Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 85 of 344
Found at i:28307857 original size:102 final size:100
Alignment explanation
Indices: 28307528--28307847 Score: 329
Period size: 101 Copynumber: 3.2 Consensus size: 100
28307518 AGGCTATACT
* * * * * *
28307528 TAGTACTACACATGTGACTTATCCATCTGATACATGTAGTAGCCTGCACTTAGTACTACACATGT
1 TAGTACTACACATGTGACCTAACAATCTGATACACGTAGTAGCCTGCACTTAGTACGACACACGT
* ** * * ** * * *
28307593 GATCAAAGTTAACAGG-TACGTAAAGTAGCCTACAC
66 GACCAAAACTATC-GGAAACACATAGTAGCCTGCTC
* * *
28307628 TTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACGACAGACG
1 -TAGTACTACACATGTGACCTAACAATCTGATACACGTAGTAGCCTGCACTTAGTACGACACACG
* ** *
28307693 TGATCAAAACTATCGGGTACGCATAGTAGCCTGCTC
65 TGACCAAAACTATCGGAAACACATAGTAGCCTGCTC
*
28307729 TTAGTACTACACATGTGACCTAACAATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACG
1 -TAGTACTACACATGTGACCTAACAATCTGATACACGTAGTAGCCTGCACTTAGTACGACACACG
**
28307794 TGACCTAAAACTATCTTAAACACATAGTAGCCTGCATAC
65 TGACC-AAAACTATCGGAAACACATAGTAGCCTGC-T-C
*
28307833 -AGTACTACAGATGTG
1 TAGTACTACACATGTG
28307848 TTCTCACAAT
Statistics
Matches: 190, Mismatches: 25, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
100 2 0.01
101 148 0.78
102 38 0.20
103 1 0.01
104 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (100 bp):
TAGTACTACACATGTGACCTAACAATCTGATACACGTAGTAGCCTGCACTTAGTACGACACACGT
GACCAAAACTATCGGAAACACATAGTAGCCTGCTC
Found at i:28310528 original size:30 final size:30
Alignment explanation
Indices: 28310493--28310561 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
28310483 ACACTAGGGG
28310493 ACACACGGCCATATAACATAACCATGTGTC
1 ACACACGGCCATATAACATAACCATGTGTC
* *
28310523 ACACACGACCATATAACATAACCGTGTGTC
1 ACACACGGCCATATAACATAACCATGTGTC
28310553 ACACACGGC
1 ACACACGGC
28310562 TGAGACTCAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.36, C:0.32, G:0.14, T:0.17
Consensus pattern (30 bp):
ACACACGGCCATATAACATAACCATGTGTC
Found at i:28315644 original size:39 final size:39
Alignment explanation
Indices: 28315590--28315715 Score: 198
Period size: 39 Copynumber: 3.2 Consensus size: 39
28315580 TTCAGTGATG
*
28315590 TATATCCGAACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
28315629 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
* * * *
28315668 TATATCCGGACTTAAGGTTCGCAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
*
28315707 TATGTCCGG
1 TATATCCGG
28315716 GCTAAAGTCC
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 81 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (39 bp):
TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
Found at i:28315730 original size:39 final size:39
Alignment explanation
Indices: 28315590--28315753 Score: 188
Period size: 39 Copynumber: 4.2 Consensus size: 39
28315580 TTCAGTGATG
* * *
28315590 TATATCCGAACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAT
* *
28315629 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAT
* *
28315668 TATATCCGGACTTAAGGTTCGCAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAT
* * * * * *
28315707 TATGTCCGGGC-TAAAGTCCCGCAGGCTTCGAGCTGGTAT
1 TATATCCGGACTTAAGGT-CCGCAGGCTACGTGCTGGAAT
28315746 TATA-CCGG
1 TATATCCGG
28315754 GTTTAAATTC
Statistics
Matches: 110, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
38 9 0.08
39 101 0.92
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (39 bp):
TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAT
Found at i:28319391 original size:12 final size:12
Alignment explanation
Indices: 28319370--28319404 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
28319360 CAAACATCTA
*
28319370 ATACAATTTCAC
1 ATACATTTTCAC
*
28319382 ATACATTTTCTC
1 ATACATTTTCAC
28319394 ATACATTTTCA
1 ATACATTTTCA
28319405 ATTTCATGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.34, C:0.23, G:0.00, T:0.43
Consensus pattern (12 bp):
ATACATTTTCAC
Found at i:28328606 original size:15 final size:16
Alignment explanation
Indices: 28328580--28328609 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28328570 AAAATAATCT
28328580 TAAAACAAAATAAAAG
1 TAAAACAAAATAAAAG
28328596 TAAAA-AAAATAAAA
1 TAAAACAAAATAAAA
28328610 TAATAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.13
Consensus pattern (16 bp):
TAAAACAAAATAAAAG
Found at i:28337197 original size:79 final size:81
Alignment explanation
Indices: 28337061--28337245 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
28337051 TTGAATGATG
*
28337061 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
28337125 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
28337140 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
28337202 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
28337220 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28337246 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:28337259 original size:40 final size:41
Alignment explanation
Indices: 28337061--28337245 Score: 231
Period size: 40 Copynumber: 4.6 Consensus size: 41
28337051 TTGAATGATG
* * *
28337061 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAT-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
28337101 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-AT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA
28337141 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
28337180 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
28337221 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28337246 AACGAGTAGC
Statistics
Matches: 127, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
39 35 0.28
40 82 0.65
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:28337267 original size:79 final size:79
Alignment explanation
Indices: 28337114--28337278 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
28337104 GGACTAAGAT
* **
28337114 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
28337179 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
28337193 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
28337256 TATATTC-GGTTAAATC
63 TAAATCCGGGTTAAATC
*
28337272 CTGAAGG
1 CCGAAGG
28337279 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.65
80 24 0.32
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:28344483 original size:38 final size:38
Alignment explanation
Indices: 28344431--28344514 Score: 141
Period size: 38 Copynumber: 2.2 Consensus size: 38
28344421 ACAAGGTATT
* *
28344431 ACATGTAGGTGCATCATTTATTTGAAGAACAAATCTGCA
1 ACATG-AGGTGCATCACTTATTTGAAGAACAAATCTACA
28344470 ACATGAGGTGCATCACTTATTTGAAGAACAAATCTACA
1 ACATGAGGTGCATCACTTATTTGAAGAACAAATCTACA
28344508 ACATGAG
1 ACATGAG
28344515 TAGCGTCATT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
38 38 0.88
39 5 0.12
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (38 bp):
ACATGAGGTGCATCACTTATTTGAAGAACAAATCTACA
Found at i:28345577 original size:35 final size:36
Alignment explanation
Indices: 28345526--28345639 Score: 108
Period size: 35 Copynumber: 3.2 Consensus size: 36
28345516 GATGAAATTC
*
28345526 ATCTCTATTTCATGTTTATT-TCTCAGATGGACTTT
1 ATCTCTATTTCGTGTTTATTATCTCAGATGGACTTT
* * * * *
28345561 ATCTTTGTTTTGTGTTTATTATCCCA-ATGGATTTT
1 ATCTCTATTTCGTGTTTATTATCTCAGATGGACTTT
* ** *
28345596 AACTCTATTTCGTGTTTATTGCCTC-GATAGACTTT
1 ATCTCTATTTCGTGTTTATTATCTCAGATGGACTTT
*
28345631 ATCGCTATT
1 ATCTCTATT
28345640 GATGTAACAC
Statistics
Matches: 60, Mismatches: 17, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
35 56 0.93
36 4 0.07
ACGTcount: A:0.19, C:0.17, G:0.13, T:0.51
Consensus pattern (36 bp):
ATCTCTATTTCGTGTTTATTATCTCAGATGGACTTT
Found at i:28348415 original size:145 final size:145
Alignment explanation
Indices: 28348217--28348490 Score: 503
Period size: 145 Copynumber: 1.9 Consensus size: 145
28348207 AACTCAAGGT
* * *
28348217 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGTACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
28348282 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
28348347 ATTTCAAGTTCGCAC
131 ATTTCAAGTTCGCAC
*
28348362 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
28348427 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATG
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATG
28348491 TACTTTAAAC
Statistics
Matches: 124, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
145 124 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.30
Consensus pattern (145 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
ATTTCAAGTTCGCAC
Found at i:28348507 original size:29 final size:30
Alignment explanation
Indices: 28348468--28348546 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
28348458 CTTAATAATC
28348468 AACCACGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
28348498 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
28348527 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
28348547 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:28356520 original size:145 final size:145
Alignment explanation
Indices: 28356322--28356595 Score: 503
Period size: 145 Copynumber: 1.9 Consensus size: 145
28356312 AACTCAAGGT
* * *
28356322 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGTACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
28356387 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
28356452 ATTTCAAGTTCGCAC
131 ATTTCAAGTTCGCAC
*
28356467 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
28356532 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATG
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATG
28356596 TACTTTAAAC
Statistics
Matches: 124, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
145 124 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.30
Consensus pattern (145 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
ATTTCAAGTTCGCAC
Found at i:28356612 original size:29 final size:30
Alignment explanation
Indices: 28356573--28356651 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
28356563 CTTAATAATC
28356573 AACCACGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
28356603 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
28356632 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
28356652 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:28358634 original size:72 final size:72
Alignment explanation
Indices: 28358541--28358687 Score: 276
Period size: 72 Copynumber: 2.0 Consensus size: 72
28358531 ATACGCCAAA
* *
28358541 AGATGTACTTAGGTGAATACTACTTTGCCAATTATACTACTTTAAGACTATACGCCAAACCTTGT
1 AGATGTACTTAGGCGAATACTACTTTGCCAATTATACTACTTTAAGACTATAAGCCAAACCTTGT
28358606 ACCCGTT
66 ACCCGTT
28358613 AGATGTACTTAGGCGAATACTACTTTGCCAATTATACTACTTTAAGACTATAAGCCAAACCTTGT
1 AGATGTACTTAGGCGAATACTACTTTGCCAATTATACTACTTTAAGACTATAAGCCAAACCTTGT
28358678 ACCCGTT
66 ACCCGTT
28358685 AGA
1 AGA
28358688 ACCTGAGTGT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (72 bp):
AGATGTACTTAGGCGAATACTACTTTGCCAATTATACTACTTTAAGACTATAAGCCAAACCTTGT
ACCCGTT
Found at i:28358931 original size:51 final size:51
Alignment explanation
Indices: 28358811--28358938 Score: 166
Period size: 51 Copynumber: 2.5 Consensus size: 51
28358801 TACCATGACA
* *
28358811 TATTTCATCTATGGGCTTACGCCATATGCCTTATACCAGACTACCATAGCC
1 TATTTCATCTATGGTCTTATGCCATATGCCTTATACCAGACTACCATAGCC
** * * * *
28358862 TCCTTCAACCATGGTCTTATGCCATATGCCTTATACTAGACTACCATTGCC
1 TATTTCATCTATGGTCTTATGCCATATGCCTTATACCAGACTACCATAGCC
**
28358913 TATTTCATCTATAATCTTATGCCATA
1 TATTTCATCTATGGTCTTATGCCATA
28358939 AACCATCGTC
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.35
Consensus pattern (51 bp):
TATTTCATCTATGGTCTTATGCCATATGCCTTATACCAGACTACCATAGCC
Found at i:28360858 original size:12 final size:11
Alignment explanation
Indices: 28360822--28360873 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
28360812 TTGACTAGAC
28360822 AAAAAAT-TTGT
1 AAAAAATATT-T
*
28360833 AAAAAA-AATT
1 AAAAAATATTT
28360843 -AAAAATATTT
1 AAAAAATATTT
28360853 AAAAAATATTT
1 AAAAAATATTT
28360864 AAAAATATAT
1 AAAAA-ATAT
28360874 AAGAATTGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
9 5 0.14
10 4 0.11
11 22 0.63
12 4 0.11
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (11 bp):
AAAAAATATTT
Found at i:28360867 original size:29 final size:29
Alignment explanation
Indices: 28360835--28360914 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 29
28360825 AAATTTGTAA
28360835 AAAAAATTAAAAATATTTAAAAAATATTT
1 AAAAAATTAAAAATATTTAAAAAATATTT
* *
28360864 AAAAATATATAAGAAT-TGT-AAAAATATTT
1 AAAAA-AT-TAAAAATATTTAAAAAATATTT
**
28360893 AAATTATTAAAAATA-TTAAAAA
1 AAAAAATTAAAAATATTTAAAAA
28360915 TTGTAAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
27 7 0.17
28 6 0.15
29 18 0.44
30 4 0.10
31 6 0.15
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAAAATTAAAAATATTTAAAAAATATTT
Found at i:28360869 original size:10 final size:10
Alignment explanation
Indices: 28360823--28360915 Score: 79
Period size: 10 Copynumber: 9.6 Consensus size: 10
28360813 TGACTAGACA
28360823 AAAAAT-TTGT
1 AAAAATATT-T
* *
28360833 AAAAAAAATT
1 AAAAATATTT
28360843 AAAAATATTT
1 AAAAATATTT
28360853 AAAAAATATTT
1 -AAAAATATTT
*
28360864 AAAAATATAT
1 AAAAATATTT
* *
28360874 AAGAAT-TGT
1 AAAAATATTT
