Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 127 of 356
Found at i:40432421 original size:27 final size:27
Alignment explanation
Indices: 40432184--40432447 Score: 199
Period size: 27 Copynumber: 9.7 Consensus size: 27
40432174 TGTAGGATAG
* * *
40432184 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCGAAATACCCTTGGTTTGTAA
* * *
40432211 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCGAAATACCCTTGGTTTGTAA
*
40432238 AATTACCGAAATACCAC-TGGTTTGTGA
1 AATTACCGAAATACC-CTTGGTTTGTAA
*
40432265 AATTACCGAAATACCAC-TGGTTTGTGA
1 AATTACCGAAATACC-CTTGGTTTGTAA
***
40432292 AATTACCGAAATACCCTCAATTTGTAA
1 AATTACCGAAATACCCTTGGTTTGTAA
* * * **
40432319 AATTACCAAAATACCCCTGATTTACAA
1 AATTACCGAAATACCCTTGGTTTGTAA
** * * *
40432346 AATTATAGAAATATCCTTGACTTTCTAAA
1 AATTACCGAAATACCCTTG-GTTTGT-AA
** * **
40432375 AATTATAGAAATACCATTGGTTTACAA
1 AATTACCGAAATACCCTTGGTTTGTAA
* *
40432402 AATTACTGAAATACCCTTGGTTTGTAG
1 AATTACCGAAATACCCTTGGTTTGTAA
* * *
40432429 ATTTACCAAAACACCCTTG
1 AATTACCGAAATACCCTTG
40432448 TAGGATGAAA
Statistics
Matches: 197, Mismatches: 36, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
26 1 0.01
27 170 0.86
28 7 0.04
29 19 0.10
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.31
Consensus pattern (27 bp):
AATTACCGAAATACCCTTGGTTTGTAA
Found at i:40433391 original size:25 final size:24
Alignment explanation
Indices: 40433353--40433422 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 24
40433343 AGGAAGTGCT
*
40433353 AAAAGGGCTCTGCCCCAGTTTACC
1 AAAAGGGCTTTGCCCCAGTTTACC
*
40433377 GAAAAGGGCTTTGCCCCAGTTTATC
1 -AAAAGGGCTTTGCCCCAGTTTACC
40433402 ATAAAGGGCTTTGCCCCAGTT
1 A-AAAGGGCTTTGCCCCAGTT
40433423 ATTAAAAGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
24 1 0.02
25 41 0.98
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTACC
Found at i:40433435 original size:24 final size:24
Alignment explanation
Indices: 40433352--40433435 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 24
40433342 GAGGAAGTGC
* *
40433352 TAAAAGGGCTCTGCCCCAGTTTACC
1 TAAAAGGGCTTTGCCCCAGTTTA-T
*
40433377 GAAAAGGGCTTTGCCCCAGTTTAT
1 TAAAAGGGCTTTGCCCCAGTTTAT
*
40433401 CATAAAGGGCTTTGCCCCAG-TTAT
1 TA-AAAGGGCTTTGCCCCAGTTTAT
40433425 TAAAAGAGGCT
1 TAAAAG-GGCT
40433436 AGGCCTCCAG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.08
24 10 0.19
25 38 0.73
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (24 bp):
TAAAAGGGCTTTGCCCCAGTTTAT
Found at i:40446566 original size:27 final size:27
Alignment explanation
Indices: 40446518--40446715 Score: 188
Period size: 27 Copynumber: 7.3 Consensus size: 27
40446508 TACTGAAATG
*
40446518 CCCTCGATTTTGTAGAATTACCATTTTA
1 CCCTCGA-TTTATAGAATTACCATTTTA
* * *
40446546 CCCTCAATTTATAGAATTACCGTTTCA
1 CCCTCGATTTATAGAATTACCATTTTA
* * * *
40446573 TCCTCGATTTACAAAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
40446600 -CCTCGATTTATAG-ATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* **
40446625 CCCTCGATTTATAGATTTACTGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* *
40446652 CCCTCGATTTACAAAATTACCATTTTTA
1 CCCTCGATTTATAGAATTACCA-TTTTA
* * *
40446680 CCCTC-AGTTTACA-ATATTATCGTTTTA
1 CCCTCGA-TTTATAGA-ATTACCATTTTA
40446707 CCCTCGATT
1 CCCTCGATT
40446716 GTAAAATTAC
Statistics
Matches: 142, Mismatches: 22, Indels: 13
0.80 0.12 0.07
Matches are distributed among these distances:
25 11 0.08
26 24 0.17
27 79 0.56
28 28 0.20
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (27 bp):
CCCTCGATTTATAGAATTACCATTTTA
Found at i:40446635 original size:79 final size:81
Alignment explanation
Indices: 40446519--40446677 Score: 241
Period size: 79 Copynumber: 2.0 Consensus size: 81
40446509 ACTGAAATGC
* *
40446519 CCTCGATTTTGTAGAATTACCATTTTACCCTCAATTTATAGAATTACCGTTTCATCCTCGATTTA
1 CCTCGATTTTATAGAATTACCATTTTACCCTCAATTTATAGAATTACCGTTTCACCCTCGATTTA
*
40446584 CAAAATTACCGTTTTA
66 CAAAATTACCATTTTA
* * * *
40446600 CCTCGA-TTTATAG-ATTACCATTTTACCCTCGATTTATAGATTTACTGTTTTACCCTCGATTTA
1 CCTCGATTTTATAGAATTACCATTTTACCCTCAATTTATAGAATTACCGTTTCACCCTCGATTTA
40446663 CAAAATTACCATTTT
66 CAAAATTACCATTTT
40446678 TACCCTCAGT
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
79 59 0.83
80 6 0.08
81 6 0.08
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (81 bp):
CCTCGATTTTATAGAATTACCATTTTACCCTCAATTTATAGAATTACCGTTTCACCCTCGATTTA
CAAAATTACCATTTTA
Found at i:40446775 original size:54 final size:54
Alignment explanation
Indices: 40446717--40446898 Score: 172
Period size: 54 Copynumber: 3.4 Consensus size: 54
40446707 CCCTCGATTG
* * * *
40446717 TAAAATTACTGAAATATCCTT-GTAGGATAGAATTACCAAAATACCCCTAGTTTA
1 TAAAATTACCGAAATACCCTTAGTAGG-TAAAATTACCAAAATACCACTAGTTTA
* ** * *
40446771 TAAAATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAATACCACTGGTTTG
1 TAAAATTACCGAAATACCCTTAGTAGGTAAAATTACCAAAATACCACTAGTTTA
* * ** *
40446825 TAAAATTACCGAAATACCCTCAATTTGTAAAATTACC-AAATACCCCT-GATTTA
1 TAAAATTACCGAAATACCCTTAGTAGGTAAAATTACCAAAATACCACTAG-TTTA
* **
40446878 CAAAATTACAAAAATACCCTT
1 TAAAATTACCGAAATACCCTT
40446899 GACTTTTTAA
Statistics
Matches: 108, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
52 1 0.01
53 29 0.27
54 75 0.69
55 3 0.03
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (54 bp):
TAAAATTACCGAAATACCCTTAGTAGGTAAAATTACCAAAATACCACTAGTTTA
Found at i:40446777 original size:27 final size:27
Alignment explanation
Indices: 40446747--40446896 Score: 180
Period size: 27 Copynumber: 5.6 Consensus size: 27
40446737 TGTAGGATAG
*
40446747 AATTACCAAAATACCCCTAGTTTATAA
1 AATTACCAAAATACCCCTAGTTTGTAA
*
40446774 AATTACCAAAATACCCTTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
* *
40446801 AATTACCAAAATACCACTGGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
* *
40446828 AATTACCGAAATA-CCCTCAATTTGTAA
1 AATTACCAAAATACCCCT-AGTTTGTAA
**
40446855 AATTACC-AAATACCCCT-GATTTACAA
1 AATTACCAAAATACCCCTAG-TTTGTAA
*
40446881 AATTACAAAAATACCC
1 AATTACCAAAATACCC
40446897 TTGACTTTTT
Statistics
Matches: 106, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
26 19 0.18
27 87 0.82
ACGTcount: A:0.43, C:0.22, G:0.06, T:0.29
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAGTTTGTAA
Found at i:40446813 original size:81 final size:80
Alignment explanation
Indices: 40446714--40446895 Score: 181
Period size: 81 Copynumber: 2.3 Consensus size: 80
40446704 TTACCCTCGA
** * * * *
40446714 TTGTAAAATTACTGAAATATC-CTTGTAGGATAGAATTACCAAAATACCC-CTAGTTTATAAAAT
1 TTGTAAAATTACCAAAATACCACTGGTAGG-TAAAATTACCAAAATACCCTC-AATTTATAAAAT
40446777 TACCAAAATACCCTTAGT
64 TACC-AAATACCCTTAGT
** * *
40446795 TTGTAAAATTACCAAAATACCACTGGTTTGTAAAATTACCGAAATACCCTCAATTTGTAAAATTA
1 TTGTAAAATTACCAAAATACCACTGGTAGGTAAAATTACCAAAATACCCTCAATTTATAAAATTA
*
40446860 CCAAATACCCCT-GAT
66 CCAAATACCCTTAG-T
** *
40446875 TTACAAAATTACAAAAATACC
1 TTGTAAAATTACCAAAATACC
40446896 CTTGACTTTT
Statistics
Matches: 84, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
79 1 0.01
80 28 0.33
81 49 0.58
82 6 0.07
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.30
Consensus pattern (80 bp):
TTGTAAAATTACCAAAATACCACTGGTAGGTAAAATTACCAAAATACCCTCAATTTATAAAATTA
CCAAATACCCTTAGT
Found at i:40446910 original size:54 final size:54
Alignment explanation
Indices: 40446747--40446974 Score: 201
Period size: 54 Copynumber: 4.2 Consensus size: 54
40446737 TGTAGGATAG
* * *
40446747 AATTACCAAAATACCCCT-AGTTTATAAAATTACCAAAATACCCTTAGTTTGTAA
1 AATTACCAAAATACCACTGA-TTTACAAAATTACCAAAATACCCTTAATTTGTAA
* ** * *
40446801 AATTACCAAAATACCACTGGTTTGTAAAATTACCGAAATACCCTCAATTTGTAA
1 AATTACCAAAATACCACTGATTTACAAAATTACCAAAATACCCTTAATTTGTAA
* * * *
40446855 AATTACC-AAATACCCCTGATTTACAAAATTACAAAAATACCCTTGACTTTTTAAA
1 AATTACCAAAATACCACTGATTTACAAAATTACCAAAATACCCTT-AATTTGT-AA
* * * ** * ** *
40446910 AATTA-TAGAAATACCATTGGTTTACAAAATTACTGAAACACCCTTGGTTTGTAG
1 AATTACCA-AAATACCACTGATTTACAAAATTACCAAAATACCCTTAATTTGTAA
*
40446964 ATTTACCAAAA
1 AATTACCAAAA
40446975 CACCCTTGTA
Statistics
Matches: 140, Mismatches: 28, Indels: 12
0.78 0.16 0.07
Matches are distributed among these distances:
53 30 0.21
54 67 0.48
55 12 0.09
56 31 0.22
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (54 bp):
AATTACCAAAATACCACTGATTTACAAAATTACCAAAATACCCTTAATTTGTAA
Found at i:40446910 original size:81 final size:82
Alignment explanation
Indices: 40446747--40446924 Score: 186
Period size: 81 Copynumber: 2.2 Consensus size: 82
40446737 TGTAGGATAG
* * * ** *
40446747 AATTACCAAAATACCCCTAGTTTATAAAATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAA
1 AATTACCGAAATACCCCTAATTTATAAAATTACCAAAATACCCTGAGTTTACAAAATTACAAAAA
*
40446812 TACCACTGGTTTGT-AA
66 TACCACTGCTTTGTAAA
*
40446828 AATTACCGAAATA-CCCTCAATTTGTAAAATTACC-AAATACCCCTGA-TTTACAAAATTACAAA
1 AATTACCGAAATACCCCT-AATTTATAAAATTACCAAAATA-CCCTGAGTTTACAAAATTACAAA
*
40446890 AATACC-CTTGACTTTTTAAA
64 AATACCAC-TG-CTTTGTAAA
**
40446910 AATTATAGAAATACC
1 AATTACCGAAATACC
40446925 ATTGGTTTAC
Statistics
Matches: 80, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
79 1 0.01
80 30 0.38
81 35 0.44
82 13 0.16
83 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.30
Consensus pattern (82 bp):
AATTACCGAAATACCCCTAATTTATAAAATTACCAAAATACCCTGAGTTTACAAAATTACAAAAA
TACCACTGCTTTGTAAA
Found at i:40446947 original size:27 final size:26
Alignment explanation
Indices: 40446904--40446959 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
40446894 CCCTTGACTT
*
40446904 TTTAAAAATTATAGAAATACCATTGG
1 TTTAAAAATTATAGAAACACCATTGG
*
40446930 TTTACAAAATTACT-GAAACACCCTTGG
1 TTTA-AAAATTA-TAGAAACACCATTGG
40446957 TTT
1 TTT
40446960 GTAGATTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 4 0.15
27 21 0.81
28 1 0.04
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (26 bp):
TTTAAAAATTATAGAAACACCATTGG
Found at i:40446962 original size:109 final size:107
Alignment explanation
Indices: 40446747--40446953 Score: 265
Period size: 109 Copynumber: 1.9 Consensus size: 107
40446737 TGTAGGATAG
* * *
40446747 AATTACCAAAATACCCCTAGTTTATAAAATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAA
1 AATTACC-AAATACCCCTAGTTTACAAAATTACAAAAATACCCTTACTTTGTAAAATTACCAAAA
** *
40446812 TACCACTGGTTTGTAAAATTACCGAAATACCCTCAATTTGTAA
65 TACCACTGGTTTACAAAATTACCGAAACACCCTCAATTTGTAA
* *
40446855 AATTACCAAATACCCCT-GATTTACAAAATTACAAAAATACCCTTGACTTTTTAAAAATTA-TAG
1 AATTACCAAATACCCCTAG-TTTACAAAATTACAAAAATACCCTT-ACTTTGT-AAAATTACCA-
* *
40446918 AAATACCATTGGTTTACAAAATTACTGAAACACCCT
62 AAATACCACTGGTTTACAAAATTACCGAAACACCCT
40446954 TGGTTTGTAG
Statistics
Matches: 85, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
106 1 0.01
107 33 0.39
108 13 0.15
109 38 0.45
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (107 bp):
AATTACCAAATACCCCTAGTTTACAAAATTACAAAAATACCCTTACTTTGTAAAATTACCAAAAT
ACCACTGGTTTACAAAATTACCGAAACACCCTCAATTTGTAA
Found at i:40447979 original size:20 final size:20
Alignment explanation
Indices: 40447956--40448034 Score: 70
Period size: 20 Copynumber: 4.0 Consensus size: 20
40447946 AATTAGGGGT
* *
40447956 ACCGTAGTGCTATCAAGAGC
1 ACCGTAGTACTATCAGGAGC
* * *
40447976 ACCGTACTACTAACAGGAGT
1 ACCGTAGTACTATCAGGAGC
*
40447996 A-CGAAAGTACTATCAGGAGC
1 ACCG-TAGTACTATCAGGAGC
* *
40448016 ACCGTAGTGCTATTAGGAG
1 ACCGTAGTACTATCAGGAG
40448035 TACGAAAGTA
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
