Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 6 of 322
Found at i:1335508 original size:27 final size:27
Alignment explanation
Indices: 1335456--1335510 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
1335446 TAAGTTATAA
* *
1335456 AAGTTATGGTATGATATATATTTATGT
1 AAGTTATGATATAATATATATTTATGT
1335483 AAGTTATGATATAATATATATTTATGT
1 AAGTTATGATATAATATATATTTATGT
1335510 A
1 A
1335511 TTATGTAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (27 bp):
AAGTTATGATATAATATATATTTATGT
Found at i:1336237 original size:12 final size:14
Alignment explanation
Indices: 1336202--1336238 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
1336192 GTCTTGACTT
1336202 AATATTTTTAAGTA
1 AATATTTTTAAGTA
1336216 AATTATTTTTAA-TA
1 AA-TATTTTTAAGTA
1336230 AA-ATTTTTA
1 AATATTTTTA
1336239 TTATTTTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.32
14 6 0.27
15 9 0.41
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (14 bp):
AATATTTTTAAGTA
Found at i:1337596 original size:14 final size:13
Alignment explanation
Indices: 1337570--1337595 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1337560 AGAAGCAGTT
1337570 TGGGAAAAAAAAA
1 TGGGAAAAAAAAA
1337583 TGGGAAAAAAAAA
1 TGGGAAAAAAAAA
1337596 AGAGATTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.23, T:0.08
Consensus pattern (13 bp):
TGGGAAAAAAAAA
Found at i:1339147 original size:40 final size:40
Alignment explanation
Indices: 1339103--1339244 Score: 135
Period size: 40 Copynumber: 3.5 Consensus size: 40
1339093 TTTTGACGGT
* * * * *
1339103 GTTTTTGAAAAAGTGTCGCTAATTCTTGATTTTTAGCAGC
1 GTTTTTCAAAAAGCGCCGCTAATACTTGATCTTTAGCAGC
* **
1339143 GTTTTTCCAAAAGCGCCGCTAATACTTGATCTTTAGTGGC
1 GTTTTTCAAAAAGCGCCGCTAATACTTGATCTTTAGCAGC
* * * * *
1339183 ATTTTTAAAAAAGCGCTGCT-A-ACTTTCGATCTTTAGCGGT
1 GTTTTTCAAAAAGCGCCGCTAATAC-TT-GATCTTTAGCAGC
1339223 GTTTTTCAAAAAGCGCCGCTAA
1 GTTTTTCAAAAAGCGCCGCTAA
1339245 GCCACTAGAT
Statistics
Matches: 82, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
38 2 0.02
39 3 0.04
40 76 0.93
41 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (40 bp):
GTTTTTCAAAAAGCGCCGCTAATACTTGATCTTTAGCAGC
Found at i:1339623 original size:22 final size:21
Alignment explanation
Indices: 1339596--1339642 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
1339586 TTAACCCTTA
*
1339596 AAACCATAAACACTAAGATCCT
1 AAACCATAAACACTAA-ACCCT
*
1339618 AAACCATAAATACTAAACCCT
1 AAACCATAAACACTAAACCCT
1339639 AAAC
1 AAAC
1339643 AACAAACTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.53, C:0.28, G:0.02, T:0.17
Consensus pattern (21 bp):
AAACCATAAACACTAAACCCT
Found at i:1339751 original size:14 final size:14
Alignment explanation
Indices: 1339717--1339764 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
1339707 CATATAAATA
*
1339717 TTAAACCATAAACC
1 TTAAACCCTAAACC
* * *
1339731 ATAAAACTCTAAATC
1 -TTAAACCCTAAACC
1339746 TTAAACCCTAAACC
1 TTAAACCCTAAACC
1339760 TTAAA
1 TTAAA
1339765 TATTAAACCC
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (14 bp):
TTAAACCCTAAACC
Found at i:1339764 original size:21 final size:22
Alignment explanation
Indices: 1339725--1339780 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
1339715 TATTAAACCA
* * *
1339725 TAAACCATAAAACTCTAAATCT
1 TAAACCCTAAACCTCTAAATAT
1339747 TAAACCCTAAACCT-TAAATAT
1 TAAACCCTAAACCTCTAAATAT
1339768 TAAACCCTAAACC
1 TAAACCCTAAACC
1339781 AAAATATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
21 19 0.61
22 12 0.39
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25
Consensus pattern (22 bp):
TAAACCCTAAACCTCTAAATAT
Found at i:1340199 original size:41 final size:41
Alignment explanation
Indices: 1340154--1340271 Score: 130
Period size: 41 Copynumber: 2.9 Consensus size: 41
1340144 CTTTATGTAC
*
1340154 CGTTTGGATTAAAAACGCCGCTATTGAT-AGGTTTTTAGTGG
1 CGTTTGGATAAAAAACGCCGCTATTGATCA-GTTTTTAGTGG
* ** * *
1340195 CGTTTGTACCAAAAACGGCGCTATTGCTCAGTTTTTAGTGG
1 CGTTTGGATAAAAAACGCCGCTATTGATCAGTTTTTAGTGG
* * * *
1340236 TGTTTGGATAAAAAAGGCCGCTATTGCTTAGTTTTT
1 CGTTTGGATAAAAAACGCCGCTATTGATCAGTTTTT
1340272 TTGTAAATGC
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 63 0.98
42 1 0.02
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37
Consensus pattern (41 bp):
CGTTTGGATAAAAAACGCCGCTATTGATCAGTTTTTAGTGG
Found at i:1340701 original size:72 final size:72
Alignment explanation
Indices: 1340584--1340822 Score: 385
Period size: 72 Copynumber: 3.3 Consensus size: 72
1340574 AGGGGAAAGT
*
1340584 ACCATTCAATTGATTTTCTGAAACATCAAAGAACT-TCAAAGATGATAACTCCCCTATAGACAAT
1 ACCATTTAATTGATTTTCTGAAACATCAAAGAA-TATCAAAGATGATAACTCCCCTATAGACAAT
1340648 GGAATTTG
65 GGAATTTG
*
1340656 ACCATTTAAATT-ATTTTCTGAAACATCAAAGAATATCAAAGATGATAACTTCCCTATAGACAAT
1 ACCATTT-AATTGATTTTCTGAAACATCAAAGAATATCAAAGATGATAACTCCCCTATAGACAAT
1340720 GGAATTTG
65 GGAATTTG
* * *
1340728 ACCATATACTTGATTTTCTGAAACATCAAACAA-ATTCAAAGATGATAACTCCCCTATAGACAAT
1 ACCATTTAATTGATTTTCTGAAACATCAAAGAATA-TCAAAGATGATAACTCCCCTATAGACAAT
1340792 GGAATTTG
65 GGAATTTG
1340800 ACCATTTAATTGATTTTCTGAAA
1 ACCATTTAATTGATTTTCTGAAA
1340823 GTTCAAGGTG
Statistics
Matches: 155, Mismatches: 8, Indels: 8
0.91 0.05 0.05
Matches are distributed among these distances:
71 5 0.03
72 146 0.94
73 4 0.03
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (72 bp):
ACCATTTAATTGATTTTCTGAAACATCAAAGAATATCAAAGATGATAACTCCCCTATAGACAATG
GAATTTG
Found at i:1348761 original size:18 final size:18
Alignment explanation
Indices: 1348703--1348795 Score: 78
Period size: 18 Copynumber: 5.2 Consensus size: 18
1348693 CCCAACTACT
* *
1348703 GTATACGTGAACAGTACC
1 GTATACGTAAATAGTACC
* *
1348721 GTATATGTAAATAGTGCC
1 GTATACGTAAATAGTACC
* * *
1348739 ATATATGTAAATAGTATC
1 GTATACGTAAATAGTACC
* * **
1348757 GTATACATGAATAGTGTC
1 GTATACGTAAATAGTACC
*
1348775 GTATACGTGAATAGTACC
1 GTATACGTAAATAGTACC
1348793 GTA
1 GTA
1348796 AACGGTCGTA
Statistics
Matches: 60, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 60 1.00
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.31
Consensus pattern (18 bp):
GTATACGTAAATAGTACC
Found at i:1350954 original size:9 final size:9
Alignment explanation
Indices: 1350930--1350964 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1350920 AAATTGTCAT
1350930 ATTAAAAAA
1 ATTAAAAAA
1350939 ATGTAAAAAA
1 AT-TAAAAAA
*
1350949 ATTAAATAA
1 ATTAAAAAA
1350958 ATTAAAA
1 ATTAAAA
1350965 GACTGAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (9 bp):
ATTAAAAAA
Found at i:1351066 original size:19 final size:20
Alignment explanation
Indices: 1351031--1351074 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
1351021 TAAAAATTCG
*
1351031 AAAAATTTATAAGAAATTTA
1 AAAAATTTATAAGAAATATA
1351051 AAAAATTT-TGAA-AAATATA
1 AAAAATTTAT-AAGAAATATA
1351070 AAAAA
1 AAAAA
1351075 AAACTATAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (20 bp):
AAAAATTTATAAGAAATATA
Found at i:1358803 original size:6 final size:6
Alignment explanation
Indices: 1358792--1358817 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1358782 GGGAAATCAT
1358792 GGGGTG GGGGTG GGGGTG GGGGTG GG
1 GGGGTG GGGGTG GGGGTG GGGGTG GG
1358818 TACCTTTGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.85, T:0.15
Consensus pattern (6 bp):
GGGGTG
Found at i:1365831 original size:8 final size:9
Alignment explanation
Indices: 1365797--1365830 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
1365787 CTTCAAAAAA
1365797 AAAAGAAATT
1 AAAA-AAATT
1365807 AAAAAAATT
1 AAAAAAATT
1365816 AAAAAAATT
1 AAAAAAATT
1365825 AAAAAA
1 AAAAAA
1365831 TATGTTATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 20 0.83
10 4 0.17
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (9 bp):
AAAAAAATT
Found at i:1367205 original size:27 final size:27
Alignment explanation
Indices: 1367174--1367227 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1367164 ACAAATTAGT
1367174 ACTGGTACTCGACCACTGAAACATATA
1 ACTGGTACTCGACCACTGAAACATATA
1367201 ACTGGTACTCGACCACTGAAACATATA
1 ACTGGTACTCGACCACTGAAACATATA
1367228 GCTATTTTGG
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:0.37, C:0.26, G:0.15, T:0.22
Consensus pattern (27 bp):
ACTGGTACTCGACCACTGAAACATATA
Found at i:1371505 original size:16 final size:16
Alignment explanation
Indices: 1371479--1371525 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1371469 TTGCAAGACT
1371479 GAAGC-AAGAAAAATC
1 GAAGCAAAGAAAAATC
* *
1371494 GAAGCAAAGAAAGAGC
1 GAAGCAAAGAAAAATC
*
1371510 AAAGCAAAGCAAAAAT
1 GAAGCAAAG-AAAAAT
1371526 TGATCAAAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
15 5 0.20
16 16 0.64
17 4 0.16
ACGTcount: A:0.62, C:0.13, G:0.21, T:0.04
Consensus pattern (16 bp):
GAAGCAAAGAAAAATC
Found at i:1373393 original size:3 final size:3
Alignment explanation
Indices: 1373385--1373411 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1373375 AGACCAGTGT
1373385 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1373412 AATCCTTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1373556 original size:3 final size:3
Alignment explanation
Indices: 1373548--1373573 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1373538 AAGAACTTCA
1373548 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
1373574 AACAAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1378963 original size:35 final size:35
Alignment explanation
Indices: 1378883--1378963 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 35
1378873 TACTTTACAC
*
1378883 ATCTATATCTGTATCTGATATGGGCTTAGGCCCGA
1 ATCTATATCTGTATCTGATATGGGCTTAGGCCCAA
* ** *
1378918 ATATGCATCTGTGTCTG-TAATGGGCTTAGGCCCAA
1 ATCTATATCTGTATCTGAT-ATGGGCTTAGGCCCAA
1378953 ATCTATATCTG
1 ATCTATATCTG
1378964 ACTGATTCTG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
34 1 0.03
35 36 0.97
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (35 bp):
ATCTATATCTGTATCTGATATGGGCTTAGGCCCAA
Found at i:1382732 original size:17 final size:18
Alignment explanation
Indices: 1382703--1382738 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1382693 TAAATTTAAT
1382703 TTTTATATTTAAAAATGA
1 TTTTATATTTAAAAATGA
*
1382721 TTTTAT-TTTAAATATGA
1 TTTTATATTTAAAAATGA
1382738 T
1 T
1382739 AATAACTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTTATATTTAAAAATGA
Found at i:1385774 original size:17 final size:17
Alignment explanation
Indices: 1385752--1385784 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1385742 GAAATACCTA
1385752 TAAATAATAATT-TTATT
1 TAAAT-ATAATTATTATT
1385769 TAAATATAATTATTAT
1 TAAATATAATTATTAT
1385785 AAATAAATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TAAATATAATTATTATT
Found at i:1394232 original size:22 final size:21
Alignment explanation
Indices: 1394207--1394255 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1394197 TTTTTTATGA
1394207 TTTTTATAAAATTTTACAATTT
1 TTTTTAT-AAATTTTACAATTT
***
1394229 TTTTTATGGTTTTTACAATTT
1 TTTTTATAAATTTTACAATTT
1394250 TTTTTA
1 TTTTTA
1394256 ATTTTTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (21 bp):
TTTTTATAAATTTTACAATTT
Found at i:1394625 original size:14 final size:14
Alignment explanation
Indices: 1394600--1394640 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1394590 CTTACCTAAT
1394600 TGTGCAAGTTGTGA
1 TGTGCAAGTTGTGA
* * *
1394614 TTTGCAAATTGTAA
1 TGTGCAAGTTGTGA
1394628 TGTGCAAGTTGTG
1 TGTGCAAGTTGTG
1394641 CAAGTTGCAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.24, C:0.07, G:0.29, T:0.39
Consensus pattern (14 bp):
TGTGCAAGTTGTGA
Found at i:1397329 original size:14 final size:14
Alignment explanation
Indices: 1397308--1397348 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1397298 CTTACCTAAT
1397308 TGTGCAAGTTGTGA
1 TGTGCAAGTTGTGA
* **
1397322 TTTGCAAGTTGCAA
1 TGTGCAAGTTGTGA
1397336 TGTGCAAGTTGTG
1 TGTGCAAGTTGTG
