTCAAACATACTTTT
5724968 ATATTAC
1 ATATTAC
5724975 AATAAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.31, C:0.15, G:0.03, T:0.51
Consensus pattern (27 bp):
ATATTACTTAGTTTCAAACATACTTTT
Found at i:5732606 original size:46 final size:46
Alignment explanation
Indices: 5732556--5732728 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
5732546 TGGTTGAGCA
*
5732556 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
5732602 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
5732649 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
5732695 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
5732729 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 61 0.57
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:5732712 original size:93 final size:93
Alignment explanation
Indices: 5732553--5732723 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
5732543 GGATGGTTGA
* *
5732553 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
5732618 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
5732646 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
5732711 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
5732724 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:5732990 original size:19 final size:20
Alignment explanation
Indices: 5732953--5732990 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
5732943 ATAAGGTGGT
5732953 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
5732973 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
5732991 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:5742127 original size:14 final size:15
Alignment explanation
Indices: 5742101--5742130 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
5742091 AAATATGGAC
5742101 TAAAATATTAAATTT
1 TAAAATATTAAATTT
5742116 TAAAAT-TTAAATTT
1 TAAAATATTAAATTT
5742130 T
1 T
5742131 TTAGTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAAATATTAAATTT
Found at i:5742138 original size:8 final size:8
Alignment explanation
Indices: 5742125--5742161 Score: 51
Period size: 7 Copynumber: 4.9 Consensus size: 8
5742115 TTAAAATTTA
5742125 AATTTTTT
1 AATTTTTT
*
5742133 AGTTTTTT
1 AATTTTTT
5742141 AA-TTTTT
1 AATTTTTT
5742148 AA-TTTTT
1 AATTTTTT
5742155 AATTTTT
1 AATTTTT
5742162 GAGTTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
7 14 0.54
8 12 0.46
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (8 bp):
AATTTTTT
Found at i:5742146 original size:6 final size:7
Alignment explanation
Indices: 5742136--5742161 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5742126 ATTTTTTAGT
5742136 TTTTTAA
1 TTTTTAA
5742143 TTTTTAA
1 TTTTTAA
5742150 TTTTTAA
1 TTTTTAA
5742157 TTTTT
1 TTTTT
5742162 GAGTTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTAA
Found at i:5742146 original size:30 final size:30
Alignment explanation
Indices: 5742111--5742167 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
5742101 TAAAATATTA
*
5742111 AATTTTAAAATTTAAATTTTTTAGTTTTTT
1 AATTTTAAAATTTAAATTTTTGAGTTTTTT
* * *
5742141 AATTTTTAATTTTTAATTTTTGAGTTT
1 AATTTTAAAATTTAAATTTTTGAGTTT
5742168 ATTTTTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (30 bp):
AATTTTAAAATTTAAATTTTTGAGTTTTTT
Found at i:5742652 original size:66 final size:66
Alignment explanation
Indices: 5742537--5742666 Score: 179
Period size: 66 Copynumber: 2.0 Consensus size: 66
5742527 TAAGGTTTGT
* * * *
5742537 TGTTTAGAGTTTTAAGGGTTTATGATTTGATATTTAGGGTCTGGTGTTTAAAGAGTTATTGATTA
1 TGTTTAGAGTTTTAAGGGTTTATGATTAGAGATTTAAGGTCTGGGGTTTAAAGAGTTATTGATTA
5742602 G
66 G
* * * * *
5742603 TGTTTATAGTTTTAGGGGTTTATGATTAGAGATTTAAGGTTTGGGGTTTAAAGGGTTGTTGATT
1 TGTTTAGAGTTTTAAGGGTTTATGATTAGAGATTTAAGGTCTGGGGTTTAAAGAGTTATTGATT
5742667 TAAAGGGTTA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.23, C:0.01, G:0.29, T:0.47
Consensus pattern (66 bp):
TGTTTAGAGTTTTAAGGGTTTATGATTAGAGATTTAAGGTCTGGGGTTTAAAGAGTTATTGATTA
G
Found at i:5743277 original size:16 final size:17
Alignment explanation
Indices: 5743258--5743316 Score: 58
Period size: 16 Copynumber: 3.8 Consensus size: 17
5743248 ATGTTTTTTG
5743258 GGGTTT-AGGGTTTTAA
1 GGGTTTAAGGGTTTTAA
*
5743274 GGG-TT-ATGG-TTT-A
1 GGGTTTAAGGGTTTTAA
*
5743287 GGGTTTAAGGTTTTTAA
1 GGGTTTAAGGGTTTTAA
5743304 -GGTTTAAGGGTTT
1 GGGTTTAAGGGTTT
5743317 AGTATTTTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
13 4 0.11
14 5 0.14
15 7 0.20
16 18 0.51
17 1 0.03
ACGTcount: A:0.19, C:0.00, G:0.36, T:0.46
Consensus pattern (17 bp):
GGGTTTAAGGGTTTTAA
Found at i:5743363 original size:18 final size:18
Alignment explanation
Indices: 5743337--5743371 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5743327 GGGTTATAGA
* *
5743337 TTAGTGTTTATGATTTTT
1 TTAGGGTTTAGGATTTTT
5743355 TTAGGGTTTAGGATTTT
1 TTAGGGTTTAGGATTTT
5743372 AGGGGTTATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.23, T:0.60
Consensus pattern (18 bp):
TTAGGGTTTAGGATTTTT
Found at i:5743431 original size:41 final size:40
Alignment explanation
Indices: 5743386--5743499 Score: 129
Period size: 41 Copynumber: 2.8 Consensus size: 40
5743376 GTTATATGAG
*
5743386 TTTTAGCAGCGTTTTATCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCAGCGTTTTA-CAAAAGCGCCGCTAATGCTCTAGT
* * * *
5743427 TTTTAGCAGCGTTTTACAGAAAGCACCGCCATTGCTCTATT
1 TTTTAGCAGCGTTTTACA-AAAGCGCCGCTAATGCTCTAGT
* **
5743468 TTTTAGCGGCGTTTTACCAAAAATGCCGCTAA
1 TTTTAGCAGCGTTTTA-CAAAAGCGCCGCTAA
5743500 AGCCCTATTT
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
40 2 0.03
41 56 0.93
42 2 0.03
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (40 bp):
TTTTAGCAGCGTTTTACAAAAGCGCCGCTAATGCTCTAGT
Found at i:5748178 original size:19 final size:21
Alignment explanation
Indices: 5748154--5748192 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
5748144 AAATTACCTG
5748154 GATGAAGAA-GGA-GAAGGAA
1 GATGAAGAACGGACGAAGGAA
5748173 GATGAAGAACGGACGAAGGA
1 GATGAAGAACGGACGAAGGA
5748193 GGAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 3 0.17
21 6 0.33
ACGTcount: A:0.49, C:0.05, G:0.41, T:0.05
Consensus pattern (21 bp):
GATGAAGAACGGACGAAGGAA
Found at i:5750306 original size:27 final size:26
Alignment explanation
Indices: 5750269--5750383 Score: 122
Period size: 27 Copynumber: 4.3 Consensus size: 26
5750259 AGCATGGCTG
*
5750269 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGTCA
* *
5750295 CCAGATACAGATAATCGGGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGTCA
5750323 CCAGAACAGATATATGTGGCAGAGTCA
1 CCAGAACAGATA-ATGTGGCAGAGTCA
* * * * *
5750350 CCAGATCAAATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGTCA
5750377 CCAGAAC
1 CCAGAAC
5750384 GCTTCCTCCA
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
26 5 0.07
27 54 0.72
28 16 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGTCA
Found at i:5750328 original size:54 final size:54
Alignment explanation
Indices: 5750269--5750383 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
5750259 AGCATGGCTG
*
5750269 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGGGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGTCACCAGAT-CAAATAATCGGGGCAGAGCCA
* * * * *
5750323 CCAGAACAGATATATGTGGCAGAGTCACCAGATCAAATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGTCACCAGATCAAATAATCGGGGCAGAGCCA
5750377 CCAGAAC
1 CCAGAAC
5750384 GCTTCCTCCA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 35 0.65
55 19 0.35
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGTCACCAGATCAAATAATCGGGGCAGAGCCA
Found at i:5751521 original size:26 final size:26
Alignment explanation
Indices: 5751483--5751644 Score: 263
Period size: 26 Copynumber: 6.2 Consensus size: 26
5751473 CATGAAATTC
5751483 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
5751509 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
5751535 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