19 2 0.04
20 41 0.91
21 2 0.04
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (20 bp):
ACCGTAGTACTATCAGGAGC
Found at i:40448051 original size:20 final size:20
Alignment explanation
Indices: 40447990--40448051 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
40447980 TACTACTAAC
*
40447990 AGGAGTACGAAAGTACTATC
1 AGGAGTACGAAAGTACTATT
* * *
40448010 AGGAGCACCG-TAGTGCTATT
1 AGGAGTA-CGAAAGTACTATT
*
40448030 AGGAGTACGAAAGTACTGTT
1 AGGAGTACGAAAGTACTATT
40448050 AG
1 AG
40448052 TAGCACTATA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 2 0.06
20 28 0.88
21 2 0.06
ACGTcount: A:0.34, C:0.15, G:0.29, T:0.23
Consensus pattern (20 bp):
AGGAGTACGAAAGTACTATT
Found at i:40448057 original size:40 final size:40
Alignment explanation
Indices: 40447972--40448154 Score: 172
Period size: 40 Copynumber: 4.6 Consensus size: 40
40447962 GTGCTATCAA
* * ** *
40447972 GAGCACCGTACTACTAACAGGAGTACGAAAGTACTATCAG
1 GAGCACCGTAGTGCTATTAGGAGTACGAAAGTACTGTCAG
*
40448012 GAGCACCGTAGTGCTATTAGGAGTACGAAAGTACTGTTAG
1 GAGCACCGTAGTGCTATTAGGAGTACGAAAGTACTGTCAG
* ** * * * *
40448052 TAGCACTATAGTGCTATCAAGAGTACAAAAGTA-TCGTTAG
1 GAGCACCGTAGTGCTATTAGGAGTACGAAAGTACT-GTCAG
* * * *
40448092 GAGCATCGTAGTGCT-TTCAAGAGTACGGAAGTACTGCCAG
1 GAGCACCGTAGTGCTATT-AGGAGTACGAAAGTACTGTCAG
*
40448132 GAGCACCGTAGTGCTATGAGGAG
1 GAGCACCGTAGTGCTATTAGGAG
40448155 CACTTATTCG
Statistics
Matches: 115, Mismatches: 24, Indels: 8
0.78 0.16 0.05
Matches are distributed among these distances:
39 2 0.02
40 111 0.97
41 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.22
Consensus pattern (40 bp):
GAGCACCGTAGTGCTATTAGGAGTACGAAAGTACTGTCAG
Found at i:40452973 original size:45 final size:45
Alignment explanation
Indices: 40452923--40453012 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
40452913 GTACTTATTT
*
40452923 TTAGGATTGTATATGGTATGCTTGGCATGTAAGAACAATAATTAA
1 TTAGGACTGTATATGGTATGCTTGGCATGTAAGAACAATAATTAA
*
40452968 TTAGGACTGTATATGGTATGCTTGGCATGTAATAACAATAATTAA
1 TTAGGACTGTATATGGTATGCTTGGCATGTAAGAACAATAATTAA
40453013 CCAATTAAGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.36
Consensus pattern (45 bp):
TTAGGACTGTATATGGTATGCTTGGCATGTAAGAACAATAATTAA
Found at i:40458222 original size:39 final size:39
Alignment explanation
Indices: 40458174--40458309 Score: 213
Period size: 39 Copynumber: 3.5 Consensus size: 39
40458164 CATATCGGAC
40458174 TAAGATCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGT
1 TAAG-TCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGT
40458214 TAAGTCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGT
1 TAAGTCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGT
*
40458253 T-AGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGC
1 TAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGT
*
40458292 TATGTCCGAAGGCATTTG
1 TAAGTCCGAAGGCATTTG
40458310 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 2, Indels: 7
0.91 0.02 0.07
Matches are distributed among these distances:
38 3 0.03
39 80 0.88
40 8 0.09
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (39 bp):
TAAGTCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGT
Found at i:40458339 original size:39 final size:39
Alignment explanation
Indices: 40458179--40458342 Score: 201
Period size: 39 Copynumber: 4.2 Consensus size: 39
40458169 CGGACTAAGA
*
40458179 TCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAG
1 TCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAT
*
40458218 TCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAGT
1 TCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAT
* *
40458257 CCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCT-AT
1 TCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGTTAAT
** *
40458295 GTCCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAAAT
1 -TCCGAAGGCATTTGTGCGAGTTA-CTAAATCCGGGTT-AAT
40458335 TCCGAAGG
1 TCCGAAGG
40458343 TACGTGATTT
Statistics
Matches: 109, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
38 7 0.06
39 98 0.90
40 4 0.04
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (39 bp):
TCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAT
Found at i:40466108 original size:40 final size:40
Alignment explanation
Indices: 40466025--40466210 Score: 252
Period size: 40 Copynumber: 4.7 Consensus size: 40
40466015 TCGAATGATG
* * * *
40466025 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
40466065 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40466105 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40466145 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
40466186 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40466211 AACGAGTAGC
Statistics
Matches: 133, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
39 1 0.01
40 122 0.92
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:40466217 original size:80 final size:79
Alignment explanation
Indices: 40466078--40466243 Score: 228
Period size: 80 Copynumber: 2.1 Consensus size: 79
40466068 GGACTAAGAT
* **
40466078 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAG-TAGCT
*
40466142 AAATCCGGGTTAAGTC
65 AAATCC-GGTTAAATC
*
40466158 CCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCT
1 CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTAGCT
* *
40466222 ATATCCGGTTAAATT
65 AAATCCGGTTAAATC
40466237 CCGAAGG
1 CCGAAGG
40466244 TACGTGATTT
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
79 16 0.21
80 59 0.77
81 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTAGCTA
AATCCGGTTAAATC
Found at i:40469232 original size:40 final size:40
Alignment explanation
Indices: 40469172--40469349 Score: 272
Period size: 40 Copynumber: 4.5 Consensus size: 40
40469162 CGGATGATAA
* *
40469172 CCGGACTAAGATC-CGAAGGCATTTGTGCTAGTGACTATAT
1 CCGGGCTAAG-TCTCGAAGGCATTTGTGCGAGTGACTATAT
*
40469212 CCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTGACTATAT
*
40469252 CCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTGACTATAT
40469292 CCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTG-CTATAT
1 CCGGGCTAAGTCTCGAAGGCATTTGTGCGAG-TGACTATAT
*
40469332 CC-GGCTAAATCTCGAAGG
1 CCGGGCTAAGTCTCGAAGG
40469350 TACTTGGGTT
Statistics
Matches: 131, Mismatches: 5, Indels: 5
0.93 0.04 0.04
Matches are distributed among these distances:
39 17 0.13
40 113 0.86
41 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (40 bp):
CCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTGACTATAT
Found at i:40470812 original size:50 final size:49
Alignment explanation
Indices: 40470581--40470870 Score: 188
Period size: 50 Copynumber: 5.8 Consensus size: 49
40470571 GTAACTGAAG
* * * * * *
40470581 CTATCTAGTACTCATAGTAGCCTGCATTTAGTACTACACATGAGACCAA
1 CTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACTAA
** * * * *
40470630 -TAAT-TCAATACACGTAGTAGCCTGAAGTTAGTACTACACACGTGAGCTAA
1 CT-ATCT-GGTACACATAGTAGCCTGCACTTAGTACTACACACGCGA-CTAA
* * * *
40470680 CCATCTGATACACATAGTAGCCTGCACTTAGTACTACACACACGATTGAA
1 CTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACT-AA
* * * * * * *
40470730 GTTGTCGGGTACGCATAGTAGACTGCACTTAGTACTACACATGCCACCTAA
1 -CTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGA-CTAA
* * * * *
40470781 CTATCTGGTACACGTAGTAGTCTGTACTTAGTACTACACATGTGACCTAAAA
1 CTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGA-CT--AA
* *** *
40470833 CCATCTTCAACACATAGTAGCCTGCACATAGTACTACA
1 CTATCTGGTACACATAGTAGCCTGCACTTAGTACTACA
40470871 TATGTGTTCT
Statistics
Matches: 187, Mismatches: 44, Indels: 17
0.75 0.18 0.07
Matches are distributed among these distances:
48 2 0.01
49 35 0.19
50 79 0.42
51 38 0.20
52 33 0.18
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (49 bp):
CTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACTAA
Found at i:40475326 original size:26 final size:26
Alignment explanation
Indices: 40475262--40475330 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 26
40475252 CATTCTGACC
* *
40475262 CACAACTGGTGTAAGTAGGCCCATTT
1 CACAACTTGTGTAAGCAGGCCCATTT
40475288 CACAACTTGTGTAAGCAGGCCCATTT
1 CACAACTTGTGTAAGCAGGCCCATTT
*
40475314 CACAGCTCT-TGTAAGCA
1 CACAACT-TGTGTAAGCA
40475331 ATGATGTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
26 38 0.97
27 1 0.03
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (26 bp):
CACAACTTGTGTAAGCAGGCCCATTT
Found at i:40481754 original size:23 final size:23
Alignment explanation
Indices: 40481702--40481748 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
40481692 GAGGGAAAGT
*
40481702 AAAAAAATTGAAGAGAAAAGGTA
1 AAAAAAATTGAAGAGAAAAGGGA
40481725 AAAAAAATTGAAGA-AAAAGGGA
1 AAAAAAATTGAAGAGAAAAGGGA
40481747 AA
1 AA
40481749 GCAAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.68, C:0.00, G:0.21, T:0.11
Consensus pattern (23 bp):
AAAAAAATTGAAGAGAAAAGGGA
Found at i:40482259 original size:40 final size:40
Alignment explanation
Indices: 40482204--40482335 Score: 203
Period size: 40 Copynumber: 3.3 Consensus size: 40
40482194 TGAATCCACA
40482204 AAAAGGTTGAAAAGGATGTATCCGAAAAGGATATCAAATG
1 AAAAGGTTGAAAAGGATGTATCCGAAAAGGATATCAAATG
40482244 AAAAGGTTGAAAAGGATGTATCCGAAAAGGATATCAAATG
1 AAAAGGTTGAAAAGGATGTATCCGAAAAGGATATCAAATG
* * ** *
40482284 AAAAGGATGAAAAAGATGTATCTAAAAAGGATAT-TAATG
1 AAAAGGTTGAAAAGGATGTATCCGAAAAGGATATCAAATG
*
40482323 AAAAGGTCGAAAA
1 AAAAGGTTGAAAA
40482336 AATATCAATG
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 15 0.18
40 70 0.82
ACGTcount: A:0.51, C:0.06, G:0.23, T:0.20
Consensus pattern (40 bp):
AAAAGGTTGAAAAGGATGTATCCGAAAAGGATATCAAATG
Found at i:40482335 original size:24 final size:23
Alignment explanation
Indices: 40482308--40482376 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
40482298 GATGTATCTA
40482308 AAAAGGATATTAATGAAAAGGTCG
1 AAAA-GATATTAATGAAAAGGTCG
* * *
40482332 AAAAAATATCAATGACAAGGTCG
1 AAAAGATATTAATGAAAAGGTCG
40482355 AAAATGATATTAATG-AAAGGTC
1 AAAA-GATATTAATGAAAAGGTC
40482377 CGTATCTCAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
23 26 0.68
24 12 0.32
ACGTcount: A:0.51, C:0.07, G:0.20, T:0.22
Consensus pattern (23 bp):
AAAAGATATTAATGAAAAGGTCG
Found at i:40498296 original size:22 final size:22
Alignment explanation
Indices: 40498254--40498297 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
40498244 ATGTTAAAAT
* *
40498254 TTTTAAAATTTTATTTCAATTA
1 TTTTAAAAATTTAATTCAATTA
40498276 TTTTAAATAATTTAATT-AATTA
1 TTTTAAA-AATTTAATTCAATTA
40498298 AATTTTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTAAAAATTTAATTCAATTA
Found at i:40498302 original size:24 final size:24
Alignment explanation
Indices: 40498275--40498337 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 24
40498265 TATTTCAATT
40498275 ATTTTAAATAATTTAATTA-ATTAA
1 ATTTTAAA-AATTTAATTAGATTAA
* *
40498299 ATTTTATAAAAATATATTTAGATTAA
1 A-TTT-TAAAAATTTAATTAGATTAA
40498325 ATTTTAAAAATTT
1 ATTTTAAAAATTT
40498338 TATTTATAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 9 0.27
25 14 0.42
26 10 0.30
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
ATTTTAAAAATTTAATTAGATTAA
Found at i:40498323 original size:26 final size:25
Alignment explanation
Indices: 40498275--40498363 Score: 81
Period size: 26 Copynumber: 3.5 Consensus size: 25
40498265 TATTTCAATT
