Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 15 of 345
Found at i:5100788 original size:18 final size:19
Alignment explanation
Indices: 5100767--5100807 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
5100757 AATGAAATGA
5100767 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
5100785 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
5100804 GAAA
1 GAAA
5100808 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:5101973 original size:15 final size:14
Alignment explanation
Indices: 5101949--5102019 Score: 54
Period size: 14 Copynumber: 4.9 Consensus size: 14
5101939 TCTAATACTA
*
5101949 TTATTCATCTAATTT
1 TTATTTATCT-ATTT
5101964 TTATTTATCTATTT
1 TTATTTATCTATTT
* * *
5101978 ATATTTCTACTATTA
1 TTATTTAT-CTATTT
5101993 TTATATT-TCTATTT
1 TTAT-TTATCTATTT
* *
5102007 CTATTTATATATT
1 TTATTTATCTATT
5102020 AATATTATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
13 2 0.04
14 23 0.51
15 18 0.40
16 2 0.04
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (14 bp):
TTATTTATCTATTT
Found at i:5101991 original size:23 final size:23
Alignment explanation
Indices: 5101973--5102025 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
5101963 TTTATTTATC
5101973 TATTTATATTTCTACTATTATTA
1 TATTTATATTTCTACTATTATTA
*
5101996 TATTTCTATTTCTA-T-TTA-TA
1 TATTTATATTTCTACTATTATTA
*
5102016 TATTAATATT
1 TATTTATATT
5102026 ATTTTCATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 10 0.37
21 3 0.11
22 1 0.04
23 13 0.48
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (23 bp):
TATTTATATTTCTACTATTATTA
Found at i:5102028 original size:29 final size:29
Alignment explanation
Indices: 5101971--5102029 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
5101961 TTTTTATTTA
* *
5101971 TCTATTTATATTTCTACTATTATTATATT
1 TCTATTTATATTTATACTATTAATATATT
*
5102000 TCTATTTCTATTTATA-TATTAATATTATT
1 TCTATTTATATTTATACTATTAATA-TATT
5102029 T
1 T
5102030 TCATTATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (29 bp):
TCTATTTATATTTATACTATTAATATATT
Found at i:5102124 original size:3 final size:3
Alignment explanation
Indices: 5102118--5102199 Score: 112
Period size: 3 Copynumber: 27.7 Consensus size: 3
5102108 TAAACTTTTT
* * ** *
5102118 TTA TTA -TA TTA TTA TTA ATA TCA TCG TCA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5102165 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5102200 TAACTATTTT
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
2 2 0.03
3 70 0.97
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:5102292 original size:28 final size:28
Alignment explanation
Indices: 5102261--5102318 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
5102251 TTTTAATTAA
* * *
5102261 ACTT-TTATTAGTTCTTATTTTTTTTTTT
1 ACTTATTATTA-TTATTATTATTTTGTTT
*
5102289 ACTTATTTTTATTATTATTATTTTGTTT
1 ACTTATTATTATTATTATTATTTTGTTT
5102317 AC
1 AC
5102319 AATCGGCTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.19, C:0.07, G:0.03, T:0.71
Consensus pattern (28 bp):
ACTTATTATTATTATTATTATTTTGTTT
Found at i:5102293 original size:16 final size:16
Alignment explanation
Indices: 5102263--5102312 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
5102253 TTAATTAAAC
5102263 TTTTATTAGTT-CTTAT
1 TTTTATTA-TTACTTAT
* *
5102279 TTTTTTTTTTACTTAT
1 TTTTATTATTACTTAT
5102295 TTTTATTATTA-TTAT
1 TTTTATTATTACTTAT
5102310 TTT
1 TTT
5102313 GTTTACAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 9 0.31
16 20 0.69
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (16 bp):
TTTTATTATTACTTAT
Found at i:5103300 original size:26 final size:24
Alignment explanation
Indices: 5103257--5103305 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