5751561 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
5751587 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
5751613 TTATCATTG-AACATTTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCCA
5751639 TTATCA
1 TTATCA
5751645 ATTTGTACCA
Statistics
Matches: 132, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
26 130 0.98
27 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:5756839 original size:23 final size:24
Alignment explanation
Indices: 5756794--5756840 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
5756784 CTTACTCTCT
*
5756794 AAAACTCTTTCAAATTTAGAAAAA
1 AAAACTCTTTCAAATTTAAAAAAA
5756818 AAAACTCTTTCAAA-TTAAAAAAA
1 AAAACTCTTTCAAATTTAAAAAAA
5756841 TATAAAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAACTCTTTCAAATTTAAAAAAA
Found at i:5760949 original size:17 final size:17
Alignment explanation
Indices: 5760923--5760964 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
5760913 ATTGCATCGG
*
5760923 AGGATTCATGAACTTGA
1 AGGATACATGAACTTGA
*
5760940 AGGATACATGTACTTGA
1 AGGATACATGAACTTGA
5760957 A-GATACAT
1 AGGATACAT
5760965 CGCATAGGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (17 bp):
AGGATACATGAACTTGA
Found at i:5765359 original size:27 final size:27
Alignment explanation
Indices: 5765320--5765372 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
5765310 TCCTATTAAC
* *
5765320 CTTTTTGGAACACTTTGAAAGGAATGG
1 CTTTGTGGAACACTCTGAAAGGAATGG
*
5765347 CTTTGTGGCACACTCTGAAAGGAATG
1 CTTTGTGGAACACTCTGAAAGGAATG
5765373 CCTTATCGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (27 bp):
CTTTGTGGAACACTCTGAAAGGAATGG
Found at i:5770657 original size:31 final size:31
Alignment explanation
Indices: 5770622--5770681 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
5770612 AATAGTATTT
5770622 TATTAATTTAATATTGAAGTGATTATCTTAA
1 TATTAATTTAATATTGAAGTGATTATCTTAA
5770653 TATTAATTTAATATTGAAGTGATTATCTT
1 TATTAATTTAATATTGAAGTGATTATCTT
5770682 GATAAATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.03, G:0.10, T:0.50
Consensus pattern (31 bp):
TATTAATTTAATATTGAAGTGATTATCTTAA
Found at i:5771258 original size:11 final size:11
Alignment explanation
Indices: 5771242--5771281 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
5771232 AAGACTTAGT
5771242 ATGATAAGAGA
1 ATGATAAGAGA
*
5771253 ATGATAACGAGC
1 ATGATAA-GAGA
5771265 AT-ATAAGAGA
1 ATGATAAGAGA
5771275 ATGATAA
1 ATGATAA
5771282 AATTGTAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 5 0.20
11 15 0.60
12 5 0.20
ACGTcount: A:0.53, C:0.05, G:0.23, T:0.20
Consensus pattern (11 bp):
ATGATAAGAGA
Found at i:5771897 original size:40 final size:40
Alignment explanation
Indices: 5771840--5771938 Score: 162
Period size: 42 Copynumber: 2.4 Consensus size: 40
5771830 AATTGAGGTT
* *
5771840 AAAAAAAGAAAGAAAAAAAATAAGAGAGGTCGAGAGAAAG
1 AAAAAAACAAGGAAAAAAAATAAGAGAGGTCGAGAGAAAG
5771880 AAAAAAACAAGGTAAAAAAAAATAAGAGAGGTCGAGAGAAAG
1 AAAAAAACAAGG--AAAAAAAATAAGAGAGGTCGAGAGAAAG
5771922 AAAAAAACAAGGAAAAA
1 AAAAAAACAAGGAAAAA
5771939 TTGAAAAAGA
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
40 15 0.27
42 40 0.73
ACGTcount: A:0.69, C:0.04, G:0.22, T:0.05
Consensus pattern (40 bp):
AAAAAAACAAGGAAAAAAAATAAGAGAGGTCGAGAGAAAG
Found at i:5771899 original size:42 final size:41
Alignment explanation
Indices: 5771852--5771938 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 41
5771842 AAAAAGAAAG
5771852 AAAAAAAATAAGAGAGGTCGAGAGAAAGAAAAAAACAAGGTA
1 AAAAAAAATAAGAGAGGTCGAGAGAAAGAAAAAAACAAGG-A
5771894 AAAAAAAATAAGAGAGGTCGAGAGAAAGAAAAAAACAAGGA
1 AAAAAAAATAAGAGAGGTCGAGAGAAAGAAAAAAACAAGGA
5771935 AAAA
1 AAAA
5771939 TTGAAAAAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 5 0.11
42 40 0.89
ACGTcount: A:0.67, C:0.05, G:0.23, T:0.06
Consensus pattern (41 bp):
AAAAAAAATAAGAGAGGTCGAGAGAAAGAAAAAAACAAGGA
Found at i:5777432 original size:49 final size:49
Alignment explanation
Indices: 5777369--5777509 Score: 129
Period size: 49 Copynumber: 2.9 Consensus size: 49
5777359 ACTGGCTAGC
* * *
5777369 ATATCAAAGTCGATGCCATGTACCAAACAGGTCTTACACTGACTTTTAT
1 ATATCAAAGTCGATGCCATGTACCAGACAGGTCTTACACTGACTCTCAT
* * * * * * * *
5777418 ATATCAAGGCCGATGTCGTGTTCTAGACAAGTCTTACACTGGCTCTCAT
1 ATATCAAAGTCGATGCCATGTACCAGACAGGTCTTACACTGACTCTCAT
* ** * * *
5777467 CTATTGATGTCGATGCCATGTCCCAGACAGGTCTTAAACTGAC
1 ATATCAAAGTCGATGCCATGTACCAGACAGGTCTTACACTGAC
5777510 ACACAACAAG
Statistics
Matches: 69, Mismatches: 23, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
49 69 1.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (49 bp):
ATATCAAAGTCGATGCCATGTACCAGACAGGTCTTACACTGACTCTCAT
Found at i:5777598 original size:48 final size:45
Alignment explanation
Indices: 5777527--5777647 Score: 136
Period size: 46 Copynumber: 2.6 Consensus size: 45
5777517 AAGCTGACGC
*
5777527 CATGTCCCAGACAGGTCTTACACTAGCCT-ATATATCTCGAGACCGATG
1 CATGTCCCAGACATGTCTTACACTAGCCTCATA-ATCT-G-G-CCGATG
* * * *
5777575 CATGTCCCAAACATGTCTTACACTTGCCCTCATAATGTGGGCGATG
1 CATGTCCCAGACATGTCTTACACTAG-CCTCATAATCTGGCCGATG
*
5777621 CATGTCTCAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
5777648 ACACATATCA
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
45 1 0.02
46 28 0.44
47 1 0.02
48 24 0.38
49 6 0.10
50 3 0.05
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (45 bp):
CATGTCCCAGACATGTCTTACACTAGCCTCATAATCTGGCCGATG
Found at i:5784460 original size:17 final size:18
Alignment explanation
Indices: 5784433--5784466 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
5784423 CAAAGGTTTT
5784433 TTTTTTGTTTTTTTTGGC
1 TTTTTTGTTTTTTTTGGC
5784451 TTTTTT-TTTTTTTTGG
1 TTTTTTGTTTTTTTTGG
5784467 TATTTGGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (18 bp):
TTTTTTGTTTTTTTTGGC
Found at i:5787345 original size:118 final size:118
Alignment explanation
Indices: 5787166--5787487 Score: 493
Period size: 118 Copynumber: 2.7 Consensus size: 118
5787156 TTCTTCATGC
* * * * * * *
5787166 TTTTCAGAGAATTCGTATGTAAATTTAAACATTCACCAACTGCTAAGTGCTGACCTTATTTGTGA
1 TTTTCATAGAATTCATATGTAAATTTGAACACTCAGCAAAT--TAAGTGCTAACCTTATTTGTGA
* * * *
5787231 TTACTATTAGTCAAATCAGTTTGCAATTGGCACTGATTTCTTTTTATATTTGTGA
64 TTATTACTAGTCAAATCAGTTTGCAATTGGCACTGATTTATTTTCATATTTGTGA
*
5787286 TTTTCATAGAATTCATATGTAAATTTGAACACTCAGTAAATTAAGTGCTAACCTTATTTGTGATT
1 TTTTCATAGAATTCATATGTAAATTTGAACACTCAGCAAATTAAGTGCTAACCTTATTTGTGATT
*
5787351 ATTACTAGTCAAATCACTTTGCAATTGGCACTGATTTATTTTCATATTTGTGA
66 ATTACTAGTCAAATCAGTTTGCAATTGGCACTGATTTATTTTCATATTTGTGA
*
5787404 TTTTCATAGAATTCATATGTAAATTTGAACACTCAGCAAATTAAGTGCTAACCTTATTTGGGATT
1 TTTTCATAGAATTCATATGTAAATTTGAACACTCAGCAAATTAAGTGCTAACCTTATTTGTGATT
5787469 ATTACTAGTCAAAT-AGTTT
66 ATTACTAGTCAAATCAGTTT
5787488 CATATTTGTG
Statistics
Matches: 186, Mismatches: 16, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
117 4 0.02
118 148 0.80
120 34 0.18
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (118 bp):
TTTTCATAGAATTCATATGTAAATTTGAACACTCAGCAAATTAAGTGCTAACCTTATTTGTGATT
ATTACTAGTCAAATCAGTTTGCAATTGGCACTGATTTATTTTCATATTTGTGA
Found at i:5788979 original size:15 final size:15
Alignment explanation
Indices: 5788959--5789008 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 15
5788949 ATTATTAACG
5788959 AATAACATATAATAT
1 AATAACATATAATAT
5788974 AATAACATATAAACTAACT
1 AATAACATAT-AA-T-A-T
5788993 AATAACATTATAATAT
1 AATAACA-TATAATAT
5789009 GCAATGGCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
15 10 0.33
16 3 0.10
17 2 0.07
18 2 0.07
19 10 0.33
20 3 0.10
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (15 bp):
AATAACATATAATAT
Found at i:5790299 original size:18 final size:19
Alignment explanation
Indices: 5790262--5790302 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5790252 TCTCAATTCA
* *
5790262 TCATTTCATATTTAATTTC
1 TCATCTCATAATTAATTTC
5790281 TCATCTCATAATT-ATTTC
