Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 102 of 378
Found at i:27947070 original size:93 final size:93
Alignment explanation
Indices: 27946958--27947128 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
27946948 GCCCATAAGT
* *
27946958 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
27947023 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
27947051 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
27947116 CGAGTTCGGATGC
66 CGAGCTCGGATGC
27947129 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:27947125 original size:46 final size:46
Alignment explanation
Indices: 27946950--27947125 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
27946940 TGTAACCCGC
* *
27946950 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
27946996 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
27947042 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
27947089 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
27947126 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 70 0.63
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:27952970 original size:40 final size:40
Alignment explanation
Indices: 27952911--27953091 Score: 267
Period size: 40 Copynumber: 4.5 Consensus size: 40
27952901 CATTTGAATG
*
27952911 ATATCCGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
27952951 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
*
27952991 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
* * * * * *
27953031 ATGTCCGGGTTAAGACCCGAAGGCAATTGGGCGTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
27953071 ATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGA-CCCGAAG
27953092 AAACTTGGGT
Statistics
Matches: 129, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
38 1 0.01
39 12 0.09
40 116 0.90
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
Found at i:27960961 original size:40 final size:40
Alignment explanation
Indices: 27960902--27961082 Score: 267
Period size: 40 Copynumber: 4.5 Consensus size: 40
27960892 CATTTGAATG
*
27960902 ATATCCGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
*
27960942 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
*
27960982 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
* * * * *
27961022 ATGTCCGGGCTAAGACCCGAAGGCAATTGGGCGTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
27961062 ATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGA-CCCGAAG
27961083 AAACTTGGGT
Statistics
Matches: 129, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
38 1 0.01
39 13 0.10
40 115 0.89
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
Found at i:27970555 original size:44 final size:44
Alignment explanation
Indices: 27970441--27970558 Score: 148
Period size: 44 Copynumber: 2.7 Consensus size: 44
27970431 GCTATAAATA
* * *
27970441 GCACTAAGTGTGCGAAAT-GGTATAGCTTCGATTAATTTTGATG
1 GCACTAAGTGTGCGGAATCGATATAGCTTCGATTAATTGTGATG
* * * *
27970484 GCACTATGTGTGCGGTACCGAGATAGCTTCGATTAATTGTGATG
1 GCACTAAGTGTGCGGAATCGATATAGCTTCGATTAATTGTGATG
* *
27970528 GCACTAAGTGTGCGGAATCGTTCTAGCTTCG
1 GCACTAAGTGTGCGGAATCGATATAGCTTCG
27970559 GCTAAACCTT
Statistics
Matches: 61, Mismatches: 13, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
43 14 0.23
44 47 0.77
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (44 bp):
GCACTAAGTGTGCGGAATCGATATAGCTTCGATTAATTGTGATG
Found at i:27976894 original size:32 final size:32
Alignment explanation
Indices: 27976853--27976913 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
27976843 TCGATGTTGC
27976853 AGGTGAATTAAATGAACTAGTATTTCCTTTGT
1 AGGTGAATTAAATGAACTAGTATTTCCTTTGT
27976885 AGGTGAATTAAATGAACTAGTATTTCCTT
1 AGGTGAATTAAATGAACTAGTATTTCCTT
27976914 CCCAACGGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (32 bp):
AGGTGAATTAAATGAACTAGTATTTCCTTTGT
Found at i:27978804 original size:46 final size:46
Alignment explanation
Indices: 27978754--27978864 Score: 179
Period size: 46 Copynumber: 2.4 Consensus size: 46
27978744 GCAAAACCAA
*
27978754 TTATGAACTTGAAGAGAAAGTAAAAAAATAAAATTCAAGAAATTAT
1 TTATGAACTTGAAGAGAAAGTAAAAAAAAAAAATTCAAGAAATTAT
27978800 TTATGAACTTGAAGAGAAAGTAAAAAAAAAAAATTCAAGAAATTAT
1 TTATGAACTTGAAGAGAAAGTAAAAAAAAAAAATTCAAGAAATTAT
* *
27978846 TAATG-ACTTTGAAAAGAAA
1 TTATGAAC-TTGAAGAGAAA
27978865 AATTTATACT
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
45 2 0.03
46 59 0.97
ACGTcount: A:0.57, C:0.05, G:0.14, T:0.25
Consensus pattern (46 bp):
TTATGAACTTGAAGAGAAAGTAAAAAAAAAAAATTCAAGAAATTAT
Found at i:27979555 original size:31 final size:33
Alignment explanation
Indices: 27979505--27979569 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
27979495 ATCTTTATGC
*
27979505 CTTAAATTGAAAATGACTTTTA-TATAGGGGAG
1 CTTAAATTGAAAATAACTTTTATTATAGGGGAG
*
27979537 CTTAAATT-AAAATAACTTTTATTATGGGGGAG
1 CTTAAATTGAAAATAACTTTTATTATAGGGGAG
27979569 C
1 C
27979570 AATCTATTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 12 0.40
32 18 0.60
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.35
Consensus pattern (33 bp):
CTTAAATTGAAAATAACTTTTATTATAGGGGAG
Found at i:27988809 original size:40 final size:40
Alignment explanation
Indices: 27988765--27988983 Score: 233
Period size: 40 Copynumber: 5.5 Consensus size: 40
27988755 GCTCGATTGT
* * * * *
27988765 CTTCGGGACGTT-GCCCGGTTATAGTGATTCGCACAATTGC
1 CTTCGGGAC-TTAACCCGGTTTTAGTAACTCGCACAAATGC
* * * *
27988805 CTTCGGGAATTAGCCCGGATTTAGTAACTCGCACGAATGC
1 CTTCGGGACTTAACCCGGTTTTAGTAACTCGCACAAATGC
*
27988845 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGACTTAACCCGGTTTTAGTAACTCGCACAAATGC
* *
27988885 CTTTGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGACTTAACCCGGTTTTAGTAACTCGCACAAATGC
* * * * * * *
27988925 CTTCGGGAATTGACCTGGATTTAGTCACTTAGCACAAAAGC
1 CTTCGGGACTTAACCCGGTTTTAGTAAC-TCGCACAAATGC
*
27988966 CTTCGGGACTTAGCCCGG
1 CTTCGGGACTTAACCCGG
27988984 ACACCATTCG
Statistics
Matches: 151, Mismatches: 26, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
39 2 0.01
40 125 0.83
41 24 0.16
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.27
Consensus pattern (40 bp):
CTTCGGGACTTAACCCGGTTTTAGTAACTCGCACAAATGC
Found at i:27993798 original size:47 final size:47
Alignment explanation
Indices: 27993744--27994151 Score: 622
Period size: 47 Copynumber: 8.7 Consensus size: 47
27993734 GATTTTATGC
* * * *
27993744 GATGAATGTGAATGTGTATGTATGAGATAAGGCCGAATGGTCGATGT
1 GATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGT
*
27993791 GATGAATGTGAAAGTGTGTATATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAA--GTGTATATATGTGATAAGGCCGAATGGCCGATGT
* *
27993840 GATAAAT-TGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGT
*
27993886 GATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGT
*
27993933 GATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGT
*
27993980 GATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGT
* *
27994027 GATGAATGTGAAGGTGTATATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGT
* * *
27994074 GATGAATGTGAAAGTGTATATATGTGAT-AGGACCGAGTGGCCAACGT
1 GATGAATGTGAAAGTGTATATATGTGATAAGG-CCGAATGGCCGATGT
* *
27994121 GATGGATGTGAAAGTGTATAAATGTGATAAG
1 GATGAATGTGAAAGTGTATATATGTGATAAG
27994152 TCCCGAAGGG
Statistics
Matches: 337, Mismatches: 19, Indels: 9
0.92 0.05 0.02
Matches are distributed among these distances:
46 43 0.13
47 251 0.74
48 7 0.02
49 36 0.11
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.29
Consensus pattern (47 bp):
GATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGT
Found at i:27997578 original size:20 final size:20
Alignment explanation
Indices: 27997553--27997604 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
27997543 GTGTGATTAC
27997553 ACACACCCGTGTGGCTTGGA
1 ACACACCCGTGTGGCTTGGA
*
27997573 ACACACCCGTGTGGCTTGGG
1 ACACACCCGTGTGGCTTGGA
27997593 ACACACCCGTGT
1 ACACACCCGTGT
27997605 CCTTAGCCCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.19, C:0.33, G:0.29, T:0.19
Consensus pattern (20 bp):
ACACACCCGTGTGGCTTGGA
Found at i:28014222 original size:63 final size:64
Alignment explanation
Indices: 28014142--28014323 Score: 210
Period size: 65 Copynumber: 2.8 Consensus size: 64
28014132 AGACATTATG
* *
28014142 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACG-GATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
28014205 ATGTAGCTAGGTCGCATGCGTGGTTCCAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGATA
1 ATGTAGCTAGGTCGCATGGGTGGTACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGATA
28014270 A
64 A
* * *
28014271 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC
28014324 CGAACTCTAT
Statistics
Matches: 99, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
62 1 0.01
63 43 0.43
64 3 0.03
65 45 0.45
66 7 0.07
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:28019871 original size:40 final size:40
Alignment explanation
Indices: 28019810--28020027 Score: 332
Period size: 40 Copynumber: 5.5 Consensus size: 40
28019800 TGGATGATAA
28019810 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
28019850 CCGAGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
28019890 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
28019930 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
28019970 CCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* * *
28020010 -CTGGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
28020028 TACTTGGCTT
Statistics
Matches: 165, Mismatches: 12, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
39 16 0.10
40 149 0.90
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:28025171 original size:40 final size:40
Alignment explanation
Indices: 28025063--28025232 Score: 225
Period size: 40 Copynumber: 4.2 Consensus size: 40
28025053 CGGGATTTAA
* * * * *
28025063 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
28025103 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
28025143 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
28025183 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
28025223 CCGGATATAT
1 CCGGATATAT
28025233 TTCCAATGTT
Statistics
Matches: 113, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
39 1 0.01
40 112 0.99
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:28031466 original size:40 final size:40
Alignment explanation
Indices: 28031421--28031587 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
28031411 CGGAATATAA
28031421 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
28031461 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
28031501 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
28031541 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
28031580 CCGGATAT
1 CCGGATAT
28031588 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:28031571 original size:80 final size:79
Alignment explanation
Indices: 28031421--28031587 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