5103247 CTTGTTTTAA
*
5103257 TATTTGTTTTTATGTTTTTAAATG
1 TATTTGTTTTTATATTTTTAAATG
5103281 TATTTGATTTATTATATTTTTAAAT
1 TATTTG-TTT-TTATATTTTTAAAT
5103306 TTTTTATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.27
25 3 0.14
26 13 0.59
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (24 bp):
TATTTGTTTTTATATTTTTAAATG
Found at i:5104161 original size:22 final size:21
Alignment explanation
Indices: 5104122--5104162 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5104112 TGTTTATCAT
* *
5104122 TTTTCTTTCAAATTTCTCTTG
1 TTTTCTCTCAAATCTCTCTTG
5104143 TTTTCTCTCATAATCTCTCT
1 TTTTCTCTCA-AATCTCTCT
5104163 AAAATTCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.15, C:0.24, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTCTCTCAAATCTCTCTTG
Found at i:5107238 original size:14 final size:15
Alignment explanation
Indices: 5107198--5107238 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
5107188 TTCTCAAACA
5107198 CTAAACTCAT-AATC
1 CTAAACTCATAAATC
* *
5107212 CCAAACTCTTAAATC
1 CTAAACTCATAAATC
5107227 CTAAA-TCATAAA
1 CTAAACTCATAAA
5107239 CTCGTAAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (15 bp):
CTAAACTCATAAATC
Found at i:5107345 original size:21 final size:20
Alignment explanation
Indices: 5107319--5107365 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
5107309 CTTGAACCTC
*
5107319 AAGGTTCAGGGTTCAAGGTTT
1 AAGGTTCAGGATTCAA-GTTT
*
5107340 AAGGTTTAGGATTCAAGTTT
1 AAGGTTCAGGATTCAAGTTT
5107360 AAGGTT
1 AAGGTT
5107366 TGAGGCTCGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.28, C:0.06, G:0.30, T:0.36
Consensus pattern (20 bp):
AAGGTTCAGGATTCAAGTTT
Found at i:5113240 original size:40 final size:35
Alignment explanation
Indices: 5113140--5113271 Score: 122
Period size: 35 Copynumber: 3.6 Consensus size: 35
5113130 TTCTCATTGA
* * * *
5113140 AATACCATACCTACATTTTACAACACGGTATGGGA-
1 AATACCATACCTACGTTTCACAACTCAGTAT-GGAT
* ** *
5113175 AATGCCATACCTACGTTTCTTAACTCATTATAGATTTGAT
1 AATACCATACCTACGTTTCACAACTCAGTAT-G----GAT
5113215 AATACCATACCTACGTTTCACAACTCAGTATGGAT
1 AATACCATACCTACGTTTCACAACTCAGTATGGAT
*
5113250 GATACCATACCTACGTTTCACA
1 AATACCATACCTACGTTTCACA
5113272 CTTTGCCATG
Statistics
Matches: 78, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
35 48 0.62
39 3 0.04
40 27 0.35
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACGTTTCACAACTCAGTATGGAT
Found at i:5120173 original size:12 final size:14
Alignment explanation
Indices: 5120133--5120170 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
5120123 TACAAATTAG
5120133 AAAT-TTTATTTAA
1 AAATATTTATTTAA
5120146 AAATATATTATTTAA
1 AAATAT-TTATTTAA
5120161 AAA-ATTTATT
1 AAATATTTATT
5120171 AAATGAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.39
14 3 0.13
15 11 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAATATTTATTTAA
Found at i:5125892 original size:46 final size:46
Alignment explanation
Indices: 5125799--5126009 Score: 216
Period size: 46 Copynumber: 4.6 Consensus size: 46
5125789 CCGTGCTGAC
* * *
5125799 GCATGT-CCATACATGTCTTACACTAGC-A-CATCTCGTA-GCCGAC
1 GCATGTCCCAGACATGTCTTACACTGGCTATCATCTCG-AGGCCGAT
*
5125842 GCATGTCCCAGACATGTCTGACACTGGCTATCATCTCGAGGCCGAT
1 GCATGTCCCAGACATGTCTTACACTGGCTATCATCTCGAGGCCGAT
* * *
5125888 GCATGTCCCAGACATGTCTTACACTGGCTCTCATACT-GTGGCTGAT
1 GCATGTCCCAGACATGTCTTACACTGGCTATCAT-CTCGAGGCCGAT
* ** * * *
5125934 GCATGTCCCAGACATGTCTTACACTAGCCCTCGTCTCAATGCCGAT
1 GCATGTCCCAGACATGTCTTACACTGGCTATCATCTCGAGGCCGAT
* *
5125980 GCCATGTCTCATACATGGTCTTACACTGGC
1 G-CATGTCCCAGACAT-GTCTTACACTGGC
5126010 ACACAAATCT
Statistics