1 TCATCTCATAATTAATTTC
5790299 TCAT
1 TCAT
5790303 ATTTGTCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.54
Consensus pattern (19 bp):
TCATCTCATAATTAATTTC
Found at i:5790327 original size:43 final size:43
Alignment explanation
Indices: 5790277--5790362 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 43
5790267 TCATATTTAA
5790277 TTTCTCATCTCATAATT-ATTTCTCATATTTGT-CATTTCAATAT
1 TTTCTCATCTCAT-ATTCATTTCTCATATTT-TCCATTTCAATAT
*
5790320 TTTCTCATCTCATATTCATTTCTCATCTTTTCCATTTCAATAT
1 TTTCTCATCTCATATTCATTTCTCATATTTTCCATTTCAATAT
5790363 CAATCACATA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
42 4 0.10
43 36 0.90
ACGTcount: A:0.23, C:0.22, G:0.01, T:0.53
Consensus pattern (43 bp):
TTTCTCATCTCATATTCATTTCTCATATTTTCCATTTCAATAT
Found at i:5791544 original size:19 final size:19
Alignment explanation
Indices: 5791506--5791544 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
5791496 ATTTATGTTC
* *
5791506 TAAGTATAAATTCTATTTT
1 TAAGTATAAATTATACTTT
5791525 TAAGTATAAATTATACTTT
1 TAAGTATAAATTATACTTT
5791544 T
1 T
5791545 CGAAATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (19 bp):
TAAGTATAAATTATACTTT
Found at i:5793227 original size:5 final size:5
Alignment explanation
Indices: 5793211--5793241 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
5793201 TATATATATA
*
5793211 TGAAT TGGAT TGAAT TGAAT TGAAT TGAAT T
1 TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT T
5793242 TAAATGAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (5 bp):
TGAAT
Found at i:5793657 original size:10 final size:10
Alignment explanation
Indices: 5793625--5793658 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
5793615 TCTAAACCAT
*
5793625 GGCAAAATAG
1 GGCAAAACAG
*
5793635 GGAAAAACAG
1 GGCAAAACAG
5793645 GGCAAAACAG
1 GGCAAAACAG
5793655 GGCA
1 GGCA
5793659 TACATATTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.50, C:0.15, G:0.32, T:0.03
Consensus pattern (10 bp):
GGCAAAACAG
Found at i:5796159 original size:38 final size:38
Alignment explanation
Indices: 5796108--5796183 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
5796098 TATTACAGTA
5796108 TGAATATGTGAATGTGAATGATTTAGGATGTAAAAATG
1 TGAATATGTGAATGTGAATGATTTAGGATGTAAAAATG
5796146 TGAATATGTGAATGTGAATGATTTAGGATGTAAAAATG
1 TGAATATGTGAATGTGAATGATTTAGGATGTAAAAATG
5796184 CGAAGCAACC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.39, C:0.00, G:0.26, T:0.34
Consensus pattern (38 bp):
TGAATATGTGAATGTGAATGATTTAGGATGTAAAAATG
Found at i:5796640 original size:56 final size:57
Alignment explanation
Indices: 5796579--5796703 Score: 144
Period size: 56 Copynumber: 2.2 Consensus size: 57
5796569 TCTTATAAAA
* * * * * **
5796579 TGATAATGGAGTATGAAATTGAAATGAAATACGTGAATTTAGTATGAGTTTAT-GAT
1 TGATAATAGAATATAAAATTAAAATGAAATACGTGAAATTAGTATGAACTTATGGAT
* * * *
5796635 TGATAATAGAATTTAAAATTAAAATGAATTATGTGAAATTGGTATGAACTTATGGAT
1 TGATAATAGAATATAAAATTAAAATGAAATACGTGAAATTAGTATGAACTTATGGAT
5796692 TGATAATAGAAT
1 TGATAATAGAAT
5796704 TTGATATAGG
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
56 42 0.74
57 15 0.26
ACGTcount: A:0.42, C:0.02, G:0.20, T:0.36
Consensus pattern (57 bp):
TGATAATAGAATATAAAATTAAAATGAAATACGTGAAATTAGTATGAACTTATGGAT
Found at i:5796718 original size:57 final size:56
Alignment explanation
Indices: 5796594--5796736 Score: 171
Period size: 57 Copynumber: 2.5 Consensus size: 56
5796584 ATGGAGTATG
* * * * * **
5796594 AAATTGAAATGAAATACGTGAATTTAGTATGAGTTTATGATTGATAATAGAATTTA
1 AAATTAAAATGAATTATGTGAAATTGGTATGAACTTATGATTGATAATAGAATTTA
*
5796650 AAATTAAAATGAATTATGTGAAATTGGTATGAACTTATGGATTGATAATAGAATTTG
1 AAATTAAAATGAATTATGTGAAATTGGTATGAACTTAT-GATTGATAATAGAATTTA
* *
5796707 ATA-TAGGAATGAATTATGTGAAATTGGTAT
1 AAATTA-AAATGAATTATGTGAAATTGGTAT
5796737 ATGCTAATAG
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
56 33 0.44
57 42 0.56
ACGTcount: A:0.42, C:0.01, G:0.20, T:0.37
Consensus pattern (56 bp):
AAATTAAAATGAATTATGTGAAATTGGTATGAACTTATGATTGATAATAGAATTTA
Found at i:5800834 original size:39 final size:39
Alignment explanation
Indices: 5800790--5800867 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
5800780 CTTGTGCGTT
*
5800790 TGAATGAAATGGTGTAATTGATGTAGTGTATATATATAA
1 TGAATGAAATAGTGTAATTGATGTAGTGTATATATATAA
*
5800829 TGAATGAAATAGTGTAATTGATGTAGTGTATATGTATAA
1 TGAATGAAATAGTGTAATTGATGTAGTGTATATATATAA
5800868 GATGTATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (39 bp):
TGAATGAAATAGTGTAATTGATGTAGTGTATATATATAA
Found at i:5811983 original size:21 final size:22
Alignment explanation
Indices: 5811937--5811993 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
5811927 CATATAACAT
*
5811937 AATAGAAAAAAATATAAGTAAG
1 AATAGTAAAAAATATAAGTAAG
** *
5811959 AATA-TAAAAAATATATTTAAT
1 AATAGTAAAAAATATAAGTAAG
*
5811980 AATAGTAAATAATA
1 AATAGTAAAAAATA
5811994 AATAAATATA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (22 bp):
AATAGTAAAAAATATAAGTAAG
Found at i:5812032 original size:8 final size:8
Alignment explanation
Indices: 5812019--5812054 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
5812009 TAATGATTTT
*
5812019 TATTATTA
1 TATTATAA
5812027 TATTATAA
1 TATTATAA
5812035 TATTATAA
1 TATTATAA
5812043 TATTAATAA
1 TATT-ATAA
5812052 TAT
1 TAT
5812055 ATTATTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
8 19 0.73
9 7 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TATTATAA
Found at i:5826269 original size:20 final size:19
Alignment explanation
Indices: 5826244--5826302 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
5826234 ACTAAAGGGC
5826244 ATTTTTTATGCAATTTTATA
1 ATTTTTTATG-AATTTTATA
*
5826264 ATTTTTTATGATTTTTATA
1 ATTTTTTATGAATTTTATA
** *
5826283 AAATTTTAT-AATTTTTTA
1 ATTTTTTATGAATTTTATA
5826301 AT
1 AT
5826303 ATATTTTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 8 0.24
19 15 0.45
20 10 0.30
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (19 bp):
ATTTTTTATGAATTTTATA
Found at i:5826270 original size:10 final size:10
Alignment explanation
Indices: 5826257--5826357 Score: 63
Period size: 9 Copynumber: 10.5 Consensus size: 10
5826247 TTTTATGCAA
5826257 TTTTATAATT
1 TTTTATAATT
*
5826267 TTTTATGA-T
1 TTTTATAATT
**
5826276 TTTTATAAAA
1 TTTTATAATT
5826286 TTTTATAATT
1 TTTTATAATT
5826296 TTTTA-ATATAT
1 TTTTATA-AT-T
5826307 TTTTAT-ATT
1 TTTTATAATT
* *
5826316 TATTACGAATT
1 TTTTA-TAATT
*
5826327 TTATAT-A-T
1 TTTTATAATT
*
5826335 TTTT-TAATA
1 TTTTATAATT
5826344 TTTTAT-ATT
1 TTTTATAATT
5826353 TTTTA
1 TTTTA
5826358 ATTAAAATTT
Statistics
Matches: 69, Mismatches: 13, Indels: 19
0.68 0.13 0.19
Matches are distributed among these distances:
7 1 0.01
8 5 0.07
9 26 0.38
10 25 0.36
11 12 0.17
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (10 bp):
TTTTATAATT
Found at i:5826279 original size:19 final size:17
Alignment explanation
Indices: 5826256--5826360 Score: 75
Period size: 17 Copynumber: 5.6 Consensus size: 17
5826246 TTTTTATGCA
*
5826256 ATTTTATAATTTTTTAT
1 ATTTTTTAATTTTTTAT
**
5826273 GATTTTTATAAAATTTTAT
1 -ATTTTT-TAATTTTTTAT
5826292 AATTTTTTAATATATTTTTAT
1 -ATTTTTT-A-AT-TTTTTAT
* *
5826313 ATTTATTACGAATTTTATAT
1 ATTT-TT--TAATTTTTTAT
*
5826333 ATTTTTTAATATTTTAT
1 ATTTTTTAATTTTTTAT
5826350 ATTTTTTAATT
1 ATTTTTTAATT
5826361 AAAATTTAAT
Statistics
Matches: 68, Mismatches: 12, Indels: 15
0.72 0.13 0.16
Matches are distributed among these distances:
17 18 0.26
18 6 0.09
19 18 0.26
20 15 0.22
21 10 0.15
22 1 0.01
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (17 bp):
ATTTTTTAATTTTTTAT
Found at i:5826367 original size:40 final size:37
Alignment explanation
Indices: 5826255--5826377 Score: 122
Period size: 40 Copynumber: 3.2 Consensus size: 37
5826245 TTTTTTATGC
* *
5826255 AATTTTATAATTTTTTATGATTTTTA-TAAAATTTTAT
1 AATTTTTTAATATTTTAT-ATTTTTATTAAAATTTTAT
* * *
5826292 AATTTTTTAATATATTTTTATATTTATTACGAATTTTAT