* * *
40498275 ATTTTAAATAATTTAATTA-ATTAA
1 ATTTTAAAAAATATATTTAGATTAA
40498299 ATTTTATAAAAATATATTTAGATTAA
1 ATTTTA-AAAAATATATTTAGATTAA
* * * **
40498325 ATTTTAAAAATTTTATTTATAGCAAA
1 ATTTTAAAAAATATATTTAGA-TTAA
40498351 ATTTTAAAAAATA
1 ATTTTAAAAAATA
40498364 AGAGATCAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
24 6 0.12
25 22 0.42
26 24 0.46
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (25 bp):
ATTTTAAAAAATATATTTAGATTAA
Found at i:40500716 original size:34 final size:34
Alignment explanation
Indices: 40500673--40500742 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
40500663 AGAAATACCA
40500673 CATAGTACTTGATATATTGGAGAATCCTTCTCAT
1 CATAGTACTTGATATATTGGAGAATCCTTCTCAT
40500707 CATAGTACTTGATATATTGGAGAATCCTTCTCAT
1 CATAGTACTTGATATATTGGAGAATCCTTCTCAT
40500741 CA
1 CA
40500743 AGGGTAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (34 bp):
CATAGTACTTGATATATTGGAGAATCCTTCTCAT
Found at i:40502629 original size:43 final size:42
Alignment explanation
Indices: 40502572--40502720 Score: 129
Period size: 42 Copynumber: 3.5 Consensus size: 42
40502562 AATGCCGACA
* * ** * *
40502572 TCCCAGACTTGGTCTTACATGTAATTTAGTATCGATGCCTCTG
1 TCCCAGACATGGTCTTACACGTAATCAAATA-CGATGCCTATG
* * *
40502615 TCCCAGACAGGGTCTTACACGAAATCAAATACGATGCTTATG
1 TCCCAGACATGGTCTTACACGTAATCAAATACGATGCCTATG
* *
40502657 TCCCAGACATGGTCTTACACGTAAATCTCAAAT-CGAGGCCTGTG
1 TCCCAGACATGGTCTTACACGT-AA--TCAAATACGATGCCTATG
* * *
40502701 TCCCAAACACGATCTTACAC
1 TCCCAGACATGGTCTTACAC
40502721 AATATCTCAG
Statistics
Matches: 86, Mismatches: 17, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
42 29 0.34
43 26 0.30
44 25 0.29
45 6 0.07
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (42 bp):
TCCCAGACATGGTCTTACACGTAATCAAATACGATGCCTATG
Found at i:40502717 original size:44 final size:41
Alignment explanation
Indices: 40502602--40502720 Score: 130
Period size: 42 Copynumber: 2.8 Consensus size: 41
40502592 GTAATTTAGT
* *
40502602 ATCGATGCCTCTGTCCCAGACAGGGTCTTACACGAAATCAA
1 ATCGATGCCTATGTCCCAGACACGGTCTTACACGAAATCAA
* *
40502643 ATACGATGCTTATGTCCCAGACATGGTCTTACACGTAAATCTCAA
1 AT-CGATGCCTATGTCCCAGACACGGTCTTACACG-AAA--TCAA
* * * *
40502688 ATCGAGGCCTGTGTCCCAAACACGATCTTACAC
1 ATCGATGCCTATGTCCCAGACACGGTCTTACAC
40502721 AATATCTCAG
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
41 2 0.03
42 29 0.45
43 3 0.05
44 25 0.38
45 6 0.09
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (41 bp):
ATCGATGCCTATGTCCCAGACACGGTCTTACACGAAATCAA
Found at i:40508144 original size:49 final size:48
Alignment explanation
Indices: 40508087--40508290 Score: 197
Period size: 49 Copynumber: 4.3 Consensus size: 48
40508077 GTAAGTTGCA
*
40508087 GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCATCTAGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATC-TCTAGGCC
* * * * * *
40508136 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATCCATGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTAT--CATCTCTAGGCC
** * * *
40508186 GACACCATGTCCTAGACATGGTATTACACTGAC-A-CATCTCGTA-GCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCTC-TAGGCC
*
40508232 GATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TACATCTCGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTAT-CATCTCTAGGCC
40508278 GATG-CATGTCCCA
1 GATGCCATGTCCCA
40508291 TGAACTATTC
Statistics
Matches: 125, Mismatches: 23, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
44 11 0.09
45 14 0.11
46 31 0.25
47 1 0.01
49 34 0.27
50 31 0.25
51 3 0.02
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.26
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCTCTAGGCC
Found at i:40508280 original size:46 final size:46
Alignment explanation
Indices: 40508087--40508290 Score: 189
Period size: 46 Copynumber: 4.3 Consensus size: 46
40508077 GTAAGTTGCA
* *
40508087 GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCATCTAGGCT
1 GATG-CATGTCCCAGACATGGTCTTACACTGGCTA-CATC-TCGAGGCC
* * * * *
40508136 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATCCATGTC
1 GATG-CATGTCCCAGACATGGTCTTACACT-G-GCT-ACATCTCGAGGCC
** * * *
40508186 GACACCATGTCCTAGACATGGTATTACACTGAC-ACATCTCGTA-GCC
1 GA-TGCATGTCCCAGACATGGTCTTACACTGGCTACATCTCG-AGGCC
40508232 GATGCATGTCCCAGACAT-GTCTTACACTGGCTTACATCTCGAGGCC
1 GATGCATGTCCCAGACATGGTCTTACACTGGC-TACATCTCGAGGCC
40508278 GATGCATGTCCCA
1 GATGCATGTCCCA
40508291 TGAACTATTC
Statistics
Matches: 128, Mismatches: 19, Indels: 19
0.77 0.11 0.11
Matches are distributed among these distances:
44 11 0.09
45 14 0.11
46 34 0.27
47 1 0.01
48 1 0.01
49 31 0.24
50 30 0.23
51 5 0.04
52 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.26
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGGTCTTACACTGGCTACATCTCGAGGCC
Found at i:40508569 original size:46 final size:47
Alignment explanation
Indices: 40508394--40508571 Score: 172
Period size: 46 Copynumber: 3.8 Consensus size: 47
40508384 TCATCATCTA
* * *
40508394 GGCCGATGCCATGTCCCAGACATGTCTTACACTGGCT-TACAT-CTCGA
1 GGCCGATGCCATGTCCCAGACATGTCTTACACTAGCTCT-CATAAT-GT
* *
40508441 GGCTGATG-CATGTCCCAGACATGTCTTACACTAGCACTCGTCTTAA--T
1 GGCCGATGCCATGTCCCAGACATGTCTTACACTAG--CTC-TCATAATGT
* * * *
40508488 -GACGTTGCCATGTTCCGGACATGGTCTTACACTAGCTCTCATAATGT
1 GGCCGATGCCATGTCCCAGACAT-GTCTTACACTAGCTCTCATAATGT
40508535 GGCCGATG-CATGTCCCAGACATGTCTTACACTAGCTC
1 GGCCGATGCCATGTCCCAGACATGTCTTACACTAGCTC
40508572 ACGTACGTGA
Statistics
Matches: 106, Mismatches: 15, Indels: 21
0.75 0.11 0.15
Matches are distributed among these distances:
45 5 0.05
46 47 0.44
47 32 0.30
48 19 0.18
49 2 0.02
50 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (47 bp):
GGCCGATGCCATGTCCCAGACATGTCTTACACTAGCTCTCATAATGT
Found at i:40514513 original size:49 final size:49
Alignment explanation
Indices: 40514453--40514718 Score: 234
Period size: 49 Copynumber: 5.6 Consensus size: 49
40514443 GTAAGTTACT
* * * *
40514453 GATGTCATGTCCCGGATATGGTCTTACACTGGCTATCATCATCGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATCATCGAGGCC
*
40514502 GATGCCATGTCCCAGACATGGTCTTATACTAGCTATCATCATCGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATCATCGAGGCC
*
40514551 GATGCCATGTCCCAGACATGGTCTTACA-TTGAC-A-CATC-TCGTA-GCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAG-CTATCATCATCG-AGGCC
* * * * * * * *
40514597 AAT-ACATGTTCTAGACAT-GTCTTACACT-GGTTTACGTC-TCGAGGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTAT-CATCATCGAGGCC
* * * * *
40514643 GATG-CATGTCCCAGGCAT-GTCTTACACTAGC-ACTCGTC-TCAATGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTA-TCATCATCGAGGCC
40514689 GATGCCATGTCCCAGACATGGTCTTACACT
1 GATGCCATGTCCCAGACATGGTCTTACACT
40514719 GGCTCACACC
Statistics
Matches: 181, Mismatches: 24, Indels: 25
0.79 0.10 0.11
Matches are distributed among these distances:
44 9 0.05
45 14 0.08
46 53 0.29
47 20 0.11
48 13 0.07
49 72 0.40
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.29
Consensus pattern (49 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATCATCGAGGCC
Found at i:40514651 original size:46 final size:46
Alignment explanation
Indices: 40514609--40514720 Score: 136
Period size: 46 Copynumber: 2.4 Consensus size: 46
40514599 TACATGTTCT
** *
40514609 AGACATGTCTTACACTGGTTTACGTCTCGAGGTCGATG-CATGTCCC
1 AGACATGTCTTACACTGGACT-CGTCTCAAGGTCGATGCCATGTCCC
* * *
40514655 AGGCATGTCTTACACTAGCACTCGTCTCAATGTCGATGCCATGTCCC
1 AGACATGTCTTACACT-GGACTCGTCTCAAGGTCGATGCCATGTCCC
40514702 AGACATGGTCTTACACTGG
1 AGACAT-GTCTTACACTGG
40514721 CTCACACCAA
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
46 29 0.53
47 16 0.29
48 10 0.18
ACGTcount: A:0.21, C:0.28, G:0.22, T:0.29
Consensus pattern (46 bp):
AGACATGTCTTACACTGGACTCGTCTCAAGGTCGATGCCATGTCCC
Found at i:40522321 original size:42 final size:46
Alignment explanation
Indices: 40522215--40522380 Score: 130
Period size: 48 Copynumber: 3.6 Consensus size: 46
40522205 GGGTTATGTA
* *
40522215 TGATCCCATGTAAGACCAT-GTCTGGGACATGGCTTTGGCATCAATATG
1 TGATCCCATGTAAGACCATAGTCTGGG--AT-GCATTGGCATCGATATG
* ** * ** *
40522263 TAATTTCGTGCGAGACCATAG-CT-GG-T-TATTGGCATCGATATG
1 TGATCCCATGTAAGACCATAGTCTGGGATGCATTGGCATCGATATG
*
40522305 TGATCCCATGTCAGACCAT-GTCTGGGACATGGCATTGGCATCGATATG
1 TGATCCCATGTAAGACCATAGTCTGGG--AT-GCATTGGCATCGATATG
*
40522353 TGATCCCATGTAAGACCATA-TCTAGGAT
1 TGATCCCATGTAAGACCATAGTCTGGGAT
40522381 ATGGCATTGG
Statistics
Matches: 91, Mismatches: 18, Indels: 20
0.71 0.14 0.16
Matches are distributed among these distances:
41 1 0.01
42 28 0.31
43 2 0.02
44 1 0.01
46 3 0.03
47 2 0.02
48 53 0.58
49 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (46 bp):
TGATCCCATGTAAGACCATAGTCTGGGATGCATTGGCATCGATATG
Found at i:40522361 original size:48 final size:48
Alignment explanation
Indices: 40522290--40522393 Score: 172
Period size: 48 Copynumber: 2.2 Consensus size: 48
40522280 ATAGCTGGTT
*
40522290 ATTGGCATCGATATGTGATCCCATGTCAGACCATGTCTGGGACATGGC
1 ATTGGCATCGATATGTGATCCCATGTAAGACCATGTCTGGGACATGGC
* * *
40522338 ATTGGCATCGATATGTGATCCCATGTAAGACCATATCTAGGATATGGC
1 ATTGGCATCGATATGTGATCCCATGTAAGACCATGTCTGGGACATGGC
40522386 ATTGGCAT
1 ATTGGCAT
40522394 ACTACCATGT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (48 bp):
ATTGGCATCGATATGTGATCCCATGTAAGACCATGTCTGGGACATGGC
Found at i:40522386 original size:90 final size:90
Alignment explanation
Indices: 40522215--40522387 Score: 231
Period size: 90 Copynumber: 1.9 Consensus size: 90
40522205 GGGTTATGTA
* ** * *
40522215 TGATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCATCAATATGTAATTTCGTGCGAGACC
1 TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGTAATCCCATGCAAGACC
*
40522280 ATAGCTGGTTATTGGCATCGATATG
66 ATAGCTGGATATTGGCATCGATATG
* * * *
40522305 TGATCCCATGTCAGACCATGTCTGGGACATGGCATTGGCATCGATATGTGATCCCATGTAAGACC
1 TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGTAATCCCATGCAAGACC
*
40522370 ATATCTAGGATA-TGGCAT
66 ATAGCT-GGATATTGGCAT
40522388 TGGCATACTA
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
90 67 0.94
91 4 0.06
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (90 bp):
TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGTAATCCCATGCAAGACC
ATAGCTGGATATTGGCATCGATATG
Found at i:40534477 original size:2 final size:2
Alignment explanation
Indices: 40534470--40534517 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
40534460 CAAAACCCTT
40534470 CA CA CA CA CA C- CA -A CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
40534510 CA CA CA CA
1 CA CA CA CA
40534518 TATATATATA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.05
2 42 0.95
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:40557601 original size:21 final size:20
Alignment explanation
Indices: 40557572--40557615 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 20
40557562 ATATGACCCT
40557572 GTTTAGTGAAAAATTTTC-TAA
1 GTTTAGTG--AAATTTTCTTAA
*
40557593 GTTTTGTGAAATTTTCTTAA
1 GTTTAGTGAAATTTTCTTAA
40557613 GTT
1 GTT
40557616 CTTGGTTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 8 0.38
20 6 0.29
21 7 0.33
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.50
Consensus pattern (20 bp):
GTTTAGTGAAATTTTCTTAA
Found at i:40557941 original size:20 final size:20
Alignment explanation
Indices: 40557918--40558015 Score: 85
Period size: 20 Copynumber: 4.9 Consensus size: 20