28360883 AAAAATATTT
1 AAAAATATTT
*
28360893 -AAATTA-TT
1 AAAAATATTT
28360901 AAAAATA-TT
1 AAAAATATTT
28360910 AAAAAT
1 AAAAAT
28360916 TGTAAAAAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 9
0.77 0.12 0.10
Matches are distributed among these distances:
8 2 0.03
9 25 0.37
10 30 0.44
11 11 0.16
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (10 bp):
AAAAATATTT
Found at i:28360921 original size:9 final size:9
Alignment explanation
Indices: 28360834--28360928 Score: 77
Period size: 9 Copynumber: 10.1 Consensus size: 9
28360824 AAAATTTGTA
*
28360834 AAAAAAATT
1 AAAAATATT
28360843 AAAAATATTT
1 AAAAATA-TT
28360853 AAAAAATATTT
1 -AAAAATA-TT
28360864 AAAAATATAT
1 AAAAATAT-T
*
28360874 AAGAAT-TGT
1 AAAAATAT-T
28360883 AAAAATATT
1 AAAAATATT
* *
28360892 TAAATTATT
1 AAAAATATT
28360901 AAAAATATT
1 AAAAATATT
28360910 AAAAAT-TGT
1 AAAAATAT-T
*
28360919 AAAAAAATT
1 AAAAATATT
28360928 A
1 A
28360929 TTGTAAAAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
8 1 0.01
9 43 0.61
10 17 0.24
11 10 0.14
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (9 bp):
AAAAATATT
Found at i:28360929 original size:30 final size:28
Alignment explanation
Indices: 28360893--28361001 Score: 83
Period size: 31 Copynumber: 3.6 Consensus size: 28
28360883 AAAAATATTT
28360893 AAATTATTAAAAATATTAAAAATTGTAAAA
1 AAATTATTAAAAA-ATTAAAAATTGT-AAA
* *
28360923 AAATTATTGTAAAAAAATAAATATTGTAAA
1 AAATTA-T-TAAAAAATTAAAAATTGTAAA
* * *
28360953 TAACTATTAAAAAATGTAAAAAGAATGTAAA
1 AAATTATTAAAAAAT-T-AAAA-ATTGTAAA
* *
28360984 AAAGTTCTTTAAAAATTA
1 AAA-TTATTAAAAAATTA
28361002 TGAATCGGTT
Statistics
Matches: 62, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
28 7 0.11
29 2 0.03
30 17 0.27
31 21 0.34
32 15 0.24
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (28 bp):
AAATTATTAAAAAATTAAAAATTGTAAA
Found at i:28360939 original size:17 final size:17
Alignment explanation
Indices: 28360909--28360952 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 17
28360899 TTAAAAATAT
*
28360909 TAAAAATTGTAAAAAAA
1 TAAATATTGTAAAAAAA
28360926 T---TATTGTAAAAAAA
1 TAAATATTGTAAAAAAA
28360940 TAAATATTGTAAA
1 TAAATATTGTAAA
28360953 TAACTATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
14 13 0.57
17 10 0.43
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (17 bp):
TAAATATTGTAAAAAAA
Found at i:28360952 original size:31 final size:30
Alignment explanation
Indices: 28360893--28360965 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
28360883 AAAAATATTT
*
28360893 AAATTATTAAAAATATTAAAAATTGTAAAA
1 AAATTATTAAAAATAATAAAAATTGTAAAA
*
28360923 AAATTATTGTAAAAA-AATAAATATTGT-AAA
1 AAATTA-T-TAAAAATAATAAAAATTGTAAAA
* *
28360953 TAACTATTAAAAA
1 AAATTATTAAAAA
28360966 ATGTAAAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
28 6 0.16
29 1 0.03
30 13 0.35
31 11 0.30
32 6 0.16
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (30 bp):
AAATTATTAAAAATAATAAAAATTGTAAAA
Found at i:28361199 original size:20 final size:20
Alignment explanation
Indices: 28361171--28361285 Score: 67
Period size: 20 Copynumber: 5.7 Consensus size: 20
28361161 GAGGATTTGA
*
28361171 TTTATTAATTATTTACAATT
1 TTTAATAATTATTTACAATT
* *
28361191 TTTAATAATT-TTTAAAGAAT
1 TTTAATAATTATTTACA-ATT
* * *
28361211 TTAAAT-ATTGTTTTATAATT
1 TTTAATAATT-ATTTACAATT
* *
28361231 TTTAATAACTTCTTTA-AAAT
1 TTTAATAA-TTATTTACAATT
* *
28361251 TTTAA-AATATTTTTAACAATA
1 TTTAATAAT-TATTT-ACAATT
28361272 TTTAATAATTATTT
1 TTTAATAATTATTT
28361286 TCTTTTACAA
Statistics
Matches: 73, Mismatches: 13, Indels: 17
0.71 0.13 0.17
Matches are distributed among these distances:
18 1 0.01
19 14 0.19
20 32 0.44
21 21 0.29
22 5 0.07
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (20 bp):
TTTAATAATTATTTACAATT
Found at i:28361200 original size:10 final size:10
Alignment explanation
Indices: 28361187--28361281 Score: 63
Period size: 10 Copynumber: 9.4 Consensus size: 10
28361177 AATTATTTAC
28361187 AATTTTTAAT
1 AATTTTTAAT
28361197 AATTTTTAA-
1 AATTTTTAAT
* *
28361206 AGAATTTAAAT
1 A-ATTTTTAAT
*
28361217 -ATTGTTTTAT
1 AATT-TTTAAT
28361227 AATTTTTAAT
1 AATTTTTAAT
28361237 AACTTCTTTAA-
1 AA-TT-TTTAAT
*
28361248 AA-TTTTAAA
1 AATTTTTAAT
*
28361257 ATATTTTTAAC
1 A-ATTTTTAAT
*
28361268 AATATTTAAT
1 AATTTTTAAT
28361278 AATT
1 AATT
28361282 ATTTTCTTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
8 5 0.08
9 5 0.08
10 37 0.56
11 14 0.21
12 5 0.08
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (10 bp):
AATTTTTAAT
Found at i:28361231 original size:40 final size:40
Alignment explanation
Indices: 28361182--28361281 Score: 123
Period size: 41 Copynumber: 2.5 Consensus size: 40
28361172 TTATTAATTA
28361182 TTTACAATTTTTAATAATT-TTTAAAGAATTT-AAATATTGT
1 TTTACAATTTTTAATAATTCTTTAAA-AATTTAAAATATT-T
* *
28361222 TTTATAATTTTTAATAACTTCTTTAAAATTTTAAAATATTT
1 TTTACAATTTTTAATAA-TTCTTTAAAAATTTAAAATATTT
* *
28361263 TTAACAATATTTAATAATT
1 TTTACAATTTTTAATAATT
28361282 ATTTTCTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
40 18 0.35
41 21 0.40
42 13 0.25
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (40 bp):
TTTACAATTTTTAATAATTCTTTAAAAATTTAAAATATTT
Found at i:28363911 original size:17 final size:17
Alignment explanation
Indices: 28363889--28363928 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
28363879 TTTTCTTATT
*
28363889 TAAAATTTTA-AAAATAA
1 TAAAATTGTATAAAA-AA
28363906 TAAAATTGTATAAAAAA
1 TAAAATTGTATAAAAAA
28363923 TAAAAT
1 TAAAAT
28363929 CAATATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
TAAAATTGTATAAAAAA
Found at i:28364530 original size:247 final size:246
Alignment explanation
Indices: 28364176--28365190 Score: 1107
Period size: 247 Copynumber: 4.1 Consensus size: 246
28364166 ATCTATTCTA
* * * * * **
28364176 TTTAATTTTTTTAAATAATGTATGCACGTGTTCGATAAAAAAACCATTCTATTATGTTTAACTTT
1 TTTAATTTATTT-AATAATGTTTGCATGT-TTCG--CAAAAAATCATTCTACCATGTTTAACTTT
* * * * * *
28364241 TCTTTTAACAATATCTACATGTGGCTAACAAAAATTCATTCAATTATATTACCGTTATGATCGAT
62 TCTTTTAACAATATCTGCACGTGTCTAACAAAAATTCATTCAATTATATTGCAGTTATGATCGAC
* * * * *
28364306 ATTGAATTACTTCTTTATATGATGTGTTTATGTTTCTAAATATGTCCTAATCATATTTGGTTCAC
127 ATTGAACTACTTCTTTATATGATGTGTCTGTGTTTCTAAATATGTCCTAATCATATTTTGTCCAC
* * *
28364371 ATTTA-ATTTTTTCGCAATGTCTGTGTGTGTCTGACAAAGATTTATTTTGTTCG-G
192 ATTTACATTTTTTCACAATGTCTGCGCGTGTCTGACAAAGATTTATTTTGTT-GTG
*
28364425 TTTAATTTATTTAATAATGTTTGCATGTATTCTGCAAAAAATCATTTTACCATGTTTAACTTTTC
1 TTTAATTTATTTAATAATGTTTGCATGT-TTC-GCAAAAAATCATTCTACCATGTTTAACTTTTC
* * * * *
28364490 ATTTAACAATATCCGCACGTGTCTAACAAAAATTCATTCAATTGTATTGCAGTTATAATTGACAT
64 TTTTAACAATATCTGCACGTGTCTAACAAAAATTCATTCAATTATATTGCAGTTATGATCGACAT
* * *
28364555 TGAACTACTGCTTTATATGATGTGTTTGTGTTTCTAAATATGTCCTAATCATATTTTGTCCACGT
129 TGAACTACTTCTTTATATGATGTGTCTGTGTTTCTAAATATGTCCTAATCATATTTTGTCCACAT
* * * ** * *
28364620 TTACAGTTTTTCACAATGTCTGTGTGTGTCCAACAAATATTTATTTTGTTTTG
194 TTACATTTTTTCACAATGTCTGCGCGTGTCTGACAAAGATTTATTTTGTTGTG
* * * *
28364673 TTTAATTTGTTTAATAATGTTTAAACATG-CTCGATAAAAAATCATTCTACCATGTTTAACTTTT
1 TTTAATTTATTTAATAATGTTT--GCATGTTTCG-CAAAAAATCATTCTACCATGTTTAACTTTT
* * ** * *
28364737 CTTTTAATAATATCTGCACGTGCCCGACAAAAATTCATTCAATTGA-ATTGTAGTTATGATCGGC
63 CTTTTAACAATATCTGCACGTGTCTAACAAAAATTCATTCAATT-ATATTGCAGTTATGATCGAC
*
28364801 ATTGAACTACTTCTTT-TCATGACT-TGTCTGTGTTTCTAAATATGTCTTAATCATATTTTGTCC
127 ATTGAACTACTTCTTTAT-ATGA-TGTGTCTGTGTTTCTAAATATGTCCTAATCATATTTTGTCC
* * * *
28364864 ACACTTA-ATTTTTTCACAATTTTTGCGCGTGTCAGACAAAGATTTATTTTGTTGTG
190 ACATTTACATTTTTTCACAATGTCTGCGCGTGTCTGACAAAGATTTATTTTGTTGTG
* * * * ** *
28364920 TTTAATTTTTTTAAAAATGTTTGCAGGTGTCCGGCAAAAAATCATTCTAATATGTTCAACTTTTC
1 TTTAATTTATTTAATAATGTTTGCATGT-TTC-GCAAAAAATCATTCTACCATGTTTAACTTTTC
* * * * * * * *
28364985 TTTTAACAATATATGCATGTGT-TCGACAAAATTTCAGTCAATTGTATTTCAGTTATGATCAACA
64 TTTTAACAATATCTGCACGTGTCT-AACAAAAATTCATTCAATTATATTGCAGTTATGATCGACA
* * * * *
28365049 TTGAACTACTTCTTTACATGATATGTCTGTGATTCTAAATATGTCATAATCATATTTTGTCCACG
128 TTGAACTACTTCTTTATATGATGTGTCTGTGTTTCTAAATATGTCCTAATCATATTTTGTCCACA
* * *
28365114 TTTACA-TTTTTCACAATGTCTGCGCGTGTTCT-ACAAAAATCTATTATGTTGTG
193 TTTACATTTTTTCACAATGTCTGCGCGTG-TCTGACAAAGATTTATTTTGTTGTG
28365167 TTT-ATTTATTTTTAATAATGTTTG
1 TTTAATTTA--TTTAATAATGTTTG
28365191 TAAGTGTCCA
Statistics
Matches: 649, Mismatches: 97, Indels: 41
0.82 0.12 0.05
Matches are distributed among these distances:
245 3 0.00
246 5 0.01
247 384 0.59
248 240 0.37
249 13 0.02
250 4 0.01
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.44
Consensus pattern (246 bp):
TTTAATTTATTTAATAATGTTTGCATGTTTCGCAAAAAATCATTCTACCATGTTTAACTTTTCTT
TTAACAATATCTGCACGTGTCTAACAAAAATTCATTCAATTATATTGCAGTTATGATCGACATTG
AACTACTTCTTTATATGATGTGTCTGTGTTTCTAAATATGTCCTAATCATATTTTGTCCACATTT
ACATTTTTTCACAATGTCTGCGCGTGTCTGACAAAGATTTATTTTGTTGTG
Found at i:28365183 original size:495 final size:496
Alignment explanation
Indices: 28364207--28365189 Score: 1287
Period size: 495 Copynumber: 2.0 Consensus size: 496
28364197 ATGCACGTGT
** * * *
28364207 TCGATAAAAAAACCATTCTATTATGTTTAACTTTTCTTTTAACAATATCTACATGTGGCTAACAA
1 TCGATAAAAAAACCATTCTACCATGTTTAACTTTTCTTTTAACAATATCTACACGTGCCCAACAA
* * * *
28364272 AAATTCATTCAATTATATTACCGTTATGATCGATATTGAATTACTTCTTTATATGATGTGTTTAT
66 AAATTCATTCAATTATATTACAGTTATGATCGACATTGAACTACTTCTTTATATGATGTGTCTAT
* * * * *
28364337 GTTTCTAAATATGTCCTAATCATATTTGGTTCACATTTAATTTTTTCGCAATGTCTGTGTGTGTC
131 GTTTCTAAATATGTCCTAATCATATTTGGTCCACACTTAATTTTTTCACAATGTCTGCGCGTGTC
* * * * *
28364402 TGACAAAGATTTATTTTGTTCGGTTTAATTTATTTAATAATGTTTGCATGTATTCTGCAAAAAAT
196 AGACAAAGATTTATTTTGTTCGGTTTAATTTATTTAAAAATGTTTGCAGGTATCCGGCAAAAAAT
* * * * *
28364467 CATTTTACCATGTTTAACTTTTCATTTAACAATATCCGCACGTGTCTAACAAAAATTCATTCAAT
261 CATTCTAACATGTTCAACTTTTCATTTAACAATATACGCACGTGTCTAACAAAAATTCAGTCAAT
** * * * *
28364532 TGTATTGCAGTTATAATTGACATTGAACTACTGCTTTATATGATGTGTTTGTGTTTCTAAATATG
326 TGTATTGCAGTTATAATCAACATTGAACTACTGCTTTACATGATATGTCTGTGATTCTAAATATG
* * * * *
28364597 TCCTAATCATATTTTGTCCACGTTTACAGTTTTTCACAATGTCTGTGTGTGTCCAACAAATATTT
391 TCATAATCATATTTTGTCCACGTTTACAGTTTTTCACAATGTCTGCGCGTGTCCAACAAAAATCT
* *
28364662 ATTTTGTTTTGTTTAATTTGTTTAATAATGTTTAAACATGC
456 ATTATGTTGTGTTTAATTTGTTTAATAATGTTTAAACATGC
* * * *
28364703 TCGAT-AAAAAATCATTCTACCATGTTTAACTTTTCTTTTAATAATATCTGCACGTGCCCGACAA
1 TCGATAAAAAAACCATTCTACCATGTTTAACTTTTCTTTTAACAATATCTACACGTGCCCAACAA
** *
28364767 AAATTCATTCAATTGA-ATTGTAGTTATGATCGGCATTGAACTACTTCTTT-TCATGACT-TGTC
66 AAATTCATTCAATT-ATATTACAGTTATGATCGACATTGAACTACTTCTTTAT-ATGA-TGTGTC
* * * * *
28364829 TGTGTTTCTAAATATGTCTTAATCATATTTTGTCCACACTTAATTTTTTCACAATTTTTGCGCGT
128 TATGTTTCTAAATATGTCCTAATCATATTTGGTCCACACTTAATTTTTTCACAATGTCTGCGCGT
* *
28364894 GTCAGACAAAGATTTATTTTGTT-GTGTTTAATTTTTTTAAAAATGTTTGCAGGTGTCCGGCAAA
193 GTCAGACAAAGATTTATTTTGTTCG-GTTTAATTTATTTAAAAATGTTTGCAGGTATCCGGCAAA
* * * * * *
28364958 AAATCATTCTAATATGTTCAACTTTTCTTTTAACAATATATGCATGTGT-TCGACAAAATTTCAG
257 AAATCATTCTAACATGTTCAACTTTTCATTTAACAATATACGCACGTGTCT-AACAAAAATTCAG
* * *
28365022 TCAATTGTATTTCAGTTATGATCAACATTGAACTACTTCTTTACATGATATGTCTGTGATTCTAA
321 TCAATTGTATTGCAGTTATAATCAACATTGAACTACTGCTTTACATGATATGTCTGTGATTCTAA
* *
28365087 ATATGTCATAATCATATTTTGTCCACGTTTACA-TTTTTCACAATGTCTGCGCGTGTTCTACAAA
386 ATATGTCATAATCATATTTTGTCCACGTTTACAGTTTTTCACAATGTCTGCGCGTGTCCAACAAA
* *
28365151 AATCTATTATGTTGTGTTTATTTATTTTTAATAATGTTT
451 AATCTATTATGTTGTGTTTAATT-TGTTTAATAATGTTT
28365190 GTAAGTGTCC
Statistics
Matches: 417, Mismatches: 64, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
494 48 0.12
495 362 0.87
496 7 0.02
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (496 bp):
TCGATAAAAAAACCATTCTACCATGTTTAACTTTTCTTTTAACAATATCTACACGTGCCCAACAA
AAATTCATTCAATTATATTACAGTTATGATCGACATTGAACTACTTCTTTATATGATGTGTCTAT
GTTTCTAAATATGTCCTAATCATATTTGGTCCACACTTAATTTTTTCACAATGTCTGCGCGTGTC
AGACAAAGATTTATTTTGTTCGGTTTAATTTATTTAAAAATGTTTGCAGGTATCCGGCAAAAAAT
CATTCTAACATGTTCAACTTTTCATTTAACAATATACGCACGTGTCTAACAAAAATTCAGTCAAT
TGTATTGCAGTTATAATCAACATTGAACTACTGCTTTACATGATATGTCTGTGATTCTAAATATG
TCATAATCATATTTTGTCCACGTTTACAGTTTTTCACAATGTCTGCGCGTGTCCAACAAAAATCT
ATTATGTTGTGTTTAATTTGTTTAATAATGTTTAAACATGC
Found at i:28365772 original size:62 final size:63
Alignment explanation
Indices: 28365675--28365792 Score: 184
Period size: 62 Copynumber: 1.9 Consensus size: 63
28365665 AAAAAGAGTA
* * * *
28365675 AACATTGTTAATGAAACATAACTCAGTTGATAAATTTACCAAAA-ACAAATCAAATTGAAGTT
1 AACATTGTCAATAAAACATAACTCAATTGATAAATTTACCAAAACAAAAATCAAATTGAAGTT
*
28365737 AACATTGTCAATAAAACATAATTCAATTGATAAATTTACCAAAACAAAAATCAAAT
1 AACATTGTCAATAAAACATAACTCAATTGATAAATTTACCAAAACAAAAATCAAAT
28365793 GGAATTTATA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
62 40 0.80
63 10 0.20
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.28
Consensus pattern (63 bp):
AACATTGTCAATAAAACATAACTCAATTGATAAATTTACCAAAACAAAAATCAAATTGAAGTT
Found at i:28365781 original size:28 final size:27
Alignment explanation
Indices: 28365688--28365782 Score: 66
Period size: 28 Copynumber: 3.2 Consensus size: 27
28365678 ATTGTTAATG
*
28365688 AAACATAACTCAGTTGATAAATTTACCAA
1 AAACATAA-TCAATTGATAAATTTACC-A
**
28365717 AAACA-AATCAAATTGAAGTTAACATTGTCAATA