1397349 CAAGTTGCAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.22, C:0.10, G:0.32, T:0.37
Consensus pattern (14 bp):
TGTGCAAGTTGTGA
Found at i:1398087 original size:281 final size:281
Alignment explanation
Indices: 1397584--1398152 Score: 1075
Period size: 281 Copynumber: 2.0 Consensus size: 281
1397574 ATCTGGATTT
1397584 ATTACGTTGTTGCTCAGGTTTTACACTAAGCTTCATACTTCCTCCGAATAAATAGTTCAAAAACC
1 ATTACGTTGTTGCTCAGGTTTTACACTAAGCTTCATACTTCCTCCGAATAAATAGTTCAAAAACC
*
1397649 TAACAAGATTTCTAGACTTGCTTTCTTACATTACCTTGATTTGATTTATGCAGATCTTTGTAAAG
66 CAACAAGATTTCTAGACTTGCTTTCTTACATTACCTTGATTTGATTTATGCAGATCTTTGTAAAG
1397714 CAATGAACTGGCTGCAGGTAACATACAAACATCCTTCATTTTTAGAGTTGCACTTGTTAGCTTGC
131 CAATGAACTGGCTGCAGGTAACATACAAACATCCTTCATTTTTAGAGTTGCACTTGTTAGCTTGC
1397779 AGTTTGGAAGATGATCCATCCCCTGTCAATGTTAATTCTACTAAATCACTAGTTGTTCTTGATCT
196 AGTTTGGAAGATGATCCATCCCCTGTCAATGTTAATTCTACTAAATCACTAGTTGTTCTTGATCT
1397844 TTCTAGGAACCAATTATCTTC
261 TTCTAGGAACCAATTATCTTC
*
1397865 ATTACGTTGTTGCTCAGGTTTTACATTAAGCTTCATACTTCCTCCGAATAAATAGTTCAAAAACC
1 ATTACGTTGTTGCTCAGGTTTTACACTAAGCTTCATACTTCCTCCGAATAAATAGTTCAAAAACC
* *
1397930 CAACAAGATTTCTAGATTTGCTTTCTTGCATTACCTTGATTTGATTTATGCAGATCTTTGTAAAG
66 CAACAAGATTTCTAGACTTGCTTTCTTACATTACCTTGATTTGATTTATGCAGATCTTTGTAAAG
* *
1397995 TAATGGACTGGCTGCAGGTAACATACAAACATCCTTCATTTTTAGAGTTGCACTTGTTAGCTTGC
131 CAATGAACTGGCTGCAGGTAACATACAAACATCCTTCATTTTTAGAGTTGCACTTGTTAGCTTGC
*
1398060 AGTTTGGAAGATGATCCATCCCCTGTCAGTGTTAATTCTACTAAATCACTAGTTGTTCTTGATCT
196 AGTTTGGAAGATGATCCATCCCCTGTCAATGTTAATTCTACTAAATCACTAGTTGTTCTTGATCT
1398125 TTCTAGGAACCAATTATCTTC
261 TTCTAGGAACCAATTATCTTC
1398146 ATTACGT
1 ATTACGT
1398153 AAGTCGATAT
Statistics
Matches: 281, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
281 281 1.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (281 bp):
ATTACGTTGTTGCTCAGGTTTTACACTAAGCTTCATACTTCCTCCGAATAAATAGTTCAAAAACC
CAACAAGATTTCTAGACTTGCTTTCTTACATTACCTTGATTTGATTTATGCAGATCTTTGTAAAG
CAATGAACTGGCTGCAGGTAACATACAAACATCCTTCATTTTTAGAGTTGCACTTGTTAGCTTGC
AGTTTGGAAGATGATCCATCCCCTGTCAATGTTAATTCTACTAAATCACTAGTTGTTCTTGATCT
TTCTAGGAACCAATTATCTTC
Found at i:1402196 original size:132 final size:132
Alignment explanation
Indices: 1401956--1402242 Score: 418
Period size: 132 Copynumber: 2.2 Consensus size: 132
1401946 TAATTATTCA
* * *
1401956 TTTAAAAATTCTTTGAAACGAAGGCGAGATTTGATATTTGGCAATTCGCGGAAATGTGCCCTAAT
1 TTTAAAAATTCTTTAAAACGAAGACGAGATTTGATATTTGGCAATTCGCGGAAATGTGCCCTAAC
* *
1402021 GTGCTGGGTTGCAATTTCGTGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCACTAATGT
66 GTGCTGGGTTGCAATTTCGTGTTTACTCAAAATAATCGAATATCCCTTCAAAATTTCACTAAGGT
1402086 CT
131 CT
*
1402088 TTTAAAAATTCTTTAAAACGAAGATGAGATTTGATATTTGGCAATTCGCGG-AATCGTGCCCTAA
1 TTTAAAAATTCTTTAAAACGAAGACGAGATTTGATATTTGGCAATTCGCGGAAAT-GTGCCCTAA
* * *
1402152 CGTGTTGGGTTGCAATTTC-TCGTTTACTCAAAATAATC-AGATATCCCTTCGAAATTTCACTCA
65 CGTGCTGGGTTGCAATTTCGT-GTTTACTCAAAATAATCGA-ATATCCCTTCAAAATTTCACTAA
1402215 GGTCT
128 GGTCT
* * *
1402220 TCTAAAAATCCTTCAAAACGAAG
1 TTTAAAAATTCTTTAAAACGAAG
1402243 GCGATACTCA
Statistics
Matches: 140, Mismatches: 12, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
131 5 0.04
132 135 0.96
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (132 bp):
TTTAAAAATTCTTTAAAACGAAGACGAGATTTGATATTTGGCAATTCGCGGAAATGTGCCCTAAC
GTGCTGGGTTGCAATTTCGTGTTTACTCAAAATAATCGAATATCCCTTCAAAATTTCACTAAGGT
CT
Found at i:1402265 original size:132 final size:131
Alignment explanation
Indices: 1401971--1402331 Score: 390
Period size: 132 Copynumber: 2.7 Consensus size: 131
1401961 AAATTCTTTG
* * *
1401971 AAACGAAGGCGAGATTTGATATTTGGCAATTCGCGGAAAT-GTGCCCTAATGTGCTGGGTTGCAA
1 AAACGAA-GAGAGATCTCATATTTGGCAATTCGCGG-AATCGTGCCCTAATGTGCTGGGTTGCAA
* * * *
1402035 TTTCGT-GTTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCACTAATGTCTTTTAAAAATTC
64 TTTC-TCGTTTACTCAAAATAATCGAATATCCCTTCAAAATTTCACTAAGGTCTTCTAAAAATCC
*
1402099 TTTA
128 TTCA
* * * *
1402103 AAACGAAGATGAGATTTGATATTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAAT
1 AAACGAAGA-GAGATCTCATATTTGGCAATTCGCGGAATCGTGCCCTAATGTGCTGGGTTGCAAT
* *
1402168 TTCTCGTTTACTCAAAATAATC-AGATATCCCTTCGAAATTTCACTCAGGTCTTCTAAAAATCCT
65 TTCTCGTTTACTCAAAATAATCGA-ATATCCCTTCAAAATTTCACTAAGGTCTTCTAAAAATCCT
1402232 TCA
129 TCA
* * * * * **
1402235 AAACGAAG-GCGATACTCAGTGTTTGACAATTCG-GGAATCATGCCCTATTGTGCTGGGTTGTGA
1 AAACGAAGAGAGAT-CTCA-TATTTGGCAATTCGCGGAATCGTGCCCTAATGTGCTGGGTTGCAA
** ** *
1402298 TTTCTCGTTTGTTCAAAACGATCGAATATTCCTT
64 TTTCTCGTTTACTCAAAATAATCGAATATCCCTT
1402332 TAGGTTTTCA
Statistics
Matches: 196, Mismatches: 26, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
130 4 0.02
131 59 0.30
132 133 0.68
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (131 bp):
AAACGAAGAGAGATCTCATATTTGGCAATTCGCGGAATCGTGCCCTAATGTGCTGGGTTGCAATT
TCTCGTTTACTCAAAATAATCGAATATCCCTTCAAAATTTCACTAAGGTCTTCTAAAAATCCTTC
A
Found at i:1404244 original size:36 final size:36
Alignment explanation
Indices: 1404204--1404314 Score: 121
Period size: 36 Copynumber: 3.3 Consensus size: 36
1404194 GGGTTACGAG
1404204 TTTGGGGTTTAAGGTTCAATTGTTTGAGGTTCTAGA
1 TTTGGGGTTTAAGGTTCAATTGTTTGAGGTTCTAGA
* * *
1404240 TTTGGGGTTT-AGG-------GTTTGAGATTATATA
1 TTTGGGGTTTAAGGTTCAATTGTTTGAGGTTCTAGA
* *
1404268 TTTAGGGTTTAAGGTTCAATTGTTTGATGTTCTAGA
1 TTTGGGGTTTAAGGTTCAATTGTTTGAGGTTCTAGA
1404304 TTTGGGGTTTA
1 TTTGGGGTTTA
1404315 GAGTTTGAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
28 21 0.36
29 3 0.05
35 3 0.05
36 31 0.53
ACGTcount: A:0.20, C:0.04, G:0.30, T:0.47
Consensus pattern (36 bp):
TTTGGGGTTTAAGGTTCAATTGTTTGAGGTTCTAGA
Found at i:1404257 original size:28 final size:28
Alignment explanation
Indices: 1404225--1404348 Score: 79
Period size: 28 Copynumber: 4.1 Consensus size: 28
1404215 AGGTTCAATT
* * *
1404225 GTTTGAGGTTCTAGATTTGGGGTTTAGG
1 GTTTGAGATTATAGATTTAGGGTTTAGG
*
1404253 GTTTGAGATTATATATTTAGGGTTTAAGG
1 GTTTGAGATTATAGATTTAGGGTTT-AGG
* * *
1404282 TTCAATTGTTTGATG-TTCTAGATTTGGGGTTTAGA
1 -------GTTTGA-GATTATAGATTTAGGGTTTAGG
* *
1404317 GTTTGAAATTATAGATTTAGGGTTTAAG
1 GTTTGAGATTATAGATTTAGGGTTTAGG
1404345 GTTT
1 GTTT
1404349 TGAGTTTGGG
Statistics
Matches: 73, Mismatches: 13, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
28 47 0.64
29 3 0.04
35 2 0.03
36 20 0.27
37 1 0.01
ACGTcount: A:0.23, C:0.02, G:0.29, T:0.46
Consensus pattern (28 bp):
GTTTGAGATTATAGATTTAGGGTTTAGG
Found at i:1404309 original size:64 final size:64
Alignment explanation
Indices: 1404208--1404347 Score: 244
Period size: 64 Copynumber: 2.2 Consensus size: 64
1404198 TACGAGTTTG
* * *
1404208 GGGTTTAAGGTTCAATTGTTTGAGGTTCTAGATTTGGGGTTTAGGGTTTGAGATTATATATTTA
1 GGGTTTAAGGTTCAATTGTTTGAGGTTCTAGATTTGGGGTTTAGAGTTTGAAATTATAGATTTA
*
1404272 GGGTTTAAGGTTCAATTGTTTGATGTTCTAGATTTGGGGTTTAGAGTTTGAAATTATAGATTTA
1 GGGTTTAAGGTTCAATTGTTTGAGGTTCTAGATTTGGGGTTTAGAGTTTGAAATTATAGATTTA
1404336 GGGTTTAAGGTT
1 GGGTTTAAGGTT
1404348 TTGAGTTTGG
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 72 1.00
ACGTcount: A:0.23, C:0.03, G:0.29, T:0.45
Consensus pattern (64 bp):
GGGTTTAAGGTTCAATTGTTTGAGGTTCTAGATTTGGGGTTTAGAGTTTGAAATTATAGATTTA
Found at i:1406459 original size:13 final size:13
Alignment explanation
Indices: 1406441--1406470 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1406431 CCTAATGGGA
1406441 TATTATAGGATAT
1 TATTATAGGATAT
*
1406454 TATTATGGGATAT
1 TATTATAGGATAT
1406467 TATT
1 TATT
1406471 TTTTAGCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (13 bp):
TATTATAGGATAT
Found at i:1408919 original size:13 final size:13
Alignment explanation
Indices: 1408901--1408925 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1408891 TATTGATGTG
1408901 ATTATTAATTTAC
1 ATTATTAATTTAC
1408914 ATTATTAATTTA
1 ATTATTAATTTA
1408926 TTTAATTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTATTAATTTAC
Found at i:1412944 original size:18 final size:18
Alignment explanation
Indices: 1412921--1412973 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
1412911 GACCATTTAC
1412921 GACACTATTTACGTATAT
1 GACACTATTTACGTATAT
*
1412939 GACACTATTCACGTATAT
1 GACACTATTTACGTATAT
** *
1412957 GGTACTATTTAGGTATA
1 GACACTATTTACGTATA
1412974 CAGTACTGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (18 bp):
GACACTATTTACGTATAT
Found at i:1412979 original size:18 final size:18
Alignment explanation
Indices: 1412942--1412996 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
1412932 CGTATATGAC
**
1412942 ACTATTCACGTATATGGT
1 ACTATTCACGTATACAGT
* *
1412960 ACTATTTAGGTATACAGT
1 ACTATTCACGTATACAGT
*
1412978 ACTGTTCACGTATACAGT
1 ACTATTCACGTATACAGT
1412996 A
1 A
1412997 GTTGGGATTG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (18 bp):
ACTATTCACGTATACAGT
Found at i:1416846 original size:12 final size:12
Alignment explanation
Indices: 1416829--1416859 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1416819 GATCAAGACT
1416829 GCAGATAATCCC
1 GCAGATAATCCC
1416841 GCAGATAATCCC
1 GCAGATAATCCC
1416853 GCAGATA
1 GCAGATA
1416860 TGATGACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.35, C:0.29, G:0.19, T:0.16
Consensus pattern (12 bp):
GCAGATAATCCC
Found at i:1419458 original size:23 final size:23
Alignment explanation
Indices: 1419431--1419474 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1419421 TTGGTAGCTA
* *
1419431 CATTAATGGAGCTAATTCAAAGG
1 CATTAAAGGAGCTAAATCAAAGG
*
1419454 CATTAAAGGTGCTAAATCAAA
1 CATTAAAGGAGCTAAATCAAA
1419475 AGGAAGTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (23 bp):
CATTAAAGGAGCTAAATCAAAGG
Found at i:1452055 original size:47 final size:47
Alignment explanation
Indices: 1451998--1452091 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
1451988 TGTTAATAAA
1451998 TTTGGAAAGAAAGCCCATTGAGGTCTTTTTTCTTATTGTTATAAATT
1 TTTGGAAAGAAAGCCCATTGAGGTCTTTTTTCTTATTGTTATAAATT
1452045 TTTGGAAAGAAAGCCCATTGAGGTCTTTTTTCTTATTGTTATAAATT
1 TTTGGAAAGAAAGCCCATTGAGGTCTTTTTTCTTATTGTTATAAATT
1452092 AGGAATTTGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.45
Consensus pattern (47 bp):
TTTGGAAAGAAAGCCCATTGAGGTCTTTTTTCTTATTGTTATAAATT
Found at i:1472111 original size:47 final size:47
Alignment explanation
Indices: 1472054--1472147 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
1472044 TGTTAATAAA
1472054 TTTGGAAAGAAAGCCCATTGAGGTCTTTTTTCTTATTGTTATAAATT
1 TTTGGAAAGAAAGCCCATTGAGGTCTTTTTTCTTATTGTTATAAATT
1472101 TTTGGAAAGAAAGCCCATTGAGGTCTTTTTTCTTATTGTTATAAATT
1 TTTGGAAAGAAAGCCCATTGAGGTCTTTTTTCTTATTGTTATAAATT
1472148 AGGAATTTGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.45
Consensus pattern (47 bp):
TTTGGAAAGAAAGCCCATTGAGGTCTTTTTTCTTATTGTTATAAATT
Found at i:1484496 original size:39 final size:39
Alignment explanation
Indices: 1484453--1484530 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
1484443 TTCTACGAGT
1484453 TTGTTTATTCTTGATCTTAGTGAAAATCATTTCAATGGG
1 TTGTTTATTCTTGATCTTAGTGAAAATCATTTCAATGGG
1484492 TTGTTTATTCTTGATCTTAGTGAAAATCATTTCAATGGG
1 TTGTTTATTCTTGATCTTAGTGAAAATCATTTCAATGGG
1484531 AGTGTACCAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.26, C:0.10, G:0.18, T:0.46
Consensus pattern (39 bp):
TTGTTTATTCTTGATCTTAGTGAAAATCATTTCAATGGG
Found at i:1488109 original size:9 final size:9
Alignment explanation
Indices: 1488097--1488121 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1488087 TTCTATTTTC
1488097 TCTACTGTT
1 TCTACTGTT
1488106 TCTACTGTT
1 TCTACTGTT
1488115 TCTACTG
1 TCTACTG
1488122 CTTTTGCGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.24, G:0.12, T:0.52
Consensus pattern (9 bp):
TCTACTGTT
Found at i:1494590 original size:20 final size:21
Alignment explanation
Indices: 1494547--1494592 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1494537 TACAATTTTT
* * *
1494547 TTTGACACACGATATTTTTCA
1 TTTGAAACACGATATTTATAA
1494568 TTTGAAACAC-ATATTTATAA
