Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 65 of 167
Found at i:20438731 original size:40 final size:39
Alignment explanation
Indices: 20438633--20438895 Score: 278
Period size: 40 Copynumber: 6.6 Consensus size: 39
20438623 TCCTCGTTCA
* * * *
20438633 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
20438672 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
20438711 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
20438751 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
20438791 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
20438831 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
20438872 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
20438896 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
39 40 0.20
40 145 0.74
41 12 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:20438855 original size:120 final size:119
Alignment explanation
Indices: 20438633--20438895 Score: 307
Period size: 120 Copynumber: 2.2 Consensus size: 119
20438623 TCCTCGTTCA
* * *
20438633 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
* * *
20438698 TAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAAC-TCGCAC
66 TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
* * * * *
20438751 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACATAACCCGG-
* * ** * *
20438816 ATTT-GTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
63 ATTTAATAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAATAACTTAGCAC
*
20438872 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
20438896 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 37 0.31
120 75 0.62
121 9 0.07
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
Found at i:20438904 original size:41 final size:41
Alignment explanation
Indices: 20438827--20438904 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
20438817 TTTGTATCTC
* * *
20438827 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
20438868 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
20438905 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:20450085 original size:50 final size:50
Alignment explanation
Indices: 20450010--20450295 Score: 572
Period size: 50 Copynumber: 5.7 Consensus size: 50
20450000 NNNNNNNNNN
20450010 CGTGCTGATGCCATGTCCCAGACATGGTCTTACACTAACTCTCACATATC
1 CGTGCTGATGCCATGTCCCAGACATGGTCTTACACTAACTCTCACATATC
20450060 CGTGCTGATGCCATGTCCCAGACATGGTCTTACACTAACTCTCACATATC
1 CGTGCTGATGCCATGTCCCAGACATGGTCTTACACTAACTCTCACATATC
20450110 CGTGCTGATGCCATGTCCCAGACATGGTCTTACACTAACTCTCACATATC
1 CGTGCTGATGCCATGTCCCAGACATGGTCTTACACTAACTCTCACATATC
20450160 CGTGCTGATGCCATGTCCCAGACATGGTCTTACACTAACTCTCACATATC
1 CGTGCTGATGCCATGTCCCAGACATGGTCTTACACTAACTCTCACATATC
20450210 CGTGCTGATGCCATGTCCCAGACATGGTCTTACACTAACTCTCACATATC
1 CGTGCTGATGCCATGTCCCAGACATGGTCTTACACTAACTCTCACATATC
20450260 CGTGCTGATGCCATGTCCCAGACATGGTCTTACACT
1 CGTGCTGATGCCATGTCCCAGACATGGTCTTACACT
20450296 GACACATTTT
Statistics
Matches: 236, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 236 1.00
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (50 bp):
CGTGCTGATGCCATGTCCCAGACATGGTCTTACACTAACTCTCACATATC
Found at i:20460841 original size:47 final size:46
Alignment explanation
Indices: 20460697--20460863 Score: 207
Period size: 46 Copynumber: 3.6 Consensus size: 46
20460687 TTAGCCGACA
20460697 CATGTCCCAGACATGTCTTACACTAGCTCTCATAATGTGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTCATAATGTGGCCGATG
* **
20460743 CATGTCCCAGACATGTCTTACACAAGCTCTTGTC-TCAA--T-GCTAATG
1 CATGTCCCAGACATGTCTTACACTAGCTC---TCAT-AATGTGGCCGATG
*
20460789 CCATGTCCCAGACATGATCTTACACTGGCTCTCATAATGTGGCCGATG
1 -CATGTCCCAGACATG-TCTTACACTAGCTCTCATAATGTGGCCGATG
*
20460837 CATGTCCTAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
20460864 ACACAAATGA
Statistics
Matches: 102, Mismatches: 9, Indels: 20
0.78 0.07 0.15
Matches are distributed among these distances:
45 4 0.04
46 45 0.44
47 31 0.30
48 18 0.18
49 4 0.04
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.29
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTAGCTCTCATAATGTGGCCGATG
Found at i:20463884 original size:48 final size:48
Alignment explanation
Indices: 20463800--20464154 Score: 359
Period size: 48 Copynumber: 7.4 Consensus size: 48
20463790 ATACTAGGGT
*
20463800 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTGA
1 TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTGA
* * * * **
20463848 TATGAGAGCTAGTGTAAGACCATTTCTTGG-ATATGGCATC-AGCCTCAA
1 TATGAGAGCCAGTGTAAGACCATGT-TTGGAACATGGCATCGA-CATTGA
20463896 TATGTA-AGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTGA
1 TATG-AGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTGA
* * * * **
20463944 TATGAGAGCTAGTGTAAGACCATTTCTTGG-ATATGGCATC-AGCCTCAA
1 TATGAGAGCCAGTGTAAGACCATGT-TTGGAACATGGCATCGA-CATTGA
20463992 TATGTA-AGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTGA
1 TATG-AGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTGA
* * * * **
20464040 TATGAGAGCTAGTGTAAGACCATTTCTTGG-ATATGGCATC-AGCCTCAA
1 TATGAGAGCCAGTGTAAGACCATGT-TTGGAACATGGCATCGA-CATTGA
* *
20464088 TATGTA-AGCCAGTGTAAGACCATGTTTGGAACATGGCAACGGCATTGA
1 TATG-AGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTGA
* *
20464136 TAGGAGAGCTAGTGTAAGA
1 TATGAGAGCCAGTGTAAGA
20464155 AGAAGTTTGA
Statistics
Matches: 248, Mismatches: 41, Indels: 36
0.76 0.13 0.11
Matches are distributed among these distances:
47 18 0.07
48 213 0.86
49 17 0.07
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.27
Consensus pattern (48 bp):
TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTGA
Found at i:20463964 original size:96 final size:96
Alignment explanation
Indices: 20463800--20464154 Score: 674
Period size: 96 Copynumber: 3.7 Consensus size: 96
20463790 ATACTAGGGT
*
20463800 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTGATATGAGAGCTAGTGTAA
1 TATGTAAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTGATATGAGAGCTAGTGTAA
20463865 GACCATTTCTTGGATATGGCATCAGCCTCAA
66 GACCATTTCTTGGATATGGCATCAGCCTCAA
20463896 TATGTAAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTGATATGAGAGCTAGTGTAA
1 TATGTAAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTGATATGAGAGCTAGTGTAA
20463961 GACCATTTCTTGGATATGGCATCAGCCTCAA
66 GACCATTTCTTGGATATGGCATCAGCCTCAA
20463992 TATGTAAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTGATATGAGAGCTAGTGTAA
1 TATGTAAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTGATATGAGAGCTAGTGTAA
20464057 GACCATTTCTTGGATATGGCATCAGCCTCAA
66 GACCATTTCTTGGATATGGCATCAGCCTCAA
* * *
20464088 TATGTAAGCCAGTGTAAGACCATGTTTGGAACATGGCAACGGCATTGATAGGAGAGCTAGTGTAA
1 TATGTAAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTGATATGAGAGCTAGTGTAA
20464153 GA
66 GA
20464155 AGAAGTTTGA
Statistics
Matches: 255, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 255 1.00
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.27
Consensus pattern (96 bp):
TATGTAAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTGATATGAGAGCTAGTGTAA
GACCATTTCTTGGATATGGCATCAGCCTCAA
Found at i:20466615 original size:18 final size:18
Alignment explanation
Indices: 20466588--20466626 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
20466578 TGCTTCTAAG
*
20466588 AAGCGCTTTTGGGACAAA
1 AAGCGCTTTTGAGACAAA
* *
20466606 AAGCGGTTTTGAGAGAAA
1 AAGCGCTTTTGAGACAAA
20466624 AAG
1 AAG
20466627 TGTTTTTCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.10, G:0.31, T:0.21
Consensus pattern (18 bp):
AAGCGCTTTTGAGACAAA
Found at i:20470123 original size:5 final size:5
Alignment explanation
Indices: 20470113--20470140 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
20470103 CCAAAAATAA
20470113 TATTT TATTT TATTT TATTT TATTT TAT
1 TATTT TATTT TATTT TATTT TATTT TAT
20470141 GGTTGGTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:20470242 original size:42 final size:42
Alignment explanation
Indices: 20470180--20470265 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
20470170 AAAATTTTGG
*
20470180 TACGAAAATTTTACCGATTGTGTGTTTAATTAGGGAAAGGAC
1 TACGAAAATTTTACCAATTGTGTGTTTAATTAGGGAAAGGAC
20470222 TACGAAAATTTTACCAATTGTGTGTTTAATTAGGGAAAGGAC
1 TACGAAAATTTTACCAATTGTGTGTTTAATTAGGGAAAGGAC
20470264 TA
1 TA
20470266 AATTACATAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.34
Consensus pattern (42 bp):
TACGAAAATTTTACCAATTGTGTGTTTAATTAGGGAAAGGAC
Found at i:20479243 original size:24 final size:24
Alignment explanation
Indices: 20479216--20479261 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
20479206 AGAAGACTAT
*
20479216 ATATAAAAATATAATAAATAAACA
1 ATATAAAAATAAAATAAATAAACA
*
20479240 ATATTAAAATAAAATAAATAAA
1 ATATAAAAATAAAATAAATAAA
20479262 TAAAAATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (24 bp):
ATATAAAAATAAAATAAATAAACA
Found at i:20479249 original size:15 final size:15
Alignment explanation
Indices: 20479218--20479269 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 15
20479208 AAGACTATAT
20479218 ATAAAAATATAATAA
1 ATAAAAATATAATAA
*
20479233 ATAAACAATATTA-AA
1 ATAAA-AATATAATAA
20479248 AT-AAAATA-AATAA
1 ATAAAAATATAATAA
20479261 ATAAAAATA
1 ATAAAAATA
20479270 CATATTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
12 1 0.03
13 8 0.25
14 8 0.25
15 9 0.28
16 6 0.19
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (15 bp):
ATAAAAATATAATAA
Found at i:20479267 original size:14 final size:14
Alignment explanation
Indices: 20479218--20479269 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
20479208 AAGACTATAT
20479218 ATAAAAATATAATAA
1 ATAAAAATA-AATAA
*
20479233 ATAAACAAT-ATTAA
1 ATAAA-AATAAATAA
20479247 A-ATAAAATAAATAA
1 ATA-AAAATAAATAA
20479261 ATAAAAATA
1 ATAAAAATA
20479270 CATATTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
13 4 0.13
14 18 0.58
15 6 0.19
16 3 0.10
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (14 bp):
ATAAAAATAAATAA
Found at i:20487681 original size:21 final size:21
Alignment explanation
Indices: 20487657--20487698 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
20487647 TTGCTTCCCA
20487657 TTTTCTTCTTTCTTTCACTTTT
1 TTTTCTT-TTTCTTTCACTTTT
*
20487679 TTTTCTTTTTCTTTCTCTTT
1 TTTTCTTTTTCTTTCACTTT
20487699 CATTTGGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTCTTTTTCTTTCACTTTT
Found at i:20487709 original size:27 final size:28
Alignment explanation
Indices: 20487657--20487711 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
20487647 TTGCTTCCCA
* *
20487657 TTTTCTTCTTTCTTTCACTTTTTTTTCT
1 TTTTCTTCTCTCTTTCACTTTGTTTTCT
20487685 TTTTCTT-TCTCTTTCA-TTTGGTTTTCT
1 TTTTCTTCTCTCTTTCACTTT-GTTTTCT
20487712 ACTCAAATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 3 0.12
27 14 0.58
28 7 0.29
ACGTcount: A:0.04, C:0.20, G:0.04, T:0.73
Consensus pattern (28 bp):
TTTTCTTCTCTCTTTCACTTTGTTTTCT
Found at i:20491244 original size:50 final size:49
Alignment explanation
Indices: 20491163--20491281 Score: 123
Period size: 49 Copynumber: 2.4 Consensus size: 49
20491153 CACTGTTGAT
* * * *
20491163 GCCACACGGCCGTGTGTGACACACGGTCTAGGCTAATTTAGGCCGTATGG
1 GCCACACGGGCATGTGGGTCACACGGTCTAGGC-AATTTAGGCCGTATGG
* * * *
20491213 GCCACACGGGCATGTGGGTCACACTGG-CTAGGCATTTTGGGTCGTGTGG
1 GCCACACGGGCATGTGGGTCACAC-GGTCTAGGCAATTTAGGCCGTATGG
* *
20491262 GCCACATGGGCTTGTGGGTC
1 GCCACACGGGCATGTGGGTC
20491282 CAAAATTTAG
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
49 30 0.52
50 26 0.45
51 2 0.03
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (49 bp):