1 AATTTTTTAATAT-TTTATATTTTTATTA-AAATTTTAT
*
5826331 ATATTTTTTAATATTTTATATTTTTTAATTAAAATTTAAT
1 A-ATTTTTTAATATTTTATA-TTTTT-ATTAAAATTTTAT
*
5826371 AACTTTT
1 AATTTTT
5826378 ATAACTTTTA
Statistics
Matches: 70, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
37 17 0.24
38 6 0.09
39 19 0.27
40 24 0.34
41 4 0.06
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (37 bp):
AATTTTTTAATATTTTATATTTTTATTAAAATTTTAT
Found at i:5828371 original size:7 final size:7
Alignment explanation
Indices: 5828339--5828370 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
5828329 TTATATACAT
5828339 AATACTA
1 AATACTA
5828346 AATACTA
1 AATACTA
5828353 AATACTA
1 AATACTA
*
5828360 AATATTA
1 AATACTA
5828367 AATA
1 AATA
5828371 TGAAATTGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.31
Consensus pattern (7 bp):
AATACTA
Found at i:5828703 original size:242 final size:245
Alignment explanation
Indices: 5828267--5828748 Score: 844
Period size: 242 Copynumber: 2.0 Consensus size: 245
5828257 TATTTACTGC
*
5828267 CCGAATTGCCGAATCCTTGTATGGTTTCCATTAAAACTATATAAACATGATAAAAATATTAGTTA
1 CCGAATTGCCGAATCCTCGTATGGTTTCCATTAAAACTATATAAACATGATAAAAATATTAGTTA
5828332 TATACATAATACTAAATACTAAATACTAAATATTAAATATGAAATTGACTGTGTTATGTGTATAT
66 TATAC---A-ACTAAATACTAAATACTAAATATTAAATATGAAATTGACTGTGTTATGTGTATAT
*
5828397 ATAGTTCAAAATGAAATAAATACTTACATGCGCTTCCAACCGTTGGTCTAATAGAAGCCGTATAT
127 ATAGTTCAAAATGAAATAAATACCTACATGCGCTTCCAACCGTTGGTCTAATAGAAGCCGTATAT
* *
5828462 CTTCAAGAGCAGTAGGTATTCCCTCGTAACTCAACAAATGGTTCCCCCGAATTG
192 CTTCAAGAGCAATAGGTATTCCCCCGTAACTCAACAAATGGTTCCCCCGAATTG
*
5828516 CCGAATTGCCGAATCCTCGTATGGTTTCCATTAAAACTATATAAACGTGATAAAAATATTAGTTA
1 CCGAATTGCCGAATCCTCGTATGGTTTCCATTAAAACTATATAAACATGATAAAAATATTAGTTA
5828581 TATAC-A-T-AATACTAAATACTAAATATTAAATATGAAATTGACTGTGTTATGTGTATATATAG
66 TATACAACTAAATACTAAATACTAAATATTAAATATGAAATTGACTGTGTTATGTGTATATATAG
* *
5828643 TTCAAAATGAAATAAATACCTACATGCGCTTCCAATCGTTGGTCTAATAGAAGTCGTATATCTTC
131 TTCAAAATGAAATAAATACCTACATGCGCTTCCAACCGTTGGTCTAATAGAAGCCGTATATCTTC
5828708 AAGAGCAATAGGTATTCCCCCGTAACTCAACAAATGGTTCC
196 AAGAGCAATAGGTATTCCCCCGTAACTCAACAAATGGTTCC
5828749 ACTTATTTAA
Statistics
Matches: 226, Mismatches: 7, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
242 156 0.69
243 1 0.00
244 1 0.00
249 68 0.30
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (245 bp):
CCGAATTGCCGAATCCTCGTATGGTTTCCATTAAAACTATATAAACATGATAAAAATATTAGTTA
TATACAACTAAATACTAAATACTAAATATTAAATATGAAATTGACTGTGTTATGTGTATATATAG
TTCAAAATGAAATAAATACCTACATGCGCTTCCAACCGTTGGTCTAATAGAAGCCGTATATCTTC
AAGAGCAATAGGTATTCCCCCGTAACTCAACAAATGGTTCCCCCGAATTG
Found at i:5831394 original size:27 final size:26
Alignment explanation
Indices: 5831357--5831468 Score: 161
Period size: 27 Copynumber: 4.2 Consensus size: 26
5831347 AGCATGGCTG
*
5831357 CCAGAACAGATAATGTGACAGAGCCA
1 CCAGAACAGATAATGTGGCAGAGCCA
5831383 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
5831411 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
5831438 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
5831465 CCAG
1 CCAG
5831469 GACGCTTCCT
Statistics
Matches: 79, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
26 6 0.08
27 55 0.70
28 18 0.23
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:5831421 original size:54 final size:54
Alignment explanation
Indices: 5831357--5831468 Score: 181
Period size: 54 Copynumber: 2.1 Consensus size: 54
5831347 AGCATGGCTG
5831357 CCAGAACAGATA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * *
5831411 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
5831465 CCAG
1 CCAG
5831469 GACGCTTCCT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
54 35 0.65
55 19 0.35
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:5833121 original size:26 final size:26
Alignment explanation
Indices: 5833090--5833197 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
5833080 TGAAATGCCC
*
5833090 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
5833116 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
5833142 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
5833168 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
5833194 ATCA
1 ATCA
5833198 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:5837464 original size:16 final size:16
Alignment explanation
Indices: 5837439--5837470 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5837429 CATTCTTTAT
*
5837439 AAAATTTTTGTTTTTG
1 AAAATCTTTGTTTTTG
5837455 AAAATCTTTGTTTTTG
1 AAAATCTTTGTTTTTG
5837471 TAAACCCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.03, G:0.12, T:0.59
Consensus pattern (16 bp):
AAAATCTTTGTTTTTG
Found at i:5840206 original size:26 final size:26
Alignment explanation
Indices: 5840175--5840282 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
5840165 TGAAATGCCC
*
5840175 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
5840201 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
5840227 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
5840253 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
5840279 ATCA
1 ATCA
5840283 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:5844806 original size:38 final size:38
Alignment explanation
Indices: 5844755--5844954 Score: 310
Period size: 38 Copynumber: 5.3 Consensus size: 38
5844745 ATATTCGATG
*
5844755 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
*
5844793 TATATCCAGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
* * *
5844831 TATATCCGAGTTAAATCCCACAGGCTTTGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
*
5844869 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
* * *
5844907 TATATCCGGGTTAAATCCCGCAGGCCTAGTGCTGATAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
*
5844945 TATATTCGGG
1 TATATCCGGG
5844955 CCTTCGTGCC
Statistics
Matches: 147, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 147 1.00
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.31
Consensus pattern (38 bp):
TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
Found at i:5844995 original size:43 final size:43
Alignment explanation
Indices: 5844947--5845230 Score: 559
Period size: 43 Copynumber: 6.6 Consensus size: 43
5844937 GCTGATATTA
*
5844947 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGGTGTG
5844990 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGGTGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGGTGTG
5845033 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGGTGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGGTGTG
5845076 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGGTGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGGTGTG
5845119 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGGTGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGGTGTG
5845162 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGGTGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGGTGTG
5845205 TATTCGGGCCTTCGTGCCTAGCAGGC
1 TATTCGGGCCTTCGTGCCTAGCAGGC
5845231 GTAATGCTGG
Statistics
Matches: 240, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 240 1.00
ACGTcount: A:0.08, C:0.26, G:0.36, T:0.30
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGGTGTG
Found at i:5848579 original size:27 final size:26
Alignment explanation
Indices: 5848544--5848658 Score: 158
Period size: 27 Copynumber: 4.3 Consensus size: 26
5848534 AGCATGGCTG
* *
5848544 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
5848570 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
5848598 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
5848625 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
5848652 CCAGAAC
1 CCAGAAC
5848659 GCTTCCTCCA
Statistics
Matches: 80, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
