Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 165 of 322
Found at i:54051223 original size:23 final size:23
Alignment explanation
Indices: 54051151--54051238 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 23
54051141 TACCTGATCA
*
54051151 AAATATGACACATAA-GTGCCTG
1 AAATATGACACACAAGGTGCCTG
* * *
54051173 -AA-ACGACACACGAGGTGCCCG
1 AAATATGACACACAAGGTGCCTG
* *
54051194 --CTGTGACACACAAGGTGCCTG
1 AAATATGACACACAAGGTGCCTG
* *
54051215 AAATATGACACATAAAGTGCCTG
1 AAATATGACACACAAGGTGCCTG
54051238 A
1 A
54051239 TCAGTAAAGC
Statistics
Matches: 49, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
20 8 0.16
21 23 0.47
23 18 0.37
ACGTcount: A:0.36, C:0.24, G:0.23, T:0.17
Consensus pattern (23 bp):
AAATATGACACACAAGGTGCCTG
Found at i:54058999 original size:10 final size:9
Alignment explanation
Indices: 54058981--54059109 Score: 70
Period size: 9 Copynumber: 13.8 Consensus size: 9
54058971 AATTTGTAAA
54058981 AAAATATTAT
1 AAAA-ATTAT
54058991 AGAAAATTAT
1 A-AAAATTAT
54059001 AAAACAATTAT
1 -AAA-AATTAT
54059012 AAAAATTA-
1 AAAAATTAT
*
54059020 AAAAATTCT
1 AAAAATTAT
*
54059029 AAAAA-AAT
1 AAAAATTAT
54059037 AAAAATGT-T
1 AAAAAT-TAT
54059046 ATAAAA-TAT
1 A-AAAATTAT
*
54059055 AAAAGTT-T
1 AAAAATTAT
*
54059063 ACAAGAATTTT
1 A-AA-AATTAT
*
54059074 AAAAATATTT
1 AAAAAT-TAT
54059084 AGAAAATTAT
1 A-AAAATTAT
*
54059094 AAAAAGTAT
1 AAAAATTAT
*
54059103 ATAAATT
1 AAAAATT
54059110 TTAATAAAAT
Statistics
Matches: 95, Mismatches: 10, Indels: 29
0.71 0.07 0.22
Matches are distributed among these distances:
8 19 0.20
9 32 0.34
10 27 0.28
11 17 0.18
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:54059011 original size:11 final size:10
Alignment explanation
Indices: 54058980--54059051 Score: 55
Period size: 10 Copynumber: 7.4 Consensus size: 10
54058970 AAATTTGTAA
54058980 AAAAATATTAT
1 AAAAA-ATTAT
*
54058991 AGAAAATTAT
1 AAAAAATTAT
54059001 AAAACAATTAT
1 AAAA-AATTAT
54059012 -AAAAA-T-T
1 AAAAAATTAT
*
54059019 AAAAAATTCT
1 AAAAAATTAT
54059029 AAAAAA--AT
1 AAAAAATTAT
*
54059037 AAAAATGTTAT
1 AAAAA-ATTAT
54059048 AAAA
1 AAAA
54059052 TATAAAAGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
7 1 0.02
8 12 0.24
9 3 0.06
10 18 0.36
11 16 0.32
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:54059024 original size:20 final size:21
Alignment explanation
Indices: 54058977--54059024 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
54058967 ATAAAATTTG
54058977 TAAAAAAATATTATAGAAAAT
1 TAAAAAAATATTATAGAAAAT
*
54058998 TATAAAACA-ATTATA-AAAAT
1 TA-AAAAAATATTATAGAAAAT
54059018 TAAAAAA
1 TAAAAAA
54059025 TTCTAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 4 0.17
20 7 0.29
21 8 0.33
22 5 0.21
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (21 bp):
TAAAAAAATATTATAGAAAAT
Found at i:54059031 original size:17 final size:18
Alignment explanation
Indices: 54058986--54059033 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
54058976 GTAAAAAAAT
54058986 ATTATAGAAAATTATAAAACA
1 ATTATA-AAAA-T-TAAAACA
54059007 ATTATAAAAATTAAAA-A
1 ATTATAAAAATTAAAACA
*
54059024 ATTCTAAAAA
1 ATTATAAAAA
54059034 AATAAAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 10 0.38
18 5 0.19
19 1 0.04
20 4 0.15
21 6 0.23
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (18 bp):
ATTATAAAAATTAAAACA
Found at i:54059586 original size:16 final size:19
Alignment explanation
Indices: 54059565--54059603 Score: 57
Period size: 16 Copynumber: 2.2 Consensus size: 19
54059555 GTTTTTAAAT
54059565 ATTTTTT-TATTT-T-ATA
1 ATTTTTTCTATTTGTAATA
54059581 ATTTTTTCTATTTGTAATA
1 ATTTTTTCTATTTGTAATA
54059600 ATTT
1 ATTT
54059604 ATATATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 5 0.25
18 1 0.05
19 7 0.35
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (19 bp):
ATTTTTTCTATTTGTAATA
Found at i:54060106 original size:11 final size:11
Alignment explanation
Indices: 54060073--54060113 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
54060063 AATGCTTAAG
54060073 TATATTTA-AT
1 TATATTTATAT
54060083 TAT-TTCATATAT
1 TATATT--TATAT
54060095 TATATTTATAT
1 TATATTTATAT
54060106 TATATTTA
1 TATATTTA
54060114 ATAAATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
9 2 0.07
10 3 0.11
11 15 0.56
12 5 0.19
13 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (11 bp):
TATATTTATAT
Found at i:54062265 original size:131 final size:131
Alignment explanation
Indices: 54062098--54062353 Score: 440
Period size: 131 Copynumber: 2.0 Consensus size: 131
54062088 TTTAGAGAAC
* * * *
54062098 ATGAGTGAATTTCTAAAGGGATATTCAATTATTTTGAACAAACGGGAAATTGCAACCCAGCACGA
1 ATGAGTAAAATTCCAAAGGAATATTCAATTATTTTGAACAAACGGGAAATTGCAACCCAGCACGA
54062163 TAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTACCTTCGTTTTAAAGAATTTTTAAAGA
66 TAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTACCTTCGTTTTAAAGAATTTTTAAAGA
54062228 T
131 T
* *
54062229 ATGAGTAAAATTCCAAAGGAATATTCGATTATTTTGAACAAACGGGAAATTGTAACCCAGCACGA
1 ATGAGTAAAATTCCAAAGGAATATTCAATTATTTTGAACAAACGGGAAATTGCAACCCAGCACGA
* *
54062294 TAGGGCACGATTCCCCGAATTGCCGAACATCGAACATTGCCTTCGTTTTAAAGAATTTTT
66 TAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTACCTTCGTTTTAAAGAATTTTT
54062354 GAATGAATAA
Statistics
Matches: 117, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
131 117 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (131 bp):
ATGAGTAAAATTCCAAAGGAATATTCAATTATTTTGAACAAACGGGAAATTGCAACCCAGCACGA
TAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTACCTTCGTTTTAAAGAATTTTTAAAGA
T
Found at i:54062707 original size:13 final size:14
Alignment explanation
Indices: 54062684--54062715 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
54062674 AAACAAAACA
54062684 ATACACACAATAAT
1 ATACACACAATAAT
54062698 ATAC-CACAATAAT
1 ATACACACAATAAT
54062711 ATACA
1 ATACA
54062716 AAGCCTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (14 bp):
ATACACACAATAAT
Found at i:54064287 original size:46 final size:47
Alignment explanation
Indices: 54064227--54064362 Score: 179
Period size: 46 Copynumber: 3.0 Consensus size: 47
54064217 TTTGACGTGA
* * * * * *
54064227 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCAGGC
*
54064273 TGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCAGGC
*
54064319 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCAG
54064363 AGAGCACACT
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
45 4 0.05
46 76 0.95
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCAGGC
Found at i:54067750 original size:21 final size:21
Alignment explanation
Indices: 54067709--54067750 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
54067699 CGTGGCGCGT
* *
54067709 GTATGGGGGCTGTGTGCTGGC
1 GTATGGAGGCTGTGGGCTGGC
54067730 GTATGGAGGC-GTGGGCGTGGC
1 GTATGGAGGCTGTGGGC-TGGC
54067751 TGCTGAAGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.07, C:0.14, G:0.55, T:0.24
Consensus pattern (21 bp):
GTATGGAGGCTGTGGGCTGGC
Found at i:54069387 original size:30 final size:30
Alignment explanation
Indices: 54069351--54069419 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
54069341 CTAGTATTTG
54069351 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* *
54069381 CCACCACCTACTCCATTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
54069411 CCACCACCA
1 CCACCACCA
54069420 CTTGTACCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.26, C:0.51, G:0.06, T:0.17
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:54069947 original size:24 final size:23
Alignment explanation
Indices: 54069899--54069950 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
54069889 TTTTTTTTGT
*
54069899 TATTATTATATTTCTTAATATTA
1 TATTATTATATTTCTTAATAATA
*
54069922 TATTATATATATATTCTT-TTAATA
1 TATTAT-TATAT-TTCTTAATAATA
54069946 TATTA
1 TATTA
54069951 GGTATATTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.24
24 14 0.56
25 5 0.20
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (23 bp):
TATTATTATATTTCTTAATAATA
Found at i:54070006 original size:27 final size:25
Alignment explanation
Indices: 54069966--54070034 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
54069956 ATTCTAAATT
*
54069966 CTATATTACGTATATATATATT-ATA
1 CTATATTATGTATATATAT-TTAATA
* *
54069991 CTATTTTATGTATATATCTTTAATA
1 CTATATTATGTATATATATTTAATA
*
54070016 CTATATTATTTATATATAT
1 CTATATTATGTATATATAT
54070035 NNNNNNNNNN
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
24 2 0.05
25 35 0.95
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.54
Consensus pattern (25 bp):
CTATATTATGTATATATATTTAATA
Found at i:54074519 original size:137 final size:136
Alignment explanation
Indices: 54074273--54074545 Score: 510
Period size: 137 Copynumber: 2.0 Consensus size: 136
54074263 GATGGAGAAA
54074273 AAGCCGTCAGAAACTTTTAGACAGTACGCGCAGAGATGGAGGGACGTCTCAGCCCAAGTGGAACC
1 AAGCCGTCAGAAACTTTTAGACAGTACGCGCAGAGATGGAGGGACGTCTCAGCCCAAGTGGAACC
54074338 CCCACTAACGAAAACGGAGATAACCGTCCTTTTTATCAACACCTTAAAGACGCCGTTTTATGACA
66 CCCACTAACGAAAACGGAGATAACCGTCCTTTTTATCAACACCTTAAAGACGCCGTTTTATGACA
54074403 AACTANG
131 AACTA-G
* *
54074410 AAGCCGTCAGAAACTTTTAGACAGTACGCGTAGAGATTGAGGGACGTCTCAGCCCAAGTGGAACC
1 AAGCCGTCAGAAACTTTTAGACAGTACGCGCAGAGATGGAGGGACGTCTCAGCCCAAGTGGAACC
*
54074475 CCCACTAACGAAAACGGAGATAACCGTCCTTTTTATCAACACCTTAAAGACGTCGTTTTATGACA
66 CCCACTAACGAAAACGGAGATAACCGTCCTTTTTATCAACACCTTAAAGACGCCGTTTTATGACA
54074540 AACTAG
131 AACTAG
54074546 TGGGAAACGC
Statistics
Matches: 133, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
136 1 0.01
137 132 0.99
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (136 bp):
AAGCCGTCAGAAACTTTTAGACAGTACGCGCAGAGATGGAGGGACGTCTCAGCCCAAGTGGAACC
CCCACTAACGAAAACGGAGATAACCGTCCTTTTTATCAACACCTTAAAGACGCCGTTTTATGACA
AACTAG
Found at i:54081683 original size:13 final size:13
Alignment explanation
Indices: 54081639--54081683 Score: 72
Period size: 13 Copynumber: 3.4 Consensus size: 13
54081629 CGCCGAGGTA
54081639 TTTTTAATTTCTG
1 TTTTTAATTTCTG
54081652 TTTTTCAATTTCTG
1 TTTTT-AATTTCTG
*
54081666 CTTTTAATTTCTG
1 TTTTTAATTTCTG
54081679 TTTTT
1 TTTTT
54081684 CAAAAATCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 17 0.59
14 12 0.41
ACGTcount: A:0.13, C:0.11, G:0.07, T:0.69
Consensus pattern (13 bp):
TTTTTAATTTCTG
Found at i:54081748 original size:100 final size:99
Alignment explanation
Indices: 54081551--54081947 Score: 401
Period size: 100 Copynumber: 4.1 Consensus size: 99
54081541 CACTGAAGTA
** * * * *
54081551 TTTTCAATTTTCTTTTTTTCAATTTATGCTTTTCAAAAATCAACTCATATTGTGAGAGGTGAGCT