40557908 CAGAGTACAT
40557918 AAGTGCAATCAGGGGTACTG
1 AAGTGCAATCAGGGGTACTG
* *
40557938 AAGTACAATCAGGGGCAC-G
1 AAGTGCAATCAGGGGTACTG
*
40557957 AAAGTGCAATCATGGGTA-TCG
1 -AAGTGCAATCAGGGGTACT-G
* * *
40557978 AAGTACAAACAGGGGCACAT-
1 AAGTGCAATCAGGGGTAC-TG
*
40557998 AAGTGCAATTAGGGGTAC
1 AAGTGCAATCAGGGGTAC
40558016 CGGAGTACAA
Statistics
Matches: 60, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
19 1 0.02
20 57 0.95
21 1 0.02
22 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.31, T:0.17
Consensus pattern (20 bp):
AAGTGCAATCAGGGGTACTG
Found at i:40557962 original size:40 final size:40
Alignment explanation
Indices: 40557918--40558048 Score: 160
Period size: 40 Copynumber: 3.3 Consensus size: 40
40557908 CAGAGTACAT
40557918 AAGTGCAATCAGGGGTACTGAAGTACAATCAGGGGCACGA
1 AAGTGCAATCAGGGGTACTGAAGTACAATCAGGGGCACGA
* *
40557958 AAGTGCAATCATGGGTA-TCGAAGTACAAACAGGGGCAC-A
1 AAGTGCAATCAGGGGTACT-GAAGTACAATCAGGGGCACGA
* * * *
40557997 TAAGTGCAATTAGGGGTACCGGAGTACAAAT-AGGGGCACGT
1 -AAGTGCAATCAGGGGTACTGAAGTAC-AATCAGGGGCACGA
40558038 AAGTGCAATCA
1 AAGTGCAATCA
40558049 TTCAATAATT
Statistics
Matches: 77, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
39 2 0.03
40 73 0.95
41 2 0.03
ACGTcount: A:0.36, C:0.17, G:0.31, T:0.17
Consensus pattern (40 bp):
AAGTGCAATCAGGGGTACTGAAGTACAATCAGGGGCACGA
Found at i:40566221 original size:28 final size:27
Alignment explanation
Indices: 40566164--40566312 Score: 226
Period size: 27 Copynumber: 5.4 Consensus size: 27
40566154 TAAATTGTGC
* *
40566164 AGCACTAAGTGTGCGAATTGAATATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
40566191 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
40566219 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
40566246 AGCACTAAGTGTGCGAGTATGATTATGT
1 AGCACTAAGTGTGCGAGT-TGACTATGT
* *
40566274 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
40566301 AGCACTGAGTGT
1 AGCACTAAGTGT
40566313 ACGGACTTAA
Statistics
Matches: 115, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
27 63 0.55
28 52 0.45
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:40566229 original size:55 final size:55
Alignment explanation
Indices: 40566164--40566312 Score: 235
Period size: 55 Copynumber: 2.7 Consensus size: 55
40566154 TAAATTGTGC
* *
40566164 AGCACTAAGTGTGCGAATTGAATATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAGTATGACTATGT
* *
40566219 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTATGATTATGT
1 AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAGTATGACTATGT
* * *
40566274 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGT
1 AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGT
40566313 ACGGACTTAA
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 87 1.00
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAGTATGACTATGT
Found at i:40570989 original size:36 final size:36
Alignment explanation
Indices: 40570949--40571021 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
40570939 TGGGTCACAT
*
40570949 TCGTAAATGGATGTATTTTCTCACTTAGTATAGAAA
1 TCGTAAATGAATGTATTTTCTCACTTAGTATAGAAA
40570985 TCGTAAATGAATGTATTTTCTCACTTAGTATAGAAA
1 TCGTAAATGAATGTATTTTCTCACTTAGTATAGAAA
40571021 T
1 T
40571022 GACTTGAGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (36 bp):
TCGTAAATGAATGTATTTTCTCACTTAGTATAGAAA
Found at i:40574138 original size:15 final size:15
Alignment explanation
Indices: 40574118--40574147 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
40574108 TTGATATACT
40574118 TTGGCAAGTTAGAGA
1 TTGGCAAGTTAGAGA
40574133 TTGGCAAGTTAGAGA
1 TTGGCAAGTTAGAGA
40574148 AGTTGATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.27
Consensus pattern (15 bp):
TTGGCAAGTTAGAGA
Found at i:40583564 original size:43 final size:41
Alignment explanation
Indices: 40583479--40583594 Score: 101
Period size: 43 Copynumber: 2.8 Consensus size: 41
40583469 GTCTGAGACA
* * *
40583479 TCGTGTAAGACCGTGTCTGGGACATAGGCCTCGATTGAGATT
1 TCGTATAAGACCATGTCTGGGACATAGGCATCGATT-AGATT
*
40583521 TATGTATAAGACCATGTCTGGGACATCA-GCATCGTATCT-GATT
1 T-CGTATAAGACCATGTCTGGGACAT-AGGCATCG-AT-TAGATT
* * * *
40583564 TCGTGTAAGACCTTGTTTGGGACAGAGGCAT
1 TCGTATAAGACCATGTCTGGGACATAGGCAT
40583595 TGATATTGAA
Statistics
Matches: 60, Mismatches: 9, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
41 1 0.02
42 24 0.40
43 31 0.52
44 3 0.05
45 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (41 bp):
TCGTATAAGACCATGTCTGGGACATAGGCATCGATTAGATT
Found at i:40591496 original size:47 final size:47
Alignment explanation
Indices: 40591442--40591729 Score: 432
Period size: 47 Copynumber: 6.1 Consensus size: 47
40591432 TTAGGATTTT
** * *
40591442 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
40591489 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
40591536 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
40591583 ATGTGGTGAATATGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
40591630 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCAAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * *
40591677 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
40591724 ATGTGA
1 ATGTGA
40591730 AATATGCATG
Statistics
Matches: 217, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 217 1.00
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:40591542 original size:22 final size:22
Alignment explanation
Indices: 40591471--40591542 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
40591461 GTATATATGA
40591471 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
* * *
40591493 GATGAATG-TGAACAT-GCATATATGT
1 GAT-AAGGCCG-A-ATGGC-CA-ATGT
40591518 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
40591540 GAT
1 GAT
40591543 GAATGTGAGC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 11 0.30
23 9 0.24
24 9 0.24
25 8 0.22
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (22 bp):
GATAAGGCCGAATGGCCAATGT
Found at i:40591858 original size:98 final size:96
Alignment explanation
Indices: 40591700--40591897 Score: 290
Period size: 98 Copynumber: 2.0 Consensus size: 96
40591690 GAACATGCAT
*
40591700 ATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGCATGAGATATGTATATGTGGTAAAGCCGA
1 ATATGTGGTAAAGCCGAATGGCTAATGTGAAATATACATGAGATATGTATATGTGGTAAAGCCGA
* *
40591765 ATGGCTAATGTGAAATATGTATGAGATATGC
66 ATGGCTAATGTGAAAAATGTAGGAGATATGC
* *
40591796 ATATGTGGTAAAGCTGAATGG-TCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGC
1 ATATGTGGTAAAGCCGAATGGCT-AATGTG-AA-ATATACATGAGATATGTATATGTGGTAAAGC
* * *
40591860 CGAATGGCTAGTGTGAAAAATGTAGGCGATGTGC
63 CGAATGGCTAATGTGAAAAATGTAGGAGATATGC
40591894 ATAT
1 ATAT
40591898 ATTGTGGCCG
Statistics
Matches: 91, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
95 1 0.01
96 26 0.29
97 2 0.02
98 62 0.68
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.30
Consensus pattern (96 bp):
ATATGTGGTAAAGCCGAATGGCTAATGTGAAATATACATGAGATATGTATATGTGGTAAAGCCGA
ATGGCTAATGTGAAAAATGTAGGAGATATGC
Found at i:40591875 original size:50 final size:48
Alignment explanation
Indices: 40591699--40591883 Score: 282
Period size: 48 Copynumber: 3.8 Consensus size: 48
40591689 TGAACATGCA
*
40591699 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGCATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
40591747 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
* * *
40591795 CATATGTGGTAAAGCTGAATGG-TCAATGTGAAATATATATATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCT-AATGTG-AA-ATATGTATGAGATATG
* *
40591845 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAAAATGTA
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTA
40591884 GGCGATGTGC
Statistics
Matches: 124, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
47 1 0.01
48 78 0.63
49 4 0.03
50 40 0.32
51 1 0.01
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.30
Consensus pattern (48 bp):
TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
Found at i:40591899 original size:50 final size:49
Alignment explanation
Indices: 40591477--40591883 Score: 262
Period size: 47 Copynumber: 8.5 Consensus size: 49
40591467 ATGAGATAAG
* ** * * *
40591477 GCCGAATGGCCAATGTGATGAATG--TGA-ACATGCATATATGTGATAAG
1 GCCGAATGGCTAATGTGAAAAATGTATGAGATATGC-TATATGTGGTAAA
* ** * *
40591524 GCCGAATGGCCAATGTGATGAATG--TGAG-CATGC-ATATGTGTGATAAG
1 GCCGAATGGCTAATGTGAAAAATGTATGAGATATGCTATATGTG-G-TAAA
* *** * * *
40591571 GCCGAATGGCCAATGTGGTGAA--TATGA-ACATGCATATATGTGATAAG
1 GCCGAATGGCTAATGTGAAAAATGTATGAGATATGC-TATATGTGGTAAA
* ** * *
40591618 GCCGAATGGCCAATGTGATGAATG--TGAG-CATGC-ATATGTGTGATAAG
1 GCCGAATGGCTAATGTGAAAAATGTATGAGATATGCTATATGTG-G-TAAA
* * *** *
40591665 GCCAAATGGCCAATGTGGTGAA--TATGA-ACATGCATATATGTGGTAAA
1 GCCGAATGGCTAATGTGAAAAATGTATGAGATATGC-TATATGTGGTAAA
* *
40591712 GCCGAATGGCTAATGTGAAATATGCATGAGATATG-TATATGTGGTAAA
1 GCCGAATGGCTAATGTGAAAAATGTATGAGATATGCTATATGTGGTAAA
*
40591760 GCCGAATGGCTAATGTGAAATATGTATGAGATATGC-ATATGTGGTAAA
1 GCCGAATGGCTAATGTGAAAAATGTATGAGATATGCTATATGTGGTAAA
* *
40591808 GCTGAATGG-TCAATGTGAAATATATATATGAGATATG-TATATGTGGTAAA
1 GCCGAATGGCT-AATGTGAAA-A-ATGTATGAGATATGCTATATGTGGTAAA
*
40591858 GCCGAATGGCTAGTGTGAAAAATGTA
1 GCCGAATGGCTAATGTGAAAAATGTA
40591884 GGCGATGTGC
Statistics
Matches: 310, Mismatches: 23, Indels: 53
0.80 0.06 0.14
Matches are distributed among these distances:
45 14 0.05
47 150 0.48
48 81 0.26
49 19 0.06
50 45 0.15
51 1 0.00
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.27
Consensus pattern (49 bp):
GCCGAATGGCTAATGTGAAAAATGTATGAGATATGCTATATGTGGTAAA
Found at i:40592137 original size:37 final size:37
Alignment explanation
Indices: 40592029--40592137 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
40592019 GCAAATATAT
* *
40592029 TCCGGGTAAGACCCGATGACTACGAGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
40592066 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
40592103 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
40592138 CGTCTGAGCT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:40594343 original size:78 final size:79
Alignment explanation
Indices: 40594230--40594423 Score: 230
Period size: 78 Copynumber: 2.5 Consensus size: 79
40594220 GCCTACGGGA
* * * * * *
40594230 CTTTAAGCCCGGATATAGTACCAGTACGAAA-CCTGCGGACCTTAAGTCCGAATATAGTACCAGT
1 CTTTAAGCCCGGATACAATTCCAGCAC-AAAGCCTGCGGACCTTAAGTCCGAATATAATACCAGC
40594294 ACGAAGCCTGCGGAT
65 ACGAAGCCTGCGGAT
* * * *
40594309 C-TTAAGTCCGGATACAATTCCAGCACAAAGCCTGCGGACCTTAAGTCGGGATATAATTCCAGCA
1 CTTTAAGCCCGGATACAATTCCAGCACAAAGCCTGCGGACCTTAAGTCCGAATATAATACCAGCA
*
40594373 CGAAGCCTGCGGGT
66 CGAAGCCTGCGGAT
* * * *
40594387 CTTTAAGCCCGGATATAATTTCAGCATATAGCCTGCG
1 CTTTAAGCCCGGATACAATTCCAGCACAAAGCCTGCG
40594424 AGTCTTTAAG
Statistics
Matches: 97, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
77 3 0.03
78 63 0.65
79 31 0.32
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.23
Consensus pattern (79 bp):
CTTTAAGCCCGGATACAATTCCAGCACAAAGCCTGCGGACCTTAAGTCCGAATATAATACCAGCA
CGAAGCCTGCGGAT
Found at i:40594404 original size:40 final size:40
Alignment explanation
Indices: 40594218--40594441 Score: 197
Period size: 39 Copynumber: 5.7 Consensus size: 40
40594208 CACCAACACA
* * * *
40594218 AAGCCTACGGGACTTTAAGCCCGGATATAGTACCAGTACG
