Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 123 of 311
Found at i:40966729 original size:40 final size:40
Alignment explanation
Indices: 40966631--40966778 Score: 179
Period size: 40 Copynumber: 3.6 Consensus size: 40
40966621 TGGGCTATTA
* * * * *
40966631 CACACTATGTGCCAATACATAGTCGAAGCTATTTTAATCTCG
1 CACACTAAGTGCC-ATACATAGCCGAAGCTATCTCAA-ATCG
*
40966673 CACACTACGTGCCATACATAGCCGAAGCTATCTCAAATCG
1 CACACTAAGTGCCATACATAGCCGAAGCTATCTCAAATCG
* * *
40966713 CACACTAAGTGTCATACATAGCCGAAGTTATCTCGAATCG
1 CACACTAAGTGCCATACATAGCCGAAGCTATCTCAAATCG
* *
40966753 CACACTAAGTGCCGTACATAACCGAA
1 CACACTAAGTGCCATACATAGCCGAA
40966779 TTGTCGTGAA
Statistics
Matches: 94, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
40 62 0.66
41 20 0.21
42 12 0.13
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.24
Consensus pattern (40 bp):
CACACTAAGTGCCATACATAGCCGAAGCTATCTCAAATCG
Found at i:40981790 original size:39 final size:38
Alignment explanation
Indices: 40981707--40981803 Score: 106
Period size: 39 Copynumber: 2.5 Consensus size: 38
40981697 TGAAACCAAT
*
40981707 TACCAGCACAAGCCTGCGGGAATTTAAACCCGGTATAA
1 TACCAGCACAAGCCTGCGGGAATTTAAACCCGGCATAA
* * * *
40981745 TACCAGCTCGAAGCCTGCGGGACTTT-AGCCCGGACATAT
1 TACCAGCAC-AAGCCTGCGGGAATTTAAACCCGG-CATAA
*
40981784 TTCCAGCACATAGCCTGCGG
1 TACCAGCACA-AGCCTGCGG
40981804 ACCTTAATTC
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
38 15 0.31
39 34 0.69
ACGTcount: A:0.27, C:0.30, G:0.24, T:0.20
Consensus pattern (38 bp):
TACCAGCACAAGCCTGCGGGAATTTAAACCCGGCATAA
Found at i:40981892 original size:39 final size:39
Alignment explanation
Indices: 40981784--40981899 Score: 169
Period size: 39 Copynumber: 3.0 Consensus size: 39
40981774 CCGGACATAT
* * *
40981784 TTCCAGCACATAGCCTGCGGACCTTAATTCCAGATATAA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCTAGATATAA
* *
40981823 TTCCAGCACATAGCCTGCAGACCCTAAGTCTGGATATAA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCTAGATATAA
* *
40981862 TTCCAGCACATAGCCAGCGGACCCTAAGTCTTGATATA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCTAGATATA
40981900 CATCACTGAA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 69 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (39 bp):
TTCCAGCACATAGCCTGCGGACCCTAAGTCTAGATATAA
Found at i:40983847 original size:21 final size:20
Alignment explanation
Indices: 40983808--40983847 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40983798 TTTGTTCTTC
*
40983808 TTTTCTTATTTCAATTAATA
1 TTTTCTTATTTCAAATAATA
*
40983828 TTTTTTTATTTCAAAATAAT
1 TTTTCTTATTTC-AAATAAT
40983848 GCAAATTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTCTTATTTCAAATAATA
Found at i:40987032 original size:14 final size:15
Alignment explanation
Indices: 40987004--40987032 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40986994 TAGTTAACTA
40987004 TACTTTAGTTACTTT
1 TACTTTAGTTACTTT
40987019 TACTTTAG-TACTTT
1 TACTTTAGTTACTTT
40987033 AGTAAAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.59
Consensus pattern (15 bp):
TACTTTAGTTACTTT
Found at i:40989982 original size:55 final size:54
Alignment explanation
Indices: 40989870--40990060 Score: 226
Period size: 55 Copynumber: 3.5 Consensus size: 54
40989860 AACTTACCAT
* * * * * * *
40989870 TGCCATGTCTTGACATGGTTTTACGTGGT-ATCCTTACCTTAT-GAACTCACCAA
1 TGCCATGCCTTGGCATGGTCTTACATGATGA-CCTTGCCTTATAGAACTCATCAA
40989923 TGCCATGCCTTGGCATGGTCTTACATGA-GACCTTTGCCTTATAGTAACTCATCAA
1 TGCCATGCCTTGGCATGGTCTTACATGATGACC-TTGCCTTATAG-AACTCATCAA
* * ** *
40989978 TGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAA
1 TGCCATGCCTTGGCATGGTCTTACATGATGACCTTGCCTTATAGAACTCATCAA
40990032 TGCCATGCCTTGGCATGGTCTTACATGAT
1 TGCCATGCCTTGGCATGGTCTTACATGAT
40990061 ATCCTTATCT
Statistics
Matches: 119, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
52 2 0.02
53 32 0.27
54 37 0.31
55 46 0.39
56 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.36
Consensus pattern (54 bp):
TGCCATGCCTTGGCATGGTCTTACATGATGACCTTGCCTTATAGAACTCATCAA
Found at i:40990099 original size:47 final size:47
Alignment explanation
Indices: 40990045--40990166 Score: 199
Period size: 47 Copynumber: 2.6 Consensus size: 47
40990035 CATGCCTTGG
*
40990045 CATGGTCTTACATGATATCCTTATCTTACCAAATGCCATATTCCAAA
1 CATGGTCTTACATGATATCCTTGTCTTACCAAATGCCATATTCCAAA
* * * *
40990092 CATGGTCTTACATGGTATCATTGTCTTACGAAATGCCATGTTCCAAA
1 CATGGTCTTACATGATATCCTTGTCTTACCAAATGCCATATTCCAAA
40990139 CATGGTCTTACATGATATCCTTGTCTTA
1 CATGGTCTTACATGATATCCTTGTCTTA
40990167 GTGCCAATGC
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 68 1.00
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (47 bp):
CATGGTCTTACATGATATCCTTGTCTTACCAAATGCCATATTCCAAA
Found at i:40992022 original size:64 final size:64
Alignment explanation
Indices: 40991942--40992124 Score: 181
Period size: 67 Copynumber: 2.8 Consensus size: 64
40991932 AGACATTATG
* * * * *
40991942 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTATGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGATACGAGATAA
* * * * *
40992006 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGATACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGATACGAGAT
40992071 AA
63 AA
* * * * *
40992073 AT-TGGCAAGGTCACATGGGTGGTACTGA-GTGTTCACCATGTGGACAAGAGAG
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAGACAAGAGAG
40992125 TTGAACTATA
Statistics
Matches: 95, Mismatches: 20, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
63 19 0.20
64 25 0.26
66 20 0.21
67 31 0.33
ACGTcount: A:0.30, C:0.15, G:0.32, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGATACGAGATAA
Found at i:40997430 original size:40 final size:40
Alignment explanation
Indices: 40997403--40997505 Score: 127
Period size: 40 Copynumber: 2.6 Consensus size: 40
40997393 TACTCGCTTG
40997403 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACA
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACA
* * * * *
40997443 AATGCCTTCGGGACTTAGCCC-GAAACTAGTCACTAGCGCA
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACA
* *
40997483 AATGCCTTTGGGACTTAGCCCGG
1 AATGCCTTCGGGACATAGCCCGG
40997506 TTATCATCCA
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.05
40 51 0.93
41 1 0.02
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.21
Consensus pattern (40 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACA
Found at i:40998768 original size:11 final size:10
Alignment explanation
Indices: 40998738--40998772 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
40998728 ACATGAGAGC
40998738 CTTTCTTTTT
1 CTTTCTTTTT
*
40998748 TTTTCTTTTT
1 CTTTCTTTTT
40998758 CTTTCTCTTTT
1 CTTTCT-TTTT
40998769 CTTT
1 CTTT
40998773 TTTCATCATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 14 0.64
11 8 0.36
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (10 bp):
CTTTCTTTTT
Found at i:41005391 original size:40 final size:40
Alignment explanation
Indices: 41005364--41005506 Score: 216
Period size: 40 Copynumber: 3.6 Consensus size: 40
41005354 TACTCACTTG
*
41005364 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
*
41005404 AATGCCTTCGGGACTTAGCCCAGATATAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
* * * *
41005444 AATGCCTTCGGGACTTAGCCC-GAAACTAGTCACTAGCGCA
1 AATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACA
41005484 AATGCCTTCGGGACTTAGCCCGG
1 AATGCCTTCGGGACTTAGCCCGG
41005507 TTATCTTACA
Statistics
Matches: 95, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
39 3 0.03
40 91 0.96
41 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.21
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
Found at i:41006757 original size:12 final size:12
Alignment explanation
Indices: 41006736--41006774 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
41006726 CATGAGAGCC
41006736 TTTC-TTTTTTT
1 TTTCTTTTTTTT
41006747 TTTCTTTTTTTT
1 TTTCTTTTTTTT
* *
41006759 TCTCTTTTCTTT
1 TTTCTTTTTTTT
41006771 TTTC
1 TTTC
41006775 ATCATCATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 4 0.17
12 20 0.83
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTCTTTTTTTT
Found at i:41010354 original size:73 final size:73
Alignment explanation
Indices: 41010225--41010361 Score: 204
Period size: 73 Copynumber: 1.9 Consensus size: 73
41010215 TGTGGAATGT
* * * *
41010225 TATCGACTGGCTCGCTAGAGTGGCACCGTGACAATGGTCTATTGACCTTATGGAGTGACACCACA
1 TATCGACTAGCTCACTAGAGTGACACCGTGACAATGGTCTATTGACCTTATAGAGTGACACCACA
41010290 ATGACAAC
66 ATGACAAC
* *
41010298 TATCGACTAGCTCACTAGAGTGACACTGTGACGATGGTCTATTGA-CTCTATAGAGTGACACCAC
1 TATCGACTAGCTCACTAGAGTGACACCGTGACAATGGTCTATTGACCT-TATAGAGTGACACCAC
41010362 GATGGTGGTT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
72 2 0.04
73 55 0.96
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (73 bp):
TATCGACTAGCTCACTAGAGTGACACCGTGACAATGGTCTATTGACCTTATAGAGTGACACCACA
ATGACAAC
Found at i:41017862 original size:42 final size:42
Alignment explanation
Indices: 41017754--41017902 Score: 192
Period size: 42 Copynumber: 3.5 Consensus size: 42
41017744 TTCCGATATG
* * *
41017754 TGATTTTGTGTAAGACCACGTTTGGGACATTGGCATCG-ATT
1 TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGTATT
*
41017795 TGATATTTACGTGTAAGACCATGTCTGGGACATTGGCATTGTATT
1 TG--ATTT-CGTGTAAGACCATGTCTGGGACATTGGCATCGTATT
*
41017840 TGATTTCGTGTAAGACCCTGTCTGGGACATTGGCATCGATATT
1 TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCG-TATT
* *
41017883 TGATTACATGTAAGACCATG
1 TGATTTCGTGTAAGACCATG
41017903 AATGGGATGT
Statistics
Matches: 94, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
41 2 0.02
42 30 0.32
43 29 0.31
44 28 0.30
45 5 0.05
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (42 bp):
TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGTATT
Found at i:41029594 original size:39 final size:39
Alignment explanation
Indices: 41029539--41029682 Score: 225
Period size: 39 Copynumber: 3.7 Consensus size: 39
41029529 CCAACATAAT
* *
41029539 TGCCTTTGGGACTTAGCCCAGATATAACACCAGCACGAA
1 TGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAA
* *
41029578 TGCCTTCGGGATTTAGCTCGGATATAACACCAGCACGAA
1 TGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAA
* *
41029617 TGCCTCCGGGACTTAGCCTGGATATAACACCAGCACGAA
1 TGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAA
*
41029656 TGCCTTCGGGACTTAGACCGGATATAA
1 TGCCTTCGGGACTTAGCCCGGATATAA
41029683 ATCTCACACA
Statistics
Matches: 94, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 94 1.00
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.22
Consensus pattern (39 bp):
TGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAA
Found at i:41031938 original size:17 final size:18
Alignment explanation
Indices: 41031909--41031948 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
41031899 TTTTAGCTCG
41031909 ATTTTTGATAATTTCTAT
1 ATTTTTGATAATTTCTAT
41031927 ATTTTTGA-AATTTCTAT
1 ATTTTTGATAATTTCTAT
*
41031944 GTTTT
1 ATTTT
41031949 GAGATGTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.62
Consensus pattern (18 bp):
ATTTTTGATAATTTCTAT
Found at i:41032680 original size:42 final size:42
Alignment explanation
Indices: 41032571--41032734 Score: 165
Period size: 43 Copynumber: 3.8 Consensus size: 42
41032561 TCCGATATGC
* *
41032571 GATTTCGTGTAAGTCCAC-ATCTGGGACGTTGGCATCG-ATTT
1 GATTTCGTGTAAGACC-CTGTCTGGGACGTTGGCATCGTATTT
* *
41032612 GATAGTTACGTGTAAGACCATGTCTGGGACATTGGCATCGTATTT
1 GAT--TT-CGTGTAAGACCCTGTCTGGGACGTTGGCATCGTATTT
* *
41032657 GATTTTGTGTAAGACCCTGTCTGGGA-TTGTGGCATCGATATTT
1 GATTTCGTGTAAGACCCTGTCTGGGACGT-TGGCATCG-TATTT
* *
41032700 GATTACATGTAAGACCAC-GTCTGGGACGTTGGCAT
1 GATTTCGTGTAAGACC-CTGTCTGGGACGTTGGCAT
41032735 TGTACGAGCT
Statistics
Matches: 103, Mismatches: 11, Indels: 16