1 TTTTCAA-TTTCTGCTTTT-AATTTCTG-TTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTT
* * * *
54081616 GAGCCTCGGGGCACGCCGAGGTATTTTTAATTTCTGT
63 GAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGT
54081653 TTTTCAATTTCTGCTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
1 TTTTCAATTTCTGCTTTTAATTTCTGTTTTT-AAAAATCAACTCATATTGCGAGAGGTGAGTTGA
* * *
54081718 GCCTCAGGGCACGTTGAGGTATTTTCAATTTCTTT
65 GCCTCAGGACACGCTGAGGTATTTTCAATTTCTGT
* ** * *
54081753 TTTTCAATTTTTGCCTTACAAATTCTGCTTTTT--AAATCAACTTATATTGCGAGAGGTGAGTTG
1 TTTTCAATTTCTG-CTTTTAATTTCTG-TTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTG
54081816 AGCCTCAGGACACGCTGAGGTATTTTCAATTT-TCGTT
64 AGCCTCAGGACACGCTGAGGTATTTTCAATTTCT-G-T
* *
54081853 TTTTCAATTTATG-TTTCTAA-----------AAAAATCAACTCATATTGCGAGAAGTGAGTTGA
1 TTTTCAATTTCTGCTTT-TAATTTCTGTTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
* *
54081906 GCCTCAGGACACGCTGAGGTAATTTCAATTTTTGT
65 GCCTCAGGACACGCTGAGGTATTTTCAATTTCTGT
*
54081941 TTGTCAA
1 TTTTCAA
54081948 AACTCAACTC
Statistics
Matches: 260, Mismatches: 26, Indels: 32
0.82 0.08 0.10
Matches are distributed among these distances:
88 7 0.03
89 60 0.23
90 1 0.00
98 3 0.01
99 65 0.25
100 93 0.36
101 19 0.07
102 12 0.05
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (99 bp):
TTTTCAATTTCTGCTTTTAATTTCTGTTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
CCTCAGGACACGCTGAGGTATTTTCAATTTCTGT
Found at i:54082057 original size:75 final size:75
Alignment explanation
Indices: 54081853--54082471 Score: 671
Period size: 75 Copynumber: 8.2 Consensus size: 75
54081843 AATTTTCGTT
* * * *
54081853 TTTTCAATTTATGTTTCT-AAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
54081917 CGCTGAGGTA
66 CGCTGAGGTA
* * * *
54081927 ATTTCAATTTTTGTTTGTC--AAAACTCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACA
1 TTTTCAATTTCTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
54081990 CGTTGAGGTA
66 CGCTGAGGTA
* * * *
54082000 TTTTTAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
54082065 CGCTGAGGTA
66 CGCTGAGGTA
* * * * *
54082075 ATTTCAATTTTTGTTTGTC--AAAAATCAATTCATATTGCAAGAGGTGAGTTAAGCCTCAAGACA
1 TTTTCAATTTCTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
54082138 CGATGAGGTA
66 CGCTGAGGTA
* * * *
54082148 TTTTCAATTTCTGTCTT-TAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTCAACCTCAAGAC
1 TTTTCAATTTCTGT-TTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAC
*
54082212 ACGCTGAGATA
65 ACGCTGAGGTA
* * * *
54082223 TTTTCAATTTCT-TTTCTTCAAAAAAATCAACGCATATTGCGATAGGTGAGTTGAGCCTCAGGAC
1 TTTTCAATTTCTGTTT-GTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAC
54082287 ACGCTGAGGTA
65 ACGCTGAGGTA
* * * * *
54082298 ATTTCAATTTTTGTTTGTC--AAAAATCAATTCATATTGCAAGAGGTGAGTTAAGCCTCAAGACA
1 TTTTCAATTTCTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
54082361 CGATGAGGTA
66 CGCTGAGGTA
* * *
54082371 TTTTCAATTGATTTTTTTTTCAATTTATGATTTGCAAAAATCAACTCATATTGCGAGAGGTGAGT
1 TTTTCAATT--TCTGTTTGTC-----A--A-----AAAAATCAACTCATATTGCGAGAGGTGAGT
* * *
54082436 TCAACCTCAAGACACGCTGAGATA
52 TGAGCCTCAAGACACGCTGAGGTA
54082460 TTTTCAATTTCT
1 TTTTCAATTTCT
54082472 TTTTTTTCAA
Statistics
Matches: 455, Mismatches: 65, Indels: 37
0.82 0.12 0.07
Matches are distributed among these distances:
73 182 0.40
74 18 0.04
75 193 0.42
76 3 0.01
87 2 0.00
89 57 0.13
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Consensus pattern (75 bp):
TTTTCAATTTCTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
CGCTGAGGTA
Found at i:54082120 original size:148 final size:148
Alignment explanation
Indices: 54081853--54082379 Score: 704
Period size: 148 Copynumber: 3.6 Consensus size: 148
54081843 AATTTTCGTT
* * * *
54081853 TTTTCAATTTATGTTTCT-AAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
54081917 CGCTGAGGTAATTTCAATTTTTGTTTGTCAAAACTCAACTCATATTGCAAGAGGTGAGTTGAGCC
66 CGCTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCC
*
54081982 TCAAGACACGTTGAGGTA
131 TCAAGACACGATGAGGTA
* * *
54082000 TTTTTAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
* *
54082065 CGCTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAATTCATATTGCAAGAGGTGAGTTAAGCC
66 CGCTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCC
54082130 TCAAGACACGATGAGGTA
131 TCAAGACACGATGAGGTA
* * * * *
54082148 TTTTCAATTTCTGTCTTTAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTCAACCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
* * * * *
54082213 CGCTGAGATATTTTCAATTTCTT-TTCT-TCAAAAAAATCAACGCATATTGCGATAGGTGAGTTG
66 CGCTGAGGTAATTTCAATTT-TTGTT-TGTC--AAAAATCAACTCATATTGCAAGAGGTGAGTTG
* *
54082276 AGCCTCAGGACACGCTGAGGTA
127 AGCCTCAAGACACGATGAGGTA
* * * * * *
54082298 ATTTCAATTTTTGTTTGTC--AAAAATCAATTCATATTGCAAGAGGTGAGTTAAGCCTCAAGACA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
* *
54082361 CGATGAGGTATTTTCAATT
66 CGCTGAGGTAATTTCAATT
54082380 GATTTTTTTT
Statistics
Matches: 337, Mismatches: 38, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
147 15 0.04
148 258 0.77
149 3 0.01
150 61 0.18
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (148 bp):
TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
CGCTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCC
TCAAGACACGATGAGGTA
Found at i:54082261 original size:223 final size:222
Alignment explanation
Indices: 54081854--54082476 Score: 865
Period size: 223 Copynumber: 2.7 Consensus size: 222
54081844 ATTTTCGTTT
* * * * * * * *
54081854 TTTCAATTTATGTTTCTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACG
1 TTTCAATTTTTGTTTGT-CAAAAATCAATTCATATTGCAAGAGGTGAGTTAAGCCTCAAGACACG
* * * * * *
54081919 CTGAGGTAATTTCAATTTTTGT-TTGT--CAAAACTCAACTCATATTGCAAGAGGTGAGTTGAGC
65 ATGAGGTATTTTCAATTTTTGTCTT-TAACAAAAATCAACTCATATTGCGAGAGGTGAGTTCAAC
* * * *
54081981 CTCAAGACACGTTGAGGTATTTTTAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGATAGG
129 CTCAAGACACGCTGAGATATTTTCAATTTCT-TTTTTCAAAAAAATCAACGCATATTGCGATAGG
54082046 TGAGTTGAGCCTCAGGACACGCTGAGGTAA
193 TGAGTTGAGCCTCAGGACACGCTGAGGTAA
54082076 TTTCAATTTTTGTTTGTCAAAAATCAATTCATATTGCAAGAGGTGAGTTAAGCCTCAAGACACGA
1 TTTCAATTTTTGTTTGTCAAAAATCAATTCATATTGCAAGAGGTGAGTTAAGCCTCAAGACACGA
* * *
54082141 TGAGGTATTTTCAATTTCTGTCTTTAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTCAACCT
66 TGAGGTATTTTCAATTTTTGTCTTTAACAAAAATCAACTCATATTGCGAGAGGTGAGTTCAACCT
54082206 CAAGACACGCTGAGATATTTTCAATTTCTTTTCTTCAAAAAAATCAACGCATATTGCGATAGGTG
131 CAAGACACGCTGAGATATTTTCAATTTCTTTT-TTCAAAAAAATCAACGCATATTGCGATAGGTG
54082271 AGTTGAGCCTCAGGACACGCTGAGGTAA
195 AGTTGAGCCTCAGGACACGCTGAGGTAA
54082299 TTTCAATTTTTGTTTGTCAAAAATCAATTCATATTGCAAGAGGTGAGTTAAGCCTCAAGACACGA
1 TTTCAATTTTTGTTTGTCAAAAATCAATTCATATTGCAAGAGGTGAGTTAAGCCTCAAGACACGA
*
54082364 TGAGGTATTTTCAATTGATTTTTTTTTCAATTTATGATTTGCAAAAATCAACTCATATTGCGAGA
66 TGAGGTATTTTC-A---A--TTTTTGTC--TTTA--A----CAAAAATCAACTCATATTGCGAGA
54082429 GGTGAGTTCAACCTCAAGACACGCTGAGATATTTTCAATTTCTTTTTT
117 GGTGAGTTCAACCTCAAGACACGCTGAGATATTTTCAATTTCTTTTTT
54082477 TTCAATTTAT
Statistics
Matches: 358, Mismatches: 25, Indels: 22
0.88 0.06 0.05
Matches are distributed among these distances:
221 61 0.17
222 20 0.06
223 194 0.54
224 1 0.00
227 1 0.00
229 6 0.02
231 4 0.01
233 1 0.00
236 2 0.01
237 68 0.19
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Consensus pattern (222 bp):
TTTCAATTTTTGTTTGTCAAAAATCAATTCATATTGCAAGAGGTGAGTTAAGCCTCAAGACACGA
TGAGGTATTTTCAATTTTTGTCTTTAACAAAAATCAACTCATATTGCGAGAGGTGAGTTCAACCT
CAAGACACGCTGAGATATTTTCAATTTCTTTTTTCAAAAAAATCAACGCATATTGCGATAGGTGA
GTTGAGCCTCAGGACACGCTGAGGTAA
Found at i:54082450 original size:89 final size:89
Alignment explanation
Indices: 54082299--54082623 Score: 462
Period size: 89 Copynumber: 3.6 Consensus size: 89
54082289 GCTGAGGTAA
* * * *
54082299 TTTCAATTTTTGTTTGTCAAAAATCAATTCATATTGCAAGAGGTGAGTTAAGCCTCAAGACACGA
1 TTTCAATTTATGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAAGACACGC
54082364 TGAGGTATTTTCAATTGATTTTTT
66 TGAGGTATTTTCAATTGATTTTTT
54082388 TTTCAATTTATGATTTG-CAAAAATCAACTCATATTGCGAGAGGTGAGTTCAA-CCTCAAGACAC
1 TTTCAATTTATG-TTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTT-AAGCCTCAAGACAC
*
54082451 GCTGAGATATTTTCAATT--TCTTTTT
64 GCTGAGGTATTTTCAATTGAT-TTTTT
*
54082476 TTTCAATTTATGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGATCAC
1 TTTCAATTTATGTTTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCA-A-GAC
*
54082541 ACGCCGAGGTATTTTCAATTGATTTTTT
62 ACGCTGAGGTATTTTCAATTGATTTTTT
* *
54082569 TTTCAATTTATGATTTG-CAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCT
1 TTTCAATTTATG-TTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCT
54082624 TGGGTCACAT
Statistics
Matches: 214, Mismatches: 10, Indels: 22
0.87 0.04 0.09
Matches are distributed among these distances:
87 5 0.02
88 18 0.08
89 70 0.33
90 42 0.20
91 36 0.17
92 20 0.09
93 18 0.08
94 5 0.02
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.38
Consensus pattern (89 bp):
TTTCAATTTATGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAAGACACGC
TGAGGTATTTTCAATTGATTTTTT
Found at i:54082880 original size:103 final size:104
Alignment explanation
Indices: 54082693--54082885 Score: 273
Period size: 103 Copynumber: 1.8 Consensus size: 104
54082683 TCAATTTCTT
**
54082693 TTTTTTTTTCAATTTATGTTTGTCAAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTC
1 TTTTTTTTTCAATTTATGTTTGTC--AAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTC
* * *
54082758 AGATCACACGCTGATGTATTTTCAATTGATTTTTATTTTTA
64 AGATCACACACCGAGGTATTTTCAATTGATTTTTATTTTTA
*
54082799 TTTTTTTTTCAATTTATGCTTTG-C-AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCG
1 TTTTTTTTTCAATTTATG-TTTGTCAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCA
* *
54082862 GGTCACATACCGAGGTATTTTCAA
65 GATCACACACCGAGGTATTTTCAA
54082886 AATCTGTTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
103 55 0.71
106 19 0.24
107 4 0.05
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.41
Consensus pattern (104 bp):
TTTTTTTTTCAATTTATGTTTGTCAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAG
ATCACACACCGAGGTATTTTCAATTGATTTTTATTTTTA
Found at i:54082969 original size:87 final size:87
Alignment explanation
Indices: 54082823--54082982 Score: 230
Period size: 87 Copynumber: 1.8 Consensus size: 87
54082813 TATGCTTTGC
* * *
54082823 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACATACCGAGGTATTTTCAAAA
1 AAAAATCAACTCATATTACGAGAAGTGAGTTGAGCCTCGGCTCACATACCGAGCTATTTTCAAAA
54082888 TCTGTTTTACAAATTTTGTTTT
66 TCTGTTTTACAAATTTTGTTTT
* * * * * **