GCCACACGGGCATGTGGGTCACACGGTCTAGGCAATTTAGGCCGTATGG
Found at i:20495424 original size:43 final size:42
Alignment explanation
Indices: 20495331--20495481 Score: 140
Period size: 43 Copynumber: 3.5 Consensus size: 42
20495321 GATTTTCGAG
* * *
20495331 ATGTGATTACATGTAAGACCATGTTTGGGACATTGGTATTGT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGT
* **
20495373 ATTGTGATTACGTGTAAGACCATGTCTAAGACATTGGCATCGTT
1 A-TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCG-T
* * * * * * * *
20495417 ATATGATTTCGTATAAGATCTTATCTGGGACAATGGCATCGAT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCG-T
*
20495460 ATGTGATAACATGTAAGACCAT
1 ATGTGATTACATGTAAGACCAT
20495482 ATCCGGGATA
Statistics
Matches: 84, Mismatches: 23, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
42 1 0.01
43 81 0.96
44 2 0.02
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (42 bp):
ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGT
Found at i:20497355 original size:31 final size:31
Alignment explanation
Indices: 20497317--20497379 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
20497307 TTTTTGTTTT
20497317 AAATTTGCATAAGATTTCTGACGATCGGAAG
1 AAATTTGCATAAGATTTCTGACGATCGGAAG
*
20497348 AAATTTGCATAAGATTTCTGACGGTCGGAAG
1 AAATTTGCATAAGATTTCTGACGATCGGAAG
20497379 A
1 A
20497380 TGTCTTCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.29
Consensus pattern (31 bp):
AAATTTGCATAAGATTTCTGACGATCGGAAG
Found at i:20511589 original size:27 final size:28
Alignment explanation
Indices: 20511507--20511601 Score: 120
Period size: 27 Copynumber: 3.4 Consensus size: 28
20511497 GAGATTGGCG
* * * *
20511507 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
20511536 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
20511564 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
20511591 CTGAGTGTGCG
1 CTAAGTGTGCG
20511602 GACTTAATAT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 23 0.39
28 21 0.36
29 15 0.25
ACGTcount: A:0.25, C:0.13, G:0.29, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:20511612 original size:27 final size:27
Alignment explanation
Indices: 20511532--20511614 Score: 87
Period size: 27 Copynumber: 3.0 Consensus size: 27
20511522 TAAATTGTAC
* * *
20511532 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
20511560 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
20511587 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
20511614 A
1 A
20511615 CTTTTAAATC
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
27 29 0.59
28 20 0.41
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:20511731 original size:29 final size:29
Alignment explanation
Indices: 20511680--20511745 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
20511670 GCGGAAAAGG
20511680 TAAGTGTGTGAACTTGAAATGCATGGCAC
1 TAAGTGTGTGAACTTGAAATGCATGGCAC
* *
20511709 TAAGTGTGTG-AGTTTAAAGTGCATGGCAC
1 TAAGTGTGTGAACTTGAAA-TGCATGGCAC
20511738 TAAGTGTG
1 TAAGTGTG
20511746 CGCGGTTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 6 0.18
29 28 0.82
ACGTcount: A:0.29, C:0.11, G:0.30, T:0.30
Consensus pattern (29 bp):
TAAGTGTGTGAACTTGAAATGCATGGCAC
Found at i:20513370 original size:23 final size:22
Alignment explanation
Indices: 20513327--20513384 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
20513317 AAAAGGTATC
* *
20513327 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
20513348 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
20513371 TGCATATCATATCT
1 TACAAATCATATCT
20513385 AAGATTGCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:20513387 original size:19 final size:19
Alignment explanation
Indices: 20513363--20513468 Score: 157
Period size: 18 Copynumber: 5.8 Consensus size: 19
20513353 AATCATATCT
20513363 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
20513382 TCTAAGATTGCA-ATGATA
1 TCTAAGATTGCATATCATA
20513400 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
20513417 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
20513436 TCAAATATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
20513454 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
20513469 TGAAGATTAT
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
17 15 0.19
18 31 0.40
19 31 0.40
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:20513461 original size:37 final size:37
Alignment explanation
Indices: 20513366--20513468 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
20513356 CATATCTTCT
* *
20513366 AAGATTGCATATCATATCTAAGATTGCA-ATGATATCT
1 AAGATTGCA-ATCATATCTAAGATTGCATATCATATCA
*
20513403 AAGATTG-TATCATATCTAAGATTGCATATCATATCA
1 AAGATTGCAATCATATCTAAGATTGCATATCATATCA
*
20513439 AATATTGCAATCATATCTAAGATTGCATAT
1 AAGATTGCAATCATATCTAAGATTGCATAT
20513469 TGAAGATTAT
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
35 18 0.31
36 13 0.22
37 28 0.47
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.36
Consensus pattern (37 bp):
AAGATTGCAATCATATCTAAGATTGCATATCATATCA
Found at i:20514003 original size:87 final size:87
Alignment explanation
Indices: 20513863--20514031 Score: 207
Period size: 87 Copynumber: 1.9 Consensus size: 87
20513853 ACAATACAGA
* *
20513863 GATGCCAAATCATCTTAGATCTACTTCAGCATAAACACGTGAAAGCCAAATCTGCTGTGTCTTCG
1 GATGCCAAATCATCTTAGATCTACTTCAGCATAAACACGTGAAAGCCAAATCTGCTATGTCTTCA
*
20513928 ATTTGCTCCTTGTAAACACAAG
66 ATCTGCTCCTTGTAAACACAAG
* * * * * *
20513950 GATGCCAAATCATCTTGGATCTGCTTCAGTA-AAATCATC-TGAAGGTCAGATCTGCTATGTCTT
1 GATGCCAAATCATCTTAGATCTACTTCAGCATAAA-CA-CGTGAAAGCCAAATCTGCTATGTCTT
* *
20514013 TAATCTGCTTCTTGTAAAC
64 CAATCTGCTCCTTGTAAAC
20514032 TTATGACTGT
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
86 3 0.04
87 65 0.94
88 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (87 bp):
GATGCCAAATCATCTTAGATCTACTTCAGCATAAACACGTGAAAGCCAAATCTGCTATGTCTTCA
ATCTGCTCCTTGTAAACACAAG
Found at i:20514217 original size:261 final size:261
Alignment explanation
Indices: 20513753--20514240 Score: 721
Period size: 261 Copynumber: 1.9 Consensus size: 261
20513743 CATGGTCCTC
**
20513753 AATCTGCTCATTGCAAACTCAAGACTGTCATGTTGATATCTTCAATCTGCTCTTTGTCAAACACA
1 AATCTGCTCATTGCAAACTCAAGACTGTCATGTTGATATCTTCAATCTGCTCTCCGTCAAACACA
* * *
20513818 GAGACGCCAAATCTGCTTTTTCGATTTGTTTTCTGACAATACAGAGATGCCAAATCATCTTAGAT
66 GAGACGCCAAATCTGATTTTTCGATTTGTTCTCTAACAATACAGAGATGCCAAATCATCTTAGAT
* * * * *
20513883 CTACTTCAGCATAAACACGTGAAAGCCAAATCTGCTGTGTCTTCGATTTGCTCCTTGTAAACACA
131 CTACTTCAGCATAAACACGCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTATAAACACA
*
20513948 AGGATGCCAAATCATCTTGGATCTGCTTCAGTAAAATCATCTGAAGGTCAGATCTGCTATGTCTT
196 AGGATGCCAAACCATCTTGGATCTGCTTCAGTAAAATCATCTGAAGGTCAGATCTGCTATGTCTT
20514013 T
261 T
* * * * * *
20514014 AATCTGCTTC-TTGTAAACTTATGACTGTCCTGTTGATATCTTCAATCTGCTCTCCG-CTGAATA
1 AATCTGC-TCATTGCAAACTCAAGACTGTCATGTTGATATCTTCAATCTGCTCTCCGTC-AAACA
20514077 CAGAGACGCCAAATCT-ATTTCTTCGATTTGTTCTCTAACAATACAGAGATGCCAAATCATCTTA
64 CAGAGACGCCAAATCTGATTT-TTCGATTTGTTCTCTAACAATACAGAGATGCCAAATCATCTTA
* * * * * *
20514141 GATTTGCTTCAGCGTAAGCACGCGAAAACCAAATCAGCTATGTCTTCGATTTGTTCCTTATAAGC
128 GATCTACTTCAGCATAAACACGCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTATAAAC
20514206 ACAAGGATGCCAAACCATCTTGGATCTGCTTCAGT
193 ACAAGGATGCCAAACCATCTTGGATCTGCTTCAGT
20514241 CATCTGAAGG
Statistics
Matches: 201, Mismatches: 23, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
260 4 0.02
261 195 0.97
262 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (261 bp):
AATCTGCTCATTGCAAACTCAAGACTGTCATGTTGATATCTTCAATCTGCTCTCCGTCAAACACA
GAGACGCCAAATCTGATTTTTCGATTTGTTCTCTAACAATACAGAGATGCCAAATCATCTTAGAT
CTACTTCAGCATAAACACGCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTATAAACACA
AGGATGCCAAACCATCTTGGATCTGCTTCAGTAAAATCATCTGAAGGTCAGATCTGCTATGTCTT
T
Found at i:20514751 original size:205 final size:201
Alignment explanation
Indices: 20514097--20514844 Score: 1187
Period size: 200 Copynumber: 3.7 Consensus size: 201
20514087 AAATCTATTT
20514097 CTTCGATTTGTTCTCT-AACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCA
1 CTTCGATTTGTTCTCTGAA-AATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCA
*
20514161 CGCGAAAACCAAATCAGCTATGTCTTCGATTTGTTCCTTATAAGCACAAGGATGCCAAACCATCT
65 CGCGAAAACCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCT
20514226 TGGATCTGCTTCAG-TCATCTGAAGGTTAGATATGCTATGTATCTGCTCTCCGTCGAAATGGAGA
130 TGGATCTGCTTCAGATCATCTGAAGGTTAGATATGCTATGTATCTGCTCTCCGTCGAAATGGAGA
20514290 TGCCAGA
195 TGCCAGA
* * *
20514297 CTTCGATTTGTTCTCTGAAAATATAGAGATGCCAAATCATCTTAGATTTGCTTCATCATAAGCAC
1 CTTCGATTTGTTCTCTGAAAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
* * *
20514362 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAATGCCAAACCATCTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
* * * *
20514427 GAATCTGCTTCA-ATCATCTAAAGGTTAGATCTGCTATGTATCTACTCTCCGTCGAAATGGAGAT
131 GGATCTGCTTCAGATCATCTGAAGGTTAGATATGCTATGTATCTGCTCTCCGTCGAAATGGAGAT
20514491 GCCAGA
196 GCCAGA
* * *
20514497 CTTCAATTTGTTCTCTGAAAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCCTAAACAC
1 CTTCGATTTGTTCTCTGAAAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
* * * *
20514562 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTGCCTTGTAAGCATAAGGATGCCAAACCATCTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
* * *
20514627 GGATCTGCTTCAGTATAAACATCTGAAGGTTAGATTTGCTATGTATTTGCTCTCCGTCGAAATAG
131 GGATCTGCTTCAG-AT---CATCTGAAGGTTAGATATGCTATGTATCTGCTCTCCGTCGAAATGG
*
20514692 AGATGCCAAA
192 AGATGCCAGA
*
20514702 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
1 CTTCGATTTGTTCTCTGAAAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
* * *
20514767 GCGAAAACAAAATCAGCTATGTCTTTGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
20514832 GGATCTTGCTTCA
131 GGATC-TGCTTCA
20514845 ACCAGATCTA
Statistics
Matches: 503, Mismatches: 37, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
200 318 0.63
201 2 0.00
202 2 0.00
205 174 0.35
206 7 0.01
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (201 bp):
CTTCGATTTGTTCTCTGAAAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
GCGAAAACCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
GGATCTGCTTCAGATCATCTGAAGGTTAGATATGCTATGTATCTGCTCTCCGTCGAAATGGAGAT
GCCAGA
Found at i:20515800 original size:7 final size:7
Alignment explanation
Indices: 20515788--20515843 Score: 60
Period size: 7 Copynumber: 7.7 Consensus size: 7
20515778 CGCCTATTCA
20515788 TTTTTCT
1 TTTTTCT
20515795 TTTTTCT
1 TTTTTCT
*
20515802 TTTTCCT
1 TTTTTCT
20515809 TTTTT-T
1 TTTTTCT
20515815 CTTTTTCTT
1 -TTTTTC-T
*
20515824 TTTTTTT
1 TTTTTCT
20515831 TCTTTTCT
1 T-TTTTCT
20515839 TTTTT
1 TTTTT
20515844 TCCCTTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
6 1 0.02
7 28 0.68
8 11 0.27
9 1 0.02
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTCT
Found at i:20515804 original size:6 final size:6
Alignment explanation
Indices: 20515788--20515842 Score: 60
Period size: 6 Copynumber: 8.8 Consensus size: 6
20515778 CGCCTATTCA
20515788 TTTTTC TTTTTTC TTTTTCC TTTTTTTC TTTTTC TTTTT- TTTTTC -TTTTC
1 TTTTTC -TTTTTC TTTTT-C --TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
20515838 TTTTT
1 TTTTT
20515843 TTCCCTTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
5 10 0.23
6 20 0.47
7 7 0.16
8 1 0.02
9 5 0.12
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTC
Found at i:20515814 original size:22 final size:22
Alignment explanation
Indices: 20515788--20515843 Score: 78
Period size: 21 Copynumber: 2.5 Consensus size: 22