28031411 CGGAATATAA
* *
28031421 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
28031486 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
28031501 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
28031563 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
28031580 CCGGATAT
1 CCGGATAT
28031588 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:28032434 original size:17 final size:19
Alignment explanation
Indices: 28032411--28032456 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
28032401 AAGAAGCATG
28032411 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
28032429 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
28032447 AATCATGCTC
1 AATCATGCTC
28032457 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:28039429 original size:40 final size:40
Alignment explanation
Indices: 28039384--28039550 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
28039374 CGGAATATAA
28039384 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
28039424 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
28039464 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
28039504 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
28039543 CCGGATAT
1 CCGGATAT
28039551 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:28039534 original size:80 final size:79
Alignment explanation
Indices: 28039384--28039550 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
28039374 CGGAATATAA
* *
28039384 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
28039449 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
28039464 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
28039526 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
28039543 CCGGATAT
1 CCGGATAT
28039551 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:28040399 original size:17 final size:19
Alignment explanation
Indices: 28040376--28040421 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
28040366 AAGAAGCATG
28040376 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
28040394 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
28040412 AATCATGCTC
1 AATCATGCTC
28040422 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:28045871 original size:25 final size:25
Alignment explanation
Indices: 28045842--28045889 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28045832 TTATAATATG
* * *
28045842 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
28045867 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
28045890 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:28045958 original size:20 final size:20
Alignment explanation
Indices: 28045933--28045991 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
28045923 TAAATATGGT
28045933 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
* *
28045953 ATGTATGCTATGCACATGAT
1 ATGTATGATATGCACATGAA
28045973 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
28045992 GGTAATCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:28046069 original size:24 final size:24
Alignment explanation
Indices: 28046042--28046183 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
28046032 GAGGAAGTGA
28046042 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
28046066 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
28046090 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
28046113 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* *
28046137 GAAAGGGCTT-TGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
28046160 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
28046184 ATGATAAAGC
Statistics
Matches: 111, Mismatches: 3, Indels: 7
0.92 0.02 0.06
Matches are distributed among these distances:
23 41 0.37
24 62 0.56
25 8 0.07
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:28046180 original size:71 final size:71
Alignment explanation
Indices: 28046042--28046184 Score: 218
Period size: 71 Copynumber: 2.0 Consensus size: 71
28046032 GAGGAAGTGA
*
28046042 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTAGGCCCC
28046107 AGTTAT
66 AGTTAT
** *
28046113 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTT-TGCCCCAGTTATTAAAAGAGGC-TAGGCCT
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTAGGCC-
28046176 CCAGTTAT
64 CCAGTTAT
28046184 A
1 A
28046185 TGATAAAGCA
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
70 22 0.33
71 44 0.67
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (71 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTAGGCCCC
AGTTAT
Found at i:28046410 original size:31 final size:31
Alignment explanation
Indices: 28046375--28046438 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
28046365 CGTTTACAGT
28046375 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
28046406 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
28046437 AA
1 AA
28046439 TATGAAAAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:28050933 original size:25 final size:25
Alignment explanation
Indices: 28050904--28050951 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28050894 TTATAATATG
* * *
28050904 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
28050929 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
28050952 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:28051020 original size:20 final size:20
Alignment explanation
Indices: 28050995--28051053 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
28050985 TAAATATGGT
28050995 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
* *
28051015 ATGTATGCTATGCACATGAT
1 ATGTATGATATGCACATGAA
28051035 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
28051054 GGTAATCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:28051172 original size:23 final size:24
Alignment explanation
Indices: 28051104--28051244 Score: 200
Period size: 24 Copynumber: 6.0 Consensus size: 24
28051094 GAGGAAGTGA
28051104 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
28051128 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
28051152 AAAAGGGCTTATG-CCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
28051174 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* *
28051198 GAAAGGGCTT-TGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
28051221 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
28051245 ATGATAAAGC
Statistics
Matches: 109, Mismatches: 3, Indels: 9
0.90 0.02 0.07
Matches are distributed among these distances:
22 13 0.12
23 36 0.33
24 52 0.48
25 8 0.07
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:28051189 original size:46 final size:47
Alignment explanation
Indices: 28051104--28051244 Score: 198
Period size: 46 Copynumber: 3.0 Consensus size: 47
28051094 GAGGAAGTGA
28051104 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
28051152 AAAAGGGCTTATG-CCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* *
28051198 GAAAGGGCTT-TGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
28051245 ATGATAAAGC
Statistics
Matches: 86, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
45 2 0.02
46 40 0.47
47 20 0.23
48 24 0.28
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:28051471 original size:31 final size:31
Alignment explanation
Indices: 28051436--28051499 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
28051426 CGTTTACAGT
28051436 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
28051467 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
28051498 AA
1 AA
28051500 TATGAAAAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:28056763 original size:46 final size:47
Alignment explanation
Indices: 28056595--28056765 Score: 131
Period size: 46 Copynumber: 3.7 Consensus size: 47
28056585 AACCCGCCCC
* * * *
28056595 TAAGTGAACTCAGAATCAACTCAACGAGCTCG-GTCATTCGCATCAAG
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGAGCCATTCGCATC-CG
* * * *
28056642 -AAGTGAACTCGGACTTAACTCAATGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCAGACTCAACTCAACGAGTTC-GA-GCC-A-TTCGCATCCG
* * * *
28056689 TCA-CGAACTCAGACTTAACTCAATGAGTTCGAG-CATTCGCATCCG
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGAGCCATTCGCATCCG
*
28056734 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCG
28056766 GATGCTCAAC
Statistics
Matches: 97, Mismatches: 17, Indels: 21
0.72 0.13 0.16
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 3 0.03
46 51 0.53
47 26 0.27
48 1 0.01
49 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (47 bp):
TAAGTGAACTCAGACTCAACTCAACGAGTTCGAGCCATTCGCATCCG
Found at i:28056763 original size:93 final size:93
Alignment explanation
Indices: 28056600--28056770 Score: 247
Period size: 93 Copynumber: 1.8 Consensus size: 93
28056590 GCCCCTAAGT
*
28056600 GAACTCAGAATCAACTCAACGAGCTCGGTCATTCGCATCAAGAAGTGAACTCGGACTTAACTCAA
1 GAACTCAGAATCAACTCAACGAGCTCGGTCATTCGCATCAAGAAGTGAACTCGGACTCAACTCAA
*
28056665 TGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * * * *
28056693 GAACTCAGACTTAACTCAATGAGTTCGAG-CATTCGCATC-CGTAAGTGAACTCGGACTCAACTC
1 GAACTCAGAATCAACTCAACGAGCTCG-GTCATTCGCATCAAG-AAGTGAACTCGGACTCAACTC
28056756 AACGAGTTCGGATGC
64 AACGAGTTCGGATGC
28056771 TCAACCATCC
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
92 1 0.01
93 67 0.97
94 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCAGAATCAACTCAACGAGCTCGGTCATTCGCATCAAGAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:28060061 original size:23 final size:23
Alignment explanation
Indices: 28060035--28060146 Score: 93
Period size: 23 Copynumber: 4.8 Consensus size: 23
28060025 AGCTTGTAAG
*
28060035 AGCTTACTGTTTTAGCTCATTAA
1 AGCTTACTGTTTCAGCTCATTAA
** * * **
28060058 AGCTTGTTGTTTTAGCTTATTGG
1 AGCTTACTGTTTCAGCTCATTAA
*
28060081 AGCTTACTG-TTCAGCTCGA-TAG
1 AGCTTACTGTTTCAGCTC-ATTAA
* *
28060103 AGCTTACCGTTTCAGCTCAATAA
1 AGCTTACTGTTTCAGCTCATTAA
28060126 AGCTTACTGTTCATCAGCTCA
1 AGCTTACTGTT--TCAGCTCA
28060147 GGAACAGCTT
Statistics
Matches: 71, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
22 17 0.24
23 46 0.65
25 8 0.11
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (23 bp):
AGCTTACTGTTTCAGCTCATTAA
Found at i:28065772 original size:49 final size:48
Alignment explanation
Indices: 28065719--28065888 Score: 162
Period size: 49 Copynumber: 3.5 Consensus size: 48
28065709 AGTCGATGAT
28065719 ATGTCCCAGACAGGTCTTACACTAACTTTCATATATCGAGGCCGATGTC
1 ATGTCCCAGACAGGTCTTACACTAACTTTCATATATCGAGGCCGATG-C
* * ** * * * *
28065768 ATGTCCCAGACAGGTCTTGCATTGGCTCTCATCTATCGATGTCGATGCC
1 ATGTCCCAGACAGGTCTTACACTAACTTTCATATATCGAGGCCGATG-C
* * * * **
28065817 ATGTCCTAGACAGGTCTTACACTAGA-TTGCATATCTCGTGGCTAATGC
1 ATGTCCCAGACAGGTCTTACACTA-ACTTTCATATATCGAGGCCGATGC
* *
28065865 ATGTCCCAGATATGTCTTACACTA
1 ATGTCCCAGACAGGTCTTACACTA
28065889 GCTCTCATCT
Statistics
Matches: 94, Mismatches: 26, Indels: 3
0.76 0.21 0.02
Matches are distributed among these distances:
48 22 0.23
49 72 0.77
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (48 bp):
ATGTCCCAGACAGGTCTTACACTAACTTTCATATATCGAGGCCGATGC
Found at i:28065828 original size:98 final size:97
Alignment explanation
Indices: 28065664--28065937 Score: 281
Period size: 98 Copynumber: 2.8 Consensus size: 97
28065654 GGTACGATGT
* * * ** *
28065664 CGATGCCATGTTCCAAACATGGTCTTACATTGGCTCACA-C-ATCTAA-GTCGATGATATGTCCC
1 CGATG-CATGTCCCAGACA-GGTCTTACATTGGCTCTCATCTATC-AATGTCGATGCCATGTCCT
*
28065726 AGACAGGTCTTACACTA-ACTTTCATATATCGAGGC
63 AGACAGGTCTTACACTAGA-TTGCATATATCGAGGC
* *
28065761 CGATGTCATGTCCCAGACAGGTCTTGCATTGGCTCTCATCTATCGATGTCGATGCCATGTCCTAG
1 CGATG-CATGTCCCAGACAGGTCTTACATTGGCTCTCATCTATCAATGTCGATGCCATGTCCTAG
* *
28065826 ACAGGTCTTACACTAGATTGCATATCTCGTGGC
65 ACAGGTCTTACACTAGATTGCATATATCGAGGC
** * * * * *
28065859 TAATGCATGTCCCAGATATGTCTTACACTAGCTCTCATCT-T-AATATCGATGCCATGTCCTTAG
1 CGATGCATGTCCCAGACAGGTCTTACATTGGCTCTCATCTATCAATGTCGATGCCATGTCC-TAG
*
28065922 ACATGTCTTACACTAG
65 ACAGGTCTTACACTAG
28065938 CACACATCCA
Statistics
Matches: 150, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
95 16 0.11
96 36 0.24
97 48 0.32
98 49 0.33
99 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (97 bp):
CGATGCATGTCCCAGACAGGTCTTACATTGGCTCTCATCTATCAATGTCGATGCCATGTCCTAGA
CAGGTCTTACACTAGATTGCATATATCGAGGC
Found at i:28070423 original size:37 final size:36
Alignment explanation
Indices: 28070355--28070451 Score: 97
Period size: 37 Copynumber: 2.6 Consensus size: 36
28070345 TAATTATTCC
* *
28070355 AAAAATAATATTATTTTAATAGTTTAATATTAAATT
1 AAAATTAATATTATCTTAATAGTTTAATATTAAATT
* * *
28070391 AAATTTAATACTTATCTTAATAGTATT-TTATTAATTT
1 AAAATTAATA-TTATCTTAATAGT-TTAATATTAAATT
28070428 AAAATTAAAGTGATTATCTTAATA
1 AAAATT-AA-T-ATTATCTTAATA
28070452 TTAAATTCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
36 8 0.16
37 25 0.50
38 4 0.08
39 12 0.24
40 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.47
Consensus pattern (36 bp):
AAAATTAATATTATCTTAATAGTTTAATATTAAATT
Found at i:28071808 original size:17 final size:18
Alignment explanation
Indices: 28071766--28071814 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
28071756 AGTTGAAAAG
28071766 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
28071785 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
28071802 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
28071815 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:28072703 original size:40 final size:40
Alignment explanation
Indices: 28072637--28072803 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
28072627 AAATTGAATG
* * *
28072637 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
28072676 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
28072716 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
28072756 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
28072796 ATATCCGG
1 ATATCCGG
28072804 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:28079810 original size:17 final size:18
Alignment explanation
Indices: 28079768--28079816 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
28079758 AGTTGAAAAG
28079768 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
28079787 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
28079804 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
28079817 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:28080761 original size:39 final size:39
Alignment explanation
Indices: 28080638--28080803 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 39
28080628 AAATTGAATG
* * **
28080638 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTG-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGC-ATTGTGC-GAGTGATT
* * *
28080677 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGATT
* *
28080717 ATATCCGGGCTAAG-GCCGAAGGCATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGATT
*
28080756 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCA-TTGTGCGA-GTGATT
28080796 ATATCCGG
1 ATATCCGG
28080804 TTATATTCCG
Statistics
Matches: 105, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
38 3 0.03
39 44 0.42
40 56 0.53
41 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGATT
Found at i:28082283 original size:30 final size:30
Alignment explanation
Indices: 28082247--28082347 Score: 118
Period size: 28 Copynumber: 3.5 Consensus size: 30
28082237 GACAAGATTG
* * *
28082247 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
28082277 GCACTAAGTGTGCGAGTTT--GATTCTATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
28082305 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
28082334 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
28082348 GTTATCACTA
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 23 0.38
29 19 0.31
30 19 0.31
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGTTTAAAATTATATA
Found at i:28090134 original size:30 final size:30
Alignment explanation
Indices: 28090098--28090198 Score: 118
Period size: 28 Copynumber: 3.5 Consensus size: 30
28090088 GACAAGATTG
* * *
28090098 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
28090128 GCACTAAGTGTGCGAGTTT--GATTCTATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
28090156 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
28090185 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
28090199 GATTCACTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 23 0.38
29 19 0.31
30 19 0.31
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGTTTAAAATTATATA
Found at i:28090210 original size:29 final size:28
Alignment explanation
Indices: 28090127--28090202 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 28
28090117 AAAATTGTAC
* *
28090127 AGCACTAAGTGTGCGAGTTTGAT-TCTAT
1 AGCACTAAGTGTGCG-GATTGATATATAT
* *
28090155 AGCACTAAGTGTGC-GAGCTGAAAATATAT
1 AGCACTAAGTGTGCGGA-TTG-ATATATAT
28090184 AGCACTAAGTGTGCGGATT
1 AGCACTAAGTGTGCGGATT
28090203 CACTATATGC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.03
27 2 0.05
28 15 0.38
29 19 0.49
30 2 0.05
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGGATTGATATATAT
Found at i:28092038 original size:40 final size:40
Alignment explanation
Indices: 28091994--28092106 Score: 138
Period size: 40 Copynumber: 2.8 Consensus size: 40
28091984 TGCTGGAAAT
* * *
28091994 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGAC
* * *
28092034 TATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTGAC
* *
28092074 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATATCCGGGCTAAGACCCGAAGGCAATTGTGC
28092107 ACGTGATTAA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
39 3 0.05
40 57 0.92
41 2 0.03
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGAC
Found at i:28102440 original size:40 final size:40
Alignment explanation
Indices: 28102395--28102506 Score: 149
Period size: 40 Copynumber: 2.9 Consensus size: 40
28102385 TTATTTGATG
*
28102395 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCTGCAGGCTTCGTGC
* *
28102435 TGGAATTGTATCCGAGCTTAAAGACCTGCAAGCTTCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCTGCAGGCTTCGTGC
* *
28102475 T-GAA-TGACATCCGGG-TTAAAAACCTGCAGGCT
1 TGGAATTG-TATCCGGGCTTAAAGACCTGCAGGCT
28102507 ATGCTAGATA
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
38 17 0.27
39 9 0.14
40 38 0.59
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
TGGAATTGTATCCGGGCTTAAAGACCTGCAGGCTTCGTGC
Found at i:28110462 original size:40 final size:40
Alignment explanation
Indices: 28110417--28110542 Score: 189
Period size: 40 Copynumber: 3.1 Consensus size: 40
28110407 TTATTTGATG
28110417 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
* * ** *
28110457 TGGAATTATTTCCGAACTTAAAGACTCGCAGGCTTCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
* *
28110497 TGGAATTGTATCCAGGCTTAAAGACCTGCAGGCTTCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
28110537 TGGAAT
1 TGGAAT
28110543 GACATCCGGG
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 74 1.00
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (40 bp):
TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
Found at i:28112650 original size:28 final size:29
Alignment explanation
Indices: 28112591--28112656 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 29
28112581 CTTTTAGTTA
* * *
28112591 TTTCACAATTTAATCCCTCAATTTACATT
1 TTTCTCAAATTAATCCCTCAATTAACATT
28112620 TTTCTCAAATTAATCCCT-AATTAACATT
1 TTTCTCAAATTAATCCCTCAATTAACATT
*
28112648 TTTGTCAAA
1 TTTCTCAAA
28112657 AATCACATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
28 17 0.52
29 16 0.48
ACGTcount: A:0.33, C:0.21, G:0.02, T:0.44
Consensus pattern (29 bp):
TTTCTCAAATTAATCCCTCAATTAACATT
Found at i:28116726 original size:80 final size:80
Alignment explanation
Indices: 28116589--28116795 Score: 231
Period size: 80 Copynumber: 2.6 Consensus size: 80
28116579 AATTAAATGA
* * ** * *
28116589 TATCCGGGCTAAGTCGCG-AGGACATTTATGCTAGTAGTTAAATCCGGGTTAAGACCCGAAGGCA
1 TATCCGGGCTAAGACCCGAAGG-CATTCGTGCAAGTAGTTAAATCCGGGCTAAGACCCGAAGGCA
*
28116653 ATTATGCTAGT-G-AC
65 ATTATGCAAGTCGTAC
* *
28116667 TAAATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGC
1 T--ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTAAATCCGGGCTAAGACCCGAAGGC
* * *
28116732 ATTTGTGCAAGTCGTTC
64 AATTATGCAAGTCGTAC
* * *
28116749 TATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTAAATCCGG
28116796 TTGTATTCCG
Statistics
Matches: 109, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
78 1 0.01
80 102 0.94
81 4 0.04
82 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTAAATCCGGGCTAAGACCCGAAGGCAA
TTATGCAAGTCGTAC
Found at i:28116773 original size:40 final size:39
Alignment explanation
Indices: 28116588--28116795 Score: 202
Period size: 40 Copynumber: 5.2 Consensus size: 39
28116578 CAATTAAATG
* * * *
28116588 ATATCCGGGCTAAGTCGCG-AGGACATTTATGCTAGTAGTT
1 ATATCCGGGCTAAGACCCGAAGG-CATTTGTGCAAGT-GTT
* * * * * *
28116628 AAATCCGGGTTAAGACCCGAAGGCAATTATGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTG-TT
* *
28116668 AAATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAG-TGTT
* *
28116708 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGT-GTT
* * *
28116748 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGT-GTT
28116788 ATATCCGG
1 ATATCCGG
28116796 TTGTATTCCG
Statistics
Matches: 143, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
39 2 0.01
40 136 0.95
41 5 0.03
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTGTT
Found at i:28122037 original size:37 final size:38
Alignment explanation
Indices: 28121993--28122089 Score: 124
Period size: 37 Copynumber: 2.5 Consensus size: 38
28121983 GGACTAGGAT
*
28121993 CCGAAGGCATTCGTGCGAGTAATAAATCCGGGCTAAG-
1 CCGAAGGCATTCGTGCGAGTAATAAACCCGGGCTAAGC
* * * *
28122030 CCGAAGGCATTTGTGCAAGTTACTAAACCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAG-TAATAAACCCGGGCTAAG-C