54082910 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATT
1 AAAAATCAACTCATATTACGAGAAGTGAGTTGAGCCTCGGCTCACATACCGAGCTATTTTCAAAA
54082975 TCTGTTTT
66 TCTGTTTT
54082983 TAATGTTTTC
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
87 63 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (87 bp):
AAAAATCAACTCATATTACGAGAAGTGAGTTGAGCCTCGGCTCACATACCGAGCTATTTTCAAAA
TCTGTTTTACAAATTTTGTTTT
Found at i:54083527 original size:18 final size:18
Alignment explanation
Indices: 54083504--54083557 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
54083494 CCACCACCAA
54083504 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
*
54083522 CT-C-C-A-CCAC-C-TA
1 CTCCACTAGCCACACTTG
54083534 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
54083552 CTCCAC
1 CTCCAC
54083558 CACCTACTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 3 0.11
13 2 0.07
14 5 0.18
15 2 0.07
16 5 0.18
17 2 0.07
18 9 0.32
ACGTcount: A:0.22, C:0.50, G:0.07, T:0.20
Consensus pattern (18 bp):
CTCCACTAGCCACACTTG
Found at i:54083530 original size:30 final size:30
Alignment explanation
Indices: 54083494--54083592 Score: 171
Period size: 30 Copynumber: 3.3 Consensus size: 30
54083484 CTAGCCTTTG
54083494 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
*
54083524 CCACCACCTACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* *
54083554 CCACCACCTACTCCATTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
54083584 CCACCACCA
1 CCACCACCA
54083593 CTTGTACCTA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 66 1.00
ACGTcount: A:0.25, C:0.51, G:0.06, T:0.18
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:54083986 original size:13 final size:13
Alignment explanation
Indices: 54083968--54083994 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
54083958 ACGGTGGCAC
54083968 CGACGGTGGCCGG
1 CGACGGTGGCCGG
54083981 CGACGGTGGCCGG
1 CGACGGTGGCCGG
54083994 C
1 C
54083995 CTTGTGGCCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.33, G:0.52, T:0.07
Consensus pattern (13 bp):
CGACGGTGGCCGG
Found at i:54084086 original size:22 final size:24
Alignment explanation
Indices: 54084037--54084082 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
54084027 TTTTTTTTGT
54084037 TATTATTATATT-TTTTAATATTA
1 TATTATTATATTCTTTTAATATTA
54084060 TATTATATATATTCTTTTAATAT
1 TATTAT-TATATTCTTTTAATAT
54084083 ATTAGGTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 6 0.29
24 6 0.29
25 9 0.43
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (24 bp):
TATTATTATATTCTTTTAATATTA
Found at i:54084140 original size:25 final size:25
Alignment explanation
Indices: 54084037--54084243 Score: 78
Period size: 23 Copynumber: 8.6 Consensus size: 25
54084027 TTTTTTTTGT
* *
54084037 TATTAT-TATAT-TTTTTAATATTA
1 TATTATGTATATATATTTAATACTA
* * *
54084060 TATTATATATAT-TCTTT--TAATA
1 TATTATGTATATATATTTAATACTA
* * * *
54084082 TATTAGGTATAT-T-CTAAATTCTA
1 TATTATGTATATATATTTAATACTA
*
54084105 TATTACGTATATATA-TT-ATACTA
1 TATTATGTATATATATTTAATACTA
* *
54084128 TTTTATGTATATATCTTTAATACTA
1 TATTATGTATATATATTTAATACTA
* * * **
54084153 TATTATTTATATTTTTTTTTCTACATGTTA
1 TATTATGTATA---TATATT-TA-ATACTA
*
54084183 TCTTATGTATATAT-TTTAAT--TA
1 TATTATGTATATATATTTAATACTA
* * * *
54084205 TATTATGTATGTATTTTTTACACTA
1 TATTATGTATATATATTTAATACTA
*
54084230 TATTATGTACATAT
1 TATTATGTATATAT
54084244 TTTTTTTATA
Statistics
Matches: 140, Mismatches: 29, Indels: 28
0.71 0.15 0.14
Matches are distributed among these distances:
21 1 0.01
22 29 0.21
23 41 0.29
24 15 0.11
25 31 0.22
26 2 0.01
27 2 0.01
28 4 0.03
29 2 0.01
30 13 0.09
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.57
Consensus pattern (25 bp):
TATTATGTATATATATTTAATACTA
Found at i:54084175 original size:78 final size:78
Alignment explanation
Indices: 54084093--54084250 Score: 176
Period size: 77 Copynumber: 2.0 Consensus size: 78
54084083 ATTAGGTATA
* *
54084093 TTCTAAAT-TCTATATTACGTATATATATTATACTATTTTATGTATATATCTTTAATACTATATT
1 TTCTAAATGT-TATATTACGTATATATATTA-ACTATATTATGTATATATCTTTAACACTATATT
* *
54084157 ATTTATAT-TTTTTT
64 ATGTACATATTTTTT
* * * * * * * *
54084171 TTCTACATGTTATCTTATGTATATATTTTAATTATATTATGTATGTATTTTTTACACTATATTAT
1 TTCTAAATGTTATATTACGTATATATATTAACTATATTATGTATATATCTTTAACACTATATTAT
54084236 GTACATATTTTTT
66 GTACATATTTTTT
54084249 TT
1 TT
54084251 ATATCTATTT
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
77 33 0.50
78 32 0.48
79 1 0.02
ACGTcount: A:0.30, C:0.08, G:0.04, T:0.58
Consensus pattern (78 bp):
TTCTAAATGTTATATTACGTATATATATTAACTATATTATGTATATATCTTTAACACTATATTAT
GTACATATTTTTT
Found at i:54084205 original size:22 final size:22
Alignment explanation
Indices: 54084180--54084246 Score: 71
Period size: 25 Copynumber: 2.9 Consensus size: 22
54084170 TTTCTACATG
*
54084180 TTATCTTATGTATATATTTTAA
1 TTATATTATGTATATATTTTAA
*
54084202 TTATATTATGTATGTATTTTTTACA
1 TTATATTATGTA--TATATTTTA-A
* *
54084227 CTATATTATGTACATATTTT
1 TTATATTATGTATATATTTT
54084247 TTTTATATCT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
22 11 0.30
23 6 0.16
24 8 0.22
25 12 0.32
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (22 bp):
TTATATTATGTATATATTTTAA
Found at i:54084230 original size:77 final size:82
Alignment explanation
Indices: 54084111--54084283 Score: 194
Period size: 77 Copynumber: 2.2 Consensus size: 82
54084101 TCTATATTAC
* * * * * *
54084111 GTATATATATTATACTATTTTATGTATATATCTTTAATACTATATTATTTATAT-TTTTTTTTCT
1 GTATATATTTTATACTATATTATGTATATATCTTTAACACTATATTATGTACATATTTTTTTTAT
*
54084175 A-C-ATGTTAT-CTTAT
66 ATCTATGTTATACATAT
* * * *
54084189 GTATATATTTTA-ATTATATTATGTATGTATTTTTTACACTATATTATGTACATATTTTTTTTAT
1 GTATATATTTTATACTATATTATGTATATATCTTTAACACTATATTATGTACATATTTTTTTTAT
*
54084253 ATCTATTTTATACATAT
66 ATCTATGTTATACATAT
*
54084270 GTATATATTATATA
1 GTATATATTTTATA
54084284 TATCTTAACA
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
77 33 0.43
78 21 0.27
79 1 0.01
80 6 0.08
81 15 0.19
82 1 0.01
ACGTcount: A:0.31, C:0.06, G:0.05, T:0.58
Consensus pattern (82 bp):
GTATATATTTTATACTATATTATGTATATATCTTTAACACTATATTATGTACATATTTTTTTTAT
ATCTATGTTATACATAT
Found at i:54089433 original size:17 final size:16
Alignment explanation
Indices: 54089401--54089434 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
54089391 TATATAAATA
*
54089401 ACAAATTTTAATTTTT
1 ACAAATTTTAAATTTT
54089417 ACAAATATTTAAATTTT
1 ACAAAT-TTTAAATTTT
54089434 A
1 A
54089435 AAAAAGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (16 bp):
ACAAATTTTAAATTTT
Found at i:54091712 original size:16 final size:17
Alignment explanation
Indices: 54091658--54091704 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
54091648 ATAGTATCTA
54091658 AAATAT-AATA-ATAATG
1 AAATATAAATAGATAA-G
54091674 AAAATATAAATAGATAAG
1 -AAATATAAATAGATAAG
54091692 AAATAT-AATAGAT
1 AAATATAAATAGAT
54091705 GAGTAATAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 7 0.25
17 12 0.43
18 5 0.18
19 4 0.14
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.28
Consensus pattern (17 bp):
AAATATAAATAGATAAG
Found at i:54091896 original size:17 final size:17
Alignment explanation
Indices: 54091874--54091913 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
54091864 AAATAGGAAT
54091874 AATAATATGGTAAAAAA
1 AATAATATGGTAAAAAA
* *
54091891 AATAATATGTTAATAAA
1 AATAATATGGTAAAAAA
54091908 AATAAT
1 AATAAT
54091914 GGTAGTAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (17 bp):
AATAATATGGTAAAAAA
Found at i:54091897 original size:23 final size:23
Alignment explanation
Indices: 54091843--54091890 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
54091833 ATATATGTTG
*
54091843 ATAACAATAATAATATATAAAAA
1 ATAAGAATAATAATATATAAAAA
* *
54091866 ATAGGAATAATAATATGGTAAAAA
1 ATAAGAATAATAATAT-ATAAAAA
54091890 A
1 A
54091891 AATAATATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.25
Consensus pattern (23 bp):
ATAAGAATAATAATATATAAAAA
Found at i:54092107 original size:3 final size:3
Alignment explanation
Indices: 54091726--54092087 Score: 143
Period size: 3 Copynumber: 121.3 Consensus size: 3
54091716 AAATGAAAAT
54091726 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
* * * * * * *
54091772 ATA A-A ATG ATA ACA GTG ATA TTA GTA ATA A-A ATA ATA GAAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
* * * * *
54091816 ATA GTA CATTA ATA ATA ATA TATG TTG ATA ACA ATA ATA ATA TATA A-A
1 ATA ATA -A-TA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA -ATA ATA
** * * * * * * *
54091864 A-A ATA GGA ATA ATA AT- ATG GTA AAA AAA ATA AT- ATG TTA ATA AAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
54091909 ATA ATG GTA GTA GTA ATA ATA ATTA ATG GTA ATA A-A ATA CATA ATA
1 ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA -ATA ATA
* * * * * *
54091955 ATA ATA ATA ATA CATT A-A ATT ACA ATA ATA A-A GTA ATA ATA GTG
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * ** * * * *
54091999 ATA ATG ATA ATA ATA ATA GTA GCA A-A A-A ATA ATA ATA TTA GTG GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
54092045 ATA ATA GTA ATA ATA AAA ATA TTA ATA TTA GTA TTA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
54092088 CGGCGTAGTA
Statistics
Matches: 266, Mismatches: 75, Indels: 36
0.71 0.20 0.10
Matches are distributed among these distances:
2 20 0.08
3 225 0.85
4 19 0.07
5 2 0.01
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:54092141 original size:28 final size:28
Alignment explanation
Indices: 54092101--54092172 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
54092091 CGTAGTAGAA
*
54092101 AATAATAATAATAATGGCAAATAA-AAAT
1 AATAATAATAATAATAGC-AATAATAAAT
*
54092129 AATAGTAATAATAATAGCAATAATAAAT
1 AATAATAATAATAATAGCAATAATAAAT
* * *
54092157 AGTACTAATAACAATA
1 AATAATAATAATAATA
54092173 ATACAAATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
27 5 0.13
28 33 0.87
ACGTcount: A:0.61, C:0.06, G:0.07, T:0.26
Consensus pattern (28 bp):
AATAATAATAATAATAGCAATAATAAAT
Found at i:54092143 original size:12 final size:12
Alignment explanation
Indices: 54092126--54092167 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
54092116 GGCAAATAAA
54092126 AATAATAGTAAT
1 AATAATAGTAAT
*
54092138 AATAATAGCAAT
1 AATAATAGTAAT
*
54092150 AATAAATAGTACT
1 AAT-AATAGTAAT
54092163 AATAA
1 AATAA
54092168 CAATAATACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.29
Consensus pattern (12 bp):
AATAATAGTAAT
Found at i:54092446 original size:3 final size:3
Alignment explanation
Indices: 54092390--54092429 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