20515778 CGCCTATTCA
20515788 TTTTTCTTTTTTCTTTTTCCTT
1 TTTTTCTTTTTTCTTTTTCCTT
**
20515810 TTTTTC-TTTTTCTTTTTTTTT
1 TTTTTCTTTTTTCTTTTTCCTT
20515831 TCTTTTCTTTTTT
1 T-TTTTCTTTTTT
20515844 TCCCTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 14 0.47
22 11 0.37
23 5 0.17
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (22 bp):
TTTTTCTTTTTTCTTTTTCCTT
Found at i:20515820 original size:16 final size:14
Alignment explanation
Indices: 20515788--20515845 Score: 73
Period size: 15 Copynumber: 4.0 Consensus size: 14
20515778 CGCCTATTCA
20515788 TTTTTC-TTTTTTC
1 TTTTTCTTTTTTTC
20515801 TTTTTCCTTTTTTTC
1 TTTTT-CTTTTTTTC
*
20515816 TTTTTCTTTTTTTTT
1 TTTTTC-TTTTTTTC
20515831 TCTTTTCTTTTTTTC
1 T-TTTTCTTTTTTTC
20515846 CCTTTTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
13 5 0.13
14 2 0.05
15 27 0.69
16 5 0.13
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTCTTTTTTTC
Found at i:20515850 original size:15 final size:14
Alignment explanation
Indices: 20515789--20515855 Score: 57
Period size: 15 Copynumber: 4.6 Consensus size: 14
20515779 GCCTATTCAT
*
20515789 TTTTC-TTTTTTCT
1 TTTTCTTTTTTTCC
*
20515802 TTTTCCTTTTTTTCT
1 TTTT-CTTTTTTTCC
*
20515817 TTTTCTTTTTTTTTTC
1 TTTTC--TTTTTTTCC
20515833 TTTTCTTTTTTTCCC
1 TTTTCTTTTTTT-CC
20515848 TTTT-TTTT
1 TTTTCTTTT
20515856 GAAATAGAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
13 4 0.09
14 13 0.28
15 17 0.37
16 12 0.26
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTCTTTTTTTCC
Found at i:20515851 original size:22 final size:20
Alignment explanation
Indices: 20515788--20515853 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
20515778 CGCCTATTCA
20515788 TTTTTCTTTTTTCTTTTTCCT
1 TTTTTCTTTTTT-TTTTTCCT
*
20515809 TTTTT-TCTTTTTCTTTT--T
1 TTTTTCT-TTTTTTTTTTCCT
20515827 TTTTTCTTTTCTTTTTTTCCCT
1 TTTTTCTTTT-TTTTTTT-CCT
20515849 TTTTT
1 TTTTT
20515854 TTGAAATAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
18 9 0.24
19 7 0.19
20 5 0.14
21 10 0.27
22 6 0.16
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTTCTTTTTTTTTTTCCT
Found at i:20517913 original size:39 final size:39
Alignment explanation
Indices: 20517878--20518329 Score: 429
Period size: 39 Copynumber: 11.5 Consensus size: 39
20517868 GGATATAGTA
* * * * *
20517878 CCAGTACGAAGCCTGCGGACCTTAAGTCCGAATATAGTA
1 CCAGCACGAAGCCTGCGGACCTTAAGTCCGGATACAATT
* * * * * *
20517917 CAAGCATGAAACCTACGGATCATAAGTCCGGATACAATT
1 CCAGCACGAAGCCTGCGGACCTTAAGTCCGGATACAATT
* * * *
20517956 CCAGCATGAAGCCTGCGGGTCTTTAAGCCCGGATACAATT
1 CCAGCACGAAGCCTGC-GGACCTTAAGTCCGGATACAATT
*
20517996 CCAGCACGAAGCCTGCAGACCTTAAGTCCGGATACAATT
1 CCAGCACGAAGCCTGCGGACCTTAAGTCCGGATACAATT
* * * * * *
20518035 CCAGCACAAAGCTTGCGGGTCTTTAAGCCCGGATATAATT
1 CCAGCACGAAGCCTGC-GGACCTTAAGTCCGGATACAATT
* * * *
20518075 CCAGCA-TATAGCCTGCGGGTCTTTAAGCCCGGATACAATT
1 CCAGCACGA-AGCCTGC-GGACCTTAAGTCCGGATACAATT
* *
20518115 CCAGCACGAAGCTTGCGGACCTTAAGTCTGGATACAATT
1 CCAGCACGAAGCCTGCGGACCTTAAGTCCGGATACAATT
*
20518154 CCAGCACGACGCCTGCGGACCTTAAGTCCGGATACAATT
1 CCAGCACGAAGCCTGCGGACCTTAAGTCCGGATACAATT
* * * * * *
20518193 CTAGCACAAAGCCTGCGGGTCTTTAAGCCCGGATATAATT
1 CCAGCACGAAGCCTGC-GGACCTTAAGTCCGGATACAATT
** * * * *
20518233 CCAGCATAAAGCCTGCGGGTCTTTAAGCCCAGATACAATT
1 CCAGCACGAAGCCTGC-GGACCTTAAGTCCGGATACAATT
* * *
20518273 CCAGCATGAAGCTTGCGGACCTTAAGTCCGGATAAAATT
1 CCAGCACGAAGCCTGCGGACCTTAAGTCCGGATACAATT
* *
20518312 CTAGCACAAAGCCTGCGG
1 CCAGCACGAAGCCTGCGG
20518330 GTCTTTAAGC
Statistics
Matches: 343, Mismatches: 65, Indels: 10
0.82 0.16 0.02
Matches are distributed among these distances:
39 175 0.51
40 167 0.49
41 1 0.00
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (39 bp):
CCAGCACGAAGCCTGCGGACCTTAAGTCCGGATACAATT
Found at i:20518148 original size:158 final size:158
Alignment explanation
Indices: 20517939--20518327 Score: 625
Period size: 158 Copynumber: 2.5 Consensus size: 158
20517929 CTACGGATCA
* * * * *
20517939 TAAGTCCGGATACAATTCCAGCATGAAGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACG
1 TAAGCCCGGATACAATTCCAGCATGAAGCTTGC-GGACCTTAAGTCCGGATACAATTCCAGCACG
*
20518004 AAGCCTGCAGACCTTAAGTCCGGATACAATTCCAGCACAAAGCTTGCGGGTCTTTAAGCCCGGAT
65 AAGCCTGCAGACCTTAAGTCCGGATACAATTCCAGCACAAAGCCTGCGGGTCTTTAAGCCCGGAT
*
20518069 ATAATTCCAGCATATAGCCTGCGGGTCTT
130 ATAATTCCAGCATAAAGCCTGCGGGTCTT
* *
20518098 TAAGCCCGGATACAATTCCAGCACGAAGCTTGCGGACCTTAAGTCTGGATACAATTCCAGCACGA
1 TAAGCCCGGATACAATTCCAGCATGAAGCTTGCGGACCTTAAGTCCGGATACAATTCCAGCACGA
* * *
20518163 CGCCTGCGGACCTTAAGTCCGGATACAATTCTAGCACAAAGCCTGCGGGTCTTTAAGCCCGGATA
66 AGCCTGCAGACCTTAAGTCCGGATACAATTCCAGCACAAAGCCTGCGGGTCTTTAAGCCCGGATA
20518228 TAATTCCAGCATAAAGCCTGCGGGTCTT
131 TAATTCCAGCATAAAGCCTGCGGGTCTT
* * * *
20518256 TAAGCCCAGATACAATTCCAGCATGAAGCTTGCGGACCTTAAGTCCGGATAAAATTCTAGCACAA
1 TAAGCCCGGATACAATTCCAGCATGAAGCTTGCGGACCTTAAGTCCGGATACAATTCCAGCACGA
20518321 AGCCTGC
66 AGCCTGC
20518328 GGGTCTTTAA
Statistics
Matches: 211, Mismatches: 19, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
158 181 0.86
159 30 0.14
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.22
Consensus pattern (158 bp):
TAAGCCCGGATACAATTCCAGCATGAAGCTTGCGGACCTTAAGTCCGGATACAATTCCAGCACGA
AGCCTGCAGACCTTAAGTCCGGATACAATTCCAGCACAAAGCCTGCGGGTCTTTAAGCCCGGATA
TAATTCCAGCATAAAGCCTGCGGGTCTT
Found at i:20518328 original size:79 final size:80
Alignment explanation
Indices: 20517939--20518346 Score: 482
Period size: 79 Copynumber: 5.2 Consensus size: 80
20517929 CTACGGATCA
* * * *
20517939 TAAGTCCGGATACAATTCCAGCATGAAGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACG
1 TAAGCCCGGATACAATTCCAGCACGAAGCTTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACA
* * *
20518004 AAGCCTGC-AGACCT
66 AAGCCTGCGGGTCTT
* * * *
20518018 TAAGTCCGGATACAATTCCAGCACAAAGCTTGCGGGTCTTTAAGCCCGGATATAATTCCAGCATA
1 TAAGCCCGGATACAATTCCAGCACGAAGCTTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACA
*
20518083 TAGCCTGCGGGTCTT
66 AAGCCTGCGGGTCTT
* * * * *
20518098 TAAGCCCGGATACAATTCCAGCACGAAGCTTGC-GGACCTTAAGTCTGGATACAATTCCAGCACG
1 TAAGCCCGGATACAATTCCAGCACGAAGCTTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACA
* * *
20518162 ACGCCTGC-GGACCT
66 AAGCCTGCGGGTCTT
* * * * * *
20518176 TAAGTCCGGATACAATTCTAGCACAAAGCCTGCGGGTCTTTAAGCCCGGATATAATTCCAGCATA
1 TAAGCCCGGATACAATTCCAGCACGAAGCTTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACA
20518241 AAGCCTGCGGGTCTT
66 AAGCCTGCGGGTCTT
* * * * * * *
20518256 TAAGCCCAGATACAATTCCAGCATGAAGCTTGC-GGACCTTAAGTCCGGATAAAATTCTAGCACA
1 TAAGCCCGGATACAATTCCAGCACGAAGCTTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACA
20518320 AAGCCTGCGGGTCTT
66 AAGCCTGCGGGTCTT
*
20518335 TAAGCTCGGATA
1 TAAGCCCGGATA
20518347 TACATCAAAT
Statistics
Matches: 275, Mismatches: 51, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
78 33 0.12
79 177 0.64
80 65 0.24
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.23
Consensus pattern (80 bp):
TAAGCCCGGATACAATTCCAGCACGAAGCTTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACA
AAGCCTGCGGGTCTT
Found at i:20518348 original size:119 final size:118
Alignment explanation
Indices: 20517842--20518346 Score: 587
Period size: 119 Copynumber: 4.3 Consensus size: 118
20517832 CAATCACCAA
* * ** * * * *
20517842 CACAAAGCCTACGGGACTTTAAGCTTGGATATAGTACCAGTACGAAGCCTGCGGACCTTAAGTCC
1 CACAAAGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCGGACCTTAAGTCC
* * * * * * * * * * *
20517907 GAATATAGTACAAGCATGAAACCTACGGATCATAAGTCCGGATACAATTCCAG
66 GGATACAATTCCAGCACGAAGCTTGCGGACCTTAAGTCCGGATACAATTCCAG
** *
20517960 CATGAAGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCAGACCTTAAGTCC
1 CACAAAGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCGGACCTTAAGTCC
* * * * *
20518025 GGATACAATTCCAGCACAAAGCTTGCGGGTCTTTAAGCCCGGATATAATTCCAG
66 GGATACAATTCCAGCACGAAGCTTGC-GGACCTTAAGTCCGGATACAATTCCAG
* * * *
20518079 CATATAGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGAAGCTTGCGGACCTTAAGTCT
1 CACAAAGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCGGACCTTAAGTCC
* * *
20518144 GGATACAATTCCAGCACGACGCCTGCGGACCTTAAGTCCGGATACAATTCTAG
66 GGATACAATTCCAGCACGAAGCTTGCGGACCTTAAGTCCGGATACAATTCCAG
* ** * * *
20518197 CACAAAGCCTGCGGGTCTTTAAGCCCGGATATAATTCCAGCATAAAGCCTGCGGGTCTTTAAGCC
1 CACAAAGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGC-GGACCTTAAGTC
* * * *
20518262 CAGATACAATTCCAGCATGAAGCTTGCGGACCTTAAGTCCGGATAAAATTCTAG
65 CGGATACAATTCCAGCACGAAGCTTGCGGACCTTAAGTCCGGATACAATTCCAG
*
20518316 CACAAAGCCTGCGGGTCTTTAAGCTCGGATA
1 CACAAAGCCTGCGGGTCTTTAAGCCCGGATA
20518347 TACATCAAAT
Statistics
Matches: 329, Mismatches: 56, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
118 138 0.42
119 191 0.58
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.22
Consensus pattern (118 bp):
CACAAAGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCGGACCTTAAGTCC
GGATACAATTCCAGCACGAAGCTTGCGGACCTTAAGTCCGGATACAATTCCAG
Found at i:20522104 original size:46 final size:46
Alignment explanation
Indices: 20522037--20522208 Score: 151
Period size: 46 Copynumber: 3.8 Consensus size: 46
20522027 TGTAACCTGC
20522037 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
* * *
20522083 CCATAAGTGAACTCAGACTCAACTCAACAAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * * *
20522133 -C-TCA-CGAACTCGGACTCAACT---CGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
* * *
20522173 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGG
20522209 ATGCCCAAAT
Statistics
Matches: 101, Mismatches: 13, Indels: 24
0.73 0.09 0.17
Matches are distributed among these distances:
39 2 0.02
40 3 0.03
41 2 0.02
42 2 0.02
43 16 0.16
44 7 0.07
46 43 0.43
47 15 0.15
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:20522192 original size:90 final size:91
Alignment explanation
Indices: 20522044--20522213 Score: 252
Period size: 90 Copynumber: 1.9 Consensus size: 91
20522034 TGCCCATAAG
* *
20522044 CGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTCAGACTCAACT--ACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
20522109 ACAAGCTCGGATGCCTAGTTACATCTCA
64 ACAAGCTCGGATGCCTAGTTACATCTCA
* * *
20522137 CGAACTCGGACTCAACT-CGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 CGAACTCAGACTCAACTACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAAC
* *
20522201 GAGTTCGGATGCC
66 AAGCTCGGATGCC
20522214 CAAATATCCT
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
90 54 0.77
93 16 0.23
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.21
Consensus pattern (91 bp):
CGAACTCAGACTCAACTACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAAC
AAGCTCGGATGCCTAGTTACATCTCA
Found at i:20522416 original size:45 final size:45
Alignment explanation
Indices: 20522366--20522477 Score: 215
Period size: 45 Copynumber: 2.5 Consensus size: 45
20522356 CATATAATTT
20522366 GACTCAACTCAACGAGTTCGGACATTCGCATCATAAGTGAACTCG
1 GACTCAACTCAACGAGTTCGGACATTCGCATCATAAGTGAACTCG
20522411 GACTCAACTCAACGAGTTCGGACATTCGCATCATAAGTGAACTCG
1 GACTCAACTCAACGAGTTCGGACATTCGCATCATAAGTGAACTCG
*
20522456 GACTCAACGCAACGAGTTCGGA
1 GACTCAACTCAACGAGTTCGGA
20522478 TGCCCAAATA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
45 66 1.00
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (45 bp):
GACTCAACTCAACGAGTTCGGACATTCGCATCATAAGTGAACTCG
Found at i:20522575 original size:268 final size:266
Alignment explanation
Indices: 20522138--20522636 Score: 860
Period size: 268 Copynumber: 1.9 Consensus size: 266
20522128 TACATCTCAC
*
20522138 GAACTCGGACTCAACTCGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGA
1 GAACTCGGACTCAACTCGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACGCAACGA
20522203 GTTCGGATGCCCAAATATCCTAGTGACATGTCACTTCTATCCTAATCCATTCCTAAGGTTCAACG
66 GTTCGGATGCCCAAATATCCTAGTGACATGTCACTTCTATCCTAATCCATTCCTAAGGTTCAACG
20522268 GGACCTTTTTTCCAATCATGTGTCTCAACCATCTTCTACGGAATGCCGTTACCGATACTCGGTAG
131 GGACCTTTTTTCCAATCATGTGTCTCAACCATCTTCTACGGAATGCCGTTACCGATACTCGGTAG
* *
20522333 TATTTCGCATTTTCCAAGTAGATCATATAATTTGACTCAACTCAACGAGTTCGGACATTCGCATC
196 TATTTCACATTTTCCAAGTAGATCACATAATTTGACTCAACTCAACGAGTTCGGACATTCGCATC
20522398 ATAAGT
261 ATAAGT
20522404 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT-CATAAGTGAACTCGGACTCAACGCAA
1 GAACTCGGACTCAACT---CGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACGCAA
* * *
20522468 CGAGTTCGGATGCCCAAATATCC-CGTTGATATGTCACTTGTATCCTAATCCATTCCTAAGGTTC
63 CGAGTTCGGATGCCCAAATATCCTAG-TGACATGTCACTTCTATCCTAATCCATTCCTAAGGTTC
*
20522532 AACGGGACC-TTTTTCCGAATCATGTGTCTCAACCATCTTCTACGGAATGTCGTTACCGATACTC
127 AACGGGACCTTTTTTCC-AATCATGTGTCTCAACCATCTTCTACGGAATGCCGTTACCGATACTC
*
20522596 GGTAGTATTTCACATTTTCCAAGTATATCACATAATTTGAC
191 GGTAGTATTTCACATTTTCCAAGTAGATCACATAATTTGAC
20522637 ATATTATCAA
Statistics
Matches: 220, Mismatches: 8, Indels: 8
0.93 0.03 0.03
Matches are distributed among these distances:
266 16 0.07
267 8 0.04
268 177 0.80
269 19 0.09
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.29
Consensus pattern (266 bp):
GAACTCGGACTCAACTCGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACGCAACGA
GTTCGGATGCCCAAATATCCTAGTGACATGTCACTTCTATCCTAATCCATTCCTAAGGTTCAACG
GGACCTTTTTTCCAATCATGTGTCTCAACCATCTTCTACGGAATGCCGTTACCGATACTCGGTAG
TATTTCACATTTTCCAAGTAGATCACATAATTTGACTCAACTCAACGAGTTCGGACATTCGCATC
ATAAGT
Found at i:20524775 original size:23 final size:23
Alignment explanation
Indices: 20524745--20524800 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
20524735 CTTCCTCATG
*
20524745 TATCCCTCCTTCTCCGGGTAAGC
1 TATCCCTCCTTCTCCGAGTAAGC
20524768 TATCCCTCCTTCTCCGAGTAAGC
1 TATCCCTCCTTCTCCGAGTAAGC
20524791 TATCCCTCCT
1 TATCCCTCCT
20524801 GACACAAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.14, C:0.41, G:0.12, T:0.32
Consensus pattern (23 bp):
TATCCCTCCTTCTCCGAGTAAGC
Found at i:20529622 original size:30 final size:31
Alignment explanation
Indices: 20529544--20529622 Score: 92
Period size: 30 Copynumber: 2.6 Consensus size: 31
20529534 CATAGTATCG
* * *
20529544 TATCTTGGGTTTCTTTA-TCCTGGATATCTT
1 TATCTTGGATTTCTTTATTCCAGGATATCTC
*
20529574 TAT-TCTGGATTTCTTTATTCCAGG-TTTCTC
1 TATCT-TGGATTTCTTTATTCCAGGATATCTC
20529604 TATCTTGGATTTCTTTATT
1 TATCTTGGATTTCTTTATT
20529623 TGGTTTTCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
29 1 0.02
30 35 0.83
31 6 0.14
ACGTcount: A:0.14, C:0.16, G:0.14, T:0.56
Consensus pattern (31 bp):
TATCTTGGATTTCTTTATTCCAGGATATCTC
Found at i:20529630 original size:14 final size:15
Alignment explanation
Indices: 20529553--20529632 Score: 76
Period size: 15 Copynumber: 5.4 Consensus size: 15
20529543 GTATCTTGGG
*
20529553 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
20529568 TATCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
20529583 TTTCTTTATTCCAGG-
1 TTTCTTTATT-CTGGA
*
20529598 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
20529613 TTTCTTTATT-TGGT
1 TTTCTTTATTCTGGA
20529627 TTTCTT
1 TTTCTT
20529633 GTTACCTTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
13 1 0.02
14 12 0.23
15 36 0.68
16 4 0.08
ACGTcount: A:0.12, C:0.16, G:0.12, T:0.59
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:20533953 original size:14 final size:14
Alignment explanation
Indices: 20533934--20533983 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
20533924 GAGTTGATTT
* *
20533934 TTGAAAAATATAAA
1 TTGAAAAACAGAAA
20533948 TTGAAAAAACAGAAA
1 TTG-AAAAACAGAAA
*
20533963 TTGAAAAGCAGAAA
1 TTGAAAAACAGAAA
20533977 TT-AAAAA
1 TTGAAAAA
20533984 GACCTCAGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 4 0.13
14 15 0.48
15 12 0.39
ACGTcount: A:0.64, C:0.04, G:0.12, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:20534122 original size:75 final size:75
Alignment explanation
Indices: 20533963--20534203 Score: 301
Period size: 76 Copynumber: 3.2 Consensus size: 75
20533953 AAAACAGAAA
* * ** *
20533963 TTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTT-GCAATA
1 TTGAAAAACAGAAATTAAAAATACCTCAGC--GTGTCCCGAGGCTCAACTCACCT-TTCGCAATA
*
20534027 TGAGTT-A-ATTT
63 TGAGTTGATTTTT
* * *
20534038 TTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTTTCGCAATATGA
1 TTGAAAAACAGAAATTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTTTCGCAATATGA
20534103 GTTGATTTTT
66 GTTGATTTTT
* *
20534113 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAA-TTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTTTCGCAATATG
20534178 AGTTGATTTTT
65 AGTTGATTTTT
**
20534189 TT-ACGAACAGAAATT
1 TTGAAAAACAGAAATT
20534204 GAAGAACAGA
Statistics
Matches: 146, Mismatches: 16, Indels: 9
0.85 0.09 0.05
Matches are distributed among these distances:
72 2 0.01
73 32 0.22
74 3 0.02
75 50 0.34
76 59 0.40
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.29
Consensus pattern (75 bp):
TTGAAAAACAGAAATTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTTTCGCAATATGA
GTTGATTTTT
Found at i:20534212 original size:14 final size:14
Alignment explanation
Indices: 20534193--20534220 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20534183 ATTTTTTTAC
20534193 GAACAGAAATTGAA
1 GAACAGAAATTGAA
20534207 GAACAGAAATTGAA
1 GAACAGAAATTGAA
20534221 AAGACCTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
GAACAGAAATTGAA
Found at i:20534265 original size:90 final size:88
Alignment explanation
Indices: 20534113--20534361 Score: 346
Period size: 90 Copynumber: 2.8 Consensus size: 88
20534103 GTTGATTTTT
*
20534113 TTGAAAAACAGAAATTTAAAAATACCTCAGC-GTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAA-TTGAAAATACCTCAGCTGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
20534177 GAGTTGATTTTTTT-ACGAACAGAAA
65 GAGTTGATTTTTTTGA--AACAGAAA
* * *
20534202 TTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTCGCAATA
1 TTGAAAAACAGAAATTGAAAATACCTCAGC-TGTG-TCCTGAGGCTCAACTCACCTCTCGCAATA
*
20534266 TGAGTTGATTTTTTTGAAACATAAA
64 TGAGTTGATTTTTTTGAAACAGAAA
*
20534291 TT-AAAAAAACGAAAATTGAAAATACCTCAG-TGTGTCCTGAGGCTCAACTCACCTCTCGCAATA
1 TTGAAAAACA-G-AAATTGAAAATACCTCAGCTGTGTCCTGAGGCTCAACTCACCTCTCGCAATA
20534354 TGAGTTGA
64 TGAGTTGA
20534362 AATTAAAACA
Statistics
Matches: 144, Mismatches: 9, Indels: 15
0.86 0.05 0.09
Matches are distributed among these distances:
87 2 0.01
88 56 0.39
89 23 0.16
90 60 0.42
91 3 0.02
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (88 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTTTTTTGAAACAGAAA
Found at i:20534406 original size:72 final size:73
Alignment explanation
Indices: 20534288--20534429 Score: 232
Period size: 72 Copynumber: 2.0 Consensus size: 73
20534278 TTTGAAACAT
* * *
20534288 AAATTAAAAAAACGAAAATTGAAAATACCTCAGTGTGTCCTGAGGCTCAACTCACCTCTCGCAAT
1 AAATTAAAAAAACAAAAATTGAAAATACCTCAGTGTGCCCCGAGGCTCAACTCACCTCTCGCAAT
20534353 ATGAGTTG
66 ATGAGTTG
* *
20534361 AAATT-AAAACACAAAAATTGAAAATACCTCAGTGTGCCCCGAGGCTCAACTCACCTCTTGCAAT
1 AAATTAAAAAAACAAAAATTGAAAATACCTCAGTGTGCCCCGAGGCTCAACTCACCTCTCGCAAT
20534425 ATGAG
66 ATGAG
20534430 CTGATTTTGA
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
72 59 0.92
73 5 0.08
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.23
Consensus pattern (73 bp):
AAATTAAAAAAACAAAAATTGAAAATACCTCAGTGTGCCCCGAGGCTCAACTCACCTCTCGCAAT
ATGAGTTG
Found at i:20534726 original size:174 final size:181
Alignment explanation
Indices: 20534404--20534734 Score: 419
Period size: 184 Copynumber: 1.9 Consensus size: 181
20534394 GTGCCCCGAG
* * *
20534404 GCTCAACTCACCTCTTGCAATATGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCAC
1 GCTCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGCAAAAATTAAAAGGTTCAACCCAC
* * * * *
20534469 CTCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGTGTCCTGAGGCT
66 CTCTCGCAATATGAGTTCAATCTTGACAAACA-AAA-T-AAATTACCTCAGCGTGCCCCGAGGCT
20534534 CAACTCACCTCTCGCAATATGAATTGAAAAAAATACCACAGTGTGTAATCTGAA
128 CAACTCACCTCTCGCAATATGAATTGAAAAAAATACCACAGTGTGTAATCTGAA
* *
20534588 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA-CAAAAATTAAAAGGCTT-AACTC
1 GCTCAACTCACCTCTCGCAATATGAGCTGA-TTTTGAAAAAGCAAAAATTAAAAGG-TTCAACCC
* **
20534651 ACCTCTCGCAATATGAG-TCAAT-TT-A-AAAC-TAA-AAA-TACCTTGGCGTGCCCCGAGGCTC
64 ACCTCTCGCAATATGAGTTCAATCTTGACAAACAAAATAAATTACCTCAGCGTGCCCCGAGGCTC
* *
20534709 AACTCACTTCTCGCAATATGAGTTGA
129 AACTCACCTCTCGCAATATGAATTGA
20534735 TTTTGAAAAA
Statistics
Matches: 130, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
174 42 0.32
175 3 0.02
178 2 0.02
180 4 0.03
181 1 0.01
182 2 0.02
183 3 0.02
184 61 0.47
185 12 0.09
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (181 bp):
GCTCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGCAAAAATTAAAAGGTTCAACCCAC
CTCTCGCAATATGAGTTCAATCTTGACAAACAAAATAAATTACCTCAGCGTGCCCCGAGGCTCAA
CTCACCTCTCGCAATATGAATTGAAAAAAATACCACAGTGTGTAATCTGAA
Found at i:20534861 original size:76 final size:72
Alignment explanation
Indices: 20534693--20534959 Score: 390
Period size: 72 Copynumber: 3.6 Consensus size: 72
20534683 AAATACCTTG
* * * * * *
20534693 GCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTTAAAA
1 GCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAACAGAAA-TTGAAA
*
20534758 ATACCTCA
65 TTACCTCA
*
20534766 GCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTAACAACAGAAATTG
1 GCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTAAAAACAGAAATTG
20534831 AAATTACCTCA
62 AAATTACCTCA
* *
20534842 GCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTAAAAACAGAAATCGAAAT
1 GCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAACAGAAATTGAAAT
20534907 TACCTCA
66 TACCTCA
*
20534914 GCGTGTCCTGAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTT
1 GCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
20534960 CCTTGGAAAG
Statistics
Matches: 177, Mismatches: 13, Indels: 9
0.89 0.07 0.05
Matches are distributed among these distances:
72 71 0.40
73 39 0.22
76 54 0.31
77 13 0.07
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (72 bp):
GCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAACAGAAATTGAAAT
TACCTCA
Found at i:20543569 original size:30 final size:30
Alignment explanation
Indices: 20543533--20543712 Score: 270
Period size: 30 Copynumber: 6.0 Consensus size: 30
20543523 TAGGTACAAG
* *
20543533 TGGTGGTGGAGAAGGTGTGACTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
* * *
20543563 TGGTGGTGGAAAAAGAGTTGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
20543593 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
* *
20543623 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
*
20543653 TGGTGGTGGAAAATGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
* *
20543683 TGGTGGTGGAAAAGGAGTGGCTAGTTGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
20543713 AAAGTTTAAG
Statistics
Matches: 135, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 135 1.00
ACGTcount: A:0.23, C:0.03, G:0.47, T:0.27
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
Found at i:20543626 original size:60 final size:60
Alignment explanation
Indices: 20543533--20543712 Score: 306
Period size: 60 Copynumber: 3.0 Consensus size: 60
20543523 TAGGTACAAG
* * *