1 AAACATAATC-AATTG-A--TAA-ATT-T-ACCA
28365750 AAACATAATTCAATTGATAAATTTACCA
1 AAACATAA-TCAATTGATAAATTTACCA
28365778 AAACA
1 AAACA
28365783 AAAATCAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 19
0.68 0.07 0.25
Matches are distributed among these distances:
27 2 0.04
28 13 0.25
29 7 0.13
30 3 0.06
31 6 0.12
32 3 0.06
33 8 0.15
34 8 0.15
35 2 0.04
ACGTcount: A:0.52, C:0.15, G:0.06, T:0.27
Consensus pattern (27 bp):
AAACATAATCAATTGATAAATTTACCA
Found at i:28366180 original size:3 final size:3
Alignment explanation
Indices: 28366174--28366211 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
28366164 GCCCTACTAC
28366174 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28366212 GAGAATTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:28380384 original size:41 final size:42
Alignment explanation
Indices: 28380282--28380418 Score: 170
Period size: 43 Copynumber: 3.2 Consensus size: 42
28380272 TGTGTGAATT
*
28380282 CATGTAAGACCATGTCTGGGACATTGGCATCGA-AGTGATAAAA
1 CATGTAAGACCATGTCTGGGACATTGGCATCGATA-T-ATGAAA
* **
28380325 CATGTAAGACCATTTCTGGGACATTGGCATC-ATATATGACT
1 CATGTAAGACCATGTCTGGGACATTGGCATCGATATATGAAA
* * *
28380366 CGTGTAAGACCCTGTCTGGGACAGTGGCATCGATATATGATAA
1 CATGTAAGACCATGTCTGGGACATTGGCATCGATATATGA-AA
28380409 CATGTAAGAC
1 CATGTAAGAC
28380419 AATATCTAGG
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
41 30 0.38
42 10 0.12
43 40 0.50
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.26
Consensus pattern (42 bp):
CATGTAAGACCATGTCTGGGACATTGGCATCGATATATGAAA
Found at i:28382922 original size:46 final size:45
Alignment explanation
Indices: 28382835--28383007 Score: 145
Period size: 46 Copynumber: 3.7 Consensus size: 45
28382825 TTATGAGAGC
* *
28382835 CAGTGTAAGACCATGTCTGGGACATGGCATCAGTATTGAGACG-AGT
1 CAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATTGAGACGAAGT
* * *
28382881 GCTAGTGTAAGACATGTTTCGGACATGCATCGGCCTTGAGACGTAAGT
1 -C-AGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACG-AAGT
* * * * **
28382929 CAATGTAAGACATGTCTGGGACATGCACCGGC-TACGAGATG-TTT
1 CAGTGTAAGACATGTCTGGGACATGCATCGGCAT-TGAGACGAAGT
*
28382973 CAGTATAAGACCATGTCTGGGACATAGCATCGGCA
1 CAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCA
28383008 CAGATATGCT
Statistics
Matches: 103, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
44 9 0.09
45 15 0.15
46 53 0.51
47 14 0.14
48 12 0.12
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (45 bp):
CAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACGAAGT
Found at i:28384031 original size:12 final size:13
Alignment explanation
Indices: 28384014--28384046 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
28384004 AGGTTTTTGC
*
28384014 ACACGGGCTA-GG
1 ACACGGGCCAGGG
28384026 ACACGGGCCAGGG
1 ACACGGGCCAGGG
28384039 ACACGGGC
1 ACACGGGC
28384047 GTGTCATAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.24, C:0.30, G:0.42, T:0.03
Consensus pattern (13 bp):
ACACGGGCCAGGG
Found at i:28389683 original size:13 final size:13
Alignment explanation
Indices: 28389665--28389689 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28389655 CCGAAACTAG
28389665 AAAGAAAAAAAAC
1 AAAGAAAAAAAAC
28389678 AAAGAAAAAAAA
1 AAAGAAAAAAAA
28389690 TGCTCATCCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.04, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAAAC
Found at i:28390952 original size:79 final size:80
Alignment explanation
Indices: 28390766--28391028 Score: 333
Period size: 79 Copynumber: 3.3 Consensus size: 80
28390756 TTGAATGATG
* * *
28390766 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT-TCCGGGCTAAGACCCGAAGGCA
* *
28390827 TTTGTGCGAGATACTAAT
63 TTTGTGCGAGTTACTAAA
28390845 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-CCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGACCCGAAGGCATTT
28390908 GTGCGAGTTACTAAA
66 GTGCGAGTTACTAAA
* * * * *
28390923 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGACCCGAAGGCATTT
*
28390988 GTGCGAATTACTATAA
66 GTGCGAGTTACTA-AA
*
28391004 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28391029 AACGAGGAGC
Statistics
Matches: 165, Mismatches: 12, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
78 44 0.27
79 59 0.36
80 59 0.36
81 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGACCCGAAGGCATTT
GTGCGAGTTACTAAA
Found at i:28391042 original size:40 final size:40
Alignment explanation
Indices: 28390766--28391028 Score: 342
Period size: 40 Copynumber: 6.7 Consensus size: 40
28390756 TTGAATGATG
* *
28390766 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-A
* * *
28390805 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
28390845 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
28390884 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28390923 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
28390963 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
28391004 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28391029 AACGAGGAGC
Statistics
Matches: 205, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
39 92 0.45
40 103 0.50
41 10 0.05
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28391046 original size:80 final size:77
Alignment explanation
Indices: 28390767--28391061 Score: 280
Period size: 79 Copynumber: 3.7 Consensus size: 77
28390757 TGAATGATGT
* * **
28390767 CCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAG-GACTA-ATCCGGGTTAAG-TCCCGAAGGCATT
*
28390829 TGTGCGAGA-TACTAATT
62 TGTGCGA-ATTACTAA-A
* *
28390846 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-CCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-GACTAA-TCCGGGTTAAGTCCCGAAGGCATTTG
*
28390909 TGCGAGTTACTAAA
64 TGCGAATTACTAAA
* *
28390923 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-GACT-AATCCGGGTTAAGTCCCGAAGGCATTT
28390988 GTGCGAATTACTATAA
63 GTGCGAATTACTA-AA
* ** * *
28391004 CCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGGA-CTA-ATCCGGGTTAAGTCCCGAAGG
28391062 TACGTGATTT
Statistics
Matches: 186, Mismatches: 18, Indels: 24
0.82 0.08 0.11
Matches are distributed among these distances:
78 43 0.23
79 75 0.40
80 66 0.35
81 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (77 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGGACTAATCCGGGTTAAGTCCCGAAGGCATTTGTG
CGAATTACTAAA
Found at i:28394722 original size:18 final size:19
Alignment explanation
Indices: 28394686--28394725 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
28394676 GTTTAAAGAC
*
28394686 TTTTAAATTATTATTTTTA
1 TTTTAAATTATTATCTTTA
*
28394705 TTTTAACTT-TTATCTTTA
1 TTTTAAATTATTATCTTTA
28394723 TTT
1 TTT
28394726 ATATTCTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTAAATTATTATCTTTA
Found at i:28394757 original size:25 final size:26
Alignment explanation
Indices: 28394719--28394776 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
28394709 AACTTTTATC
28394719 TTTA-TTTATATTC-TTTAAGTACT-T
1 TTTATTTTATATTCTTTTAA-TACTAT
*
28394743 TTTATTTTATCTTCTTTTAATACTAT
1 TTTATTTTATATTCTTTTAATACTAT
*
28394769 TTCATTTT
1 TTTATTTT
28394777 TAGGTTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 4 0.14
25 12 0.41
26 13 0.45
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (26 bp):
TTTATTTTATATTCTTTTAATACTAT
Found at i:28399231 original size:19 final size:20
Alignment explanation
Indices: 28399207--28399244 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
28399197 GGTACCACCA
28399207 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
28399226 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
28399245 ACCACATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:28399641 original size:46 final size:46
Alignment explanation
Indices: 28399469--28399641 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
28399459 AACCCGCCCC
* *
28399469 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
28399515 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* * *
28399563 TCA-CGAGCTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
28399608 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
28399642 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 60 0.57
47 28 0.26
48 2 0.02
49 1 0.01
50 4 0.04
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:28404639 original size:35 final size:35
Alignment explanation
Indices: 28404599--28404671 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
28404589 AGATCAGACC
28404599 CTTCACATGTGATTATGCCAACAGTGGTTGAGATT
1 CTTCACATGTGATTATGCCAACAGTGGTTGAGATT
28404634 CTTCACATGTGATTATGCCAACAGTGGTTGAGATT
1 CTTCACATGTGATTATGCCAACAGTGGTTGAGATT
28404669 CTT
1 CTT
28404672 TCGGACATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.36
Consensus pattern (35 bp):
CTTCACATGTGATTATGCCAACAGTGGTTGAGATT
Found at i:28406217 original size:46 final size:45
Alignment explanation
Indices: 28406158--28406293 Score: 134
Period size: 46 Copynumber: 3.0 Consensus size: 45
28406148 TTGAGATATG
*
28406158 GCATCGGCATTGAGA-TAAGTGCTAGTGTAAGACATGTCTAGGACAT
1 GCATCAGCATTGAGAGTAAGT-C-AGTGTAAGACATGTCTAGGACAT
* *
28406204 GCATCAGCCTTGAGATGTAAGTCAGTGTAAGACATGTCTGGGACAT
1 GCATCAGCATTGAGA-GTAAGTCAGTGTAAGACATGTCTAGGACAT
* * ** *
28406250 GCATC-G-ACTGCGAGATGTGTCAGTGTAAGACCATGTCTGGGACA
1 GCATCAGCATTGAGAG-TAAGTCAGTGTAAGA-CATGTCTAGGACA
28406294 CGGCATCGAC
Statistics
Matches: 78, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
43 1 0.01
44 17 0.22
45 14 0.18
46 40 0.51
47 1 0.01
48 5 0.06
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (45 bp):
GCATCAGCATTGAGAGTAAGTCAGTGTAAGACATGTCTAGGACAT
Found at i:28406301 original size:46 final size:44
Alignment explanation
Indices: 28406181--28406303 Score: 158
Period size: 46 Copynumber: 2.7 Consensus size: 44
28406171 GATAAGTGCT
* * *
28406181 AGTGTAAGACATGTCTAGGACATGCATCAGCCTTGAGATGTAAGTC
1 AGTGTAAGACATGTCTGGGACATGCATC-GACTCGAGATGT-AGTC
28406227 AGTGTAAGACATGTCTGGGACATGCATCGACTGCGAGATGT-GTC
1 AGTGTAAGACATGTCTGGGACATGCATCGACT-CGAGATGTAGTC
*
28406271 AGTGTAAGACCATGTCTGGGACACGGCATCGAC
1 AGTGTAAGA-CATGTCTGGGACA-TGCATCGAC
28406304 ACAAATATGC
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
44 12 0.17
45 16 0.23
46 42 0.60
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.24
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGACTCGAGATGTAGTC
Found at i:28409383 original size:27 final size:27
Alignment explanation
Indices: 28409353--28409530 Score: 171
Period size: 27 Copynumber: 6.6 Consensus size: 27
28409343 ATATTGAGCC
* *
28409353 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
28409380 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
28409407 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
** ** *
28409435 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* * **
28409462 CACACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
28409489 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
28409516 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28409531 GTACAATTTA
Statistics
Matches: 127, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
27 102 0.80
28 25 0.20
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:28429027 original size:40 final size:40
Alignment explanation
Indices: 28428967--28429150 Score: 235
Period size: 40 Copynumber: 4.6 Consensus size: 40
28428957 TATTCGAATG
* *
28428967 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
* * * * *
28429007 ATATCCAGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGACT
* * *
28429047 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
* * *
28429087 ATATCTGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
28429127 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
28429151 CTTGTGCGAG
Statistics
Matches: 121, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
39 1 0.01
40 118 0.98
41 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
Found at i:28431398 original size:41 final size:42
Alignment explanation
Indices: 28431341--28431419 Score: 124
Period size: 41 Copynumber: 1.9 Consensus size: 42
28431331 GTGTGAATTT
* *
28431341 GTGTAAGACCATGTCTGGGACATTGGCATTG-TATATGTCTC
1 GTGTAAGACCATGTCTGGGACAGTGGCATCGATATATGTCTC
*
28431382 GTGTAAGACCCTGTCTGGGACAGTGGCATCGATATATG
1 GTGTAAGACCATGTCTGGGACAGTGGCATCGATATATG
28431420 ATAACATGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
41 28 0.82
42 6 0.18
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (42 bp):
GTGTAAGACCATGTCTGGGACAGTGGCATCGATATATGTCTC
Found at i:28433293 original size:20 final size:20
Alignment explanation
Indices: 28433256--28433293 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28433246 TACAACCAAT
*
28433256 CATTCATTACATTACCAAAC
1 CATTCATTACAGTACCAAAC
*
28433276 CATTCATTACAGTGCCAA
1 CATTCATTACAGTACCAA
28433294 TCAATCAACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.29, G:0.05, T:0.29
Consensus pattern (20 bp):
CATTCATTACAGTACCAAAC
Found at i:28435346 original size:46 final size:46
Alignment explanation
Indices: 28435323--28435538 Score: 351
Period size: 46 Copynumber: 4.7 Consensus size: 46
28435313 TTGTCATGTC
** *** *
28435323 GCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTT
1 GCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTT
*
28435370 GCCATGATATCTTTCAACCATGGTCTTACACATTTCATATCAGGTT
1 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTT
*
28435416 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATTAGGTT
1 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTT
28435462 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTT
1 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTT
28435508 GCCATGGTATCTTTCAACCATGGTCTTACAC
1 GCCATGGTATCTTTCAACCATGGTCTTACAC
28435539 CCATGGTTTT
Statistics
Matches: 159, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
46 130 0.82
47 29 0.18
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.38
Consensus pattern (46 bp):
GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTT
Found at i:28435492 original size:92 final size:93
Alignment explanation
Indices: 28435276--28435648 Score: 451
Period size: 92 Copynumber: 3.9 Consensus size: 93
28435266 TTCGACATGA
* * * * * ** * * *
28435276 TGCCATAATATCTTTCAACTATGGTTTTACTCGTTTTTTGTCATGTCGCCATGGTATCTTTCAAC
1 TGCCATGATATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
** * * *
28435341 CATGGTCTTATTCATTTTCCCGTCATGT
66 CATGGTCTTACACATTTTCACATCAGGT
28435369 TGCCATGATATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
1 TGCCATGATATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
* *
28435434 CATGGTCTTACACA-TTTCATATTAGGT
66 CATGGTCTTACACATTTTCACATCAGGT
*
28435461 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
1 TGCCATGATATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
28435526 CATGGTCTTACACCCATGGTTTTACACATTTCATATCAGGT
66 CATGGTCTTACA--CA---TTTT---CA---C--ATCAGGT
*
28435567 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
1 TGCCATGATATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
28435632 CATGGTCTTACACATTT
66 CATGGTCTTACACATTT
28435649 CATTTCAGAG
Statistics
Matches: 246, Mismatches: 20, Indels: 20
0.86 0.07 0.07
Matches are distributed among these distances:
92 84 0.34
93 67 0.27
94 2 0.01
98 3 0.01
101 5 0.02
104 2 0.01
106 83 0.34
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.39
Consensus pattern (93 bp):
TGCCATGATATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
CATGGTCTTACACATTTTCACATCAGGT
Found at i:28435558 original size:60 final size:60
Alignment explanation
Indices: 28435479--28435598 Score: 231
Period size: 60 Copynumber: 2.0 Consensus size: 60
28435469 TATCTTTCAA
28435479 CCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 CCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
*
28435539 CCATGGTTTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 CCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
28435599 ATTTCATATC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (60 bp):
CCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
Found at i:28435567 original size:106 final size:106
Alignment explanation
Indices: 28435433--28435644 Score: 406
Period size: 106 Copynumber: 2.0 Consensus size: 106
28435423 TATCTTTCAA
*
28435433 CCATGGTCTTACACATTTCATATTAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
1 CCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
28435498 ATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
66 ATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
*
28435539 CCATGGTTTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
1 CCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
28435604 ATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
66 ATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
28435645 ATTTCATTTC
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 104 1.00
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.37
Consensus pattern (106 bp):
CCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
ATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
Found at i:28435591 original size:46 final size:46
Alignment explanation
Indices: 28435539--28435656 Score: 218
Period size: 46 Copynumber: 2.6 Consensus size: 46
28435529 GGTCTTACAC
*
28435539 CCATGGTTTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAA
1 CCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAA
28435585 CCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAA
1 CCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAA
*
28435631 CCATGGTCTTACACATTTCATTTCAG
1 CCATGGTCTTACACATTTCATATCAG
28435657 AGAGCACACT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 70 1.00
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.38
Consensus pattern (46 bp):
CCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAA
Found at i:28437839 original size:18 final size:19
Alignment explanation
Indices: 28437790--28437839 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
28437780 TATAATATAA
28437790 TTATTTAATTAATAAATATC
1 TTATTTAA-TAATAAATATC
28437810 TT-TTATAAAATAATAAATAT-
1 TTATT-T--AATAATAAATATC
28437830 TTATTTAATA
1 TTATTTAATA
28437840 TCTAATACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
18 4 0.15
19 2 0.08
20 6 0.23
21 12 0.46
22 2 0.08
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TTATTTAATAATAAATATC
Found at i:28445727 original size:47 final size:47
Alignment explanation
Indices: 28444967--28445715 Score: 1214
Period size: 47 Copynumber: 16.2 Consensus size: 47
28444957 ATGATAGTAT
*
28444967 ATGTGTATGTGTGATAAGGCCGAATGG-CAATGTGATGAAAGTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
28445013 ATGTGTATGTGTGATAAGG-CGAATGG-CAATGTGATGAA-GTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
*
28445057 ATGTGTATGTGTGATAAGACCGAATGGCCAATGTGATGAATGTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
* * *
28445104 ATG-ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
28445150 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
*
28445197 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
* *
28445244 ATGTGTATGTGTGATAAGGCCAAATGGCCAATGTGATGAAAGTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
*
28445291 ATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
28445338 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
*
28445385 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
*
28445432 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
* *
28445479 ATGTATATGTGTGATAA-GCCGAATGGCCAATGTGATGAAAGTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
* *
28445525 ATGTGTATGTGTGATAA--ACGAATGG-CAATGTGATGAAAGTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
* *
28445569 ATGTATATGTGTGACAAGGCCGAATGGCCAATGTGATGAATGTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
* * *
28445616 ATGTGTATGTGTGATAAGGCCGAGTGGCCAATGTGATAAATGTGAGC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
* * *
28445663 ATGTGTATGTGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAA-
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
28445709 A-GTGTAT
1 ATGTGTAT
28445716 AAATGTGATA
Statistics
Matches: 663, Mismatches: 33, Indels: 15
0.93 0.05 0.02
Matches are distributed among these distances:
44 58 0.09
45 39 0.06
46 126 0.19
47 440 0.66
ACGTcount: A:0.32, C:0.10, G:0.31, T:0.27
Consensus pattern (47 bp):
ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
Found at i:28445902 original size:37 final size:37
Alignment explanation
Indices: 28445846--28445925 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
28445836 CCGGGCTCTA
* * *
28445846 AAGACCCGATGACTGCGTGTGG-GAATTTTGTCCGGGT
1 AAGACTCGATAACTGCGTGTGGAG-ATTATGTCCGGGT
*
28445883 AAGACTCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACTCGATAACTGCGTGTGGAGATTATGTCCGGGT
28445920 AAGACT
1 AAGACT
28445926 TCGTAATAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (37 bp):
AAGACTCGATAACTGCGTGTGGAGATTATGTCCGGGT
Found at i:28447778 original size:40 final size:40
Alignment explanation
Indices: 28447721--28448164 Score: 390
Period size: 40 Copynumber: 11.1 Consensus size: 40
28447711 TCGAATGATG
* * *
28447721 TCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAATTGA-TATA
*
28447761 TCCGGACTAAGATCCGAAGGCATTTATGCGAATTGATATA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAATTGATATA
* *
28447801 TCCGGGA-TAAGACCCGAAGGCATTTATGCGAATTGATATA
1 TCC-GGACTAAGATCCGAAGGCATTTGTGCGAATTGATATA
*
28447841 TCCGGGA-TAAGACCCGAAGGCATTTGTGCGAATTGATATA
1 TCC-GGACTAAGATCCGAAGGCATTTGTGCGAATTGATATA
*
28447881 TCCGGACTAAGATCCGAAGGCATTTATGCGAATTGATATA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAATTGATATA
* *
28447921 TCCGGGA-TAAGACCCGAAGGCATTTATGCGAATTGATATA
1 TCC-GGACTAAGATCCGAAGGCATTTGTGCGAATTGATATA
* *
28447961 TCCGGGA-TAAGACCCGAAGGCGTTTGTGCGAATTGATATA
1 TCC-GGACTAAGATCCGAAGGCATTTGTGCGAATTGATATA
* * * * *
28448001 TCCGGGCTAAG-TCCCGAAGAGCATTCGTGC-TAGTGATGTA
1 TCCGGACTAAGAT-CCGAAG-GCATTTGTGCGAATTGATATA
* * * * *
28448041 TCCGGGCTAAG-TCCCGAAGAGCATTCGTGC-TAGTGATGTA
1 TCCGGACTAAGAT-CCGAAG-GCATTTGTGCGAATTGATATA
* * * * * *
28448081 TCCGGGCTAAGTTCCGAAGAGCATTCGTGC-TAGTGATGTA
1 TCCGGACTAAGATCCGAAG-GCATTTGTGCGAATTGATATA
* * * * * *
28448121 TCCGGGCTAGGTTCCGAAGAGCATTCGTGC-TAGTGATATA
1 TCCGGACTAAGATCCGAAG-GCATTTGTGCGAATTGATATA
28448161 TCCG
1 TCCG
28448165 TGCTAAATCC
Statistics
Matches: 375, Mismatches: 20, Indels: 18
0.91 0.05 0.04
Matches are distributed among these distances:
39 5 0.01
40 343 0.91
41 27 0.07
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGACTAAGATCCGAAGGCATTTGTGCGAATTGATATA
Found at i:28447858 original size:80 final size:80
Alignment explanation
Indices: 28447721--28448065 Score: 446
Period size: 80 Copynumber: 4.3 Consensus size: 80
28447711 TCGAATGATG
* * * * * *
28447721 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCC-GGACTAAGATCCGAAGGCAT
1 TCCGGGATAAGACCCGAAGGCATTTATGCGAATTGA-TATATCCGGGA-TAAGACCCGAAGGCAT
28447784 TTATGCGAATTGATATA
64 TTATGCGAATTGATATA
28447801 TCCGGGATAAGACCCGAAGGCATTTATGCGAATTGATATATCCGGGATAAGACCCGAAGGCATTT
1 TCCGGGATAAGACCCGAAGGCATTTATGCGAATTGATATATCCGGGATAAGACCCGAAGGCATTT
*
28447866 GTGCGAATTGATATA
66 ATGCGAATTGATATA
*
28447881 TCC-GGACTAAGATCCGAAGGCATTTATGCGAATTGATATATCCGGGATAAGACCCGAAGGCATT
1 TCCGGGA-TAAGACCCGAAGGCATTTATGCGAATTGATATATCCGGGATAAGACCCGAAGGCATT
28447945 TATGCGAATTGATATA
65 TATGCGAATTGATATA
* * * *
28447961 TCCGGGATAAGACCCGAAGGCGTTTGTGCGAATTGATATATCCGGGCTAAGTCCCGAAGAGCATT
1 TCCGGGATAAGACCCGAAGGCATTTATGCGAATTGATATATCCGGGATAAGACCCGAAG-GCATT
** * * *
28448026 CGTGC-TAGTGATGTA
65 TATGCGAATTGATATA
* *
28448041 TCCGGGCTAAGTCCCGAAGAGCATT
1 TCCGGGATAAGACCCGAAG-GCATT
28448066 CGTGCTAGTG
Statistics
Matches: 237, Mismatches: 22, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
79 3 0.01
80 205 0.86
81 29 0.12
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (80 bp):
TCCGGGATAAGACCCGAAGGCATTTATGCGAATTGATATATCCGGGATAAGACCCGAAGGCATTT
ATGCGAATTGATATA
Found at i:28447934 original size:120 final size:119
Alignment explanation
Indices: 28447721--28448065 Score: 514
Period size: 120 Copynumber: 2.9 Consensus size: 119
28447711 TCGAATGATG
* * * *
28447721 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGATAAGACCCGAAGGCTTTGTGCGAATTGA-TATATCCGGACTAAGATCCGAAGGCATTT
28447786 ATGCGAATTGATATATCCGGGATAAGACCCGAAGGCATTTATGCGAATTGATATA
65 ATGCGAATTGATATATCCGGGATAAGACCCGAAGGCATTTATGCGAATTGATATA
28447841 TCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGATATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGATAAGACCCGAAGGC-TTTGTGCGAATTGATATATCCGGACTAAGATCCGAAGGCATTT
28447906 ATGCGAATTGATATATCCGGGATAAGACCCGAAGGCATTTATGCGAATTGATATA
65 ATGCGAATTGATATATCCGGGATAAGACCCGAAGGCATTTATGCGAATTGATATA
*
28447961 TCCGGGATAAGACCCGAAGGCGTTTGTGCGAATTGATATATCCGGGCTAAG-TCCCGAAGAGCAT
1 TCCGGGATAAGACCCGAAGGC-TTTGTGCGAATTGATATATCCGGACTAAGAT-CCGAAG-GCAT
** * * * * *
28448025 TCGTGC-TAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATT
63 TTATGCGAATTGATATATCCGGGATAAGACCCGAAG-GCATT
28448066 CGTGCTAGTG
Statistics
Matches: 208, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
119 1 0.00
120 182 0.88
121 25 0.12
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (119 bp):
TCCGGGATAAGACCCGAAGGCTTTGTGCGAATTGATATATCCGGACTAAGATCCGAAGGCATTTA
TGCGAATTGATATATCCGGGATAAGACCCGAAGGCATTTATGCGAATTGATATA
Found at i:28448032 original size:23 final size:23
Alignment explanation
Indices: 28448006--28448072 Score: 56
Period size: 23 Copynumber: 3.2 Consensus size: 23
28447996 ATATATCCGG
28448006 GCTAAGTCCCGAAGAGCATTCGT
1 GCTAAGTCCCGAAGAGCATTCGT
* * * *
28448029 GCT-AGT---G-A-TGTATCCGG
1 GCTAAGTCCCGAAGAGCATTCGT
28448046 GCTAAGTCCCGAAGAGCATTCGT
1 GCTAAGTCCCGAAGAGCATTCGT
28448069 GCTA
1 GCTA
28448073 GTGATGTATC
Statistics
Matches: 30, Mismatches: 8, Indels: 12
0.60 0.16 0.24
Matches are distributed among these distances:
17 8 0.27
18 4 0.13
19 1 0.03
21 1 0.03
22 4 0.13
23 12 0.40
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (23 bp):
GCTAAGTCCCGAAGAGCATTCGT
Found at i:28448083 original size:80 final size:80
Alignment explanation
Indices: 28447721--28448190 Score: 441
Period size: 80 Copynumber: 5.9 Consensus size: 80
28447711 TCGAATGATG
* *
28447721 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTGA-TATATCCGGGCTAAG-TCCCGAAGGCAT
* *
28447784 TTATGCGAATTGATATA
64 TCATGCGAAGTGATATA