1 AAGCCTGCGGGACTTTAAGCCCGGATATAATTCCAGCACG
* * * * * * *
40594258 AAACCTGC-GGACCTTAAGTCCGAATATAGTACCAGTACG
1 AAGCCTGCGGGACTTTAAGCCCGGATATAATTCCAGCACG
* * *
40594297 AAGCCTGC-GGA-TCTTAAGTCCGGATACAATTCCAGCACA
1 AAGCCTGCGGGACT-TTAAGCCCGGATATAATTCCAGCACG
* * *
40594336 AAGCCTGC-GGACCTTAAGTCGGGATATAATTCCAGCACG
1 AAGCCTGCGGGACTTTAAGCCCGGATATAATTCCAGCACG
* * *
40594375 AAGCCTGCGGGTCTTTAAGCCCGGATATAATTTCAGCA-T
1 AAGCCTGCGGGACTTTAAGCCCGGATATAATTCCAGCACG
* *
40594414 ATAGCCTGCGAGTCTTTAAGCCCGGATA
1 A-AGCCTGCGGGACTTTAAGCCCGGATA
40594442 CACATCAAAT
Statistics
Matches: 156, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
39 101 0.65
40 55 0.35
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.22
Consensus pattern (40 bp):
AAGCCTGCGGGACTTTAAGCCCGGATATAATTCCAGCACG
Found at i:40599254 original size:85 final size:84
Alignment explanation
Indices: 40599124--40599278 Score: 222
Period size: 85 Copynumber: 1.8 Consensus size: 84
40599114 TACCATACCA
* * * *
40599124 ATGCCATATCCCAGATATGGTCTTACATGTAATCTCGTATCGATGCCAATAGCCCAGCTATAGTC
1 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCATATAGATGCC-ATAGCCCAGATATAGTC
40599189 TTACACGAAATCTCATATCG
65 TTACACGAAATCTCATATCG
* * *
40599209 ATGCCATATCCTAGATATGGTCTTACACG-AAGTCTCATATAGATGCCATATCCCAGATATGGTC
1 ATGCCATATCCCAGATATGGTCTTACACGTAA-TCTCATATAGATGCCATAGCCCAGATATAGTC
40599273 TTACAC
65 TTACAC
40599279 ATAGTCTTAG
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
84 22 0.35
85 40 0.65
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (84 bp):
ATGCCATATCCCAGATATGGTCTTACACGTAATCTCATATAGATGCCATAGCCCAGATATAGTCT
TACACGAAATCTCATATCG
Found at i:40599285 original size:42 final size:42
Alignment explanation
Indices: 40599124--40599278 Score: 220
Period size: 42 Copynumber: 3.7 Consensus size: 42
40599114 TACCATACCA
* * *
40599124 ATGCCATATCCCAGATATGGTCTTACATGTAATCTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* * *
40599166 ATGCCAATAGCCCAGCTATAGTCTTACACGAAATCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* * *
40599209 ATGCCATATCCTAGATATGGTCTTACACGAAGTCTCATATAG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
40599251 ATGCCATATCCCAGATATGGTCTTACAC
1 ATGCCATATCCCAGATATGGTCTTACAC
40599279 ATAGTCTTAG
Statistics
Matches: 99, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 63 0.64
43 36 0.36
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
Found at i:40604229 original size:47 final size:47
Alignment explanation
Indices: 40604120--40604231 Score: 127
Period size: 47 Copynumber: 2.4 Consensus size: 47
40604110 ACAGTAATGC
40604120 AAATAAATTGCCACATAATAAAAATCATGGACAAGCCACCAAAATCTA
1 AAATAAATTGCCA-ATAATAAAAATCATGGACAAGCCACCAAAATCTA
* * ** * *
40604168 AAATATATTTCCAATAATCGAAATCATGGACAAGCCATCAAAGTCGT-
1 AAATAAATTGCCAATAATAAAAATCATGGACAAGCCACCAAAATC-TA
* *
40604215 AGATAAACTGCCAATAA
1 AAATAAATTGCCAATAA
40604232 CTTCCAACTT
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
47 41 0.77
48 12 0.23
ACGTcount: A:0.48, C:0.20, G:0.11, T:0.21
Consensus pattern (47 bp):
AAATAAATTGCCAATAATAAAAATCATGGACAAGCCACCAAAATCTA
Found at i:40613916 original size:15 final size:15
Alignment explanation
Indices: 40613878--40613907 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40613868 ATCTCACCCC
40613878 AAATCAGATACAAAA
1 AAATCAGATACAAAA
*
40613893 AAATTAGATACAAAA
1 AAATCAGATACAAAA
40613908 TTATCAGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.10, G:0.07, T:0.17
Consensus pattern (15 bp):
AAATCAGATACAAAA
Found at i:40619128 original size:17 final size:17
Alignment explanation
Indices: 40619103--40619143 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
40619093 ATTTTTGTCC
*
40619103 AAAACTTAGAAATTGGG
1 AAAATTTAGAAATTGGG
40619120 AAAATTTAGAAATTGGG
1 AAAATTTAGAAATTGGG
40619137 AAAATTT
1 AAAATTT
40619144 CTCTTTAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.49, C:0.02, G:0.20, T:0.29
Consensus pattern (17 bp):
AAAATTTAGAAATTGGG
Found at i:40630991 original size:47 final size:46
Alignment explanation
Indices: 40630885--40631196 Score: 190
Period size: 46 Copynumber: 6.6 Consensus size: 46
40630875 GTGCTAATGC
* * *
40630885 AAGACATGTCTGGGACATGCATTGGCCA-C-ATTATGAG-GCCAATGT
1 AAGACATGTCTGGGACATGCATCGG-CATCGA-GATGAGAGCCAGTGT
* * *
40630930 AAGACCATGCCTGGGACATGGCATCGGTATTGAGATGAGAGCCAGTGT
1 AAGA-CATGTCTGGGACAT-GCATCGGCATCGAGATGAGAGCCAGTGT
* *
40630978 AAGACATGTCTGGGACATGCATCGCCCTCGAGATGTA-AGCCAGTGT
1 AAGACATGTCTGGGACATGCATCGGCATCGAGATG-AGAGCCAGTGT
* * * *
40631024 AAGACATGTCTGGGACATGCATCGGC-TAC-AAAAG-GTGTCAGTGT
1 AAGACATGTCTGGGACATGCATCGGCAT-CGAGATGAGAGCCAGTGT
* * * *
40631068 AAGACAATGTTTGGGACATGGCATCGACA-CGGATATGTGAGAGCTAGTGT
1 AAGAC-ATGTCTGGGACAT-GCATCGGCATC-GAGA--TGAGAGCCAGTGT
* * * * ** * * *
40631118 AAGACCATGTTTGGGATATGGCATCAGCCTCGATTTTGATAGTCAGTTT
1 AAGA-CATGTCTGGGACAT-GCATCGGCATCGA-GATGAGAGCCAGTGT
*
40631167 AAGACCATGTCTGGGACATGGCATCAGCAT
1 AAGA-CATGTCTGGGACAT-GCATCGGCAT
40631197 TATACCCTAT
Statistics
Matches: 213, Mismatches: 35, Indels: 34
0.76 0.12 0.12
Matches are distributed among these distances:
44 12 0.06
45 21 0.10
46 69 0.32
47 27 0.13
48 12 0.06
49 37 0.17
50 32 0.15
51 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (46 bp):
AAGACATGTCTGGGACATGCATCGGCATCGAGATGAGAGCCAGTGT
Found at i:40631188 original size:49 final size:51
Alignment explanation
Indices: 40631060--40631194 Score: 161
Period size: 49 Copynumber: 2.7 Consensus size: 51
40631050 TACAAAAGGT
* *
40631060 GTCAGTGTAAGACAATGTTTGGGACATGGCATC-GACACGGATATGTGAGA
1 GTCAGTGTAAGACCATGTTTGGGACATGGCATCAGCCACGGATATGTGAGA
* * * *
40631110 G-CTAGTGTAAGACCATGTTTGGGATATGGCATCAGCCTC-GAT-TTTGATA
1 GTC-AGTGTAAGACCATGTTTGGGACATGGCATCAGCCACGGATATGTGAGA
* *
40631159 GTCAGTTTAAGACCATGTCTGGGACATGGCATCAGC
1 GTCAGTGTAAGACCATGTTTGGGACATGGCATCAGC
40631195 ATTATACCCT
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
49 37 0.51
50 33 0.45
51 3 0.04
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (51 bp):
GTCAGTGTAAGACCATGTTTGGGACATGGCATCAGCCACGGATATGTGAGA
Found at i:40635629 original size:40 final size:40
Alignment explanation
Indices: 40635467--40635630 Score: 233
Period size: 40 Copynumber: 4.1 Consensus size: 40
40635457 CGGATGATAA
* * *
40635467 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
40635507 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
40635547 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
40635587 CCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
40635627 CCGG
1 CCGG
40635631 TTAAATCCGA
Statistics
Matches: 114, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
39 3 0.03
40 111 0.97
ACGTcount: A:0.21, C:0.25, G:0.29, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:40643517 original size:40 final size:40
Alignment explanation
Indices: 40643462--40643676 Score: 265
Period size: 40 Copynumber: 5.4 Consensus size: 40
40643452 ATGATAACCA
* ** * *
40643462 GGCTAAGTCCCGAAGGAATTTACGCTAGTGACTAGT-TCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TATCCG
40643502 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
*
40643542 GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
*
40643582 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
* * * * *
40643622 GGCTATGTCCCAAAGGCATTCGAGTGAG-TAGCTATATCC-
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCG
* *
40643661 GGTTAAATCCCGAAGG
1 GGCTAAGTCCCGAAGG
40643677 TACCTGGCTT
Statistics
Matches: 155, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
39 15 0.10
40 140 0.90
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
Found at i:40646547 original size:21 final size:21
Alignment explanation
Indices: 40646522--40646562 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
40646512 GTCATAATAG
40646522 CCACACGGGCGTGTTGCCCTT
1 CCACACGGGCGTGTTGCCCTT
*
40646543 CCACATGGGCGTGTTGCCCT
1 CCACACGGGCGTGTTGCCCT
40646563 GCTTCAAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.37, G:0.29, T:0.24
Consensus pattern (21 bp):
CCACACGGGCGTGTTGCCCTT
Found at i:40648003 original size:49 final size:48
Alignment explanation
Indices: 40647884--40648022 Score: 172
Period size: 51 Copynumber: 2.8 Consensus size: 48
40647874 TTGTGAGGTT
* *
40647884 GCATGTGTAGTACTAAGTACAGGCTACTATGCGTACCCGAAAACTGTGATC
1 GCATGTGTAGTACTAAGTGCAGGCTACTATGCGTA-CC--AGACTGTGATC
* * * * *
40647935 ACATGTGTAATACTAAGTGCAGGCTACTACGTGTACCAGACTGTTGGTC
1 GCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGACTG-TGATC
40647984 GCATGTGTAGTACTAAGTGCA-GCTACTATGCGTACCAGA
1 GCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA
40648023 TAGCTTCGGC
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
48 21 0.28
49 23 0.30
50 2 0.03
51 30 0.39
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (48 bp):
GCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGACTGTGATC
Found at i:40658473 original size:47 final size:49
Alignment explanation
Indices: 40658399--40658528 Score: 164
Period size: 46 Copynumber: 2.8 Consensus size: 49
40658389 AACCCGCCCC
*
40658399 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-AGTTACATCCA
* * *
40658447 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTTGCATCCA
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTACATCCA
*
40658492 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
40658529 TCAACCATCC
Statistics
Matches: 70, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
43 6 0.09
44 2 0.03
45 2 0.03
46 29 0.41
47 29 0.41
48 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (49 bp):
TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTACATCCA
Found at i:40658544 original size:46 final size:45
Alignment explanation
Indices: 40658401--40658544 Score: 136
Period size: 46 Copynumber: 3.1 Consensus size: 45
40658391 CCCGCCCCTA
40658401 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCT
* * * *
40658448 CA-CGAACTCGGACTCAACTCAACGAGTTCGGACAT-TTGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCT-CAACCATCT
40658494 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT-CT
40658540 AGTGA
1 AGTGA
40658545 CATGTCACTT
Statistics
Matches: 79, Mismatches: 8, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
44 8 0.10
45 2 0.03
46 33 0.42
47 31 0.39
48 1 0.01
49 3 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCT
Found at i:40664018 original size:40 final size:40
Alignment explanation
Indices: 40663963--40664165 Score: 284
Period size: 40 Copynumber: 5.1 Consensus size: 40
40663953 TGGATGATAA
* * *
40663963 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
*
40664003 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
40664043 CCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
40664083 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
40664123 CCGGGCTATGTCCCGAAGGAATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
40664163 CCG
1 CCG
40664166 ATTAAATCCC
Statistics
Matches: 150, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
39 3 0.02
40 147 0.98
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:40673873 original size:24 final size:24
Alignment explanation
Indices: 40673845--40673892 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
40673835 GTCTAGGGCT
*
40673845 GTAAAACTATTTTCAAAGTTCCAA