1 TTTGAAACACGATATTTATAA
1494588 TTTGA
1 TTTGA
1494593 GAAATTTACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (21 bp):
TTTGAAACACGATATTTATAA
Found at i:1512809 original size:68 final size:68
Alignment explanation
Indices: 1512700--1512831 Score: 237
Period size: 68 Copynumber: 1.9 Consensus size: 68
1512690 ACAACAGGGG
*
1512700 AAAATACATCATTGTAGTCAATTCCCTCCTTCTGAGCGTAGCCTTTAGCTACCAATCTTGCCTTA
1 AAAATACATCATTATAGTCAATTCCCTCCTTCTGAGCGTAGCCTTTAGCTACCAATCTTGCCTTA
1512765 GGA
66 GGA
* *
1512768 AAAATACATTATTATAGTCAATTCCCTCCTTCTGAGCGTAGCCTTTAGCTACTAATCTTGCCTT
1 AAAATACATCATTATAGTCAATTCCCTCCTTCTGAGCGTAGCCTTTAGCTACCAATCTTGCCTT
1512832 GTAGCGAACA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.27, C:0.26, G:0.13, T:0.35
Consensus pattern (68 bp):
AAAATACATCATTATAGTCAATTCCCTCCTTCTGAGCGTAGCCTTTAGCTACCAATCTTGCCTTA
GGA
Found at i:1513256 original size:21 final size:21
Alignment explanation
Indices: 1513230--1513270 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1513220 ATCTGCTCAA
* *
1513230 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
1513251 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
1513271 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:1515222 original size:134 final size:134
Alignment explanation
Indices: 1514982--1515236 Score: 456
Period size: 134 Copynumber: 1.9 Consensus size: 134
1514972 TCATCTTTGA
*
1514982 ATGTCTCATCCATATTTAGCAAATCAGTGACTAACTGATTAAATTTGGTGATGTGATCATTCATT
1 ATGTCTCATCCATACTTAGCAAATCAGTGACTAACTGATTAAATTTGGTGATGTGATCATTCATT
* * * *
1515047 GTGGTACTTGGGACGTATGTGAAGCGAAACAGTCTTTTCTTCAAGTGGAGCTTATTTTGACTGTT
66 GTGGTACCTCGGACGTAAGTGAAACGAAACAGTCTTTTCTTCAAGTGGAGCTTATTTTGACTGTT
1515112 TTTT
131 TTTT
1515116 ATGTCTCATCCATACTTAGCAAATCAGTGACTAACTGATTAAATTTGGTGATGTGATCATTCATT
1 ATGTCTCATCCATACTTAGCAAATCAGTGACTAACTGATTAAATTTGGTGATGTGATCATTCATT
*
1515181 GTGGTACCTCGGACGTAAGTGAAACGAAATAGTCTTTTCTTCAAGTGGAGCTTATT
66 GTGGTACCTCGGACGTAAGTGAAACGAAACAGTCTTTTCTTCAAGTGGAGCTTATT
1515237 CTAACTATTT
Statistics
Matches: 115, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
134 115 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.37
Consensus pattern (134 bp):
ATGTCTCATCCATACTTAGCAAATCAGTGACTAACTGATTAAATTTGGTGATGTGATCATTCATT
GTGGTACCTCGGACGTAAGTGAAACGAAACAGTCTTTTCTTCAAGTGGAGCTTATTTTGACTGTT
TTTT
Found at i:1519479 original size:52 final size:54
Alignment explanation
Indices: 1519334--1519491 Score: 171
Period size: 54 Copynumber: 3.0 Consensus size: 54
1519324 GGACCATGTC
* * * * *
1519334 AACAAGTGATAAGCGATAT-CCATATAATACCATAAT-TGGGCTATGGCATCGAAA
1 AACAAGTGATAAGTGAT-TCCCGTATAAGACCAT-ATCTGGGCTATGGCATTGGAA
* *
1519388 AACAAGTGATAAGTGATTCCCGTATAAGACCATAGCTGGGCTATGGCATTGGAG
1 AACAAGTGATAAGTGATTCCCGTATAAGACCATATCTGGGCTATGGCATTGGAA
* * * *
1519442 AA-AAGTGATAAGTGCTT-TCGTGTAAGACCATATCTGGGATATGGCATTGG
1 AACAAGTGATAAGTGATTCCCGTATAAGACCATATCTGGGCTATGGCATTGG
1519492 TATGATATAT
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
52 29 0.32
53 16 0.18
54 45 0.50
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (54 bp):
AACAAGTGATAAGTGATTCCCGTATAAGACCATATCTGGGCTATGGCATTGGAA
Found at i:1524850 original size:16 final size:17
Alignment explanation
Indices: 1524800--1524850 Score: 50
Period size: 19 Copynumber: 2.9 Consensus size: 17
1524790 ATGGAAATAT
* *
1524800 AATCTTTAAGGATATTC
1 AATCTTGAAGGATATGC
*
1524817 AATCTTAGATATGATATGC
1 AATCTT-GA-AGGATATGC
1524836 AATCTTGAA-GATATG
1 AATCTTGAAGGATATG
1524851 ATCTTGTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 6 0.21
17 7 0.24
18 3 0.10
19 13 0.45
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (17 bp):
AATCTTGAAGGATATGC
Found at i:1524869 original size:22 final size:21
Alignment explanation
Indices: 1524810--1524852 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
1524800 AATCTTTAAG
*
1524810 GATATTCAATCTT--AGATAT
1 GATATGCAATCTTGAAGATAT
1524829 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTTGAAGATAT
1524850 GAT
1 GAT
1524853 CTTGTAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.57
21 9 0.43
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (21 bp):
GATATGCAATCTTGAAGATAT
Found at i:1527114 original size:95 final size:95
Alignment explanation
Indices: 1526951--1527140 Score: 362
Period size: 95 Copynumber: 2.0 Consensus size: 95
1526941 TTTGGCTGTA
1526951 GAGCTTACTTCATAGGTGAAGCCGTAATTCAAATTCAAGAGATAGCTGATCATTTACAGATACTG
1 GAGCTTACTTCATAGGTGAAGCCGTAATTCAAATTCAAGAGATAGCTGATCATTTACAGATACTG
1527016 GTAGAAAGGGCAAGCACGTTGAGCACCAAT
66 GTAGAAAGGGCAAGCACGTTGAGCACCAAT
* *
1527046 GAGCTTACTTCATAGTTGAAGCTGTAATTCAAATTCAAGAGATAGCTGATCATTTACAGATACTG
1 GAGCTTACTTCATAGGTGAAGCCGTAATTCAAATTCAAGAGATAGCTGATCATTTACAGATACTG
1527111 GTAGAAAGGGCAAGCACGTTGAGCACCAAT
66 GTAGAAAGGGCAAGCACGTTGAGCACCAAT
1527141 ATGAGCTACA
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 93 1.00
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (95 bp):
GAGCTTACTTCATAGGTGAAGCCGTAATTCAAATTCAAGAGATAGCTGATCATTTACAGATACTG
GTAGAAAGGGCAAGCACGTTGAGCACCAAT
Found at i:1529839 original size:21 final size:21
Alignment explanation
Indices: 1529799--1529858 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
1529789 TTTTATTTAA
*
1529799 AAAAAGGGAAAAAAAGAAAAG
1 AAAAAGAGAAAAAAAGAAAAG
1529820 AAAAAGAGAAAAATAA-AAAA-
1 AAAAAGAGAAAAA-AAGAAAAG
1529840 AATAAA-A-AAAAAAAGAAAA
1 AA-AAAGAGAAAAAAAGAAAA
1529859 AATGGAGAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
18 2 0.06
19 9 0.26
20 3 0.09
21 19 0.54
22 2 0.06
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (21 bp):
AAAAAGAGAAAAAAAGAAAAG
Found at i:1529840 original size:9 final size:9
Alignment explanation
Indices: 1529828--1529861 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
1529818 AGAAAAAGAG
1529828 AAAAATAAA
1 AAAAATAAA
1529837 AAAAATAAA
1 AAAAATAAA
*
1529846 AAAAAAAAGA
1 AAAAATAA-A
1529856 AAAAAT
1 AAAAAT
1529862 GGAGAGGCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.88, C:0.00, G:0.03, T:0.09
Consensus pattern (9 bp):
AAAAATAAA
Found at i:1529850 original size:27 final size:28
Alignment explanation
Indices: 1529807--1529859 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
1529797 AAAAAAAGGG
*
1529807 AAAAAAAGAAAAGAAAAAGAGAAAAATA
1 AAAAAAAGAAAAGAAAAAAAGAAAAATA
*
1529835 AAAAAAATAAAA-AAAAAAAGAAAAA
1 AAAAAAAGAAAAGAAAAAAAGAAAAA
1529860 ATGGAGAGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.87, C:0.00, G:0.09, T:0.04
Consensus pattern (28 bp):
AAAAAAAGAAAAGAAAAAAAGAAAAATA
Found at i:1529860 original size:28 final size:28
Alignment explanation
Indices: 1529807--1529861 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
1529797 AAAAAAAGGG
* *
1529807 AAAAAAAGAAAAGAAAAAGAGAAAAATA
1 AAAAAAAAAAAAAAAAAAGAGAAAAATA
1529835 AAAAAAATAAAAAAAAAAAGA-AAAAAT
1 AAAAAAA-AAAAAAAAAAAGAGAAAAAT
1529862 GGAGAGGCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.05
Consensus pattern (28 bp):
AAAAAAAAAAAAAAAAAAGAGAAAAATA
Found at i:1530912 original size:41 final size:41
Alignment explanation
Indices: 1530863--1531000 Score: 122
Period size: 41 Copynumber: 3.3 Consensus size: 41
1530853 GATCTTATCT
*
1530863 CCCTAAGCAGTAGTGGAGTAGATCAAAGACTCGCCTTAATC
1 CCCTAAGCAGTAGTGGAGCAGATCAAAGACTCGCCTTAATC
* * * *
1530904 CCCTAAGCAGTAG-GGTAACAG-GCTAAA-ATTACAGATCTT-ATC
1 CCCTAAGCAGTAGTGG-AGCAGATC-AAAGACT-C-G-CCTTAATC
* * *
1530946 TCCCTAAGCAGTAGTGGAGCAAATCGAAGACCCGCCTTAATC
1 -CCCTAAGCAGTAGTGGAGCAGATCAAAGACTCGCCTTAATC
1530988 CCCTAAGCAGTAG
1 CCCTAAGCAGTAG
1531001 GGTAACAGGC
Statistics
Matches: 75, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
40 5 0.07
41 36 0.48
42 8 0.11
43 22 0.29
44 4 0.05
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (41 bp):
CCCTAAGCAGTAGTGGAGCAGATCAAAGACTCGCCTTAATC
Found at i:1530951 original size:84 final size:84
Alignment explanation
Indices: 1530810--1531203 Score: 513
Period size: 84 Copynumber: 4.6 Consensus size: 84
1530800 CAAAATTCAG
* * * * *
1530810 CGCCTTAATCCCCTAAGCAATTGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAGATCTTATCTCCCTAAGCAGTA
*
1530875 GTGGAGTAGATCAAAGACT
66 GTGGAGCAGATCAAAGACT
1530894 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAGATCTTATCTCCCTAAGCAGTA
* * *
1530959 GTGGAGCAAATCGAAGACC
66 GTGGAGCAGATCAAAGACT
*
1530978 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAGATCTTATCTCCCTAAACAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAGATCTTATCTCCCTAAGCAGTA
*
1531043 GAGGAGCAGATCGAAGATGA-T
66 GTGGAGCAGATC-AA-A-GACT
* *
1531064 GCGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAAATCTTATCTCCCTAAGCAGT
1 -CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAGATCTTATCTCCCTAAGCAGT
** **
1531129 AGTGGAGTGGATTGAAGACT
65 AGTGGAGCAGATCAAAGACT
* * * * *
1531149 CGCCTTAA-CTCTCTAAGTAGTAGGGTAATAGGCTAAGATATAGCAGATCTGATCT
1 CGCCTTAATC-CCCTAAGCAGTAGGGTAACAGGCTAAAAT-TA-CAGATCTTATCT
1531204 TCACGTGTTT
Statistics
Matches: 274, Mismatches: 28, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
83 1 0.00
84 184 0.67
85 5 0.02
86 12 0.04
87 72 0.26
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.24
Consensus pattern (84 bp):
CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAGATCTTATCTCCCTAAGCAGTA
GTGGAGCAGATCAAAGACT
Found at i:1531115 original size:171 final size:168
Alignment explanation
Indices: 1530810--1531203 Score: 531
Period size: 171 Copynumber: 2.3 Consensus size: 168
1530800 CAAAATTCAG
* * * * * *
1530810 CGCCTTAATCCCCTAAGCAATTGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAGATCTTATCTCCCTAAACAGTA
* * * *
1530875 GTGGAGTAGATCAAAGACTCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAGAT
66 GAGGAGCAGATCAAAGACTCGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAAAT
1530940 CTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACC
131 CTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACC
1530978 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAGATCTTATCTCCCTAAACAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAGATCTTATCTCCCTAAACAGTA
1531043 GAGGAGCAGATCGAAGATGA-TGCGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTAC
66 GAGGAGCAGATC-AA-A-GACT-CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTAC
*** * *
1531107 AAATCTTATCTCCCTAAGCAGTAGTGGAGTGGATTGAAGACT
127 AAATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACC
* * * * *
1531149 CGCCTTAA-CTCTCTAAGTAGTAGGGTAATAGGCTAAGATATAGCAGATCTGATCT
1 CGCCTTAATC-CCCTAAGCAGTAGGGTAACAGGCTAAAAT-TA-CAGATCTTATCT
1531204 TCACGTGTTT
Statistics
Matches: 199, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
168 69 0.35
169 2 0.01
170 3 0.02
171 112 0.56
172 2 0.01
173 11 0.06
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.24
Consensus pattern (168 bp):
CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAGATCTTATCTCCCTAAACAGTA
GAGGAGCAGATCAAAGACTCGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAAAT
CTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACC
Found at i:1531296 original size:44 final size:44
Alignment explanation
Indices: 1531233--1531933 Score: 349
Period size: 44 Copynumber: 15.9 Consensus size: 44
1531223 CGGATCTAAG
* *
1531233 CAGATTTGGTGTCTCTGTATTGTCAGAGAGCAGATTGAAGACAA
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGACAA
* * **
1531277 CAGATTTGGCGTTTCTGTATTGGCAGAGAGCAGATCGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGACAA
* * *
1531321 CTGATTTGGCATCTCTGTATTTGGT-GGAGAGCAGATCGAAGACATA
1 CAGATTTGGCGTCTCTGTA-TT-GTCAGAGAGCAGATCGAAGACA-A
* * * * * *
1531367 GCTGATTTGGC-TTTCATGTGTT-T-ACGTTGAAGCAAATCTAAG---A
1 -CAGATTTGGCGTCTC-TGTATTGTCA-G-AG-AGCAGATCGAAGACAA
* * * * *
1531410 -TGATTTTGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGACAA
* * * * **
1531453 CAAATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGA
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGACAA
* * * *
1531497 CAGATTTTGCATCTCTGTATTCGGCGGAGAGCAGATCGAAGACATA
1 CAGATTTGGCGTCTCTGTATT-GTCAGAGAGCAGATCGAAGACA-A
* * * * *
1531543 GCTGATTTGGCTTCCACATGT-TTACGT-TGA-AGCA-AGTCTAAG---A
1 -CAGATTTGGCGT-CTC-TGTATT--GTCAGAGAGCAGA-TCGAAGACAA
* * * * *
1531586 -TGATTTGGCATCTCTGTATTGAT-AGAGAGTAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTG-TCAGAGAGCAGATCGAAGACAA
* * * * **
1531629 CAGATTTGGCATCTTTGTATTGGCAGAGAGCAGATCAAAGATGA
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGACAA
** * * *
1531673 CAGATTTGGTATCTCTGTATTTGGCGGAGAGTAGATCGAAGACATA
1 CAGATTTGGCGTCTCTGTA-TTGTCAGAGAGCAGATCGAAGACA-A
* * * * *
1531719 GCTGATTTGGCTTCCACGTGT-TTACGTTA-A-AGCA-AGTCTAAG---A
1 -CAGATTTGGCGT-CTC-TGTATT--GTCAGAGAGCAGA-TCGAAGACAA
* * * *
1531762 -TGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGACAA
*** * *
1531805 CAGATTTGATATCTCTGTATTGGCAGAGAGCAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGACAA
* * *
1531849 TAGATTTGGCATCTCTGTATTGGT-AGAGAGCAGATCGAAGATAGA
1 CAGATTTGGCGTCTCTGTATT-GTCAGAGAGCAGATCGAAGACA-A
*
1531894 -AGATTTGGCGTCTCTGTATTGTCAGAGAGCATATCGAAGA
1 CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGA
1531934 GAAGAACGAC
Statistics
Matches: 520, Mismatches: 87, Indels: 100
0.74 0.12 0.14
Matches are distributed among these distances:
38 3 0.01
39 10 0.02
40 35 0.07
41 36 0.07
42 4 0.01
43 8 0.02
44 276 0.53
45 58 0.11
46 12 0.02
47 60 0.12
48 9 0.02
49 9 0.02
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.30
Consensus pattern (44 bp):
CAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGACAA
Found at i:1531511 original size:176 final size:176
Alignment explanation
Indices: 1531205--1531889 Score: 1014
Period size: 176 Copynumber: 3.9 Consensus size: 176
1531195 ATCTGATCTT
* ** ** * *
1531205 CACGTGTTTACGCTGAAGCGGATCTAAGCA-GATTTGGTGTCTCTGTATTGTCAGAGAGCAGATT
1 CACGTGTTTACGTTGAAGCAAATCTAAG-ATGATTTGGCATCTCTGTATTGGCAGAGAGCAGATC
* * * * *
1531269 GAAGACAACAGATTTGGCGTTTCTGTATTGGCAGAGAGCAGATCGAAGATGACTGATTTGGCATC
65 GAAGATAACAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATC
* *
1531334 TCTGTATTTGGTGGAGAGCAGATCGAAGACATAGCTGATTTGGCTTT
130 TCTGTATTTGGCGGAGAGCAGATCGAAGACATAGCTGATTTGGCTTC
* *
1531381 CATGTGTTTACGTTGAAGCAAATCTAAGATGATTTTGCATCTCTGTATTGGCAGAGAGCAGATCG
1 CACGTGTTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCG
* *
1531446 AAGATAACAAATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGACAGATTTTGCATCT
66 AAGATAACAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCT
*
1531511 CTGTATTCGGCGGAGAGCAGATCGAAGACATAGCTGATTTGGCTTC
131 CTGTATTTGGCGGAGAGCAGATCGAAGACATAGCTGATTTGGCTTC
* * ** *
1531557 CACATGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGATAGAGAGTAGATCG
1 CACGTGTTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCG
* * *
1531622 AAGATAGCAGATTTGGCATCTTTGTATTGGCAGAGAGCAGATCAAAGATGACAGATTTGGTATCT
66 AAGATAACAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCT
*
1531687 CTGTATTTGGCGGAGAGTAGATCGAAGACATAGCTGATTTGGCTTC
131 CTGTATTTGGCGGAGAGCAGATCGAAGACATAGCTGATTTGGCTTC
* *
1531733 CACGTGTTTACGTTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCG
1 CACGTGTTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCG
** * * *
1531798 AAGATAACAGATTTGATATCTCTGTATTGGCAGAGAGCAGATCGAAGATAATAGATTTGGCATCT
66 AAGATAACAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCT
**
1531863 CTGTA-TTGGTAGAGAGCAGATCGAAGA
131 CTGTATTTGGCGGAGAGCAGATCGAAGA
1531890 TAGAAGATTT
Statistics
Matches: 459, Mismatches: 49, Indels: 3
0.90 0.10 0.01
Matches are distributed among these distances:
175 20 0.04
176 439 0.96
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (176 bp):
CACGTGTTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCG
AAGATAACAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCT
CTGTATTTGGCGGAGAGCAGATCGAAGACATAGCTGATTTGGCTTC
Found at i:1532112 original size:44 final size:45
Alignment explanation
Indices: 1532063--1532247 Score: 173
Period size: 44 Copynumber: 4.2 Consensus size: 45
1532053 TATTTTAACA
**
1532063 TGGCATCCCTGTGTTTATTGGGAACAAG-TTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTACAGGGAACAAGATTGAAGATAGCAGATT
** *
1532107 TGGCATCCCTGTGTTTACAGGGAAC-AGATCAAAGACATAGCAGATC
1 TGGCATCCCTGTGTTTACAGGGAACAAGATTGAAG--ATAGCAGATT
* * * * * * **
1532153 TGACATTCCTATGCTTACAGCGAAGAAGATTGAAGATTTCAGCA--
1 TGGCATCCCTGTGTTTACAGGGAACAAGATTGAAGATAGCAG-ATT
* *
1532197 TGGCATCCCTGTGTTTATAGGGAACAAG-TTGAAGATAGTAGATT
1 TGGCATCCCTGTGTTTACAGGGAACAAGATTGAAGATAGCAGATT
1532241 TGGCATC
1 TGGCATC
1532248 TCCATATTCG
Statistics
Matches: 109, Mismatches: 25, Indels: 14
0.74 0.17 0.09
Matches are distributed among these distances:
42 1 0.01
43 12 0.11
44 55 0.50
45 5 0.05
46 29 0.27
47 7 0.06
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (45 bp):
TGGCATCCCTGTGTTTACAGGGAACAAGATTGAAGATAGCAGATT
Found at i:1532171 original size:46 final size:46
Alignment explanation
Indices: 1531987--1532172 Score: 134
Period size: 44 Copynumber: 4.1 Consensus size: 46
1531977 ATCCAAGTGT
* *
1531987 TTACAGGGAACAGATTGAAGACATAGCAGATCTGACATTCCTGTGC
1 TTACAGGGAACAGATCGAAGACATAGCAGATCTGACATCCCTGTGC
* * *** * *
1532033 TTACAGCGAAGCAGATC-AA-ATATTTTA-A-CATGGCATCCCTGTGT
1 TTACAGGGAA-CAGATCGAAGACATAGCAGATC-TGACATCCCTGTGC
** * * * *
1532077 TTATTGGGAACA-AGTTGAAG--ATAGCAGATTTGGCATCCCTGTGT
1 TTACAGGGAACAGA-TCGAAGACATAGCAGATCTGACATCCCTGTGC
* * *
1532121 TTACAGGGAACAGATCAAAGACATAGCAGATCTGACATTCCTATGC
1 TTACAGGGAACAGATCGAAGACATAGCAGATCTGACATCCCTGTGC
1532167 TTACAG
1 TTACAG
1532173 CGAAGAAGAT
Statistics
Matches: 104, Mismatches: 26, Indels: 20
0.69 0.17 0.13
Matches are distributed among these distances:
42 1 0.01
43 7 0.07
44 50 0.48
45 5 0.05
46 36 0.35
47 5 0.05
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (46 bp):
TTACAGGGAACAGATCGAAGACATAGCAGATCTGACATCCCTGTGC
Found at i:1532223 original size:134 final size:136
Alignment explanation
Indices: 1531978--1532324 Score: 448
Period size: 134 Copynumber: 2.6 Consensus size: 136
1531968 GGGGAGCAGA
* * *
1531978 TCCAAGTGTTTACAGGGAACAGATTGAAGACATAGCAGATCTGACATTCCTGTGCTTACAGCGAA
1 TCCATGTGTTTACAGGGAACAGATTAAAGACATAGCAGATCTGACATTCCTATGCTTACAGCGAA
* * * *
1532043 GCAGATCAAATATTTTAACATGGCATCCCTGTGTTTATTGGGAACAAGTTGAAGATAGCAGATTT
66 GAAGATCAAAGATTTCAACATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTT
1532108 GGCATC
131 GGCATC
*
1532114 -CC-TGTGTTTACAGGGAACAGATCAAAGACATAGCAGATCTGACATTCCTATGCTTACAGCGAA
1 TCCATGTGTTTACAGGGAACAGATTAAAGACATAGCAGATCTGACATTCCTATGCTTACAGCGAA
** * *
1532177 GAAGATTGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGTAGATTT
66 GAAGATCAAAGATTTCAACATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTT
1532242 GGCATC
131 GGCATC
* ** * * * * * * * *
1532248 TCCATAT-TCGACGGGGAGCAGATTAAAGACATAGTAGATCTGACCTTCATGTGTTTACATCGAA
1 TCCATGTGTTTACAGGGAACAGATTAAAGACATAGCAGATCTGACATTCCTATGCTTACAGCGAA
* *
1532312 GCAGATCCAAGAT
66 GAAGATCAAAGAT
1532325 GACAGATTTG
Statistics
Matches: 182, Mismatches: 27, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
134 120 0.66
135 60 0.33
136 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (136 bp):
TCCATGTGTTTACAGGGAACAGATTAAAGACATAGCAGATCTGACATTCCTATGCTTACAGCGAA
GAAGATCAAAGATTTCAACATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTT
GGCATC
Found at i:1532391 original size:45 final size:45
Alignment explanation
Indices: 1532320--1532465 Score: 186
Period size: 45 Copynumber: 3.3 Consensus size: 45
1532310 AAGCAGATCC
* * *
1532320 AAGATGACAGATTTGGCATCTTTGTATTAGACGGGGAGCAAATTG
1 AAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATTA
* *
1532365 GAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATTA
1 AAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATTA
* * * * *
1532410 AAGA-AGCAAATTTGGCGTCTCTGTATTAGACGGGGAGCATATCA
1 AAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATTA
*
1532454 AAGATAGCAGAT
1 AAGATAACAGAT
1532466 ATCGCCTTCC
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
44 39 0.44
45 49 0.56
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.26
Consensus pattern (45 bp):
AAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATTA
Found at i:1532437 original size:44 final size:45
Alignment explanation
Indices: 1532330--1532462 Score: 178
Period size: 44 Copynumber: 3.0 Consensus size: 45
1532320 AAGATGACAG
* ** * *
1532330 ATTTGGCATCTTTGTATTAGACGGGGAGCAAATTGGAGATAACAG
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAAATTAAAGATAGCAA
*
1532375 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATTAAAGA-AGCAA
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAAATTAAAGATAGCAA
* * *
1532419 ATTTGGCGTCTCTGTATTAGACGGGGAGCATATCAAAGATAGCA
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAAATTAAAGATAGCA
1532463 GATATCGCCT
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
44 39 0.50
45 39 0.50
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.27
Consensus pattern (45 bp):
ATTTGGCATCTCTGTATTAGACGGGGAGCAAATTAAAGATAGCAA
Found at i:1532837 original size:19 final size:19
Alignment explanation
Indices: 1532813--1532909 Score: 162
Period size: 19 Copynumber: 5.1 Consensus size: 19
1532803 ATCTTTAAGA
1532813 ATATGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
1532832 ATATGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
1532851 ATA--CAATCTTAGATATG
1 ATATGCAATCTTAGATATG
1532868 ATATGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
1532887 ATATGCAATCTTGAAGATATG
1 ATATGCAATCTT--AGATATG
1532908 AT
1 AT
1532910 CTTGTAATCT
Statistics
Matches: 74, Mismatches: 0, Indels: 6
0.93 0.00 0.08
Matches are distributed among these distances:
17 17 0.23
19 48 0.65
21 9 0.12
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (19 bp):
ATATGCAATCTTAGATATG
Found at i:1532858 original size:36 final size:37
Alignment explanation
Indices: 1532817--1532909 Score: 152
Period size: 36 Copynumber: 2.5 Consensus size: 37
1532807 TTAAGAATAT
1532817 GCAATCTTAGATATGATATGCAATCTTAGATATGATA
1 GCAATCTTAGATATGATATGCAATCTTAGATATGATA
1532854 -CAATCTTAGATATGATATGCAATCTTAGATATGATA
1 GCAATCTTAGATATGATATGCAATCTTAGATATGATA
1532890 TGCAATCTTGAAGATATGAT
1 -GCAATCTT--AGATATGAT
1532910 CTTGTAATCT
Statistics
Matches: 52, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
36 36 0.69
38 7 0.13
40 9 0.17
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (37 bp):
GCAATCTTAGATATGATATGCAATCTTAGATATGATA
Found at i:1534634 original size:43 final size:43
Alignment explanation
Indices: 1534567--1534730 Score: 213
Period size: 43 Copynumber: 3.8 Consensus size: 43
1534557 GAAAAAAAGT
* *
1534567 GCCGCTAAAAGTGCTACCTTTTTAGCGGCATTTTCTAAAAAACC
1 GCCGCTAAAAGTGCTGCC-TTTTAGCGGCGTTTTCTAAAAAACC
*
1534611 GCCGCTAAAAGTGCTGCCTTTTAGCGACGTTTTCTAAAAAACC
1 GCCGCTAAAAGTGCTGCCTTTTAGCGGCGTTTTCTAAAAAACC
* * * *
1534654 ACCGCGAAAAGTGCTGCCTTTTAGCGGCGTTTGCTAAAAAAGC
1 GCCGCTAAAAGTGCTGCCTTTTAGCGGCGTTTTCTAAAAAACC
* *
1534697 GCCGCTAAAAGT-CATGGCTTTTAGCTGCGCTTTT
1 GCCGCTAAAAGTGC-TGCCTTTTAGCGGCG-TTTT
1534731 TTAGCAAACT
Statistics
Matches: 105, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
42 1 0.01
43 84 0.80
44 20 0.19
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (43 bp):
GCCGCTAAAAGTGCTGCCTTTTAGCGGCGTTTTCTAAAAAACC
Found at i:1534831 original size:31 final size:32
Alignment explanation
Indices: 1534796--1534878 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 32
1534786 CTTCCTGCAT
*
1534796 TAAAATCCAACCAAAAACAATAAATATAG-TA
1 TAAAATACAACCAAAAACAATAAATATAGATA
** * *
1534827 TAAAATACAGTCAAAAACAGTAAATTTAGCATA
1 TAAAATACAACCAAAAACAATAAATATAG-ATA
*
1534860 AAAAATACAACCAAAAACA
1 TAAAATACAACCAAAAACA
1534879 TTAATTCTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 24 0.57
33 18 0.43