* * * * * * *
28447801 TCCGGGATAAGACCCGAAGGCATTTATGCGAATTGATATATCCGGGATAAGACCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTGATATATCCGGGCTAAGTCCCGAAGGCATTC
* *
28447866 GTGCGAATTGATATA
66 ATGCGAAGTGATATA
* * * * *
28447881 TCCGGACTAAGAT-CCGAAGGCATTTATGCGAATTGATATATCCGGGATAAGACCCGAAGGCATT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAAGTGATATATCCGGGCTAAGTCCCGAAGGCATT
* *
28447945 TATGCGAATTGATATA
65 CATGCGAAGTGATATA
* * * *
28447961 TCCGGGATAAGACCCGAAGGCGTTTGTGCGAATTGATATATCCGGGCTAAGTCCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTGATATATCCGGGCTAAGTCCCGAAG-GCATT
* * *
28448026 CGTGC-TAGTGATGTA
65 CATGCGAAGTGATATA
* * * *
28448041 TCCGGGCTAAGTCCCGAAGAGCATTCGTGC-TAGTGATGTATCCGGGCTAAGTTCCGAAGAGCAT
1 TCCGGGCTAAGTCCCGAAG-GCATTTGTGCGAAGTGATATATCCGGGCTAAGTCCCGAAG-GCAT
* * *
28448105 TCGTGC-TAGTGATGTA
64 TCATGCGAAGTGATATA
* * * * * * * *
28448121 TCCGGGCTAGGTTCCGAAGAGCATTCGTGC-TAGTGATATATCCGTGCTAAATCCTGAAGAGCAA
1 TCCGGGCTAAGTCCCGAAG-GCATTTGTGCGAAGTGATATATCCGGGCTAAGTCCCGAAG-GCAT
28448185 TCATGC
64 TCATGC
28448191 TGGTGATGTG
Statistics
Matches: 342, Mismatches: 42, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
80 315 0.92
81 27 0.08
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTGATATATCCGGGCTAAGTCCCGAAGGCATTC
ATGCGAAGTGATATA
Found at i:28448083 original size:120 final size:120
Alignment explanation
Indices: 28447721--28448164 Score: 486
Period size: 120 Copynumber: 3.7 Consensus size: 120
28447711 TCGAATGATG
* * *
28447721 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGATAAGACCCGAAGGCATTTGTGCGAAGTGA-TATATCCGGACTAAGATCCGAAGGCATT
* * * *
28447785 TATGCGAATTGATATATCCGGGATAAGACCCGAAGGCATTTATGCGAATTGATATA
65 CATGCGAAGTGATATATCCGGGATAAGACCCGAAGGCATTCATGCGAAGTGATATA
* *
28447841 TCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGATATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGATAAGACCCGAAGGCATTTGTGCGAAGTGATATATCCGGACTAAGATCCGAAGGCATTC
* * *
28447906 ATGCGAATTGATATATCCGGGATAAGACCCGAAGGCATTTATGCGAATTGATATA
66 ATGCGAAGTGATATATCCGGGATAAGACCCGAAGGCATTCATGCGAAGTGATATA
* * *
28447961 TCCGGGATAAGACCCGAAGGCGTTTGTGCGAATTGATATATCCGGGCTAAG-TCCCGAAGAGCAT
1 TCCGGGATAAGACCCGAAGGCATTTGTGCGAAGTGATATATCCGGACTAAGAT-CCGAAG-GCAT
* * * * * * * *
28448025 TCGTGC-TAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGC-TAGTGATGTA
64 TCATGCGAAGTGATATATCCGGGATAAGACCCGAAG-GCATTCATGCGAAGTGATATA
* ** * * * * * *
28448081 TCCGGGCTAAGTTCCGAAGAGCATTCGTGC-TAGTGATGTATCCGGGCTAGGTTCCGAAGAGCAT
1 TCCGGGATAAGACCCGAAG-GCATTTGTGCGAAGTGATATATCCGGACTAAGATCCGAAG-GCAT
* *
28448145 TCGTGC-TAGTGATATATCCG
64 TCATGCGAAGTGATATATCCG
28448165 TGCTAAATCC
Statistics
Matches: 290, Mismatches: 28, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
119 1 0.00
120 252 0.87
121 37 0.13
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGATAAGACCCGAAGGCATTTGTGCGAAGTGATATATCCGGACTAAGATCCGAAGGCATTC
ATGCGAAGTGATATATCCGGGATAAGACCCGAAGGCATTCATGCGAAGTGATATA
Found at i:28448180 original size:40 final size:39
Alignment explanation
Indices: 28447994--28448199 Score: 295
Period size: 40 Copynumber: 5.2 Consensus size: 39
28447984 TTGTGCGAAT
*
28447994 TGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAG
1 TGATGTATCCGGGCTAAGT-CCGAAGAGCATTCGTGCTAG
28448034 TGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAG
1 TGATGTATCCGGGCTAAGT-CCGAAGAGCATTCGTGCTAG
28448074 TGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAG
1 TGATGTATCCGGGCTAAG-TCCGAAGAGCATTCGTGCTAG
*
28448114 TGATGTATCCGGGCTAGGTTCCGAAGAGCATTCGTGCTAG
1 TGATGTATCCGGGCTAAG-TCCGAAGAGCATTCGTGCTAG
* * * * * *
28448154 TGATATATCCGTGCTAAATCCTGAAGAGCAATCATGCTGG
1 TGATGTATCCGGGCTAAGTCC-GAAGAGCATTCGTGCTAG
28448194 TGATGT
1 TGATGT
28448200 GTATTCGGGC
Statistics
Matches: 154, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
39 3 0.02
40 150 0.97
41 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (39 bp):
TGATGTATCCGGGCTAAGTCCGAAGAGCATTCGTGCTAG
Found at i:28452510 original size:23 final size:23
Alignment explanation
Indices: 28452484--28452558 Score: 59
Period size: 23 Copynumber: 3.2 Consensus size: 23
28452474 CGAATGGCCA
28452484 ATGTGATGAAAGTGAACATGTGT
1 ATGTGATGAAAGTGAACATGTGT
* *
28452507 ATGTG-TGATAAG-G-CCGAATG-GCCA
1 ATGTGATGA-AAGTGAAC--ATGTG--T
28452531 ATGTGATGAAAGTGAACATGTGT
1 ATGTGATGAAAGTGAACATGTGT
28452554 ATGTG
1 ATGTG
28452559 TGATAAGGCC
Statistics
Matches: 39, Mismatches: 4, Indels: 18
0.64 0.07 0.30
Matches are distributed among these distances:
21 1 0.03
22 5 0.13
23 16 0.41
24 11 0.28
25 5 0.13
26 1 0.03
ACGTcount: A:0.32, C:0.08, G:0.32, T:0.28
Consensus pattern (23 bp):
ATGTGATGAAAGTGAACATGTGT
Found at i:28452528 original size:47 final size:47
Alignment explanation
Indices: 28452459--28453008 Score: 836
Period size: 47 Copynumber: 12.1 Consensus size: 47
28452449 ATTGATGAAA
28452459 GTGTATGTGT-A-AA-GCCGAATGGCCAATGTGATGAAAGTGAACAT
1 GTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACAT
28452503 GTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACAT
1 GTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACAT
28452550 GTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACAT
1 GTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACAT
* *
28452597 GTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACAT
1 GTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACAT
28452644 GTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG-AAG-GAA-AT
1 GTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACAT
28452688 GTGTATGTGTGATAA-G-CGAATGG-CAATGT-ATGAAAGTGAACAT
1 GTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACAT
28452731 GT-TA---GTGATAA-GCCGAATGGCCAATGTGATGAAAGTGAACAT
1 GTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACAT
28452773 GTGTATGTGTGATAA-GCCGAATGGCCAATGTGATGAAAGTGAACAT
1 GTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACAT
*
28452819 GTATATGTGTGATAA-GCCGAATGGCCAATGTGATGAAAGTGAACAT
1 GTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACAT
* * *
28452865 GTATATGTGTGACAAGGCCGAATGGCCAATGTGATGAATGTGAACAT
1 GTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACAT
* *
28452912 GTGTATGTGTGATAAGGCCGAGTGGCCAATGTGAT-AAATGTGAGCAT
1 GTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAA-GTGAACAT
* * * *
28452959 GTGTATGTGAGA-AAGGCCTAATGGCCGATGTGATGAATGTGAA-A-
1 GTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACAT
28453003 GTGTAT
1 GTGTAT
28453009 AAATGTGATA
Statistics
Matches: 472, Mismatches: 18, Indels: 32
0.90 0.03 0.06
Matches are distributed among these distances:
39 8 0.02
40 10 0.02
41 15 0.03
42 28 0.06
43 7 0.01
44 33 0.07
45 5 0.01
46 126 0.27
47 240 0.51
ACGTcount: A:0.32, C:0.10, G:0.31, T:0.26
Consensus pattern (47 bp):
GTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACAT
Found at i:28452781 original size:23 final size:23
Alignment explanation
Indices: 28452754--28452873 Score: 58
Period size: 23 Copynumber: 5.2 Consensus size: 23
28452744 CGAATGGCCA
28452754 ATGTGATGAAAGTGAACATGTGT
1 ATGTGATGAAAGTGAACATGTGT
* *
28452777 ATGTG-TGATAAGCCG-A-ATG-GCCA
1 ATGTGATGA-AAG-TGAACATGTG--T
*
28452800 ATGTGATGAAAGTGAACATGTAT
1 ATGTGATGAAAGTGAACATGTGT
* *
28452823 ATGTG-TGATAAGCCG-A-ATG-GCCA
1 ATGTGATGA-AAG-TGAACATGTG--T
*
28452846 ATGTGATGAAAGTGAACATGTAT
1 ATGTGATGAAAGTGAACATGTGT
28452869 ATGTG
1 ATGTG
28452874 TGACAAGGCC
Statistics
Matches: 70, Mismatches: 11, Indels: 32
0.62 0.10 0.28
Matches are distributed among these distances:
21 1 0.01
22 14 0.20
23 41 0.59
24 14 0.20
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.28
Consensus pattern (23 bp):
ATGTGATGAAAGTGAACATGTGT
Found at i:28452900 original size:268 final size:262
Alignment explanation
Indices: 28452424--28452946 Score: 899
Period size: 268 Copynumber: 2.0 Consensus size: 262
28452414 ATGATAGTAT
*
28452424 ATGTGTATGTGTGATAAGGAATCCAATTGATGAAAGTGTATGTGTAAAGCCGAATGGCCAATGTG
1 ATGTGTATGTGTGATAAGGAATCCAATTGATGAAAGTGCATGTGTAAAGCCGAATGGCCAATGTG
*
28452489 ATGAAAGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACATGTGT
66 ATGAAAGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACATGTAT
*
28452554 ATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACATGTATATGTGTGATAAGGCCGAA
131 ATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACATGTATATGTGTGACAAGGCCGAA
28452619 TGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAGG
196 TGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAGG
28452684 AA
261 AA
*
28452686 ATGTGTATGTGTGATAAGCGAATGGCAA-TGTATGAAAGTGAACATGTTAGTGATAAGCCGAATG
1 ATGTGTATGTGTGATAAG-GAAT-CCAATTG-ATGAAAGTG--CATG-T-GT-A-AAGCCGAATG
28452750 GCCAATGTGATGAAAGTGAACATGTGTATGTGTGATAA-GCCGAATGGCCAATGTGATGAAAGTG
57 GCCAATGTGATGAAAGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTG
28452814 AACATGTATATGTGTGATAA-GCCGAATGGCCAATGTGATGAAAGTGAACATGTATATGTGTGAC
122 AACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACATGTATATGTGTGAC
*
28452878 AAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAGTGGCCAATG
187 AAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATG
28452943 TGAT
252 TGAT
28452947 AAATGTGAGC
Statistics
Matches: 247, Mismatches: 5, Indels: 12
0.94 0.02 0.05
Matches are distributed among these distances:
262 18 0.07
263 6 0.02
264 12 0.05
266 3 0.01
267 1 0.00
268 113 0.46
269 46 0.19
270 48 0.19
ACGTcount: A:0.33, C:0.10, G:0.31, T:0.26
Consensus pattern (262 bp):
ATGTGTATGTGTGATAAGGAATCCAATTGATGAAAGTGCATGTGTAAAGCCGAATGGCCAATGTG
ATGAAAGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACATGTAT
ATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACATGTATATGTGTGACAAGGCCGAA
TGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAGG
AA
Found at i:28453195 original size:37 final size:37
Alignment explanation
Indices: 28453139--28453218 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
28453129 CCGGGCTCTA
* * *
28453139 AAGACCCGATGACTGCGTGTGG-GAATTTTGTCCGGGT
1 AAGACTCGATAACTGCGTGTGGAG-ATTATGTCCGGGT
*
28453176 AAGACTCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACTCGATAACTGCGTGTGGAGATTATGTCCGGGT
28453213 AAGACT
1 AAGACT
28453219 TCGTAATAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (37 bp):
AAGACTCGATAACTGCGTGTGGAGATTATGTCCGGGT
Found at i:28455062 original size:40 final size:40
Alignment explanation
Indices: 28455005--28455448 Score: 390
Period size: 40 Copynumber: 11.1 Consensus size: 40
28454995 TCGAATGATG
* * *
28455005 TCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAATTGA-TATA
*
28455045 TCCGGACTAAGATCCGAAGGCATTTATGCGAATTGATATA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAATTGATATA
* *
28455085 TCCGGGA-TAAGACCCGAAGGCATTTATGCGAATTGATATA
1 TCC-GGACTAAGATCCGAAGGCATTTGTGCGAATTGATATA
*
28455125 TCCGGGA-TAAGACCCGAAGGCATTTGTGCGAATTGATATA
1 TCC-GGACTAAGATCCGAAGGCATTTGTGCGAATTGATATA
*
28455165 TCCGGACTAAGATCCGAAGGCATTTATGCGAATTGATATA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAATTGATATA
* *
28455205 TCCGGGA-TAAGACCCGAAGGCATTTATGCGAATTGATATA
1 TCC-GGACTAAGATCCGAAGGCATTTGTGCGAATTGATATA
* *
28455245 TCCGGGA-TAAGACCCGAAGGCGTTTGTGCGAATTGATATA
1 TCC-GGACTAAGATCCGAAGGCATTTGTGCGAATTGATATA
* * * * *
28455285 TCCGGGCTAAG-TCCCGAAGAGCATTCGTGC-TAGTGATGTA
1 TCCGGACTAAGAT-CCGAAG-GCATTTGTGCGAATTGATATA
* * * * *
28455325 TCCGGGCTAAG-TCCCGAAGAGCATTCGTGC-TAGTGATGTA
1 TCCGGACTAAGAT-CCGAAG-GCATTTGTGCGAATTGATATA
* * * * * *
28455365 TCCGGGCTAAGTTCCGAAGAGCATTCGTGC-TAGTGATGTA
1 TCCGGACTAAGATCCGAAG-GCATTTGTGCGAATTGATATA
* * * * * *
28455405 TCCGGGCTAGGTTCCGAAGAGCATTCGTGC-TAGTGATATA
1 TCCGGACTAAGATCCGAAG-GCATTTGTGCGAATTGATATA
28455445 TCCG
1 TCCG
28455449 TGCTAAATCC
Statistics
Matches: 375, Mismatches: 20, Indels: 18
0.91 0.05 0.04
Matches are distributed among these distances:
39 5 0.01
40 343 0.91
41 27 0.07
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGACTAAGATCCGAAGGCATTTGTGCGAATTGATATA
Found at i:28455142 original size:80 final size:80
Alignment explanation
Indices: 28455005--28455349 Score: 446
Period size: 80 Copynumber: 4.3 Consensus size: 80
28454995 TCGAATGATG
* * * * * *
28455005 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCC-GGACTAAGATCCGAAGGCAT
1 TCCGGGATAAGACCCGAAGGCATTTATGCGAATTGA-TATATCCGGGA-TAAGACCCGAAGGCAT
28455068 TTATGCGAATTGATATA
64 TTATGCGAATTGATATA
28455085 TCCGGGATAAGACCCGAAGGCATTTATGCGAATTGATATATCCGGGATAAGACCCGAAGGCATTT
1 TCCGGGATAAGACCCGAAGGCATTTATGCGAATTGATATATCCGGGATAAGACCCGAAGGCATTT
*
28455150 GTGCGAATTGATATA
66 ATGCGAATTGATATA
*
28455165 TCC-GGACTAAGATCCGAAGGCATTTATGCGAATTGATATATCCGGGATAAGACCCGAAGGCATT
1 TCCGGGA-TAAGACCCGAAGGCATTTATGCGAATTGATATATCCGGGATAAGACCCGAAGGCATT
28455229 TATGCGAATTGATATA
65 TATGCGAATTGATATA
* * * *
28455245 TCCGGGATAAGACCCGAAGGCGTTTGTGCGAATTGATATATCCGGGCTAAGTCCCGAAGAGCATT
1 TCCGGGATAAGACCCGAAGGCATTTATGCGAATTGATATATCCGGGATAAGACCCGAAG-GCATT
** * * *
28455310 CGTGC-TAGTGATGTA
65 TATGCGAATTGATATA
* *
28455325 TCCGGGCTAAGTCCCGAAGAGCATT
1 TCCGGGATAAGACCCGAAG-GCATT
28455350 CGTGCTAGTG
Statistics
Matches: 237, Mismatches: 22, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
79 3 0.01
80 205 0.86
81 29 0.12
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (80 bp):