0.79 0.08 0.12
Matches are distributed among these distances:
41 4 0.04
42 27 0.26
43 36 0.35
44 29 0.28
45 7 0.07
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (42 bp):
GATTTCGTGTAAGACCCTGTCTGGGACGTTGGCATCGTATTT
Found at i:41040838 original size:40 final size:40
Alignment explanation
Indices: 41040781--41041038 Score: 319
Period size: 40 Copynumber: 6.5 Consensus size: 40
41040771 CGGATGATAA
* * * * *
41040781 CCGGGCTAAGCCCCGAAGGTATTTGTTCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATA-T
* * *
41040821 CTGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAT
41040861 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAT
* *
41040901 CTGGGCTAAGTCCCGAAGGCATTTGTCCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAT
* *
41040941 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAT
*
41040981 CCGGGCTAAG-CCCTGAAGGCATTTG-AGTGAG-TAGCTATAT
1 CCGGGCTAAGTCCC-GAAGGCATTTGTA-CGAGTTA-CTATAT
*
41041021 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
41041039 TACTTGGTTT
Statistics
Matches: 196, Mismatches: 17, Indels: 11
0.88 0.08 0.05
Matches are distributed among these distances:
39 16 0.08
40 179 0.91
41 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAT
Found at i:41047548 original size:40 final size:40
Alignment explanation
Indices: 41047493--41047713 Score: 304
Period size: 40 Copynumber: 5.5 Consensus size: 40
41047483 TATTCGAATG
*
41047493 ATATCCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCT
* *
41047533 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAG-TGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTG-CT
* *
41047573 ATATCCGGGCTAAGTCCCGAAGGTATTTGTGCTA-TTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTG-CT
*
41047613 ATATCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCT
* * *
41047653 ATATCCGGGCCAAGACCCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCT
* *
41047693 ATATCC-GGCTAAATCTCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
41047714 ATGCTTGGGT
Statistics
Matches: 162, Mismatches: 16, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
39 13 0.08
40 146 0.90
41 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.29
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCT
Found at i:41078023 original size:119 final size:120
Alignment explanation
Indices: 41077817--41078039 Score: 283
Period size: 119 Copynumber: 1.9 Consensus size: 120
41077807 TCCTCGTTCA
*
41077817 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAGAT
* *
41077882 TTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTAGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * * ** *
41077937 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTT-TGGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCAG
* * *
41077999 ATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
64 ATATAGTAAC-TAGCACAAATGCCTTCGGGACTTAACCCGGA
41078040 CATCATTCAA
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
118 4 0.05
119 64 0.73
120 20 0.23
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAGAT
ATAGTAACTAGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:41078039 original size:40 final size:40
Alignment explanation
Indices: 41077815--41078039 Score: 269
Period size: 40 Copynumber: 5.7 Consensus size: 40
41077805 GCTCCTCGTT
* *
41077815 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
41077855 CAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
41077895 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
41077935 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * * *
41077974 CAAATGCCTT-TGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
41078015 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41078040 CATCATTCAA
Statistics
Matches: 160, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
38 2 0.01
39 30 0.19
40 116 0.73
41 12 0.08
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:41085423 original size:27 final size:26
Alignment explanation
Indices: 41085367--41085423 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
41085357 CAACCTTAAC
* * *
41085367 CCTAGGGGTATATCAGTAATTTTACT
1 CCTAGGGGTAAATCAGTAATTGTACA
* *
41085393 CCTAGGGGTAAATCTGTAAATTGTCCA
1 CCTAGGGGTAAATCAGT-AATTGTACA
41085420 CCTA
1 CCTA
41085424 TGAAGGTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (26 bp):
CCTAGGGGTAAATCAGTAATTGTACA
Found at i:41101947 original size:48 final size:48
Alignment explanation
Indices: 41101798--41101951 Score: 150
Period size: 48 Copynumber: 3.2 Consensus size: 48
41101788 GTGAGTTGCT
* *
41101798 GATGCCATGTTCCAAACATGGTCTTACA-TTGGCTC-ACATGTCGAGCCC
1 GATGCCATGTTCCAAACATGGTCTTACACTT-GCTCTA-ATATCGTGCCC
* * * *** * * *
41101846 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCGCAACATCCCC
1 GATGCCATGTTCCAAACATGGTCTTACACTTGCTCTAATATCGTGCCC
* * *
41101894 AATGCCATGTTCCAAATATGGTCTTACACTTGCTCTAATATCGTGGCC
1 GATGCCATGTTCCAAACATGGTCTTACACTTGCTCTAATATCGTGCCC
41101942 GATGCCATGT
1 GATGCCATGT
41101952 CCTAGATGTG
Statistics
Matches: 80, Mismatches: 24, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
48 79 0.99
49 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (48 bp):
GATGCCATGTTCCAAACATGGTCTTACACTTGCTCTAATATCGTGCCC
Found at i:41106879 original size:30 final size:30
Alignment explanation
Indices: 41106834--41106893 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
41106824 ATTTAATACG
41106834 AACTTTGGCAAAATTACA-TTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTT-CCCCTA
* *
41106864 AACTTTTGCATAATTACACTTTTTCCCCTA
1 AACTTTGGCAAAATTACACTTTTTCCCCTA
41106894 GGCTCGAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.28, C:0.25, G:0.07, T:0.40
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTTCCCCTA
Found at i:41111141 original size:13 final size:13
Alignment explanation
Indices: 41111123--41111148 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41111113 TTGAATCCCT
41111123 ACCAAAACAATCA
1 ACCAAAACAATCA
41111136 ACCAAAACAATCA
1 ACCAAAACAATCA
41111149 TGAAGCATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.31, G:0.00, T:0.08
Consensus pattern (13 bp):
ACCAAAACAATCA
Found at i:41114678 original size:48 final size:48
Alignment explanation
Indices: 41114622--41114951 Score: 210
Period size: 48 Copynumber: 6.9 Consensus size: 48
41114612 GGTGAGTTGC
*
41114622 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATGTCGAGAT
1 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCGAGAT
* * * * ** * * * *
41114670 TGATGCCATGTCCCAGACATAGTCTTACACTAACTCTCGTCTCAATG-T
1 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCGA-GAT
* * * *
41114718 CGATGCCATG-TCCTAGACATGGTCTTACACTGGCTCCCATAAT-GTGGT
1 CGATGCCATGTTCC-AAACATGGTCTTACACTGGCTCACAT-ATCGAGAT
* * * * * *
41114766 CGATGCCATGTCCCAAACATGGTCCTACACTAG-TGGACATATCAATAT
1 CGATGCCATGTTCCAAACATGGTCTTACACTGGCT-CACATATCGAGAT
* *
41114814 CGATGCCATG-TCTCAAACATGGTCTTACACTGGCTCTCACAACATC--G-C
1 CGATGCCATGTTC-CAAACATGGTCTTACACTGG--CTCAC-ATATCGAGAT
** * * * *
41114862 CGATTTCATGTTCCAAACATGGTCTTACATTGGCTCTCATATCGTG-G
1 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCGAGAT
* * * ** *
41114909 CAATGCCATGTCCCAGATGTGGTCTTACACTGGCACACATATC
1 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATC
41114952 ACCCAAATGT
Statistics
Matches: 214, Mismatches: 53, Indels: 31
0.72 0.18 0.10
Matches are distributed among these distances:
45 4 0.02
46 4 0.02
47 41 0.19
48 152 0.71
49 6 0.03
50 2 0.01
51 5 0.02
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.28
Consensus pattern (48 bp):
CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCGAGAT
Found at i:41114795 original size:96 final size:96
Alignment explanation
Indices: 41114622--41114849 Score: 257
Period size: 96 Copynumber: 2.4 Consensus size: 96
41114612 GGTGAGTTGC
* * *
41114622 CGATGCCATGTTCC-AAACATGGTCTTACACTGGCTCACATGTCGAGATTGATGCCATGTCCCAG
1 CGATGCCATG-TCCTAAACATGGTCTTACACTGGCTCACATATCGAGATCGATGCCATGTCCCAA
* * * * *
41114686 ACATAGTCTTACACTAACT-CTCGTCTCAATGT
65 ACATAGTCCTACACT-ACTGCACATATCAATAT
* * * *
41114718 CGATGCCATGTCCTAGACATGGTCTTACACTGGCTCCCATAAT-GTGGTCGATGCCATGTCCCAA
1 CGATGCCATGTCCTAAACATGGTCTTACACTGGCTCACAT-ATCGAGATCGATGCCATGTCCCAA
* * *
41114782 ACATGGTCCTACACTAGTGGACATATCAATAT
65 ACATAGTCCTACACTACTGCACATATCAATAT
41114814 CGATGCCATGT-CTCAAACATGGTCTTACACTGGCTC
1 CGATGCCATGTCCT-AAACATGGTCTTACACTGGCTC
41114850 TCACAACATC
Statistics
Matches: 112, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
95 7 0.06
96 104 0.93
97 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (96 bp):
CGATGCCATGTCCTAAACATGGTCTTACACTGGCTCACATATCGAGATCGATGCCATGTCCCAAA
CATAGTCCTACACTACTGCACATATCAATAT
Found at i:41114872 original size:96 final size:96
Alignment explanation
Indices: 41114711--41114890 Score: 236
Period size: 96 Copynumber: 1.9 Consensus size: 96
41114701 AACTCTCGTC
* * * ** * *
41114711 TCAATGTCGATGCCATGTCCTAGACATGGTCTTACACTGGCTCCCATAATGTGGTCGATGCCATG
1 TCAATATCGATGCCATGTCCTAAACATGGTCTTACACTGGCTCCCACAACATCGCCGATGCCATG
41114776 TCCCAAACATGGTCCTACACTAGTGGACATA
66 TCCCAAACATGGTCCTACACTAGTGGACATA
* **
41114807 TCAATATCGATGCCATGT-CTCAAACATGGTCTTACACTGGCTCTCACAACATCGCCGATTTCAT
1 TCAATATCGATGCCATGTCCT-AAACATGGTCTTACACTGGCTCCCACAACATCGCCGATGCCAT
* *
41114871 GTTCCAAACATGGTCTTACA
65 GTCCCAAACATGGTCCTACA
41114891 TTGGCTCTCA
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
95 2 0.03
96 69 0.97
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (96 bp):
TCAATATCGATGCCATGTCCTAAACATGGTCTTACACTGGCTCCCACAACATCGCCGATGCCATG
TCCCAAACATGGTCCTACACTAGTGGACATA
Found at i:41134250 original size:119 final size:120
Alignment explanation
Indices: 41134072--41134296 Score: 296
Period size: 119 Copynumber: 1.9 Consensus size: 120
41134062 GCTACTCATT
*
41134072 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCAAAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCAAAAATGCCTTCGGGACTTAGCCCGG
* *
41134137 TTATAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
41134192 CAAATGCCTTCGGG-CTTAGCCCGGA-ATAAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACATAGCCCGGATAT-AGTAACTCGCAAAAATGCCTTCGGGA-CTTAGCCC
* * * *
41134254 GGATATGGTCACTTATCACAAAGCCTTCGGGACTTAGCCCGGA
64 GGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
41134297 CATCATTCAA
Statistics
Matches: 91, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
118 5 0.05
119 65 0.71
120 21 0.23
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCAAAAATGCCTTCGGGACTTAGCCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:41134296 original size:40 final size:40
Alignment explanation
Indices: 41134072--41134296 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
41134062 GCTACTCATT
* *
41134072 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
41134112 AAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
41134152 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
41134192 CAAATGCCTTCGGG-CTTAGCCCGGA-ATAAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATAT-AGTAACTCGCA
* * * **
41134231 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTATCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
41134272 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41134297 CATCATTCAA
Statistics
Matches: 163, Mismatches: 16, Indels: 12
0.85 0.08 0.06
Matches are distributed among these distances:
38 3 0.02
39 31 0.19
40 117 0.72
41 12 0.07
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:41135837 original size:13 final size:13
Alignment explanation
Indices: 41135819--41135844 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41135809 GACCTATCAC
41135819 ATTTCAAAATTAT
1 ATTTCAAAATTAT