ACGTcount: A:0.61, C:0.16, G:0.05, T:0.18
Consensus pattern (32 bp):
TAAAATACAACCAAAAACAATAAATATAGATA
Found at i:1535146 original size:21 final size:21
Alignment explanation
Indices: 1535122--1535162 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1535112 GCTCGTGCCT
*
1535122 CTGCCTCTCTCGCTGCTACCG
1 CTGCCTCCCTCGCTGCTACCG
*
1535143 CTGCCTCCCTCTCTGCTACC
1 CTGCCTCCCTCGCTGCTACC
1535163 TCCGCTCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.05, C:0.51, G:0.15, T:0.29
Consensus pattern (21 bp):
CTGCCTCCCTCGCTGCTACCG
Found at i:1540475 original size:27 final size:27
Alignment explanation
Indices: 1540444--1540501 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 27
1540434 TCGTAAGTTG
1540444 TTATGTACA-TTATGTGAGTTATGTAAA
1 TTATGTA-ATTTATGTGAGTTATGTAAA
*
1540471 TTATGTAATTTATGTGAGTTATGTAAG
1 TTATGTAATTTATGTGAGTTATGTAAA
1540498 TTAT
1 TTAT
1540502 TTTTTAAGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 1 0.03
27 28 0.97
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (27 bp):
TTATGTAATTTATGTGAGTTATGTAAA
Found at i:1540483 original size:18 final size:18
Alignment explanation
Indices: 1540443--1540501 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
1540433 TTCGTAAGTT
* *
1540443 GTTATGTACATTATGTGA
1 GTTATGTAAATTATGTAA
1540461 GTTATGTAAATTATGTAA
1 GTTATGTAAATTATGTAA
* * *
1540479 TTTATGTGAGTTATGTAA
1 GTTATGTAAATTATGTAA
1540497 GTTAT
1 GTTAT
1540502 TTTTTAAGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47
Consensus pattern (18 bp):
GTTATGTAAATTATGTAA
Found at i:1540923 original size:241 final size:241
Alignment explanation
Indices: 1540500--1541174 Score: 1246
Period size: 241 Copynumber: 2.8 Consensus size: 241
1540490 TATGTAAGTT
*
1540500 ATTTTTTAAGATTCATCATACGTGGCGTTATTACACCTAGGGAGGATCCATTATATCTTACAGCT
1 ATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTACAGCT
*
1540565 CGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAA
66 CGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAAAA
1540630 GGTTGGAGAGAAGGTCAGCTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGGTAATAAATA
131 GGTTGGAGAGAAGGTCAGCTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGGTAATAAATA
1540695 TTCAATAGTAAATGAGCTCGATAGAACTT-TTGTCAAGTCTTTTTGA
196 TTCAATAGTAAATGAGCTCGATAGAACTTCTT-TCAAGTCTTTTTGA
* *
1540741 ATTTTTTAAGATTCATCATACGCGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCT
1 ATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTACAGCT
1540806 CGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAAAA
66 CGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAAAA
* *
1540871 GGTTGGAAAGAAGGTCAACTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGGTAATAAATA
131 GGTTGGAGAGAAGGTCAGCTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGGTAATAAATA
1540936 TTCAATAGTAAATGAGCTCGATAGAACTTCTTTCAAGTCTTTTTGA
196 TTCAATAGTAAATGAGCTCGATAGAACTTCTTTCAAGTCTTTTTGA
1540982 ATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTACAGCT
1 ATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTACAGCT
*
1541047 CGATATAAGGCAACCCGCCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAAAA
66 CGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAAAA
*
1541112 GGTTTGAGAGAAGGTCAGCTATTGTTGTAATTTTAAAT-GACAAGCAAGCTACATGGTAATAAA
131 GGTTGGAGAGAAGGTCAGCTATTGTTGTAATTTT-AATGGACAAGCAAGCTACATGGTAATAAA
1541175 ATTAATTCAT
Statistics
Matches: 420, Mismatches: 12, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
241 415 0.99
242 5 0.01
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (241 bp):
ATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTACAGCT
CGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAAAA
GGTTGGAGAGAAGGTCAGCTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGGTAATAAATA
TTCAATAGTAAATGAGCTCGATAGAACTTCTTTCAAGTCTTTTTGA
Found at i:1543366 original size:25 final size:25
Alignment explanation
Indices: 1543338--1543393 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
1543328 GAGAAGCAGC
1543338 AGAGGGATGCCAACGAAGATGTAGA
1 AGAGGGATGCCAACGAAGATGTAGA
* * * * *
1543363 AGAGAGATGCCGATGGAGATGTAGC
1 AGAGGGATGCCAACGAAGATGTAGA
1543388 AGAGGG
1 AGAGGG
1543394 CTACCGACAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.11, G:0.41, T:0.12
Consensus pattern (25 bp):
AGAGGGATGCCAACGAAGATGTAGA
Found at i:1545441 original size:20 final size:18
Alignment explanation
Indices: 1545396--1545433 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1545386 GAAAGGTTGA
*
1545396 GAAAGAAAAGGGAATTGG
1 GAAAGAAAAGGGAATGGG
1545414 GAAAGAAAAGGGAATCGGG
1 GAAAGAAAAGGGAAT-GGG
1545433 G
1 G
1545434 GAGAGAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.47, C:0.03, G:0.42, T:0.08
Consensus pattern (18 bp):
GAAAGAAAAGGGAATGGG
Found at i:1545671 original size:22 final size:20
Alignment explanation
Indices: 1545644--1545700 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 20
1545634 TGTTTGACTT
1545644 TTTTATAATTTTTATATTGAA
1 TTTTATAATTTTTATATT-AA
1545665 TTATTAT-ATCTTTTATATTAA
1 TT-TTATAAT-TTTTATATTAA
1545686 TTTTAAATAATTTTT
1 TTTT--ATAATTTTT
1545701 TTAAAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
20 2 0.06
21 8 0.26
22 19 0.61
23 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTATAATTTTTATATTAA
Found at i:1546164 original size:7 final size:7
Alignment explanation
Indices: 1546033--1546164 Score: 77
Period size: 7 Copynumber: 18.6 Consensus size: 7
1546023 TCCCCTAAAT
*
1546033 TAAACCC
1 TAAACCA
*
1546040 TAAATCA
1 TAAACCA
1546047 TACAA-CA
1 TA-AACCA
* *
1546054 TAACCCT
1 TAAACCA
1546061 TAAACCCA
1 TAAA-CCA
*
1546069 TAACCCA
1 TAAACCA
*
1546076 TAATCCA
1 TAAACCA
* *
1546083 TAACCCC
1 TAAACCA
*
1546090 TAAACCT
1 TAAACCA
1546097 TAAACCA
1 TAAACCA
* * *
1546104 CAACCCT
1 TAAACCA
*
1546111 TAAACTA
1 TAAACCA
*
1546118 TAAACTA
1 TAAACCA
1546125 TAAACCA
1 TAAACCA
*
1546132 TAATCCA
1 TAAACCA
1546139 TAAACCCA
1 TAAA-CCA
*
1546147 TAATCCA
1 TAAACCA
*
1546154 TAAACCT
1 TAAACCA
1546161 TAAA
1 TAAA
1546165 ATAGTAACTC
Statistics
Matches: 95, Mismatches: 26, Indels: 8
0.74 0.20 0.06
Matches are distributed among these distances:
6 1 0.01
7 81 0.85
8 13 0.14
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCA
Found at i:1546477 original size:24 final size:24
Alignment explanation
Indices: 1546449--1546497 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
1546439 CCAAAATAAC
* *
1546449 AATTAATTTTTATATAGACTTTTA
1 AATTAAATTTTATATAAACTTTTA
1546473 AATTAAATTTTATATAAACTTTTA
1 AATTAAATTTTATATAAACTTTTA
1546497 A
1 A
1546498 TAAATATAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (24 bp):
AATTAAATTTTATATAAACTTTTA
Found at i:1546500 original size:11 final size:12
Alignment explanation
Indices: 1546456--1546501 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
1546446 AACAATTAAT
*
1546456 TTTTATATAGAC
1 TTTTATATAAAC
*
1546468 TTTTAAATTAAA-
1 TTTTATA-TAAAC
1546480 TTTTATATAAAC
1 TTTTATATAAAC
1546492 TTTTA-ATAAA
1 TTTTATATAAA
1546502 TATAGGAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 9 0.31
12 17 0.59
13 3 0.10
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.50
Consensus pattern (12 bp):
TTTTATATAAAC
Found at i:1550595 original size:26 final size:26
Alignment explanation
Indices: 1550564--1550671 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
1550554 TGAAATGCCC
*
1550564 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
1550590 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
1550616 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
1550642 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
1550668 ATCA
1 ATCA
1550672 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:1557694 original size:26 final size:26
Alignment explanation
Indices: 1557663--1557770 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
1557653 TGAAATGCCC
*
1557663 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
1557689 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
1557715 ATCATGGAATATTTGCCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
1557741 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
1557767 ATCA
1 ATCA
1557771 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:1558798 original size:21 final size:21
Alignment explanation
Indices: 1558768--1558807 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1558758 TAAAAATATA
*
1558768 AAAAAAAATATTAAAACAAAT
1 AAAAAAAATACTAAAACAAAT
*
1558789 AAAAATAATACTAAAACAA
1 AAAAAAAATACTAAAACAA
1558808 TTCTTAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.17
Consensus pattern (21 bp):
AAAAAAAATACTAAAACAAAT
Found at i:1561339 original size:42 final size:41
Alignment explanation
Indices: 1561270--1561400 Score: 140
Period size: 42 Copynumber: 3.1 Consensus size: 41
1561260 AGCGGCGTTT
*
1561270 GCGGTGCTTTTACTGA-AAACGCTGCTATAGAACATGCCTTTA
1 GCGG-GCTTTTACT-ACAAACGCCGCTATAGAACATGCCTTTA
*
1561312 G-GAGCGCTTTTACTACAAACGCCGCTATAGAACATGAGCTTTA
1 GCG-G-GCTTTTACTACAAACGCCGCTATAGAACATG-CCTTTA
** * *
1561355 GCGGTATTTTACTACAAACGCCACTATAGAACATTACCTTTA
1 GCGGGCTTTTACTACAAACGCCGCTATAGAACA-TGCCTTTA
1561397 GCGG
1 GCGG
1561401 CACTTCCAAG
Statistics
Matches: 76, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
41 2 0.03
42 65 0.86
43 8 0.11
44 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (41 bp):
GCGGGCTTTTACTACAAACGCCGCTATAGAACATGCCTTTA
Found at i:1561466 original size:42 final size:42
Alignment explanation
Indices: 1561393--1561493 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
1561383 GAACATTACC
* * *
1561393 TTTAGCGGCACTTCCAAGCAAAATGCCGCTAAAGAATAAGACT
1 TTTAGCGGCACTT-TAAGAAAAATGCCGCTAAAGAACAAGACT
* * *
1561436 TTTAGCGGCGCTTTAAGAAAAATGCTGCTAACGAACAAGACT
1 TTTAGCGGCACTTTAAGAAAAATGCCGCTAAAGAACAAGACT
*
1561478 TTTAGTGGCACTTTAA
1 TTTAGCGGCACTTTAA
1561494 TCAAATACGT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
42 38 0.76
43 12 0.24
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (42 bp):
TTTAGCGGCACTTTAAGAAAAATGCCGCTAAAGAACAAGACT
Found at i:1561676 original size:19 final size:19
Alignment explanation
Indices: 1561627--1561676 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
1561617 CACCAAAAAT
* *
1561627 AGCAAATACAAAGCCATCT
1 AGCAAATACAAAGCCAACC
1561646 AGCAAATACAAAGCCAACC
1 AGCAAATACAAAGCCAACC
1561665 AG-AAATAGCAAA
1 AGCAAATA-CAAA
1561677 TATAAATGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 5 0.18
19 23 0.82
ACGTcount: A:0.54, C:0.24, G:0.12, T:0.10
Consensus pattern (19 bp):
AGCAAATACAAAGCCAACC
Found at i:1562702 original size:17 final size:17
Alignment explanation
Indices: 1562680--1562713 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1562670 GTTGGAATAA
1562680 CTTTTGTAGTGCAATTC
1 CTTTTGTAGTGCAATTC
1562697 CTTTTGTAGTGCAATTC
1 CTTTTGTAGTGCAATTC
1562714 TTAGTGAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.47
Consensus pattern (17 bp):
CTTTTGTAGTGCAATTC
Found at i:1563233 original size:85 final size:85
Alignment explanation
Indices: 1563135--1563569 Score: 446
Period size: 86 Copynumber: 5.1 Consensus size: 85
1563125 GAAAAAAATA
* * * *
1563135 CCGCTAAAAACCAGGACCTTTAGCGGCGCTCTTAAAAAAACGCCGCCAAAGACCAGGACCTATAG
1 CCGCTAAAGACCAGGAACTTTAGCGGCGCTTTTAAAAAAACGCCGCCAAAGACCAGGACCTTTAG
*
1563200 CGGCG-TTTTTTATAAAAGCG
66 CGGCGCTTTTTTA-AAAAACG
* * * * *
1563220 CCGCTAAAGACCAGGACCTTTAGCGGCGCTCTTAAAAAAGCGACGCCAAAGACCAGGACCTATAG
1 CCGCTAAAGACCAGGAACTTTAGCGGCGCTTTTAAAAAAACGCCGCCAAAGACCAGGACCTTTAG
** *
1563285 CAACG-TTTTTTATAAAAGCG
66 CGGCGCTTTTTTA-AAAAACG
* * * * *
1563305 CCGCTAAAAGTA-CA-GTACTATAGCGGCGTTTTTTATAAAAGCGCCGCCAAAGACCAGGACCTT
1 CCGCT-AAAG-ACCAGGAACTTTAGCGGCG-CTTTTAAAAAAACGCCGCCAAAGACCAGGACCTT
*
1563368 TAGCGGGGCTTTTTTAAAAAACG
63 TAGCGGCGCTTTTTTAAAAAACG
** * * * * * * *
1563391 CCGCTGTAGACCAAGAACTTTAGCGGCGCTTTTATAAAAAACGTCGCTATAGACCTGTACTTTTA