20543533 TGGTGGTGGAGAAGGTGTGACTAGTGGAGTTGGTGGTGGAAAAAGAGTTGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
20543593 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
* * *
20543653 TGGTGGTGGAAAATGTGTGGCTAGTGGAGTTGGTGGTGGAAAAGGAGTGGCTAGTTGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
20543713 AAAGTTTAAG
Statistics
Matches: 114, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 114 1.00
ACGTcount: A:0.23, C:0.03, G:0.47, T:0.27
Consensus pattern (60 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
Found at i:20544079 original size:21 final size:21
Alignment explanation
Indices: 20544053--20544126 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 21
20544043 GAAAATCATG
20544053 AAATAGGTAAAATTTACCATA
1 AAATAGGTAAAATTTACCATA
* * ** *
20544074 AAATAGCTAATCCATGGAAAACCATG
1 AAATAGGTAA--AAT---TTACCATA
20544100 AAATAGGTAAAATTTACCATA
1 AAATAGGTAAAATTTACCATA
20544121 AAATAG
1 AAATAG
20544127 ATTCAGACAG
Statistics
Matches: 38, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
21 20 0.53
23 2 0.05
24 2 0.05
26 14 0.37
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.24
Consensus pattern (21 bp):
AAATAGGTAAAATTTACCATA
Found at i:20544088 original size:47 final size:47
Alignment explanation
Indices: 20544034--20544126 Score: 177
Period size: 47 Copynumber: 2.0 Consensus size: 47
20544024 AATTACTAGT
*
20544034 TAATCCATGGAAAATCATGAAATAGGTAAAATTTACCATAAAATAGC
1 TAATCCATGGAAAACCATGAAATAGGTAAAATTTACCATAAAATAGC
20544081 TAATCCATGGAAAACCATGAAATAGGTAAAATTTACCATAAAATAG
1 TAATCCATGGAAAACCATGAAATAGGTAAAATTTACCATAAAATAG
20544127 ATTCAGACAG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (47 bp):
TAATCCATGGAAAACCATGAAATAGGTAAAATTTACCATAAAATAGC
Found at i:20546967 original size:23 final size:22
Alignment explanation
Indices: 20546924--20546981 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
20546914 AAAAGGTATC
* *
20546924 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
20546945 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
20546968 TGCATATCATATCT
1 TACAAATCATATCT
20546982 AAGATTGCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:20546975 original size:17 final size:19
Alignment explanation
Indices: 20546960--20547082 Score: 159
Period size: 19 Copynumber: 6.8 Consensus size: 19
20546950 AATCATATCT
20546960 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
20546979 TCTAAGATTGCA-ATGATA
1 TCTAAGATTGCATATCATA
20546997 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
*
20547014 TCTAAGATTGCATATCATG
1 TCTAAGATTGCATATCATA
* *
20547033 TCAAATATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
*
20547051 TCTAAGATTG--TATCACA
1 TCTAAGATTGCATATCATA
20547068 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
20547083 TGAAGATTAT
Statistics
Matches: 89, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
17 30 0.34
18 28 0.31
19 31 0.35
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:20547028 original size:54 final size:54
Alignment explanation
Indices: 20546960--20547082 Score: 201
Period size: 54 Copynumber: 2.3 Consensus size: 54
20546950 AATCATATCT
* * *
20546960 TCTAAGATTGCATATCATATCTAAGATTGCAATGATATCTAAGATTGTATCATA
1 TCTAAGATTGCATATCATATCAAAGATTGCAATCATATCTAAGATTGTATCACA
* *
20547014 TCTAAGATTGCATATCATGTCAAATATTGCAATCATATCTAAGATTGTATCACA
1 TCTAAGATTGCATATCATATCAAAGATTGCAATCATATCTAAGATTGTATCACA
20547068 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
20547083 TGAAGATTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 64 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (54 bp):
TCTAAGATTGCATATCATATCAAAGATTGCAATCATATCTAAGATTGTATCACA
Found at i:20547079 original size:35 final size:36
Alignment explanation
Indices: 20546960--20547079 Score: 145
Period size: 35 Copynumber: 3.3 Consensus size: 36
20546950 AATCATATCT
* *
20546960 TCTAAGATTGCATATCATATCTAAGATTGCAATGATA
1 TCTAAGATTGCA-ATCATATCTAAGATTGCTATCATA
* *
20546997 TCTAAGATTG-TATCATATCTAAGATTGCATATCATG
1 TCTAAGATTGCAATCATATCTAAGATTGC-TATCATA
* * *
20547033 TCAAATATTGCAATCATATCTAAGATTG-TATCACA
1 TCTAAGATTGCAATCATATCTAAGATTGCTATCATA
20547068 TCTAAGATTGCA
1 TCTAAGATTGCA
20547080 TATTGAAGAT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
35 32 0.46
36 12 0.17
37 26 0.37
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (36 bp):
TCTAAGATTGCAATCATATCTAAGATTGCTATCATA
Found at i:20548182 original size:46 final size:48
Alignment explanation
Indices: 20548055--20548270 Score: 209
Period size: 45 Copynumber: 4.6 Consensus size: 48
20548045 GAGAGCCAAC
* * * * * *
20548055 GTAAGACCATGTCTGGGACATGGCATCAG-TATTGAGACGAAAGCTAAT
1 GTAAGACCATGTCTGGGACATGGCATCGGCTA-CGAGATGTAAGCCAGT
20548103 GTAAGA-CATGTCTGGG-CAT-GCATCGGCCT-CGAGATGTAAGCCAGT
1 GTAAGACCATGTCTGGGACATGGCATCGG-CTACGAGATGTAAGCCAGT
* * *
20548148 GTAAGA-CATGTATGGGACAT-GCATCGGCTACGAGATGT-A-TCAGG
1 GTAAGACCATGTCTGGGACATGGCATCGGCTACGAGATGTAAGCCAGT
*
20548192 GTAAGACCATGTCCGGGACATGGCATCGGC-ACAGAGATGTTAGAGCCAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCTAC-GAGATG-TA-AGCCAGT
* *
20548242 ATAAGACCATGTCTAGGACATGGCATCGG
1 GTAAGACCATGTCTGGGACATGGCATCGG
20548271 TATTACAACC
Statistics
Matches: 141, Mismatches: 16, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
44 9 0.06
45 49 0.35
46 35 0.25
47 12 0.09
48 6 0.04
49 1 0.01
50 29 0.21
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.21
Consensus pattern (48 bp):
GTAAGACCATGTCTGGGACATGGCATCGGCTACGAGATGTAAGCCAGT
Found at i:20550042 original size:28 final size:28
Alignment explanation
Indices: 20550007--20550073 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
20549997 AAAAAAAATT
* *
20550007 GCACTAAGTGTGCAAG-TCTGATTATTGA
1 GCACTAAGTGTGCAAGCT-TAAGTATTGA
*
20550035 GCACTAAGTGTGCAAGCTTAAGTATTTA
1 GCACTAAGTGTGCAAGCTTAAGTATTGA
20550063 GCACTAAGTGT
1 GCACTAAGTGT
20550074 ACGAATTTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
28 34 0.97
29 1 0.03
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGCTTAAGTATTGA
Found at i:20561073 original size:11 final size:11
Alignment explanation
Indices: 20561057--20561083 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
20561047 GAACAAACAT
20561057 GTCACACATGG
1 GTCACACATGG
20561068 GTCACACATGG
1 GTCACACATGG
20561079 GTCAC
1 GTCAC
20561084 TTTTCATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.19
Consensus pattern (11 bp):
GTCACACATGG
Found at i:20565667 original size:46 final size:46
Alignment explanation
Indices: 20565489--20565850 Score: 212
Period size: 49 Copynumber: 7.7 Consensus size: 46
20565479 TTTGTGTATT
* *
20565489 AGTGTAAGA-CATGTCTGGGACATGCATCGGCCAC-ATTAT-TAAAGCT
1 AGTGTAAGACCATGTCTGGGACATGCATCGG-CACGA-GATGT-AAGCC
* * * * *
20565535 AGTGTAAGACCATGTTTGGGACATGGCACCGGCATTGAGACG-AGAGCT
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGGCA-CGAGATGTA-AGCC
*
20565583 AGTGTAAGA-CATGTCTGGG-CATGCATCGGCCTCGAGATGTAAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATCGG-CACGAGATGTAAGCC
* *
20565628 AGTGTAAGA-TATGTCTGGGACATGCATCGGCTACGAGATGT--GTC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGC-ACGAGATGTAAGCC
* * * * *
20565672 AGTGTAAGACTATGTCCGGGACAAGGCATCAGCATGGAGAT-TGAGAGCC
1 AGTGTAAGACCATGTCTGGGAC-ATGCATCGGCA-CGAGATGT-A-AGCC
* * * *
20565721 AGTGTAAGACCATGTCTGGGACATGGCGTCAGCTTCGA-AT-TCAATAGTC
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGGC-ACGAGATGT--A-AGCC
* * ** *
20565770 AGTATAAAACCATGTCTGGGACATGGCATC-G-ACTTGATGGATGAGCC
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGGCACGAGAT-G-TAAGCC
*
20565817 AATGTAAGACCATGTCTGGGACATGGCATCGGCA
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGGCA
20565851 TTACACCCTA
Statistics
Matches: 251, Mismatches: 39, Indels: 49
0.74 0.12 0.14
Matches are distributed among these distances:
44 11 0.04
45 46 0.18
46 46 0.18
47 57 0.23
48 26 0.10
49 64 0.25
50 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACCATGTCTGGGACATGCATCGGCACGAGATGTAAGCC
Found at i:20567016 original size:21 final size:20
Alignment explanation
Indices: 20566992--20567031 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
20566982 GTTATAATGA
*
20566992 CCACACGTGCGTGTTGCCCTT
1 CCACACGGGCGTG-TGCCCTT
*
20567013 CCACATGGGCGTGTGCCCT
1 CCACACGGGCGTGTGCCCT
20567032 ATTTCAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.10, C:0.38, G:0.28, T:0.25
Consensus pattern (20 bp):
CCACACGGGCGTGTGCCCTT
Found at i:20580302 original size:19 final size:19
Alignment explanation
Indices: 20580278--20580315 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
20580268 TATAATTCTT
20580278 TTACCTGCAAAAACTTTCG
1 TTACCTGCAAAAACTTTCG
*
20580297 TTACCTGCATAAACTTTCG
1 TTACCTGCAAAAACTTTCG
20580316 CTTATTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (19 bp):
TTACCTGCAAAAACTTTCG
Found at i:20586900 original size:3 final size:3
Alignment explanation
Indices: 20586892--20586916 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20586882 AGATATTTAC
20586892 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
20586917 CAATTAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:20586959 original size:41 final size:40
Alignment explanation
Indices: 20586914--20586994 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 40
20586904 TTATTATTAT
*
20586914 TATCAATTAATTGAGATAATGACAAATGTATGGTGATGAA
1 TATCAATTAATTGAGATAATGACAAATGTATGATGATGAA
20586954 NTATCAATTAATTGAGATAATGACAAATGTATGATGATGAA
1 -TATCAATTAATTGAGATAATGACAAATGTATGATGATGAA
20586995 ATATTACATG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.32
Consensus pattern (40 bp):
TATCAATTAATTGAGATAATGACAAATGTATGATGATGAA
Found at i:20587115 original size:12 final size:12
Alignment explanation
Indices: 20587098--20587123 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20587088 AAAGAAATAA
20587098 AATAAATAAAAG
1 AATAAATAAAAG
20587110 AATAAATAAAAG
1 AATAAATAAAAG
20587122 AA
1 AA
20587124 AGAAAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (12 bp):
AATAAATAAAAG
Found at i:20587169 original size:15 final size:15
Alignment explanation
Indices: 20587119--20587173 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
20587109 GAATAAATAA
* *
20587119 AAGAAAGAAAAACAAG
1 AAGAAAGAAATA-GAG
*
20587135 AA-AAAGAAGTAGAG
1 AAGAAAGAAATAGAG
20587149 AAGAAACGAAATAGA-
1 AAGAAA-GAAATAGAG
20587164 AAGAAAGAAA
1 AAGAAAGAAA
20587174 GAAGAAAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 8 0.24
15 16 0.48
16 9 0.27
ACGTcount: A:0.71, C:0.04, G:0.22, T:0.04
Consensus pattern (15 bp):
AAGAAAGAAATAGAG
Found at i:20587198 original size:26 final size:25
Alignment explanation
Indices: 20587105--20587199 Score: 70
Period size: 26 Copynumber: 3.6 Consensus size: 25
20587095 TAAAATAAAT
*
20587105 AAAAGAATAAATA-AAAGAAAGAAAA-
1 AAAAGAA-AAAGAGAAAG-AAGAAAAG
* * *
20587130 ACAAGAAAAAGAAGTAGAGAAGAAACG
1 AAAAGAAAAAG-AG-AAAGAAGAAAAG
20587157 AAATAGAAAGAA-AGAAAGAAGAAAAG
1 AAA-AGAAA-AAGAGAAAGAAGAAAAG
20587183 AAAAGAAAAAGGAGAAA
1 AAAAGAAAAA-GAGAAA
20587200 TTAGGGTTTG
Statistics
Matches: 55, Mismatches: 7, Indels: 15
0.71 0.09 0.19
Matches are distributed among these distances:
24 5 0.09
25 12 0.22
26 24 0.44
27 7 0.13
28 5 0.09
29 2 0.04
ACGTcount: A:0.73, C:0.02, G:0.21, T:0.04
Consensus pattern (25 bp):
AAAAGAAAAAGAGAAAGAAGAAAAG
Found at i:20590060 original size:17 final size:17
Alignment explanation
Indices: 20590038--20590078 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
20590028 GGAATGATAG
20590038 TAAAATTATTAATTTGT
1 TAAAATTATTAATTTGT
20590055 TAAAATTATTAATTTGT
1 TAAAATTATTAATTTGT