54092380 AACGATAGTT
*
54092390 ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
54092430 AATTTTTGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:54092904 original size:29 final size:29
Alignment explanation
Indices: 54092848--54092904 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
54092838 ATAAATCCAA
* *
54092848 TTTTTTTTAAAAAGTTCATTTCTGCTCTG
1 TTTTTTTAAAAAAGTTCATTTCTCCTCTG
*
54092877 TTTTTTTAAAAAAAGTT-ATTTTTCCTCT
1 TTTTTTT-AAAAAAGTTCATTTCTCCTCT
54092905 TTGCTCTCTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.25, C:0.12, G:0.07, T:0.56
Consensus pattern (29 bp):
TTTTTTTAAAAAAGTTCATTTCTCCTCTG
Found at i:54104428 original size:22 final size:22
Alignment explanation
Indices: 54104403--54104447 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
54104393 GTGAACCNAT
*
54104403 TTTTTGCATTACAGTATTACAC
1 TTTTTGCATCACAGTATTACAC
*
54104425 TTTTTGCATCACGGTATTACAC
1 TTTTTGCATCACAGTATTACAC
54104447 T
1 T
54104448 CTGCCGCCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.44
Consensus pattern (22 bp):
TTTTTGCATCACAGTATTACAC
Found at i:54108783 original size:9 final size:9
Alignment explanation
Indices: 54108769--54108809 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
54108759 ATAAGTATAA
54108769 AATTAACCG
1 AATTAACCG
54108778 AATTAACCG
1 AATTAACCG
*
54108787 AATTACCCG
1 AATTAACCG
*
54108796 AATTAACAG
1 AATTAACCG
54108805 AATTA
1 AATTA
54108810 TTTTTATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:54108846 original size:14 final size:14
Alignment explanation
Indices: 54108821--54108867 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
54108811 TTTTATAAAA
54108821 TTATATTTTTTATATT
1 TTATA-TTTTTAT-TT
54108837 TT-TATTTTTATTT
1 TTATATTTTTATTT
*
54108850 TTAGATTTTTATTT
1 TTATATTTTTATTT
54108864 TTAT
1 TTAT
54108868 TTATTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 4 0.14
14 20 0.71
15 2 0.07
16 2 0.07
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (14 bp):
TTATATTTTTATTT
Found at i:54108850 original size:5 final size:6
Alignment explanation
Indices: 54108828--54108869 Score: 57
Period size: 6 Copynumber: 6.5 Consensus size: 6
54108818 AAATTATATT
54108828 TTTTATA TTTTTA TTTTTA TTTTTAGA TTTTTA TTTTTA TTT
1 TTTT-TA TTTTTA TTTTTA TTTTT--A TTTTTA TTTTTA TTT
54108870 ATTACATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
6 23 0.70
7 4 0.12
8 6 0.18
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:54108852 original size:20 final size:20
Alignment explanation
Indices: 54108827--54108869 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
54108817 AAAATTATAT
*
54108827 TTTTTATATTTTTATTTTTA
1 TTTTTAGATTTTTATTTTTA
54108847 TTTTTAGATTTTTATTTTTA
1 TTTTTAGATTTTTATTTTTA
54108867 TTT
1 TTT
54108870 ATTACATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (20 bp):
TTTTTAGATTTTTATTTTTA
Found at i:54109785 original size:20 final size:20
Alignment explanation
Indices: 54109760--54109830 Score: 79
Period size: 20 Copynumber: 3.2 Consensus size: 20
54109750 TTCAATAATC
54109760 TTAACATGATGTATACATGT
1 TTAACATGATGTATACATGT
54109780 TTAACATGATACATGATGTATACATGT
1 TTAAC-------ATGATGTATACATGT
54109807 TTAACATGATGTATACATGT
1 TTAACATGATGTATACATGT
54109827 TTAA
1 TTAA
54109831 GTTTGGTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
20 24 0.55
27 20 0.45
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (20 bp):
TTAACATGATGTATACATGT
Found at i:54109793 original size:27 final size:27
Alignment explanation
Indices: 54109763--54109816 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
54109753 AATAATCTTA
54109763 ACATGATGTATACATGTTTAACATGAT
1 ACATGATGTATACATGTTTAACATGAT
54109790 ACATGATGTATACATGTTTAACATGAT
1 ACATGATGTATACATGTTTAACATGAT
54109817 GTATACATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (27 bp):
ACATGATGTATACATGTTTAACATGAT
Found at i:54109804 original size:11 final size:11
Alignment explanation
Indices: 54109788--54109825 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
54109778 GTTTAACATG
54109788 ATACATGATGT
1 ATACATGATGT
*
54109799 ATACATG-TTT
1 ATACATGATGT
54109809 A-ACATGATGT
1 ATACATGATGT
54109819 ATACATG
1 ATACATG
54109826 TTTAAGTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 5 0.22
10 6 0.26
11 12 0.52
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (11 bp):
ATACATGATGT
Found at i:54114519 original size:28 final size:28
Alignment explanation
Indices: 54114483--54114539 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
54114473 ATGTAATTTG
* *
54114483 ACAAGAAAATTATCAAAGTACAAGTTTA
1 ACAAAAAAATTATCAAAATACAAGTTTA
54114511 ACAAAAAAATTATCAAAATACAAGTTTA
1 ACAAAAAAATTATCAAAATACAAGTTTA
54114539 A
1 A
54114540 GAGATCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.58, C:0.11, G:0.07, T:0.25
Consensus pattern (28 bp):
ACAAAAAAATTATCAAAATACAAGTTTA
Found at i:54114593 original size:16 final size:17
Alignment explanation
Indices: 54114553--54114600 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
54114543 ATCAAAAGGT
* *
54114553 AAAATAAAATTAAATGG
1 AAAATAAAAATAAATAG
*
54114570 AGAATAAAAAT-AATAG
1 AAAATAAAAATAAATAG
*
54114586 AAAATAAAAAAAAAT
1 AAAATAAAAATAAAT
54114601 CATTACTACC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (17 bp):
AAAATAAAAATAAATAG
Found at i:54118011 original size:4 final size:4
Alignment explanation
Indices: 54118002--54118314 Score: 626
Period size: 4 Copynumber: 78.2 Consensus size: 4
54117992 GATCTAAATG
54118002 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
54118050 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
54118098 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
54118146 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
54118194 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
54118242 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
54118290 GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT G
54118315 AGTTTGTGAT
Statistics
Matches: 309, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 309 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:54122389 original size:29 final size:31
Alignment explanation
Indices: 54122331--54122403 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 31
54122321 AAAATTCAAA
*
54122331 AAAAATTACATCTTAGACCCCTAAACTTTCCT
1 AAAAATTACATTTTAGACCCCTAAACTTT-CT
* *
54122363 -TAAATTACATTTTA-A-CCCTAAATTTTCT
1 AAAAATTACATTTTAGACCCCTAAACTTTCT
54122391 AAAAATTACATTT
1 AAAAATTACATTT
54122404 AGCCCCAGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 2 0.06
29 21 0.58
30 1 0.03
31 12 0.33
ACGTcount: A:0.40, C:0.21, G:0.01, T:0.38
Consensus pattern (31 bp):
AAAAATTACATTTTAGACCCCTAAACTTTCT
Found at i:54124881 original size:803 final size:803
Alignment explanation
Indices: 54123337--54124942 Score: 3203
Period size: 803 Copynumber: 2.0 Consensus size: 803
54123327 AATCGGCCCC
54123337 TATTTCCAATTTTCTTTTGTTTTTTTTTAATTCTAACCCTCAAATTTCGTTTGGTTTTTGATTAG
1 TATTTCCAATTTTCTTTTGTTTTTTTTTAATTCTAACCCTCAAATTTCGTTTGGTTTTTGATTAG
54123402 GTCCCTGATGAACTTTCCAGTATTTATAATTTTGTACCCCAATTTTTAACTCGTTTTCAACCATG
66 GTCCCTGATGAACTTTCCAGTATTTATAATTTTGTACCCCAATTTTTAACTCGTTTTCAACCATG
54123467 TCCTAAATCTATTTAATCCATTTATTAACTTTTAAAAAAAATAATATTTCACCTATGTGTTATTT
131 TCCTAAATCTATTTAATCCATTTATTAACTTTTAAAAAAAATAATATTTCACCTATGTGTTATTT
54123532 AAAATATTTTATATGTTATTTACTTTACATCTATTCCAACTTATTTTAATGTATTGTTTGTTTAA
196 AAAATATTTTATATGTTATTTACTTTACATCTATTCCAACTTATTTTAATGTATTGTTTGTTTAA
54123597 ATTCTTATTATTTATTTTAACTTGCTTTATGCATATATTTTATATTGGTCTATTTTATATATATT
261 ATTCTTATTATTTATTTTAACTTGCTTTATGCATATATTTTATATTGGTCTATTTTATATATATT
54123662 ATTTATTCCTTACCTACTATATATATGTGTACATATATTCTATTTTTAAATTGTTTTGTACATTG
326 ATTTATTCCTTACCTACTATATATATGTGTACATATATTCTATTTTTAAATTGTTTTGTACATTG
54123727 TTGATTAAATTTCTTTTCTCATTATTTATTTTAAATTCATTTATTAATTATTTTGAAATTTGTTT
391 TTGATTAAATTTCTTTTCTCATTATTTATTTTAAATTCATTTATTAATTATTTTGAAATTTGTTT
54123792 TACGTTTTAGTCATTTTAGTTTGCGTTATAATATTTTTAATTCACTTGTCTTTGATTATTAATGA
456 TACGTTTTAGTCATTTTAGTTTGCGTTATAATATTTTTAATTCACTTGTCTTTGATTATTAATGA
54123857 TTAGTATTCAAGTTACATATGTTATGTGATTATTGCCATTGTGTATGGTATAATTAGTTTATTCG
521 TTAGTATTCAAGTTACATATGTTATGTGATTATTGCCATTGTGTATGGTATAATTAGTTTATTCG
54123922 TATTTTCGTTATTGCCATTTGCTTGTATAATATTGTATTTGTGTTGTTATTACGTACTCTATGTT
586 TATTTTCGTTATTGCCATTTGCTTGTATAATATTGTATTTGTGTTGTTATTACGTACTCTATGTT
54123987 ATATTTTTGTTTTATCTAGTTTAAATCATATCATACATTAACCCAACATACTTGCCCGACTTGGA
651 ATATTTTTGTTTTATCTAGTTTAAATCATATCATACATTAACCCAACATACTTGCCCGACTTGGA
54124052 TCGCTTGATTTTTTTTATTCCAAACAAATAATATACGTCGTTCAAATGCCATATTCGCTACTACT
716 TCGCTTGATTTTTTTTATTCCAAACAAATAATATACGTCGTTCAAATGCCATATTCGCTACTACT
54124117 CAAAAACGAAATTTTCCAAATAA
781 CAAAAACGAAATTTTCCAAATAA
54124140 TATTTCCAATTTTCTTTTGTTTTTTTTTAATTCTAACCCTCAAATTTCGTTTGGTTTTTGATTAG
1 TATTTCCAATTTTCTTTTGTTTTTTTTTAATTCTAACCCTCAAATTTCGTTTGGTTTTTGATTAG
54124205 GTCCCTGATGAACTTTCCAGTATTTATAATTTTGTACCCCAATTTTTAACTCGTTTTCAACCATG
66 GTCCCTGATGAACTTTCCAGTATTTATAATTTTGTACCCCAATTTTTAACTCGTTTTCAACCATG
54124270 TCCTAAATCTATTTAATCCATTTATTAACTTTTAAAAAAAATAATATTTCACCTATGTGTTATTT
131 TCCTAAATCTATTTAATCCATTTATTAACTTTTAAAAAAAATAATATTTCACCTATGTGTTATTT
54124335 AAAATATTTTATATGTTATTTACTTTACATCTATTCCAACTTATTTTAATGTATTGTTTGTTTAA
196 AAAATATTTTATATGTTATTTACTTTACATCTATTCCAACTTATTTTAATGTATTGTTTGTTTAA
54124400 ATTCTTATTATTTATTTTAACTTGCTTTATGCATATATTTTATATTGGTCTATTTTATATATATT
261 ATTCTTATTATTTATTTTAACTTGCTTTATGCATATATTTTATATTGGTCTATTTTATATATATT
54124465 ATTTATTCCTTACCTACTATATATATGTGTACATATATTCTATTTTTAAATTGTTTTGTACATTG
326 ATTTATTCCTTACCTACTATATATATGTGTACATATATTCTATTTTTAAATTGTTTTGTACATTG
54124530 TTGATTAAATTTCTTTTCTCATTATTTATTTTAAATTCATTTATTAATTATTTTGAAATTTGTTT
391 TTGATTAAATTTCTTTTCTCATTATTTATTTTAAATTCATTTATTAATTATTTTGAAATTTGTTT
54124595 TACGTTTTAGTCATTTTAGTTTGCGTTATAATATTTTTAATTCACTTGTCTTTGATTATTAATGA
456 TACGTTTTAGTCATTTTAGTTTGCGTTATAATATTTTTAATTCACTTGTCTTTGATTATTAATGA
54124660 TTAGTATTCAAGTTACATATGTTATGTGATTATTGCCATTGTGTATGGTATAATTAGTTTATTCG
521 TTAGTATTCAAGTTACATATGTTATGTGATTATTGCCATTGTGTATGGTATAATTAGTTTATTCG
54124725 TATTTTCGTTATTGCCATTTGCTTGTATAATATTGTATTTGTGTTGTTATTACGTACTCTATGTT
586 TATTTTCGTTATTGCCATTTGCTTGTATAATATTGTATTTGTGTTGTTATTACGTACTCTATGTT
54124790 ATATTTTTGTTTTATCTAGTTTAAATCATATCATACATTAACCCAACATACTTGCCCGACTTGGA
651 ATATTTTTGTTTTATCTAGTTTAAATCATATCATACATTAACCCAACATACTTGCCCGACTTGGA
*
54124855 TCGCTTGATTTTTTTTATTCCAAACAAATAATGTACGTCGTTCAAATGCCATATTCGCTACTACT
716 TCGCTTGATTTTTTTTATTCCAAACAAATAATATACGTCGTTCAAATGCCATATTCGCTACTACT