28122070 CCGAAGGCATTCGTGCGAGT
1 CCGAAGGCATTCGTGCGAGT
28122090 CGCTATAACC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
37 17 0.34
38 15 0.30
39 1 0.02
40 17 0.34
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.22
Consensus pattern (38 bp):
CCGAAGGCATTCGTGCGAGTAATAAACCCGGGCTAAGC
Found at i:28122074 original size:77 final size:78
Alignment explanation
Indices: 28121940--28122089 Score: 198
Period size: 77 Copynumber: 1.9 Consensus size: 78
28121930 TCGAATGATG
* * *
28121940 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATTC
1 TCCGGGCTAAG-CCCGAAGGCTTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
28122005 GTGCGAGTAATAAA
65 GTGCGAGTAATAAA
* **
28122019 TCCGGGCTAAG-CCGAAGGCATTTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCATT
1 TCCGGGCTAAGCCCGAAGGC-TTTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCATT
28122081 CGTGCGAGT
64 CGTGCGAGT
28122090 CGCTATAACC
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
76 1 0.02
77 44 0.70
78 7 0.11
79 11 0.17
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.23
Consensus pattern (78 bp):
TCCGGGCTAAGCCCGAAGGCTTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTCG
TGCGAGTAATAAA
Found at i:28122077 original size:40 final size:40
Alignment explanation
Indices: 28121940--28122122 Score: 162
Period size: 40 Copynumber: 4.7 Consensus size: 40
28121930 TCGAATGATG
* *
28121940 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-AAGTTACTAAA
* * * * *
28121980 TCCGGACTAGGAT-CCGAAGGCATTCGTGCGAG-TAATAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCAAGTTACTAAA
28122019 TCCGGGCTAAG--CCGAAGGCATTTGTGCAAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTAAA
* * * * **
28122057 CCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCGCTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTA-AA
**
28122098 -CCGGGCTTCGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28122123 AGCGAGTCGT
Statistics
Matches: 115, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
37 17 0.15
38 15 0.13
39 13 0.11
40 61 0.53
41 9 0.08
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.23
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTAAA
Found at i:28125649 original size:41 final size:41
Alignment explanation
Indices: 28125534--28125669 Score: 145
Period size: 40 Copynumber: 3.4 Consensus size: 41
28125524 ATTATGTTTC
* * * * *
28125534 GCACTTAGTGTGTGTATC-GAGATAGCTTCAGCTTTATAAA
1 GCACTTAGTGTGCGAAACGGAGATAGCTTCAGCTATATAAG
* *
28125574 GCACTTAGTGTGCGAATCGGA-ATAGCTTCAGCTATATATG
1 GCACTTAGTGTGCGAAACGGAGATAGCTTCAGCTATATAAG
* *
28125614 GCACTTAGTGTGC-AAGACTGAGATAGCTTCGGCTATGA-AAG
1 GCACTTAGTGTGCGAA-ACGGAGATAGCTTCAGCTAT-ATAAG
28125655 GCACTTAGTGTGCGA
1 GCACTTAGTGTGCGA
28125670 GATTATAATT
Statistics
Matches: 82, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
39 2 0.02
40 48 0.59
41 30 0.37
42 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (41 bp):
GCACTTAGTGTGCGAAACGGAGATAGCTTCAGCTATATAAG
Found at i:28132785 original size:28 final size:28
Alignment explanation
Indices: 28132742--28132934 Score: 242
Period size: 28 Copynumber: 6.9 Consensus size: 28
28132732 ATGCCTTTGA
* * *
28132742 ATACTCAATATTTCGCACACTAAGTGCT
1 ATACTCAATGTCTCGCACACTAAGTGCC
*
28132770 ATACCCAATGTCTCGCACACTAAGTGCC
1 ATACTCAATGTCTCGCACACTAAGTGCC
* * *
28132798 ATACTCAATGTTTCGCACACTAAATGTC
1 ATACTCAATGTCTCGCACACTAAGTGCC
* *
28132826 ATGCTCAATGTCTGGCACACTAAGTGCC
1 ATACTCAATGTCTCGCACACTAAGTGCC
*
28132854 ATACTCAATTTCTCGCACACTAAGTGCC
1 ATACTCAATGTCTCGCACACTAAGTGCC
** **
28132882 ATACTCAATGTCTCATACACTAAGTTTC
1 ATACTCAATGTCTCGCACACTAAGTGCC
* *
28132910 ATATTCAATGTTTCGCACACTAAGT
1 ATACTCAATGTCTCGCACACTAAGT
28132935 CCCGTATATA
Statistics
Matches: 140, Mismatches: 25, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 140 1.00
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.30
Consensus pattern (28 bp):
ATACTCAATGTCTCGCACACTAAGTGCC
Found at i:28138238 original size:41 final size:40
Alignment explanation
Indices: 28138101--28138240 Score: 171
Period size: 40 Copynumber: 3.5 Consensus size: 40
28138091 GATTATGTTT
* *
28138101 GGCACTTAGTGTGCG-TATCGAGATAGCTTCGGCCATATAAA
1 GGCACTTAGTGTGCGAGATTGAGATAGCTTCGG-C-TATAAA
* *
28138142 -GCACTTAGTGTGCGA-ATTG-GAATAGCTTGGGCTATATA
1 GGCACTTAGTGTGCGAGATTGAG-ATAGCTTCGGCTATAAA
28138180 GGCACTTAGTGTGCGAGATTGAGATAGCTTCGGCTATGAAA
1 GGCACTTAGTGTGCGAGATTGAGATAGCTTCGGCTAT-AAA
*
28138221 GGCACTTAGTGTACGAGATT
1 GGCACTTAGTGTGCGAGATT
28138241 ATAATTGCTT
Statistics
Matches: 87, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
38 5 0.06
39 17 0.20
40 43 0.49
41 22 0.25
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (40 bp):
GGCACTTAGTGTGCGAGATTGAGATAGCTTCGGCTATAAA
Found at i:28138251 original size:41 final size:39
Alignment explanation
Indices: 28138101--28138257 Score: 140
Period size: 40 Copynumber: 3.9 Consensus size: 39
28138091 GATTATGTTT
* * *
28138101 GGCACTTAGTGTGCG-TATCGAGATAGCTTCGGCCATATAAA
1 GGCACTTAGTGTGCGAGAT-TAAATAGCTTCGG-C-TATAAA
* * *
28138142 -GCACTTAGTGTGCGA-ATTGGAATAGCTTGGGCTATATA
1 GGCACTTAGTGTGCGAGATT-AAATAGCTTCGGCTATAAA
*
28138180 GGCACTTAGTGTGCGAGATTGAGATAGCTTCGGCTATGAAA
1 GGCACTTAGTGTGCGAGATT-AAATAGCTTCGGCTAT-AAA
* * *
28138221 GGCACTTAGTGTACGAGATTATAATTGCTTCAGCTAT
1 GGCACTTAGTGTGCGAGATTA-AATAGCTTCGGCTAT
28138258 GCTTTGTCAC
Statistics
Matches: 97, Mismatches: 13, Indels: 12
0.80 0.11 0.10
Matches are distributed among these distances:
38 5 0.05
39 16 0.16
40 43 0.44
41 33 0.34
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (39 bp):
GGCACTTAGTGTGCGAGATTAAATAGCTTCGGCTATAAA
Found at i:28138258 original size:41 final size:41
Alignment explanation
Indices: 28138142--28138258 Score: 123
Period size: 41 Copynumber: 2.9 Consensus size: 41
28138132 GCCATATAAA
* * ** *
28138142 GCACTTAGTGTGCGA-ATTGGAATAGCTTGGGCTAT-ATAG
1 GCACTTAGTGTACGAGATTGAAATAGCTTCAGCTATGAAAG
* * *
28138181 GCACTTAGTGTGCGAGATTGAGATAGCTTCGGCTATGAAAG
1 GCACTTAGTGTACGAGATTGAAATAGCTTCAGCTATGAAAG
*
28138222 GCACTTAGTGTACGAGATT-ATAATTGCTTCAGCTATG
1 GCACTTAGTGTACGAGATTGA-AATAGCTTCAGCTATG
28138259 CTTTGTCACT
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
39 15 0.22
40 18 0.27
41 34 0.51
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (41 bp):
GCACTTAGTGTACGAGATTGAAATAGCTTCAGCTATGAAAG
Found at i:28139199 original size:79 final size:79
Alignment explanation
Indices: 28139108--28139266 Score: 291
Period size: 79 Copynumber: 2.0 Consensus size: 79
28139098 ATTTTTGTCC
* *
28139108 AAACGAGCAGAGACACGGGCGTGTGTCTCGTCCGTGTGCAACACATGATTAAGTTACACGACCGT
1 AAACGAGCAGAGACACGGGCGTGTGTCTCATCCGTGTGCAACACACGATTAAGTTACACGACCGT
28139173 GTGTCCCCTGGGGT
66 GTGTCCCCTGGGGT
*
28139187 AAACGAGCAGAGACACGGGCGTGTGTCTCATCCGTGTGCAACACACGATTAAGTTACTCGACCGT
1 AAACGAGCAGAGACACGGGCGTGTGTCTCATCCGTGTGCAACACACGATTAAGTTACACGACCGT
28139252 GTGTCCCCTGGGGT
66 GTGTCCCCTGGGGT
28139266 A
1 A
28139267 CCTTTCGAGT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.23, C:0.26, G:0.30, T:0.21
Consensus pattern (79 bp):
AAACGAGCAGAGACACGGGCGTGTGTCTCATCCGTGTGCAACACACGATTAAGTTACACGACCGT
GTGTCCCCTGGGGT
Found at i:28155091 original size:40 final size:40
Alignment explanation
Indices: 28155046--28155181 Score: 125
Period size: 40 Copynumber: 3.4 Consensus size: 40
28155036 ATTATGTTTC
* * *
28155046 GCACTTAGTGTGTGTATA-GAGATAGCTTCAGCTTTATAAA
1 GCACTTAGTGTGCGAATAGGA-ATAGCTTCAGCTATATAAA
* **
28155086 GCACTTAGTGTGCGAATCGGAATAGCTTCAGCTATATATG
1 GCACTTAGTGTGCGAATAGGAATAGCTTCAGCTATATAAA
* * * *
28155126 GCACTTAGTGTGC-AAGACTGAGATAGCTTCGGCTATGA-AAG
1 GCACTTAGTGTGCGAATA-GGA-ATAGCTTCAGCTAT-ATAAA
28155167 GCACTTAGTGTGCGA
1 GCACTTAGTGTGCGA
28155182 GATTATAATT
Statistics
Matches: 80, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
39 2 0.03
40 46 0.57
41 30 0.38
42 2 0.03
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (40 bp):
GCACTTAGTGTGCGAATAGGAATAGCTTCAGCTATATAAA
Found at i:28155161 original size:41 final size:41
Alignment explanation
Indices: 28155064--28155181 Score: 143
Period size: 40 Copynumber: 2.9 Consensus size: 41
28155054 TGTGTGTATA
* * *
28155064 GAGATAGCTTCAGCTTTATAAAGCACTTAGTGTGCGAATCG
1 GAGATAGCTTCAGCTATATAAGGCACTTAGTGTGCGAAACG
* *
28155105 GA-ATAGCTTCAGCTATATATGGCACTTAGTGTGC-AAGACT
1 GAGATAGCTTCAGCTATATAAGGCACTTAGTGTGCGAA-ACG
*
28155145 GAGATAGCTTCGGCTATGA-AAGGCACTTAGTGTGCGA
1 GAGATAGCTTCAGCTAT-ATAAGGCACTTAGTGTGCGA
28155182 GATTATAATT
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
39 2 0.03
40 32 0.48
41 30 0.45
42 2 0.03
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (41 bp):
GAGATAGCTTCAGCTATATAAGGCACTTAGTGTGCGAAACG
Found at i:28162309 original size:28 final size:28
Alignment explanation
Indices: 28162274--28162478 Score: 277
Period size: 28 Copynumber: 7.3 Consensus size: 28
28162264 ATATTTCGCG
* * **
28162274 CACTAAGTGCCATACCCAATTTCTTGCA
1 CACTAAGTGCCATACTCAATGTCTCACA
* * *
28162302 CAATAAGTGCCA-AGCTCGATGTCTCGCA
1 CACTAAGTGCCATA-CTCAATGTCTCACA
28162330 CACTAAGTGCCATACTCAATGTCTCACA
1 CACTAAGTGCCATACTCAATGTCTCACA
* *
28162358 AACTAAGTGCCATTCTCAATGTCTCACA
1 CACTAAGTGCCATACTCAATGTCTCACA
*
28162386 CACTAAGTGCCATTCTCAATGTCTCACA
1 CACTAAGTGCCATACTCAATGTCTCACA
*
28162414 CACTAAGTGCTATACTCAATGTCTCACA
1 CACTAAGTGCCATACTCAATGTCTCACA
* *
28162442 CACTAAGTGCCATATTCAATGTTTCACA
1 CACTAAGTGCCATACTCAATGTCTCACA
28162470 CACTAAGTG
1 CACTAAGTG
28162479 TCGTATATAG
Statistics
Matches: 159, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
27 1 0.01
28 157 0.99
29 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CACTAAGTGCCATACTCAATGTCTCACA
Found at i:28163497 original size:23 final size:23
Alignment explanation
Indices: 28163466--28163514 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
28163456 ACATTTAACA
28163466 TATAAGATGCCACTTTTGCATTT
1 TATAAGATGCCACTTTTGCATTT
* *
28163489 TATAGGATGCTACTTTTGCATTT
1 TATAAGATGCCACTTTTGCATTT
28163512 TAT
1 TAT
28163515 GCGATTTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.47
Consensus pattern (23 bp):
TATAAGATGCCACTTTTGCATTT
Found at i:28169117 original size:40 final size:39
Alignment explanation
Indices: 28169073--28169187 Score: 122
Period size: 40 Copynumber: 2.9 Consensus size: 39
28169063 AAGTGACTAT
* * *
28169073 ATCCGGACTAAGATCTGAAGGCGTTCGTGCGAGTTAATAA
1 ATCCGGACTAAG-CCCGAAGGCATTCGTGCGAGTTAATAA
* * *
28169113 ATCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 ATCCGGACTAAGCCCGAAGGCATTCGTGCGAGTTAATAA
* ** *
28169152 ACCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTA
1 ATCCGGACTAAG-CCCGAAGGCATTCGTGCGAGTTA
28169188 CTATAACCGG
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
39 32 0.48
40 34 0.52
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (39 bp):
ATCCGGACTAAGCCCGAAGGCATTCGTGCGAGTTAATAA
Found at i:28169188 original size:40 final size:39
Alignment explanation
Indices: 28169089--28169225 Score: 170