1 CCGCTAAAGACCAGGAACTTTAGCGGCGCTTTTA-AAAAAACGCCGCCAAAGACCAGGACCTTTA
1563456 GCGGCGCTTTTTTAAAAAACG
65 GCGGCGCTTTTTTAAAAAACG
** * * * * * * *
1563477 CCGCTGTAGACCAAGAACTTTAGCGGCGCTTTTATAAAAAACGTCGCTATAGACCTGTACTTTTA
1 CCGCTAAAGACCAGGAACTTTAGCGGCGCTTTTA-AAAAAACGCCGCCAAAGACCAGGACCTTTA
1563542 GCGGCGCTTTTTTAAAAAACG
65 GCGGCGCTTTTTTAAAAAACG
1563563 CCGCTAA
1 CCGCTAA
1563570 TTTGCTCAGT
Statistics
Matches: 310, Mismatches: 33, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
84 1 0.00
85 105 0.34
86 196 0.63
87 8 0.03
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (85 bp):
CCGCTAAAGACCAGGAACTTTAGCGGCGCTTTTAAAAAAACGCCGCCAAAGACCAGGACCTTTAG
CGGCGCTTTTTTAAAAAACG
Found at i:1563236 original size:43 final size:43
Alignment explanation
Indices: 1563135--1563569 Score: 368
Period size: 43 Copynumber: 10.2 Consensus size: 43
1563125 GAAAAAAATA
* * * *
1563135 CCGCTAAAAACCAGGACCTTTAGCGGCG-CTCTTAAAAAAACG
1 CCGCTAAAGACCAGGACCTTTAGCGGCGTTTTTTATAAAAACG
* * *
1563177 CCGCCAAAGACCAGGACCTATAGCGGCGTTTTTTATAAAAGCG
1 CCGCTAAAGACCAGGACCTTTAGCGGCGTTTTTTATAAAAACG
* *
1563220 CCGCTAAAGACCAGGACCTTTAGCGGCG-CTCTTA-AAAAAGCG
1 CCGCTAAAGACCAGGACCTTTAGCGGCGTTTTTTATAAAAA-CG
* * * ** *
1563262 ACGCCAAAGACCAGGACCTATAGCAACGTTTTTTATAAAAGCG
1 CCGCTAAAGACCAGGACCTTTAGCGGCGTTTTTTATAAAAACG
* * *
1563305 CCGCTAAAAGTA-CAGTA-CTATAGCGGCGTTTTTTATAAAAGCG
1 CCGCT-AAAG-ACCAGGACCTTTAGCGGCGTTTTTTATAAAAACG
* *
1563348 CCGCCAAAGACCAGGACCTTTAGCGGGGCTTTTTTA-AAAAACG
1 CCGCTAAAGACCAGGACCTTTAGCGGCG-TTTTTTATAAAAACG
** * * *
1563391 CCGCTGTAGACCAAGAACTTTAGCGGCG-CTTTTATAAAAAACG
1 CCGCTAAAGACCAGGACCTTTAGCGGCGTTTTTTAT-AAAAACG
* * * * *
1563434 TCGCTATAGACCTGTACTTTTAGCGGCGCTTTTTTA-AAAAACG
1 CCGCTAAAGACCAGGACCTTTAGCGGCG-TTTTTTATAAAAACG
** * * *
1563477 CCGCTGTAGACCAAGAACTTTAGCGGCG-CTTTTATAAAAAACG
1 CCGCTAAAGACCAGGACCTTTAGCGGCGTTTTTTAT-AAAAACG
* * * * *
1563520 TCGCTATAGACCTGTACTTTTAGCGGCGCTTTTTTA-AAAAACG
1 CCGCTAAAGACCAGGACCTTTAGCGGCG-TTTTTTATAAAAACG
1563563 CCGCTAA
1 CCGCTAA
1563570 TTTGCTCAGT
Statistics
Matches: 313, Mismatches: 63, Indels: 33
0.77 0.15 0.08
Matches are distributed among these distances:
41 15 0.05
42 62 0.20
43 206 0.66
44 19 0.06
45 11 0.04
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (43 bp):
CCGCTAAAGACCAGGACCTTTAGCGGCGTTTTTTATAAAAACG
Found at i:1563489 original size:129 final size:128
Alignment explanation
Indices: 1563152--1563569 Score: 436
Period size: 129 Copynumber: 3.3 Consensus size: 128
1563142 AAACCAGGAC
* * *
1563152 CTTTAGCGGCGCTCTTA-AAAAAACGCCGCCAAAGACCAGGACCTATAGCGGCGTTTTTTATAAA
1 CTTTAGCGGCGCTTTTATAAAAAACGCCGCTAAAGACCAGTA-CTATAGCGGCGTTTTTTATAAA
* * * * *
1563216 AGCGCCGCTAAAGACCAGGACCTTTAGCGGCGC--TCTTAAAAAAGCGACGCCAAAGACCAGGAC
65 AGCGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTTTAAAAAA-CGACGCTATAGACCAAGAA
* ** * *
1563279 CTATAGCAACG-TTTTTTATAAAAGCGCCGCTAAAAGTA-CAGTACTATAGCGGCGTTTTTTATA
1 CTTTAGCGGCGCTTTTATA-AAAAACGCCGCT-AAAG-ACCAGTACTATAGCGGCGTTTTTTATA
* * * *
1563342 AAAGCGCCGCCAAAGACCAGGACCTTTAGCGGGGCTTTTTTAAAAAACGCCGCTGTAGACCAAGA
63 AAAGCGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTTTAAAAAACGACGCTATAGACCAAGA
1563407 A
128 A
* * * *
1563408 CTTTAGCGGCGCTTTTATAAAAAACGTCGCTATAGACCTGTACTTTTAGCGGCGCTTTTTTA-AA
1 CTTTAGCGGCGCTTTTATAAAAAACGCCGCTAAAGACCAGTAC-TATAGCGGCG-TTTTTTATAA
* ** * * * * * *
1563472 AAACGCCGCTGTAGACCAAGAACTTTAGCGGCGCTTTTATAAAAAACGTCGCTATAGACC-TGTA
64 AAGCGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTTTAAAAAACGACGCTATAGACCAAGAA
*
1563536 CTTTTAGCGGCGCTTTTTTAAAAAACGCCGCTAA
1 C-TTTAGCGGCGCTTTTATAAAAAACGCCGCTAA
1563570 TTTGCTCAGT
Statistics
Matches: 239, Mismatches: 41, Indels: 20
0.80 0.14 0.07
Matches are distributed among these distances:
126 3 0.01
127 10 0.04
128 74 0.31
129 129 0.54
130 23 0.10
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (128 bp):
CTTTAGCGGCGCTTTTATAAAAAACGCCGCTAAAGACCAGTACTATAGCGGCGTTTTTTATAAAA
GCGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTTTAAAAAACGACGCTATAGACCAAGAA
Found at i:1564480 original size:18 final size:18
Alignment explanation
Indices: 1564448--1564485 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1564438 TACAATATAG
1564448 TAGTAAAAATATTATTTAA
1 TAGTAAAAATATTA-TTAA
*
1564467 TAGTAAAAA-GTTATTAA
1 TAGTAAAAATATTATTAA
1564484 TA
1 TA
1564486 CTTGATAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
TAGTAAAAATATTATTAA
Found at i:1565563 original size:25 final size:26
Alignment explanation
Indices: 1565535--1565583 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
1565525 ACATTACATA
1565535 TAAATAAAAAATCATAAA-ATCTTAC
1 TAAATAAAAAATCATAAATATCTTAC
* * *
1565560 TAAATCATAAATCGTAAATATCTT
1 TAAATAAAAAATCATAAATATCTT
1565584 CGTCCACATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (26 bp):
TAAATAAAAAATCATAAATATCTTAC
Found at i:1570052 original size:21 final size:21
Alignment explanation
Indices: 1570028--1570067 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1570018 AAATTAATTC
*
1570028 ATACTTAAGTTGAATCAAATA
1 ATACTTAAGTTGAACCAAATA
1570049 ATACTTAAGTTGAACCAAA
1 ATACTTAAGTTGAACCAAA
1570068 ATATAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.30
Consensus pattern (21 bp):
ATACTTAAGTTGAACCAAATA
Found at i:1570512 original size:21 final size:21
Alignment explanation
Indices: 1570488--1570527 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1570478 AAATTAATTC
*
1570488 ATACTTAAGTTGAATCAAATA
1 ATACTTAAGTTGAACCAAATA
1570509 ATACTTAAGTTGAACCAAA
1 ATACTTAAGTTGAACCAAA
1570528 ATATAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.30
Consensus pattern (21 bp):
ATACTTAAGTTGAACCAAATA
Found at i:1571315 original size:477 final size:477
Alignment explanation
Indices: 1569675--1574709 Score: 9569
Period size: 477 Copynumber: 10.7 Consensus size: 477
1569665 TATAACAAAA
*
1569675 TTTTAAAGACATTTAAAAATAATAAATATTAAAATCAAACATGT-TTAATATAACAAAATAGTAA
1 TTTTAAAGACATTTAAAAATATTAAATATTAAAATCAAACAT-TATTAATATAACAAAATAGTAA
1569739 TTTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATT
65 TTTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATT
1569804 AAGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAATTCTTTTTGAATTTTTTAAGATTC
130 AAGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAATTCTTTTTGAATTTTTTAAGATTC
1569869 ATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAAC
195 ATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAAC
1569934 CCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATGGACAAGCA
260 CCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATGGACAAGCA
*
1569999 AGCTACATATATGGTAAT--AA--AA-T--TA---ATTCATACTTAAGTTGAATCAAATAATACT
325 AGCTACATATATGGTAATAAAATTAATTCATACTTATTCATACTTAAGTTGAATCAAATAATAAT
*
1570054 TAAGTTGAACCAAAATATAAAAACTTATTCATAC---TTCA-A-AT--AATAATTAA-TAATACT
390 TAAGTTGAACCAAAATATAAAAACTTATTCATACTTATTCATACTTCAAATAA-TAATTAATACT
*
1570111 ATTTTGATAAAAATTAGTTATAAA
454 ATTTTGATAAAAATTAGTTATAAC
*
1570135 TTTTAAAGACATTTAAAAATAATAAATATTAAAATCAAACATGT-TTAATATAACAAAATAGTAA
1 TTTTAAAGACATTTAAAAATATTAAATATTAAAATCAAACAT-TATTAATATAACAAAATAGTAA
1570199 TTTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATT
65 TTTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATT
1570264 AAGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAATTCTTTTTGAATTTTTTAAGATTC
130 AAGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAATTCTTTTTGAATTTTTTAAGATTC
1570329 ATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAAC
195 ATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAAC
1570394 CCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATGGACAAGCA
260 CCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATGGACAAGCA
*
1570459 AGCTACATATATGGTAAT--AA--AA-T--TA---ATTCATACTTAAGTTGAATCAAATAATACT
325 AGCTACATATATGGTAATAAAATTAATTCATACTTATTCATACTTAAGTTGAATCAAATAATAAT
1570514 TAAGTTGAACCAAAATATAAAAACTTATTCATACTTATTCATACTTCAAATAATAATTAATACTA
390 TAAGTTGAACCAAAATATAAAAACTTATTCATACTTATTCATACTTCAAATAATAATTAATACTA
1570579 TTTTGATAAAAATTAGTTATAAC
455 TTTTGATAAAAATTAGTTATAAC
1570602 TTTTAAAGACATTTAAAAATATTAAATATTAAAATCAAACATGT-TTAATATAACAAAATAGTAA
1 TTTTAAAGACATTTAAAAATATTAAATATTAAAATCAAACAT-TATTAATATAACAAAATAGTAA
1570666 TTTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATT
65 TTTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATT
1570731 AAGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAATTCTTTTTGAATTTTTTAAGATTC
130 AAGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAATTCTTTTTGAATTTTTTAAGATTC
1570796 ATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAAC
195 ATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAAC
1570861 CCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATGGACAAGCA
260 CCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATGGACAAGCA
1570926 AGCTACATATATGGTAATAAAATTAATTCATACTTATTCATACTTAAGTTGAATCAAATAATAAT
325 AGCTACATATATGGTAATAAAATTAATTCATACTTATTCATACTTAAGTTGAATCAAATAATAAT
1570991 TAAGTTGAACCAAAATATAAAAACTTATTCATACTTATTCATACTTCAAATAATAATTAATACTA
390 TAAGTTGAACCAAAATATAAAAACTTATTCATACTTATTCATACTTCAAATAATAATTAATACTA
1571056 TTTTGATAAAAATTAGTTATAAC
455 TTTTGATAAAAATTAGTTATAAC
1571079 TTTTAAAGACATTTAAAAATATTAAATATTAAAATCAAACATTATTAATATAACAAAATAGTAAT
1 TTTTAAAGACATTTAAAAATATTAAATATTAAAATCAAACATTATTAATATAACAAAATAGTAAT
1571144 TTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTA
66 TTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTA
1571209 AGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAATTCTTTTTGAATTTTTTAAGATTCA
131 AGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAATTCTTTTTGAATTTTTTAAGATTCA
1571274 TCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAACC
196 TCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAACC
1571339 CGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATGGACAAGCAA
261 CGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATGGACAAGCAA
1571404 GCTACATATATGGTAATAAAATTAATTCATACTTATTCATACTTAAGTTGAATCAAATAATAATT
326 GCTACATATATGGTAATAAAATTAATTCATACTTATTCATACTTAAGTTGAATCAAATAATAATT
1571469 AAGTTGAACCAAAATATAAAAACTTATTCATACTTATTCATACTTCAAATAATAATTAATACTAT
391 AAGTTGAACCAAAATATAAAAACTTATTCATACTTATTCATACTTCAAATAATAATTAATACTAT
1571534 TTTGATAAAAATTAGTTATAAC
456 TTTGATAAAAATTAGTTATAAC
1571556 TTTTAAAGACATTTAAAAATATTAAATATTAAAATCAAACATTATTAATATAACAAAATAGTAAT
1 TTTTAAAGACATTTAAAAATATTAAATATTAAAATCAAACATTATTAATATAACAAAATAGTAAT
*
1571621 TTGAATATAATAATATCAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTA
66 TTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTA
1571686 AGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAATTCTTTTTGAATTTTTTAAGATTCA
131 AGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAATTCTTTTTGAATTTTTTAAGATTCA
1571751 TCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAACC
196 TCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAACC
1571816 CGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATGGACAAGCAA
261 CGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATGGACAAGCAA
1571881 GCTACATATATGGTAATAAAATTAATTCATACTTATTCATACTTAAGTTGAATCAAATAATAATT
326 GCTACATATATGGTAATAAAATTAATTCATACTTATTCATACTTAAGTTGAATCAAATAATAATT
1571946 AAGTTGAACCAAAATATAAAAACTTATTCATACTTATTCATACTTCAAATAATAATTAATACTAT
391 AAGTTGAACCAAAATATAAAAACTTATTCATACTTATTCATACTTCAAATAATAATTAATACTAT
*
1572011 TTTGATAAAAATTATTTATAAC
456 TTTGATAAAAATTAGTTATAAC
1572033 TTTTAAAGACATTTAAAAATATTAAATATTAAAATCAAACATTATTAATATAACAAAATAGTAAT
1 TTTTAAAGACATTTAAAAATATTAAATATTAAAATCAAACATTATTAATATAACAAAATAGTAAT
1572098 TTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTA
66 TTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTA
1572163 AGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAATTCTTTTTGAATTTTTTAAGATTCA