54124920 CAAAAACGAAATTTTCCAAATAA
781 CAAAAACGAAATTTTCCAAATAA
54124943 GGCAATGTTA
Statistics
Matches: 802, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
803 802 1.00
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.50
Consensus pattern (803 bp):
TATTTCCAATTTTCTTTTGTTTTTTTTTAATTCTAACCCTCAAATTTCGTTTGGTTTTTGATTAG
GTCCCTGATGAACTTTCCAGTATTTATAATTTTGTACCCCAATTTTTAACTCGTTTTCAACCATG
TCCTAAATCTATTTAATCCATTTATTAACTTTTAAAAAAAATAATATTTCACCTATGTGTTATTT
AAAATATTTTATATGTTATTTACTTTACATCTATTCCAACTTATTTTAATGTATTGTTTGTTTAA
ATTCTTATTATTTATTTTAACTTGCTTTATGCATATATTTTATATTGGTCTATTTTATATATATT
ATTTATTCCTTACCTACTATATATATGTGTACATATATTCTATTTTTAAATTGTTTTGTACATTG
TTGATTAAATTTCTTTTCTCATTATTTATTTTAAATTCATTTATTAATTATTTTGAAATTTGTTT
TACGTTTTAGTCATTTTAGTTTGCGTTATAATATTTTTAATTCACTTGTCTTTGATTATTAATGA
TTAGTATTCAAGTTACATATGTTATGTGATTATTGCCATTGTGTATGGTATAATTAGTTTATTCG
TATTTTCGTTATTGCCATTTGCTTGTATAATATTGTATTTGTGTTGTTATTACGTACTCTATGTT
ATATTTTTGTTTTATCTAGTTTAAATCATATCATACATTAACCCAACATACTTGCCCGACTTGGA
TCGCTTGATTTTTTTTATTCCAAACAAATAATATACGTCGTTCAAATGCCATATTCGCTACTACT
CAAAAACGAAATTTTCCAAATAA
Found at i:54125304 original size:45 final size:45
Alignment explanation
Indices: 54125247--54125334 Score: 167
Period size: 45 Copynumber: 2.0 Consensus size: 45
54125237 GATTTTTAAT
54125247 TTTCGACATTAAGACACTAACTAATCAATTCGGTACCAATTTTAC
1 TTTCGACATTAAGACACTAACTAATCAATTCGGTACCAATTTTAC
*
54125292 TTTCGACATTAAGACAGTAACTAATCAATTCGGTACCAATTTT
1 TTTCGACATTAAGACACTAACTAATCAATTCGGTACCAATTTT
54125335 TTGGGCATGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.34
Consensus pattern (45 bp):
TTTCGACATTAAGACACTAACTAATCAATTCGGTACCAATTTTAC
Found at i:54129685 original size:24 final size:24
Alignment explanation
Indices: 54129657--54129706 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
54129647 ATACCCCTAA
*
54129657 TCCATATCCAAACGAACCCCAACC
1 TCCATATCCAAACCAACCCCAACC
*
54129681 TCCATATCCAAACCAACCCCGACC
1 TCCATATCCAAACCAACCCCAACC
54129705 TC
1 TC
54129707 GAAATTATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.34, C:0.48, G:0.04, T:0.14
Consensus pattern (24 bp):
TCCATATCCAAACCAACCCCAACC
Found at i:54136785 original size:79 final size:79
Alignment explanation
Indices: 54136695--54136841 Score: 231
Period size: 79 Copynumber: 1.9 Consensus size: 79
54136685 TTTTTGTTTC
* * *
54136695 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAATCACGCCCTGAGGTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAACCTCAAATCACACCCTGAGATATTTTCAA
54136760 TTTCTGTTTTTCAA
66 TTTCTGTTTTTCAA
* ** *
54136774 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAACCTTAGGTCACACGCTGAGATATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAACCTCAAATCACACCCTGAGATATTTTCAA
54136839 TTT
66 TTT
54136842 TTTTTTGCTT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
79 61 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (79 bp):
AAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAACCTCAAATCACACCCTGAGATATTTTCAA
TTTCTGTTTTTCAA
Found at i:54137098 original size:12 final size:11
Alignment explanation
Indices: 54137080--54137118 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
54137070 CCAAAATTTC
54137080 AAAAAAATAAA
1 AAAAAAATAAA
54137091 ATAAAAAATAAA
1 A-AAAAAATAAA
*
54137103 AAAAAATTCAAA
1 AAAAAAAT-AAA
54137115 AAAA
1 AAAA
54137119 TTACATCTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 7 0.28
12 18 0.72
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.13
Consensus pattern (11 bp):
AAAAAAATAAA
Found at i:54137172 original size:29 final size:31
Alignment explanation
Indices: 54137114--54137186 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 31
54137104 AAAAATTCAA
*
54137114 AAAAATTACATCTTAGACCCCTAAACTTTCCT
1 AAAAATTACATTTTAGACCCCTAAACTTT-CT
* *
54137146 -TAAATTACATTTTA-A-CCCTAAATTTTCT
1 AAAAATTACATTTTAGACCCCTAAACTTTCT
54137174 AAAAATTACATTT
1 AAAAATTACATTT
54137187 AGCACCAGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 2 0.06
29 21 0.58
30 1 0.03
31 12 0.33
ACGTcount: A:0.40, C:0.21, G:0.01, T:0.38
Consensus pattern (31 bp):
AAAAATTACATTTTAGACCCCTAAACTTTCT
Found at i:54140874 original size:13 final size:14
Alignment explanation
Indices: 54140848--54140876 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
54140838 ATATAAATTA
54140848 TATAATTGTATAAT
1 TATAATTGTATAAT
54140862 TATAATT-TATAAT
1 TATAATTGTATAAT
54140875 TA
1 TA
54140877 CGAATTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (14 bp):
TATAATTGTATAAT
Found at i:54141825 original size:19 final size:18
Alignment explanation
Indices: 54141801--54141842 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
54141791 AAGATATAAA
54141801 AAAAAAGTATAATCTTT-TT
1 AAAAAA-TATAAT-TTTATT
*
54141820 AAAAAATTTAATTTTATT
1 AAAAAATATAATTTTATT
54141838 AAAAA
1 AAAAA
54141843 TTAATTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 3 0.14
18 12 0.57
19 6 0.29
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (18 bp):
AAAAAATATAATTTTATT
Found at i:54143248 original size:22 final size:22
Alignment explanation
Indices: 54143187--54143248 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
54143177 GGATTTACAG
* *
54143187 TATATGATTAAGGGTTTAATGTT
1 TATA-GATTATGGGTTTAAGGTT
***
54143210 TAT-GAGTTATTATTTTAAGGTT
1 TATAGA-TTATGGGTTTAAGGTT
54143232 TATAGATTATGGGTTTA
1 TATAGATTATGGGTTTA
54143249 GGGATTATGG
Statistics
Matches: 29, Mismatches: 8, Indels: 5
0.69 0.19 0.12
Matches are distributed among these distances:
21 2 0.07
22 22 0.76
23 5 0.17
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (22 bp):
TATAGATTATGGGTTTAAGGTT
Found at i:54143284 original size:25 final size:25
Alignment explanation
Indices: 54143243--54143290 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
54143233 ATAGATTATG
54143243 GGTTTAGGGATTATGGTTTAAGGGT
1 GGTTTAGGGATTATGGTTTAAGGGT
*
54143268 GGTTTAAGGG-TTGTGGTTTAAGG
1 GGTTT-AGGGATTATGGTTTAAGG
54143291 TTTAAGTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.19, C:0.00, G:0.42, T:0.40
Consensus pattern (25 bp):
GGTTTAGGGATTATGGTTTAAGGGT
Found at i:54143357 original size:7 final size:7
Alignment explanation
Indices: 54143347--54143381 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
54143337 AAGATTTATA
54143347 GTTTAGG
1 GTTTAGG
54143354 GTTTAGG
1 GTTTAGG
*
54143361 GATTAGG
1 GTTTAGG
54143368 AGTTTAGG
1 -GTTTAGG
54143376 GTTTAG
1 GTTTAG
54143382 ATTAATTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (7 bp):
GTTTAGG
Found at i:54143479 original size:14 final size:14
Alignment explanation
Indices: 54143462--54143500 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
54143452 ATCATTATAG
54143462 TTTAGGGTTTATGA
1 TTTAGGGTTTATGA
* *
54143476 TTTAGGGTATATGG
1 TTTAGGGTTTATGA
*
54143490 TTTAGAGTTTA
1 TTTAGGGTTTA
54143501 AAGTGTATGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (14 bp):
TTTAGGGTTTATGA
Found at i:54143542 original size:15 final size:15
Alignment explanation
Indices: 54143524--54143571 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
54143514 ATTATTTTAA
54143524 GGTTTATGGATTATG
1 GGTTTATGGATTATG
*
54143539 GGTTTAGGGATTAT-
1 GGTTTATGGATTATG
* *
54143553 GGTTTATGGTTTAAG
1 GGTTTATGGATTATG
54143568 GGTT
1 GGTT
54143572 GGGGTTTAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (15 bp):
GGTTTATGGATTATG
Found at i:54143544 original size:22 final size:21
Alignment explanation
Indices: 54143519--54143568 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
54143509 GAGTTATTAT
*
54143519 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGATTATGGATTAT-GG
* *
54143541 TTTAGGGATTATGGTTTATGG
1 TTTAAGGATTATGGATTATGG
54143562 TTTAAGG
1 TTTAAGG
54143569 GTTGGGGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.46
Consensus pattern (21 bp):
TTTAAGGATTATGGATTATGG
Found at i:54143577 original size:14 final size:15
Alignment explanation
Indices: 54143560--54143600 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
54143550 TATGGTTTAT
54143560 GGTTTAAGGGTT-GG
1 GGTTTAAGGGTTAGG
*
54143574 GGTTTAAGGCTTAGG
1 GGTTTAAGGGTTAGG
54143589 GG-TTAAGGGTTA
1 GGTTTAAGGGTTA
54143601 AGTGTTAGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 20 0.83
15 4 0.17
ACGTcount: A:0.20, C:0.02, G:0.44, T:0.34
Consensus pattern (15 bp):
GGTTTAAGGGTTAGG
Found at i:54143591 original size:21 final size:21
Alignment explanation
Indices: 54143553--54143592 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
54143543 TAGGGATTAT
* *
54143553 GGTTTATGGTTTAAGGGTTGG
1 GGTTTAAGGCTTAAGGGTTGG
*
54143574 GGTTTAAGGCTTAGGGGTT
1 GGTTTAAGGCTTAAGGGTT
54143593 AAGGGTTAAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.15, C:0.03, G:0.42, T:0.40
Consensus pattern (21 bp):
GGTTTAAGGCTTAAGGGTTGG
Found at i:54152159 original size:11 final size:11
Alignment explanation
Indices: 54152140--54152172 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
54152130 TTTGATGATT
54152140 ATTTG-TTTAA
1 ATTTGTTTTAA
54152150 ATTTGTTTTAA
1 ATTTGTTTTAA
*
54152161 ATTTTTTTTAA
1 ATTTGTTTTAA
54152172 A
1 A
54152173 GTAAATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (11 bp):
ATTTGTTTTAA
Found at i:54155137 original size:16 final size:16
Alignment explanation
Indices: 54155086--54155137 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
54155076 AACGGCATGT
54155086 TAAAACATCAGAAGTA
1 TAAAACATCAGAAGTA
* * * *
54155102 TAAATCTAACA-CAGTT
1 TAAAAC-ATCAGAAGTA
54155118 TAAAACATCAGAAGTA
1 TAAAACATCAGAAGTA
54155134 TAAA
1 TAAA
54155138 TCTAAACCCG
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
15 3 0.12
16 20 0.77
17 3 0.12
ACGTcount: A:0.54, C:0.13, G:0.10, T:0.23
Consensus pattern (16 bp):
TAAAACATCAGAAGTA
Found at i:54155246 original size:204 final size:204
Alignment explanation
Indices: 54154892--54155502 Score: 1197
Period size: 204 Copynumber: 3.0 Consensus size: 204
54154882 AATAATAGTT
*
54154892 AGAA-TATAAATCTAACACAGATTAAAACATCAGAAGTATAAATCTAAACCCGACAAGCAACTCT
1 AGAAGTATAAATCTAACACAGTTTAAAACATCAGAAGTATAAATCTAAACCCGACAAGCAACTCT
*
54154956 GCCTTCAGCCAACCATATCTAGATATATGATACATAACACAACCTCGCATTAAAATTTTGCGGGT
66 GCCTTCAGCCAACCATATCTAGATATATGATACATAACACAACCTCACATTAAAATTTTGCGGGT
54155021 AAAGAATCAGTTCATAGATATGGTAAATGATATATTGCCCTATAATGTCAGCAGCAACGGCATGT
131 AAAGAATCAGTTCATAGATATGGTAAATGATATATTGCCCTATAATGTCAGCAGCAACGGCATGT
54155086 TAAAACATC
196 TAAAACATC
54155095 AGAAGTATAAATCTAACACAGTTTAAAACATCAGAAGTATAAATCTAAACCCGACAAGCAACTCT
1 AGAAGTATAAATCTAACACAGTTTAAAACATCAGAAGTATAAATCTAAACCCGACAAGCAACTCT
54155160 GCCTTCAGCCAACCATATCTAGATATATGATACATAACACAACCTCACATTAAAATTTTGCGGGT