Period size: 40 Copynumber: 3.5 Consensus size: 39
28169079 ACTAAGATCT
* * * *
28169089 GAAGGCGTTCGTGCGAGTTAATAAATCCGGGCTAAG-CCC
1 GAAGGCATTTGTGCGAGTTACTAAA-CCGGGTTAAGTCCC
28169128 GAAGGCATTTGTGCGAGTTACTAAACCCGGGTTAAGTCCC
1 GAAGGCATTTGTGCGAGTTACTAAA-CCGGGTTAAGTCCC
*
28169168 GAAGGCATTTGTGCGAGTTACTATAACCGGGCTT-TGTCCC
1 GAAGGCATTTGTGCGAGTTACTA-AACCGGG-TTAAGTCCC
*
28169208 GAAGGCATTTGAGCGAGT
1 GAAGGCATTTGTGCGAGT
28169226 CGTTATATCC
Statistics
Matches: 88, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
39 31 0.35
40 53 0.60
41 4 0.05
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.25
Consensus pattern (39 bp):
GAAGGCATTTGTGCGAGTTACTAAACCGGGTTAAGTCCC
Found at i:28170628 original size:16 final size:16
Alignment explanation
Indices: 28170604--28170635 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28170594 AACGGACTCG
*
28170604 GGTACGGGGTGTTACA
1 GGTAAGGGGTGTTACA
28170620 GGTAAGGGGTGTTACA
1 GGTAAGGGGTGTTACA
28170636 CGTACTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.09, G:0.44, T:0.25
Consensus pattern (16 bp):
GGTAAGGGGTGTTACA
Found at i:28171544 original size:17 final size:17
Alignment explanation
Indices: 28171505--28171565 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 17
28171495 TGTCCTCTAG
* *
28171505 GCGATACAATCCGCCAG
1 GCGATACAATCCACCAA
* *
28171522 GTGATACAATGCACCAA
1 GCGATACAATCCACCAA
* **
28171539 GCGATACTATCCTTCAA
1 GCGATACAATCCACCAA
28171556 GCGATACAAT
1 GCGATACAAT
28171566 TCATCAAAGA
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.20
Consensus pattern (17 bp):
GCGATACAATCCACCAA
Found at i:28171572 original size:17 final size:17
Alignment explanation
Indices: 28171505--28171572 Score: 55
Period size: 17 Copynumber: 4.0 Consensus size: 17
28171495 TGTCCTCTAG
** *
28171505 GCGATACAATCCGCCAG
1 GCGATACAATCCATCAA
* * *
28171522 GTGATACAATGCACCAA
1 GCGATACAATCCATCAA
* *
28171539 GCGATACTATCCTTCAA
1 GCGATACAATCCATCAA
*
28171556 GCGATACAATTCATCAA
1 GCGATACAATCCATCAA
28171573 AGATGTATGT
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.35, C:0.28, G:0.16, T:0.21
Consensus pattern (17 bp):
GCGATACAATCCATCAA
Found at i:28176425 original size:18 final size:19
Alignment explanation
Indices: 28176388--28176428 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
28176378 ATTTAGAATC
28176388 AAAACTAAAATAAATAATA
1 AAAACTAAAATAAATAATA
* *
28176407 AAAACTAGATTAAAT-ATA
1 AAAACTAAAATAAATAATA
28176425 AAAA
1 AAAA
28176429 TATCAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (19 bp):
AAAACTAAAATAAATAATA
Found at i:28176430 original size:31 final size:31
Alignment explanation
Indices: 28176354--28176427 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
28176344 TCAAGTTATC
*
28176354 TTAAATATTAAAATAAAAATAAAAATTTAGAA
1 TTAAATA-TAAAATAAAAATAAAAATCTAGAA
*
28176386 TCAAA-ACTAAAATAAATAATAAAAA-CTAG-A
1 TTAAATA-TAAAATAAA-AATAAAAATCTAGAA
28176416 TTAAATATAAAA
1 TTAAATATAAAA
28176428 ATATCAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
30 10 0.28
31 14 0.39
32 12 0.33
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.27
Consensus pattern (31 bp):
TTAAATATAAAATAAAAATAAAAATCTAGAA
Found at i:28178000 original size:38 final size:38
Alignment explanation
Indices: 28177949--28178024 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
28177939 AATACTTAAC
28177949 CAACTTAAAACTACTACTACTAATAGAAACTGGTCCCT
1 CAACTTAAAACTACTACTACTAATAGAAACTGGTCCCT
28177987 CAACTTAAAACTACTACTACTAATAGAAACTGGTCCCT
1 CAACTTAAAACTACTACTACTAATAGAAACTGGTCCCT
28178025 ATATGCACCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.39, C:0.26, G:0.08, T:0.26
Consensus pattern (38 bp):
CAACTTAAAACTACTACTACTAATAGAAACTGGTCCCT
Found at i:28178425 original size:2 final size:2
Alignment explanation
Indices: 28178413--28178447 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
28178403 AAAATATGCT
*
28178413 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28178448 TTATCTTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:28179966 original size:18 final size:18
Alignment explanation
Indices: 28179943--28179986 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
28179933 AGGGATTTTG
* *
28179943 GGGGAAATTTAG-GGATT
1 GGGGAAATGTAGAGAATT
28179960 AGGGGAAATGTAGAGAATT
1 -GGGGAAATGTAGAGAATT
28179979 GGGGAAAT
1 GGGGAAAT
28179987 CTATTTTGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.36, C:0.00, G:0.41, T:0.23
Consensus pattern (18 bp):
GGGGAAATGTAGAGAATT
Found at i:28180209 original size:74 final size:74
Alignment explanation
Indices: 28180117--28180341 Score: 396
Period size: 74 Copynumber: 3.0 Consensus size: 74
28180107 CGTCATTTTC
* *
28180117 ATAGTGTTTTTTGTGGCGTTTTTTAAAAAAAGCCACTAATCTCTTAATTTACATATTTATTTTTA
1 ATAGTGTTTTTTGTGGCGTTTTTTAAAAAACGCCACTAATCTCTTAATTTTCATATTTATTTTTA
*
28180182 TTTTTTATA
66 TTTGTTATA
*
28180191 ATAGTGTTTTTTGTGGCGTTTTTTTAAAAAACGCCACTAATCTTTTAATTTTCATATTTATTTTT
1 ATAGTGTTTTTTGTGGCG-TTTTTTAAAAAACGCCACTAATCTCTTAATTTTCATATTTATTTTT
28180256 ATTTGTTATA
65 ATTTGTTATA
*
28180266 ATAGTGTTTTTTGTGGCGTTTTTTTAAAAACGCCACTAATCTCTTAATTTTCATATTTATTTTTA
1 ATAGTGTTTTTTGTGGCGTTTTTTAAAAAACGCCACTAATCTCTTAATTTTCATATTTATTTTTA
28180331 TTTGTTATA
66 TTTGTTATA
28180340 AT
1 AT
28180342 TTGGAAGCCA
Statistics
Matches: 144, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
74 74 0.51
75 70 0.49
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (74 bp):
ATAGTGTTTTTTGTGGCGTTTTTTAAAAAACGCCACTAATCTCTTAATTTTCATATTTATTTTTA
TTTGTTATA
Found at i:28180239 original size:75 final size:75
Alignment explanation
Indices: 28180117--28180341 Score: 400
Period size: 75 Copynumber: 3.0 Consensus size: 75
28180107 CGTCATTTTC
* *
28180117 ATAGTGTTTTTTGTGGCG-TTTTTTAAAAAAAGCCACTAATCTCTTAATTTACATATTTATTTTT
1 ATAGTGTTTTTTGTGGCGTTTTTTTAAAAAACGCCACTAATCTCTTAATTTTCATATTTATTTTT
*
28180181 ATTTTTTATA
66 ATTTGTTATA
*
28180191 ATAGTGTTTTTTGTGGCGTTTTTTTAAAAAACGCCACTAATCTTTTAATTTTCATATTTATTTTT
1 ATAGTGTTTTTTGTGGCGTTTTTTTAAAAAACGCCACTAATCTCTTAATTTTCATATTTATTTTT
28180256 ATTTGTTATA
66 ATTTGTTATA
28180266 ATAGTGTTTTTTGTGGCGTTTTTTT-AAAAACGCCACTAATCTCTTAATTTTCATATTTATTTTT
1 ATAGTGTTTTTTGTGGCGTTTTTTTAAAAAACGCCACTAATCTCTTAATTTTCATATTTATTTTT
28180330 ATTTGTTATA
66 ATTTGTTATA
28180340 AT
1 AT
28180342 TTGGAAGCCA
Statistics
Matches: 145, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
74 68 0.47
75 77 0.53
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (75 bp):
ATAGTGTTTTTTGTGGCGTTTTTTTAAAAAACGCCACTAATCTCTTAATTTTCATATTTATTTTT
ATTTGTTATA
Found at i:28180585 original size:7 final size:7
Alignment explanation
Indices: 28180550--28180655 Score: 54
Period size: 7 Copynumber: 14.9 Consensus size: 7
28180540 TAACATTTAC
28180550 CCCTAAA
1 CCCTAAA
* *
28180557 TCTTAAA
1 CCCTAAA
*
28180564 TCCTAAA
1 CCCTAAA
*
28180571 TCCTAAA
1 CCCTAAA
28180578 CCCTAAA
1 CCCTAAA
28180585 CCC-ATAA
1 CCCTA-AA
*
28180592 CCC-ATAT
1 CCCTA-AA
* *
28180599 CTCTTAA
1 CCCTAAA
28180606 CCCTTAAA
1 CCC-TAAA
*
28180614 ACCTAAA
1 CCCTAAA
*
28180621 CCCTTAA
1 CCCTAAA
* *
28180628 CACATAAC
1 C-CCTAAA
28180636 CCCTAAA
1 CCCTAAA
*
28180643 CCTTAAA
1 CCCTAAA
28180650 CCCTAA
1 CCCTAA
28180656 CACATAATCC
Statistics
Matches: 75, Mismatches: 20, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
6 1 0.01
7 65 0.87
8 9 0.12
ACGTcount: A:0.41, C:0.36, G:0.00, T:0.24
Consensus pattern (7 bp):
CCCTAAA
Found at i:28180623 original size:36 final size:36
Alignment explanation
Indices: 28180565--28180669 Score: 106
Period size: 36 Copynumber: 2.9 Consensus size: 36
28180555 AATCTTAAAT
* *
28180565 CCTAAATCC-TAAACCCTAAACCCATAACCCATATCT
1 CCTAAA-CCTTAAACCCTAAACCCATAACCCATAACC
* * * * *
28180601 CTTAACCCTTAAAACCTAAACCCTTAACACATAACC
1 CCTAAACCTTAAACCCTAAACCCATAACCCATAACC
* *
28180637 CCTAAACCTTAAACCCT-AACACATAATCCATAA
1 CCTAAACCTTAAACCCTAAACCCATAACCCATAA
28180670 ACCATAATCC
Statistics
Matches: 54, Mismatches: 14, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
35 14 0.26
36 40 0.74
ACGTcount: A:0.42, C:0.36, G:0.00, T:0.22
Consensus pattern (36 bp):
CCTAAACCTTAAACCCTAAACCCATAACCCATAACC
Found at i:28180624 original size:15 final size:15
Alignment explanation
Indices: 28180604--28180653 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
28180594 CATATCTCTT
28180604 AACCCTTAAAACCTA
1 AACCCTTAAAACCTA
* *
28180619 AACCCTTAACACAT-
1 AACCCTTAAAACCTA
*
28180633 AACCCCT-AAACCTTA
1 AACCCTTAAAACC-TA
28180648 AACCCT
1 AACCCT
28180654 AACACATAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
13 3 0.11
14 7 0.26
15 17 0.63
ACGTcount: A:0.42, C:0.38, G:0.00, T:0.20
Consensus pattern (15 bp):
AACCCTTAAAACCTA
Found at i:28180648 original size:43 final size:44
Alignment explanation
Indices: 28180548--28180653 Score: 119
Period size: 43 Copynumber: 2.5 Consensus size: 44
28180538 TCTAACATTT
* * * *
28180548 ACCCCTAAATCTTAAATCC-TAAATCCTAAACCCTAAACCCATA
1 ACCCCTAAACCTTAAACCCTTAAAACCTAAACCCTAAACACATA
* * *
28180591 ACCCAT-ATCTCTT-AACCCTTAAAACCTAAACCCTTAACACATA
1 ACCCCTAAAC-CTTAAACCCTTAAAACCTAAACCCTAAACACATA
28180634 ACCCCTAAACCTTAAACCCT
1 ACCCCTAAACCTTAAACCCT
28180654 AACACATAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
42 5 0.10
43 37 0.74
44 8 0.16
ACGTcount: A:0.40, C:0.37, G:0.00, T:0.24
Consensus pattern (44 bp):
ACCCCTAAACCTTAAACCCTTAAAACCTAAACCCTAAACACATA
Found at i:28180722 original size:7 final size:7
Alignment explanation
Indices: 28180712--28180776 Score: 51
Period size: 7 Copynumber: 9.0 Consensus size: 7
28180702 ATAAACCATA
28180712 AACCCCT
1 AACCCCT
28180719 AACCCC-
1 AACCCCT
28180725 AATCCCCTT
1 AA-CCCC-T
*
28180734 AACGCCT
1 AACCCCT
*
28180741 AACCCTT
1 AACCCCT
*
28180748 ATCCCCTT
1 AACCCC-T
*
28180756 AACGCCT
1 AACCCCT
28180763 AACCCCT
1 AACCCCT
*
28180770 ATCCCCT
1 AACCCCT
28180777 TAAAACCTGT
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
6 2 0.04
7 33 0.73
8 8 0.18
9 2 0.04
ACGTcount: A:0.25, C:0.51, G:0.03, T:0.22
Consensus pattern (7 bp):
AACCCCT
Found at i:28180741 original size:22 final size:22
Alignment explanation
Indices: 28180716--28180779 Score: 110
Period size: 22 Copynumber: 2.9 Consensus size: 22
28180706 ACCATAAACC
*
28180716 CCTAACCCCAATCCCCTTAACG
1 CCTAACCCCTATCCCCTTAACG
*
28180738 CCTAACCCTTATCCCCTTAACG
1 CCTAACCCCTATCCCCTTAACG
28180760 CCTAACCCCTATCCCCTTAA
1 CCTAACCCCTATCCCCTTAA
28180780 AACCTGTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.25, C:0.48, G:0.03, T:0.23
Consensus pattern (22 bp):
CCTAACCCCTATCCCCTTAACG
Found at i:28180872 original size:7 final size:7
Alignment explanation
Indices: 28180860--28180977 Score: 53
Period size: 7 Copynumber: 16.6 Consensus size: 7
28180850 ACTAATTAAT
28180860 CTAAACC
1 CTAAACC
28180867 CTAAACC
1 CTAAACC
*
28180874 TCTTAACCC
1 -C-TAAACC
*
28180883 CT-ATCC
1 CTAAACC
*
28180889 CATAAACA
1 C-TAAACC
*
28180897 CTAAACT
1 CTAAACC
28180904 CTAAACC
1 CTAAACC
*
28180911 CTTAACC