Matches: 142, Mismatches: 18, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
43 6 0.04
44 18 0.13
45 4 0.03
46 88 0.62
47 14 0.10
48 12 0.08
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (46 bp):
GCATGTCCCAGACATGTCTTACACTGGCTATCATCTCGAGGCCGAT
Found at i:5129847 original size:20 final size:19
Alignment explanation
Indices: 5129806--5129858 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
5129796 TTTTAAAACT
*
5129806 TTTTAATATATTTTTTACAA
1 TTTTAATA-ATTTTTAACAA
*
5129826 TTTTAATAATTTTGTAATAA
1 TTTTAATAATTTT-TAACAA
*
5129846 TTTCAACTAATTT
1 TTTTAA-TAATTT
5129859 CTTTGCAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 5 0.18
20 17 0.61
21 6 0.21
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTTAATAATTTTTAACAA
Found at i:5129928 original size:19 final size:19
Alignment explanation
Indices: 5129904--5129941 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5129894 TTTTTCTAGA
5129904 TTTTTT-AAATAATTTATAT
1 TTTTTTCAAA-AATTTATAT
*
5129923 TTTTTTCTAAAATTTATAT
1 TTTTTTCAAAAATTTATAT
5129942 ATATTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTTTCAAAAATTTATAT
Found at i:5159919 original size:50 final size:50
Alignment explanation
Indices: 5159841--5160476 Score: 503
Period size: 50 Copynumber: 12.7 Consensus size: 50
5159831 ATCCATTATG
* * * *
5159841 AGTCATGTGTGTAGTACTAAGTGCAGGCTACTACATGTATCAAATGGTTA
1 AGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATTGTTA
* * * *
5159891 AGTCACGTGTGTAGTACTAACTGTAGGCTACTACGTGTACCAGATTGATA
1 AGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATTGTTA
* ** * * * * * * *
5159941 GGTTGCATGTGTAATACTAAGTGCAGGCTACTATGCGTACCCG-TTAACTT-
1 AGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATT--GTTA
* * *
5159991 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAAATGGTTA
1 AG-TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATTGTTA
* * * *
5160042 AGTCACATGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATTGATA
1 AGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATTGTTA
* * * * ** * * *
5160092 GGTCACATGTGTAGTACTAAGTGCAGGCTATTATGCATACCCG-TTAACTT-
1 AGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATT--GTTA
* * * *
5160142 TGATCACGTGTGTAATACAAAGTGCAGGCTACTACGTGTATCAGATGGTTA
1 AG-TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATTGTTA
* * * * * *
5160193 AGTCACGTGTATAGTACTAATTGTAGGCTACTACGTGTACCAGATTGATG
1 AGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATTGTTA
* ** * * ** * * *
5160243 GGTTGCATGTGTAGTACTAAGTGCAGGCTACTATGCATACCCG-TTAACTT-
1 AGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATT--GTTA
* * * *
5160293 TGATCACGTGTGTGGTACTAAGTGCAAGCTACTACGTGTATCAGATGGTTA
1 AG-TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATTGTTA
* * * *
5160344 AGTCACGTATGTAGTACTAAGTGCAAGCTACTACGTGTA-CTATATTGATA
1 AGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATC-AGATTGTTA
* ** * * *
5160394 GGTCATATGTGTAGTACTAAGTGCGGGCTACTACGTGTATTAGATTGATA
1 AGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATTGTTA
* *
5160444 GGTCACATGTGTAGTACTAAGTGCAGGCTACTA
1 AGTCACGTGTGTAGTACTAAGTGCAGGCTACTA
5160477 TGCGTACCAG
Statistics
Matches: 457, Mismatches: 112, Indels: 34
0.76 0.19 0.06
Matches are distributed among these distances:
49 7 0.02
50 346 0.76
51 101 0.22
52 3 0.01
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (50 bp):
AGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATTGTTA
Found at i:5160121 original size:151 final size:151
Alignment explanation
Indices: 5159847--5160426 Score: 899
Period size: 151 Copynumber: 3.8 Consensus size: 151
5159837 TATGAGTCAT
* *