*
20590072 TACAATT
1 TAAAATT
20590079 TAGTACAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.51
Consensus pattern (17 bp):
TAAAATTATTAATTTGT
Found at i:20600720 original size:25 final size:25
Alignment explanation
Indices: 20600672--20600719 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
20600662 TCAAAAGGTT
20600672 AAAAAATTATAAAAATTATTAAAAG
1 AAAAAATTATAAAAATTATTAAAAG
*
20600697 AAAAACTTAT-AAAATTATTAAAA
1 AAAAAATTATAAAAATTATTAAAA
20600720 ATATTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (25 bp):
AAAAAATTATAAAAATTATTAAAAG
Found at i:20601116 original size:16 final size:17
Alignment explanation
Indices: 20601095--20601127 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
20601085 ACTCAATAAA
20601095 AAATAAAATGTC-CTAT
1 AAATAAAATGTCACTAT
*
20601111 AAATAAATTGTCACTAT
1 AAATAAAATGTCACTAT
20601128 TTTTTGACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (17 bp):
AAATAAAATGTCACTAT
Found at i:20603712 original size:82 final size:82
Alignment explanation
Indices: 20603618--20603923 Score: 612
Period size: 82 Copynumber: 3.7 Consensus size: 82
20603608 TATGATAGTG
20603618 ATAGGGTTTTTTACCCTGGAAAAAAAATTATTTACCACAATTATTAACTGAAATAATATGTTTTT
1 ATAGGGTTTTTTACCCTGGAAAAAAAATTATTTACCACAATTATTAACTGAAATAATATGTTTTT
20603683 AGGCTCATGAATTAGGA
66 AGGCTCATGAATTAGGA
20603700 ATAGGGTTTTTTACCCTGGAAAAAAAATTATTTACCACAATTATTAACTGAAATAATATGTTTTT
1 ATAGGGTTTTTTACCCTGGAAAAAAAATTATTTACCACAATTATTAACTGAAATAATATGTTTTT
20603765 AGGCTCATGAATTAGGA
66 AGGCTCATGAATTAGGA
20603782 ATAGGGTTTTTTACCCTGGAAAAAAAATTATTTACCACAATTATTAACTGAAATAATATGTTTTT
1 ATAGGGTTTTTTACCCTGGAAAAAAAATTATTTACCACAATTATTAACTGAAATAATATGTTTTT
20603847 AGGCTCATGAATTAGGA
66 AGGCTCATGAATTAGGA
20603864 ATAGGGTTTTTTACCCTGGAAAAAAAATTATTTACCACAATTATTAACTGAAATAATATG
1 ATAGGGTTTTTTACCCTGGAAAAAAAATTATTTACCACAATTATTAACTGAAATAATATG
20603924 AAGGGTTTCC
Statistics
Matches: 224, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 224 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (82 bp):
ATAGGGTTTTTTACCCTGGAAAAAAAATTATTTACCACAATTATTAACTGAAATAATATGTTTTT
AGGCTCATGAATTAGGA
Found at i:20609831 original size:20 final size:19
Alignment explanation
Indices: 20609810--20609851 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
20609800 TTAAAAAATA
*
20609810 TATAAAT-TTTAGAATTTT
1 TATAAATATTTTGAATTTT
20609828 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
20609847 T-TAAA
1 TATAAA
20609852 ATCATTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:20609853 original size:19 final size:21
Alignment explanation
Indices: 20609815--20609873 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
20609805 AAATATATAA
20609815 ATTTTAGAA-TTTTTATAAAT-
1 ATTTT-GAATTTTTTATAAATC
20609835 ATTTTGAATTTTTTA-AAATC
1 ATTTTGAATTTTTTATAAATC
* *
20609855 ATTTTAAATTACTTTATAA
1 ATTTTGAATT-TTTTATAA
20609874 TTTTTATTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 7 0.21
20 20 0.61
21 4 0.12
22 2 0.06
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (21 bp):
ATTTTGAATTTTTTATAAATC
Found at i:20609858 original size:20 final size:20
Alignment explanation
Indices: 20609810--20609864 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
20609800 TTAAAAAATA
*
20609810 TATAAAT-TTTAGAA-TTTT
1 TATAAATATTTTGAATTTTT
20609828 TATAAATATTTTGAATTTTT
1 TATAAATATTTTGAATTTTT
*
20609848 TA-AAATCATTTTAAATT
1 TATAAAT-ATTTTGAATT
20609865 ACTTTATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 7 0.22
19 10 0.31
20 15 0.47
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (20 bp):
TATAAATATTTTGAATTTTT
Found at i:20612106 original size:48 final size:47
Alignment explanation
Indices: 20612036--20612258 Score: 196
Period size: 49 Copynumber: 4.6 Consensus size: 47
20612026 CCCCTATGCG
* * *
20612036 TTTGGGAGCAAAGTTTTATTATTA-CTTCCCTAAGCCTCTCTCAATACA
1 TTTGGGAG-AAGGTTTTATTATTACCTTCCGTAAGCCTCTCTC-ACACA
* * * * *
20612084 TTTGGGAGTAAGGTTTTGTTATTACCTTCCGTAAGCTTCCCCCTACGCA
1 TTTGGGAG-AAGGTTTTATTATTACCTTCCGTAAGCCTCTCTC-ACACA
* * *
20612133 TCTAGGAGAAAGGTTTTATTATTACCTTCCGTAAGCCTCCTCTCACACG
1 TTTGGGAG-AAGGTTTTATTATTACCTTCCGTAAGCCT-CTCTCACACA
* * **
20612182 TTTGGGAGAAGGGTTTTATTAATACCTTCCGTAAGCCTCCCATCGTACA
1 TTTGGGAGAA-GGTTTTATTATTACCTTCCGTAAGCCTCTC-TCACACA
* * *
20612231 TCTGGAAGCAAAGTTTTATTATTACCTT
1 TTTGGGAG-AAGGTTTTATTATTACCTT
20612259 TTGTAAGTGT
Statistics
Matches: 140, Mismatches: 30, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
48 25 0.18
49 110 0.79
50 5 0.04
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (47 bp):
TTTGGGAGAAGGTTTTATTATTACCTTCCGTAAGCCTCTCTCACACA
Found at i:20612208 original size:98 final size:97
Alignment explanation
Indices: 20611999--20612255 Score: 265
Period size: 98 Copynumber: 2.6 Consensus size: 97
20611989 CCAATAATGA
* ** * * * * * *
20611999 GTTTTATTATTACCTTTTGTTAGTCTCCCCCTATGCGTTTGGGAGCAAAGTTTTATTATTACTTC
1 GTTTTATTAATACCTTCCGTAAGCCTCCCCCTACGCATCTAGGAGCAAAGTTTTATTATTACTTC
*
20612064 CCTAAGCCTCTCTCAATACATTTGGGAGTAAG
66 CCTAAGCCTCTCTCAACACATTTGGGAGTAAG
* * *
20612096 GTTTTGTTATTACCTTCCGTAAGCTTCCCCCTACGCATCTAGGAG-AAAGGTTTTATTATTACCT
1 GTTTTATTAATACCTTCCGTAAGCCTCCCCCTACGCATCTAGGAGCAAA-GTTTTATTATTA-CT
* *
20612160 TCCGTAAGCCTCCTCTC-ACACGTTTGGGAG-AAGG
64 TCCCTAAGCCT-CTCTCAACACATTTGGGAGTAA-G
*
20612194 GTTTTATTAATACCTTCCGTAAGCCT-CCCAT-CGTACATCT-GGAAGCAAAGTTTTATTATTAC
1 GTTTTATTAATACCTTCCGTAAGCCTCCCCCTACG--CATCTAGG-AGCAAAGTTTTATTATTAC
20612256 CTTTTGTAAG
Statistics
Matches: 135, Mismatches: 17, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
96 5 0.04
97 56 0.41
98 66 0.49
99 8 0.06
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (97 bp):
GTTTTATTAATACCTTCCGTAAGCCTCCCCCTACGCATCTAGGAGCAAAGTTTTATTATTACTTC
CCTAAGCCTCTCTCAACACATTTGGGAGTAAG
Found at i:20612265 original size:98 final size:97
Alignment explanation
Indices: 20612040--20612258 Score: 270
Period size: 98 Copynumber: 2.2 Consensus size: 97
20612030 TATGCGTTTG
* * *
20612040 GGAGCAAAGTTTTATTATTA-CTTCCCTAAGCCTCTCTCAATACATTTGGGAGTAAGGTTTTGTT
1 GGAGCAAAGTTTTATTATTACCTTCCGTAAGCCTCTCTCAACACATTTGGGAGTAAGGTTTTATT
* *
20612104 ATTACCTTCCGTAAGCTTCCCCCTACGCATCTA
66 AATACCTTCCGTAAGCCTCCCCCTAC-CATCTA
*
20612137 GGAG-AAAGGTTTTATTATTACCTTCCGTAAGCCTCCTCTC-ACACGTTTGGGAG-AAGGGTTTT
1 GGAGCAAA-GTTTTATTATTACCTTCCGTAAGCCT-CTCTCAACACATTTGGGAGTAA-GGTTTT
*
20612199 ATTAATACCTTCCGTAAGCCTCCCATCGTA-CATCT-
63 ATTAATACCTTCCGTAAGCCTCCC--CCTACCATCTA
20612234 GGAAGCAAAGTTTTATTATTACCTT
1 GG-AGCAAAGTTTTATTATTACCTT
20612259 TTGTAAGTGT
Statistics
Matches: 107, Mismatches: 7, Indels: 15
0.83 0.05 0.12
Matches are distributed among these distances:
96 3 0.03
97 20 0.19
98 73 0.68
99 8 0.07
100 3 0.03
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (97 bp):
GGAGCAAAGTTTTATTATTACCTTCCGTAAGCCTCTCTCAACACATTTGGGAGTAAGGTTTTATT
AATACCTTCCGTAAGCCTCCCCCTACCATCTA
Found at i:20614816 original size:18 final size:18
Alignment explanation
Indices: 20614793--20614830 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
20614783 TAGCCGTGTG
*
20614793 TTCTTTCTCTTCTTTTCT
1 TTCTTTCTCTTCTTTCCT
*
20614811 TTCTTTCTTTTCTTTCCT
1 TTCTTTCTCTTCTTTCCT
20614829 TT
1 TT
20614831 TTAATTTGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (18 bp):
TTCTTTCTCTTCTTTCCT
Found at i:20622950 original size:21 final size:20
Alignment explanation
Indices: 20622910--20622951 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
20622900 GGATTTAGAA
*
20622910 TTGAATTATAAATTTATTTT
1 TTGAATTATAAATGTATTTT
20622930 TTGAGATTA-AAATGTATTTT
1 TTGA-ATTATAAATGTATTTT
20622950 TT
1 TT
20622952 ATTAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (20 bp):
TTGAATTATAAATGTATTTT
Found at i:20625352 original size:19 final size:18
Alignment explanation
Indices: 20625324--20625359 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
20625314 AAGTTACCTT
20625324 CTTTGTTTCTGGTTTTGA
1 CTTTGTTTCTGGTTTTGA
*
20625342 CTTTGGTTTCTGTTTTTG
1 CTTT-GTTTCTGGTTTTG
20625360 TTTGTGGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.03, C:0.11, G:0.22, T:0.64
Consensus pattern (18 bp):
CTTTGTTTCTGGTTTTGA
Found at i:20628483 original size:11 final size:10
Alignment explanation
Indices: 20628463--20628498 Score: 63
Period size: 10 Copynumber: 3.5 Consensus size: 10
20628453 TTCATTTTCT
20628463 AAAAGCAAAAA
1 AAAAG-AAAAA
20628474 AAAAGAAAAA
1 AAAAGAAAAA
20628484 AAAAGAAAAA
1 AAAAGAAAAA
20628494 AAAAG
1 AAAAG
20628499 GTTTGGCACA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 20 0.80
11 5 0.20
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:20637002 original size:2 final size:2
Alignment explanation
Indices: 20636162--20636985 Score: 1648
Period size: 2 Copynumber: 412.0 Consensus size: 2
20636152 TACTCTGTAC
20636162 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
20636204 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
20636246 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
20636288 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
20636330 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
20636372 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
20636414 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
20636456 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
20636498 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
20636540 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
20636582 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
20636624 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
20636666 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
20636708 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
20636750 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
20636792 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
20636834 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
20636876 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
20636918 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
20636960 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
20636986 CTTGATGAAG
Statistics
Matches: 822, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 822 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:20637659 original size:25 final size:27
Alignment explanation
Indices: 20637603--20637659 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
20637593 TTCTTCAATA
**
20637603 TAATTATTATAGGTATTTTAATAAATT
1 TAATTATTATAAATATTTTAATAAATT
*
20637630 AAATTATTATAAATA-TTT-ATAAATT
1 TAATTATTATAAATATTTTAATAAATT
20637655 TAATT
1 TAATT
20637660 TAAGTTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 11 0.42
26 3 0.12
27 12 0.46
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (27 bp):
TAATTATTATAAATATTTTAATAAATT
Found at i:20646136 original size:40 final size:40
Alignment explanation
Indices: 20646063--20646167 Score: 104
Period size: 40 Copynumber: 2.6 Consensus size: 40
20646053 ACTATGTTTG
* * *
20646063 GCACTTAGTGTGCGATTCGAGATAGCTTTGGCTATATAAA
1 GCACTTAGTGTGCGATACGAGATAACTTCGGCTATATAAA
* ***
20646103 GCACTTAGTGTGCGAATAGGA-ATAACTTCGGCTATATGTG
1 GCACTTAGTGTGCG-ATACGAGATAACTTCGGCTATATAAA
* *
20646143 GCACTAAGTGTGTGATACCGAGATA
1 GCACTTAGTGTGCGATA-CGAGATA
20646168 GTTTCAGTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
39 3 0.06
40 42 0.81
41 7 0.13
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.30
Consensus pattern (40 bp):
GCACTTAGTGTGCGATACGAGATAACTTCGGCTATATAAA
Found at i:20650529 original size:25 final size:27
Alignment explanation