1 CTAAACC
*
28180918 CTTAACC
1 CTAAACC
* *
28180925 TTTAACC
1 CTAAACC
*
28180932 CCAAACC
1 CTAAACC
*
28180939 CTTACACC
1 C-TAAACC
* *
28180947 TTAAACT
1 CTAAACC
28180954 CT-AACC
1 CTAAACC
28180960 CT-AACC
1 CTAAACC
*
28180966 ATTAAACC
1 -CTAAACC
28180974 CTAA
1 CTAA
28180978 TTAATCATAA
Statistics
Matches: 84, Mismatches: 20, Indels: 14
0.71 0.17 0.12
Matches are distributed among these distances:
6 13 0.15
7 53 0.63
8 13 0.15
9 5 0.06
ACGTcount: A:0.37, C:0.39, G:0.00, T:0.24
Consensus pattern (7 bp):
CTAAACC
Found at i:28180937 original size:28 final size:28
Alignment explanation
Indices: 28180906--28180960 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
28180896 ACTAAACTCT
* *
28180906 AAACCCTTA-ACCCTTAACCTTTAACCCC
1 AAACCCTTACA-CCTTAAACTCTAACCCC
28180934 AAACCCTTACACCTTAAACTCTAACCC
1 AAACCCTTACACCTTAAACTCTAACCC
28180961 TAACCATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.35, C:0.42, G:0.00, T:0.24
Consensus pattern (28 bp):
AAACCCTTACACCTTAAACTCTAACCCC
Found at i:28180959 original size:21 final size:21
Alignment explanation
Indices: 28180905--28180977 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
28180895 CACTAAACTC
*
28180905 TAAACCCTTAACCCTTAACCTT
1 TAAACCC-TAACCCTTAACCAT
* *
28180927 TAACCCCAAACCCTTACACC-T
1 TAAACCCTAACCCTTA-ACCAT
*
28180948 TAAACTCTAACCC-TAACCAT
1 TAAACCCTAACCCTTAACCAT
28180968 TAAACCCTAA
1 TAAACCCTAA
28180978 TTAATCATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 12 0.28
21 19 0.44
22 9 0.21
ACGTcount: A:0.37, C:0.38, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAACCCTAACCCTTAACCAT
Found at i:28181065 original size:21 final size:21
Alignment explanation
Indices: 28181041--28181114 Score: 76
Period size: 21 Copynumber: 3.3 Consensus size: 21
28181031 ACTCCTAAAC
28181041 CTTAAACCCTAAACTATATAT
1 CTTAAACCCTAAACTATATAT
* * *
28181062 CTTAAACCATAGTTAACTCATAAAC
1 CTTAAACCCTA---AACT-ATATAT
*
28181087 CTTAAACCCTAAACCATATAT
1 CTTAAACCCTAAACTATATAT
28181108 CTTAAAC
1 CTTAAAC
28181115 AATAAACCAT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
21 21 0.50
22 3 0.07
24 4 0.10
25 14 0.33
ACGTcount: A:0.43, C:0.26, G:0.01, T:0.30
Consensus pattern (21 bp):
CTTAAACCCTAAACTATATAT
Found at i:28181078 original size:46 final size:46
Alignment explanation
Indices: 28181025--28181114 Score: 162
Period size: 46 Copynumber: 2.0 Consensus size: 46
28181015 CTTCAAATAC
* *
28181025 TAGTTAACTCCTAAACCTTAAACCCTAAACTATATATCTTAAACCA
1 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA
28181071 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAAC
1 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAAC
28181115 AATAAACCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.42, C:0.26, G:0.02, T:0.30
Consensus pattern (46 bp):
TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA
Found at i:28181092 original size:25 final size:25
Alignment explanation
Indices: 28180962--28181094 Score: 82
Period size: 25 Copynumber: 5.4 Consensus size: 25
28180952 CTCTAACCCT
*
28180962 AACCATTAAACCCTAATTAA-TCATA
1 AACC-TTAAACCATAATTAACTCATA
* * *
28180987 ATCCCTAAACCCATAATTCA-TCATA
1 AACCTTAAA-CCATAATTAACTCATA
* * *
28181012 AACCTTCAAA-TACTAGTTAACTCCTA
1 AACCTT-AAACCA-TAATTAACTCATA
*
28181038 AACCTTAAACCCT-A--AACT-ATA
1 AACCTTAAACCATAATTAACTCATA
* * *
28181059 TATCTTAAACCATAGTTAACTCATA
1 AACCTTAAACCATAATTAACTCATA
28181084 AACCTTAAACC
1 AACCTTAAACC
28181095 CTAAACCATA
Statistics
Matches: 79, Mismatches: 20, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
21 12 0.15
22 4 0.05
24 9 0.11
25 41 0.52
26 13 0.16
ACGTcount: A:0.43, C:0.27, G:0.02, T:0.29
Consensus pattern (25 bp):
AACCTTAAACCATAATTAACTCATA
Found at i:28181120 original size:21 final size:21
Alignment explanation
Indices: 28181041--28181125 Score: 62
Period size: 21 Copynumber: 3.9 Consensus size: 21
28181031 ACTCCTAAAC
** *
28181041 CTTAAACCCTAAACTATATAT
1 CTTAAACAATAAACCATATAT
* * *
28181062 CTTAAACCATAGTTAACTCATAAAC
1 CTTAAA-CA-A-TAAAC-CATATAT
**
28181087 CTTAAACCCTAAACCATATAT
1 CTTAAACAATAAACCATATAT
28181108 CTTAAACAATAAACCATA
1 CTTAAACAATAAACCATA
28181126 AACTATAATG
Statistics
Matches: 47, Mismatches: 13, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
21 27 0.57
22 5 0.11
24 5 0.11
25 10 0.21
ACGTcount: A:0.46, C:0.25, G:0.01, T:0.28
Consensus pattern (21 bp):
CTTAAACAATAAACCATATAT
Found at i:28181336 original size:41 final size:41
Alignment explanation
Indices: 28181290--28181416 Score: 141
Period size: 41 Copynumber: 3.1 Consensus size: 41
28181280 GTTATATGAC
*
28181290 TTTTAGTGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
* * *
28181331 TTTTAGCGGCGTTTTGCCAAAAGCACCGCTAATGCTCT-AT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
* * * * *
28181371 TTTTCGCGGCATTTTTTACTAAAA-TGCCGCTATTGCTCTGGT
1 TTTTAGCGGC-GTTTTT-CCAAAAGCGCCGCTAATGCTCTGGT
28181413 TTTT
1 TTTT
28181417 GTGGCATTTT
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
40 10 0.14
41 51 0.72
42 10 0.14
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.39
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
Found at i:28187339 original size:39 final size:40
Alignment explanation
Indices: 28187244--28187465 Score: 267
Period size: 40 Copynumber: 5.6 Consensus size: 40
28187234 CGGATGATAA
* * *
28187244 CCGGGCTAAGTCCCG-AGAGCATTTGAGCTAG-TGGCTA-ATT
1 CCGGGCTAAGTCCCGAAG-GCATTTGTGCGAGCT-ACTATA-T
*
28187284 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
* *
28187324 CC-GGCTAAGTCCCGAAGGCGTTTGTGCGAGCTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
* *
28187363 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
* * * *
28187402 CCGGGCTAAGT-CCGAAGGCATTTGTGCAAGTTACCATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
28187441 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
28187466 AGCTAGTGGC
Statistics
Matches: 164, Mismatches: 12, Indels: 12
0.87 0.06 0.06
Matches are distributed among these distances:
38 24 0.15
39 58 0.35
40 78 0.48
41 4 0.02
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
Found at i:28187464 original size:78 final size:79
Alignment explanation
Indices: 28187284--28187498 Score: 265
Period size: 78 Copynumber: 2.7 Consensus size: 79
28187274 GTGGCTAATT
* *
28187284 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATATCCGGCTAAGTCCCGAAGGCGTTTGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGCTAAGTCCCGAAGGCATTTGT
* ** *
28187349 GCGAGCTATTATAT
66 GCAAGCTACCATAA
* *
28187363 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATA-CCGGGCTAAGT-CCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCC-GGCTAAGTCCCGAAGGCATTTG
*
28187426 TGCAAGTTACCATAA
65 TGCAAGCTACCATAA
* * * **
28187441 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAG-TGGCTATATCCGGCTAAACCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCT-ACTATATCCGGCTAAGTCCCGAAGG
28187499 TACTTGGTTT
Statistics
Matches: 117, Mismatches: 15, Indels: 8
0.84 0.11 0.06
Matches are distributed among these distances:
77 1 0.01
78 63 0.54
79 53 0.45
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.24
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGCTAAGTCCCGAAGGCATTTGT
GCAAGCTACCATAA
Found at i:28187487 original size:39 final size:39
Alignment explanation
Indices: 28187244--28187498 Score: 261
Period size: 40 Copynumber: 6.5 Consensus size: 39
28187234 CGGATGATAA
* * *
28187244 CCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTA-ATT
1 CCGGGCTAAGTCCCGAAG-GCATTTGTGCGAGT-ACTATA-T
*
28187284 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT
* *
28187324 CC-GGCTAAGTCCCGAAGGCGTTTGTGCGAGCTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT
*
28187363 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT
* * *
28187402 CCGGGCTAAGT-CCGAAGGCATTTGTGCAAGTTACCATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT
* * *
28187441 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT-ACTATAT
**
28187481 CC-GGCTAAACCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
28187499 TACTTGGTTT
Statistics
Matches: 189, Mismatches: 19, Indels: 15
0.85 0.09 0.07
Matches are distributed among these distances:
38 24 0.13
39 73 0.39
40 88 0.47
41 4 0.02
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATAT
Found at i:28196698 original size:29 final size:29
Alignment explanation
Indices: 28196666--28196800 Score: 155
Period size: 29 Copynumber: 4.7 Consensus size: 29
28196656 ATACCCTCCG
** * *
28196666 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
* * * *
28196695 AGCTTGCACACATAGTGTCATATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
28196724 AGCAT-GCACACTTAGTGCCTTATATTTCC
1 AGC-TCGCACACTTAGTGCCATATATTTCC
*
28196753 AGCACGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
28196782 AGCACGCACACTTAGTGCC
1 AGCTCGCACACTTAGTGCC
28196801 GATCTCGTCA
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
29 92 0.99
30 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.30
Consensus pattern (29 bp):
AGCTCGCACACTTAGTGCCATATATTTCC
Found at i:28196733 original size:58 final size:58
Alignment explanation
Indices: 28196612--28196801 Score: 179
Period size: 58 Copynumber: 3.3 Consensus size: 58
28196602 TACTCGATTT
* * * *** *
28196612 CGCACACTTAGTGCCACGTA-ATTT-AAGCCCGCACACACAGTGCCATA-CCCTCCGAGCT
1 CGCACACTTAGTG-C-CGTATATTTCCAGCACGCACACATAGTGCCATATATTTCC-AGCA
** * ** * *
28196670 CGCACACCCAGTGCCGTATTTTTCCAGCTTGCACACATAGTGTCATATTTTTCCAGCA
1 CGCACACTTAGTGCCGTATATTTCCAGCACGCACACATAGTGCCATATATTTCCAGCA
* * *
28196728 TGCACACTTAGTGCCTTATATTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCGTATATTTCCAGCACGCACACATAGTGCCATATATTTCCAGCA
28196786 CGCACACTTAGTGCCG
1 CGCACACTTAGTGCCG
28196802 ATCTCGTCAC
Statistics
Matches: 105, Mismatches: 24, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
56 4 0.04
57 4 0.04
58 94 0.90
59 3 0.03
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.26
Consensus pattern (58 bp):
CGCACACTTAGTGCCGTATATTTCCAGCACGCACACATAGTGCCATATATTTCCAGCA
Found at i:28209691 original size:80 final size:80
Alignment explanation
Indices: 28209607--28209755 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
28209597 TATGGTAACC
* * * *
28209607 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
28209671 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
28209687 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
28209752 CCGG
66 CCGG
28209756 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:28209697 original size:40 final size:38
Alignment explanation
Indices: 28209648--28209755 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
28209638 ATCACGATTT
*
28209648 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
28209688 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
28209728 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