1 GTAAAACTATTGTCAAAGTTCCAA
40673869 GTAAAACTATTGTCAAAGTTCCAA
1 GTAAAACTATTGTCAAAGTTCCAA
40673893 TACCTAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (24 bp):
GTAAAACTATTGTCAAAGTTCCAA
Found at i:40681084 original size:24 final size:24
Alignment explanation
Indices: 40681021--40681085 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
40681011 AATAATAGTA
*
40681021 AATGATAGAAAAAAATAATTAATT
1 AATGATAGAAAAAAATAAATAATT
* *
40681045 AATTATA-AAAACAAATAAATCATT
1 AATGATAGAAAA-AAATAAATAATT
* *
40681069 GATGATAGAATAAAATA
1 AATGATAGAAAAAAATA
40681086 GTAAATTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
23 4 0.12
24 26 0.79
25 3 0.09
ACGTcount: A:0.62, C:0.03, G:0.08, T:0.28
Consensus pattern (24 bp):
AATGATAGAAAAAAATAAATAATT
Found at i:40681360 original size:20 final size:20
Alignment explanation
Indices: 40681335--40681374 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40681325 CTAGTGAATG
*
40681335 TTAGTTGTCATATATTAGAA
1 TTAGTTATCATATATTAGAA
*
40681355 TTAGTTATTATATATTAGAA
1 TTAGTTATCATATATTAGAA
40681375 CAGGAGGGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (20 bp):
TTAGTTATCATATATTAGAA
Found at i:40686583 original size:82 final size:83
Alignment explanation
Indices: 40686430--40686595 Score: 262
Period size: 82 Copynumber: 2.0 Consensus size: 83
40686420 GTTAACGAAC
* *
40686430 ATGAAACAATGAACGGATACATGAAAGATACTCGGAACACCCTAAATAGTGTGCACAAGCACGAA
1 ATGAAACAATGAACGGATACATGAAAAATACTCGGAACACCCTAAATAGTGTGCACAAGCACCAA
** *
40686495 GTGAATAGCAGTACTCCA
66 CCGAATAGCAATACTCCA
* *
40686513 ATGAAACAATGACCGGATACATGAAAAATACTC-GAACACTCTAAATAGTGTGCACAAGCACCAA
1 ATGAAACAATGAACGGATACATGAAAAATACTCGGAACACCCTAAATAGTGTGCACAAGCACCAA
40686577 CCGAATAGCAATACTCCA
66 CCGAATAGCAATACTCCA
40686595 A
1 A
40686596 AGTAAGGTTG
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
82 45 0.59
83 31 0.41
ACGTcount: A:0.43, C:0.22, G:0.17, T:0.17
Consensus pattern (83 bp):
ATGAAACAATGAACGGATACATGAAAAATACTCGGAACACCCTAAATAGTGTGCACAAGCACCAA
CCGAATAGCAATACTCCA
Found at i:40686755 original size:7 final size:7
Alignment explanation
Indices: 40686743--40686772 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
40686733 AACTTAATAA
40686743 ATATTAT
1 ATATTAT
40686750 ATATTAT
1 ATATTAT
40686757 ATATTAT
1 ATATTAT
40686764 ATATTAT
1 ATATTAT
40686771 AT
1 AT
40686773 GCATTAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATATTAT
Found at i:40700503 original size:17 final size:17
Alignment explanation
Indices: 40700447--40700503 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
40700437 AAAACTTAAA
40700447 TGTAAAAGAAAAGTATG
1 TGTAAAAGAAAAGTATG
* * * * *
40700464 TGTATACATATTAAGTGTA
1 TGTA-AAAGA-AAAGTATG
40700483 TGTAAAAGAAAAGTATG
1 TGTAAAAGAAAAGTATG
40700500 TGTA
1 TGTA
40700504 TGTCATTCAA
Statistics
Matches: 28, Mismatches: 10, Indels: 4
0.67 0.24 0.10
Matches are distributed among these distances:
17 13 0.46
18 6 0.21
19 9 0.32
ACGTcount: A:0.46, C:0.02, G:0.21, T:0.32
Consensus pattern (17 bp):
TGTAAAAGAAAAGTATG
Found at i:40700595 original size:15 final size:15
Alignment explanation
Indices: 40700575--40700605 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
40700565 AAAGTGATAA
40700575 TAGATATGCAATTTG
1 TAGATATGCAATTTG
40700590 TAGATATGCAATTTG
1 TAGATATGCAATTTG
40700605 T
1 T
40700606 TGATTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.42
Consensus pattern (15 bp):
TAGATATGCAATTTG
Found at i:40707247 original size:16 final size:17
Alignment explanation
Indices: 40707220--40707252 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
40707210 CAATGTTTAT
40707220 ATGAATTATTATAAAAG
1 ATGAATTATTATAAAAG
*
40707237 ATGAA-TATTATTAAAG
1 ATGAATTATTATAAAAG
40707253 TAGGTTCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (17 bp):
ATGAATTATTATAAAAG
Found at i:40710017 original size:3 final size:3
Alignment explanation
Indices: 40710009--40710055 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
40709999 TAATACAAAT
40710009 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
40710056 TAATAATAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:40710114 original size:34 final size:34
Alignment explanation
Indices: 40710076--40710179 Score: 101
Period size: 34 Copynumber: 3.1 Consensus size: 34
40710066 AATAATAATC
40710076 TAAATTTTGAAATTACATAAAAGTAATAAACAAA
1 TAAATTTTGAAATTACATAAAAGTAATAAACAAA
** * * **
40710110 TAAATAAT-AACA-AAAAT-AAA-TAATAATA-ATC
1 TAAATTTTGAA-ATTACATAAAAGTAATAA-ACAAA
40710141 TAAATTTTGAAATTACATAAAAGTAATAAACAAA
1 TAAATTTTGAAATTACATAAAAGTAATAAACAAA
40710175 TAAAT
1 TAAAT
40710180 AATGAAATAA
Statistics
Matches: 51, Mismatches: 12, Indels: 14
0.66 0.16 0.18
Matches are distributed among these distances:
31 14 0.27
32 9 0.18
33 9 0.18
34 19 0.37
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.29
Consensus pattern (34 bp):
TAAATTTTGAAATTACATAAAAGTAATAAACAAA
Found at i:40710132 original size:65 final size:63
Alignment explanation
Indices: 40710060--40710201 Score: 248
Period size: 65 Copynumber: 2.2 Consensus size: 63
40710050 CAACAATAAT
40710060 AATAATAATAATAATCTAAATTTTGAAATTACATAAAAGTAATAAACAAATAAATAATAACAAA
1 AATAATAATAATAATCTAAATTTTGAAATTACATAAAAGTAATAAACAAATAAATAATAA-AAA
* *
40710124 AATAAATAATAATAATCTAAATTTTGAAATTACATAAAAGTAATAAACAAATAAATAATGAAAT
1 AAT-AATAATAATAATCTAAATTTTGAAATTACATAAAAGTAATAAACAAATAAATAATAAAAA
40710188 AATAATAATAATAA
1 AATAATAATAATAA
40710202 AGGAAAAATA
Statistics
Matches: 75, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
63 11 0.15
64 8 0.11
65 56 0.75
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.29
Consensus pattern (63 bp):
AATAATAATAATAATCTAAATTTTGAAATTACATAAAAGTAATAAACAAATAAATAATAAAAA
Found at i:40710168 original size:31 final size:31
Alignment explanation
Indices: 40710068--40710169 Score: 91
Period size: 31 Copynumber: 3.2 Consensus size: 31
40710058 ATAATAATAA
40710068 TAATAATCTAAATTTTGAAATTACATAAAAG
1 TAATAATCTAAATTTTGAAATTACATAAAAG
* ** * * *
40710099 TAATAAACAAATAAATAAT-AACA-AAAATAAATAA
1 TAATAATC---TAAATTTTGAA-ATTACATAAA-AG
40710133 TAATAATCTAAATTTTGAAATTACATAAAAG
1 TAATAATCTAAATTTTGAAATTACATAAAAG
40710164 TAATAA
1 TAATAA
40710170 ACAAATAAAT
Statistics
Matches: 52, Mismatches: 12, Indels: 14
0.67 0.15 0.18
Matches are distributed among these distances:
31 21 0.40
32 8 0.15
33 8 0.15
34 15 0.29
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (31 bp):
TAATAATCTAAATTTTGAAATTACATAAAAG
Found at i:40710317 original size:12 final size:12
Alignment explanation
Indices: 40710289--40710338 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
40710279 AAAATTGAAC
40710289 TTAAAT-AAATAA
1 TTAAATAAAAT-A
*
40710301 ATAAATAAAATA
1 TTAAATAAAATA
*
40710313 TTAAATGAAATA
1 TTAAATAAAATA
40710325 TTAAATAAAATA
1 TTAAATAAAATA
40710337 TT
1 TT
40710339 TTTTAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
12 29 0.88
13 4 0.12
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (12 bp):
TTAAATAAAATA
Found at i:40710329 original size:24 final size:24
Alignment explanation
Indices: 40710289--40710338 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
40710279 AAAATTGAAC
40710289 TTAAATAAATAAATAAATAAAATA
1 TTAAATAAATAAATAAATAAAATA
*
40710313 TTAAATGAAAT-ATTAAATAAAATA
1 TTAAAT-AAATAAATAAATAAAATA
40710337 TT
1 TT
40710339 TTTTAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (24 bp):
TTAAATAAATAAATAAATAAAATA
Found at i:40716257 original size:31 final size:30
Alignment explanation
Indices: 40716222--40716286 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
40716212 GCAATTACGC
*
40716222 ACATGAAACTTGAATTGTGGTTC-ATATGTAT
1 ACATGAAACTTGAATT-TGATTCAAT-TGTAT
* *
40716253 ACATGAAATTTTAATTTGATTCAATTGTAT
1 ACATGAAACTTGAATTTGATTCAATTGTAT
40716283 ACAT
1 ACAT
40716287 TTATTTTCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 14 0.47
31 16 0.53
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (30 bp):
ACATGAAACTTGAATTTGATTCAATTGTAT
Found at i:40716284 original size:30 final size:31
Alignment explanation
Indices: 40716222--40716286 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
40716212 GCAATTACGC
*
40716222 ACATGAAACTTGAATTGTGGTTCATATGTAT
1 ACATGAAACTTGAATTGTGATTCATATGTAT
* *
40716253 ACATGAAATTTTAATT-TGATTCA-ATTGTAT
1 ACATGAAACTTGAATTGTGATTCATA-TGTAT
40716283 ACAT
1 ACAT
40716287 TTATTTTCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 1 0.03
30 15 0.50
31 14 0.47
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (31 bp):
ACATGAAACTTGAATTGTGATTCATATGTAT
Found at i:40716444 original size:31 final size:31
Alignment explanation
Indices: 40716403--40716474 Score: 110
Period size: 31 Copynumber: 2.3 Consensus size: 31
40716393 TAATCTAAAT
* *
40716403 TTCATATATAACATTGC-ATATTAGTTCAAAG
1 TTCATGTATAACATT-CAACATTAGTTCAAAG
40716434 TTCATGTATAACATTCAACATTAGTTCAAAG
1 TTCATGTATAACATTCAACATTAGTTCAAAG
40716465 TTCATGTATA
1 TTCATGTATA
40716475 GTTTTAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 1 0.03
31 37 0.97
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.39
Consensus pattern (31 bp):
TTCATGTATAACATTCAACATTAGTTCAAAG
Found at i:40717180 original size:128 final size:126
Alignment explanation
Indices: 40716949--40717193 Score: 364
Period size: 128 Copynumber: 1.9 Consensus size: 126
40716939 TAATTCCAGA
* * * *
40716949 TTCTTTAATTGTTTTAGATTGAAGAAAAGTGTAAAAAGGTGAGGCCTTTGGCTCGATAGAATGCA
1 TTCTCTAATTGTTTTAGATTGAAGAAAAATATAAAAAGGTGAGGCCTTTGACTCGATAGAATGCA
*** *
40717014 TTGCAGTCAGGAGTGTTGAAGTTAATGTTGATGCCTCTAGTGCAAAAATGTTGGCAATTAG
66 CCACAGTCACGAGTGTTGAAGTTAATGTTGATGCCTCTAGTGCAAAAATGTTGGCAATTAG
* *
40717075 TTCTCTAATTGTTTTAGATTGAAGAAAAAATATAAAAAGGGTGAGGCCTTTGACTCGATGGAGTG
1 TTCTCTAATTGTTTTAGATTGAAG-AAAAATATAAAAA-GGTGAGGCCTTTGACTCGATAGAATG
* *
40717140 CACCACAGTTACGAGTGTTGAAGTTAATGTTGATGCCTCTAGTGCAAAAGTGTT
64 CACCACAGTCACGAGTGTTGAAGTTAATGTTGATGCCTCTAGTGCAAAAATGTT
40717194 AGTAATTAAG
Statistics
Matches: 105, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
126 23 0.22
127 11 0.10
128 71 0.68
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (126 bp):
TTCTCTAATTGTTTTAGATTGAAGAAAAATATAAAAAGGTGAGGCCTTTGACTCGATAGAATGCA
CCACAGTCACGAGTGTTGAAGTTAATGTTGATGCCTCTAGTGCAAAAATGTTGGCAATTAG
Found at i:40724332 original size:12 final size:12
Alignment explanation
Indices: 40724315--40724381 Score: 71
Period size: 12 Copynumber: 5.5 Consensus size: 12
40724305 TATAAAAAGC
40724315 AACAATAAGCAT
1 AACAATAAGCAT
* * *
40724327 AACAATGTATCAA
1 AACAAT-AAGCAT
40724340 AACAATAAGCAT
1 AACAATAAGCAT
* *
40724352 AACAATAAACAC
1 AACAATAAGCAT
*
40724364 AACAATAAGTAT
1 AACAATAAGCAT
40724376 AACAAT
1 AACAAT
40724382 GTATTAAAAT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
12 34 0.79
13 9 0.21
ACGTcount: A:0.60, C:0.16, G:0.06, T:0.18
Consensus pattern (12 bp):
AACAATAAGCAT
Found at i:40724343 original size:25 final size:25
Alignment explanation
Indices: 40724315--40724390 Score: 100
Period size: 25 Copynumber: 3.1 Consensus size: 25
40724305 TATAAAAAGC
40724315 AACAATAAGCATAACAATGTATCAA
1 AACAATAAGCATAACAATGTATCAA
* * *
40724340 AACAATAAGCATAACAAT-AAACAC
1 AACAATAAGCATAACAATGTATCAA
* *
40724364 AACAATAAGTATAACAATGTATTAA
1 AACAATAAGCATAACAATGTATCAA
40724389 AA
1 AA