41135832 ATTTCAAAATTAT
1 ATTTCAAAATTAT
41135845 CTCACATAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTTCAAAATTAT
Found at i:41142314 original size:40 final size:39
Alignment explanation
Indices: 41142194--41142369 Score: 234
Period size: 39 Copynumber: 4.5 Consensus size: 39
41142184 GCTACTCGTT
*
41142194 CAAATGCCTTCGGACATAGCCC-ATTATAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGATTATAGTAACTCGCA
41142232 CAAATGCCTTCGGGACTTAGCCCG-TTATAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGATTATAGTAACTCGCA
*
41142271 CAAATGCCTTCGGTACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGG-ACTTAGCCC-GATTATAGTAACTCGCA
* * *
41142311 CAAATGCCTTCGGGCTTAGCCCGGAATA-AGTATCTCGCA
1 CAAATGCCTTCGGACTTAGCCC-GATTATAGTAACTCGCA
41142350 CAAATGCCTTCGGATCTTAG
1 CAAATGCCTTCGGA-CTTAG
41142370 TCCGGATATG
Statistics
Matches: 124, Mismatches: 7, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
38 13 0.10
39 78 0.63
40 31 0.25
41 2 0.02
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGACTTAGCCCGATTATAGTAACTCGCA
Found at i:41142375 original size:79 final size:79
Alignment explanation
Indices: 41142194--41142415 Score: 251
Period size: 79 Copynumber: 2.8 Consensus size: 79
41142184 GCTACTCGTT
* * *
41142194 CAAATGCCTTCGGA-CATAGCC-CATTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGT
1 CAAATGCCTTCGGATCTTAGCCGGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
41142257 TATAGTAACTCGCA
66 AATAGTAACTCGCA
*
41142271 CAAATGCCTTCGG-TACTTAACCCGGATT-TAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCC
1 CAAATGCCTTCGGAT-CTT-AGCCGGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
*
41142333 GGAATAAGTATCTCGCA
64 GGAAT-AGTAACTCGCA
* * ** *
41142350 CAAATGCCTTCGGATCTTAGTCCGGA-TATGGTCACTTATCACAAA-GCTTTCGGGACTTAGCCC
1 CAAATGCCTTCGGATCTTAG-CCGGATTATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCC
41142413 GGA
64 GGA
41142416 CATCATTCAA
Statistics
Matches: 123, Mismatches: 12, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
77 13 0.11
78 15 0.12
79 73 0.59
80 22 0.18
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGATCTTAGCCGGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
AATAGTAACTCGCA
Found at i:41150422 original size:39 final size:40
Alignment explanation
Indices: 41150298--41150479 Score: 183
Period size: 40 Copynumber: 4.6 Consensus size: 40
41150288 GCTACTCGTT
*
41150298 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* * *
41150338 CAAATTCCTTCGGGACTTAACCCGGATTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * *
41150378 CAAATGCCTT-GGGGCTTAGCCCGGAATTAGTATCTCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
41150417 TAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
41150458 CAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCC
41150480 AGACATCATT
Statistics
Matches: 114, Mismatches: 23, Indels: 10
0.78 0.16 0.07
Matches are distributed among these distances:
39 34 0.30
40 69 0.61
41 11 0.10
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:41150442 original size:79 final size:81
Alignment explanation
Indices: 41150265--41150479 Score: 203
Period size: 79 Copynumber: 2.7 Consensus size: 81
41150255 AAATCACGTA
* ** * *
41150265 CCTTCGGGATTTAA-CCGGATATAGCT-ACTC-GTTCAAATGCCTTCGGGACATAGCCCGGTTAT
1 CCTTCGGGACTTAACCCGGATATAG-TAACTCAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
*
41150327 AGTAACTCGCACAAATT
65 AGTAACTCGCACAAATG
* *
41150344 CCTTCGGGACTTAACCCGGATTTAGTAACTCA-CACAAATGCCTT-GGGGCTTAGCCCGGA-ATT
1 CCTTCGGGACTTAACCCGGATATAGTAACTCAGCACAAATGCCTTCGGGACTTAGCCCGGATA-T
* * *
41150406 AGTATCTCGGATAAATG
65 AGTAACTCGCACAAATG
** * * *
41150423 CCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CCTTCGGGA-CTTAACCCGGATATAGTAACTCAGCACAAATGCCTTCGGGACTTAGCCC
41150480 AGACATCATT
Statistics
Matches: 111, Mismatches: 18, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
78 4 0.04
79 67 0.60
80 40 0.36
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (81 bp):
CCTTCGGGACTTAACCCGGATATAGTAACTCAGCACAAATGCCTTCGGGACTTAGCCCGGATATA
GTAACTCGCACAAATG
Found at i:41162129 original size:22 final size:21
Alignment explanation
Indices: 41162102--41162156 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 21
41162092 TAATTAACTT
41162102 ATTTCTTGATTTTTAAATTTTA
1 ATTTCTTGATTTTTAAA-TTTA
* *
41162124 ATTTCTTAATTTTGAAATTTA
1 ATTTCTTGATTTTTAAATTTA
41162145 A-TT-TTGATTTTT
1 ATTTCTTGATTTTT
41162157 TAAAAATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 7 0.24
20 2 0.07
21 5 0.17
22 15 0.52
ACGTcount: A:0.27, C:0.04, G:0.05, T:0.64
Consensus pattern (21 bp):
ATTTCTTGATTTTTAAATTTA
Found at i:41162212 original size:19 final size:19
Alignment explanation
Indices: 41162110--41162227 Score: 80
Period size: 19 Copynumber: 5.9 Consensus size: 19
41162100 TTATTTCTTG
*
41162110 ATTTTTAAATTTTAATTTCTT
1 ATTTTTAAA-ATTAATTT-TT
* * *
41162131 AATTTTGAAATTTAATTTTG
1 -ATTTTTAAAATTAATTTTT
*
41162151 ATTTTTTAAAAATAA-TTTT
1 A-TTTTTAAAATTAATTTTT
*
41162170 A-TTTTAAACTATAATTAATTT
1 ATTTTTAAAAT-TAATT--TTT
*
41162191 ATTTCTT-TAATTAATTTTT
1 ATTT-TTAAAATTAATTTTT
41162210 ATTTTTAAAATTAATTTT
1 ATTTTTAAAATTAATTTT
41162228 AGTTTAATTC
Statistics
Matches: 77, Mismatches: 11, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
17 7 0.09
18 5 0.06
19 23 0.30
20 11 0.14
21 17 0.22
22 12 0.16
23 2 0.03
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTTTAAAATTAATTTTT
Found at i:41162261 original size:18 final size:18
Alignment explanation
Indices: 41162238--41162370 Score: 105
Period size: 18 Copynumber: 7.6 Consensus size: 18
41162228 AGTTTAATTC
*
41162238 ATTTAATTTTACAACCAT
1 ATTTAATTTTAAAACCAT
* * ** *
41162256 ATTTAAATCTAAAATTAA
1 ATTTAATTTTAAAACCAT
41162274 ATATT--TTTTAAAACCAT
1 AT-TTAATTTTAAAACCAT
*
41162291 ATTTAATTTTACAACCAT
1 ATTTAATTTTAAAACCAT
* *
41162309 ATTGAATTTTAAAA--TT
1 ATTTAATTTTAAAACCAT
**
41162325 AAAT-ATTTTAAAACCAT
1 ATTTAATTTTAAAACCAT
* *
41162342 ATTTAATTTTAAAGCAAT
1 ATTTAATTTTAAAACCAT
41162360 ATTTAATTTTA
1 ATTTAATTTTA
41162371 TTTTATTTTA
Statistics
Matches: 86, Mismatches: 23, Indels: 12
0.71 0.19 0.10
Matches are distributed among these distances:
15 9 0.10
16 4 0.05
17 12 0.14
18 59 0.69
19 2 0.02
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTTAATTTTAAAACCAT
Found at i:41162299 original size:53 final size:51
Alignment explanation
Indices: 41162238--41162365 Score: 186
Period size: 53 Copynumber: 2.5 Consensus size: 51
41162228 AGTTTAATTC
41162238 ATTTAATTTTACAACCATATTTAAATCTAAAATTAAATATTTTTTAAAACCAT
1 ATTTAATTTTACAACCATATTTAAATCTAAAATTAAATA--TTTTAAAACCAT
* * *
41162291 ATTTAATTTTACAACCATATTGAATTTTAAAATTAAATATTTTAAAACCAT
1 ATTTAATTTTACAACCATATTTAAATCTAAAATTAAATATTTTAAAACCAT
*
41162342 ATTTAATTTTA-AAGCAATATTTAA
1 ATTTAATTTTACAA-CCATATTTAA
41162366 TTTTATTTTA
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
50 2 0.03
51 31 0.45
53 36 0.52
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (51 bp):
ATTTAATTTTACAACCATATTTAAATCTAAAATTAAATATTTTAAAACCAT
Found at i:41162362 original size:51 final size:52
Alignment explanation
Indices: 41162238--41162370 Score: 198
Period size: 51 Copynumber: 2.6 Consensus size: 52
41162228 AGTTTAATTC
* *
41162238 ATTTAATTTTACAACCATATTTAAATCTAAAATTAAATATTTTTTAAAACCAT
1 ATTTAATTTTACAACCATATTTAATTTTAAAATTAAATA-TTTTTAAAACCAT
*
41162291 ATTTAATTTTACAACCATATTGAATTTTAAAATTAAATA-TTTTAAAACCAT
1 ATTTAATTTTACAACCATATTTAATTTTAAAATTAAATATTTTTAAAACCAT
*
41162342 ATTTAATTTTA-AAGCAATATTTAATTTTA
1 ATTTAATTTTACAA-CCATATTTAATTTTA
41162371 TTTTATTTTA
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
50 2 0.03
51 36 0.49
53 36 0.49
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (52 bp):
ATTTAATTTTACAACCATATTTAATTTTAAAATTAAATATTTTTAAAACCAT
Found at i:41178406 original size:47 final size:47
Alignment explanation
Indices: 41178332--41178850 Score: 558
Period size: 47 Copynumber: 10.5 Consensus size: 47
41178322 TCGGGACTTT
* * * * * * * * *
41178332 TCACATTTATATACTTTCACATCCATCACGTTGGCCACTCGGCCCTG
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
41178379 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
*
41178426 TCACATATATACACTTTCACATTCTTCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
* *
41178473 TCACATATATATACACTTTCATATTCATCACATCGGCTATTAGGCCTTA
1 TCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
41178522 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
* *
41178569 TCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
*
41178616 TCACATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
* * **
41178663 TCGCATCGGCCATTAGGCCTTATCACATATATACACTTTCAT-ATTCATC-G-CATCGGCCATTA
1 TCACAT-----A-TA-----TA-CAC-T-T-T-CACATTCATCA--CATCGGCCAT---TA----
41178725 GGCCTTA
41 GGCCTTA
* *
41178732 TCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
*
41178779 TCACATATATACACTTTCAAATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
41178826 TCACATATATATACACTTTCACATT
1 TCAC--ATATATACACTTTCACATT
41178851 TATTCAAATA
Statistics
Matches: 407, Mismatches: 33, Indels: 62
0.81 0.07 0.12
Matches are distributed among these distances:
47 278 0.68
49 62 0.15
51 1 0.00
52 4 0.01
53 11 0.03
54 5 0.01
55 1 0.00
56 1 0.00
57 3 0.01
58 3 0.01
59 3 0.01
60 1 0.00
61 1 0.00
62 5 0.01
63 11 0.03
64 5 0.01
69 12 0.03
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
Found at i:41178672 original size:22 final size:22
Alignment explanation
Indices: 41178644--41178686 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
41178634 ACATTCATCA
41178644 CATCGGCCATTAGGCCTTATCG
1 CATCGGCCATTAGGCCTTATCG
41178666 CATCGGCCATTAGGCCTTATC
1 CATCGGCCATTAGGCCTTATC
41178687 ACATATATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.21, T:0.28
Consensus pattern (22 bp):
CATCGGCCATTAGGCCTTATCG
Found at i:41178682 original size:69 final size:69
Alignment explanation
Indices: 41178601--41178733 Score: 230
Period size: 69 Copynumber: 1.9 Consensus size: 69
41178591 TCATCACATT
*
41178601 GGCCATTCGGCCTTATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCG
1 GGCCATTAGGCCTTATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCG
41178666 CATC
66 CATC
* * *
41178670 GGCCATTAGGCCTTATCACATATATACACTTTCATATTCATCGCATCGGCCATTAGGCCTTATC
1 GGCCATTAGGCCTTATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
41178734 ACATATATAC
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.25, C:0.31, G:0.14, T:0.31
Consensus pattern (69 bp):
GGCCATTAGGCCTTATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCG
CATC
Found at i:41178689 original size:163 final size:163
Alignment explanation
Indices: 41178503--41178827 Score: 605
Period size: 163 Copynumber: 2.0 Consensus size: 163
41178493 ATATTCATCA
*
41178503 CATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
41178568 ATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACACACTTT
66 ATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACACACTTT
*
41178633 CACATTCATCACATCGGCCATTAGGCCTTATCG
131 CAAATTCATCACATCGGCCATTAGGCCTTATCG
* *
41178666 CATCGGCCATTAGGCCTTATCACATATATACACTTTCATATTCATCGCATCGGCCATTAGGCCTT
1 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
*
41178731 ATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTT
66 ATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACACACTTT
41178796 CAAATTCATCACATCGGCCATTAGGCCTTATC
131 CAAATTCATCACATCGGCCATTAGGCCTTATC
41178828 ACATATATAT
Statistics
Matches: 157, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
163 157 1.00
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.32
Consensus pattern (163 bp):
CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
ATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACACACTTT
CAAATTCATCACATCGGCCATTAGGCCTTATCG
Found at i:41178703 original size:116 final size:116
Alignment explanation
Indices: 41178550--41178780 Score: 399
Period size: 116 Copynumber: 2.0 Consensus size: 116
41178540 ACATTCATCA
* *
41178550 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
41178615 ATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCG
66 ATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCG
* *
41178666 CATCGGCCATTAGGCCTTATCACATATATACACTTTCATATTCATCGCATCGGCCATTAGGCCTT
1 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
* * *
41178731 ATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATC
66 ATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
41178781 ACATATATAC
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
116 108 1.00
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.32
Consensus pattern (116 bp):
CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
ATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCG
Found at i:41180361 original size:13 final size:13
Alignment explanation
Indices: 41180343--41180367 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41180333 TACTAAATTT
41180343 TCATGGATTCAAA
1 TCATGGATTCAAA
41180356 TCATGGATTCAA
1 TCATGGATTCAA
41180368 TATACCATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAA
Found at i:41191603 original size:49 final size:49
Alignment explanation
Indices: 41191531--41191719 Score: 236
Period size: 49 Copynumber: 3.8 Consensus size: 49
41191521 TGAGGTCACG
* *
41191531 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAGTTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAGTTGGTCGCA
** * * * * * *
41191580 TGTGTAGTACTAAGTGCAGGCTACTATACGTACCCGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAG-ATAGT-TGGTCGCA
*
41191631 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTA-TTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGA-TAGTTGGTCGCA
*
41191680 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAG
1 TGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAG
41191720 CTTCAGCTAC
Statistics
Matches: 117, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
48 2 0.02
49 72 0.62
50 5 0.04
51 38 0.32
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAGTTGGTCGCA
Found at i:41191699 original size:100 final size:100
Alignment explanation
Indices: 41191526--41191713 Score: 342
Period size: 100 Copynumber: 1.9 Consensus size: 100
41191516 TATTGTGAGG
*
41191526 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAGTTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTGGTCGCATGTGTAGTACT
41191591 AAGTGCAGGCTACTATACGTACCCGAAAACTGTGA
66 AAGTGCAGGCTACTATACGTACCCGAAAACTGTGA
41191626 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTA-TTGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA-TAGTTGGTCGCATGTGTAGTAC
*
41191690 TAAGTGCAGGCTACTATGCGTACC
65 TAAGTGCAGGCTACTATACGTACC
41191714 AGATAGCTTC
Statistics
Matches: 85, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
100 83 0.98
101 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (100 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTGGTCGCATGTGTAGTACT
AAGTGCAGGCTACTATACGTACCCGAAAACTGTGA
Found at i:41194183 original size:19 final size:19
Alignment explanation
Indices: 41194137--41194183 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
41194127 ACATAACTAA
*
41194137 TGACTTTCCATACATAAGT
1 TGACTTTCTATACATAAGT
41194156 TGACTTTCTATACATAAGT
1 TGACTTTCTATACATAAGT
*
41194175 TGTCTTTCT
1 TGACTTTCT
41194184 TCTTAAAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.45
Consensus pattern (19 bp):
TGACTTTCTATACATAAGT
Found at i:41195412 original size:38 final size:38
Alignment explanation
Indices: 41195370--41195448 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
41195360 TACGTGGACT
41195370 TCAAATCAGAATCTATCTATTCATGTTATCATGATTAG
1 TCAAATCAGAATCTATCTATTCATGTTATCATGATTAG
*
41195408 TCAAATCAGAATCTATCTATTCATGTTGTCATGATTAG
1 TCAAATCAGAATCTATCTATTCATGTTATCATGATTAG
41195446 TCA
1 TCA
41195449 CCAATTACAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.39
Consensus pattern (38 bp):
TCAAATCAGAATCTATCTATTCATGTTATCATGATTAG
Found at i:41197732 original size:14 final size:15
Alignment explanation
Indices: 41197697--41197734 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
41197687 AAAAGTTTAA
**
41197697 AATTTAATTTTTATT
1 AATTTAATTTTTAGG
41197712 AATTTAATTTTTAGG
1 AATTTAATTTTTAGG
41197727 AA-TTAATT
1 AATTTAATT
41197735 ATAATCGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (15 bp):
AATTTAATTTTTAGG
Found at i:41202611 original size:18 final size:18
Alignment explanation
Indices: 41202590--41202627 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
41202580 GTATCAGAAC
*
41202590 AGGAACCTGTGTCAAAAT
1 AGGAACCTGAGTCAAAAT
41202608 AGGAACCTGAGTCAAAAT
1 AGGAACCTGAGTCAAAAT
41202626 AG
1 AG
41202628 ATTTGAGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.18
Consensus pattern (18 bp):
AGGAACCTGAGTCAAAAT
Found at i:41205555 original size:30 final size:30
Alignment explanation
Indices: 41205517--41205582 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
41205507 TATAGGTAGG
**
41205517 CCGTGTCTCTCACATGGCCAAGAAACACGC
1 CCGTGTCTCTCACACAGCCAAGAAACACGC
*
41205547 CTGTGTCTCTCACACAGCCAAGAAACACGC
1 CCGTGTCTCTCACACAGCCAAGAAACACGC
41205577 CCGTGT
1 CCGTGT
41205583 GTTTTCTACT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.36, G:0.20, T:0.18
Consensus pattern (30 bp):
CCGTGTCTCTCACACAGCCAAGAAACACGC
Found at i:41220738 original size:12 final size:12
Alignment explanation
Indices: 41220701--41220781 Score: 83
Period size: 12 Copynumber: 6.8 Consensus size: 12
41220691 CATGTGGCAT
*
41220701 GCCCATGTCTTA
1 GCCCGTGTCTTA
*
41220713 GGCCGTGT-TCTA
1 GCCCGTGTCT-TA
*
41220725 GCCTGTGTCTTA
1 GCCCGTGTCTTA
41220737 GCCCGTGTCTTA
1 GCCCGTGTCTTA
* * *
41220749 GCCTGTGCCCTA
1 GCCCGTGTCTTA
*
41220761 GCCCATGTCTTA
1 GCCCGTGTCTTA
41220773 GCCCGTGTC
1 GCCCGTGTC
41220782 CTTACTCATG
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
11 1 0.02
12 52 0.96
13 1 0.02
ACGTcount: A:0.10, C:0.33, G:0.25, T:0.32
Consensus pattern (12 bp):
GCCCGTGTCTTA
Found at i:41222095 original size:24 final size:24
Alignment explanation
Indices: 41222030--41222097 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
41222020 GAAAGCTTGT
* *
41222030 AAAGAGCCATAATCGGGAAGTTCAC
1 AAAGAACCAT-ATCGGGAAGTTCAA
* *
41222055 AAAGAATCTTATCGGGAAGTTCAA
1 AAAGAACCATATCGGGAAGTTCAA
*
41222079 AAAGAACCATATTGGGAAG
1 AAAGAACCATATCGGGAAG
41222098 CTCCGGATAG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
24 29 0.81
25 7 0.19
ACGTcount: A:0.43, C:0.15, G:0.24, T:0.19
Consensus pattern (24 bp):
AAAGAACCATATCGGGAAGTTCAA
Found at i:41223667 original size:16 final size:15
Alignment explanation
Indices: 41223640--41223673 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
41223630 ATAACAAGTA
*
41223640 TATAATTATATTTAT
1 TATAATTATATTAAT
41223655 TATAATATATATTAAT
1 TATAAT-TATATTAAT
41223671 TAT
1 TAT
41223674 TATCAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATAATTATATTAAT
Found at i:41225234 original size:37 final size:37
Alignment explanation
Indices: 41225184--41225333 Score: 230
Period size: 37 Copynumber: 4.1 Consensus size: 37
41225174 CTTTAGCTCA
* * *
41225184 GACAAAATCTCCACACGAAGTTATCGGGTCTTACCCG
1 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
* *
41225221 GACA-AATTCTCCACACGTAGTCATTGGGTCTTATCCG
1 GACATAA-TCTCCACACGTAGTCATCGGGTCTTACCCG
*
41225258 AACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
1 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
41225295 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
1 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
41225332 GA
1 GA
41225334 ATATATTTCC
Statistics
Matches: 103, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
36 2 0.02
37 99 0.96
38 2 0.02
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
Found at i:41225592 original size:47 final size:47
Alignment explanation
Indices: 41225540--41225733 Score: 280
Period size: 47 Copynumber: 4.1 Consensus size: 47
41225530 CATACATATT
* * * *
41225540 TCACATTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* *
41225587 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* *
41225634 TCGCATTGGCCATTCGGTCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * **
41225681 TCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
41225728 TCACAT
1 TCACAT
41225734 AAAATCCTAA
Statistics
Matches: 131, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 131 1.00
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.34
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:41228870 original size:536 final size:536
Alignment explanation
Indices: 41227858--41228929 Score: 2090
Period size: 536 Copynumber: 2.0 Consensus size: 536
41227848 TTAAAATTTC
41227858 ACAATTTGACATAATATACTAACCTTTTTAATGACTCAAGTGACCCAAAAATTCTTCCCCTCCTT
1 ACAATTTGACATAATATACTAACCTTTTTAATGACTCAAGTGACCCAAAAATTCTTCCCCTCCTT
41227923 TGTTTCTTCTATTCAGCCAAGTTGAACAACAAAGAAAGAACTTTGTTTTTTCCTCCCCTTTCTCT
66 TGTTTCTTCTATTCAGCCAAGTTGAACAACAAAGAAAGAACTTTGTTTTTTCCTCCCCTTTCTCT
*
41227988 AGTCACGGCAATGGGGAGTAAGGGGGAGACAACTTTGGTTTCTCCTCCCACTCCCCTCATATTTT
131 AGTCACGGCAATGAGGAGTAAGGGGGAGACAACTTTGGTTTCTCCTCCCACTCCCCTCATATTTT
41228053 ATTATTCTTCCCACACATATTAGCATAAAATGTCTATAATATGTTTTACCCCATAGCATGGCCGG
196 ATTATTCTTCCCACACATATTAGCATAAAATGTCTATAATATGTTTTACCCCATAGCATGGCCGG
*
41228118 CCACTATCTAGATTTTTGGCTAATTTGACATGCAAACCCTTCTTTTATACAACATGCATTAATAG
261 CCACCATCTAGATTTTTGGCTAATTTGACATGCAAACCCTTCTTTTATACAACATGCATTAATAG
41228183 GTCCTTATAGATTAACCTATCGCATTTCAAAAGTGTCACACATAAGTCCTATTACTAAATTCACA
326 GTCCTTATAGATTAACCTATCGCATTTCAAAAGTGTCACACATAAGTCCTATTACTAAATTCACA
41228248 TGCAATCGACTAAATCGAAGCTTAAAACTTTCACACATTCATATTCACATATAATAAACATAAAA
391 TGCAATCGACTAAATCGAAGCTTAAAACTTTCACACATTCATATTCACATATAATAAACATAAAA
*
41228313 TATGATGGCTAATTATTTTTATGACTCGATTTTGTGGTCCCGAAACCATTTTTCGACTAGGGTCA
456 TATGACGGCTAATTATTTTTATGACTCGATTTTGTGGTCCCGAAACCATTTTTCGACTAGGGTCA
41228378 AATTAGGGGTGTCACA
521 AATTAGGGGTGTCACA
41228394 ACAATTTGACATAATATACTAACCTTTTTAATGACTCAAGTGACCCAAAAATTCTTCCCCTCCTT
1 ACAATTTGACATAATATACTAACCTTTTTAATGACTCAAGTGACCCAAAAATTCTTCCCCTCCTT
*
41228459 TGTTTCTTCTATTCGGCCAAGTTGAACAACAAAGAAAGAACTTTGTTTTTTCCTCCCCTTTCTCT
66 TGTTTCTTCTATTCAGCCAAGTTGAACAACAAAGAAAGAACTTTGTTTTTTCCTCCCCTTTCTCT
41228524 AGTCACGGCAATGAGGAGTAAGGGGGAGACAACTTTGGTTTCTCCTCCCACTCCCCTCATATTTT
131 AGTCACGGCAATGAGGAGTAAGGGGGAGACAACTTTGGTTTCTCCTCCCACTCCCCTCATATTTT
* *
41228589 ATTATTCTTCCCACACGTATTAGCATAAAATGTCTATAATATGTTTTACCCCATAGCATGGCTGG
196 ATTATTCTTCCCACACATATTAGCATAAAATGTCTATAATATGTTTTACCCCATAGCATGGCCGG
41228654 CCACCATCTAGATTTTTGGCTAATTTGACATGCAAACCCTTCTTTTATACAACATGCATTAATAG
261 CCACCATCTAGATTTTTGGCTAATTTGACATGCAAACCCTTCTTTTATACAACATGCATTAATAG
41228719 GTCCTTATAGATTAACCTATCGCATTTCAAAAGTGTCACACATAAGTCCTATTACTAAATTCACA
326 GTCCTTATAGATTAACCTATCGCATTTCAAAAGTGTCACACATAAGTCCTATTACTAAATTCACA
41228784 TGCAATCGACTAAATCGAAGCTTAAAACTTTCACACATTCATATTCACATATAATAAACATAAAA
391 TGCAATCGACTAAATCGAAGCTTAAAACTTTCACACATTCATATTCACATATAATAAACATAAAA
41228849 TATGACGGCTAATTATTTTTATGACTCGATTTTGTGGTCCCGAAACCATTTTTCGACTAGGGTCA
456 TATGACGGCTAATTATTTTTATGACTCGATTTTGTGGTCCCGAAACCATTTTTCGACTAGGGTCA
41228914 AATTAGGGGTGTCACA
521 AATTAGGGGTGTCACA
41228930 GAAATGGTAA
Statistics
Matches: 530, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
536 530 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (536 bp):
ACAATTTGACATAATATACTAACCTTTTTAATGACTCAAGTGACCCAAAAATTCTTCCCCTCCTT