131 AGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAATTCTTTTTGAATTTTTTAAGATTCA
1572228 TCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAACC
196 TCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAACC
1572293 CGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATGGACAAGCAA
261 CGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATGGACAAGCAA
1572358 GCTACATATATGGTAATAAAATTAATTCATACTTATTCATACTTAAGTTGAATCAAATAATAATT
326 GCTACATATATGGTAATAAAATTAATTCATACTTATTCATACTTAAGTTGAATCAAATAATAATT
1572423 AAGTTGAACCAAAATATAAAAACTTATTCATACTTATTCATACTTCAAATAATAATTAATACTAT
391 AAGTTGAACCAAAATATAAAAACTTATTCATACTTATTCATACTTCAAATAATAATTAATACTAT
1572488 TTTGATAAAAATTAGTTATAAC
456 TTTGATAAAAATTAGTTATAAC
*
1572510 TTTTAAAGACATTTAAAAATATTAAATATTAAAATCAAACATTTTTAATATAACAAAATAGTAAT
1 TTTTAAAGACATTTAAAAATATTAAATATTAAAATCAAACATTATTAATATAACAAAATAGTAAT
1572575 TTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTA
66 TTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTA
1572640 AGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAATTCTTTTTGAATTTTTTAAGATTCA
131 AGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAATTCTTTTTGAATTTTTTAAGATTCA
1572705 TCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAACC
196 TCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAACC
1572770 CGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATGGACAAGCAA
261 CGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATGGACAAGCAA
1572835 GCTACATATATGGTAATAAAATTAATTCATACTTATTCATACTTAAGTTGAATCAAATAATAATT
326 GCTACATATATGGTAATAAAATTAATTCATACTTATTCATACTTAAGTTGAATCAAATAATAATT
1572900 AAGTTGAACCAAAATATAAAAACTTATTCATACTTATTCATACTTCAAATAATAATTAATACTAT
391 AAGTTGAACCAAAATATAAAAACTTATTCATACTTATTCATACTTCAAATAATAATTAATACTAT
1572965 TTTGATAAAAATTAGTTATAAC
456 TTTGATAAAAATTAGTTATAAC
*
1572987 TTTTAAAGACATTTAAAAATATTAAATATTAAAATCACACATTATTAATATAACAAAATAGTAAT
1 TTTTAAAGACATTTAAAAATATTAAATATTAAAATCAAACATTATTAATATAACAAAATAGTAAT
1573052 TTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTA
66 TTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTA
1573117 AGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAATTCTTTTTGAATTTTTTAAGATTCA
131 AGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAATTCTTTTTGAATTTTTTAAGATTCA
1573182 TCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAACC
196 TCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAACC
1573247 CGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATGGACAAGCAA
261 CGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATGGACAAGCAA
1573312 GCTACATATATGGTAATAAAATTAATTCATACTTATTCATACTTAAGTTGAATCAAATAATAATT
326 GCTACATATATGGTAATAAAATTAATTCATACTTATTCATACTTAAGTTGAATCAAATAATAATT
1573377 AAGTTGAACCAAAATATAAAAACTTATTCATACTTATTCATACTTCAAATAATAATTAATACTAT
391 AAGTTGAACCAAAATATAAAAACTTATTCATACTTATTCATACTTCAAATAATAATTAATACTAT
1573442 TTTGATAAAAATTAGTTATAAC
456 TTTGATAAAAATTAGTTATAAC
1573464 TTTTAAAGACATTTAAAAATATTAAATATTAAAATCAAACATTATTAATATAACAAAATAGTAAT
1 TTTTAAAGACATTTAAAAATATTAAATATTAAAATCAAACATTATTAATATAACAAAATAGTAAT
1573529 TTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTA
66 TTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTA
1573594 AGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAATTCTTTTTGAATTTTTTAAGATTCA
131 AGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAATTCTTTTTGAATTTTTTAAGATTCA
1573659 TCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAACC
196 TCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAACC
1573724 CGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATGGACAAGCAA
261 CGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATGGACAAGCAA
*
1573789 GCTACATATATGGTAAT--AA--AA-T--TA---ATTCATACTTAAGTTGAATCAAATAATACTT
326 GCTACATATATGGTAATAAAATTAATTCATACTTATTCATACTTAAGTTGAATCAAATAATAATT
*
1573844 AAGTTGAACCAAAATATAAAAACTTATTCATACTTATTCATACTTCAAATAATTATTAATACTAT
391 AAGTTGAACCAAAATATAAAAACTTATTCATACTTATTCATACTTCAAATAATAATTAATACTAT
1573909 TTTGATAAAAATTAGTTATAAC
456 TTTGATAAAAATTAGTTATAAC
1573931 TTTTAAAGACATTTAAAAATATTAAATATTAAAATCAAACATTATTAATATAACAAAATAGTAAT
1 TTTTAAAGACATTTAAAAATATTAAATATTAAAATCAAACATTATTAATATAACAAAATAGTAAT
1573996 TTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTA
66 TTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTA
1574061 AGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAATTCTTTTTGAATTTTTTAAGATTCA
131 AGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAATTCTTTTTGAATTTTTTAAGATTCA
1574126 TCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAACC
196 TCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAACC
1574191 CGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATGGACAAGCAA
261 CGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATGGACAAGCAA
1574256 GCTACATATATGGTAAT--AA--AA-T--TA---ATTCATACTTAAGTTGAATCAAATAATAATT
326 GCTACATATATGGTAATAAAATTAATTCATACTTATTCATACTTAAGTTGAATCAAATAATAATT
1574311 AAGTTGAACCAAAATATAAAAACTTATTCATACTTATTCATACTTCAAATAATAATTAATACTAT
391 AAGTTGAACCAAAATATAAAAACTTATTCATACTTATTCATACTTCAAATAATAATTAATACTAT
1574376 TTTGATAAAAATTAGTTATAAC
456 TTTGATAAAAATTAGTTATAAC
1574398 TTTTAAAGACATTTAAAAATATTAAATATTAAAATCAAACATTATTAATATAACAAAATAGTAAT
1 TTTTAAAGACATTTAAAAATATTAAATATTAAAATCAAACATTATTAATATAACAAAATAGTAAT
1574463 TTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTA
66 TTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTA
1574528 AGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAATTCTTTTTGAATTTTTTAAGATTCA
131 AGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAATTCTTTTTGAATTTTTTAAGATTCA
1574593 TCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAACC
196 TCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAACC
1574658 CGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGG
261 CGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGG
1574710 TTGGAGAGAA
Statistics
Matches: 4540, Mismatches: 16, Indels: 31
0.99 0.00 0.01
Matches are distributed among these distances:
460 413 0.09
463 4 0.00
464 1 0.00
465 1 0.00
466 3 0.00
467 1269 0.28
469 2 0.00
470 2 0.00
471 2 0.00
472 2 0.00
473 2 0.00
474 2 0.00
475 2 0.00
476 1 0.00
477 2834 0.62
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (477 bp):
TTTTAAAGACATTTAAAAATATTAAATATTAAAATCAAACATTATTAATATAACAAAATAGTAAT
TTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTA
AGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAATTCTTTTTGAATTTTTTAAGATTCA
TCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAGCTCGATATAAGGCAACC
CGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGAATGGACAAGCAA
GCTACATATATGGTAATAAAATTAATTCATACTTATTCATACTTAAGTTGAATCAAATAATAATT
AAGTTGAACCAAAATATAAAAACTTATTCATACTTATTCATACTTCAAATAATAATTAATACTAT
TTTGATAAAAATTAGTTATAAC
Found at i:1573841 original size:21 final size:21
Alignment explanation
Indices: 1573817--1573856 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1573807 AAATTAATTC
*
1573817 ATACTTAAGTTGAATCAAATA
1 ATACTTAAGTTGAACCAAATA
1573838 ATACTTAAGTTGAACCAAA
1 ATACTTAAGTTGAACCAAA
1573857 ATATAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.30
Consensus pattern (21 bp):
ATACTTAAGTTGAACCAAATA
Found at i:1576635 original size:133 final size:133
Alignment explanation
Indices: 1576397--1576648 Score: 486
Period size: 133 Copynumber: 1.9 Consensus size: 133
1576387 GAATTCAGCA
1576397 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
1 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
**
1576462 TAAGTTGGATAGAAACATGGTAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
66 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
1576527 ATT
131 ATT
1576530 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
1 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
1576595 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAAT
66 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAAT
1576649 GGAATCACCA
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
133 117 1.00
ACGTcount: A:0.51, C:0.19, G:0.11, T:0.20
Consensus pattern (133 bp):
ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
ATT
Found at i:1578444 original size:45 final size:45
Alignment explanation
Indices: 1578394--1578482 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
1578384 ACAGCACCAG
1578394 AAACACCAGACCCGGTATTGGGTTTACTTAAAACAAGGGTATAAA
1 AAACACCAGACCCGGTATTGGGTTTACTTAAAACAAGGGTATAAA
*
1578439 AAACACCAGACCTGGTATTGGGTTTACTTAAAACAAGGGTATAA
1 AAACACCAGACCCGGTATTGGGTTTACTTAAAACAAGGGTATAA
1578483 TCATCGAGAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (45 bp):
AAACACCAGACCCGGTATTGGGTTTACTTAAAACAAGGGTATAAA
Found at i:1580043 original size:15 final size:15
Alignment explanation
Indices: 1580025--1580056 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1580015 AAATAATATT
*
1580025 TTATATATATTTATC
1 TTATATACATTTATC
1580040 TTATATACATTTATC
1 TTATATACATTTATC
1580055 TT
1 TT
1580057 CTAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATATACATTTATC
Found at i:1580976 original size:14 final size:14
Alignment explanation
Indices: 1580957--1580993 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
1580947 AATGATAATT
1580957 AATTCAATATTTTA
1 AATTCAATATTTTA
1580971 AATTCAATATTTTA
1 AATTCAATATTTTA
1580985 AATTCAATA
1 AATTCAATA
1580994 CTATCTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (14 bp):
AATTCAATATTTTA
Found at i:1581315 original size:41 final size:41
Alignment explanation
Indices: 1581121--1581299 Score: 288
Period size: 41 Copynumber: 4.4 Consensus size: 41
1581111 GGTTATGGGG
* *
1581121 TTTTAGCAGCGTTTTACCTAAAGCGCCGCTAATGCCCTGGT
1 TTTTAGCGGCGTTTTAACTAAAGCGCCGCTAATGCCCTGGT
1581162 TTTTAGCGGCGTTTTAACTAAAGCGCCGCTAATGCCCTGGT
1 TTTTAGCGGCGTTTTAACTAAAGCGCCGCTAATGCCCTGGT
*
1581203 TTTTAGTGGCGTTTTAACTAAAGCGCCGCTAATGCCCTGGT
1 TTTTAGCGGCGTTTTAACTAAAGCGCCGCTAATGCCCTGGT
* * *
1581244 TTTTAGCGGCGTTTTACCTAAAGCGTCGCTAATGCTCT-GT
1 TTTTAGCGGCGTTTTAACTAAAGCGCCGCTAATGCCCTGGT
*
1581284 TTTTAGCGGCATTTTA
1 TTTTAGCGGCGTTTTA
1581300 GTAAAAAACG
Statistics
Matches: 130, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
40 17 0.13
41 113 0.87
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTAACTAAAGCGCCGCTAATGCCCTGGT
Found at i:1581339 original size:81 final size:82
Alignment explanation
Indices: 1581121--1581339 Score: 255
Period size: 82 Copynumber: 2.7 Consensus size: 82
1581111 GGTTATGGGG
* * * * *
1581121 TTTTAGCAGCGTTTTACCTAAAGCGCCGCTAATGCCCTGGTTTTTAGCGGCGTTTTAACTAAAGC
1 TTTTAGCGGCATTTTAACAAAAACGCCGCTAATGCCCTGGTTTTTAGCGGCGTTTTAACTAAAGC
1581186 GCCGCTAATGCCCTGGT
66 GCCGCTAATGCCCTGGT
* * * * *
1581203 TTTTAGTGGCGTTTTAACTAAAGCGCCGCTAATGCCCTGGTTTTTAGCGGCGTTTTACCTAAAGC
1 TTTTAGCGGCATTTTAACAAAAACGCCGCTAATGCCCTGGTTTTTAGCGGCGTTTTAACTAAAGC
* *
1581268 GTCGCTAATGCTCT-GT
66 GCCGCTAATGCCCTGGT
* ** *
1581284 TTTTAGCGGCATTTTAGTA-AAAAACGCCGCTATTGTTCT-GTTTTTACCGGCGTTTT
1 TTTTAGCGGCATTTTA--ACAAAAACGCCGCTAATGCCCTGGTTTTTAGCGGCGTTTT
1581340 TTTGGAACGC
Statistics
Matches: 121, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
81 32 0.26
82 88 0.73
83 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.36
Consensus pattern (82 bp):
TTTTAGCGGCATTTTAACAAAAACGCCGCTAATGCCCTGGTTTTTAGCGGCGTTTTAACTAAAGC
GCCGCTAATGCCCTGGT
Found at i:1593904 original size:9 final size:9
Alignment explanation
Indices: 1593890--1593965 Score: 71
Period size: 9 Copynumber: 8.1 Consensus size: 9
1593880 TTTAAGGAAA
*
1593890 TTATGTGAG
1 TTATGTAAG
1593899 TTATGTAAGTTG
1 TTATGTAA---G
*
1593911 TTATGTAAA
1 TTATGTAAG
1593920 TTATGTAAG
1 TTATGTAAG
* *
1593929 TTATATGAG
1 TTATGTAAG
1593938 TTATGTAAG
1 TTATGTAAG
*
1593947 TTATGTAAT
1 TTATGTAAG
*
1593956 TTATTTAAG
1 TTATGTAAG
1593965 T
1 T
1593966 AATGATCAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