40724391 TAAGGGAATA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
24 20 0.48
25 22 0.52
ACGTcount: A:0.59, C:0.14, G:0.07, T:0.20
Consensus pattern (25 bp):
AACAATAAGCATAACAATGTATCAA
Found at i:40724577 original size:7 final size:7
Alignment explanation
Indices: 40724567--40724592 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
40724557 ATGTGAGTCA
40724567 AGAAATG
1 AGAAATG
40724574 AGAAATG
1 AGAAATG
40724581 AGAAATG
1 AGAAATG
40724588 AGAAA
1 AGAAA
40724593 CATTTAGGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.27, T:0.12
Consensus pattern (7 bp):
AGAAATG
Found at i:40730271 original size:40 final size:40
Alignment explanation
Indices: 40730220--40730522 Score: 423
Period size: 40 Copynumber: 7.6 Consensus size: 40
40730210 TTGAATGCTG
* * * * *
40730220 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAG-TGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTG-TTAAA
* *
40730260 TCCGGATTAAGTTCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
*
40730300 TCCGGGTTAAGTCCAGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
40730340 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
*
40730380 TCCGGGTTAAGTCCCGAAGGCATACGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
*
40730420 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
* * **
40730460 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
* *
40730499 TCCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
40730523 TGAACGAGGA
Statistics
Matches: 242, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
39 35 0.14
40 199 0.82
41 8 0.03
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
Found at i:40737978 original size:40 final size:40
Alignment explanation
Indices: 40737927--40738229 Score: 432
Period size: 40 Copynumber: 7.6 Consensus size: 40
40737917 TTGAATGCTG
* * * * *
40737927 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAG-TGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTG-TTAAA
* *
40737967 TCCGGATTAAGTTCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
40738007 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
40738047 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
*
40738087 TCCGGGTTAAGTCCCGAAGGCATACGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
*
40738127 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
* * **
40738167 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
* *
40738206 TCCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
40738230 TGAACGAGGA
Statistics
Matches: 244, Mismatches: 17, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
39 35 0.14
40 201 0.82
41 8 0.03
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
Found at i:40742387 original size:47 final size:47
Alignment explanation
Indices: 40742309--40742795 Score: 636
Period size: 47 Copynumber: 10.1 Consensus size: 47
40742299 CCCTTCGGGA
* * * * * * *
40742309 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*** *
40742356 CCCGTCACATATATACACTTTCATATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
** *
40742403 CTTATCACATATATACACTTTCACATTCATCACACACATTCATCACA-TCGGC
1 CTTATCACATATATACACTTTCACATTCAT----CACA-TCGGC-CATTAGGC
*
40742455 CATTAGGC-CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 C-TTA-TCAC--A-T----ATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40742510 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTGGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40742557 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40742604 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40742651 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40742698 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40742745 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40742792 CTTA
1 CTTA
40742796 CTATCATTTC
Statistics
Matches: 390, Mismatches: 33, Indels: 34
0.85 0.07 0.07
Matches are distributed among these distances:
47 328 0.84
51 5 0.01
52 9 0.02
53 7 0.02
54 7 0.02
55 9 0.02
56 5 0.01
60 20 0.05
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:40742442 original size:13 final size:13
Alignment explanation
Indices: 40742424--40742449 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40742414 TATACACTTT
40742424 CACATTCATCACA
1 CACATTCATCACA
40742437 CACATTCATCACA
1 CACATTCATCACA
40742450 TCGGCCATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.23
Consensus pattern (13 bp):
CACATTCATCACA
Found at i:40742456 original size:60 final size:60
Alignment explanation
Indices: 40742380--40742496 Score: 225
Period size: 60 Copynumber: 1.9 Consensus size: 60
40742370 ACACTTTCAT
40742380 ATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACACAC
1 ATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACACAC
*
40742440 ATTCATCACATCGGCCATTAGGCCTTATTACATATATACACTTTCACATTCATCACA
1 ATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
40742497 TCGGCCATTA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.32, C:0.30, G:0.07, T:0.32
Consensus pattern (60 bp):
ATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACACAC
Found at i:40756823 original size:44 final size:44
Alignment explanation
Indices: 40756755--40756838 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
40756745 CCAAAACATG
*
40756755 TGTCCCATATATCATGAACTCAGACCACAACTCATGAGTTTAGA
1 TGTCACATATATCATGAACTCAGACCACAACTCATGAGTTTAGA
*
40756799 TGTCACATATATCATGAACTCAGACCATAACTCATGAGTT
1 TGTCACATATATCATGAACTCAGACCACAACTCATGAGTT
40756839 CAAATCACAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.29
Consensus pattern (44 bp):
TGTCACATATATCATGAACTCAGACCACAACTCATGAGTTTAGA
Found at i:40761433 original size:29 final size:29
Alignment explanation
Indices: 40761391--40761514 Score: 189
Period size: 29 Copynumber: 4.3 Consensus size: 29
40761381 TGTGTGTACC
*
40761391 ATGTGAAAAGGGATAGCTTCAGCTATCGA
1 ATGTGAAAAGGGATAGCTTCGGCTATCGA
*
40761420 ATGTGAAAAGGGATAGCTTCGACTATCGA
1 ATGTGAAAAGGGATAGCTTCGGCTATCGA
*
40761449 ATGTGAAAAGGGGATAGCTTCGGCTATCAA
1 ATGTGAAAA-GGGATAGCTTCGGCTATCGA
*
40761479 ATGTGAAAAGGGATAGCTTTGGC--TCGA
1 ATGTGAAAAGGGATAGCTTCGGCTATCGA
40761506 ATGTGAAAA
1 ATGTGAAAA
40761515 TGTTAGGTAT
Statistics
Matches: 88, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
27 12 0.14
29 49 0.56
30 27 0.31
ACGTcount: A:0.35, C:0.12, G:0.29, T:0.24
Consensus pattern (29 bp):
ATGTGAAAAGGGATAGCTTCGGCTATCGA
Found at i:40761475 original size:59 final size:56
Alignment explanation
Indices: 40761391--40761514 Score: 185
Period size: 59 Copynumber: 2.2 Consensus size: 56
40761381 TGTGTGTACC
*
40761391 ATGTGAAAAGGGATAGCTTCAGCTATCGAATGTGAAAAGGGATAGCTTCGACTATCGA
1 ATGTGAAAAGGGATAGCTTCAGCTATCAAATGTGAAAAGGGATAGCTTCGAC--TCGA
* * *
40761449 ATGTGAAAAGGGGATAGCTTCGGCTATCAAATGTGAAAAGGGATAGCTTTGGCTCGA
1 ATGTGAAAA-GGGATAGCTTCAGCTATCAAATGTGAAAAGGGATAGCTTCGACTCGA
40761506 ATGTGAAAA
1 ATGTGAAAA
40761515 TGTTAGGTAT
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
57 13 0.21
58 9 0.15
59 39 0.64
ACGTcount: A:0.35, C:0.12, G:0.29, T:0.24
Consensus pattern (56 bp):
ATGTGAAAAGGGATAGCTTCAGCTATCAAATGTGAAAAGGGATAGCTTCGACTCGA
Found at i:40761547 original size:33 final size:33
Alignment explanation
Indices: 40761519--40761638 Score: 152
Period size: 33 Copynumber: 3.7 Consensus size: 33
40761509 TGAAAATGTT
**
40761519 AGGTATACTTTGTGTATACCACATGAAAAGGTT
1 AGGTATACTTTGTGTATACCACATGAAAAGGAA
* * * *
40761552 ATGTACACTTTGTGTGTA-CACTTGAAAAGGAA
1 AGGTATACTTTGTGTATACCACATGAAAAGGAA
*
40761584 AGGTATACTTTGTGTATACCATATGAAAAGGAA
1 AGGTATACTTTGTGTATACCACATGAAAAGGAA
* *
40761617 ATGTATACTTTGTGTGTACCAC
1 AGGTATACTTTGTGTATACCAC
40761639 TTAGAAAGAA
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
32 26 0.36
33 46 0.64
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (33 bp):
AGGTATACTTTGTGTATACCACATGAAAAGGAA
Found at i:40761578 original size:65 final size:66
Alignment explanation
Indices: 40761519--40761645 Score: 202
Period size: 65 Copynumber: 1.9 Consensus size: 66
40761509 TGAAAATGTT
**
40761519 AGGTATACTTTGTGTATACCACATGAAAAGGTTATGTACACTTTGTGTGTA-CACTTGAAAAGGA
1 AGGTATACTTTGTGTATACCACATGAAAAGGAAATGTACACTTTGTGTGTACCACTTGAAAAGGA
40761583 A
66 A
* *
40761584 AGGTATACTTTGTGTATACCATATGAAAAGGAAATGTATACTTTGTGTGTACCACTTAGAAA
1 AGGTATACTTTGTGTATACCACATGAAAAGGAAATGTACACTTTGTGTGTACCACTT-GAAA
40761646 GAAACGTACA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
65 47 0.84
66 5 0.09
67 4 0.07
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (66 bp):
AGGTATACTTTGTGTATACCACATGAAAAGGAAATGTACACTTTGTGTGTACCACTTGAAAAGGA
A
Found at i:40770849 original size:20 final size:19
Alignment explanation
Indices: 40770826--40770883 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
40770816 ATTTTAAGGC
*
40770826 TAAAAAAGTAATTTAGTAAA
1 TAAAAAA-TAATTAAGTAAA
40770846 TAAAAGAATAATTAAGTAAA
1 TAAAA-AATAATTAAGTAAA
*
40770866 TAAAAAATGAATGAAGTA
1 TAAAAAAT-AATTAAGTA
40770884 TCATCTGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.09
20 29 0.85
21 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (19 bp):
TAAAAAATAATTAAGTAAA
Found at i:40774317 original size:27 final size:27
Alignment explanation
Indices: 40774287--40774464 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
40774277 ATATTGAGTC
* * * *
40774287 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
40774314 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40774341 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
40774369 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
40774396 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
40774423 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40774450 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40774465 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:40774426 original size:82 final size:81
Alignment explanation
Indices: 40774308--40774463 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40774298 TGCTATATAA
* *
40774308 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40774373 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40774390 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40774454 CACTTAGTGC
65 CACTTAGTGC
40774464 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40776721 original size:42 final size:40
Alignment explanation
Indices: 40776674--40776752 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 40
40776664 ACAGGGATTT
*
40776674 TCACACGACCAGACACACGCCCATGTCATTGGCCCGTGTCCC
1 TCACACGACCAGA-ACACGCCCATGTC-TTAGCCCGTGTCCC
* * * *
40776716 TCACACGGCCATAAGACGCCCGTGTCTTAGCCCGTGT
1 TCACACGACCAGAACACGCCCATGTCTTAGCCCGTGT
40776753 GCAAAAACCT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 10 0.31
41 11 0.34
42 11 0.34
ACGTcount: A:0.20, C:0.39, G:0.22, T:0.19
Consensus pattern (40 bp):
TCACACGACCAGAACACGCCCATGTCTTAGCCCGTGTCCC
Found at i:40777764 original size:47 final size:47
Alignment explanation
Indices: 40777690--40777962 Score: 237
Period size: 47 Copynumber: 5.8 Consensus size: 47
40777680 GTAAGGTGCC
* *
40777690 GATGCCATGTCCCAGACATGGTTTTACACTGGCTCAT-ATCTCAAGTT
1 GATG-CATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAAGCT
* *
40777737 GATGCAATGTCCTAGACATGGTCTTACACTGACT-ATCATCTCGTAA-CAT