TCCGGGATAAGACCCGAAGGCATTTATGCGAATTGATATATCCGGGATAAGACCCGAAGGCATTT
ATGCGAATTGATATA
Found at i:28455218 original size:120 final size:119
Alignment explanation
Indices: 28455005--28455349 Score: 514
Period size: 120 Copynumber: 2.9 Consensus size: 119
28454995 TCGAATGATG
* * * *
28455005 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGATAAGACCCGAAGGCTTTGTGCGAATTGA-TATATCCGGACTAAGATCCGAAGGCATTT
28455070 ATGCGAATTGATATATCCGGGATAAGACCCGAAGGCATTTATGCGAATTGATATA
65 ATGCGAATTGATATATCCGGGATAAGACCCGAAGGCATTTATGCGAATTGATATA
28455125 TCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGATATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGATAAGACCCGAAGGC-TTTGTGCGAATTGATATATCCGGACTAAGATCCGAAGGCATTT
28455190 ATGCGAATTGATATATCCGGGATAAGACCCGAAGGCATTTATGCGAATTGATATA
65 ATGCGAATTGATATATCCGGGATAAGACCCGAAGGCATTTATGCGAATTGATATA
*
28455245 TCCGGGATAAGACCCGAAGGCGTTTGTGCGAATTGATATATCCGGGCTAAG-TCCCGAAGAGCAT
1 TCCGGGATAAGACCCGAAGGC-TTTGTGCGAATTGATATATCCGGACTAAGAT-CCGAAG-GCAT
** * * * * *
28455309 TCGTGC-TAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATT
63 TTATGCGAATTGATATATCCGGGATAAGACCCGAAG-GCATT
28455350 CGTGCTAGTG
Statistics
Matches: 208, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
119 1 0.00
120 182 0.88
121 25 0.12
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (119 bp):
TCCGGGATAAGACCCGAAGGCTTTGTGCGAATTGATATATCCGGACTAAGATCCGAAGGCATTTA
TGCGAATTGATATATCCGGGATAAGACCCGAAGGCATTTATGCGAATTGATATA
Found at i:28455316 original size:23 final size:23
Alignment explanation
Indices: 28455290--28455356 Score: 56
Period size: 23 Copynumber: 3.2 Consensus size: 23
28455280 ATATATCCGG
28455290 GCTAAGTCCCGAAGAGCATTCGT
1 GCTAAGTCCCGAAGAGCATTCGT
* * * *
28455313 GCT-AGT---G-A-TGTATCCGG
1 GCTAAGTCCCGAAGAGCATTCGT
28455330 GCTAAGTCCCGAAGAGCATTCGT
1 GCTAAGTCCCGAAGAGCATTCGT
28455353 GCTA
1 GCTA
28455357 GTGATGTATC
Statistics
Matches: 30, Mismatches: 8, Indels: 12
0.60 0.16 0.24
Matches are distributed among these distances:
17 8 0.27
18 4 0.13
19 1 0.03
21 1 0.03
22 4 0.13
23 12 0.40
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (23 bp):
GCTAAGTCCCGAAGAGCATTCGT
Found at i:28455367 original size:80 final size:80
Alignment explanation
Indices: 28455005--28455474 Score: 441
Period size: 80 Copynumber: 5.9 Consensus size: 80
28454995 TCGAATGATG
* *
28455005 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTGA-TATATCCGGGCTAAG-TCCCGAAGGCAT
* *
28455068 TTATGCGAATTGATATA
64 TCATGCGAAGTGATATA
* * * * * * *
28455085 TCCGGGATAAGACCCGAAGGCATTTATGCGAATTGATATATCCGGGATAAGACCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTGATATATCCGGGCTAAGTCCCGAAGGCATTC
* *
28455150 GTGCGAATTGATATA
66 ATGCGAAGTGATATA
* * * * *
28455165 TCCGGACTAAGAT-CCGAAGGCATTTATGCGAATTGATATATCCGGGATAAGACCCGAAGGCATT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAAGTGATATATCCGGGCTAAGTCCCGAAGGCATT
* *
28455229 TATGCGAATTGATATA
65 CATGCGAAGTGATATA
* * * *
28455245 TCCGGGATAAGACCCGAAGGCGTTTGTGCGAATTGATATATCCGGGCTAAGTCCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTGATATATCCGGGCTAAGTCCCGAAG-GCATT
* * *
28455310 CGTGC-TAGTGATGTA
65 CATGCGAAGTGATATA
* * * *
28455325 TCCGGGCTAAGTCCCGAAGAGCATTCGTGC-TAGTGATGTATCCGGGCTAAGTTCCGAAGAGCAT
1 TCCGGGCTAAGTCCCGAAG-GCATTTGTGCGAAGTGATATATCCGGGCTAAGTCCCGAAG-GCAT
* * *
28455389 TCGTGC-TAGTGATGTA
64 TCATGCGAAGTGATATA
* * * * * * * *
28455405 TCCGGGCTAGGTTCCGAAGAGCATTCGTGC-TAGTGATATATCCGTGCTAAATCCTGAAGAGCAA
1 TCCGGGCTAAGTCCCGAAG-GCATTTGTGCGAAGTGATATATCCGGGCTAAGTCCCGAAG-GCAT
28455469 TCATGC
64 TCATGC
28455475 TGGTGATGTG
Statistics
Matches: 342, Mismatches: 42, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
80 315 0.92
81 27 0.08
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTGATATATCCGGGCTAAGTCCCGAAGGCATTC
ATGCGAAGTGATATA
Found at i:28455367 original size:120 final size:120
Alignment explanation
Indices: 28455005--28455448 Score: 486
Period size: 120 Copynumber: 3.7 Consensus size: 120
28454995 TCGAATGATG
* * *
28455005 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGATAAGACCCGAAGGCATTTGTGCGAAGTGA-TATATCCGGACTAAGATCCGAAGGCATT
* * * *
28455069 TATGCGAATTGATATATCCGGGATAAGACCCGAAGGCATTTATGCGAATTGATATA
65 CATGCGAAGTGATATATCCGGGATAAGACCCGAAGGCATTCATGCGAAGTGATATA
* *
28455125 TCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGATATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGATAAGACCCGAAGGCATTTGTGCGAAGTGATATATCCGGACTAAGATCCGAAGGCATTC
* * *
28455190 ATGCGAATTGATATATCCGGGATAAGACCCGAAGGCATTTATGCGAATTGATATA
66 ATGCGAAGTGATATATCCGGGATAAGACCCGAAGGCATTCATGCGAAGTGATATA
* * *
28455245 TCCGGGATAAGACCCGAAGGCGTTTGTGCGAATTGATATATCCGGGCTAAG-TCCCGAAGAGCAT
1 TCCGGGATAAGACCCGAAGGCATTTGTGCGAAGTGATATATCCGGACTAAGAT-CCGAAG-GCAT
* * * * * * * *
28455309 TCGTGC-TAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGC-TAGTGATGTA
64 TCATGCGAAGTGATATATCCGGGATAAGACCCGAAG-GCATTCATGCGAAGTGATATA
* ** * * * * * *
28455365 TCCGGGCTAAGTTCCGAAGAGCATTCGTGC-TAGTGATGTATCCGGGCTAGGTTCCGAAGAGCAT
1 TCCGGGATAAGACCCGAAG-GCATTTGTGCGAAGTGATATATCCGGACTAAGATCCGAAG-GCAT
* *
28455429 TCGTGC-TAGTGATATATCCG
64 TCATGCGAAGTGATATATCCG
28455449 TGCTAAATCC
Statistics
Matches: 290, Mismatches: 28, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
119 1 0.00
120 252 0.87
121 37 0.13
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGATAAGACCCGAAGGCATTTGTGCGAAGTGATATATCCGGACTAAGATCCGAAGGCATTC
ATGCGAAGTGATATATCCGGGATAAGACCCGAAGGCATTCATGCGAAGTGATATA
Found at i:28455464 original size:40 final size:39
Alignment explanation
Indices: 28455278--28455483 Score: 295
Period size: 40 Copynumber: 5.2 Consensus size: 39
28455268 TTGTGCGAAT
*
28455278 TGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAG
1 TGATGTATCCGGGCTAAGT-CCGAAGAGCATTCGTGCTAG
28455318 TGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAG
1 TGATGTATCCGGGCTAAGT-CCGAAGAGCATTCGTGCTAG
28455358 TGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAG
1 TGATGTATCCGGGCTAAG-TCCGAAGAGCATTCGTGCTAG
*
28455398 TGATGTATCCGGGCTAGGTTCCGAAGAGCATTCGTGCTAG
1 TGATGTATCCGGGCTAAG-TCCGAAGAGCATTCGTGCTAG
* * * * * *
28455438 TGATATATCCGTGCTAAATCCTGAAGAGCAATCATGCTGG
1 TGATGTATCCGGGCTAAGTCC-GAAGAGCATTCGTGCTAG
28455478 TGATGT
1 TGATGT
28455484 GTATTCGGGC
Statistics
Matches: 154, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
39 3 0.02
40 150 0.97
41 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (39 bp):
TGATGTATCCGGGCTAAGTCCGAAGAGCATTCGTGCTAG
Found at i:28460340 original size:23 final size:23
Alignment explanation
Indices: 28460267--28460341 Score: 59
Period size: 23 Copynumber: 3.2 Consensus size: 23
28460257 CGAATGGCCA
28460267 ATGTGATGAAAGTGAACATGTAT
1 ATGTGATGAAAGTGAACATGTAT
* *
28460290 ATGTG-TGATAAAGCCG-A-ATGGCCA-
1 ATGTGATG--AAAG-TGAACAT-G-TAT
28460314 ATGTGATGAAAGTGAACATGTAT
1 ATGTGATGAAAGTGAACATGTAT
28460337 ATGTG
1 ATGTG
28460342 TGACAAGGCC
Statistics
Matches: 39, Mismatches: 4, Indels: 18
0.64 0.07 0.30
Matches are distributed among these distances:
22 4 0.10
23 18 0.46
24 13 0.33
25 4 0.10
ACGTcount: A:0.36, C:0.08, G:0.28, T:0.28
Consensus pattern (23 bp):
ATGTGATGAAAGTGAACATGTAT
Found at i:28460489 original size:47 final size:47
Alignment explanation
Indices: 28459720--28460477 Score: 1261
Period size: 47 Copynumber: 16.2 Consensus size: 47
28459710 ATGATAGTAT
28459720 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAAC
28459767 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAAC
* *
28459814 ATGTGTATGTGTGATAAGACCGAATGGCCAATGTGATGAATGTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAAC
** * * * *
28459861 ATGCATATATGAGATAAGGCCAAATGGCCAATGTGATGAATGTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAAC
*
28459908 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAAC
28459955 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAAC
* *
28460002 ATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAAC
*
28460049 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAAC
28460096 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAAC
28460143 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAAC
*
28460190 ATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAAC
*
28460237 ATGTGTATGTGTGATAAGACCGAATGGCCAATGTGATGAAAGTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAAC
* *
28460284 ATGTATATGTGTGATAAAGCCGAATGGCCAATGTGATGAAAGTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAAC
* * *
28460331 ATGTATATGTGTGACAAGGCCGAATGGCCAATGTGATGAATGTGAAC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAAC
* *
28460378 ATGTGTATGTGTGATAAGGCCGAGTGGCCAATGTGAT-AAATGTGAGC
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAA-GTGAAC
* * * *
28460425 ATGTGTATGTGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAA-
1 ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAAC
28460471 A-GTGTAT
1 ATGTGTAT
28460478 AAATGTGATA
Statistics
Matches: 671, Mismatches: 38, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
45 6 0.01
46 3 0.00
47 660 0.98
48 2 0.00
ACGTcount: A:0.32, C:0.11, G:0.31, T:0.26
Consensus pattern (47 bp):
ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAAC
Found at i:28460664 original size:37 final size:37
Alignment explanation
Indices: 28460608--28460687 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
28460598 CCGGGCTCTA
* * *
28460608 AAGACCCGATGACTGCGTGTGG-GAATTTTGTCCGGGT
1 AAGACTCGATAACTGCGTGTGGAG-ATTATGTCCGGGT
*
28460645 AAGACTCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACTCGATAACTGCGTGTGGAGATTATGTCCGGGT
28460682 AAGACT
1 AAGACT
28460688 TCGTAATAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (37 bp):
AAGACTCGATAACTGCGTGTGGAGATTATGTCCGGGT
Found at i:28474893 original size:38 final size:37
Alignment explanation
Indices: 28474842--28474916 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 37
28474832 ACATAACATC
* *
28474842 ATTAACAACATTAATAATCTAATGCTATGGAAATTAA
1 ATTAACAAAATTAACAATCTAATGCTATGGAAATTAA
*
28474879 ATTAACAAAAATTAACAATCTAATTCTATGGAAATTAA
1 ATTAAC-AAAATTAACAATCTAATGCTATGGAAATTAA
28474917 CTTATTCTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 6 0.18
38 28 0.82
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.32
Consensus pattern (37 bp):
ATTAACAAAATTAACAATCTAATGCTATGGAAATTAA
Found at i:28480165 original size:63 final size:63
Alignment explanation
Indices: 28480066--28480189 Score: 212
Period size: 63 Copynumber: 2.0 Consensus size: 63
28480056 TTGCTGTGTG
*
28480066 CACACGTGCTAGGAAAACGAGCATGTGTCCAGGCTATGTAACTCACTATTTGCAAATTAGAGC
1 CACACGTGCTAGGAAAAAGAGCATGTGTCCAGGCTATGTAACTCACTATTTGCAAATTAGAGC
* **
28480129 CACACGTGCTAGGAAAAAGAGCATGTGTCCTGGCTATGTAACTCACTATTTGTGAATTAGA
1 CACACGTGCTAGGAAAAAGAGCATGTGTCCAGGCTATGTAACTCACTATTTGCAAATTAGA
28480190 ATCACATGGG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (63 bp):
CACACGTGCTAGGAAAAAGAGCATGTGTCCAGGCTATGTAACTCACTATTTGCAAATTAGAGC
Found at i:28486675 original size:23 final size:22
Alignment explanation
Indices: 28486642--28486712 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
28486632 CCTGAGCTAA
* *
28486642 TGAACGATAAGCTCTAT-TGAGC
1 TGAACGGTAAGCTC-ATGCGAGC
28486664 TGAAACGGTAAGCTCATGCGAGC
1 TG-AACGGTAAGCTCATGCGAGC
* * *
28486687 TGAACAGTAAGCTCATACAAGC
1 TGAACGGTAAGCTCATGCGAGC
28486709 TGAA
1 TGAA
28486713 TCAATAAGCT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
22 25 0.60
23 17 0.40
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.21
Consensus pattern (22 bp):
TGAACGGTAAGCTCATGCGAGC
Found at i:28486699 original size:22 final size:22
Alignment explanation
Indices: 28486660--28486723 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
28486650 AAGCTCTATT
* *
28486660 GAGCTGAAACGGTAAGCTCATGC
1 GAGCTG-AACAGTAAGCTCATAC
28486683 GAGCTGAACAGTAAGCTCATAC
1 GAGCTGAACAGTAAGCTCATAC
* *
28486705 AAGCTGAATCAATAAGCTC
1 GAGCTGAA-CAGTAAGCTC
28486724 TAATAATCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
22 21 0.58
23 15 0.42
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (22 bp):
GAGCTGAACAGTAAGCTCATAC
Found at i:28495375 original size:44 final size:41
Alignment explanation
Indices: 28495304--28495465 Score: 146
Period size: 42 Copynumber: 3.8 Consensus size: 41
28495294 TGTCTTATCG
* * * *
28495304 TGTAAGACCACGTCTGGGGC-TTGGGCATCAATTTGTTATTTACA
1 TGTAAGACCATGTCTGGGACAGT-GGCATCAATATG--ATTT-CA
* *
28495348 TGTAAGACCATGTCTGGGACATTGGCATCGTATATGATTTCA
1 TGTAAGACCATGTCTGGGACAGTGGCATC-AATATGATTTCA
* * * *
28495390 TGTAAGACCCTGTCTAGGACAGTGGCAACATATATGATTTCG
1 TGTAAGACCATGTCTGGGACAGTGGCATCA-ATATGATTTCA
* * *
28495432 TATAAGACCTTGTCTGGGACAGTGGCATCGATAT
1 TGTAAGACCATGTCTGGGACAGTGGCATCAATAT
28495466 TTGATTACTT
Statistics
Matches: 100, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.04
42 62 0.62
43 4 0.04
44 24 0.24
45 6 0.06
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (41 bp):
TGTAAGACCATGTCTGGGACAGTGGCATCAATATGATTTCA
Found at i:28495404 original size:42 final size:42
Alignment explanation
Indices: 28495341--28495471 Score: 163
Period size: 42 Copynumber: 3.1 Consensus size: 42
28495331 TCAATTTGTT
*
28495341 ATTTACATGTAAGACCATGTCTGGGACATTGGCATCGTATATG