26 6 0.08
27 57 0.71
28 17 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.16
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:5848603 original size:54 final size:54
Alignment explanation
Indices: 5848544--5848658 Score: 178
Period size: 54 Copynumber: 2.1 Consensus size: 54
5848534 AGCATGGCTG
*
5848544 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * *
5848598 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
5848652 CCAGAAC
1 CCAGAAC
5848659 GCTTCCTCCA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
54 38 0.68
55 18 0.32
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.16
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:5851844 original size:48 final size:48
Alignment explanation
Indices: 5851773--5851867 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
5851763 TATGGAAAGA
5851773 TAGAATGAAACAAATGATAGCCATTTTCTTTTCTTTAATTTTGACTTT
1 TAGAATGAAACAAATGATAGCCATTTTCTTTTCTTTAATTTTGACTTT
*
5851821 TAGAATGAAA-ATGATGATAGCCATTTTCTTTTCTTTAATTTTGACTT
1 TAGAATGAAACA-AATGATAGCCATTTTCTTTTCTTTAATTTTGACTT
5851868 ATTTTGATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
47 1 0.02
48 44 0.98
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.46
Consensus pattern (48 bp):
TAGAATGAAACAAATGATAGCCATTTTCTTTTCTTTAATTTTGACTTT
Found at i:5858202 original size:426 final size:427
Alignment explanation
Indices: 5857408--5858260 Score: 1555
Period size: 426 Copynumber: 2.0 Consensus size: 427
5857398 CTGCAGGTTT
* *
5857408 GTTTAGAAAGGAAATCAGCTTTGAGCGTGAAAAACTAACAAAAGGAAAATAACATACCTGCTGTC
1 GTTTAGAAAGGAAATCAGCTTTGAGCGCGAAAAACTAACAAAAGGAAAATAACATACCTGCTGCC
5857473 TGGGTTGTGGAAGTTCTACCTCTGGACAATGATTAAGGGTTGCAATTGAAGCTTGGAAGTTGCTT
66 TGGGTTGTGGAAGTTCTACCTCTGGACAATGATTAAGGGTTGCAATTGAAGCTTGGAAGTTGCTT
5857538 TTGGTGTTTGATTTGGTAAAAGTTTGATAGGTTTAAGAAACTGATTTATGGTCTGTAATTCTTGA
131 TTGGTGTTTGATTTGGTAAAAGTTTGATAGGTTTAAGAAACTGATTTATGGTCTGTAATTCTTGA
*
5857603 ACAATGCTAGAAATGGGAATAAGAAGGTGAAGAAGATCAAGATAACACTTTACACCTAAAGCTAA
196 ACAATGCTAGAAATGGGAATAAGAAGATGAAGAAGATCAAGATAACACTTTACACCTAAAGCTAA
* *
5857668 AAGTTGCTTCATACAATCCGACCGTAGCATAATTTATCATGCATCTATACCATCTTTGAAATTAT
261 AAGTTGCTTCATACAATCAGAACGTAGCATAATTTATCATGCATCTATACCATCTTTGAAATTAT
*
5857733 CTTCTTTATCAAACGAAAGAGTTCACATGCTTATAGTGTTTACTTTACCCTATTCTCACAAGGAT
326 CTTCTTTATCAAACGAAAGAGTTCACATGCTTATAGCGTTTACTTTACCCTATTCTCACAAGGAT
*
5857798 TTAGAGATGAGATACCACTGAAATTTGTTCTCTTTAG
391 TTAGAGATAAGATACCACTGAAATTTGTTCTCTTTAG
* * * * *
5857835 GTTTAGAAAGGAAATCTGCTTTGAGGGCGAAAAGCTAACAAAAGGGAAATAACCTACCTGCTGCC
1 GTTTAGAAAGGAAATCAGCTTTGAGCGCGAAAAACTAACAAAAGGAAAATAACATACCTGCTGCC
*
5857900 TGGGTTGTGGAAGTTCTACCTCTGGGCAATGATTAAGGGTTGCAATTGAAGCTTGGAAGTTGCTT
66 TGGGTTGTGGAAGTTCTACCTCTGGACAATGATTAAGGGTTGCAATTGAAGCTTGGAAGTTGCTT
5857965 TTGGTGTTTGATTTGGT-AAAGTTTGATAGGTTTAAGAAACTGATTTATGGTCTGTAATTCTTGA
131 TTGGTGTTTGATTTGGTAAAAGTTTGATAGGTTTAAGAAACTGATTTATGGTCTGTAATTCTTGA
5858029 ACAATGCTAGAAATGGGAATAAGAAGATGAAGAAGATCAAGATAACACTTTACACCTAAAGCTAA
196 ACAATGCTAGAAATGGGAATAAGAAGATGAAGAAGATCAAGATAACACTTTACACCTAAAGCTAA
*
5858094 AAGTTGCTTCATACAATCAGAAGGTAGCATAATTTATCATGCATCTATACCATCTTTGAAATTAT
261 AAGTTGCTTCATACAATCAGAACGTAGCATAATTTATCATGCATCTATACCATCTTTGAAATTAT
*
5858159 CTTCTTTATCAAATGAAAGAGTTCACATGCTTATAGCGTTTACTTTACCCTATTCTCACAAGGAT
326 CTTCTTTATCAAACGAAAGAGTTCACATGCTTATAGCGTTTACTTTACCCTATTCTCACAAGGAT
*
5858224 TTAGAGGTAAGATACCACTGAAATTTGTTCTCTTTAG
391 TTAGAGATAAGATACCACTGAAATTTGTTCTCTTTAG
5858261 ATAACAACAG
Statistics
Matches: 410, Mismatches: 16, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
426 271 0.66
427 139 0.34
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (427 bp):
GTTTAGAAAGGAAATCAGCTTTGAGCGCGAAAAACTAACAAAAGGAAAATAACATACCTGCTGCC
TGGGTTGTGGAAGTTCTACCTCTGGACAATGATTAAGGGTTGCAATTGAAGCTTGGAAGTTGCTT
TTGGTGTTTGATTTGGTAAAAGTTTGATAGGTTTAAGAAACTGATTTATGGTCTGTAATTCTTGA
ACAATGCTAGAAATGGGAATAAGAAGATGAAGAAGATCAAGATAACACTTTACACCTAAAGCTAA
AAGTTGCTTCATACAATCAGAACGTAGCATAATTTATCATGCATCTATACCATCTTTGAAATTAT
CTTCTTTATCAAACGAAAGAGTTCACATGCTTATAGCGTTTACTTTACCCTATTCTCACAAGGAT
TTAGAGATAAGATACCACTGAAATTTGTTCTCTTTAG
Found at i:5863767 original size:5 final size:5
Alignment explanation
Indices: 5863757--5863783 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
5863747 ATATTTTCAA
5863757 AAAAG AAAAG AAAAG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AA
5863784 TATATAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:5880314 original size:22 final size:22
Alignment explanation
Indices: 5880288--5880343 Score: 94
Period size: 23 Copynumber: 2.5 Consensus size: 22
5880278 AGCTCGAAAT
5880288 CTTACTGTTCAGCTCAATAGAG
1 CTTACTGTTCAGCTCAATAGAG
*
5880310 CTTACCGTTTCAGCTCAATAGAG
1 CTTACTG-TTCAGCTCAATAGAG
5880333 CTTACTGTTCA
1 CTTACTGTTCA
5880344 TTGACTCAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 10 0.32
23 21 0.68
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (22 bp):
CTTACTGTTCAGCTCAATAGAG
Found at i:5881978 original size:42 final size:43
Alignment explanation
Indices: 5881913--5882034 Score: 149
Period size: 43 Copynumber: 2.8 Consensus size: 43
5881903 AGTCAACTTA
5881913 TGATTTACGTGTAAGACCATGTCTGGGACA-TCGGCATCG-TATT
1 TGATTT-CGTGTAAGACCATGTCTGGGACAGT-GGCATCGATATT
*
5881956 TGATTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCGATATT
1 TGATTTCGTGTAAGACCATGTCTGGGACAGTGGCATCGATATT
* * * * * *
5881999 TGATTACATGTAAGACTACGTCTTGGACATTGGCAT
1 TGATTTCGTGTAAGACCATGTCTGGGACAGTGGCAT
5882035 TGTACCAGCT
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
42 29 0.42
43 40 0.58
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (43 bp):
TGATTTCGTGTAAGACCATGTCTGGGACAGTGGCATCGATATT
Found at i:5885501 original size:42 final size:42
Alignment explanation
Indices: 5885450--5885530 Score: 162
Period size: 42 Copynumber: 1.9 Consensus size: 42
5885440 CCTATTAGGG
5885450 TCTAAATCGGGCTGTTACAATATATACATATGTGTATTAGAA
1 TCTAAATCGGGCTGTTACAATATATACATATGTGTATTAGAA
5885492 TCTAAATCGGGCTGTTACAATATATACATATGTGTATTA
1 TCTAAATCGGGCTGTTACAATATATACATATGTGTATTA
5885531 TGATCAAGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (42 bp):
TCTAAATCGGGCTGTTACAATATATACATATGTGTATTAGAA
Found at i:5894853 original size:27 final size:27
Alignment explanation
Indices: 5894815--5894868 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
5894805 CTAGCGAGTT
5894815 TGATTATAATAATGGAGATTCTTGTAG
1 TGATTATAATAATGGAGATTCTTGTAG
5894842 TGATTATAATAATGGAGATTCTTGTAG
1 TGATTATAATAATGGAGATTCTTGTAG
5894869 ATGAAGTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.04, G:0.22, T:0.41
Consensus pattern (27 bp):
TGATTATAATAATGGAGATTCTTGTAG
Found at i:5895809 original size:23 final size:23
Alignment explanation
Indices: 5895782--5895839 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
5895772 ACAGCTCGTA
*
5895782 AGAGCTTACTGTTTCAGCTCATT
1 AGAGCTTACTGTTTCAGCTCAAT
* * *
5895805 GGAGCTTACCGATTCAGCTCAAT
1 AGAGCTTACTGTTTCAGCTCAAT
5895828 AGAGCTTACTGT
1 AGAGCTTACTGT
5895840 CCATCAACTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (23 bp):
AGAGCTTACTGTTTCAGCTCAAT
Found at i:5900686 original size:43 final size:42
Alignment explanation
Indices: 5900561--5900722 Score: 171
Period size: 42 Copynumber: 3.8 Consensus size: 42
5900551 AGGGTTACTA
* * *
5900561 AGATTATGTGTAAGACCATATCTGGGATATGACATCTATATG
1 AGATTTTGTGTAAGACCATATCTGGGATATGGCATCGATATG
* * * * *
5900603 CGACTTCGCGTAAGACCATATCTGTGATATGGCATCGATATG
1 AGATTTTGTGTAAGACCATATCTGGGATATGGCATCGATATG
* *
5900645 AGATTTTGTGTAAGACCATAGCTGGGCTATTGGCATCGATATG
1 AGATTTTGTGTAAGACCATATCTGGGATA-TGGCATCGATATG
**** * *
5900688 AGATCCCATATAAGACCATATATGGGATATGGCAT
1 AGATTTTGTGTAAGACCATATCTGGGATATGGCAT
5900723 TGGTATGGTA
Statistics
Matches: 96, Mismatches: 23, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
42 62 0.65
43 34 0.35