Indices: 20650492--20650544 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
20650482 TTAAACATGC
20650492 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
20650518 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
20650544 A
1 A
20650545 AAACTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:20652063 original size:26 final size:26
Alignment explanation
Indices: 20652033--20652114 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
20652023 TGAAATGCCC
20652033 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
20652059 ATCATGGAACATTTACCGAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
20652085 ATCATGGAACATTTACATAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
20652111 ATCA
1 ATCA
20652115 ATTTTTATCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.37, C:0.26, G:0.09, T:0.29
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:20658585 original size:25 final size:27
Alignment explanation
Indices: 20658548--20658600 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
20658538 TTAAACATGC
20658548 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
20658574 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
20658600 A
1 A
20658601 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:20660092 original size:40 final size:40
Alignment explanation
Indices: 20659994--20660256 Score: 307
Period size: 40 Copynumber: 6.6 Consensus size: 40
20659984 TCCTCGTTCA
* * * * *
20659994 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
20660033 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
20660073 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCTCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
20660113 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
20660153 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
20660193 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
20660233 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
20660257 CAGCATTCAA
Statistics
Matches: 198, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
39 37 0.19
40 153 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:20660265 original size:41 final size:41
Alignment explanation
Indices: 20660188--20660265 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
20660178 TTAGTATCTC
* * *
20660188 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
20660229 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
20660266 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:20663283 original size:26 final size:26
Alignment explanation
Indices: 20663253--20663308 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
20663243 TGAAATGCCC
20663253 ATCATGAAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
*
20663279 ATCATGGAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
20663305 ATCA
1 ATCA
20663309 ATTTTTATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.30
Consensus pattern (26 bp):
ATCATGAAACATTTACCTAACCCATT
Found at i:20664139 original size:15 final size:16
Alignment explanation
Indices: 20664111--20664141 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
20664101 GGATGTGAAT
20664111 TTGAGTAGTGAAATGG
1 TTGAGTAGTGAAATGG
20664127 TTGAGTA-TGAAATGG
1 TTGAGTAGTGAAATGG
20664142 CATGAAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (16 bp):
TTGAGTAGTGAAATGG
Found at i:20667874 original size:21 final size:20
Alignment explanation
Indices: 20667850--20667888 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
20667840 AAACTTGTTT
20667850 ATCTATCAACAAACATTCATA
1 ATCTATCAACAAA-ATTCATA
*
20667871 ATCTATCAATAAAATTCA
1 ATCTATCAACAAAATTCA
20667889 AAATACACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.31
Consensus pattern (20 bp):
ATCTATCAACAAAATTCATA
Found at i:20673540 original size:42 final size:43
Alignment explanation
Indices: 20673486--20673595 Score: 136
Period size: 43 Copynumber: 2.6 Consensus size: 43
20673476 ATTTACGTGC
* *
20673486 AAGACGATGTTTGGGACA-TCGGCATCG-TATTTGATTTCATGT
1 AAGACCATGTTTGGGACAGT-GGCATCGATATTTGATTACATGT
*
20673528 AAGACCATGTTTGGGATAGTGGCATCGATATTTGATTACATGT
1 AAGACCATGTTTGGGACAGTGGCATCGATATTTGATTACATGT
* *
20673571 AAGACCACGTCTGGGAC-GTTGGCAT
1 AAGACCATGTTTGGGACAG-TGGCAT
20673596 TGTACGAGCT
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
42 24 0.41
43 35 0.59
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.32
Consensus pattern (43 bp):
AAGACCATGTTTGGGACAGTGGCATCGATATTTGATTACATGT
Found at i:20673594 original size:43 final size:43
Alignment explanation
Indices: 20673451--20673595 Score: 134
Period size: 43 Copynumber: 3.4 Consensus size: 43
20673441 TAAGGTCACA
* * * * *
20673451 TCTGGGATGTTGGCATCGAT-TTGAGATTTACGTGCAAGACGATG
1 TCTGGGACGTTGGCATCGATATT-TGA-TTACATGTAAGACCATG
* * * *
20673495 TTTGGGACATCGGCATCG-TATTTGATTTCATGTAAGACCATG
1 TCTGGGACGTTGGCATCGATATTTGATTACATGTAAGACCATG
* * *
20673537 TTTGGGATAG-TGGCATCGATATTTGATTACATGTAAGACCACG
1 TCTGGGA-CGTTGGCATCGATATTTGATTACATGTAAGACCATG
20673580 TCTGGGACGTTGGCAT
1 TCTGGGACGTTGGCAT
20673596 TGTACGAGCT
Statistics
Matches: 81, Mismatches: 16, Indels: 9
0.76 0.15 0.08
Matches are distributed among these distances:
42 28 0.35
43 37 0.46
44 16 0.20
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.33
Consensus pattern (43 bp):
TCTGGGACGTTGGCATCGATATTTGATTACATGTAAGACCATG
Found at i:20676426 original size:30 final size:30
Alignment explanation
Indices: 20676392--20676458 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
20676382 ACTAGGGGAT
20676392 ACACGGCCGTGTAACATGCCCGTGTATCAC
1 ACACGGCCGTGTAACATGCCCGTGTATCAC
**
20676422 ACACGGCCGTGTAACATGCTTGTGTATCAC
1 ACACGGCCGTGTAACATGCCCGTGTATCAC
20676452 ACACGGC
1 ACACGGC
20676459 TGAGACACAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (30 bp):
ACACGGCCGTGTAACATGCCCGTGTATCAC
Found at i:20687173 original size:14 final size:15
Alignment explanation
Indices: 20687154--20687183 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
20687144 ATATTTAACT
20687154 TGTTCTTAATT-ATG
1 TGTTCTTAATTCATG
20687168 TGTTCTTAATTCATG
1 TGTTCTTAATTCATG
20687183 T
1 T
20687184 TTTGATATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.20, C:0.10, G:0.13, T:0.57
Consensus pattern (15 bp):
TGTTCTTAATTCATG
Found at i:20689698 original size:174 final size:174
Alignment explanation
Indices: 20689407--20689732 Score: 589
Period size: 174 Copynumber: 1.9 Consensus size: 174
20689397 AACTCAAGGT
* *
20689407 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
20689472 GAAAATATATATTGAGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGAGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
20689537 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTTGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTTGCAC
*
20689581 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
* *
20689646 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGTCATGT
66 GAAAATATATATTGAGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
*
20689711 ACTTTAAACTCGCACACTTAGT
131 ACTTTAAACTCACACACTTAGT
20689733 TCTGTACAAT
Statistics
Matches: 145, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
174 145 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGAGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTTGCAC
Found at i:20689726 original size:29 final size:29
Alignment explanation
Indices: 20689687--20689762 Score: 102
Period size: 29 Copynumber: 2.6 Consensus size: 29
20689677 CTTAATAATC
20689687 AACCACGCACACTTAGTGTCATGTAC-TTTA
1 AACC-CGCACACTTAGTGTC-TGTACATTTA
*
20689717 AACTCGCACACTTAGT-TCTGTACAATTTA
1 AACCCGCACACTTAGTGTCTGTAC-ATTTA
20689746 AACCCGCACACTTAGTG
1 AACCCGCACACTTAGTG
20689763 CCAATCTCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
28 2 0.05
29 31 0.76
30 3 0.07
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (29 bp):
AACCCGCACACTTAGTGTCTGTACATTTA
Found at i:20692307 original size:32 final size:30
Alignment explanation
Indices: 20692266--20692327 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 30
20692256 CCAACATTCA
20692266 CCCGGATAGTGTCT-ACTATAATCCCTACAC
1 CCCGGATAGTGTCTCA-TATAATCCCTACAC
20692296 NNCCCGGATAGTGTCTCATATAATCCCTACAC
1 --CCCGGATAGTGTCTCATATAATCCCTACAC
20692328 GGTTGAGCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 28 0.97
33 1 0.03
ACGTcount: A:0.26, C:0.32, G:0.13, T:0.26
Consensus pattern (30 bp):
CCCGGATAGTGTCTCATATAATCCCTACAC
Found at i:20697596 original size:81 final size:81
Alignment explanation
Indices: 20697461--20697622 Score: 324
Period size: 81 Copynumber: 2.0 Consensus size: 81
20697451 TGATTGAAGT
20697461 ATAAGTTATGAATGTGGGAAAGAACAGGTGAATTGTTTATCGAAAAATGATATCGGACTTCGGGC
1 ATAAGTTATGAATGTGGGAAAGAACAGGTGAATTGTTTATCGAAAAATGATATCGGACTTCGGGC
20697526 CTAGCAGGCTATGATG
66 CTAGCAGGCTATGATG
20697542 ATAAGTTATGAATGTGGGAAAGAACAGGTGAATTGTTTATCGAAAAATGATATCGGACTTCGGGC
1 ATAAGTTATGAATGTGGGAAAGAACAGGTGAATTGTTTATCGAAAAATGATATCGGACTTCGGGC
20697607 CTAGCAGGCTATGATG
66 CTAGCAGGCTATGATG
20697623 CCGGTGAAAT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.27
Consensus pattern (81 bp):
ATAAGTTATGAATGTGGGAAAGAACAGGTGAATTGTTTATCGAAAAATGATATCGGACTTCGGGC
CTAGCAGGCTATGATG
Found at i:20697669 original size:45 final size:45
Alignment explanation
Indices: 20697605--20697806 Score: 279
Period size: 45 Copynumber: 4.6 Consensus size: 45
20697595 CGGACTTCGG
*
20697605 GCCTAGCAGGCTATGATGCCGGTGAAATACTATTCGGGCCTTTGA
1 GCCTAGCAGGCTATAATGCCGGTGAAATACTATTCGGGCCTTTGA
* * *
20697650 GCCTAGCAGGCTATGATGCCGGTGAGATATTATTCGGGCCTTTGA
1 GCCTAGCAGGCTATAATGCCGGTGAAATACTATTCGGGCCTTTGA
*
20697695 GCCTAGCAGGCTATAATGCCGGTGAGATACTATTCGGG-CTTTCGA
1 GCCTAGCAGGCTATAATGCCGGTGAAATACTATTCGGGCCTTT-GA
*
20697740 GCCTAGCAGGCTATAATGCCGGTGAAATGA-TA-TCGGGCC-TCGA
1 GCCTAGCAGGCTATAATGCCGGTGAAAT-ACTATTCGGGCCTTTGA
* *
20697783 GCCTAGCAGGCGA-AATGCCAGTGA
1 GCCTAGCAGGCTATAATGCCGGTGA
20697807 TTAGAGAAAA
Statistics
Matches: 146, Mismatches: 8, Indels: 9
0.90 0.05 0.06
Matches are distributed among these distances:
42 10 0.07
43 14 0.10
44 10 0.07
45 111 0.76
46 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.24
Consensus pattern (45 bp):
GCCTAGCAGGCTATAATGCCGGTGAAATACTATTCGGGCCTTTGA
Found at i:20704084 original size:40 final size:40
Alignment explanation
Indices: 20704029--20704166 Score: 156
Period size: 40 Copynumber: 3.5 Consensus size: 40
20704019 TGGATGATAA
* *
20704029 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTCGCGCGAGTGACTA-TAT
* *
20704069 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGCGCGAGTGACTATAT
* * *
20704109 CCGGGCTATGTCCTGAAGGCATTCGAGCGAGT-AGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGCGCGAGTGA-CTATAT
* *
20704149 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
20704167 TACTTGGCTT
Statistics
Matches: 85, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
39 14 0.16
40 71 0.84
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTCGCGCGAGTGACTATAT
Found at i:20716541 original size:40 final size:40
Alignment explanation
Indices: 20716486--20716667 Score: 267
Period size: 40 Copynumber: 4.6 Consensus size: 40
20716476 TATTCGGATG
20716486 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* *
20716526 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
20716566 ATTTCCGGGCTAAGACCCGAAGGCATGTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * * *
20716606 ATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTGCG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