66 GCCTTCAGCCAACCATATCTAGATATATGATACATAACACAACCTCACATTAAAATTTTGCGGGT
54155225 AAAGAATCAGTTCATAGATATGGTAAATGATATATTGCCCTATAATGTCAGCAGCAACGGCATGT
131 AAAGAATCAGTTCATAGATATGGTAAATGATATATTGCCCTATAATGTCAGCAGCAACGGCATGT
54155290 TAAAACATC
196 TAAAACATC
54155299 AGAAGTATAAATCTAACACAGTTTAAAACATCAGAAGTATAAATCTAAACCCGACAAGCAACTCT
1 AGAAGTATAAATCTAACACAGTTTAAAACATCAGAAGTATAAATCTAAACCCGACAAGCAACTCT
54155364 GCCTTCAGCCAACCATATCTAGATATATGATACATAACACAACCTCACATTAAAATTTTGCGGGT
66 GCCTTCAGCCAACCATATCTAGATATATGATACATAACACAACCTCACATTAAAATTTTGCGGGT
54155429 AAAGAATCAGTTCATAGATATGGTAAATGATATATTGCCCTATAATGTCAGCAGCAACGGCATGT
131 AAAGAATCAGTTCATAGATATGGTAAATGATATATTGCCCTATAATGTCAGCAGCAACGGCATGT
54155494 TAAAACATC
196 TAAAACATC
54155503 TAAGCAAGTG
Statistics
Matches: 405, Mismatches: 2, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
203 4 0.01
204 401 0.99
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (204 bp):
AGAAGTATAAATCTAACACAGTTTAAAACATCAGAAGTATAAATCTAAACCCGACAAGCAACTCT
GCCTTCAGCCAACCATATCTAGATATATGATACATAACACAACCTCACATTAAAATTTTGCGGGT
AAAGAATCAGTTCATAGATATGGTAAATGATATATTGCCCTATAATGTCAGCAGCAACGGCATGT
TAAAACATC
Found at i:54155341 original size:16 final size:16
Alignment explanation
Indices: 54155290--54155341 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
54155280 AACGGCATGT
54155290 TAAAACATCAGAAGTA
1 TAAAACATCAGAAGTA
* * * *
54155306 TAAATCTAACA-CAGTT
1 TAAAAC-ATCAGAAGTA
54155322 TAAAACATCAGAAGTA
1 TAAAACATCAGAAGTA
54155338 TAAA
1 TAAA
54155342 TCTAAACCCG
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
15 3 0.12
16 20 0.77
17 3 0.12
ACGTcount: A:0.54, C:0.13, G:0.10, T:0.23
Consensus pattern (16 bp):
TAAAACATCAGAAGTA
Found at i:54159403 original size:5 final size:5
Alignment explanation
Indices: 54159393--54159424 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
54159383 CCCAATTCAA
*
54159393 AATAT AATAT AATAT AATAT AATAT GATAT AA
1 AATAT AATAT AATAT AATAT AATAT AATAT AA
54159425 AAATTATCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:54168352 original size:25 final size:25
Alignment explanation
Indices: 54168296--54168352 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
54168286 ATATTTGCAA
* * *
54168296 CATATTTCACATTCTATTTTTCATT
1 CATATTTCACATTCCATTTCTCATC
54168321 CACTATTTCAC-TTCCATTTCTCATAC
1 CA-TATTTCACATTCCATTTCTCAT-C
54168347 CATATT
1 CATATT
54168353 ATTTCAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 17 0.63
26 10 0.37
ACGTcount: A:0.25, C:0.26, G:0.00, T:0.49
Consensus pattern (25 bp):
CATATTTCACATTCCATTTCTCATC
Found at i:54168544 original size:37 final size:38
Alignment explanation
Indices: 54168449--54168546 Score: 101
Period size: 40 Copynumber: 2.6 Consensus size: 38
54168439 ACACACCAAT
*
54168449 TTGGCACCCAGTGCCTCATCGGATAATTCGAAGTAATAAA
1 TTGGCACCCAGTGCCTCATCGGATAACTCGAAG--ATAAA
* * * *
54168489 TTGACATCCAGTGTCTCATCGGCTAAACT-GAAG-TAAA
1 TTGGCACCCAGTGCCTCATCGGAT-AACTCGAAGATAAA
*
54168526 TTGGCACCCAATGCCTCATCG
1 TTGGCACCCAGTGCCTCATCG
54168547 AATATATCCG
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
37 21 0.44
40 24 0.50
41 3 0.06
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (38 bp):
TTGGCACCCAGTGCCTCATCGGATAACTCGAAGATAAA
Found at i:54169904 original size:20 final size:20
Alignment explanation
Indices: 54169876--54169916 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
54169866 AATCTCAAAA
* * *
54169876 ACTGTCACTTAGGTATTGAT
1 ACTGACACTAAGGTACTGAT
54169896 ACTGACACTAAGGTACTGAT
1 ACTGACACTAAGGTACTGAT
54169916 A
1 A
54169917 TTTTCTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (20 bp):
ACTGACACTAAGGTACTGAT
Found at i:54171469 original size:40 final size:40
Alignment explanation
Indices: 54171425--54171508 Score: 159
Period size: 40 Copynumber: 2.1 Consensus size: 40
54171415 TATTTATTTT
54171425 ATTTTATTTTATTTTTATGAGTTTTAGATGACCTTGAATA
1 ATTTTATTTTATTTTTATGAGTTTTAGATGACCTTGAATA
*
54171465 ATTTTATTTTATTTTTATGAGTTTTAGATGAGCTTGAATA
1 ATTTTATTTTATTTTTATGAGTTTTAGATGACCTTGAATA
54171505 ATTT
1 ATTT
54171509 AGTTAATATT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.27, C:0.04, G:0.13, T:0.56
Consensus pattern (40 bp):
ATTTTATTTTATTTTTATGAGTTTTAGATGACCTTGAATA
Found at i:54174734 original size:28 final size:28
Alignment explanation
Indices: 54174703--54174765 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
54174693 TTTATCTTTA
* *
54174703 TTTTTTAGATGTTACAATTTTTCCCCTT
1 TTTTTTAAATGTTACAATTTTACCCCTT
* * *
54174731 TTTTTCCAAATTTTACAATTTTACCTCTT
1 TTTTT-TAAATGTTACAATTTTACCCCTT
54174760 TTTTTT
1 TTTTTT
54174766 TTCCAGATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.19, C:0.17, G:0.03, T:0.60
Consensus pattern (28 bp):
TTTTTTAAATGTTACAATTTTACCCCTT
Found at i:54174823 original size:28 final size:28
Alignment explanation
Indices: 54174792--54174870 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 28
54174782 TTTTCTCATA
* * *
54174792 TTTTCTAGATTTTATAGTTTT-GCCTTT
1 TTTTCTAGATTTTACAGTTTTACCCTAT
* *
54174819 GTTTTCCAAATTTTACAGTTTTACCCTAT
1 -TTTTCTAGATTTTACAGTTTTACCCTAT
54174848 TTTT-TAGATTTTACAGTTTTACC
1 TTTTCTAGATTTTACAGTTTTACC
54174871 TAGAATTATA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
27 17 0.40
28 22 0.51
29 4 0.09
ACGTcount: A:0.20, C:0.15, G:0.09, T:0.56
Consensus pattern (28 bp):
TTTTCTAGATTTTACAGTTTTACCCTAT
Found at i:54177365 original size:11 final size:11
Alignment explanation
Indices: 54177349--54177377 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
54177339 AGAAGGAAGA
54177349 AGAAACAGCAG
1 AGAAACAGCAG
54177360 AGAAACAGCAG
1 AGAAACAGCAG
54177371 AGAAACA
1 AGAAACA
54177378 AAAGTCTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.59, C:0.17, G:0.24, T:0.00
Consensus pattern (11 bp):
AGAAACAGCAG
Found at i:54184641 original size:12 final size:12
Alignment explanation
Indices: 54184626--54184656 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
54184616 CAAAATAATC
54184626 ATAAAAAGAAAA
1 ATAAAAAGAAAA
54184638 ATAAAAAGAAAA
1 ATAAAAAGAAAA
54184650 ATAAAAA
1 ATAAAAA
54184657 TAAGACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.06, T:0.10
Consensus pattern (12 bp):
ATAAAAAGAAAA
Found at i:54184657 original size:6 final size:6
Alignment explanation
Indices: 54184626--54184659 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
54184616 CAAAATAATC
* *
54184626 ATAAAA AGAAAA ATAAAA AGAAAA ATAAAA ATAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAA
54184660 GACAAAAGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (6 bp):
ATAAAA
Found at i:54186757 original size:15 final size:14
Alignment explanation
Indices: 54186737--54186793 Score: 78
Period size: 15 Copynumber: 3.9 Consensus size: 14
54186727 CGATGAATTT
54186737 ATTGAATCTATATTG
1 ATTGAAT-TATATTG
*
54186752 ATTGAAATTATTTTG
1 ATTG-AATTATATTG
54186767 ATTGAATTTATATTG
1 ATTGAA-TTATATTG
54186782 ATTGAATTATAT
1 ATTGAATTATAT
54186794 AATATACATG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
14 8 0.21
15 27 0.71
16 3 0.08
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (14 bp):
ATTGAATTATATTG
Found at i:54187224 original size:21 final size:21
Alignment explanation
Indices: 54187170--54187228 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
54187160 ACCGATCAGA
54187170 CACTTTATGTGTCGTATTTTAGG
1 CACTTTATGTGTCG--TTTTAGG
* **
54187193 CACCTCGTGTGTCGTTTTAGG
1 CACTTTATGTGTCGTTTTAGG
54187214 CACTTTATGTGTCGT
1 CACTTTATGTGTCGT
54187229 ATACTGATCA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 19 0.63
23 11 0.37
ACGTcount: A:0.14, C:0.19, G:0.24, T:0.44
Consensus pattern (21 bp):
CACTTTATGTGTCGTTTTAGG
Found at i:54188144 original size:15 final size:15
Alignment explanation
Indices: 54188111--54188144 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
54188101 AGTTATGTCT
*
54188111 ATGTATGGAATTATA
1 ATGTATGGAATTAGA
*
54188126 ATGTATGGAATTAGC
1 ATGTATGGAATTAGA
54188141 ATGT
1 ATGT
54188145 CAAAAAGATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (15 bp):
ATGTATGGAATTAGA
Found at i:54189054 original size:19 final size:19
Alignment explanation
Indices: 54189032--54189071 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
54189022 TTAAACTTTT
* *
54189032 ATTATACTTTTCTATTCTA
1 ATTAAACTTTTCGATTCTA
54189051 ATTAAACTTTTCGATTCTA
1 ATTAAACTTTTCGATTCTA
54189070 AT
1 AT
54189072 AAAAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.30, C:0.15, G:0.03, T:0.53
Consensus pattern (19 bp):
ATTAAACTTTTCGATTCTA
Found at i:54190761 original size:30 final size:30
Alignment explanation
Indices: 54190705--54190761 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
54190695 ACAGTCATGA
* * *
54190705 CACACGGGCGTATGGTTTGCCTGTGTGTAT
1 CACACGGGCGTATGGATTACCCGTGTGTAT
*
54190735 CACACGGGCGTGTGGATTACCCGTGTG
1 CACACGGGCGTATGGATTACCCGTGTG
54190762 GAAGTGTCTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.14, C:0.23, G:0.35, T:0.28
Consensus pattern (30 bp):
CACACGGGCGTATGGATTACCCGTGTGTAT
Found at i:54192591 original size:6 final size:6
Alignment explanation
Indices: 54192568--54192658 Score: 130
Period size: 6 Copynumber: 15.3 Consensus size: 6
54192558 TCAAAATATG
* *
54192568 AAAA-A AAAATA AACATA AAAATA AAAATA AAAATA AACATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
* * *
54192615 AAAATA AAAATA AACATA AAAATA AAAATA AACATA AAGATA AA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AA
54192659 TGAACTCAAT
Statistics
Matches: 77, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
5 4 0.05
6 73 0.95
ACGTcount: A:0.79, C:0.04, G:0.01, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:54192599 original size:24 final size:24
Alignment explanation
Indices: 54192568--54192658 Score: 157
Period size: 24 Copynumber: 3.8 Consensus size: 24
54192558 TCAAAATATG
54192568 AAAA-AAAAATAAACATAAAAATA
1 AAAATAAAAATAAACATAAAAATA
54192591 AAAATAAAAATAAACATAAAAATA
1 AAAATAAAAATAAACATAAAAATA
54192615 AAAATAAAAATAAACATAAAAATA
1 AAAATAAAAATAAACATAAAAATA
* *
54192639 AAAATAAACATAAAGATAAA
1 AAAATAAAAATAAACATAAA
54192659 TGAACTCAAT
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
23 4 0.06
24 61 0.94
ACGTcount: A:0.79, C:0.04, G:0.01, T:0.15
Consensus pattern (24 bp):
AAAATAAAAATAAACATAAAAATA
Found at i:54193983 original size:21 final size:21
Alignment explanation
Indices: 54193949--54194011 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
54193939 ATAAAATAAC
*
54193949 AAAT-AAGAATTAAAGAAAGA
1 AAATAAAGAAATAAAGAAAGA
*
54193969 AAATAAAGAAATAAAGAATGA