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.30
Consensus pattern (42 bp):
AGATTTTGTGTAAGACCATATCTGGGATATGGCATCGATATG
Found at i:5906827 original size:22 final size:21
Alignment explanation
Indices: 5906786--5906831 Score: 51
Period size: 21 Copynumber: 2.1 Consensus size: 21
5906776 ATTAATCTTA
5906786 TATAAATTATATCCATTAAAAT
1 TATAAATTATATCCATT-AAAT
5906808 TATAAATTTATTAT-CA-TAAAT
1 TATAAA-TTA-TATCCATTAAAT
5906829 TAT
1 TAT
5906832 GTTAGAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
21 7 0.32
22 7 0.32
23 5 0.23
24 3 0.14
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (21 bp):
TATAAATTATATCCATTAAAT
Found at i:5906972 original size:23 final size:26
Alignment explanation
Indices: 5906920--5906977 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 26
5906910 AAAATTAAAT
* *
5906920 TATTAAATATTCATAATTTAAATTCT
1 TATTAAATATTCATAATATAAATTCA
5906946 TATTAAATATT-ATAA-AT-AATTCA
1 TATTAAATATTCATAATATAAATTCA
*
5906969 TATTTAATA
1 TATTAAATA
5906978 ATAGATATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.45
24 1 0.03
25 4 0.14
26 11 0.38
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (26 bp):
TATTAAATATTCATAATATAAATTCA
Found at i:5915853 original size:28 final size:28
Alignment explanation
Indices: 5915819--5915876 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
5915809 CCTAAACAAT
5915819 GTAAAAAATTGATGTTGTGTAGTCTAGG
1 GTAAAAAATTGATGTTGTGTAGTCTAGG
5915847 GTAAAAAATTGATGTTGTGTAGTCTAGG
1 GTAAAAAATTGATGTTGTGTAGTCTAGG
5915875 GT
1 GT
5915877 CACACGGCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.03, G:0.29, T:0.36
Consensus pattern (28 bp):
GTAAAAAATTGATGTTGTGTAGTCTAGG
Found at i:5922732 original size:18 final size:20
Alignment explanation
Indices: 5922703--5922743 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
5922693 ATTTGGCCTA
5922703 ATATACTTTTCATATGCA-C
1 ATATACTTTTCATATGCATC
*
5922722 ATATA-TTTTCATTTGCATC
1 ATATACTTTTCATATGCATC
5922741 ATA
1 ATA
5922744 AATAATTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.32, C:0.17, G:0.05, T:0.46
Consensus pattern (20 bp):
ATATACTTTTCATATGCATC
Found at i:5923026 original size:40 final size:40
Alignment explanation
Indices: 5922978--5923110 Score: 169
Period size: 40 Copynumber: 3.2 Consensus size: 40
5922968 TCCCAGATAG
5922978 GGTCTTACACAATCAAATACGATACCGATGTCCTAGACAA
1 GGTCTTACACAATCAAATACGATACCGATGTCCTAGACAA
* * * * * *
5923018 GGTCTTACACGTAATCACATATCGATGCC-ACTATCCCAGATAG
1 GGTCTTACAC--AATCAAATA-CGATACCGA-TGTCCTAGACAA
5923061 GGTCTTACACAATCAAATACGATACCGATGTCCTAGACAA
1 GGTCTTACACAATCAAATACGATACCGATGTCCTAGACAA
5923101 GGTCTTACAC
1 GGTCTTACAC
5923111 GTAATCACAT
Statistics
Matches: 76, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
40 34 0.45
41 9 0.12
42 9 0.12
43 24 0.32
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (40 bp):
GGTCTTACACAATCAAATACGATACCGATGTCCTAGACAA
Found at i:5923032 original size:83 final size:83
Alignment explanation
Indices: 5922929--5923153 Score: 423
Period size: 83 Copynumber: 2.7 Consensus size: 83
5922919 CCAACATCTC
* *
5922929 AGACATGGTCTTACATGTAATCACATATCGATGCCACTATCCCAGATAGGGTCTTACACAATCAA
1 AGACAAGGTCTTACACGTAATCACATATCGATGCCACTATCCCAGATAGGGTCTTACACAATCAA
5922994 ATACGATACCGATGTCCT
66 ATACGATACCGATGTCCT
5923012 AGACAAGGTCTTACACGTAATCACATATCGATGCCACTATCCCAGATAGGGTCTTACACAATCAA
1 AGACAAGGTCTTACACGTAATCACATATCGATGCCACTATCCCAGATAGGGTCTTACACAATCAA
5923077 ATACGATACCGATGTCCT
66 ATACGATACCGATGTCCT
*
5923095 AGACAAGGTCTTACACGTAATCACATATCGATGCCACTATCCCAGACAGGGTCTTACAC
1 AGACAAGGTCTTACACGTAATCACATATCGATGCCACTATCCCAGATAGGGTCTTACAC
5923154 GTAATTACAT
Statistics
Matches: 139, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 139 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (83 bp):
AGACAAGGTCTTACACGTAATCACATATCGATGCCACTATCCCAGATAGGGTCTTACACAATCAA
ATACGATACCGATGTCCT
Found at i:5923173 original size:43 final size:43
Alignment explanation
Indices: 5922928--5923173 Score: 274
Period size: 43 Copynumber: 5.9 Consensus size: 43
5922918 GCCAACATCT
* *
5922928 CAGACATGGTCTTACATGTAATCACATATCGATGCCACTATCC
1 CAGACAGGGTCTTACACGTAATCACATATCGATGCCACTATCC
* * * *
5922971 CAGATAGGGTCTTACAC--AATCAAATA-CGATACCGA-TGTCC
1 CAGACAGGGTCTTACACGTAATCACATATCGATGCC-ACTATCC
* *
5923011 TAGACAAGGTCTTACACGTAATCACATATCGATGCCACTATCC
1 CAGACAGGGTCTTACACGTAATCACATATCGATGCCACTATCC
* * * *
5923054 CAGATAGGGTCTTACAC--AATCAAATA-CGATACCGA-TGTCC
1 CAGACAGGGTCTTACACGTAATCACATATCGATGCC-ACTATCC
* *
5923094 TAGACAAGGTCTTACACGTAATCACATATCGATGCCACTATCC
1 CAGACAGGGTCTTACACGTAATCACATATCGATGCCACTATCC
* *
5923137 CAGACAGGGTCTTACACGTAATTACATATCAATGCCA
1 CAGACAGGGTCTTACACGTAATCACATATCGATGCCA
5923174 ACGTCCCAGA
Statistics
Matches: 165, Mismatches: 28, Indels: 20
0.77 0.13 0.09
Matches are distributed among these distances:
40 48 0.29
41 18 0.11
42 18 0.11
43 81 0.49
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.25
Consensus pattern (43 bp):
CAGACAGGGTCTTACACGTAATCACATATCGATGCCACTATCC
Found at i:5926626 original size:93 final size:93
Alignment explanation
Indices: 5926514--5926684 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
5926504 GCCCATAAGT
* *
5926514 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
5926579 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
5926607 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
5926672 CGAGTTCGGATGC
66 CGAGTTCGGATGC
5926685 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:5926681 original size:46 final size:46
Alignment explanation
Indices: 5926506--5926681 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
5926496 TGTAACCCGC
* * *
5926506 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
5926552 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
5926602 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
5926645 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
5926682 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:5929116 original size:30 final size:30
Alignment explanation
Indices: 5929072--5929160 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
5929062 CAAAGATAAC
*
5929072 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAACCCGGAATAAAGAAATCCAAGATA
*
5929101 GAGAAACCCGGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGGAATAAAGAAATCCAAG-ATA
* * *
5929131 AAGAGATCCAGG-ATAAAGAAACCCAAGATA
1 AAGA-AACCCGGAATAAAGAAATCCAAGATA
5929161 CGATACTATG
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 9 0.18
30 34 0.68
31 7 0.14
ACGTcount: A:0.56, C:0.16, G:0.18, T:0.10
Consensus pattern (30 bp):
AAGAAACCCGGAATAAAGAAATCCAAGATA
Found at i:5929120 original size:15 final size:14
Alignment explanation
Indices: 5929072--5929154 Score: 58
Period size: 15 Copynumber: 5.6 Consensus size: 14
5929062 CAAAGATAAC
*
5929072 AAGAAAACCGAATA
1 AAGAAACCCGAATA
* *
5929086 AAGAAATCCAAGATA
1 AAGAAACCCGA-ATA
*
5929101 GAGAAACCCGGAATA
1 AAGAAACCC-GAATA
*
5929116 AAGAAATCCAGAATA
1 AAGAAA-CCCGAATA
* * *
5929131 AAGAGATCCAGGATA
1 AAGA-AACCCGAATA
5929146 AAGAAACCC
1 AAGAAACCC
5929155 AAGATACGAT
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
14 12 0.22
15 38 0.70
16 4 0.07
ACGTcount: A:0.55, C:0.17, G:0.18, T:0.10
Consensus pattern (14 bp):
AAGAAACCCGAATA
Found at i:5929160 original size:15 final size:15
Alignment explanation
Indices: 5929083--5929160 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
5929073 AGAAAACCGA
5929083 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* **
5929098 ATAGAGAAA-CCCGG
1 ATAAAGAAATCCAAG
5929112 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
5929127 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
5929143 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
5929158 ATA
1 ATA
5929161 CGATACTATG
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
14 3 0.06