20716646 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
20716668 TACTTGGTTT
Statistics
Matches: 126, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 14 0.11
40 112 0.89
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:20723654 original size:23 final size:24
Alignment explanation
Indices: 20723593--20723671 Score: 83
Period size: 23 Copynumber: 3.4 Consensus size: 24
20723583 AGCTGATGGG
*
20723593 CAGTAAGCTCTAT-TGAGCTGAAA
1 CAGTAAGCTCTATACGAGCTGAAA
* * *
20723616 CGGTAAGCTCT-GACGAGCTGAAT
1 CAGTAAGCTCTATACGAGCTGAAA
*
20723639 CAGTAAGCT-TATACGAGATGAGAA
1 CAGTAAGCTCTATACGAGCTGA-AA
20723663 CAGTAAGCT
1 CAGTAAGCT
20723672 TTTACAAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
22 1 0.02
23 34 0.76
24 10 0.22
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (24 bp):
CAGTAAGCTCTATACGAGCTGAAA
Found at i:20727959 original size:27 final size:27
Alignment explanation
Indices: 20727918--20727971 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
20727908 TGTCATGTGA
* * *
20727918 AATTGAATGGCAAATTATTGTTACATG
1 AATTGAATGACAAATTACTATTACATG
*
20727945 AATTGAATGATAAATTACTATTACATG
1 AATTGAATGACAAATTACTATTACATG
20727972 GGTTGTATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (27 bp):
AATTGAATGACAAATTACTATTACATG
Found at i:20728350 original size:50 final size:49
Alignment explanation
Indices: 20728217--20728400 Score: 201
Period size: 50 Copynumber: 3.7 Consensus size: 49
20728207 ATCTATTGTG
* * *
20728217 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCGATAACTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGACTACTACGTGTA-TCGATAA-TT
* * * **
20728268 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGACTACTACGTGTATC-GATAATT
* *
20728318 AGGTCACGTGTGTAGTACTAAGTGCAGACTACTACATGTACTGGATAATT
1 AGGTCACGTGTGTAGTACTAAGTGCAGACTACTACGTGTA-TCGATAATT
* *
20728368 -GGTCGA-ATGTGTAGTACTAAGTACAGACTACTA
1 AGGTC-ACGTGTGTAGTACTAAGTGCAGACTACTA
20728401 TGCATACCAG
Statistics
Matches: 115, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
49 29 0.25
50 46 0.40
51 40 0.35
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (49 bp):
AGGTCACGTGTGTAGTACTAAGTGCAGACTACTACGTGTATCGATAATT
Found at i:20730152 original size:14 final size:14
Alignment explanation
Indices: 20730133--20730167 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
20730123 TGTTTCACTA
*
20730133 AAAATGGTTTTCAG
1 AAAATGATTTTCAG
*
20730147 AAAATGATTTTTAG
1 AAAATGATTTTCAG
20730161 AAAATGA
1 AAAATGA
20730168 CTTACTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.03, G:0.17, T:0.34
Consensus pattern (14 bp):
AAAATGATTTTCAG
Found at i:20731246 original size:14 final size:14
Alignment explanation
Indices: 20731229--20731255 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20731219 GTAAAACAAT
20731229 GAAAATATTTTACA
1 GAAAATATTTTACA
20731243 GAAAATATTTTAC
1 GAAAATATTTTAC
20731256 TTACAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (14 bp):
GAAAATATTTTACA
Found at i:20733577 original size:22 final size:22
Alignment explanation
Indices: 20733539--20733580 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
20733529 GGGTGGACTG
20733539 TTTTGGGGAGAAGATTAAGGGA
1 TTTTGGGGAGAAGATTAAGGGA
*
20733561 TTTTGGTGAGGAA-ATTAAGG
1 TTTTGGGGA-GAAGATTAAGG
20733581 AGTGAGGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.31, C:0.00, G:0.38, T:0.31
Consensus pattern (22 bp):
TTTTGGGGAGAAGATTAAGGGA
Found at i:20755764 original size:56 final size:56
Alignment explanation
Indices: 20755682--20755800 Score: 168
Period size: 56 Copynumber: 2.1 Consensus size: 56
20755672 TTACTCGTAA
* * * *
20755682 ACACATA-TCGAATCACATATCAATGCCAACGTATTAAACGTGGTCTTACTCACAC
1 ACACATATTGGAATCAAATATCAATGCCAACGTATTAAACATGGTCTAACTCACAC
* * *
20755737 ATACATATTGGAATCAAATATCGATGCCAACGTATTAAACATGGTCTAACTCGCAC
1 ACACATATTGGAATCAAATATCAATGCCAACGTATTAAACATGGTCTAACTCACAC
20755793 ACACATAT
1 ACACATAT
20755801 CATACAATGC
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
55 6 0.11
56 49 0.89
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (56 bp):
ACACATATTGGAATCAAATATCAATGCCAACGTATTAAACATGGTCTAACTCACAC
Found at i:20755946 original size:84 final size:85
Alignment explanation
Indices: 20755815--20756354 Score: 645
Period size: 84 Copynumber: 6.4 Consensus size: 85
20755805 CAATGCCAAC
* * * *
20755815 GTCCCAGACGTGGTCTTACATGTGATTACATATCGATGCC-ACTGTCCCAGGTA-G-GGTCTTAC
1 GTCCCAGACATGGTCTTACACGTAATCACATATCGATGCCAAC-GTCCCA-GTACGTGGTCTTAC
20755877 -TCGAATCAAATATGATGCTGAT
64 AT-GAATCAAATATGATGCTGAT
* * * * *
20755899 GTCTCAGATATGGTCTTACATGTAATCACATATC-ATTTCCAACGTCCCA-AACGTGGTCTTACA
1 GTCCCAGACATGGTCTTACACGTAATCACATATCGA-TGCCAACGTCCCAGTACGTGGTCTTACA
* *
20755962 CGAATCAAATATAATGCTGAT
65 TGAATCAAATATGATGCTGAT
* * *
20755983 GTCCCAGACATGGTCTTACACGTAATCACATATCGATGACAACGTCCTAG-ACGAT-ATCTTACA
1 GTCCCAGACATGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGTACG-TGGTCTTACA
* **
20756046 TGAATCAAAAATGATGCCAAT
65 TGAATCAAATATGATGCTGAT
* ** *
20756067 GTCCCAGACATGGTCTTACACGTAATCACATATCGATGACAACGTCATAG-ACGAT-ATCTTACA
1 GTCCCAGACATGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGTACG-TGGTCTTACA
* **
20756130 TGAATCAAAAATGATGCCAAT
65 TGAATCAAATATGATGCTGAT
*
20756151 GTCCCAGACATGGTCTTACACGTAATCACATATCGATGCCAACGCCCCAG-ACGTGGTCTTACAT
1 GTCCCAGACATGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGTACGTGGTCTTACAT
*
20756215 GAATCAAATACGATGCTGAT
66 GAATCAAATATGATGCTGAT
** * *
20756235 GTCCCAGACATGGTCTTACACGTAATCACATATCGATGCCAAAATCCTAG-ACGTGGTCTTACAC
1 GTCCCAGACATGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGTACGTGGTCTTACAT
* *
20756299 GAATCAAATACGATGTTGAT
66 GAATCAAATATGATGCTGAT
*
20756319 GTCCTAGACATGGTCTTACACGTAATCACATATCGA
1 GTCCCAGACATGGTCTTACACGTAATCACATATCGA
20756355 AAATCCTATG
Statistics
Matches: 409, Mismatches: 38, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
82 1 0.00
83 3 0.01
84 401 0.98
85 4 0.01
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (85 bp):
GTCCCAGACATGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGTACGTGGTCTTACAT
GAATCAAATATGATGCTGAT
Found at i:20756252 original size:252 final size:252
Alignment explanation
Indices: 20755871--20756354 Score: 713
Period size: 252 Copynumber: 1.9 Consensus size: 252
20755861 CCAGGTAGGG
* ** * * *
20755871 TCTTACTCGAATCAAATATGATGCTGATGTCTCAGATATGGTCTTACATGTAATCACATATCATT
1 TCTTACTCGAATCAAAAATGATGCCAATGTCCCAGACATGGTCTTACACGTAATCACATATCATT
* * *
20755936 TCCAACGTCCCAAACGTGGTCTTACACGAATCAAATATAATGCTGATGTCCCAGACATGGTCTTA
66 GCCAACGCCCCAAACGTGGTCTTACACGAATCAAATACAATGCTGATGTCCCAGACATGGTCTTA
** * *
20756001 CACGTAATCACATATCGATGACAACGTCCTAGACGAT-ATCTTACATGAATCAAAAATGATGCCA
131 CACGTAATCACATATCGATGACAAAATCCTAGACG-TGATCTTACACGAATCAAAAACGATGCCA
20756065 ATGTCCCAGACATGGTCTTACACGTAATCACATATCGATGACAACGTCATAGACGATA
195 ATGTCCCAGACATGGTCTTACACGTAATCACATATCGATGACAACGTCATAGACGATA
20756123 TCTTACAT-GAATCAAAAATGATGCCAATGTCCCAGACATGGTCTTACACGTAATCACATATCGA
1 TCTTAC-TCGAATCAAAAATGATGCCAATGTCCCAGACATGGTCTTACACGTAATCACATATC-A
* * *
20756187 -TGCCAACGCCCCAGACGTGGTCTTACATGAATCAAATACGATGCTGATGTCCCAGACATGGTCT
64 TTGCCAACGCCCCAAACGTGGTCTTACACGAATCAAATACAATGCTGATGTCCCAGACATGGTCT
* * * **
20756251 TACACGTAATCACATATCGATGCCAAAATCCTAGACGTGGTCTTACACGAATCAAATACGATGTT
129 TACACGTAATCACATATCGATGACAAAATCCTAGACGTGATCTTACACGAATCAAAAACGATGCC
* *
20756316 GATGTCCTAGACATGGTCTTACACGTAATCACATATCGA
194 AATGTCCCAGACATGGTCTTACACGTAATCACATATCGA
20756355 AAATCCTATG
Statistics
Matches: 206, Mismatches: 23, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
251 1 0.00
252 203 0.99
253 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (252 bp):
TCTTACTCGAATCAAAAATGATGCCAATGTCCCAGACATGGTCTTACACGTAATCACATATCATT
GCCAACGCCCCAAACGTGGTCTTACACGAATCAAATACAATGCTGATGTCCCAGACATGGTCTTA
CACGTAATCACATATCGATGACAAAATCCTAGACGTGATCTTACACGAATCAAAAACGATGCCAA
TGTCCCAGACATGGTCTTACACGTAATCACATATCGATGACAACGTCATAGACGATA
Found at i:20759017 original size:28 final size:26
Alignment explanation
Indices: 20758985--20759050 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 26
20758975 TTGGAGGAAG
20758985 TACTGTATTAGTGGCTTTGCCACGTAAT
1 TACTGTATTAGTGGCTTTGCCACGT--T
* *
20759013 TACTGCT-CTGGTGGCTTTGCCACGTT
1 TACTG-TATTAGTGGCTTTGCCACGTT
20759039 TACTGTCATTAG
1 TACTGT-ATTAG
20759051 CAGCCTTGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
25 1 0.03
26 6 0.19
27 2 0.06
28 21 0.68
29 1 0.03
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.39
Consensus pattern (26 bp):
TACTGTATTAGTGGCTTTGCCACGTT
Found at i:20775023 original size:44 final size:43
Alignment explanation
Indices: 20774929--20775038 Score: 123
Period size: 44 Copynumber: 2.5 Consensus size: 43
20774919 ACAATGCCGA
** * *
20774929 TGTCCCAGACGTGGTCTTACATGTAATTCAATATCGATGCCTC
1 TGTCCCAGACACGGTCTTACACGTAATTCAATATCGAGGCCTC
* * *
20774972 TGTCCCAGATAGGGTCTTACACGTAAATCTCAA-ATCGAGGCCTG
1 TGTCCCAGACACGGTCTTACACGT-AAT-TCAATATCGAGGCCTC
*
20775016 TGTCCCAGACACAGTCTTACACG
1 TGTCCCAGACACGGTCTTACACG
20775039 ATATTTCAGA
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
43 20 0.36
44 32 0.57
45 4 0.07
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (43 bp):
TGTCCCAGACACGGTCTTACACGTAATTCAATATCGAGGCCTC
Found at i:20779033 original size:12 final size:12
Alignment explanation
Indices: 20779016--20779041 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20779006 ACCGAGTACT
20779016 AATTCAATGCCA
1 AATTCAATGCCA
20779028 AATTCAATGCCA
1 AATTCAATGCCA
20779040 AA
1 AA
20779042 CTCAGCTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (12 bp):
AATTCAATGCCA
Found at i:20785490 original size:42 final size:43
Alignment explanation
Indices: 20785411--20785520 Score: 127
Period size: 42 Copynumber: 2.6 Consensus size: 43
20785401 CAATGTCGAC
* * * **
20785411 GTCCCAAACGTGGTCTTACATGTAATTCAGTATCGATGCCTCT
1 GTCCCAGACATGGTCTTACACGTAATTCAGTATCGATGCCGAT
*
20785454 GTCTCAGACA-GTGTCTTACACG-AATTCAG-ATACGATGCCGAT
1 GTCCCAGACATG-GTCTTACACGTAATTCAGTAT-CGATGCCGAT
20785496 GTCCCAGACATGGTCTTACACGTAA
1 GTCCCAGACATGGTCTTACACGTAA
20785521 ATCTCAAATC
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
41 2 0.04
42 35 0.62
43 19 0.34
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.28
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACACGTAATTCAGTATCGATGCCGAT
Found at i:20787164 original size:48 final size:48
Alignment explanation
Indices: 20787042--20787318 Score: 168
Period size: 48 Copynumber: 5.7 Consensus size: 48
20787032 ATGAGATCTT
* * * * *
20787042 ATGTAAGACCATGTCTGGGACATGGCATCGGCATCCGAGATGAGAGCCA
1 ATGTAAGACCATGTCTGAGATATGGCATCGGCAT-CAATATGAGTGCCA
* * * * * * * *
20787091 GTGTAAAACCATGTCTGGGAAATGGCATTGGCGTTAATATGTGTGCCA
1 ATGTAAGACCATGTCTGAGATATGGCATCGGCATCAATATGAGTGCCA
* ** **
20787139 ATGTAAGACCATGTCTGAGATATGGCATCGGCGTTGATATGTTTGCCA
1 ATGTAAGACCATGTCTGAGATATGGCATCGGCATCAATATGAGTGCCA
* * * * * *
20787187 GTGTAAGACTATAT-TTAGGATATGGCATCGGCATCAGTATGAGAT-CCC
1 ATGTAAGACCATGTCTGA-GATATGGCATCGGCATCAATATGAG-TGCCA
* * **
20787235 ATGTAAGACCATATCT-AGGATATGGCATTGGCATCGCTATGAG-GTCC-
1 ATGTAAGACCATGTCTGA-GATATGGCATCGGCATCAATATGAGTG-CCA
* * * *
20787282 ATTTACAAGACCATGTCTGGGACATGGCATCGACATC
1 ATGT--AAGACCATGTCTGAGATATGGCATCGGCATC
20787319 GACATGAGAC
Statistics
Matches: 181, Mismatches: 39, Indels: 16
0.77 0.17 0.07
Matches are distributed among these distances:
47 5 0.03
48 120 0.66
49 56 0.31
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (48 bp):
ATGTAAGACCATGTCTGAGATATGGCATCGGCATCAATATGAGTGCCA
Done.