1 GATGC-ATGTCCCAGACATGGTCTTACACTGGCTCATCATCTC--AAGC-T
* *
40777786 -ATGCATGTCCCAGACATGGTCTTACACTGACT-ATCATCTCGTAATC-
1 GATGCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTC--AAGCT
* * *
40777832 GATGCATGTCCTAGACAT-GTCTTGA-ACTGGCTTA-CGTCTCAAGGCT
1 GATGCATGTCCCAGACATGGTCTT-ACACTGGCTCATCATCTCAA-GCT
* * *
40777878 GATGCATGTCCCAGACAT-GTCTTACACTAGCTC-TCGTCTCAATGCC
1 GATGCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAA-GCT
* *
40777924 GATGCCGTGTCCCAGACATAGTCTTACACTGGCTC-TCAT
1 GATG-CATGTCCCAGACATGGTCTTACACTGGCTCATCAT
40777963 AATGTGGCCG
Statistics
Matches: 194, Mismatches: 17, Indels: 29
0.81 0.07 0.12
Matches are distributed among these distances:
44 2 0.01
45 2 0.01
46 61 0.31
47 104 0.54
48 22 0.11
49 3 0.02
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (47 bp):
GATGCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAAGCT
Found at i:40783402 original size:40 final size:40
Alignment explanation
Indices: 40783358--40783621 Score: 342
Period size: 40 Copynumber: 6.7 Consensus size: 40
40783348 GCTCCTCGTT
* * *
40783358 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
40783398 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
40783438 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
40783478 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
40783518 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* ** * *
40783557 CAAATGCCTT-TGGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGAT-TTAGTAAC-TCGCA
*
40783598 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
40783622 CAGCATTCAA
Statistics
Matches: 204, Mismatches: 14, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
38 2 0.01
39 47 0.23
40 146 0.72
41 9 0.04
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:40791360 original size:40 final size:40
Alignment explanation
Indices: 40791316--40791619 Score: 386
Period size: 40 Copynumber: 7.7 Consensus size: 40
40791306 GCTCCTCGTT
* * * *
40791316 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTTGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
*
40791356 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCTCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
40791396 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
40791436 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
40791476 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * * *
40791516 CAAATGCCTTCGGG-CTTAGCCCAGAATTAGTATCTTGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* ** * *
40791555 CAAATGCCTT-TGGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGAT-TTAGTAAC-TCGCA
*
40791596 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
40791620 CAGCATTAAA
Statistics
Matches: 238, Mismatches: 20, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
38 2 0.01
39 45 0.19
40 182 0.76
41 9 0.04
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:40796593 original size:46 final size:46
Alignment explanation
Indices: 40796462--40796716 Score: 223
Period size: 46 Copynumber: 5.5 Consensus size: 46
40796452 GCCATATCCT
* *
40796462 AGACATGGTCTTACACTGGCTCAT-ATCTC-AAGTCGATGCCATGCCCC
1 AGACAT-GTCTTACACTGGCTC-TCATCTCGAGGTCGATG-CATGTCCC
* * ** * * **
40796509 AGACATAGTCTTACGCTGACAATCATCTAGTA-GCCGATGCATGTCAT
1 AGACAT-GTCTTACACTGGCTCTCATCTCG-AGGTCGATGCATGTCCC
*
40796556 AGACATGTCTTACACTGGCT-TACGTCTCGAGGTCGATGCATGTCCC
1 AGACATGTCTTACACTGGCTCT-CATCTCGAGGTCGATGCATGTCCC
* * * * *
40796602 AGACATGTCTTACACTAGCTCTCATCTCCATGCCAATGCCATGTCCC
1 AGACATGTCTTACACTGGCTCTCATCTCGAGGTCGATG-CATGTCCC
* *
40796649 AGACATGGTCTTACACTGGCTCTCATAAT-GTGGTCGATGCATGTCCC
1 AGACAT-GTCTTACACTGGCTCTCAT-CTCGAGGTCGATGCATGTCCC
*
40796696 AGACATGTCTTACACTAGCTC
1 AGACATGTCTTACACTGGCTC
40796717 ACACACAAAT
Statistics
Matches: 167, Mismatches: 32, Indels: 19
0.77 0.15 0.09
Matches are distributed among these distances:
45 2 0.01
46 73 0.44
47 61 0.37
48 29 0.17
49 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (46 bp):
AGACATGTCTTACACTGGCTCTCATCTCGAGGTCGATGCATGTCCC
Found at i:40796669 original size:94 final size:94
Alignment explanation
Indices: 40796450--40796716 Score: 289
Period size: 94 Copynumber: 2.9 Consensus size: 94
40796440 TAAGGTGCAT
* * * * *
40796450 ATGCCATATCCTAGACATGGTCTTACACTGGCTCATATCTC-AAGTCGATGCCATGCCCCAGACA
1 ATGCCATGTCCTAGACATGGTCTTACACTGGCTTACATCTCGAGGTCGATG-CATGTCCCAGACA
* ** *
40796514 TAGTCTTACGCT-GACAATCATCTAGTAGCCG
65 T-GTCTTACACTAG-CTCTCATCTAGTAGCCA
* *
40796545 ATG-CATGTCATAGACAT-GTCTTACACTGGCTTACGTCTCGAGGTCGATGCATGTCCCAGACAT
1 ATGCCATGTCCTAGACATGGTCTTACACTGGCTTACATCTCGAGGTCGATGCATGTCCCAGACAT
40796608 GTCTTACACTAGCTCTCATCTCCA-T-GCCA
66 GTCTTACACTAGCTCTCATCT--AGTAGCCA
* * *
40796637 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAAT-GTGGTCGATGCATGTCCCAGAC
1 ATGCCATGTCCTAGACATGGTCTTACACTGGCT-TACAT-CTCGAGGTCGATGCATGTCCCAGAC
40796700 ATGTCTTACACTAGCTC
64 ATGTCTTACACTAGCTC
40796717 ACACACAAAT
Statistics
Matches: 148, Mismatches: 16, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
92 22 0.15
93 46 0.31
94 75 0.51
95 5 0.03
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (94 bp):
ATGCCATGTCCTAGACATGGTCTTACACTGGCTTACATCTCGAGGTCGATGCATGTCCCAGACAT
GTCTTACACTAGCTCTCATCTAGTAGCCA
Found at i:40800606 original size:17 final size:17
Alignment explanation
Indices: 40800586--40800621 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
40800576 ATGTGAAAAG
40800586 TATATGAATATGAAACT
1 TATATGAATATGAAACT
40800603 TATATGAATATGAAACT
1 TATATGAATATGAAACT
40800620 TA
1 TA
40800622 GTTATTATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (17 bp):
TATATGAATATGAAACT
Found at i:40809500 original size:53 final size:53
Alignment explanation
Indices: 40809300--40809506 Score: 193
Period size: 53 Copynumber: 3.8 Consensus size: 53
40809290 ATTAGGGTTT
* * *
40809300 AAGGATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTT-ATACTAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATA--AGGC
* * * * * * * *
40809354 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAACTACGGTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAGGC
* * * * *
40809409 AAAGAT-CCTATGTAAGACCATGCCAAGTCAAGCCAATGGTGAGTTCATAAGGC
1 AAGGATACC-ATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
* *
40809462 AAGGATACCATGTAAGACCATGTCAAGACATGGAAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
40809507 TAAAAAGGAA
Statistics
Matches: 119, Mismatches: 29, Indels: 11
0.75 0.18 0.07
Matches are distributed among these distances:
53 41 0.34
54 40 0.34
55 36 0.30
57 2 0.02
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
Found at i:40830031 original size:24 final size:24
Alignment explanation
Indices: 40829960--40830037 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
40829950 TGAAAGAGAG
* *
40829960 TCCCGTTATTAGCTC-TCATGAGCT
1 TCCCATTAATAGCTCTTC-TGAGCT
* * *
40829984 TCCCGTTAAATGGTTCTTGC-GAGCT
1 TCCCATT-AATAGCTCTT-CTGAGCT
*
40830009 TCCCATTAATAGCTCTTCTGAGCA
1 TCCCATTAATAGCTCTTCTGAGCT
40830033 TCCCA
1 TCCCA
40830038 ATTGGTTGTG
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
23 1 0.02
24 24 0.56
25 16 0.37
26 1 0.02
27 1 0.02
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.35
Consensus pattern (24 bp):
TCCCATTAATAGCTCTTCTGAGCT
Found at i:40830250 original size:25 final size:25
Alignment explanation
Indices: 40830202--40830271 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 25
40830192 CCCAATTATG
* *
40830202 ATGAGCTTTCCATTACATGACTCAT
1 ATGAGCTTCCCATTACATGACTCAA
* * *
40830227 ATGAGCTTCCCGTTATATGGCTCAA
1 ATGAGCTTCCCATTACATGACTCAA
* *
40830252 AAGAGCTTTCCATTTACATG
1 ATGAGCTTCCCA-TTACATG
40830272 TTTGCATGAG
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
25 29 0.83
26 6 0.17
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (25 bp):
ATGAGCTTCCCATTACATGACTCAA
Found at i:40850842 original size:39 final size:40
Alignment explanation
Indices: 40850684--40850855 Score: 285
Period size: 40 Copynumber: 4.3 Consensus size: 40
40850674 GCTCCTCGTT
* * *
40850684 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
*
40850724 CAAATGCCTTCGAGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
40850764 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
40850804 CAAATGCCTTCGGGACTTAACCC-GATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
40850843 CAAATGCCTTCGG
1 CAAATGCCTTCGG
40850856 ATCTTAGTCT
Statistics
Matches: 126, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
39 29 0.23
40 95 0.75
41 2 0.02
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:40858635 original size:40 final size:40
Alignment explanation
Indices: 40858591--40858815 Score: 307
Period size: 40 Copynumber: 5.7 Consensus size: 40
40858581 GCTCCTCGTT
* * *
40858591 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
40858631 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
40858671 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
40858711 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * *
40858751 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTTACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGAT-TTAGTAAC-TCGCA
*
40858792 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
40858816 CAGCATTCAA
Statistics
Matches: 172, Mismatches: 8, Indels: 11
0.90 0.04 0.06
Matches are distributed among these distances:
39 19 0.11
40 144 0.84
41 9 0.05
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:40859912 original size:13 final size:13
Alignment explanation
Indices: 40859894--40859918 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40859884 AGGATGAGCA
40859894 TTTTTTTTCTTTG
1 TTTTTTTTCTTTG
40859907 TTTTTTTTCTTT
1 TTTTTTTTCTTT
40859919 CTAGTTTCGG
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:0.00, C:0.08, G:0.04, T:0.88
Consensus pattern (13 bp):
TTTTTTTTCTTTG
Found at i:40860470 original size:15 final size:15
Alignment explanation
Indices: 40860422--40860501 Score: 76
Period size: 15 Copynumber: 5.4 Consensus size: 15
40860412 CTGTCACAAC
*
40860422 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
40860436 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
40860451 GAGAAA-CACGGAATA
1 AAGAAATC-CAGAATA
40860466 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
40860481 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
40860496 AAGAAA
1 AAGAAA
40860502 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
14 10 0.19
15 41 0.77
16 2 0.04
ACGTcount: A:0.59, C:0.12, G:0.19, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:40860510 original size:15 final size:15
Alignment explanation
Indices: 40860433--40860510 Score: 63
Period size: 15 Copynumber: 5.2 Consensus size: 15
40860423 AGAAAACCGA
40860433 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
40860448 ATAGAGAAA--CACGG
1 ATAAAGAAATCCA-AG
40860462 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
40860477 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
40860493 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
40860508 ATA
1 ATA
40860511 CGATACTATG
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
13 2 0.04
14 1 0.02
15 44 0.90
16 1 0.02
17 1 0.02
ACGTcount: A:0.56, C:0.14, G:0.18, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Done.