15 44 0.88
16 3 0.06
ACGTcount: A:0.55, C:0.15, G:0.18, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:5932195 original size:93 final size:93
Alignment explanation
Indices: 5932083--5932253 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
5932073 GCCCATAAGT
* *
5932083 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
5932148 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
5932176 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
5932241 CGAGTTCGGATGC
66 CGAGTTCGGATGC
5932254 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:5932250 original size:46 final size:46
Alignment explanation
Indices: 5932075--5932250 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
5932065 TGTAACCCGC
* * *
5932075 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
5932121 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
5932171 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
5932214 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
5932251 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:5937337 original size:43 final size:43
Alignment explanation
Indices: 5937276--5937542 Score: 246
Period size: 43 Copynumber: 6.3 Consensus size: 43
5937266 TCACACATAT
* *
5937276 CATA-CGATGCCAAC-ATCCCAGACATGGTCTTACATGTAATCA
1 CATATCGATGCC-ACTATCCCAGACAGGGTCTTACACGTAATCA
*
5937318 CATATCGATGCCACTATCCCAGATAGGGTCTTACAC-TAATCA
1 CATATCGATGCCACTATCCCAGACAGGGTCTTACACGTAATCA
* * * * * * *
5937360 AATAT-AATATCGA-TGTCCCAGACATGGTTTTACACGTAATCA
1 CATATCGAT-GCCACTATCCCAGACAGGGTCTTACACGTAATCA
* * * *
5937402 CATATTGATGCCAAC-GTCCCAGAC-GTGTCTTACACG-AGAACA
1 CATATCGATGCC-ACTATCCCAGACAGGGTCTTACACGTA-ATCA
* *
5937444 CATATCGATGCCACTGTCCCAGACAGGGTCTTACACG-AGAACA
1 CATATCGATGCCACTATCCCAGACAGGGTCTTACACGTA-ATCA
* * *
5937487 CATATCGATGCTACTATCCTAGACAGGGTCTTTCACGTAATCA
1 CATATCGATGCCACTATCCCAGACAGGGTCTTACACGTAATCA
*
5937530 CATATCAATGCCA
1 CATATCGATGCCA
5937543 ACGTCCCAAA
Statistics
Matches: 186, Mismatches: 28, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
41 23 0.12
42 61 0.33
43 101 0.54
44 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (43 bp):
CATATCGATGCCACTATCCCAGACAGGGTCTTACACGTAATCA
Found at i:5943767 original size:93 final size:93
Alignment explanation
Indices: 5943660--5943830 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
5943650 GCCCCTAAGT
* *
5943660 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
5943725 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
5943753 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
5943818 CGAGTTCGGATGC
66 CGAGTTCGGATGC
5943831 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:5943827 original size:46 final size:46
Alignment explanation
Indices: 5943655--5943827 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
5943645 AACCCGCCCC
* * *
5943655 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
5943701 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
5943749 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
5943794 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
5943828 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 61 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:5944284 original size:30 final size:30
Alignment explanation
Indices: 5944250--5944309 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
5944240 ATTTAATACG
5944250 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
5944280 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
5944310 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:5945161 original size:20 final size:20
Alignment explanation
Indices: 5945136--5945177 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
5945126 GATAAGTATG
5945136 TAAGATTAATCTTTGAGTGA
1 TAAGATTAATCTTTGAGTGA
5945156 TAAGATTAATCTTTGAGTGA
1 TAAGATTAATCTTTGAGTGA
5945176 TA
1 TA
5945178 TTGATTGTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (20 bp):
TAAGATTAATCTTTGAGTGA
Found at i:5945573 original size:29 final size:28
Alignment explanation
Indices: 5945523--5945633 Score: 105
Period size: 29 Copynumber: 3.9 Consensus size: 28
5945513 GTGAGCATGA
* * *
5945523 ATATGAATGTGACTGGGACTAATGGGCC
1 ATATAAATGTGATTGGGCCTAATGGGCC
* * *
5945551 ACATAAATGTGATTTGGGCCTAACGGACC
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
* *
5945580 ATATACAGGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
* * *
5945609 ATATGAATATGATTGGGCTTAATGG
1 ATATAAATGTGATTGGGCCTAATGG
5945634 ACCAGATACA
Statistics
Matches: 66, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
28 22 0.33
29 44 0.67
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (28 bp):
ATATAAATGTGATTGGGCCTAATGGGCC
Found at i:5945643 original size:57 final size:58
Alignment explanation
Indices: 5945536--5945646 Score: 152
Period size: 57 Copynumber: 1.9 Consensus size: 58
5945526 TGAATGTGAC
* *
5945536 TGGGACTAATGGGCCACATAAATGTGATTTGGGCCTAACGGACCATATACAGGTGATT
1 TGGGACTAATGGGCCACATAAATATGATTTGGGCCTAACGGACCAGATACAGGTGATT
* * * * *
5945594 TGGGCCTAATGGGCCATATGAATATGA-TTGGGCTTAATGGACCAGATACAGGT
1 TGGGACTAATGGGCCACATAAATATGATTTGGGCCTAACGGACCAGATACAGGT
5945647 ATGTGAAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 23 0.50
58 23 0.50
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (58 bp):
TGGGACTAATGGGCCACATAAATATGATTTGGGCCTAACGGACCAGATACAGGTGATT
Found at i:5951934 original size:605 final size:605
Alignment explanation
Indices: 5950784--5951993 Score: 2294
Period size: 605 Copynumber: 2.0 Consensus size: 605
5950774 CCCTGATGCA
5950784 ATAAGCCGAATTTGTCAATTTGTCCACTATGACCCATATGGCATCTTTCTTTTTTGGAGTCTTAG
1 ATAAGCCGAATTTGTCAATTTGTCCACTATGACCCATATGGCATCTTTCTTTTTTGGAGTCTTAG
* * *
5950849 GTATTCCTATCACGAAGTCCATGGTAATTCTATCCCACTTCCATTCGGTGACCATTACAGGCTGT
66 GTAGTCCTATCACGAAGTCCATGGTAAGTCTATCCCACTTCCATTCGGTGACCATTACAGGCTAT
5950914 AACATACCTGAAGGCACTTGATGTTCAACTTTAACTTACTGACATACGACGCATTTCGATACAAA
131 AACATACCTGAAGGCACTTGATGTTCAACTTTAACTTACTGACATACGACGCATTTCGATACAAA
*
5950979 TTCAGAAACATCTCTTTTCATGCCGTTCCACTAGTACATCTTCTTTAAATCATTGTACATCTTGG
196 TTCAGAAACATCTCTTTTCATGCCGTTCCACCAGTACATCTTCTTTAAATCATTGTACATCTTGG
*
5951044 TACTTCCCGGGTGAATAGACAAATGACTGTTATGTGCTTCTTGCAAAATCTTCTGAATAAGTTCA
261 TACTTCCCGGGTGAATAGACAAATGACTGTTATGTGCTTCTTGCAAAATCTTCTAAATAAGTTCA
5951109 TTGTCTTTGGGTACACAAACCCTATCTTTGAACATCAAACATCCATCAGGACTAATTTGAAAATC
326 TTGTCTTTGGGTACACAAACCCTATCTTTGAACATCAAACATCCATCAGGACTAATTTGAAAATC
5951174 GGACTCAATCCCAGACTCACATTGAGCCCTTTTTGCTTGCAAGTCATCATCATTTAACTGAGCAT
391 GGACTCAATCCCAGACTCACATTGAGCCCTTTTTGCTTGCAAGTCATCATCATTTAACTGAGCAT
5951239 CATGAATTTCTTGCAGAAATGTTGGCCTAGCCTCCAGCTCGGCCAAAACTAAACCATCATCAAAC
456 CATGAATTTCTTGCAGAAATGTTGGCCTAGCCTCCAGCTCGGCCAAAACTAAACCATCATCAAAC
*
5951304 AAGGTCAAAGGAGCATCGATAGCTCTCAAGACATACAAGGATTTTCTACTCAGTGCATCAGCGAC
521 AAGGTCAAACGAGCATCGATAGCTCTCAAGACATACAAGGATTTTCTACTCAGTGCATCAGCGAC
*
5951369 CACATTCGCCTTTCCCGGGT
586 CACATCCGCCTTTCCCGGGT
*
5951389 ATAAGCCGAATTTGTCAATTTGTCCACTATGACCTATATGGCATCTTTCTTTTTTGGAGTCTTAG
1 ATAAGCCGAATTTGTCAATTTGTCCACTATGACCCATATGGCATCTTTCTTTTTTGGAGTCTTAG
*
5951454 GTAGTCCTGTCACGAAGTCCATGGTAAGTCTATCCCACTTCCATTCGGTGACCATTACAGGCTAT
66 GTAGTCCTATCACGAAGTCCATGGTAAGTCTATCCCACTTCCATTCGGTGACCATTACAGGCTAT
* * *
5951519 AACATACCTGAAGGCACTTGATGTTCAACTTTAACTTGCTGACATACTATGCATTTCGATACAAA
131 AACATACCTGAAGGCACTTGATGTTCAACTTTAACTTACTGACATACGACGCATTTCGATACAAA
5951584 TTCAGAAACATCTCTTTTCATGCCGTTCCACCAGTACATCTTCTTTAAATCATTGTACATCTTGG
196 TTCAGAAACATCTCTTTTCATGCCGTTCCACCAGTACATCTTCTTTAAATCATTGTACATCTTGG
5951649 TACTTCCCGGGTGAATAGACAAATGACTGTTATGTGCTTCTTGCAAAATCTTCTAAATAAGTTCA
261 TACTTCCCGGGTGAATAGACAAATGACTGTTATGTGCTTCTTGCAAAATCTTCTAAATAAGTTCA
5951714 TTGTCTTTGGGTACACAAACCCTATCTTTGAACATCAAACATCCATCAGGACTAATTTGAAAATC
326 TTGTCTTTGGGTACACAAACCCTATCTTTGAACATCAAACATCCATCAGGACTAATTTGAAAATC