9 45 0.83
12 9 0.17
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.49
Consensus pattern (9 bp):
TTATGTAAG
Found at i:1594975 original size:19 final size:19
Alignment explanation
Indices: 1594951--1595012 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
1594941 TTTTTACCAA
1594951 CACAAATGAATAAAGAGAT
1 CACAAATGAATAAAGAGAT
* * ** * *
1594970 CACAAAGGGAT-TTGATAA
1 CACAAATGAATAAAGAGAT
1594988 CACAAATGAATAAAGAGAT
1 CACAAATGAATAAAGAGAT
1595007 CACAAA
1 CACAAA
1595013 AGGATTGATA
Statistics
Matches: 30, Mismatches: 12, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
18 12 0.40
19 18 0.60
ACGTcount: A:0.55, C:0.13, G:0.16, T:0.16
Consensus pattern (19 bp):
CACAAATGAATAAAGAGAT
Found at i:1594990 original size:37 final size:36
Alignment explanation
Indices: 1594949--1595022 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 36
1594939 ATTTTTTACC
*
1594949 AACACAAATGAATAAAGAGATCACAAAGGGATTTGAT
1 AACACAAATGAATAAAGAGATCACAAAAGGA-TTGAT
1594986 AACACAAATGAATAAAGAGATCACAAAAGGATTGAT
1 AACACAAATGAATAAAGAGATCACAAAAGGATTGAT
1595022 A
1 A
1595023 GATACCAAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 6 0.17
37 30 0.83
ACGTcount: A:0.54, C:0.11, G:0.18, T:0.18
Consensus pattern (36 bp):
AACACAAATGAATAAAGAGATCACAAAAGGATTGAT
Found at i:1597512 original size:84 final size:84
Alignment explanation
Indices: 1597371--1597565 Score: 293
Period size: 84 Copynumber: 2.3 Consensus size: 84
1597361 CAGTTTTTTT
* **
1597371 GTGGCGTTT-TTAGGATAGCGCCACTAATTCCTAAACCGTGCCACATAAAACGACGTAGTTTTCA
1 GTGGCGTTTATAAGG-TAGCGCCACTAATTCCTAAACCGCACCACATAAAACGACGTAGTTTTCA
*
1597435 TTCGAATTCTCATATTCTTA
65 TTCGAATTCTCATATTATTA
*
1597455 GTGGCGTTTATAAGGTAGCTCCACTAATTCCTAAACCGCACCACATAAAACGACGTAGTTTTCAT
1 GTGGCGTTTATAAGGTAGCGCCACTAATTCCTAAACCGCACCACATAAAACGACGTAGTTTTCAT
* * *
1597520 TCGATTTTTTATATTATTA
66 TCGAATTCTCATATTATTA
*
1597539 GTGGCGTTTATAAGATAGCGCCACTAA
1 GTGGCGTTTATAAGGTAGCGCCACTAA
1597566 ATCCACTACC
Statistics
Matches: 100, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
84 96 0.96
85 4 0.04
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (84 bp):
GTGGCGTTTATAAGGTAGCGCCACTAATTCCTAAACCGCACCACATAAAACGACGTAGTTTTCAT
TCGAATTCTCATATTATTA
Found at i:1597917 original size:15 final size:15
Alignment explanation
Indices: 1597897--1597941 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
1597887 AATCCCAAAA
1597897 CCAATACACTAAACC
1 CCAATACACTAAACC
*
1597912 CCAATACCCTAAA-C
1 CCAATACACTAAACC
* *
1597926 CCTATAGACTAAACC
1 CCAATACACTAAACC
1597941 C
1 C
1597942 TAAACCAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.42, C:0.40, G:0.02, T:0.16
Consensus pattern (15 bp):
CCAATACACTAAACC
Found at i:1597929 original size:7 final size:7
Alignment explanation
Indices: 1597905--1597997 Score: 64
Period size: 7 Copynumber: 13.1 Consensus size: 7
1597895 AACCAATACA
1597905 CTAAACC
1 CTAAACC
*
1597912 CCAATACC
1 CTAA-ACC
1597920 CTAAACC
1 CTAAACC
* **
1597927 CTATAGA
1 CTAAACC
1597934 CTAAACC
1 CTAAACC
1597941 CTAAA-C
1 CTAAACC
* *
1597947 CAAATACA
1 CTAA-ACC
1597955 C-AATACC
1 CTAA-ACC
1597962 CTAAACC
1 CTAAACC
1597969 CTAAACC
1 CTAAACC
* **
1597976 CTATAGA
1 CTAAACC
1597983 CTAAACC
1 CTAAACC
1597990 CTAAACC
1 CTAAACC
1597997 C
1 C
1597998 AATACCCAGT
Statistics
Matches: 65, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
6 4 0.06
7 52 0.80
8 9 0.14
ACGTcount: A:0.44, C:0.38, G:0.02, T:0.16
Consensus pattern (7 bp):
CTAAACC
Found at i:1597943 original size:21 final size:21
Alignment explanation
Indices: 1597917--1597997 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 21
1597907 AAACCCCAAT
1597917 ACCCTAAACCCTATAGACTAA
1 ACCCTAAACCCTATAGACTAA
* * *
1597938 ACCCTAAACCAAATACACAATACCCTAA
1 ACCCTAAACC--CT--A-TAGA-C-TAA
1597966 ACCCTAAACCCTATAGACTAA
1 ACCCTAAACCCTATAGACTAA
1597987 ACCCTAAACCC
1 ACCCTAAACCC
1597998 AATACCCAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
21 24 0.51
22 1 0.02
23 3 0.06
24 1 0.02
25 1 0.02
26 3 0.06
27 1 0.02
28 13 0.28
ACGTcount: A:0.44, C:0.37, G:0.02, T:0.16
Consensus pattern (21 bp):
ACCCTAAACCCTATAGACTAA
Found at i:1597970 original size:49 final size:48
Alignment explanation
Indices: 1597894--1598016 Score: 169
Period size: 49 Copynumber: 2.5 Consensus size: 48
1597884 ATTAATCCCA
*
1597894 AAACCAATACACTAA-ACCCCAATACCCTAAACCCTATAGACTAAACCCT
1 AAACCAATACAC-AATACCCTAA-ACCCTAAACCCTATAGACTAAACCCT
1597943 AAACCAAATACACAATACCCTAAACCCTAAACCCTATAGACTAAACCCT
1 AAACC-AATACACAATACCCTAAACCCTAAACCCTATAGACTAAACCCT
* *
1597992 AAACCCAATACCCAGT-CCCTAAACC
1 AAA-CCAATACACAATACCCTAAACC
1598017 TTATAAACCA
Statistics
Matches: 68, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
48 9 0.13
49 44 0.65
50 15 0.22
ACGTcount: A:0.45, C:0.37, G:0.02, T:0.15
Consensus pattern (48 bp):
AAACCAATACACAATACCCTAAACCCTAAACCCTATAGACTAAACCCT
Found at i:1598035 original size:41 final size:41
Alignment explanation
Indices: 1597967--1598045 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
1597957 ATACCCTAAA
* *
1597967 CCCTAAACCCTATAGACTAAACCCTAAACCCAATACCCAGT
1 CCCTAAACCCTATAAACCAAACCCTAAACCCAATACCCAGT
* ** *
1598008 CCCTAAACCTTATAAACCAAATTCTAAACCCAGTACCC
1 CCCTAAACCCTATAAACCAAACCCTAAACCCAATACCC
1598046 TAAACCTTGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.39, C:0.38, G:0.04, T:0.19
Consensus pattern (41 bp):
CCCTAAACCCTATAAACCAAACCCTAAACCCAATACCCAGT
Found at i:1598457 original size:15 final size:15
Alignment explanation
Indices: 1598439--1598502 Score: 51
Period size: 15 Copynumber: 4.4 Consensus size: 15
1598429 AAAATTTATT
* *
1598439 TTTAAGATTTTAGGG
1 TTTAAGATTTAAGAG
*
1598454 TTTATGATTTAAGAG
1 TTTAAGATTTAAGAG
* *
1598469 TTTAGGATTT-ATAG
1 TTTAAGATTTAAGAG
* *
1598483 TTTAAGGTTTGAGA-
1 TTTAAGATTTAAGAG
1598497 TTTAAG
1 TTTAAG
1598503 GCCTATAGTT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 17 0.43
15 23 0.57
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (15 bp):
TTTAAGATTTAAGAG
Found at i:1598467 original size:22 final size:22
Alignment explanation
Indices: 1598439--1598500 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
1598429 AAAATTTATT
* *
1598439 TTTAAGATTTTAGGGTTTAT-G
1 TTTAAGAGTTTAGGATTTATAG
1598460 ATTTAAGAGTTTAGGATTTATAG
1 -TTTAAGAGTTTAGGATTTATAG
1598483 TTTAAG-GTTT-GAGATTTA
1 TTTAAGAGTTTAG-GATTTA
1598501 AGGCCTATAG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
20 1 0.03
21 10 0.28
22 24 0.67
23 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (22 bp):
TTTAAGAGTTTAGGATTTATAG
Found at i:1601737 original size:6 final size:6
Alignment explanation
Indices: 1601726--1601768 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
1601716 GTTGAAGCTT
*
1601726 TTGCCC TTGCCC TTGCCC TTGCCC TTGCCC TTGCCT TTGCCC T
1 TTGCCC TTGCCC TTGCCC TTGCCC TTGCCC TTGCCC TTGCCC T
1601769 ATCGATGCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.00, C:0.47, G:0.16, T:0.37
Consensus pattern (6 bp):
TTGCCC
Found at i:1604376 original size:72 final size:72
Alignment explanation
Indices: 1604254--1604394 Score: 203
Period size: 72 Copynumber: 2.0 Consensus size: 72
1604244 GAGGAAAAGT
* * * *
1604254 ACCATTTAATTGATTATCTGTAACATCAAAGAACTTCAAAGATGATAACTCCCCTATAGACAATG
1 ACCACTTAATTGATTATCTGAAACATCAAAGAAATACAAAGATGATAACTCCCCTATAGACAATG
1604319 GAATTTG
66 GAATTTG
* * *
1604326 ACCACTTAATTGATTTTCT-AAAGCATCAAAGAAATACAAAGATGATAACTCCCCTATGGACACT
1 ACCACTTAATTGATTATCTGAAA-CATCAAAGAAATACAAAGATGATAACTCCCCTATAGACAAT
1604390 GGAAT
65 GGAAT
1604395 GGGACCAAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
71 2 0.03
72 59 0.97
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (72 bp):
ACCACTTAATTGATTATCTGAAACATCAAAGAAATACAAAGATGATAACTCCCCTATAGACAATG
GAATTTG
Found at i:1607031 original size:34 final size:34
Alignment explanation
Indices: 1606988--1607055 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
1606978 GACAAATGTT
*
1606988 TTATGCTGGATGTGAGTCAGCTTGAGAAAAGTGC
1 TTATGCTGGATGTGAGTCAACTTGAGAAAAGTGC
1607022 TTATGCTGGATGTGAGTCAACTTGAGAAAAGTGC
1 TTATGCTGGATGTGAGTCAACTTGAGAAAAGTGC
1607056 CTAAACAAGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.28, C:0.12, G:0.31, T:0.29
Consensus pattern (34 bp):
TTATGCTGGATGTGAGTCAACTTGAGAAAAGTGC
Found at i:1613276 original size:23 final size:20
Alignment explanation
Indices: 1613220--1613284 Score: 87
Period size: 20 Copynumber: 3.1 Consensus size: 20
1613210 TTGCACCTCC
1613220 CACCATTTTTGACTTTTCAA
1 CACCATTTTTGACTTTTCAA
1613240 CACCATTTTTGAC-TTTCAA
1 CACCATTTTTGACTTTTCAA
1613259 CACCTACCTTATTTGACTTTTCAA
1 CACC-A--TT-TTTGACTTTTCAA
1613283 CA
1 CA
1613285 ATCTCCACCT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
19 10 0.25
20 14 0.35
22 2 0.05
23 6 0.15
24 8 0.20
ACGTcount: A:0.26, C:0.28, G:0.05, T:0.42
Consensus pattern (20 bp):
CACCATTTTTGACTTTTCAA
Found at i:1615215 original size:21 final size:21
Alignment explanation
Indices: 1615189--1615229 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1615179 ATCTGCTCAA
* *
1615189 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
1615210 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
1615230 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:1629294 original size:21 final size:21
Alignment explanation
Indices: 1629268--1629308 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1629258 AGACGAGCAA
* *
1629268 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
1629289 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
1629309 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:1631247 original size:16 final size:16
Alignment explanation
Indices: 1631214--1631247 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1631204 GGAGATTGTT
* *
1631214 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
1631230 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
1631246 AA
1 AA
1631248 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:1637753 original size:21 final size:22
Alignment explanation
Indices: 1637727--1637773 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
1637717 ATCTACTCAA
* *
1637727 ACTCCACCTGTTTTGGAGTA-C
1 ACTCCACCTGCTGTGGAGTATC
1637748 ACTCCACCTGCTGTGGAGTATC
1 ACTCCACCTGCTGTGGAGTATC
1637770 ACTC
1 ACTC
1637774 GTCTGAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.19, C:0.32, G:0.19, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGTGGAGTATC
Found at i:1641036 original size:24 final size:24
Alignment explanation
Indices: 1641004--1641053 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1640994 AATACAATTA
1641004 AACACAATCACATATTATCAAAGC
1 AACACAATCACATATTATCAAAGC
1641028 AACACAATCACATATTATCAAAGC
1 AACACAATCACATATTATCAAAGC
1641052 AA
1 AA
1641054 GCTTGAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.24, G:0.04, T:0.20
Consensus pattern (24 bp):
AACACAATCACATATTATCAAAGC
Found at i:1662536 original size:10 final size:10
Alignment explanation
Indices: 1662521--1662572 Score: 68
Period size: 10 Copynumber: 5.1 Consensus size: 10
1662511 TAATTTTAGG
1662521 ATTTATTTTT
1 ATTTATTTTT
*
1662531 ATTTATCTTT
1 ATTTATTTTT
*
1662541 ATTTATCTTT
1 ATTTATTTTT
*
1662551 ATTTATTTGT
1 ATTTATTTTT
1662561 ATTTATCTTTT
1 ATTTAT-TTTT
1662572 A
1 A
1662573 CAATTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
10 33 0.89
11 4 0.11
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.71
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:1663495 original size:12 final size:12
Alignment explanation
Indices: 1663478--1663510 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
1663468 CTACTTCCCC
1663478 TTTACTATTATT
1 TTTACTATTATT
1663490 TTTACTATTATT
1 TTTACTATTATT
1663502 TTTACTATT
1 TTTACTATT
1663511 TTATAGGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTACTATTATT
Done.