1 ATTT-CATGTAAGACCATGTCTGGGACAGTGGCATCGTATATG
* * * *
28495384 ATTTCATGTAAGACCCTGTCTAGGACAGTGGCAACATATATG
1 ATTTCATGTAAGACCATGTCTGGGACAGTGGCATCGTATATG
* * * *
28495426 ATTTCGTATAAGACCTTGTCTGGGACAGTGGCATCGATATTTG
1 ATTTCATGTAAGACCATGTCTGGGACAGTGGCATCG-TATATG
28495469 ATT
1 ATT
28495472 ACTTATAAGG
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
42 63 0.84
43 12 0.16
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (42 bp):
ATTTCATGTAAGACCATGTCTGGGACAGTGGCATCGTATATG
Found at i:28500659 original size:16 final size:16
Alignment explanation
Indices: 28500638--28500672 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28500628 CATGCCGATG
28500638 TTTCAGCT-TTTCGGCT
1 TTTCAGCTATTT-GGCT
28500654 TTTCAGCTATTTGGCT
1 TTTCAGCTATTTGGCT
28500670 TTT
1 TTT
28500673 AACAGTTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.09, C:0.20, G:0.17, T:0.54
Consensus pattern (16 bp):
TTTCAGCTATTTGGCT
Found at i:28512856 original size:28 final size:28
Alignment explanation
Indices: 28512824--28512893 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
28512814 AATGAGATTG
*
28512824 GCACTAAGTGTGCGAGTTTAATT-GTATA
1 GCACTAAGTGTGCGAGTTTAATTATTA-A
*
28512852 GCACTAAGTGTGCGAGTTTGATTATTAA
1 GCACTAAGTGTGCGAGTTTAATTATTAA
28512880 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
28512894 GACTTACTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 37 0.95
29 2 0.05
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTATTAA
Found at i:28519117 original size:93 final size:93
Alignment explanation
Indices: 28518958--28519128 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
28518948 GGATGGTTGA
*** * *
28518958 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCTGAACTTGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACACCCGAACTCGTTGAGT
28519023 TGAGTCCGAGTTCGTAAGATGTAACTAG
66 TGAGTCCGAGTTCGTAAGATGTAACTAG
** * *
28519051 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAGCACCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACACCCGAACTCGTTGAGT
28519116 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
28519129 ACTTAGGGGC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACACCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTAAGATGTAACTAG
Found at i:28519125 original size:46 final size:46
Alignment explanation
Indices: 28518956--28519129 Score: 188
Period size: 46 Copynumber: 3.8 Consensus size: 46
28518946 TAGGATGGTT
**
28518956 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATATATGGATGC
*** * * * * * *
28519002 GAATGTCTGAACTTGTTGAGTTGAGTCCGAGTTCGTAAGATGTA-AC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAT-ATATGGATGC
* *
28519048 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGC
1 GA-GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATATATGGATGC
* *
28519095 GAGCACCCGAGCTCGTTGAGTTGAGTCCGAGTTCA
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCA
28519130 CTTAGGGGCG
Statistics
Matches: 100, Mismatches: 25, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
46 66 0.66
47 34 0.34
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATATATGGATGC
Found at i:28526604 original size:46 final size:45
Alignment explanation
Indices: 28526537--28526704 Score: 168
Period size: 46 Copynumber: 3.7 Consensus size: 45
28526527 TGGTTGAGCA
28526537 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATCGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTAT-GATGCGAATG
* *
28526583 TCCGAACTCGTTGAGTTGAGT-CGAGTT--CGTGA-GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCT-ATGATGCGAA-T--G
*
28526627 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCA-TTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTAT-GATGCGAATG
* * *
28526674 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCAC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCAC
28526705 TTAGGGGCGG
Statistics
Matches: 102, Mismatches: 7, Indels: 26
0.76 0.05 0.19
Matches are distributed among these distances:
41 2 0.02
42 5 0.05
43 2 0.02
44 2 0.02
45 33 0.32
46 42 0.41
47 8 0.08
48 1 0.01
49 5 0.05
50 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGATGCGAATG
Found at i:28526701 original size:92 final size:92
Alignment explanation
Indices: 28526534--28526702 Score: 286
Period size: 92 Copynumber: 1.8 Consensus size: 92
28526524 GGATGGTTGA
*
28526534 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATCGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATCGATGCGAATGCCCGAACTCGTTGAGT
28526599 TGAGTCGAGTTCGTGAGATGTAACTAG
66 TGAGTCGAGTTCGTGAGATGTAACTAG
* * *
28526626 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCA-TTATGGATGCGAATGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATCGATGCGAATGCCCGAACTCGTTGAGT
28526690 TGAGTCTGAGTTC
66 TGAGTC-GAGTTC
28526703 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
91 33 0.46
92 39 0.54
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATCGATGCGAATGCCCGAACTCGTTGAGT
TGAGTCGAGTTCGTGAGATGTAACTAG
Found at i:28526962 original size:19 final size:20
Alignment explanation
Indices: 28526925--28526962 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
28526915 ATAAGGTGGT
28526925 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
28526945 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
28526963 TGGTGTACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:28528999 original size:52 final size:51
Alignment explanation
Indices: 28528879--28529057 Score: 222
Period size: 51 Copynumber: 3.5 Consensus size: 51
28528869 ACTAGTGACT
* *
28528879 CAAGTGTGGTACTATGTGAAGGCCGCTTTGAGAAG-AGATAGC-TTGATCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTTGATCA
*
28528928 CAAATGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGATCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAG-AAGATAGCTTTGATCA
* * * * *
28528980 CAAGTGTTGTACTATGTGAAGGCCAATTTATGAAGAAGGTAGATTTGA-CTA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTTGATC-A
*
28529031 CAAG-GCTGGTACTATGTGCAGGCCACT
1 CAAGTG-TGGTACTATGTGAAGGCCACT
28529058 GGGTATCCGT
Statistics
Matches: 113, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
49 32 0.28
50 2 0.02
51 41 0.36
52 38 0.34
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (51 bp):
CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTTGATCA
Found at i:28529048 original size:51 final size:52
Alignment explanation
Indices: 28528879--28529055 Score: 188
Period size: 52 Copynumber: 3.5 Consensus size: 52
28528869 ACTAGTGACT
** *
28528879 CAAGTGTGGTACTATGTGAAGGCC-GCTT-TG-AGAAGAGATAG-CTTGATCA
1 CAAGTGTGGTACTATGTGAAGGCCAATTTATGAAGAA-AGATAGATTTGATCA
* * * *
28528928 CAAATGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGATCA
1 CAAGTGTGGTACTATGTGAAGGCCAATTTATGAAGAAAGATAGATTTGATCA
* *
28528980 CAAGTGTTGTACTATGTGAAGGCCAATTTATGAAG-AAGGTAGATTTGA-CTA
1 CAAGTGTGGTACTATGTGAAGGCCAATTTATGAAGAAAGATAGATTTGATC-A
*
28529031 CAAG-GCTGGTACTATGTGCAGGCCA
1 CAAGTG-TGGTACTATGTGAAGGCCA
28529056 CTGGGTATCC
Statistics
Matches: 110, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
49 23 0.21
50 4 0.04
51 41 0.37
52 42 0.38
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (52 bp):
CAAGTGTGGTACTATGTGAAGGCCAATTTATGAAGAAAGATAGATTTGATCA
Found at i:28532531 original size:51 final size:50
Alignment explanation
Indices: 28532476--28532574 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 50
28532466 CTACCACATA
* *
28532476 ACATGTAA-CACATCCATAATGAACTCGGACCTCTCAACGAGCTTGGATGTT
1 ACATG-AATCACATCC-TAATGAACTCAGACCTCTCAACAAGCTTGGATGTT
* * *
28532527 ACATGAATCGCATCCTTATGAACTCAGACCTGTCAACAAGCTTGGATG
1 ACATGAATCACATCCTAATGAACTCAGACCTCTCAACAAGCTTGGATG
28532575 CTGGCATCCA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
50 31 0.74
51 11 0.26
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (50 bp):
ACATGAATCACATCCTAATGAACTCAGACCTCTCAACAAGCTTGGATGTT
Found at i:28534175 original size:44 final size:42
Alignment explanation
Indices: 28534092--28534195 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 42
28534082 GCGATGACTG
* *
28534092 AATAAATGACACTAAGTGTGCGATATAGATATAAATTCGGTTT
1 AATAAATGGCACTAAGTGTGCGATATAGATATAAATTCGG-CT
* **
28534135 AATGAAATGGCACTAAGTGTGCGATATTA-TTATAGCTTCGGCT
1 AAT-AAATGGCACTAAGTGTGCGATA-TAGATATAAATTCGGCT
*
28534178 AATTAATGGCACT-AGTGT
1 AATAAATGGCACTAAGTGT
28534196 ACGAGTTCAT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
41 5 0.09
42 9 0.17
43 7 0.13
44 30 0.57
45 2 0.04
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.33
Consensus pattern (42 bp):
AATAAATGGCACTAAGTGTGCGATATAGATATAAATTCGGCT
Found at i:28539914 original size:19 final size:20
Alignment explanation
Indices: 28539890--28539927 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28539880 CACTTGAAGC
28539890 AAGGC-ACACGCCCGTGTGA
1 AAGGCAACACGCCCGTGTGA
*
28539909 AAGGCAACACGCTCGTGTG
1 AAGGCAACACGCCCGTGTG
28539928 GCCACTATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.26, C:0.29, G:0.32, T:0.13
Consensus pattern (20 bp):
AAGGCAACACGCCCGTGTGA
Found at i:28565202 original size:27 final size:27
Alignment explanation
Indices: 28565167--28565335 Score: 185
Period size: 27 Copynumber: 6.3 Consensus size: 27
28565157 ATTACTAAAA
* **
28565167 TACCTTCGATTTGTAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
* * * *
28565194 TTCCCTCGATTTATAGAATTATCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
* * *
28565221 CACCCTCGATTTACAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
** *
28565248 TACCCTTAATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
* *
28565275 TACCCTCGATTTACAGAATTATCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
* *
28565302 TACCCTTGATTTACAAAATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
28565329 TACCCTC
1 TACCCTC
28565336 AGTTTAAAAA
Statistics
Matches: 116, Mismatches: 26, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 116 1.00
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.41
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCATTT
Found at i:28565293 original size:81 final size:81
Alignment explanation
Indices: 28565175--28565334 Score: 266
Period size: 81 Copynumber: 2.0 Consensus size: 81
28565165 AATACCTTCG
* * *
28565175 ATTTGTAGAATTACCATTTTTCCCTCGATTTATAGAATTATCGTTTCACCCTCGATTTACAAAAT
1 ATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTATCGTTTCACCCTCGATTTACAAAAT
*
28565240 TACCGTTTTACCCTTA
66 TACCATTTTACCCTTA
* *
28565256 ATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTATCGTTTTACCCTTGATTTACAAAAT
1 ATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTATCGTTTCACCCTCGATTTACAAAAT
28565321 TACCATTTTACCCT
66 TACCATTTTACCCT
28565335 CAGTTTAAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 73 1.00
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.42
Consensus pattern (81 bp):
ATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTATCGTTTCACCCTCGATTTACAAAAT
TACCATTTTACCCTTA
Found at i:28565358 original size:54 final size:54
Alignment explanation
Indices: 28565222--28565366 Score: 166
Period size: 54 Copynumber: 2.7 Consensus size: 54
28565212 TTATCGTTTC
* * * * *
28565222 ACCCTCGATTTACAAAATTACCGTTTTACCCTTAATTTATAGAATTACCATTTT
1 ACCCTCGATTTAAAAAATTATCGCTTTACCCTTAATTTACAAAATTACCATTTT
* * * *
28565276 ACCCTCGATTTACAGAATTATCGTTTTACCCTTGATTTACAAAATTACCATTTT
1 ACCCTCGATTTAAAAAATTATCGCTTTACCCTTAATTTACAAAATTACCATTTT
* * *
28565330 ACCCTC-AGTTTAAAAAATTGTTGCTTTACCCTCAATT
1 ACCCTCGA-TTTAAAAAATTATCGCTTTACCCTTAATT
28565367 GTGAAATTAC
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
53 1 0.01
54 77 0.99
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (54 bp):
ACCCTCGATTTAAAAAATTATCGCTTTACCCTTAATTTACAAAATTACCATTTT
Found at i:28565428 original size:27 final size:27
Alignment explanation
Indices: 28565398--28565523 Score: 164
Period size: 27 Copynumber: 4.7 Consensus size: 27
28565388 TGTAGGATAG
28565398 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
28565425 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
* * * *
28565452 AATTACCGAAATACCACTGGTTTGTGA
1 AATTACCAAAATACCCCTAGTTTGTAA
* * *
28565479 AATTATCGAAATA-CCCTCAATTTGTAA
1 AATTACCAAAATACCCCT-AGTTTGTAA
*
28565506 AATGACCAAAATACCCCT
1 AATTACCAAAATACCCCT
28565524 GATTTACAAA
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
26 3 0.04
27 78 0.92
28 4 0.05
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.29
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAGTTTGTAA
Found at i:28565437 original size:54 final size:54
Alignment explanation
Indices: 28565365--28565520 Score: 154
Period size: 54 Copynumber: 2.9 Consensus size: 54
28565355 TTACCCTCAA
* * *
28565365 TTGTGAAATTACTGAAATACCCCT-GTAGGATAGAATTACCAAAATACCCCTAGT
1 TTGTGAAATTACCGAAATACCCCTAGTAGG-TAAAATTACCAAAATACCACTAGT
* * ** * *
28565419 TTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCGAAATACCACTGGT
1 TTGTGAAATTACCGAAATACCCCTAGTAGGTAAAATTACCAAAATACCACTAGT
* * ** *
28565473 TTGTGAAATTATCGAAATA-CCCTCAATTTGTAAAATGACCAAAATACC
1 TTGTGAAATTACCGAAATACCCCT-AGTAGGTAAAATTACCAAAATACC
28565521 CCTGATTTAC
Statistics
Matches: 85, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
53 4 0.05
54 78 0.92
55 3 0.04