TGTTTCTTCTATTCAGCCAAGTTGAACAACAAAGAAAGAACTTTGTTTTTTCCTCCCCTTTCTCT
AGTCACGGCAATGAGGAGTAAGGGGGAGACAACTTTGGTTTCTCCTCCCACTCCCCTCATATTTT
ATTATTCTTCCCACACATATTAGCATAAAATGTCTATAATATGTTTTACCCCATAGCATGGCCGG
CCACCATCTAGATTTTTGGCTAATTTGACATGCAAACCCTTCTTTTATACAACATGCATTAATAG
GTCCTTATAGATTAACCTATCGCATTTCAAAAGTGTCACACATAAGTCCTATTACTAAATTCACA
TGCAATCGACTAAATCGAAGCTTAAAACTTTCACACATTCATATTCACATATAATAAACATAAAA
TATGACGGCTAATTATTTTTATGACTCGATTTTGTGGTCCCGAAACCATTTTTCGACTAGGGTCA
AATTAGGGGTGTCACA
Found at i:41245714 original size:49 final size:49
Alignment explanation
Indices: 41245638--41245872 Score: 326
Period size: 49 Copynumber: 4.8 Consensus size: 49
41245628 TAGCCGAAGC
* *
41245638 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
* * * * *
41245687 AATTTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAGT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAAT
* * * *
41245738 TTTCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
* *
41245787 TATCCGGTACACGTAGGAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
*
41245836 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACA
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACA
41245873 AACGTTGTAA
Statistics
Matches: 162, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
49 121 0.75
50 2 0.01
51 39 0.24
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (49 bp):
TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
Found at i:41245757 original size:100 final size:98
Alignment explanation
Indices: 41245638--41245872 Score: 344
Period size: 100 Copynumber: 2.4 Consensus size: 98
41245628 TAGCCGAAGC
* **
41245638 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATTTGGTACACGTAG
1 TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAG
* * *
41245703 TAGCCTGCACTTAGTACTACACACGTGATCACAGT
66 GAGCCTGCACTTAGTACTACACACGCGA-C-CAAT
* * *
41245738 TTTCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAG
1 TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAG
*
41245803 GAGCCTGCACTTAGTACTACACATGCGACCAAT
66 GAGCCTGCACTTAGTACTACACACGCGACCAAT
* *
41245836 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACA
1 TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACA
41245873 AACGTTGTAA
Statistics
Matches: 122, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
98 36 0.30
99 1 0.01
100 85 0.70
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (98 bp):
TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAG
GAGCCTGCACTTAGTACTACACACGCGACCAAT
Found at i:41262423 original size:16 final size:17
Alignment explanation
Indices: 41262391--41262424 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
41262381 GAGGATGGCA
41262391 TTTGTTTGATGTTTATT
1 TTTGTTTGATGTTTATT
*
41262408 TTTGTTTGGT-TTTATT
1 TTTGTTTGATGTTTATT
41262424 T
1 T
41262425 CATAATATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.09, C:0.00, G:0.18, T:0.74
Consensus pattern (17 bp):
TTTGTTTGATGTTTATT
Found at i:41282661 original size:28 final size:28
Alignment explanation
Indices: 41282598--41282695 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
41282588 ATATTAAGTC
*
41282598 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
41282625 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
41282653 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
41282682 CGCACACTTAGTGC
1 CGCACACTTAGTGC
41282696 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:41283161 original size:18 final size:18
Alignment explanation
Indices: 41283140--41283175 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
41283130 TGGGCATACT
41283140 TATGTATATATACATATA
1 TATGTATATATACATATA
* *
41283158 TATGTGTATATATATATA
1 TATGTATATATACATATA
41283176 CTTTGGAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (18 bp):
TATGTATATATACATATA
Found at i:41314382 original size:27 final size:26
Alignment explanation
Indices: 41314334--41314385 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
41314324 GAGAGGCTAC
*
41314334 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
41314360 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
41314386 TTGTAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:41315085 original size:27 final size:27
Alignment explanation
Indices: 41315055--41315285 Score: 318
Period size: 27 Copynumber: 8.5 Consensus size: 27
41315045 CCCCAAAAGA
* *
41315055 GTATCTCGGTAATTTTACCCTACAGGG
1 GTATTTCGGTAATTCTACCCTACAGGG
* * *
41315082 GTATTTCAGTATTTCTACCCTACAAGG
1 GTATTTCGGTAATTCTACCCTACAGGG
*
41315109 GTATTTCGGTAATTCTACCCTATAGGG
1 GTATTTCGGTAATTCTACCCTACAGGG
* **
41315136 GTATTTCAGTAATTCTACCCTGTAGGG
1 GTATTTCGGTAATTCTACCCTACAGGG
*
41315163 GTATTTCGGTAATTCTACCTTACAGGG
1 GTATTTCGGTAATTCTACCCTACAGGG
*
41315190 GTATTTCAGTAATTCTACCCTACAGGG
1 GTATTTCGGTAATTCTACCCTACAGGG
*
41315217 GTATTTCAGTAATTCTACCCTACAGGG
1 GTATTTCGGTAATTCTACCCTACAGGG
* *
41315244 GTATTTCGGTAATTCTACCTTATAGGG
1 GTATTTCGGTAATTCTACCCTACAGGG
*
41315271 GTATTTTTGGTAATT
1 GTA-TTTCGGTAATT
41315286 TTACAAACCA
Statistics
Matches: 182, Mismatches: 21, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
27 172 0.95
28 10 0.05
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (27 bp):
GTATTTCGGTAATTCTACCCTACAGGG
Found at i:41315313 original size:27 final size:27
Alignment explanation
Indices: 41315269--41315340 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
41315259 TACCTTATAG
41315269 GGGTATTTTTGGTAATTTTACAAACCAA
1 GGGTA-TTTTGGTAATTTTACAAACCAA
* * * *
41315297 GGGTATTTTGGTAATTTTGCTAATCGA
1 GGGTATTTTGGTAATTTTACAAACCAA
41315324 GGGTATTTTGGTAATTT
1 GGGTATTTTGGTAATTT
41315341 GGTAAACTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 35 0.88
28 5 0.12
ACGTcount: A:0.25, C:0.07, G:0.24, T:0.44
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAA
Found at i:41317440 original size:27 final size:26
Alignment explanation
Indices: 41317392--41317451 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
41317382 GCAAGGCTGC
*
41317392 CAGATATTGTGACAAAGTCACCAGATA
1 CAGATATTGTGACAAAGCCACCAGA-A
* * *
41317419 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACAAAGCCACCAGAA
41317445 CAGATAT
1 CAGATAT
41317452 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACAAAGCCACCAGAA
Found at i:41318208 original size:27 final size:27
Alignment explanation
Indices: 41318178--41318456 Score: 260
Period size: 27 Copynumber: 10.4 Consensus size: 27
41318168 GGGGAAAAAT
* *
41318178 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTTTACCCTACAAGGGTATTTC
41318205 GGTAATTTTACCCTACAAGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTC
*
41318232 AGT-ATTTCTACCCTACAAGGGT-TTTC
1 GGTAATTT-TACCCTACAAGGGTATTTC
* * *
41318258 GGTAATTCTACCATACAGGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTC
* *
41318285 AGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTC
* *
41318312 GATAATTTTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTC
* * * * *
41318339 GGTAATTATACCTTATAGGGGTATTTT
1 GGTAATTTTACCCTACAAGGGTATTTC
* * *
41318366 AGTAA-TCTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTC
* * * * *
41318392 GATAATTCTACCTTACAGGGGTATTTTT
1 GGTAATTTTACCCTACAAGGGTA-TTTC
** * *
41318420 GGTAATTTTA-CAAACCAGGGGTATTTT
1 GGTAATTTTACCCTA-CAAGGGTATTTC
41318447 GGTAATTTTA
1 GGTAATTTTA
41318457 ATAATCGAGG
Statistics
Matches: 214, Mismatches: 32, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
26 42 0.20
27 153 0.71
28 19 0.09
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.37
Consensus pattern (27 bp):
GGTAATTTTACCCTACAAGGGTATTTC
Found at i:41318280 original size:53 final size:54
Alignment explanation
Indices: 41318179--41318430 Score: 294
Period size: 53 Copynumber: 4.7 Consensus size: 54
41318169 GGGAAAAATG
* * * *
41318179 GTAATTTTACCCCACAAGGGTATCTCGGTAATTTTACCCTACAAGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTTTACCCTACAGGGGTATTTCA
* * *
41318233 GTATTTCTACCCTACAAGGGT-TTTCGGTAATTCTACCATACAGGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTTTACCCTACAGGGGTATTTCA
* *
41318286 GTAATTCTACCCTACAAGGGTATTTCGATAATTTTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTTTACCCTACAGGGGTATTTCA
* * * * ** *
41318340 GTAATTATACCTTATAGGGGTATTTTAGTAA-TCTACCCTACAGGGGTATTTC-
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTTTACCCTACAGGGGTATTTCA
* * *
41318392 GATAATTCTACCTTACAGGGGTATTTTTGGTAATTTTAC
1 G-TAATTCTACCCTACAAGGGTA-TTTCGGTAATTTTAC
41318431 AAACCAGGGG
Statistics
Matches: 170, Mismatches: 24, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
52 1 0.01
53 87 0.51
54 78 0.46
55 4 0.02
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (54 bp):
GTAATTCTACCCTACAAGGGTATTTCGGTAATTTTACCCTACAGGGGTATTTCA
Found at i:41318311 original size:80 final size:80
Alignment explanation
Indices: 41318178--41318445 Score: 301
Period size: 80 Copynumber: 3.3 Consensus size: 80
41318168 GGGGAAAAAT
** * * * *
41318178 GGTAATTTTACCCCACAAGGGTATCTCGGTAATTTTACCCTACAAGGGTATTTC-AGTATTTCTA
1 GGTAATTTTACCATACAGGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCGA-TATTTCTA
*
41318242 CCCTACAAGGGTTTTC
65 CCCTACAGGGGTTTTC
*
41318258 GGTAATTCTACCATACAGGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCGATAATTT-TA
1 GGTAATTTTACCATACAGGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCGAT-ATTTCTA
41318322 CCCTACAGGGGTATTTC
65 CCCTACAGGGGT-TTTC
* * * * * *
41318339 GGTAATTATACCTTATAGGGGTATTTTAGTAA-TCTACCCTACAGGGGTATTTCGATAATTCTAC
1 GGTAATTTTACCATACAGGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCGATATTTCTAC
* *
41318403 CTTACAGGGGTATTTTT
66 CCTACAGGGG--TTTTC
*
41318420 GGTAATTTTA-CAAACCAGGGGTATTT
1 GGTAATTTTACCATA-CAGGGGTATTT
41318446 TGGTAATTTT
Statistics
Matches: 161, Mismatches: 20, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
79 3 0.02
80 98 0.61
81 59 0.37
82 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.36
Consensus pattern (80 bp):
GGTAATTTTACCATACAGGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCGATATTTCTAC
CCTACAGGGGTTTTC
Found at i:41318375 original size:107 final size:106
Alignment explanation
Indices: 41318179--41318453 Score: 311
Period size: 107 Copynumber: 2.6 Consensus size: 106
41318169 GGGAAAAATG
* * * * * * *
41318179 GTAATTTTACCCCACAAGGGTATCTCGGTAATTTTACCCTACAAGGGTATTTCAGTATTTCTACC
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTTTACCCTACAGGGGTATTTCGGTAATTATACC
*
41318244 CTACAAGGGTTTTCGGTAATTCTACCATACAGGGGTATTTC
66 CTACAAGGGTTTTCAGTAATTCTACCATACAGGGGTATTTC
*
41318285 AGTAATTCTACCCTACAAGGGTATTTCGATAATTTTACCCTACAGGGGTATTTCGGTAATTATAC
1 -GTAATTCTACCCTACAAGGGTATTTCGGTAATTTTACCCTACAGGGGTATTTCGGTAATTATAC
* * * * *
41318350 CTTATAGGGGTATTTTAGTAA-TCTACCCTACAGGGGTATTTC
65 CCTACAAGGGT-TTTCAGTAATTCTACCATACAGGGGTATTTC
* * * ** *
41318392 GATAATTCTACCTTACAGGGGTATTTTTGGTAATTTTA-CAAACCAGGGGTATTTTGGTAATT
1 G-TAATTCTACCCTACAAGGGTA-TTTCGGTAATTTTACCCTA-CAGGGGTATTTCGGTAATT
41318454 TTAATAATCG
Statistics
Matches: 143, Mismatches: 21, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
106 1 0.01
107 105 0.73
108 37 0.26
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.37
Consensus pattern (106 bp):
GTAATTCTACCCTACAAGGGTATTTCGGTAATTTTACCCTACAGGGGTATTTCGGTAATTATACC
CTACAAGGGTTTTCAGTAATTCTACCATACAGGGGTATTTC
Found at i:41318468 original size:27 final size:27
Alignment explanation
Indices: 41318410--41318508 Score: 128
Period size: 27 Copynumber: 3.6 Consensus size: 27
41318400 TACCTTACAG
* *
41318410 GGGTATTTTTGGTAATTTTACA-AACCAG
1 GGGTA-TTTTGGTAATTTTA-ATAATCAA
*
41318438 GGGTATTTTGGTAATTTTAATAATCGA
1 GGGTATTTTGGTAATTTTAATAATCAA
**
41318465 GGGTATTTTGGTAATTTTGCTAATCAA
1 GGGTATTTTGGTAATTTTAATAATCAA
41318492 GGGTATTTTGGTAATTT