28209756 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:28209946 original size:21 final size:22
Alignment explanation
Indices: 28209922--28209963 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
28209912 CCCGGGTAAT
*
28209922 TCAATACTCATACACA-CATAA
1 TCAATAATCATACACATCATAA
28209943 TCAATAATCATACACATCATA
1 TCAATAATCATACACATCATA
28209964 TTTCATTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (22 bp):
TCAATAATCATACACATCATAA
Found at i:28213572 original size:37 final size:37
Alignment explanation
Indices: 28213522--28213596 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
28213512 AGGGGGTTAG
28213522 AAACTCTAATTACAAATTCAGTAGACTCCACAAGCAA
1 AAACTCTAATTACAAATTCAGTAGACTCCACAAGCAA
28213559 AAACTCTAATTACAAATTCAGTAGACTCCACAAGCAA
1 AAACTCTAATTACAAATTCAGTAGACTCCACAAGCAA
28213596 A
1 A
28213597 GTCTTACTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.47, C:0.24, G:0.08, T:0.21
Consensus pattern (37 bp):
AAACTCTAATTACAAATTCAGTAGACTCCACAAGCAA
Found at i:28216401 original size:8 final size:8
Alignment explanation
Indices: 28216367--28216402 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
28216357 TGAATCGGTG
28216367 AAAGTCGA
1 AAAGTCGA
*
28216375 AATGTCGA
1 AAAGTCGA
*
28216383 AATGTCGA
1 AAAGTCGA
28216391 AAAGTCGA
1 AAAGTCGA
28216399 AAAG
1 AAAG
28216403 GCAAAAGGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.47, C:0.11, G:0.25, T:0.17
Consensus pattern (8 bp):
AAAGTCGA
Found at i:28216698 original size:29 final size:27
Alignment explanation
Indices: 28216656--28216762 Score: 108
Period size: 29 Copynumber: 3.8 Consensus size: 27
28216646 ATAATATGTT
*
28216656 TTGGGCCTAATGGGCCATATGAAGGTGAA
1 TTGGGCCTAGTGGGCCATATGAA--TGAA
*
28216685 TTGGGCCTAGTGGGCCATAAGAATATGAA
1 TTGGGCCTAGTGGGCCATATG-A-ATGAA
* *
28216714 TTGGGCC-AGATGGGCCATTTGAATAAGA
1 TTGGGCCTAG-TGGGCCATATGAATGA-A
*
28216742 TTGGGCCTAGTGGGCTATATG
1 TTGGGCCTAGTGGGCCATATG
28216763 TATGTATGTA
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
27 3 0.05
28 20 0.30
29 41 0.62
30 1 0.02
31 1 0.02
ACGTcount: A:0.26, C:0.14, G:0.34, T:0.26
Consensus pattern (27 bp):
TTGGGCCTAGTGGGCCATATGAATGAA
Found at i:28217832 original size:17 final size:18
Alignment explanation
Indices: 28217802--28217835 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28217792 TTTAAAAAGG
28217802 GTTTTCAATGAAAACACA
1 GTTTTCAATGAAAACACA
*
28217820 GTTTTCACT-AAAACAC
1 GTTTTCAATGAAAACAC
28217836 TTCAATGTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (18 bp):
GTTTTCAATGAAAACACA
Found at i:28219350 original size:42 final size:43
Alignment explanation
Indices: 28219261--28219406 Score: 129
Period size: 43 Copynumber: 3.4 Consensus size: 43
28219251 TGCCAACGTT
* *** *
28219261 CCAGATGTGGTCTTACATGTAATCAAATATCGATGCCACTGTC
1 CCAGACGTGGTCTTACACAAAATCAAATATCGATGCCACTATC
28219304 CCAGACAG-GGTCTTACACAAAATCAAATA-CGATGCCAAC-ATC
1 CCAGAC-GTGGTCTTACACAAAATCAAATATCGATGCC-ACTATC
** * * *
28219346 CCAGACGTGGTCTTACATGTAAATACCAA-ATCGATGCCAATGTC
1 CCAGACGTGGTCTTACA-CAAAAT-CAAATATCGATGCCACTATC
*
28219390 CCAGATGTGGTCTTACA
1 CCAGACGTGGTCTTACA
28219407 TGATATCACA
Statistics
Matches: 85, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
41 1 0.01
42 24 0.28
43 31 0.36
44 29 0.34
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (43 bp):
CCAGACGTGGTCTTACACAAAATCAAATATCGATGCCACTATC
Found at i:28239299 original size:48 final size:48
Alignment explanation
Indices: 28239228--28239711 Score: 860
Period size: 48 Copynumber: 10.0 Consensus size: 48
28239218 CAAGATAAAT
*
28239228 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
* *
28239276 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTG-AA-ATATGTATGAG
28239326 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
28239374 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
28239422 ATATGTATATGTGGTGAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
28239470 ATATGTATATGTGGTGAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
28239518 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
* *
28239566 ATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
28239614 ATATGTATATGTGGTAAAGCTGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
28239662 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
28239710 AT
1 AT
28239712 GCGTGTATAT
Statistics
Matches: 420, Mismatches: 14, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
48 372 0.89
49 4 0.01
50 44 0.10
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.31
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
Found at i:28239959 original size:37 final size:37
Alignment explanation
Indices: 28239851--28239959 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
28239841 GGAAATATAT
*
28239851 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
28239888 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* * *
28239925 TCCGGGTAAAACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
28239960 CATCTGAGCT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:28241366 original size:17 final size:17
Alignment explanation
Indices: 28241344--28241376 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
28241334 TTCCCATGTG
28241344 GGGCCCATGTGCCCGTA
1 GGGCCCATGTGCCCGTA
28241361 GGGCCCATGTGCCCGT
1 GGGCCCATGTGCCCGT
28241377 TTCGGCCAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.09, C:0.36, G:0.36, T:0.18
Consensus pattern (17 bp):
GGGCCCATGTGCCCGTA
Found at i:28250686 original size:39 final size:40
Alignment explanation
Indices: 28250618--28250787 Score: 229
Period size: 40 Copynumber: 4.3 Consensus size: 40
28250608 AAACCAAGTA
* * *
28250618 CCTTCGGGATTTAG-TCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
28250657 CCTGCGGGACTTAGCCCGAATATAGT-ACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
28250696 CCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
28250736 CCTTTGGGACTTAGCCCGGATATATTAACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
28250776 CCTTCGGGACTT
1 CCTTCGGGACTT
28250788 GGCCTGGTTG
Statistics
Matches: 116, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
39 48 0.41
40 68 0.59
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:28250748 original size:79 final size:79
Alignment explanation
Indices: 28250618--28250787 Score: 227
Period size: 79 Copynumber: 2.2 Consensus size: 79
28250608 AAACCAAGTA
* * *
28250618 CCTTCGGGATTTAGTCGGATATAGCTACTCGCTCAAATGCCTGCGGGACTTAGCCCGAATATAGT
1 CCTTCGGGACTTAGCCGGATATAGCTACTCGCACAAATGCCTGCGGGACTTAGCCCGAATATAGT
*
28250683 -ACTCGCACAAATG
66 AACTAGCACAAATG
* ** *
28250696 CCTTCGGGACTTAGCCCGGATTTAG-TAACTCGCACAAATGCCTTTGGGACTTAGCCCGGATATA
1 CCTTCGGGACTTAG-CCGGATATAGCT-ACTCGCACAAATGCCTGCGGGACTTAGCCCGAATATA
*
28250760 TTAACTAGCACAAATG
64 GTAACTAGCACAAATG
28250776 CCTTCGGGACTT
1 CCTTCGGGACTT
28250788 GGCCTGGTTG
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
78 14 0.17
79 42 0.52
80 24 0.30
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (79 bp):
CCTTCGGGACTTAGCCGGATATAGCTACTCGCACAAATGCCTGCGGGACTTAGCCCGAATATAGT
AACTAGCACAAATG
Found at i:28258698 original size:40 final size:40
Alignment explanation
Indices: 28258637--28258814 Score: 261
Period size: 40 Copynumber: 4.5 Consensus size: 40
28258627 AAACCAAGTA
* * *
28258637 CCTTCGGGATTTAG-TCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
28258676 CCTGCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
28258716 CCTTCGGGTCATAGCCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
28258756 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
28258796 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
28258815 TTGCCATCCG
Statistics
Matches: 124, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
39 13 0.10
40 111 0.90
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:28264774 original size:43 final size:43
Alignment explanation
Indices: 28264713--28264795 Score: 141
Period size: 43 Copynumber: 1.9 Consensus size: 43
28264703 CCTTTCTTGG
28264713 GGACACATATTACAGGGCTTACCCACAAGCTGTTCGAGATTAA
1 GGACACATATTACAGGGCTTACCCACAAGCTGTTCGAGATTAA
*
28264756 GGACACAT-TGTACAGGGCTTACCCACGAGCTGTTCGAGAT
1 GGACACATAT-TACAGGGCTTACCCACAAGCTGTTCGAGAT
28264796 CGAATTCAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 1 0.03
43 37 0.97
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (43 bp):
GGACACATATTACAGGGCTTACCCACAAGCTGTTCGAGATTAA
Found at i:28271841 original size:43 final size:43
Alignment explanation
Indices: 28271761--28271886 Score: 137
Period size: 43 Copynumber: 2.9 Consensus size: 43
28271751 TATCATATAT
* * ** *
28271761 CGATGCCACTGTCCCAGACAGGGTCTTAAACAAAATCA-ATTAA
1 CGATGCCAATGTCCCAGACATGGTCTTAAATGAAATCACAAT-A
* *
28271804 CGATGCCAATGTCCCAGACATGGTCTTATATGCAATCACAATA
1 CGATGCCAATGTCCCAGACATGGTCTTAAATGAAATCACAATA
* * * *
28271847 CAATGCCAATGTCCTAGACATGGTCTTACATGTAATCACA
1 CGATGCCAATGTCCCAGACATGGTCTTAAATGAAATCACA
28271887 TCTCGGTAAC
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
43 69 0.97
44 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (43 bp):
CGATGCCAATGTCCCAGACATGGTCTTAAATGAAATCACAATA
Found at i:28278168 original size:54 final size:54
Alignment explanation
Indices: 28278046--28278542 Score: 334
Period size: 54 Copynumber: 9.3 Consensus size: 54
28278036 TTAGTTTACC
* * *
28278046 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCGAAATACCCCTAGTTTATAAAATTACCAAAATACCCTC-GATTTGTA
* *
28278100 AAATTGTA-AG-AATACCCCTAGTTTATAAAATTACCAAAATACCC-CTGATTTGTG
1 AAA-T-TACCGAAATACCCCTAGTTTATAAAATTACCAAAATACCCTC-GATTTGTA
* * ** * *** *
28278154 AAATTACTGAAATA-CCCTCGACCTGTAAAATTATTGAAATACCCTCGACTTGTA
1 AAATTACCGAAATACCCCTAG-TTTATAAAATTACCAAAATACCCTCGATTTGTA
* * * *
28278208 AAATTACC-AAAGTACCCCGA-TTTATAAAATTACCTAAATATCCTCGATTAGTA
1 AAATTACCGAAA-TACCCCTAGTTTATAAAATTACCAAAATACCCTCGATTTGTA
* ** **
28278261 AAATTACCGAAATACCTC-AGTTTGCAAAATTACTGAAATACCCTCGATTTGTA
1 AAATTACCGAAATACCCCTAGTTTATAAAATTACCAAAATACCCTCGATTTGTA
* * ** * *** **
28278314 AAATTACTGAAATACTCCT-GTAAGATAGAATTACCATTTTACCCTCGATTTACA
1 AAATTACCGAAATACCCCTAGT-TTATAAAATTACCAAAATACCCTCGATTTGTA
* *** * * *** **
28278368 GAATTACCGTTTTA-CCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACA
1 AAATTACCGAAATACCCCTAG-TTTATAAAATTACCAAAATACCCTCGATTTGTA
* * * ***
28278422 AAATTACTGAAATACCCTTAGTTTACAAAATTACCAAAATACCCTCGATCAATA
1 AAATTACCGAAATACCCCTAGTTTATAAAATTACCAAAATACCCTCGATTTGTA
* * * *
28278476 AAATTACCAAAATA-CCCTGGTTTGTAAAATTACCAAAATACCC-CTGATTTGTG
1 AAATTACCGAAATACCCCTAGTTTATAAAATTACCAAAATACCCTC-GATTTGTA
*
28278529 GAATTACCGAAATA
1 AAATTACCGAAATA
28278543 TAGGGTAGAA
Statistics
Matches: 343, Mismatches: 84, Indels: 33
0.75 0.18 0.07
Matches are distributed among these distances:
52 4 0.01
53 135 0.39
54 192 0.56
55 10 0.03
56 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (54 bp):
AAATTACCGAAATACCCCTAGTTTATAAAATTACCAAAATACCCTCGATTTGTA
Found at i:28278266 original size:80 final size:79