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (54 bp):
TTGTGAAATTACCGAAATACCCCTAGTAGGTAAAATTACCAAAATACCACTAGT
Found at i:28565536 original size:54 final size:55
Alignment explanation
Indices: 28565402--28565549 Score: 167
Period size: 54 Copynumber: 2.7 Consensus size: 55
28565392 GGATAGAATT
* * * *
28565402 ACCAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCC-CTAGTTTGTAAAATT
1 ACCAAAATACCCCTGA-TTTGTAAAATTATCGAAATACCCTCTAATTTGTAAAATG
* * * *
28565456 ACCGAAATACCACTGGTTTGTGAAATTATCGAAATACCCTC-AATTTGTAAAATG
1 ACCAAAATACCCCTGATTTGTAAAATTATCGAAATACCCTCTAATTTGTAAAATG
** *
28565510 ACCAAAATACCCCTGATTTACAAAATTATAGAAATACCCT
1 ACCAAAATACCCCTGATTTGTAAAATTATCGAAATACCCT
28565550 TGACTTTCTA
Statistics
Matches: 77, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
54 76 0.99
55 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (55 bp):
ACCAAAATACCCCTGATTTGTAAAATTATCGAAATACCCTCTAATTTGTAAAATG
Found at i:28565544 original size:27 final size:27
Alignment explanation
Indices: 28565514--28565607 Score: 111
Period size: 27 Copynumber: 3.4 Consensus size: 27
28565504 AAAATGACCA
*
28565514 AAATACCCCTGATTTACAAAATTATAG
1 AAATACCCTTGATTTACAAAATTATAG
28565541 AAATACCCTTGACTTT-CTAAAAATTATAG
1 AAATACCCTTGA-TTTAC--AAAATTATAG
* *
28565570 AAATACCATTGGTTTACAAAATTACT-G
1 AAATACCCTTGATTTACAAAATTA-TAG
28565597 AAATACCCTTG
1 AAATACCCTTG
28565608 GTTTGTAGAT
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
27 30 0.52
28 7 0.12
29 21 0.36
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (27 bp):
AAATACCCTTGATTTACAAAATTATAG
Found at i:28565722 original size:53 final size:54
Alignment explanation
Indices: 28565617--28565759 Score: 209
Period size: 53 Copynumber: 2.7 Consensus size: 54
28565607 GGTTTGTAGA
* *
28565617 TTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTACCAT
1 TTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACCAT
*
28565671 TTTACCCTCGATTTATAGAATTA-CGTTTTACCCTCGATTTACAAAATTACCAT
1 TTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACCAT
* * *
28565724 TTTACCCTC-AGTTTAAAAAATTATCATTTTACCCTC
1 TTTACCCTCGA-TTTATAGAATTACCATTTTACCCTC
28565760 AATTGTGAAA
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
52 1 0.01
53 46 0.57
54 34 0.42
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.41
Consensus pattern (54 bp):
TTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACCAT
Found at i:28565760 original size:27 final size:27
Alignment explanation
Indices: 28565617--28565759 Score: 209
Period size: 27 Copynumber: 5.3 Consensus size: 27
28565607 GGTTTGTAGA
28565617 TTTACCCTCGATTTATAGAATTACCAT
1 TTTACCCTCGATTTATAGAATTACCAT
28565644 TTTACCCTCGATTTATAGAATTACCAT
1 TTTACCCTCGATTTATAGAATTACCAT
*
28565671 TTTACCCTCGATTTATAGAATTA-CGT
1 TTTACCCTCGATTTATAGAATTACCAT
* *
28565697 TTTACCCTCGATTTACAAAATTACCAT
1 TTTACCCTCGATTTATAGAATTACCAT
* * *
28565724 TTTACCCTC-AGTTTAAAAAATTATCAT
1 TTTACCCTCGA-TTTATAGAATTACCAT
28565751 TTTACCCTC
1 TTTACCCTC
28565760 AATTGTGAAA
Statistics
Matches: 108, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
26 24 0.22
27 84 0.78
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.41
Consensus pattern (27 bp):
TTTACCCTCGATTTATAGAATTACCAT
Found at i:28565783 original size:80 final size:80
Alignment explanation
Indices: 28565619--28565783 Score: 192
Period size: 80 Copynumber: 2.1 Consensus size: 80
28565609 TTTGTAGATT
* * * * *
28565619 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATT
1 TACCCTCGATTTACAAAATTACCATTTTACCCTCGATTTAAAAAATTACCATTTTACCCTCAATT
* ***
28565684 TATAGAATTACGTTT
66 TAGAGAATTACGAAA
*
28565699 TACCCTCGATTTACAAAATTACCATTTTACCCTC-AGTTTAAAAAATTATCATTTTACCCTCAAT
1 TACCCTCGATTTACAAAATTACCATTTTACCCTCGA-TTTAAAAAATTACCATTTTACCCTCAAT
28565763 TGT-GA-AATTACTGAAA
65 T-TAGAGAATTAC-GAAA
28565779 TACCC
1 TACCC
28565784 CTGTAAGATA
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
79 7 0.10
80 64 0.89
81 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.38
Consensus pattern (80 bp):
TACCCTCGATTTACAAAATTACCATTTTACCCTCGATTTAAAAAATTACCATTTTACCCTCAATT
TAGAGAATTACGAAA
Found at i:28565825 original size:27 final size:27
Alignment explanation
Indices: 28565795--28566030 Score: 174
Period size: 27 Copynumber: 8.7 Consensus size: 27
28565785 TGTAAGATAG
28565795 AATTACCAAAATACCCTTAGTTTGTAA
1 AATTACCAAAATACCCTTAGTTTGTAA
*
28565822 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCTTAGTTTGTAA
* * *
28565849 AATTACCGAAATACCAC-TGGTTTGTGA
1 AATTACCAAAATACC-CTTAGTTTGTAA
* * * *
28565876 AATTATCGAAATACCCTCAATTTGTAA
1 AATTACCAAAATACCCTTAGTTTGTAA
* **
28565903 AATTACCAAAATACCCCT-GATTTACAA
1 AATTACCAAAATACCCTTAG-TTTGTAA
* *
28565930 AATTA-CAGAAATACCCTTGACTTTCTAAA
1 AATTACCA-AAATACCCTT-AGTTTGT-AA
* * * **
28565959 AATTA-TAGAAATACCATTGGTTTACAA
1 AATTACCA-AAATACCCTTAGTTTGTAA
** * *
28565986 AATTACTGAAATACCCTTGGTTTGTAG
1 AATTACCAAAATACCCTTAGTTTGTAA
* *
28566013 ATTTACCAAAACACCCTT
1 AATTACCAAAATACCCTT
28566031 GTAGGATGAA
Statistics
Matches: 166, Mismatches: 35, Indels: 16
0.76 0.16 0.07
Matches are distributed among these distances:
26 3 0.02
27 137 0.83
28 8 0.05
29 18 0.11
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.31
Consensus pattern (27 bp):
AATTACCAAAATACCCTTAGTTTGTAA
Found at i:28565836 original size:54 final size:54
Alignment explanation
Indices: 28565762--28565917 Score: 156
Period size: 54 Copynumber: 2.9 Consensus size: 54
28565752 TTACCCTCAA
* *
28565762 TTGTGAAATTACTGAAATACCCCT-GTAAGATAGAATTACCAAAATACC-CTTAGT
1 TTGTGAAATTACCGAAATACCCCTAGTAAG-TAAAATTACCAAAATACCAC-TAGT
* * ** * *
28565816 TTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCGAAATACCACTGGT
1 TTGTGAAATTACCGAAATACCCCTAGTAAGTAAAATTACCAAAATACCACTAGT
* * **
28565870 TTGTGAAATTATCGAAATA-CCCTCAATTTGTAAAATTACCAAAATACC
1 TTGTGAAATTACCGAAATACCCCT-AGTAAGTAAAATTACCAAAATACC
28565918 CCTGATTTAC
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
53 4 0.05
54 78 0.91
55 4 0.05
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (54 bp):
TTGTGAAATTACCGAAATACCCCTAGTAAGTAAAATTACCAAAATACCACTAGT
Found at i:28565956 original size:397 final size:398
Alignment explanation
Indices: 28565222--28566019 Score: 1454
Period size: 397 Copynumber: 2.0 Consensus size: 398
28565212 TTATCGTTTC
* *
28565222 ACCCTCGATTTACAAAATTACCGTTTTACCCTTAATTTATAGAATTACCATTTTACCCTCGATTT
1 ACCCTCGATTTACAAAATTACCATTTTACCCTCAATTTATAGAATTACCATTTTACCCTCGATTT
* * *
28565287 ACAGAATTATCGTTTTACCCTTGATTTACAAAATTACCATTTTACCCTCAGTTTAAAAAATTGTT
66 ACAGAATTATCGTTTTACCCTCGATTTACAAAATTACCATTTTACCCTCAGTTTAAAAAATTATC
* *
28565352 GCTTTACCCTCAATTGTGAAATTACTGAAATACCCCTGTAGGATAGAATTACCAAAATACCCCTA
131 ACTTTACCCTCAATTGTGAAATTACTGAAATACCCCTGTAAGATAGAATTACCAAAATACCCCTA
28565417 GTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCGAAATACCACTGGTTTGTGAAAT
196 GTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCGAAATACCACTGGTTTGTGAAAT
*
28565482 TATCGAAATACCCTCAATTTGTAAAATGACCAAAATACCCCTGATTTACAAAATTATAGAAATAC
261 TATCGAAATACCCTCAATTTGTAAAATGACCAAAATACCCCTGATTTACAAAATTACAGAAATAC
28565547 CCTTGACTTTCTAAAAATTATAGAAATACCATTGGTTTACAAAATTACTGAAATACCCTTGGTTT
326 CCTTGACTTTCTAAAAATTATAGAAATACCATTGGTTTACAAAATTACTGAAATACCCTTGGTTT
28565612 GTAGATTT
391 GTAGATTT
* * *
28565620 ACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTT
1 ACCCTCGATTTACAAAATTACCATTTTACCCTCAATTTATAGAATTACCATTTTACCCTCGATTT
*
28565685 ATAGAATTA-CGTTTTACCCTCGATTTACAAAATTACCATTTTACCCTCAGTTTAAAAAATTATC
66 ACAGAATTATCGTTTTACCCTCGATTTACAAAATTACCATTTTACCCTCAGTTTAAAAAATTATC
* *
28565749 ATTTTACCCTCAATTGTGAAATTACTGAAATACCCCTGTAAGATAGAATTACCAAAATACCCTTA
131 ACTTTACCCTCAATTGTGAAATTACTGAAATACCCCTGTAAGATAGAATTACCAAAATACCCCTA
28565814 GTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCGAAATACCACTGGTTTGTGAAAT
196 GTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCGAAATACCACTGGTTTGTGAAAT
*
28565879 TATCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAATTACAGAAATAC
261 TATCGAAATACCCTCAATTTGTAAAATGACCAAAATACCCCTGATTTACAAAATTACAGAAATAC
28565944 CCTTGACTTTCTAAAAATTATAGAAATACCATTGGTTTACAAAATTACTGAAATACCCTTGGTTT
326 CCTTGACTTTCTAAAAATTATAGAAATACCATTGGTTTACAAAATTACTGAAATACCCTTGGTTT
28566009 GTAGATTT
391 GTAGATTT
28566017 ACC
1 ACC
28566020 AAAACACCCT
Statistics
Matches: 385, Mismatches: 15, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
397 317 0.82
398 68 0.18
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (398 bp):
ACCCTCGATTTACAAAATTACCATTTTACCCTCAATTTATAGAATTACCATTTTACCCTCGATTT
ACAGAATTATCGTTTTACCCTCGATTTACAAAATTACCATTTTACCCTCAGTTTAAAAAATTATC
ACTTTACCCTCAATTGTGAAATTACTGAAATACCCCTGTAAGATAGAATTACCAAAATACCCCTA
GTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCGAAATACCACTGGTTTGTGAAAT
TATCGAAATACCCTCAATTTGTAAAATGACCAAAATACCCCTGATTTACAAAATTACAGAAATAC
CCTTGACTTTCTAAAAATTATAGAAATACCATTGGTTTACAAAATTACTGAAATACCCTTGGTTT
GTAGATTT
Found at i:28566125 original size:27 final size:27
Alignment explanation
Indices: 28566061--28566125 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
28566051 TACCCCAATA
*
28566061 GGTAAAAAGACCGTAAAGCCCATGTAG
1 GGTAAAATGACCGTAAAGCCCATGTAG
* * *
28566088 GGTAAAGTGACCGTAATA-CCCCTGTAT
1 GGTAAAATGACCGTAA-AGCCCATGTAG
28566115 GGTAAAATGAC
1 GGTAAAATGAC
28566126 GAATATGCCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCATGTAG
Found at i:28566975 original size:25 final size:24
Alignment explanation
Indices: 28566937--28567003 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 24
28566927 AGGAAGTGCT
* *
28566937 AAAAGGGCTCTGCCCCAATTTACTG
1 AAAAGGGCTTTGCCCCAATTTA-TC
* *
28566962 AAAAGGGCTTTGCCCTAGTTTATC
1 AAAAGGGCTTTGCCCCAATTTATC
*
28566986 AGAAAGGGCTTTACCCCA
1 A-AAAGGGCTTTGCCCCA
28567004 GTTATTAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 2 0.06
25 33 0.94
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.25
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAATTTATC
Found at i:28567019 original size:24 final size:24
Alignment explanation
Indices: 28566937--28567019 Score: 69
Period size: 25 Copynumber: 3.4 Consensus size: 24
28566927 AGGAAGTGCT
* * * *
28566937 AAAAGGGCTCTGCCCCAATTTACTG
1 AAAAGGGCTTTACCCCAGTTTA-TC
* *
28566962 AAAAGGGCTTTGCCCTAGTTTATC
1 AAAAGGGCTTTACCCCAGTTTATC
*
28566986 AGAAAGGGCTTTACCCCAG-TTATT
1 A-AAAGGGCTTTACCCCAGTTTATC
28567010 AAAAGAGGCT
1 AAAAG-GGCT
28567020 AGGCCTCTAG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
23 4 0.08
24 11 0.22
25 34 0.69
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTTACCCCAGTTTATC
Found at i:28567213 original size:42 final size:42
Alignment explanation
Indices: 28567154--28567245 Score: 175
Period size: 42 Copynumber: 2.2 Consensus size: 42
28567144 TAGTCTCCCC
*
28567154 AAATGGGCTTGCATACATTTATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCTATTGACATTACATGTGATATTG
28567196 AAATGGGCTTGCATACATCTATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCTATTGACATTACATGTGATATTG
28567238 AAATGGGC
1 AAATGGGC
28567246 CTAAGGGCCA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCTATTGACATTACATGTGATATTG
Found at i:28567304 original size:31 final size:31
Alignment explanation
Indices: 28567269--28567352 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
28567259 CATTTACAGT
28567269 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* *
28567300 AAAGGCTTCAGCCCAGTGATATGATTTATGG
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
28567331 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
28567353 CCAAGACTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
30 5 0.10
31 45 0.90
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:28568572 original size:31 final size:31
Alignment explanation
Indices: 28568531--28568590 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
28568521 CCTTTTCATA
*
28568531 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAGATTTCATAACACTGGGCCGAAGCCT
**
28568562 TTTCAGATTTCATATTACTGGGCCGAAGC
1 TTTCAGATTTCATAACACTGGGCCGAAGC
28568591 ATTTACTGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.33
Consensus pattern (31 bp):
TTTCAGATTTCATAACACTGGGCCGAAGCCT
Found at i:28568839 original size:24 final size:24
Alignment explanation
Indices: 28568788--28568905 Score: 152
Period size: 23 Copynumber: 5.0 Consensus size: 24
28568778 GCTTTATCAT
*
28568788 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
28568813 ATAACTAGGGCAAAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
28568837 ATAACTGGGGCATAAGCCC-TTCA
1 ATAACTGGGGCATAAGCCCTTTTA
*
28568860 ATAACTGTGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
28568883 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
28568906 GCACTTCCTC
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
23 42 0.51
24 29 0.35
25 11 0.13
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:28568980 original size:20 final size:20
Alignment explanation
Indices: 28568953--28568999 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
28568943 TTATGAATAA
28568953 ACCATGTGCATATCATACAT
1 ACCATGTGCATATCATACAT
*
28568973 ATCATGTGCATATCATACAT
1 ACCATGTGCATATCATACAT
28568993 ACCATGT
1 ACCATGT
28569000 TTATCAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (20 bp):
ACCATGTGCATATCATACAT
Done.