1 AAATAAAGAAATAAAGAAAGA
*
54193990 AAATGAAACAAAAATAAAGAAA
1 AAAT--AA-AGAAATAAAGAAA
54194012 AAGTTAGGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 4 0.11
21 18 0.51
23 2 0.06
24 11 0.31
ACGTcount: A:0.73, C:0.02, G:0.13, T:0.13
Consensus pattern (21 bp):
AAATAAAGAAATAAAGAAAGA
Found at i:54206715 original size:26 final size:27
Alignment explanation
Indices: 54206686--54206748 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
54206676 ATTAAATTGT
54206686 ATTAATAATAATTATGA-TAAAATATA
1 ATTAATAATAATTATGATTAAAATATA
* * *
54206712 ATTAA-ATTATTTATTATTAAAATATA
1 ATTAATAATAATTATGATTAAAATATA
*
54206738 TTTAATAATAA
1 ATTAATAATAA
54206749 GCTTATTAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
25 8 0.28
26 18 0.62
27 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
ATTAATAATAATTATGATTAAAATATA
Found at i:54212209 original size:22 final size:24
Alignment explanation
Indices: 54212160--54212237 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 24
54212150 ATTCAATTTG
*
54212160 AATATATAAACTATATTTTAAATATTAA
1 AATATAT-AACT-TA-TATAAAT-TTAA
54212188 AATATTATAA-TTA-A-AAATTTAA
1 AATA-TATAACTTATATAAATTTAA
*
54212210 AATATATAACTTATATATATTTAA
1 AATATATAACTTATATAAATTTAA
54212234 AATA
1 AATA
54212238 AATTTTAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
21 5 0.11
22 11 0.25
23 5 0.11
24 11 0.25
26 2 0.05
27 1 0.02
28 6 0.14
29 3 0.07
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (24 bp):
AATATATAACTTATATAAATTTAA
Found at i:54212495 original size:22 final size:22
Alignment explanation
Indices: 54212464--54212512 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
54212454 AAACATAATA
54212464 AAAAATTTATA-ATGAAATTATTT
1 AAAAATTTATATAT-AAATT-TTT
*
54212487 AAAAA-TTATATATATATTTTT
1 AAAAATTTATATATAAATTTTT
54212508 AAAAA
1 AAAAA
54212513 AAAACCTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 8 0.33
22 9 0.38
23 7 0.29
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AAAAATTTATATATAAATTTTT
Found at i:54213838 original size:15 final size:15
Alignment explanation
Indices: 54213799--54213841 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
54213789 GGTTTTATAT
54213799 TTGATATTTATT-AA
1 TTGATATTTATTAAA
* *
54213813 TGTTATTTTTATTAAA
1 T-TGATATTTATTAAA
54213829 TTGATATTTATTA
1 TTGATATTTATTA
54213842 TGAAATAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 1 0.04
15 19 0.83
16 3 0.13
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (15 bp):
TTGATATTTATTAAA
Found at i:54214222 original size:15 final size:15
Alignment explanation
Indices: 54214183--54214225 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
54214173 GGTTTTATAT
54214183 TTGATATTTATT-AA
1 TTGATATTTATTAAA
* *
54214197 TGTTATTTTTATTAAA
1 T-TGATATTTATTAAA
54214213 TTGATATTTATTA
1 TTGATATTTATTA
54214226 TGAAATAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 1 0.04
15 19 0.83
16 3 0.13
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (15 bp):
TTGATATTTATTAAA
Found at i:54214365 original size:384 final size:384
Alignment explanation
Indices: 54213656--54214423 Score: 1536
Period size: 384 Copynumber: 2.0 Consensus size: 384
54213646 TGTGAAATTT
54213656 TAATTGTAAATTAAAAGAAAAAAAGAGGACCAAAATGGAATTATGCCATTTGTCCTAAGTGAGGC
1 TAATTGTAAATTAAAAGAAAAAAAGAGGACCAAAATGGAATTATGCCATTTGTCCTAAGTGAGGC
54213721 GGCAAATACATAAAAATCAAAATTTTTATGCATAAATATGTATATTAAATTATTATTATTATTAT
66 GGCAAATACATAAAAATCAAAATTTTTATGCATAAATATGTATATTAAATTATTATTATTATTAT
54213786 TATGGTTTTATATTTGATATTTATTAATGTTATTTTTATTAAATTGATATTTATTATGAAATAAA
131 TATGGTTTTATATTTGATATTTATTAATGTTATTTTTATTAAATTGATATTTATTATGAAATAAA
54213851 TTAAAAGTTGACAAATGTATGGTAATAAAATATACATGTGTAATGAATTAAATACATACATGTGT
196 TTAAAAGTTGACAAATGTATGGTAATAAAATATACATGTGTAATGAATTAAATACATACATGTGT
54213916 AATACAATTATATAATTACTTATAATATAAGAATTATTATTATTTTATTTATTATAATATATATA
261 AATACAATTATATAATTACTTATAATATAAGAATTATTATTATTTTATTTATTATAATATATATA
54213981 CATGGTAAAGTAAATGAAATAAAGAAACAAAAGAAAAAGAAAAAGAAAGGAGAAAGAAC
326 CATGGTAAAGTAAATGAAATAAAGAAACAAAAGAAAAAGAAAAAGAAAGGAGAAAGAAC
54214040 TAATTGTAAATTAAAAGAAAAAAAGAGGACCAAAATGGAATTATGCCATTTGTCCTAAGTGAGGC
1 TAATTGTAAATTAAAAGAAAAAAAGAGGACCAAAATGGAATTATGCCATTTGTCCTAAGTGAGGC
54214105 GGCAAATACATAAAAATCAAAATTTTTATGCATAAATATGTATATTAAATTATTATTATTATTAT
66 GGCAAATACATAAAAATCAAAATTTTTATGCATAAATATGTATATTAAATTATTATTATTATTAT
54214170 TATGGTTTTATATTTGATATTTATTAATGTTATTTTTATTAAATTGATATTTATTATGAAATAAA
131 TATGGTTTTATATTTGATATTTATTAATGTTATTTTTATTAAATTGATATTTATTATGAAATAAA
54214235 TTAAAAGTTGACAAATGTATGGTAATAAAATATACATGTGTAATGAATTAAATACATACATGTGT
196 TTAAAAGTTGACAAATGTATGGTAATAAAATATACATGTGTAATGAATTAAATACATACATGTGT
54214300 AATACAATTATATAATTACTTATAATATAAGAATTATTATTATTTTATTTATTATAATATATATA
261 AATACAATTATATAATTACTTATAATATAAGAATTATTATTATTTTATTTATTATAATATATATA
54214365 CATGGTAAAGTAAATGAAATAAAGAAACAAAAGAAAAAGAAAAAGAAAGGAGAAAGAAC
326 CATGGTAAAGTAAATGAAATAAAGAAACAAAAGAAAAAGAAAAAGAAAGGAGAAAGAAC
54214424 CGAGAGCAGG
Statistics
Matches: 384, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
384 384 1.00
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.36
Consensus pattern (384 bp):
TAATTGTAAATTAAAAGAAAAAAAGAGGACCAAAATGGAATTATGCCATTTGTCCTAAGTGAGGC
GGCAAATACATAAAAATCAAAATTTTTATGCATAAATATGTATATTAAATTATTATTATTATTAT
TATGGTTTTATATTTGATATTTATTAATGTTATTTTTATTAAATTGATATTTATTATGAAATAAA
TTAAAAGTTGACAAATGTATGGTAATAAAATATACATGTGTAATGAATTAAATACATACATGTGT
AATACAATTATATAATTACTTATAATATAAGAATTATTATTATTTTATTTATTATAATATATATA
CATGGTAAAGTAAATGAAATAAAGAAACAAAAGAAAAAGAAAAAGAAAGGAGAAAGAAC
Found at i:54214471 original size:19 final size:19
Alignment explanation
Indices: 54214447--54214483 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
54214437 GAAATAAGGG
*
54214447 AAGGAAAGAAGGAAAAAGA
1 AAGGAAAGAAAGAAAAAGA
54214466 AAGGAAAGAAAGAAAAAG
1 AAGGAAAGAAAGAAAAAG
54214484 GGAAAATTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
AAGGAAAGAAAGAAAAAGA
Found at i:54215704 original size:18 final size:18
Alignment explanation
Indices: 54215683--54215722 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
54215673 AACGACTGAA
54215683 ACTGAATAAATGAATATT
1 ACTGAATAAATGAATATT
* * *
54215701 ACTGATTAACTGATTATT
1 ACTGAATAAATGAATATT
54215719 ACTG
1 ACTG
54215723 TTGACTAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (18 bp):
ACTGAATAAATGAATATT
Found at i:54220689 original size:15 final size:15
Alignment explanation
Indices: 54220650--54220692 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
54220640 GGTTTTATAT
54220650 TTGATATTTATT-AA
1 TTGATATTTATTAAA
* *
54220664 TGTTATTTTTATTAAA
1 T-TGATATTTATTAAA
54220680 TTGATATTTATTA
1 TTGATATTTATTA
54220693 TGAAATAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 1 0.04
15 19 0.83
16 3 0.13
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (15 bp):
TTGATATTTATTAAA
Found at i:54221972 original size:6 final size:6
Alignment explanation
Indices: 54221961--54221987 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
54221951 TGTGCACCGC
54221961 TACTGT TACTGT TACTGT TACTGT TAC
1 TACTGT TACTGT TACTGT TACTGT TAC
54221988 CCTTACAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:54227580 original size:46 final size:46
Alignment explanation
Indices: 54227465--54227591 Score: 152
Period size: 46 Copynumber: 2.8 Consensus size: 46
54227455 GATCAGAGGG
*
54227465 TGCCATGGTGTCTTTCAA-TCATGGTCTTATTCA-TTCTCGACTTGA
1 TGCCATAGTGTCTTTCAACT-ATGGTCTTATTCATTTCTCGACTTGA
* * * * * *
54227510 TGCCACAGTGCCTTTCAACCATGGTCTTATTCATTTTTCG-TTGTGT
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCTCGACT-TGA
54227556 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTT
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTT
54227592 GATTCGTGAT
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
45 29 0.42
46 40 0.58
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.44
Consensus pattern (46 bp):
TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCTCGACTTGA
Found at i:54227644 original size:45 final size:45
Alignment explanation
Indices: 54227595--54227768 Score: 152
Period size: 45 Copynumber: 3.9 Consensus size: 45
54227585 TTCATTTGAT
* ** *
54227595 TCGTGATGTCATATTGTCTTTCAG-TGATGGTCTTACTCGATAAAA
1 TCGTGATGCCATAAAGTATTTCAGCT-ATGGTCTTACTCGATAAAA
* * *
54227640 TCGTGATGCCATAAAGTATTTCTGCTATGGTTTTACTCGATAGAA
1 TCGTGATGCCATAAAGTATTTCAGCTATGGTCTTACTCGATAAAA
* * ** * * * *
54227685 TCATGATGCCATAACGCCTTTTAGCTATCGTCTTACTTGATAGAA
1 TCGTGATGCCATAAAGTATTTCAGCTATGGTCTTACTCGATAAAA
* * * * *
54227730 TAGTGATGCCATAACGTCTTTCAACTATGATCTTACTCG
1 TCGTGATGCCATAAAGTATTTCAGCTATGGTCTTACTCG
54227769 TTTCTAGTAT
Statistics
Matches: 104, Mismatches: 24, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
45 103 0.99
46 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (45 bp):
TCGTGATGCCATAAAGTATTTCAGCTATGGTCTTACTCGATAAAA
Found at i:54228196 original size:16 final size:16
Alignment explanation
Indices: 54228158--54228190 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
54228148 CCATTTTGCC
*
54228158 ATTAAA-ATAACATAT
1 ATTAAATATAAAATAT
54228173 ATTAAATATAAAATAT
1 ATTAAATATAAAATAT
54228189 AT
1 AT
54228191 GTAATAACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTAAATATAAAATAT
Found at i:54236794 original size:26 final size:26
Alignment explanation
Indices: 54236765--54236872 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
54236755 TGGTACAAAT
54236765 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
54236791 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
54236817 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
54236843 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
54236869 TGAT
1 TGAT
54236873 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:54239668 original size:22 final size:23
Alignment explanation
Indices: 54239640--54239717 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 23
54239630 TCATAAATAT
*
54239640 TATATTATTAATAAACT-TAT-AA
1 TATATTA-GAATAAACTATATAAA
*
54239662 TATATTAGATTAAACTATATAAA
1 TATATTAGAATAAACTATATAAA
* *
54239685 TATATTTGAAAAAAAAACTATATAAA
1 TATA-TT--AGAATAAACTATATAAA
54239711 TATATTA
1 TATATTA
54239718 TTTATAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
21 7 0.15
22 10 0.22
23 7 0.15
24 2 0.04
25 2 0.04
26 18 0.39
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.40
Consensus pattern (23 bp):
TATATTAGAATAAACTATATAAA
Found at i:54240667 original size:15 final size:16
Alignment explanation