1 GGGTATTTTGGTAATTT
41318509 GGTAAACTAA
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
26 1 0.02
27 58 0.91
28 5 0.08
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.44
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTAATAATCAA
Found at i:41323808 original size:41 final size:41
Alignment explanation
Indices: 41323763--41323845 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
41323753 TAATGCCCCT
41323763 AGCAGCCCATATTTTTCATTTATTTTACATTTTAACCACTA
1 AGCAGCCCATATTTTTCATTTATTTTACATTTTAACCACTA
41323804 AGCAGCCCATATTTTTCATTTATTTTACATTTTAACCACTA
1 AGCAGCCCATATTTTTCATTTATTTTACATTTTAACCACTA
41323845 A
1 A
41323846 CTTTACACAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.30, C:0.22, G:0.05, T:0.43
Consensus pattern (41 bp):
AGCAGCCCATATTTTTCATTTATTTTACATTTTAACCACTA
Found at i:41324600 original size:17 final size:18
Alignment explanation
Indices: 41324567--41324601 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
41324557 GGGGATGGCA
41324567 TTTGTTTGATGTTTATTT
1 TTTGTTTGATGTTTATTT
*
41324585 TTTGTTTGGT-TTTATTT
1 TTTGTTTGATGTTTATTT
41324602 CATAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.09, C:0.00, G:0.17, T:0.74
Consensus pattern (18 bp):
TTTGTTTGATGTTTATTT
Found at i:41325398 original size:46 final size:46
Alignment explanation
Indices: 41325280--41325456 Score: 218
Period size: 46 Copynumber: 3.8 Consensus size: 46
41325270 AAATGATGTT
* * *
41325280 AATGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-T
1 AATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG
41325322 AACTAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG
1 AA-T--G--TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG
*
41325373 AATGTCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCG
1 AATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG
* * *
41325419 AACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 AATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
41325457 GGGGCGGGTT
Statistics
Matches: 118, Mismatches: 8, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
42 2 0.02
43 1 0.01
45 1 0.01
46 75 0.64
47 29 0.25
48 3 0.03
50 5 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (46 bp):
AATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG
Found at i:41327743 original size:48 final size:48
Alignment explanation
Indices: 41327678--41327919 Score: 246
Period size: 48 Copynumber: 5.1 Consensus size: 48
41327668 AAAATTACAT
* * *
41327678 TCACATAGTAGGATGCCAATGCCATTTCCCAAATATGGTCTTACATGGGA
1 TCACATA-TA-GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
*
41327728 TCACATATAGATGCCAATGCCATGTCCCAGACATGGTCTTACATAGGA
1 TCACATATAGATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
* * * * *
41327776 TCATGCATATCGAAGCCGAT---A-G-CCCAG-CTATGGTCTTACACGATG-
1 TCA--CATATAGATGCCAATGCCATGTCCCAGAC-ATGGTCTTACATG-GGA
* * *
41327821 TCTCATATTGATGCCAATGCCATGTTCCAGACATGGTCTTACATGGGA
1 TCACATATAGATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
* * *
41327869 TCACATTTCGATGCCAATGCCATGTCCCAGACATGGTCTTACATAGGA
1 TCACATATAGATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
41327917 TCA
1 TCA
41327920 TGCATATCCC
Statistics
Matches: 159, Mismatches: 22, Indels: 24
0.78 0.11 0.12
Matches are distributed among these distances:
43 12 0.08
44 1 0.01
45 18 0.11
46 3 0.02
47 3 0.02
48 100 0.63
49 3 0.02
50 19 0.12
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (48 bp):
TCACATATAGATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
Found at i:41335201 original size:57 final size:58
Alignment explanation
Indices: 41335129--41335237 Score: 166
Period size: 57 Copynumber: 1.9 Consensus size: 58
41335119 GCCCACTGAT
* *
41335129 CGATCTCGCACACATAGTGCTTGGTT-GAAGAACTCGCACACACAGTGCCTCAATTAC
1 CGATCTCGCACACATAGTGCTCGGTTAAAAGAACTCGCACACACAGTGCCTCAATTAC
* * *
41335186 CGATTTCGCACACATAGTGCTCGGTTAAAAGAATTTGCACACACAGTGCCTC
1 CGATCTCGCACACATAGTGCTCGGTTAAAAGAACTCGCACACACAGTGCCTC
41335238 TAATCATTCG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
57 24 0.52
58 22 0.48
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.24
Consensus pattern (58 bp):
CGATCTCGCACACATAGTGCTCGGTTAAAAGAACTCGCACACACAGTGCCTCAATTAC
Found at i:41335481 original size:40 final size:40
Alignment explanation
Indices: 41335449--41335756 Score: 458
Period size: 40 Copynumber: 7.7 Consensus size: 40
41335439 CCAGCATGAT
* * * *
41335449 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * * *
41335489 TGCTCTTCGAGG-TTTAGCACGGATATATTACTAGCACGAA
1 TGCTCTTCG-GGACTTAGCCCGGATACATCACTAGCACGAA
*
41335529 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
41335569 TGCTCTTCGGGACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
41335609 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
41335649 TGCTCTTCGGAACTTAGCCCGGGTACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
41335689 TGCTCTTCGGGACTTAGCCCAGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
41335729 TGCTCTTCGGGACTTAGCCCGGAT-CATC
1 TGCTCTTCGGGACTTAGCCCGGATACATC
41335757 GTCGAGACCT
Statistics
Matches: 243, Mismatches: 23, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
39 5 0.02
40 236 0.97
41 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:41337321 original size:22 final size:22
Alignment explanation
Indices: 41337296--41337367 Score: 96
Period size: 22 Copynumber: 3.3 Consensus size: 22
41337286 CACAAAACCG
41337296 AAGGGTACATGACCAACAACAA
1 AAGGGTACATGACCAACAACAA
*
41337318 AAGGGT--A-GTCCTATACAACAA
1 AAGGGTACATGACC-A-ACAACAA
41337339 AAGGGTACATGACCAACAACAA
1 AAGGGTACATGACCAACAACAA
41337361 AAGGGTA
1 AAGGGTA
41337368 GTCCTATACG
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
19 3 0.07
20 2 0.05
21 13 0.30
22 20 0.47
23 2 0.05
24 3 0.07
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.12
Consensus pattern (22 bp):
AAGGGTACATGACCAACAACAA
Found at i:41337337 original size:21 final size:21
Alignment explanation
Indices: 41337311--41337376 Score: 82
Period size: 21 Copynumber: 3.1 Consensus size: 21
41337301 TACATGACCA
41337311 ACAACAAAAGGGTAGTCCTAT
1 ACAACAAAAGGGTAGTCCTAT
*
41337332 ACAACAAAAGGGTACATGACC-A-
1 ACAACAAAAGGGT--A-GTCCTAT
41337354 ACAACAAAAGGGTAGTCCTAT
1 ACAACAAAAGGGTAGTCCTAT
41337375 AC
1 AC
41337377 GTGCTATGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
19 3 0.08
20 2 0.05
21 15 0.39
22 13 0.34
23 2 0.05
24 3 0.08
ACGTcount: A:0.45, C:0.21, G:0.18, T:0.15
Consensus pattern (21 bp):
ACAACAAAAGGGTAGTCCTAT
Found at i:41338994 original size:27 final size:28
Alignment explanation
Indices: 41338964--41339032 Score: 122
Period size: 27 Copynumber: 2.5 Consensus size: 28
41338954 ATATTAAGTC
*
41338964 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
41338991 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
41339019 CGCACACTTAGTGC
1 CGCACACTTAGTGC
41339033 CAATCTCATA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.55
28 18 0.45
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:41347269 original size:28 final size:28
Alignment explanation
Indices: 41347206--41347303 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
41347196 ATATTAAGTC
*
41347206 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
41347233 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
41347261 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
41347290 CGCACACTTAGTGC
1 CGCACACTTAGTGC
41347304 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:41394483 original size:22 final size:22
Alignment explanation
Indices: 41394453--41394494 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
41394443 ACGATCAAAT
* *
41394453 TATTGAATATATATTATTTTAA
1 TATTGAATACAAATTATTTTAA
*
41394475 TATTTAATACAAATTATTTT
1 TATTGAATACAAATTATTTT
41394495 GGAATGTGTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
TATTGAATACAAATTATTTTAA
Found at i:41399021 original size:46 final size:45
Alignment explanation
Indices: 41398971--41399236 Score: 283
Period size: 46 Copynumber: 5.8 Consensus size: 45
41398961 TGGTTGAGCA
*
41398971 TCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGTTAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-TAATG
* *
41399017 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAA-T--G
*
41399062 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-TAATG
* *
41399110 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAA-T--G
* *
41399155 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-TAATG
* *
41399203 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
41399237 GGGGCGGGTT
Statistics
Matches: 187, Mismatches: 15, Indels: 36
0.79 0.06 0.15
Matches are distributed among these distances:
42 5 0.03
43 10 0.05
45 6 0.03
46 89 0.48
47 58 0.31
48 6 0.03
50 9 0.05
51 4 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAATG
Found at i:41399127 original size:93 final size:93
Alignment explanation
Indices: 41398968--41399231 Score: 474
Period size: 93 Copynumber: 2.8 Consensus size: 93
41398958 GGATGGTTGA
* **
41398968 GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGTTAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
41399033 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
41399061 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
41399126 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
41399154 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
41399219 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
41399232 ACTTAGGGGC
Statistics
Matches: 165, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 165 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:41401922 original size:48 final size:48
Alignment explanation
Indices: 41401857--41402091 Score: 241
Period size: 48 Copynumber: 4.9 Consensus size: 48
41401847 AAAATTACAT
* * *
41401857 TCACATAGTAGGATGCCAATGCCATTTCCCAAATATGGTCTTACATGGGA
1 TCACATA-TA-GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
*
41401907 TCACATATAGATGCCAATGCCATGTCCCAGACATGGTCTTACATAGGA
1 TCACATATAGATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
* * * * *
41401955 TCATGCATATCGAAGCCGAT---A-G-CCCAG-CTATGGTCTTACACGATG-
1 TCA--CATATAGATGCCAATGCCATGTCCCAGAC-ATGGTCTTACATG-GGA
* * *
41402000 TCTCATATTGATGCCAATGCCATGTTCCAGACATGGTCTTACATGGGA
1 TCACATATAGATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
* *
41402048 TCACATTTCGATGCCAATGCCATGTCCCAGACATGGTCTTACAT
1 TCACATATAGATGCCAATGCCATGTCCCAGACATGGTCTTACAT
41402092 AGTATCATGC
Statistics
Matches: 153, Mismatches: 21, Indels: 24
0.77 0.11 0.12
Matches are distributed among these distances:
43 12 0.08
44 1 0.01
45 18 0.12
46 3 0.02
47 3 0.02
48 94 0.61
49 3 0.02
50 19 0.12
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (48 bp):
TCACATATAGATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
Found at i:41409357 original size:57 final size:58
Alignment explanation
Indices: 41409285--41409393 Score: 175
Period size: 57 Copynumber: 1.9 Consensus size: 58
41409275 GCCCACTGAT
*
41409285 CGATCTCGCACACATAGTGCTTGGTT-GAAGAACTCGCACACACAGTGCCTCAATTAC
1 CGATCTCGCACACATAGTGCTTGGTTAAAAGAACTCGCACACACAGTGCCTCAATTAC
* * *
41409342 CGATTTCGCACACATAGTGCTTGGTTAAAAGAATTTGCACACACAGTGCCTC
1 CGATCTCGCACACATAGTGCTTGGTTAAAAGAACTCGCACACACAGTGCCTC
41409394 TAATCATTCG
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 25 0.53
58 22 0.47
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (58 bp):
CGATCTCGCACACATAGTGCTTGGTTAAAAGAACTCGCACACACAGTGCCTCAATTAC
Found at i:41409649 original size:40 final size:40
Alignment explanation
Indices: 41409605--41409912 Score: 449
Period size: 40 Copynumber: 7.7 Consensus size: 40
41409595 CCAGCATGAT