5951779 GGACTCAATCCCAGACTCACATTGAGCCCTTTTTGCTTGCAAGTCATCATCATTTAACTGAGCAT
391 GGACTCAATCCCAGACTCACATTGAGCCCTTTTTGCTTGCAAGTCATCATCATTTAACTGAGCAT
*
5951844 CATGAATTTCTTGCAGAAATGTTGGCCTAGCCTCCAGCTCGGCCAAAACTAAACCATCATCAAGC
456 CATGAATTTCTTGCAGAAATGTTGGCCTAGCCTCCAGCTCGGCCAAAACTAAACCATCATCAAAC
5951909 AAGGTCAAACGAGCATCGATAGCTCTCAAGACATACAAGGATTTTCTACTCAGTGCATCAGCGAC
521 AAGGTCAAACGAGCATCGATAGCTCTCAAGACATACAAGGATTTTCTACTCAGTGCATCAGCGAC
*
5951974 CATATCCGCCTTTCCCGGGT
586 CACATCCGCCTTTCCCGGGT
5951994 TGTAGTCGAT
Statistics
Matches: 591, Mismatches: 14, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
605 591 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (605 bp):
ATAAGCCGAATTTGTCAATTTGTCCACTATGACCCATATGGCATCTTTCTTTTTTGGAGTCTTAG
GTAGTCCTATCACGAAGTCCATGGTAAGTCTATCCCACTTCCATTCGGTGACCATTACAGGCTAT
AACATACCTGAAGGCACTTGATGTTCAACTTTAACTTACTGACATACGACGCATTTCGATACAAA
TTCAGAAACATCTCTTTTCATGCCGTTCCACCAGTACATCTTCTTTAAATCATTGTACATCTTGG
TACTTCCCGGGTGAATAGACAAATGACTGTTATGTGCTTCTTGCAAAATCTTCTAAATAAGTTCA
TTGTCTTTGGGTACACAAACCCTATCTTTGAACATCAAACATCCATCAGGACTAATTTGAAAATC
GGACTCAATCCCAGACTCACATTGAGCCCTTTTTGCTTGCAAGTCATCATCATTTAACTGAGCAT
CATGAATTTCTTGCAGAAATGTTGGCCTAGCCTCCAGCTCGGCCAAAACTAAACCATCATCAAAC
AAGGTCAAACGAGCATCGATAGCTCTCAAGACATACAAGGATTTTCTACTCAGTGCATCAGCGAC
CACATCCGCCTTTCCCGGGT
Found at i:5958736 original size:43 final size:43
Alignment explanation
Indices: 5958688--5958810 Score: 158
Period size: 43 Copynumber: 2.9 Consensus size: 43
5958678 CACATGTATC
* *
5958688 GCATCCATTATGAACTCGGACCACTCAACGAGCTCGGATGCTA
1 GCATCCATAATGAACTCGGACCACTCAACGAGCTCGGATGCCA
*
5958731 GCATCCATAATGATCTCGGACCACTCAACGAGCTCGGATGCCA
1 GCATCCATAATGAACTCGGACCACTCAACGAGCTCGGATGCCA
** * * * *
5958774 -CATATATCACGAACCCGGACCACTCAACGAGTTCGGA
1 GCATCCATAATGAACTCGGACCACTCAACGAGCTCGGA
5958811 CTTCTTAATT
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
42 30 0.43
43 40 0.57
ACGTcount: A:0.29, C:0.32, G:0.20, T:0.19
Consensus pattern (43 bp):
GCATCCATAATGAACTCGGACCACTCAACGAGCTCGGATGCCA
Found at i:5958810 original size:42 final size:43
Alignment explanation
Indices: 5958699--5958810 Score: 145
Period size: 42 Copynumber: 2.6 Consensus size: 43
5958689 CATCCATTAT
* * *
5958699 GAACTCGGACCACTCAACGAGCTCGGATGCTAGCATCCATAAT
1 GAACTCGGACCACTCAACGAGCTCGGATGCCAGCATACATAAC
* * *
5958742 GATCTCGGACCACTCAACGAGCTCGGATGCCA-CATATATCAC
1 GAACTCGGACCACTCAACGAGCTCGGATGCCAGCATACATAAC
* *
5958784 GAACCCGGACCACTCAACGAGTTCGGA
1 GAACTCGGACCACTCAACGAGCTCGGA
5958811 CTTCTTAATT
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 30 0.50
43 30 0.50
ACGTcount: A:0.29, C:0.32, G:0.21, T:0.17
Consensus pattern (43 bp):
GAACTCGGACCACTCAACGAGCTCGGATGCCAGCATACATAAC
Found at i:5958975 original size:43 final size:43
Alignment explanation
Indices: 5958927--5959049 Score: 158
Period size: 43 Copynumber: 2.9 Consensus size: 43
5958917 CACATGTATC
* *
5958927 GCATCCATTATGAACTCGGACCACTCAACGAGCTCGGATGCTA
1 GCATCCATAATGAACTCGGACCACTCAACGAGCTCGGATGCCA
*
5958970 GCATCCATAATGATCTCGGACCACTCAACGAGCTCGGATGCCA
1 GCATCCATAATGAACTCGGACCACTCAACGAGCTCGGATGCCA
** * * * *
5959013 -CATATATCACGAACCCGGACCACTCAACGAGTTCGGA
1 GCATCCATAATGAACTCGGACCACTCAACGAGCTCGGA
5959050 CTTCTTAATT
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
42 30 0.43
43 40 0.57
ACGTcount: A:0.29, C:0.32, G:0.20, T:0.19
Consensus pattern (43 bp):
GCATCCATAATGAACTCGGACCACTCAACGAGCTCGGATGCCA
Found at i:5959007 original size:239 final size:239
Alignment explanation
Indices: 5958588--5959066 Score: 958
Period size: 239 Copynumber: 2.0 Consensus size: 239
5958578 GTAACTACAC
5958588 GTGCTGCTCACAAAAGTTGTCAGGTATCCGACCACTCAAGGATTACCTAGCCACCGATAGGACAC
1 GTGCTGCTCACAAAAGTTGTCAGGTATCCGACCACTCAAGGATTACCTAGCCACCGATAGGACAC
5958653 ACAAAACCATTGCCCAAAGCTCAATCACATGTATCGCATCCATTATGAACTCGGACCACTCAACG
66 ACAAAACCATTGCCCAAAGCTCAATCACATGTATCGCATCCATTATGAACTCGGACCACTCAACG
5958718 AGCTCGGATGCTAGCATCCATAATGATCTCGGACCACTCAACGAGCTCGGATGCCACATATATCA
131 AGCTCGGATGCTAGCATCCATAATGATCTCGGACCACTCAACGAGCTCGGATGCCACATATATCA
5958783 CGAACCCGGACCACTCAACGAGTTCGGACTTCTTAATTCCTAGT
196 CGAACCCGGACCACTCAACGAGTTCGGACTTCTTAATTCCTAGT
5958827 GTGCTGCTCACAAAAGTTGTCAGGTATCCGACCACTCAAGGATTACCTAGCCACCGATAGGACAC
1 GTGCTGCTCACAAAAGTTGTCAGGTATCCGACCACTCAAGGATTACCTAGCCACCGATAGGACAC
5958892 ACAAAACCATTGCCCAAAGCTCAATCACATGTATCGCATCCATTATGAACTCGGACCACTCAACG
66 ACAAAACCATTGCCCAAAGCTCAATCACATGTATCGCATCCATTATGAACTCGGACCACTCAACG
5958957 AGCTCGGATGCTAGCATCCATAATGATCTCGGACCACTCAACGAGCTCGGATGCCACATATATCA
131 AGCTCGGATGCTAGCATCCATAATGATCTCGGACCACTCAACGAGCTCGGATGCCACATATATCA
5959022 CGAACCCGGACCACTCAACGAGTTCGGACTTCTTAATTCCTAGT
196 CGAACCCGGACCACTCAACGAGTTCGGACTTCTTAATTCCTAGT
5959066 G
1 G
5959067 ACATGTCACT
Statistics
Matches: 240, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
239 240 1.00
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.21
Consensus pattern (239 bp):
GTGCTGCTCACAAAAGTTGTCAGGTATCCGACCACTCAAGGATTACCTAGCCACCGATAGGACAC
ACAAAACCATTGCCCAAAGCTCAATCACATGTATCGCATCCATTATGAACTCGGACCACTCAACG
AGCTCGGATGCTAGCATCCATAATGATCTCGGACCACTCAACGAGCTCGGATGCCACATATATCA
CGAACCCGGACCACTCAACGAGTTCGGACTTCTTAATTCCTAGT
Found at i:5959049 original size:42 final size:43
Alignment explanation
Indices: 5958938--5959049 Score: 145
Period size: 42 Copynumber: 2.6 Consensus size: 43
5958928 CATCCATTAT
* * *
5958938 GAACTCGGACCACTCAACGAGCTCGGATGCTAGCATCCATAAT
1 GAACTCGGACCACTCAACGAGCTCGGATGCCAGCATACATAAC
* * *
5958981 GATCTCGGACCACTCAACGAGCTCGGATGCCA-CATATATCAC
1 GAACTCGGACCACTCAACGAGCTCGGATGCCAGCATACATAAC
* *
5959023 GAACCCGGACCACTCAACGAGTTCGGA
1 GAACTCGGACCACTCAACGAGCTCGGA
5959050 CTTCTTAATT
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 30 0.50
43 30 0.50
ACGTcount: A:0.29, C:0.32, G:0.21, T:0.17
Consensus pattern (43 bp):
GAACTCGGACCACTCAACGAGCTCGGATGCCAGCATACATAAC
Found at i:5961306 original size:19 final size:19
Alignment explanation
Indices: 5961261--5961307 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
5961251 ATCAAATTAA
*
5961261 AATAAAAATAAAAATATAG
1 AATAAAAATAAAAATAAAG
* *
5961280 AATCAAAACT-AAAATAAAT
1 AAT-AAAAATAAAAATAAAG
5961299 AATAAAAAT
1 AATAAAAAT
5961308 TAGATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAAAATAAAAATAAAG
Found at i:5964179 original size:81 final size:81
Alignment explanation
Indices: 5964044--5964194 Score: 198
Period size: 81 Copynumber: 1.9 Consensus size: 81
5964034 ATTCTGAAGT
* * * * * * *
5964044 CAACAGCCAAGATACACAAGCATGTGATAAACATCTGCAAAATTTTCCCACTGAAAATTTATTAC
1 CAACAGCCAAGATACACAAGCAAGTGACAAAAATATGCAAAATATTCCCACTGAAAATCTATCAC
5964109 AAATTAAACAATGTAC
66 AAATTAAACAATGTAC
*
5964125 CAACAGCCAAGATACACAAGTAAGTGACAAAGAATAT-CAATAA-ATTCCCACTGAAAATCTATC
1 CAACAGCCAAGATACACAAGCAAGTGACAAA-AATATGCAA-AATATTCCCACTGAAAATCTATC
5964188 ACAAATT
64 ACAAATT
5964195 CAAAAAGGTA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
81 55 0.92
82 5 0.08
ACGTcount: A:0.46, C:0.21, G:0.10, T:0.23
Consensus pattern (81 bp):
CAACAGCCAAGATACACAAGCAAGTGACAAAAATATGCAAAATATTCCCACTGAAAATCTATCAC
AAATTAAACAATGTAC
Found at i:5965936 original size:17 final size:18
Alignment explanation
Indices: 5965903--5965936 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5965893 TCTCTCTTAA
5965903 ATAATTTAAACTATATTG
1 ATAATTTAAACTATATTG
*
5965921 ATAATTTTAA-TATATT
1 ATAATTTAAACTATATT
5965937 AAAACAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
ATAATTTAAACTATATTG
Found at i:5966779 original size:15 final size:15
Alignment explanation
Indices: 5966756--5966790 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
5966746 CCCTAACCCT
*
5966756 TAAAC-CATAATCCC
1 TAAACTCATAATCCA
5966770 TAAACTCATAATCCA
1 TAAACTCATAATCCA
5966785 TAAACT
1 TAAACT
5966791 TAAAATAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAACTCATAATCCA
Done.