Indices: 54240634--54240671 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
54240624 TATATTTTAA
*
54240634 ATAAATATTAATTACT
1 ATAAAAATTAATTACT
*
54240650 ATAAAAATT-ATTAGT
1 ATAAAAATTAATTACT
54240665 ATAAAAA
1 ATAAAAA
54240672 AATAATTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (16 bp):
ATAAAAATTAATTACT
Found at i:54245519 original size:180 final size:180
Alignment explanation
Indices: 54245217--54245572 Score: 493
Period size: 180 Copynumber: 2.0 Consensus size: 180
54245207 ATGTGAATAG
* * *
54245217 TATAGTTTAAATAATAATAGTGAACTTAGGTTGTAAATAAGAACACTCATGTCAAGAAACTGGCA
1 TATAGTTTAAATAATAATAATGAACTTAGGTAGTAAACAAGAACACTCATGTCAAGAAACTGGCA
* * * ** *
54245282 ATGGATACTCAGAGGGAGGCATTCTTAAATTTAGAATGCCTTTCTATTTCACTTCTAATTACCTG
66 ATAGATACTCAGAGGAAAGCATTCTTAAAGATAGAATACCTTTCTATTTCACTTCTAATTACCTG
*
54245347 CACTGCAACTTACTTGAGATTGTAATGAAGTCCTTCATTTCTTTTTATTT
131 CACTGCAACTTACCTGAGATTGTAATGAAGTCCTTCATTTCTTTTTATTT
* *
54245397 TATAGTTTAAGCT-ATAATAATGAACTTAGGTAGTAACCAAGAA-A-TCCTATGTCAAGAAACTG
1 TATAGTTTAA-ATAATAATAATGAACTTAGGTAGTAAACAAGAACACT-C-ATGTCAAGAAACTG
* ** *
54245459 GCAATAGATATTCAGAGGAAAGCATTCTTAAAGATAGTGTACCTTTCTTTTTCACTTCTAATTAC
63 GCAATAGATACTCAGAGGAAAGCATTCTTAAAGATAGAATACCTTTCTATTTCACTTCTAATTAC
* * *
54245524 CTGCACTGCAACTTACCTGAGATTGTGATGAATTCCTTCTTTTCTTTTT
128 CTGCACTGCAACTTACCTGAGATTGTAATGAAGTCCTTCATTTCTTTTT
54245573 GGTTTATGCT
Statistics
Matches: 154, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
178 1 0.01
179 2 0.01
180 150 0.97
181 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (180 bp):
TATAGTTTAAATAATAATAATGAACTTAGGTAGTAAACAAGAACACTCATGTCAAGAAACTGGCA
ATAGATACTCAGAGGAAAGCATTCTTAAAGATAGAATACCTTTCTATTTCACTTCTAATTACCTG
CACTGCAACTTACCTGAGATTGTAATGAAGTCCTTCATTTCTTTTTATTT
Found at i:54248626 original size:5 final size:5
Alignment explanation
Indices: 54248616--54248642 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
54248606 CACCACCACC
54248616 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
54248643 ACAACTAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:54258005 original size:18 final size:17
Alignment explanation
Indices: 54257975--54258008 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
54257965 AATGACTTAG
54257975 AAAATATAATAAATATA
1 AAAATATAATAAATATA
*
54257992 AAAATTATACTAAATAT
1 AAAA-TATAATAAATAT
54258009 TGTTATATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATATAATAAATATA
Found at i:54259591 original size:19 final size:19
Alignment explanation
Indices: 54259552--54259590 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
54259542 TACTTATAAA
* *
54259552 TTATATTTATTTATATATT
1 TTATATATATATATATATT
54259571 TTATATATATATATAT-TT
1 TTATATATATATATATATT
54259589 TT
1 TT
54259591 TTAAAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATATATATATATATATT
Found at i:54259696 original size:17 final size:17
Alignment explanation
Indices: 54259674--54259708 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
54259664 TTCATTATAT
54259674 TTACATTTTATTACATA
1 TTACATTTTATTACATA
*
54259691 TTACATTTTATTATATA
1 TTACATTTTATTACATA
54259708 T
1 T
54259709 ATTTTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (17 bp):
TTACATTTTATTACATA
Found at i:54259719 original size:17 final size:18
Alignment explanation
Indices: 54259699--54259752 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 18
54259689 TATTACATTT
54259699 TATTA-TATATATTTTTA
1 TATTATTATATATTTTTA
*
54259716 TATTACTTATTATATGGTTTA
1 TATTA-TTA-TATAT-TTTTA
54259737 TATTATTATATATTTT
1 TATTATTATATATTTT
54259753 GGTTATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 5 0.16
18 2 0.06
19 7 0.23
20 8 0.26
21 9 0.29
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (18 bp):
TATTATTATATATTTTTA
Found at i:54263795 original size:15 final size:15
Alignment explanation
Indices: 54263773--54263819 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
54263763 TGTCCTTTTG
54263773 GCAT-TCATGCATTT
1 GCATCTCATGCATTT
54263787 GCATCTCATAGCATTT
1 GCATCTCAT-GCATTT
*
54263803 -CATCGCAT-CATTT
1 GCATCTCATGCATTT
54263816 GCAT
1 GCAT
54263820 TCAAAGTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 5 0.17
14 7 0.24
15 11 0.38
16 6 0.21
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (15 bp):
GCATCTCATGCATTT
Found at i:54270335 original size:17 final size:17
Alignment explanation
Indices: 54270315--54270730 Score: 139
Period size: 17 Copynumber: 23.3 Consensus size: 17
54270305 ACGAAAGTTT
54270315 TTTTTAAAACACGAGAA
1 TTTTTAAAACACGAGAA
54270332 TTTTTGAAAACACGAGAA
1 TTTTT-AAAACACGAGAA
*
54270350 TTTGT-AAACAC--GAA
1 TTTTTAAAACACGAGAA
* *
54270364 TATTTTAGAAAAACGAAAA
1 T-TTTTA-AAACACGAGAA
*
54270383 TTTTTGGAAAAAAACGA-AA
1 TTTTT---AAAACACGAGAA
* *
54270402 TTTTCTACAAACACGACATTTT
1 TTTT-TA-AAACACGAGA---A
* *
54270424 TTTTTGAAACACGGGAA
1 TTTTTAAAACACGAGAA
* * *
54270441 TTTTTAAAACAAGACAT
1 TTTTTAAAACACGAGAA
** ***
54270458 TTTTTCAAAACAAAATTT
1 TTTTT-AAAACACGAGAA
*
54270476 TTTCTTAAAA-A--AAAA
1 TTT-TTAAAACACGAGAA
* *
54270491 ATTTT-AAATACGAGAA
1 TTTTTAAAACACGAGAA
*
54270507 TTTTTAAAACACGAAAA
1 TTTTTAAAACACGAGAA
*
54270524 TTTTTAAAACACGGAAATA
1 TTTTTAAAACAC-GAGA-A
*
54270543 TTTTTTTTTAAAACACGAAAA
1 ----TTTTTAAAACACGAGAA
* *
54270564 TTTTTTTTTTGAAAACAAGAAAA
1 -----TTTTT-AAAACACGAGAA
* *
54270587 TTTTTGAAACACTAGAA
1 TTTTTAAAACACGAGAA
*
54270604 TTTTGAAAACACGA-AGA
1 TTTTTAAAACACGAGA-A
* *
54270621 TTTTTGAAACATGAGAA
1 TTTTTAAAACACGAGAA
*
54270638 TTTTTAAAAGCACGAGGA
1 TTTTTAAAA-CACGAGAA
* * *
54270656 TTATTGAAAGCACGAAAA
1 TT-TTTAAAACACGAGAA
* * *
54270674 TTTGTAAAAAACGACAA
1 TTTTTAAAACACGAGAA
* *
54270691 TTTTTGAAATACGAGAAA
1 TTTTTAAAACACGAG-AA
* * *
54270709 TTTTTTAAACGCGAAAA
1 TTTTTAAAACACGAGAA
54270726 TTTTT
1 TTTTT
54270731 TTCAAACACG
Statistics
Matches: 308, Mismatches: 57, Indels: 68
0.71 0.13 0.16
Matches are distributed among these distances:
13 3 0.01
14 7 0.02
15 6 0.02
16 14 0.05
17 118 0.38
18 82 0.27
19 18 0.06
20 17 0.06
21 3 0.01
22 17 0.06
23 23 0.07
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (17 bp):
TTTTTAAAACACGAGAA
Found at i:54270475 original size:16 final size:18
Alignment explanation
Indices: 54270441--54270479 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
54270431 AACACGGGAA
54270441 TTTTT-AAAACAAGACAT
1 TTTTTCAAAACAAGACAT
54270458 TTTTTCAAAACAA-A-AT
1 TTTTTCAAAACAAGACAT
54270474 TTTTTC
1 TTTTTC
54270480 TTAAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.38
17 6 0.29
18 7 0.33
ACGTcount: A:0.41, C:0.13, G:0.03, T:0.44
Consensus pattern (18 bp):
TTTTTCAAAACAAGACAT
Found at i:54270513 original size:16 final size:16
Alignment explanation
Indices: 54270487--54270764 Score: 88
Period size: 17 Copynumber: 15.4 Consensus size: 16
54270477 TTCTTAAAAA
* *
54270487 AAAAATTTTAAATACG
1 AAAATTTTTAAACACG
*
54270503 AGAATTTTTAAAACACG
1 AAAATTTTT-AAACACG
54270520 AAAATTTTTAAAACACGG
1 AAAATTTTT-AAACAC-G
54270538 AAATATTTTTTTTTAAAACACG
1 AAA-A----TTTTT-AAACACG
*
54270560 AAAATTTTTTTTTTGAAAACAAG
1 AAAA-----TTTTT--AAACACG
*
54270583 AAAATTTTTGAAACACT
1 AAAATTTTT-AAACACG
* *
54270600 AGAATTTTGAAAACACG
1 AAAATTTT-TAAACACG
* *
54270617 AAGATTTTTGAAACATG
1 AAAATTTTT-AAACACG
*
54270634 AGAATTTTTAAAAGCACG
1 AAAATTTTT-AAA-CACG
** *
54270652 AGGATTATTGAAAGCACG
1 AAAATT-TTTAAA-CACG
* *
54270670 AAAATTTGTAAAAAACG
1 AAAATTT-TTAAACACG
* *
54270687 ACAATTTTTGAAATACG
1 AAAATTTTT-AAACACG
*
54270704 AGAAATTTTTTAAACGCG
1 A-AAA-TTTTTAAACACG
54270722 AAAATTTTTTTCAAACACG
1 AAAA--TTTTT-AAACACG
* *
54270741 AAAACTTTTGAAAACGCG
1 AAAA-TTTT-TAAACACG
54270759 AAAATT
1 AAAATT
54270765 CGAAAATTTC
Statistics
Matches: 207, Mismatches: 35, Indels: 39
0.74 0.12 0.14
Matches are distributed among these distances:
16 8 0.04
17 83 0.40
18 61 0.29
19 18 0.09
21 1 0.00
22 13 0.06
23 23 0.11
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (16 bp):
AAAATTTTTAAACACG
Found at i:54270551 original size:23 final size:22
Alignment explanation
Indices: 54270524--54270591 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 22
54270514 AACACGAAAA
*
54270524 TTTTTAAAACACGGAAATATTTT
1 TTTTTAAAACACGAAAAT-TTTT
54270547 TTTTTAAAACACGAAAATTTTT
1 TTTTTAAAACACGAAAATTTTT
*
54270569 TTTTTGAAAACAAGAAAATTTTT
1 TTTTT-AAAACACGAAAATTTTT
54270592 GAAACACTAG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
22 9 0.21
23 33 0.79
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (22 bp):
TTTTTAAAACACGAAAATTTTT
Found at i:54270562 original size:22 final size:21
Alignment explanation
Indices: 54270507--54270591 Score: 97
Period size: 23 Copynumber: 4.0 Consensus size: 21
54270497 AATACGAGAA
54270507 TTTTTAAAACACGAAAA----
1 TTTTTAAAACACGAAAATTTT
54270524 TTTTTAAAACACGGAAATATTTT
1 TTTTTAAAACAC-GAAA-ATTTT
54270547 TTTTTAAAACACGAAAATTTTT
1 TTTTTAAAACACGAAAA-TTTT
*
54270569 TTTTTGAAAACAAGAAAATTTT
1 TTTTT-AAAACACGAAAATTTT
54270591 T
1 T
54270592 GAAACACTAG
Statistics
Matches: 59, Mismatches: 1, Indels: 11
0.83 0.01 0.15
Matches are distributed among these distances:
17 12 0.20
18 4 0.07
19 1 0.02
21 1 0.02
22 18 0.31
23 23 0.39
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (21 bp):
TTTTTAAAACACGAAAATTTT
Found at i:54270698 original size:35 final size:32
Alignment explanation
Indices: 54270570--54270730 Score: 115
Period size: 35 Copynumber: 4.6 Consensus size: 32
54270560 AAAATTTTTT
* *
54270570 TTTTGAAAACAAGAAAATTTTTGAAACACTAGAA
1 TTTT-AAAACACG-AAATTTTTGAAACACGAGAA
*
54270604 TTTTGAAAACACGAAGATTTTTGAAACATGAGAA
1 TTTT-AAAACACGAA-ATTTTTGAAACACGAGAA
* * *
54270638 TTTTTAAAAGCACGAGGATTATTGAAAGCACGAAAA
1 -TTTTAAAA-CACGA-AATTTTTGAAA-CACGAGAA
* *
54270674 TTTGTAAAAAACGACAATTTTTGAAATACGAGAAA
1 TTT-TAAAACACGA-AATTTTTGAAACACGAG-AA
* *
54270709 TTTTTTAAACGCGAAAATTTTT
1 -TTTTAAAACACG-AAATTTTT
54270731 TTCAAACACG
Statistics
Matches: 102, Mismatches: 16, Indels: 17
0.76 0.12 0.13
Matches are distributed among these distances:
33 2 0.02
34 36 0.35
35 49 0.48
36 15 0.15
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.31
Consensus pattern (32 bp):
TTTTAAAACACGAAATTTTTGAAACACGAGAA
Found at i:54270760 original size:18 final size:19
Alignment explanation
Indices: 54270715--54270763 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
54270705 GAAATTTTTT
* **
54270715 AAACGCGAAAATTTTTTTC
1 AAACGCGAAAATCTTTTGA
*
54270734 AAACACGAAAA-CTTTTGA
1 AAACGCGAAAATCTTTTGA
54270752 AAACGCGAAAAT
1 AAACGCGAAAAT
54270764 TCGAAAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.24
Consensus pattern (19 bp):
AAACGCGAAAATCTTTTGA
Done.