* * * *
41409605 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * * *
41409645 TGCTCTTCGAGG-TTTAGCACGGATATATTACTAGCACGAA
1 TGCTCTTCG-GGACTTAGCCCGGATACATCACTAGCACGAA
* *
41409685 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACAAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
41409725 TGCTCTTCGGGACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* **
41409765 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCATTAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
41409805 TGCTCTTCGGGACTTAGCCCGGGTACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
41409845 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
41409885 TGCTCTTCGGGACTTAGCCCGGAT-CATC
1 TGCTCTTCGGGACTTAGCCCGGATACATC
41409913 GTCGAGACCT
Statistics
Matches: 241, Mismatches: 25, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
39 5 0.02
40 234 0.97
41 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:41412055 original size:37 final size:37
Alignment explanation
Indices: 41412005--41412083 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
41411995 TTATTACGAA
* * *
41412005 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
41412042 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
41412079 GTCTT
1 GTCTT
41412084 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:41412280 original size:47 final size:47
Alignment explanation
Indices: 41412202--41412413 Score: 343
Period size: 47 Copynumber: 4.5 Consensus size: 47
41412192 CCCTTCGGGA
* * * * * * *
41412202 CTTATCACATTTATACACTTTCACATCCATCACGTTGGTCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41412249 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41412296 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41412343 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41412390 CTTATCACATATATACACTTTCAC
1 CTTATCACATATATACACTTTCAC
41412414 GTATACACAC
Statistics
Matches: 154, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 154 1.00
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:41416761 original size:40 final size:40
Alignment explanation
Indices: 41416707--41416938 Score: 333
Period size: 40 Copynumber: 5.8 Consensus size: 40
41416697 CATTTGAATG
41416707 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
* * * *
41416747 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
* *
41416787 TTATCTGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
* * * *
41416827 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
*
41416867 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
41416907 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC
41416939 TTGTGGTTAT
Statistics
Matches: 166, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
39 6 0.04
40 154 0.93
41 6 0.04
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
Found at i:41416846 original size:80 final size:80
Alignment explanation
Indices: 41416708--41416939 Score: 428
Period size: 80 Copynumber: 2.9 Consensus size: 80
41416698 ATTTGAATGA
41416708 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATACCCGGGTTAAGACCCGAAGGCAA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATACCCGGGTTAAGACCCGAAGGCAA
41416773 TTGTGCTAGTGATTT
66 TTGTGCTAGTGATTT
*
41416788 TATCTGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATACCCGGGTTAAGACCCGAAGGCAA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATACCCGGGTTAAGACCCGAAGGCAA
41416853 TTGTGCTAGTGATTT
66 TTGTGCTAGTGATTT
* * *
41416868 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCAT
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATACCCGGGTTAAGACCCGAAGGCAA
41416933 TTGTGCT
66 TTGTGCT
41416940 TGTGGTTATA
Statistics
Matches: 147, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 147 1.00
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (80 bp):
TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATACCCGGGTTAAGACCCGAAGGCAA
TTGTGCTAGTGATTT
Found at i:41438883 original size:17 final size:17
Alignment explanation
Indices: 41438861--41438893 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41438851 GTTAGTGAAC
*
41438861 ATTGTCGTTGCATTTTT
1 ATTGTCATTGCATTTTT
41438878 ATTGTCATTGCATTTT
1 ATTGTCATTGCATTTT
41438894 AATGTTAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.58
Consensus pattern (17 bp):
ATTGTCATTGCATTTTT
Found at i:41439234 original size:81 final size:81
Alignment explanation
Indices: 41439099--41439259 Score: 322
Period size: 81 Copynumber: 2.0 Consensus size: 81
41439089 TGAACGAGTT
41439099 GCATAAATTTGACTGAATGTTGTATCTTCAATTCTTTGATGAATGATTTAGGTTCCATTAGTAAT
1 GCATAAATTTGACTGAATGTTGTATCTTCAATTCTTTGATGAATGATTTAGGTTCCATTAGTAAT
41439164 GGATGACAAGTAGCAA
66 GGATGACAAGTAGCAA
41439180 GCATAAATTTGACTGAATGTTGTATCTTCAATTCTTTGATGAATGATTTAGGTTCCATTAGTAAT
1 GCATAAATTTGACTGAATGTTGTATCTTCAATTCTTTGATGAATGATTTAGGTTCCATTAGTAAT
41439245 GGATGACAAGTAGCA
66 GGATGACAAGTAGCA
41439260 TTCCTTGAAT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.37
Consensus pattern (81 bp):
GCATAAATTTGACTGAATGTTGTATCTTCAATTCTTTGATGAATGATTTAGGTTCCATTAGTAAT
GGATGACAAGTAGCAA
Found at i:41457843 original size:40 final size:40
Alignment explanation
Indices: 41457791--41457883 Score: 109
Period size: 40 Copynumber: 2.3 Consensus size: 40
41457781 CTCGGTATCA
*
41457791 CACACTTAGTGCC-TCATATAGCCGAAGCTATTCCAACAT-G
1 CACACTTAGTGCCAT-ATATAGCCAAAGCTATTCCAA-ATCG
* * * *
41457831 CACACTTAGTGCCATTTGTAGCCAAAGCTATTTCGAATCG
1 CACACTTAGTGCCATATATAGCCAAAGCTATTCCAAATCG
41457871 CACACTTAGTGCC
1 CACACTTAGTGCC
41457884 GAACGATTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
39 2 0.04
40 43 0.93
41 1 0.02
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (40 bp):
CACACTTAGTGCCATATATAGCCAAAGCTATTCCAAATCG
Found at i:41464501 original size:43 final size:43
Alignment explanation
Indices: 41464448--41464602 Score: 258
Period size: 43 Copynumber: 3.6 Consensus size: 43
41464438 CCAGCATTAT
*
41464448 GCCTACTAGGCACGAAGGCCCGAATACACATCACCGGCATGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCATGAA
* *
41464491 GCCTGCTAGGCACGAAGGCTCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCATGAA
*
41464534 GCCTGCTAGGCACGAAGGCCCAAATACACATCACCGGCACT-AA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCA-TGAA
41464577 GCCTGCTAGGCACGAAGGCCCGAATA
1 GCCTGCTAGGCACGAAGGCCCGAATA
41464603 TAATACCAGC
Statistics
Matches: 104, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
43 104 1.00
ACGTcount: A:0.31, C:0.33, G:0.25, T:0.12
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCATGAA
Found at i:41464649 original size:38 final size:38
Alignment explanation
Indices: 41464595--41464678 Score: 132
Period size: 38 Copynumber: 2.2 Consensus size: 38
41464585 GGCACGAAGG
* * *
41464595 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAT
1 CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
41464633 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAA
41464671 CCCGAATA
1 CCCGAATA
41464679 CACATCAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (38 bp):
CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:41478496 original size:68 final size:67
Alignment explanation
Indices: 41478415--41478570 Score: 147
Period size: 68 Copynumber: 2.3 Consensus size: 67
41478405 CATCATGTGT
* * * * * *
41478415 ACAAGA-AGGCTACGAGATACTATATAGTAGCTAGGTCACATGTGTGA-TACGGGATGTATC-CC
1 ACAAGAGA-GCTACGAGAGA-TAAAT-GTAGCTAGGTCACATGCGTGATTAAGGGAAGGA-CACC
41478477 ATGTAG
62 ATGTAG
* *
41478483 ACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCGCATGCGTGATTCTAAGTGAAGGACACC
1 ACAAGAGAGCTAC--GAGAGATAAATGTAGCTAGGTCACATGCGTGA-T-TAAGGGAAGGACACC
41478548 ATGTAG
62 ATGTAG
41478554 ACAAGAGAGCTACGAGA
1 ACAAGAGAGCTACGAGA
41478571 CAAATCGGCT
Statistics
Matches: 73, Mismatches: 8, Indels: 13
0.78 0.09 0.14
Matches are distributed among these distances:
68 30 0.41
69 9 0.12
70 6 0.08
71 28 0.38
ACGTcount: A:0.35, C:0.16, G:0.28, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGAGAGATAAATGTAGCTAGGTCACATGCGTGATTAAGGGAAGGACACCATGT
AG
Found at i:41483956 original size:11 final size:11
Alignment explanation
Indices: 41483940--41483964 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41483930 GCCTGGACTG
41483940 ATAATCTTGCC
1 ATAATCTTGCC
41483951 ATAATCTTGCC
1 ATAATCTTGCC
41483962 ATA
1 ATA
41483965 TATGTGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (11 bp):
ATAATCTTGCC
Found at i:41498652 original size:3 final size:3
Alignment explanation
Indices: 41498644--41498687 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
41498634 GATAAGTTAA
*
41498644 AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
41498688 ACAAAACATG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:41511550 original size:40 final size:40
Alignment explanation
Indices: 41511472--41511694 Score: 299
Period size: 40 Copynumber: 5.6 Consensus size: 40
41511462 ACCCAATTAT
* * *
41511472 CTTCGGGATTTAGCCCGG--ATGAACAACCAGCACAAATGC
1 CTTCGGGACTTAACCCGGAAAT-AACAACCAGCACGAATGC
* *
41511511 CTTCGGGACTTAACCCGGAAATAGCAACCAGCATGAATGC
1 CTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATGC
*
41511551 CTTCGGGACTTAACCCAGAAATAACAACCAGCACGAATGC
1 CTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATGC
** *
41511591 CTTCATGACTTAACCCAGG-AATAACAACCGGCACGAATGC
1 CTTCGGGACTTAACCC-GGAAATAACAACCAGCACGAATGC
* *
41511631 CTTCGGGACTTAACCCGAAAATAACAACCAGCATGAATGC
1 CTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATGC
*
41511671 CTTCGGGACTTAACCCGGATATAA
1 CTTCGGGACTTAACCCGGAAATAA
41511695 TCCTCAATTT
Statistics
Matches: 161, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 17 0.11
40 141 0.88
41 3 0.02
ACGTcount: A:0.34, C:0.28, G:0.20, T:0.18
Consensus pattern (40 bp):
CTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATGC
Found at i:41520691 original size:27 final size:26
Alignment explanation
Indices: 41520629--41520838 Score: 170
Period size: 27 Copynumber: 7.8 Consensus size: 26
41520619 AAACTTACAT
**
41520629 CACATAAGGGAAAAATAGTCAGCTTAC
1 CACATAAGGGAAAAA-AGTCATTTTAC
* * *
41520656 CATATAAGGGAAAAAAGTTATATTAC
1 CACATAAGGGAAAAAAGTCATTTTAC
* * * *
41520682 CACATAAAGGCAAAACAGTTATTTTGC
1 CACAT-AAGGGAAAAAAGTCATTTTAC
* *
41520709 CACATAAGGGCAAAACAGTCATTTTGC
1 CACATAAGGG-AAAAAAGTCATTTTAC
*
41520736 CACATAAGGGCAAAACAA-TCATTTTGC
1 CACATAAGGG-AAAA-AAGTCATTTTAC
* * *
41520763 CGCATAAGGGCAAAACAGTCATTTTGC
1 CACATAAGGG-AAAAAAGTCATTTTAC
* * *
41520790 CACATAAGAGCAAAATAGTCATTTTGC
1 CACATAAG-GGAAAAAAGTCATTTTAC
*
41520817 CACATAAGGGCAAAACAGTCAT
1 CACATAAGGG-AAAAAAGTCAT
41520839 GTCATCAAAT
Statistics
Matches: 158, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
26 18 0.11
27 138 0.87
28 2 0.01
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.22
Consensus pattern (26 bp):
CACATAAGGGAAAAAAGTCATTTTAC
Found at i:41520748 original size:54 final size:54
Alignment explanation
Indices: 41520629--41520838 Score: 269
Period size: 54 Copynumber: 3.9 Consensus size: 54
41520619 AAACTTACAT
* * ** * * * * * *
41520629 CACATAAGGGAAAAATAGTCAGCTTACCATATAAGGG-AAAAAAGTTATATTAC
1 CACATAAGGGCAAAACAGTCATTTTGCCACATAAGGGCAAAACAGTCATTTTGC
* *
41520682 CACATAAAGGCAAAACAGTTATTTTGCCACATAAGGGCAAAACAGTCATTTTGC
1 CACATAAGGGCAAAACAGTCATTTTGCCACATAAGGGCAAAACAGTCATTTTGC
* *
41520736 CACATAAGGGCAAAACAATCATTTTGCCGCATAAGGGCAAAACAGTCATTTTGC
1 CACATAAGGGCAAAACAGTCATTTTGCCACATAAGGGCAAAACAGTCATTTTGC
* *
41520790 CACATAAGAGCAAAATAGTCATTTTGCCACATAAGGGCAAAACAGTCAT
1 CACATAAGGGCAAAACAGTCATTTTGCCACATAAGGGCAAAACAGTCAT
41520839 GTCATCAAAT
Statistics
Matches: 136, Mismatches: 20, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
53 29 0.21
54 107 0.79