Alignment explanation
Indices: 28278125--28278328 Score: 220
Period size: 80 Copynumber: 2.5 Consensus size: 79
28278115 CCCTAGTTTA
* **
28278125 TAAAATTACCAAAATACCCCTGATTTGTGAAATTA-CTGAAATACCCTCGACCTGTAAAATTATT
1 TAAAATTACC-AAATACCCC-GATTTGTAAAATTACCTGAAATACCCTCGACCTGTAAAATTACC
28278189 GAAATACCCTC-GACTTG
64 GAAATA-CCTCAG-CTTG
* * *
28278206 TAAAATTACCAAAGTACCCCGATTTATAAAATTACCT-AAATATCCTCGA-TTAGTAAAATTACC
1 TAAAATTACCAAA-TACCCCGATTTGTAAAATTACCTGAAATACCCTCGACCT-GTAAAATTACC
*
28278269 GAAATACCTCAGTTTG
64 GAAATACCTCAGCTTG
* *
28278285 CAAAATTACTGAAATACCCTCGATTTGTAAAATTA-CTGAAATAC
1 TAAAATTAC-CAAATACCC-CGATTTGTAAAATTACCTGAAATAC
28278329 TCCTGTAAGA
Statistics
Matches: 105, Mismatches: 11, Indels: 15
0.80 0.08 0.11
Matches are distributed among these distances:
79 23 0.22
80 64 0.61
81 18 0.17
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.30
Consensus pattern (79 bp):
TAAAATTACCAAATACCCCGATTTGTAAAATTACCTGAAATACCCTCGACCTGTAAAATTACCGA
AATACCTCAGCTTG
Found at i:28278492 original size:81 final size:79
Alignment explanation
Indices: 28278036--28278518 Score: 287
Period size: 81 Copynumber: 6.0 Consensus size: 79
28278026 TTAGAATACT
* * * * * *
28278036 TTAGTTTACCAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGGTTTGTAA
1 TTAGTTTACAAAATTACCAAAATACCCCGA-TTTATAAAATTACCAAAATA-CCCTCGATTATAA
* *
28278101 AATT-GTAAGAATACCC
64 AATTACTGA-AATACCC
* * * * ** * *
28278117 CTAGTTTATAAAATTACCAAAATACCCCTGATTTGTGAAATTACTGAAATACCCTCGACCTGTAA
1 TTAGTTTACAAAATTACCAAAATACCCC-GATTTATAAAATTACCAAAATACCCTCGA-TTATAA
*
28278182 AATTATTGAAATACCC
64 AATTACTGAAATACCC
* * * * *
28278198 TCGACTTGT--AAAATTACCAAAGTACCCCGATTTATAAAATTACCTAAATATCCTCGATTAGTA
1 T-TAGTT-TACAAAATTACCAAAATACCCCGATTTATAAAATTACCAAAATACCCTCGATTA-TA
*
28278261 AAATTACCGAAATA-CC
63 AAATTACTGAAATACCC
* * ** * ** **
28278277 TCAGTTTGCAAAATTACTGAAATACCCTCGATTTGTAAAATTACTGAAATACTCCT-GTAAGATA
1 TTAGTTTACAAAATTACCAAAATACCC-CGATTTATAAAATTACCAAAATAC-CCTCG-ATTATA
* * **
28278341 GAATTAC-CATTTTACCC
63 AAATTACTGA-AATACCC
* * **** * *** *
28278358 -TCGATTTACAGAATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACA
1 TTAG-TTTACAAAATTACCAAAATACCC-CGATTTATAAAATTACCAAAATACCCTCGA-TTATA
28278422 AAATTACTGAAATACCC
63 AAATTACTGAAATACCC
** * * *
28278439 TTAGTTTACAAAATTACCAAAATACCCTCGATCAATAAAATTACCAAAATACCCTGGTTTGTAAA
1 TTAGTTTACAAAATTACCAAAATACCC-CGATTTATAAAATTACCAAAATACCCTCGATTATAAA
**
28278504 ATTACCAAAATACCC
65 ATTACTGAAATACCC
28278519 CTGATTTGTG
Statistics
Matches: 304, Mismatches: 80, Indels: 37
0.72 0.19 0.09
Matches are distributed among these distances:
77 1 0.00
78 3 0.01
79 20 0.07
80 97 0.32
81 173 0.57
82 9 0.03
83 1 0.00
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (79 bp):
TTAGTTTACAAAATTACCAAAATACCCCGATTTATAAAATTACCAAAATACCCTCGATTATAAAA
TTACTGAAATACCC
Found at i:28278533 original size:27 final size:26
Alignment explanation
Indices: 28278046--28278542 Score: 257
Period size: 27 Copynumber: 18.5 Consensus size: 26
28278036 TTAGTTTACC
28278046 AAATTACCAAAATACCCCT-AGTTTGTA
1 AAATTACCAAAATA-CCCTGA-TTTGTA
*
28278073 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATA-CCCTGATTTGTA
** *
28278100 AAATT-GTAAGAATACCCCT-AGTTTATA
1 AAATTACCAA-AATA-CCCTGA-TTTGTA
*
28278127 AAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATA-CCCTGATTTGTA
** **
28278154 AAATTACTGAAATACCCTCGACCTGTA
1 AAATTACCAAAATACCCT-GATTTGTA
*** *
28278181 AAATTATTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCT-GATTTGTA
* * *
28278208 AAATTACCAAAGTACCCCGATTTATA
1 AAATTACCAAAATACCCTGATTTGTA
* * *
28278234 AAATTACCTAAATATCCTCGATTAGTA
1 AAATTACCAAAATACCCT-GATTTGTA
* * *
28278261 AAATTACCGAAATA-CCTCAGTTTGCA
1 AAATTACCAAAATACCCTGA-TTTGTA
**
28278287 AAATTACTGAAATACCCTCGATTTGTA
1 AAATTACCAAAATACCCT-GATTTGTA
** **
28278314 AAATTACTGAAATACTCCTG-TAAGATA
1 AAATTACCAAAATAC-CCTGATTTG-TA
* *** **
28278341 GAATTACCATTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCT-GATTTGTA
* **** *
28278368 GAATTACCGTTTTACCCTCGATTTATA
1 AAATTACCAAAATACCCT-GATTTGTA
* *** **
28278395 GAATTACCATTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCT-GATTTGTA
** * **
28278422 AAATTACTGAAATACCCTTAGTTTACA
1 AAATTACCAAAATACCCTGA-TTTGTA
***
28278449 AAATTACCAAAATACCCTCGATCAATA
1 AAATTACCAAAATACCCT-GATTTGTA
*
28278476 AAATTACCAAAATACCCTGGTTTGTA
1 AAATTACCAAAATACCCTGATTTGTA
*
28278502 AAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATA-CCCTGATTTGTA
* *
28278529 GAATTACCGAAATA
1 AAATTACCAAAATA
28278543 TAGGGTAGAA
Statistics
Matches: 380, Mismatches: 73, Indels: 34
0.78 0.15 0.07
Matches are distributed among these distances:
25 1 0.00
26 70 0.18
27 300 0.79
28 9 0.02
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (26 bp):
AAATTACCAAAATACCCTGATTTGTA
Found at i:28278573 original size:27 final size:27
Alignment explanation
Indices: 28278543--28278961 Score: 615
Period size: 27 Copynumber: 15.6 Consensus size: 27
28278533 TACCGAAATA
* *
28278543 TAGGGTAGAATTATCGAAATACCCTTG
1 TAGGGTAGAATTACCGAAATACCCCTG
** * *
28278570 TAGGGTAGAATTATTGCAATACCCCTA
1 TAGGGTAGAATTACCGAAATACCCCTG
28278597 TAGGGTAGAATTACCGAAATACCCCTG
1 TAGGGTAGAATTACCGAAATACCCCTG
28278624 TAGGGTAGAATTACCGAAATACCCCTG
1 TAGGGTAGAATTACCGAAATACCCCTG
* *
28278651 TAGGGTAGAATTAGCGCAATACCCCTG
1 TAGGGTAGAATTACCGAAATACCCCTG
*
28278678 TAGGGTAGAATTACCGAAATACCCCTA
1 TAGGGTAGAATTACCGAAATACCCCTG
* *
28278705 TAGGGTAGAATTAGCGCAATACCCCTG
1 TAGGGTAGAATTACCGAAATACCCCTG
*
28278732 TAGAGTAGAATTACCGAAATACCCCTG
1 TAGGGTAGAATTACCGAAATACCCCTG
*
28278759 TAGGGTAGAATTACCGGAATACCCCTG
1 TAGGGTAGAATTACCGAAATACCCCTG
*
28278786 TAGGGTAGAATTACCGGAATACCCCTG
1 TAGGGTAGAATTACCGAAATACCCCTG
** *
28278813 TAGGGTAGAATTATTGAAATACCCTTG
1 TAGGGTAGAATTACCGAAATACCCCTG
28278840 TAGGGTAGAATTACCGAAATACCCCTG
1 TAGGGTAGAATTACCGAAATACCCCTG
*
28278867 TAGGGTAGAATTACCGAAATACCCTTG
1 TAGGGTAGAATTACCGAAATACCCCTG
*
28278894 TAGGGTAGAATTACCAAAATACCCCTG
1 TAGGGTAGAATTACCGAAATACCCCTG
* * *
28278921 TAGTGTAGAATTACCGAGATA-CCTTG
1 TAGGGTAGAATTACCGAAATACCCCTG
* *
28278947 TGGGGTAAAATTACC
1 TAGGGTAGAATTACC
28278962 ATTTTGCCCC
Statistics
Matches: 354, Mismatches: 38, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
26 16 0.05
27 338 0.95
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (27 bp):
TAGGGTAGAATTACCGAAATACCCCTG
Found at i:28279440 original size:22 final size:22
Alignment explanation
Indices: 28279388--28279452 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
28279378 TTAAAGCCTT
* *
28279388 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
* *
28279410 CT-ACATATGGCTCTATGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
*
28279432 CTGATTATGGCTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
28279453 ACGTATTTTC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
21 1 0.03
22 32 0.94
23 1 0.03
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.34
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:28279641 original size:27 final size:26
Alignment explanation
Indices: 28279611--28279712 Score: 89
Period size: 27 Copynumber: 3.8 Consensus size: 26
28279601 ATTCTGTTAA
* *
28279611 GTGGCTTTGCCATATTATCTGTTTCTG
1 GTGGCTATGCCA-AATATCTGTTTCTG
28279638 GTGGCTATGACACAAATATCTG-TTCTG
1 GTGGCTATG-C-CAAATATCTGTTTCTG
* *
28279665 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTATGCCA-AATATCTGTTTCTG
* * *
28279692 GTGACTCTGTCACAATATCTG
1 GTGGCTATGCCA-AATATCTG
28279713 ATAACTGAGC
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
25 2 0.03
26 9 0.14
27 44 0.68
28 8 0.12
29 2 0.03
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.37
Consensus pattern (26 bp):
GTGGCTATGCCAAATATCTGTTTCTG
Found at i:28279669 original size:54 final size:53
Alignment explanation
Indices: 28279611--28279712 Score: 132
Period size: 54 Copynumber: 1.9 Consensus size: 53
28279601 ATTCTGTTAA
* * * * *
28279611 GTGGCTTTGCCATATTATCTGTTTCTGGTGGCTATGACACAAATATCTGTTCTG
1 GTGGCTCTGCCACAATATCTGTATCTGGTGACTATGACAC-AATATCTGTTCTG
* *
28279665 GTGGCTCTGCCACAATATCTGTATCTGGTGACTCTGTCACAATATCTG
1 GTGGCTCTGCCACAATATCTGTATCTGGTGACTATGACACAATATCTG
28279713 ATAACTGAGC
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
53 8 0.20
54 33 0.80
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.37
Consensus pattern (53 bp):
GTGGCTCTGCCACAATATCTGTATCTGGTGACTATGACACAATATCTGTTCTG
Found at i:28279887 original size:6 final size:6
Alignment explanation
Indices: 28279849--28280011 Score: 102
Period size: 6 Copynumber: 26.3 Consensus size: 6
28279839 TTGCATTCAC
* * *
28279849 ATTCTG ATTTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTTTG ATTCTG
1 ATTCTG A-TTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * * *
28279899 -TTACCTG ATACTG ATTTTG ATTTTG ATTCT- ATTACCTG ATACTA ATTCTG
1 ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG
* * *
28279949 CTTCTG ATTCTG ATTCTG ATTCTG CCA-CCTG ATTCTG ACTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG --ATTCTG ATTCTG ATTCTG ATTCTG
28279998 ATTCT- AGTTCTG AT
1 ATTCTG A-TTCTG AT
28280012 AATGTTTCTT
Statistics
Matches: 122, Mismatches: 20, Indels: 30
0.71 0.12 0.17
Matches are distributed among these distances:
5 9 0.07
6 91 0.75
7 17 0.14
8 5 0.04
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:28279895 original size:31 final size:31
Alignment explanation
Indices: 28279849--28279960 Score: 170
Period size: 31 Copynumber: 3.6 Consensus size: 31
28279839 TTGCATTCAC
28279849 ATTCTGATTTTTGATTCTGTTACCTGATACTG
1 ATTCTGA-TTTTGATTCTGTTACCTGATACTG
28279881 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
* * *
28279912 ATTTTGATTTTGATTCTATTACCTGATACTA
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
* *
28279943 ATTCTGCTTCTGATTCTG
1 ATTCTGATTTTGATTCTG
28279961 ATTCTGATTC
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
31 66 0.90
32 7 0.10
ACGTcount: A:0.20, C:0.16, G:0.14, T:0.50
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTTACCTGATACTG
Found at i:28279906 original size:25 final size:24
Alignment explanation
Indices: 28279849--28280011 Score: 102
Period size: 25 Copynumber: 6.6 Consensus size: 24
28279839 TTGCATTCAC
*
28279849 ATTCTGATTTTTGATTCTG-TTACCTG
1 ATTCTGA-TTCTGATTCTGATT--CTG
* *
28279875 ATACTGATTCTGATTTTGATTCTG
1 ATTCTGATTCTGATTCTGATTCTG
* * *
28279899 -TTACCTGATACTGATTTTGATTTTG
1 ATT--CTGATTCTGATTCTGATTCTG
* *
28279924 ATTCT-ATTACCTGATACTAATTCTG
1 ATTCTGATT--CTGATTCTGATTCTG
*
28279949 CTTCTGATTCTGATTCTGATTCTG
1 ATTCTGATTCTGATTCTGATTCTG
* *
28279973 CCA-CCTGATTCTGACTCTGATTCTG
1 --ATTCTGATTCTGATTCTGATTCTG
28279998 ATTCT-AGTTCTGAT
1 ATTCTGA-TTCTGAT
28280012 AATGTTTCTT
Statistics
Matches: 107, Mismatches: 19, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
23 5 0.05
24 26 0.24
25 63 0.59
26 13 0.12
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.48
Consensus pattern (24 bp):
ATTCTGATTCTGATTCTGATTCTG
Done.