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.22
Consensus pattern (54 bp):
CACATAAGGGCAAAACAGTCATTTTGCCACATAAGGGCAAAACAGTCATTTTGC
Found at i:41520788 original size:81 final size:81
Alignment explanation
Indices: 41520684--41520838 Score: 265
Period size: 81 Copynumber: 1.9 Consensus size: 81
41520674 TATATTACCA
* *
41520684 CATAAAGGCAAAACAGTTATTTTGCCACATAAGGGCAAAACAGTCATTTTGCCACATAAGGGCAA
1 CATAAAGGCAAAACAGTCATTTTGCCACATAAGAGCAAAACAGTCATTTTGCCACATAAGGGCAA
41520749 AACAATCATTTTGCCG
66 AACAATCATTTTGCCG
* *
41520765 CATAAGGGCAAAACAGTCATTTTGCCACATAAGAGCAAAATAGTCATTTTGCCACATAAGGGCAA
1 CATAAAGGCAAAACAGTCATTTTGCCACATAAGAGCAAAACAGTCATTTTGCCACATAAGGGCAA
*
41520830 AACAGTCAT
66 AACAATCAT
41520839 GTCATCAAAT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 69 1.00
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (81 bp):
CATAAAGGCAAAACAGTCATTTTGCCACATAAGAGCAAAACAGTCATTTTGCCACATAAGGGCAA
AACAATCATTTTGCCG
Found at i:41522852 original size:28 final size:28
Alignment explanation
Indices: 41522821--41522901 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 28
41522811 TGGTAAGTAG
*
41522821 TTGGGCCTAATGGGCCATATGAATGTGA
1 TTGGGCCTAATGGGCCATATGAATGAGA
* * * *
41522849 TTGGGCCTGATAGGCCATGTGAACGAGA
1 TTGGGCCTAATGGGCCATATGAATGAGA
* *
41522877 TTGGGCCTAAAAGGGCCAAATGAAT
1 TTGGGCCT-AATGGGCCATATGAAT
41522902 AAGTGTAGAT
Statistics
Matches: 41, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
28 31 0.76
29 10 0.24
ACGTcount: A:0.28, C:0.16, G:0.32, T:0.23
Consensus pattern (28 bp):
TTGGGCCTAATGGGCCATATGAATGAGA
Found at i:41523231 original size:27 final size:27
Alignment explanation
Indices: 41523213--41523325 Score: 165
Period size: 27 Copynumber: 4.2 Consensus size: 27
41523203 ATTGCTGAAA
41523213 TACCCCCAATTTGTAAAATTATCGAAG
1 TACCCCCAATTTGTAAAATTATCGAAG
41523240 TATCCCCC-ATTTGTAAAATTATCGAAG
1 TA-CCCCCAATTTGTAAAATTATCGAAG
* *
41523267 TACCCTCAGTTTGTAAAATTATCGAAG
1 TACCCCCAATTTGTAAAATTATCGAAG
* * *
41523294 TACCCCCAGTTTGTAAAATTATAGAAA
1 TACCCCCAATTTGTAAAATTATCGAAG
41523321 TACCC
1 TACCC
41523326 TTGTAGTGTA
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
26 4 0.05
27 70 0.89
28 5 0.06
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (27 bp):
TACCCCCAATTTGTAAAATTATCGAAG
Found at i:41523280 original size:54 final size:54
Alignment explanation
Indices: 41523209--41523326 Score: 184
Period size: 54 Copynumber: 2.2 Consensus size: 54
41523199 ATAAATTGCT
* *
41523209 GAAATACCCCCAATTTGTAAAATTATCGAAGTATCCCCCA-TTTGTAAAATTATC
1 GAAATACCCTCAATTTGTAAAATTATCGAAGTA-CCCCCAGTTTGTAAAATTATA
* *
41523263 GAAGTACCCTCAGTTTGTAAAATTATCGAAGTACCCCCAGTTTGTAAAATTATA
1 GAAATACCCTCAATTTGTAAAATTATCGAAGTACCCCCAGTTTGTAAAATTATA
41523317 GAAATACCCT
1 GAAATACCCT
41523327 TGTAGTGTAT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
53 6 0.10
54 52 0.90
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (54 bp):
GAAATACCCTCAATTTGTAAAATTATCGAAGTACCCCCAGTTTGTAAAATTATA
Found at i:41523335 original size:27 final size:27
Alignment explanation
Indices: 41523305--41523393 Score: 124
Period size: 27 Copynumber: 3.3 Consensus size: 27
41523295 ACCCCCAGTT
**
41523305 TGTAAAATTATAGAAATACCCTTGTAG
1 TGTAAAATTACCGAAATACCCTTGTAG
*
41523332 TGTATAATTACCGAAATACCCTTGTAG
1 TGTAAAATTACCGAAATACCCTTGTAG
* *
41523359 TGTAAAATGACCGACATACCCTTGTAG
1 TGTAAAATTACCGAAATACCCTTGTAG
*
41523386 GGTAAAAT
1 TGTAAAAT
41523394 GACTATTTTG
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (27 bp):
TGTAAAATTACCGAAATACCCTTGTAG
Found at i:41523341 original size:54 final size:53
Alignment explanation
Indices: 41523209--41523352 Score: 164
Period size: 54 Copynumber: 2.7 Consensus size: 53
41523199 ATAAATTGCT
* * * *
41523209 GAAATACCCCCAATTTGTAAAATTATCGAAGTATCCCCCATTTGTAAAATTATC
1 GAAATACCCTCAGTGTGTAAAATTATCGAAGTA-CCCCCATTTGTAAAATTATA
* *
41523263 GAAGTACCCTCAGTTTGTAAAATTATCGAAGTACCCCCAGTTTGTAAAATTATA
1 GAAATACCCTCAGTGTGTAAAATTATCGAAGTACCCCCA-TTTGTAAAATTATA
* * * *
41523317 GAAATACCCT-TGTAGTGTATAATTACCGAAATACCC
1 GAAATACCCTCAGT-GTGTAAAATTATCGAAGTACCC
41523353 TTGTAGTGTA
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
53 8 0.10
54 70 0.90
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (53 bp):
GAAATACCCTCAGTGTGTAAAATTATCGAAGTACCCCCATTTGTAAAATTATA
Found at i:41528355 original size:14 final size:14
Alignment explanation
Indices: 41528336--41528362 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41528326 ACAGCGGTCA
41528336 CACGCCCATGTGGT
1 CACGCCCATGTGGT
41528350 CACGCCCATGTGG
1 CACGCCCATGTGG
41528363 GCAGACCGTG
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:0.15, C:0.37, G:0.30, T:0.19
Consensus pattern (14 bp):
CACGCCCATGTGGT
Found at i:41530629 original size:40 final size:43
Alignment explanation
Indices: 41530580--41530679 Score: 134
Period size: 40 Copynumber: 2.4 Consensus size: 43
41530570 CAATGGTATT
* *
41530580 TGGCACTAAGTGTGCGATTCA-AAATAGCTTCAGCTATTTG-A
1 TGGCACTAAGTGTGCGATACAGAAATAGCTTCAGCTAATTGAA
* *
41530621 -GGCACTAAGTGTGCGATACAGAGATAGCTTCAGTTAATTGAAA
1 TGGCACTAAGTGTGCGATACAGAAATAGCTTCAGCTAATTG-AA
41530664 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
41530680 GATGTTAAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
40 19 0.37
41 16 0.31
43 1 0.02
44 15 0.29
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (43 bp):
TGGCACTAAGTGTGCGATACAGAAATAGCTTCAGCTAATTGAA
Found at i:41536531 original size:105 final size:105
Alignment explanation
Indices: 41536386--41536595 Score: 296
Period size: 105 Copynumber: 2.0 Consensus size: 105
41536376 AAGTGTTAAA
* * *
41536386 TGTAAGACCATAGCTGGGCTATGGCATTTTAGTGAAAAGACCATAACTAGGTTATGGCACTGTGA
1 TGTAAGACCATAGCTGGGCTATGGCATCTGAGTGAAAAGACCATAACTAGGTTATGGCACTATGA
* *
41536451 ACGTAAGACCATGGTTGGACCATGACAGTATATGTATAAG
66 ACGTAAGACCATGGTAGGACCATGACAATATATGTATAAG
* *
41536491 TGTAAGACCATAGCTGGGCTATGGCATCCTGA-TGATAAGACTATAACTAGGTTATGGCACTATG
1 TGTAAGACCATAGCTGGGCTATGGCAT-CTGAGTGAAAAGACCATAACTAGGTTATGGCACTATG
** * * *
41536555 AGTGTAAGACCATGGTAGGGCCATGGCAATATATGTGTAAG
65 AACGTAAGACCATGGTAGGACCATGACAATATATGTATAAG
41536596 ACCATAGTTG
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
105 90 0.98
106 2 0.02
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (105 bp):
TGTAAGACCATAGCTGGGCTATGGCATCTGAGTGAAAAGACCATAACTAGGTTATGGCACTATGA
ACGTAAGACCATGGTAGGACCATGACAATATATGTATAAG
Found at i:41549229 original size:14 final size:15
Alignment explanation
Indices: 41549197--41549231 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
41549187 GTGTGCCACC
41549197 TTTTAAAAAACCTAA
1 TTTTAAAAAACCTAA
*
41549212 TTTTAGAAAACC-AA
1 TTTTAAAAAACCTAA
41549226 TTTTAA
1 TTTTAA
41549232 TCTTTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.37
Consensus pattern (15 bp):
TTTTAAAAAACCTAA
Found at i:41550172 original size:27 final size:26
Alignment explanation
Indices: 41550124--41550183 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
41550114 GCGAGGTTGC
*
41550124 CAGATATTGTGACAAAGTCACCAGATA
1 CAGATATTGTGACAAAGCCACCAGA-A
* * *
41550151 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACAAAGCCACCAGAA
*
41550177 CAAATAT
1 CAGATAT
41550184 ATATATGTGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACAAAGCCACCAGAA
Found at i:41553042 original size:31 final size:31
Alignment explanation
Indices: 41552982--41553043 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
41552972 GATCTTTGAG
** *
41552982 ATTGTGCATAGATTACGGACAACTGAACAAT
1 ATTGTGCATAGATTACAAACAACTAAACAAT
*
41553013 ATTGTGCATAGATTACAAACAGCTAAACAAT
1 ATTGTGCATAGATTACAAACAACTAAACAAT
41553044 GTCACAATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (31 bp):
ATTGTGCATAGATTACAAACAACTAAACAAT
Found at i:41556384 original size:49 final size:47
Alignment explanation
Indices: 41556327--41556501 Score: 171
Period size: 49 Copynumber: 3.7 Consensus size: 47
41556317 TGATGTGTGT
*
41556327 GCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCAAGATATGCAA
1 GCTAGTGTAAGACCTATCTGGGACATGGCATCGG-CTC-AGATATGCAA
* * *
41556376 GCTAGTGTAAGACCTATCTGGGACATGGCATCGGCTTGAGGTGTG---
1 GCTAGTGTAAGACCTATCTGGGACATGGCATCGGC-TCAGATATGCAA
* * * *
41556421 TCT-GTGTAAAACCTATCTGGGACATGGCATCGACACAGATGA-GCGAGA
1 GCTAGTGTAAGACCTATCTGGGACATGGCATCGGCTCAGAT-ATGC-A-A
* *
41556469 GCCAGTGTAAGACCTGTCTGGGACATGGCATCG
1 GCTAGTGTAAGACCTATCTGGGACATGGCATCG
41556502 ACTTAGGTGT
Statistics
Matches: 103, Mismatches: 15, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
43 4 0.04
44 29 0.28
45 2 0.02
48 7 0.07
49 61 0.59
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (47 bp):
GCTAGTGTAAGACCTATCTGGGACATGGCATCGGCTCAGATATGCAA
Found at i:41556482 original size:93 final size:94
Alignment explanation
Indices: 41556321--41556512 Score: 250
Period size: 93 Copynumber: 2.1 Consensus size: 94
41556311 TTTGGGTGAT
* * * * *
41556321 GTGTGTGCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCAAGATATGCAAGCTAGTGTAA
1 GTGTGTGCTAGTGTAAAACCTATCTGGGACATGGCATCGGACACAAGATATGCAAGCCAGTGTAA
*
41556386 GACCTATCTGGGACATGGCATCGGCTTGAG
66 GACCTATCTGGGACATGGCATCGACTT-AG
41556416 GTGTGT-CT-GTGTAAAACCTATCTGGGACATGGCATC-GACAC-AGATGA-GCGAGAGCCAGTG
1 GTGTGTGCTAGTGTAAAACCTATCTGGGACATGGCATCGGACACAAGAT-ATGC-A-AGCCAGTG
*
41556476 TAAGACCTGTCTGGGACATGGCATCGACTTAG
63 TAAGACCTATCTGGGACATGGCATCGACTTAG
41556508 GTGTG
1 GTGTG
41556513 AGAGCCAGTG
Statistics
Matches: 87, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
91 6 0.07
92 12 0.14
93 61 0.70
94 2 0.02
95 6 0.07
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (94 bp):
GTGTGTGCTAGTGTAAAACCTATCTGGGACATGGCATCGGACACAAGATATGCAAGCCAGTGTAA
GACCTATCTGGGACATGGCATCGACTTAG
Found at i:41556502 original size:49 final size:49
Alignment explanation
Indices: 41556330--41556552 Score: 169
Period size: 49 Copynumber: 4.7 Consensus size: 49
41556320 TGTGTGTGCT
* * *
41556330 AGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCAAGAT-ATGC-A-AGCT
1 AGTGTAAGACCTGTCTGGGACATGGCATC-GACAC-AGATGA-GCGAGAGCC
* * * * * *
41556379 AGTGTAAGACCTATCTGGGACATGGCATCG--GC--TTGAG-GTGTGTC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACACAGATGAGCGAGAGCC
* * *
41556423 TGTGTAAAACCTATCTGGGACATGGCATCGACACAGATGAGCGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACACAGATGAGCGAGAGCC
** * *
41556472 AGTGTAAGACCTGTCTGGGACATGGCATCGACTTAG--GTGTGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACACAGATGAGCGAGAGCC
* * *
41556519 AGTGTAAGACCATGTTTGGAACATGGCTTCGACA
1 AGTGTAAGACC-TGTCTGGGACATGGCATCGACA
41556553 TCGTACCCTA
Statistics
Matches: 140, Mismatches: 25, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
43 2 0.01
44 30 0.21
46 2 0.01
47 20 0.14
48 23 0.16
49 63 0.45
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.23
Consensus pattern (49 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCGACACAGATGAGCGAGAGCC
Found at i:41559430 original size:64 final size:64
Alignment explanation
Indices: 41559350--41559533 Score: 176
Period size: 67 Copynumber: 2.8 Consensus size: 64
41559340 AGACACTATG
* * *
41559350 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGAGAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
41559414 ATGTAGCTAGGTCGCATGCGTGGCT-CCAGGTGAAGGACACCATGTAGACAGGAGAGCTACGAGA
1 ATGTAGCTAGGTCGCATGGGT-GATACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGA
41559478 TAA
62 TAA
* * * * *
41559481 AT-TGGCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
41559534 CGAACTCTAT
Statistics
Matches: 95, Mismatches: 19, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
62 1 0.01
63 18 0.19
64 23 0.24
65 4 0.04
66 19 0.20
67 30 0.32
ACGTcount: A:0.29, C:0.17, G:0.32, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Done.