5159847 GTGTGTAGTACTAAGTGCAGGCTACTACATGTATCAAATGGTTAAGTCACGTGTGTAGTACTAAC
1 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAAATGGTTAAGTCACGTGTGTAGTACTAAG
* ** *
5159912 TGTAGGCTACTACGTGTACCAGATTGATAGGTTGCATGTGTAATACTAAGTGCAGGCTACTATGC
66 TGCAGGCTACTACGTGTACCAGATTGATAGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGC
* *
5159977 GTACCCGTTAACTTCGATCAC
131 ATACCCGTTAACTTTGATCAC
*
5159998 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAAATGGTTAAGTCACATGTGTAGTACTAAG
1 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAAATGGTTAAGTCACGTGTGTAGTACTAAG
* *
5160063 TGCAGGCTACTACATGTACCAGATTGATAGGTCACATGTGTAGTACTAAGTGCAGGCTATTATGC
66 TGCAGGCTACTACGTGTACCAGATTGATAGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGC
5160128 ATACCCGTTAACTTTGATCAC
131 ATACCCGTTAACTTTGATCAC
* * * * *
5160149 GTGTGTAATACAAAGTGCAGGCTACTACGTGTATCAGATGGTTAAGTCACGTGTATAGTACTAAT
1 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAAATGGTTAAGTCACGTGTGTAGTACTAAG
* * **
5160214 TGTAGGCTACTACGTGTACCAGATTGATGGGTTGCATGTGTAGTACTAAGTGCAGGCTACTATGC
66 TGCAGGCTACTACGTGTACCAGATTGATAGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGC
5160279 ATACCCGTTAACTTTGATCAC
131 ATACCCGTTAACTTTGATCAC
* * * *
5160300 GTGTGTGGTACTAAGTGCAAGCTACTACGTGTATCAGATGGTTAAGTCACGTATGTAGTACTAAG
1 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAAATGGTTAAGTCACGTGTGTAGTACTAAG
* * * * *
5160365 TGCAAGCTACTACGTGTACTATATTGATAGGTCATATGTGTAGTACTAAGTGCGGGCTACTA
66 TGCAGGCTACTACGTGTACCAGATTGATAGGTCACATGTGTAGTACTAAGTGCAGGCTACTA
5160427 CGTGTATTAG
Statistics
Matches: 390, Mismatches: 39, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
151 390 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (151 bp):
GTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAAATGGTTAAGTCACGTGTGTAGTACTAAG
TGCAGGCTACTACGTGTACCAGATTGATAGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGC
ATACCCGTTAACTTTGATCAC
Found at i:5160201 original size:201 final size:200
Alignment explanation
Indices: 5159994--5160476 Score: 508
Period size: 201 Copynumber: 2.4 Consensus size: 200
5159984 TTAACTTCGA
* * * *
5159994 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAAATGGTTAAGTCACATGTGTAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATTGATAGGTCACATGTGTAGTAC
* * *
5160059 TAAGTGCAGGCTACTACATG-TACCAGATTGA-TAGGTCACATGTGTAGTACTAAGTGCAGGCTA
66 TAAGTGCAGGCTACTA-ATGATACCAG-TTAACTAGATCACATGTGTAGTACTAAGTGCAAGCTA
* * * * * * *
5160122 TTATGCATACCCGTTAACTTTGA-TCACGTGTGTAATACAAAGTGCAGGCTACTACGTGTA-TCA
129 CTACGCATACCAG--AACGTTAAGTCACGTATGTAATACAAAGTGCAAGCTACTACGTGTACT-A
*
5160185 GATGGTTAAG
191 GATGGATAAG
* * * * * **
5160195 TCACGTGTATAGTACTAATTGTAGGCTACTACGTGTACCAGATTGATGGGTTGCATGTGTAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATTGATAGGTCACATGTGTAGTAC
* * * *
5160260 TAAGTGCAGGCTACT-ATGCATACCCGTTAACTTTGATCACGTGTGTGGTACTAAGTGCAAGCTA
66 TAAGTGCAGGCTACTAATG-ATACCAGTTAAC-TAGATCACATGTGTAGTACTAAGTGCAAGCTA
** * ** * * *
5160324 CTACGTGTATCAGATGGTTAAGTCACGTATGTAGTACTAAGTGCAAGCTACTACGTGTACTATAT
129 CTACGCATACCAGAACGTTAAGTCACGTATGTAATACAAAGTGCAAGCTACTACGTGTACTAGAT
* *
5160389 TGATAGG
194 GGATAAG
** * *
5160396 TCATATGTGTAGTACTAAGTGCGGGCTACTACGTGTATTAGATTGATAGGTCACATGTGTAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATTGATAGGTCACATGTGTAGTAC
5160461 TAAGTGCAGGCTACTA
66 TAAGTGCAGGCTACTA
5160477 TGCGTACCAG
Statistics
Matches: 228, Mismatches: 47, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
199 3 0.01
200 7 0.03
201 183 0.80
202 35 0.15
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (200 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATTGATAGGTCACATGTGTAGTAC
TAAGTGCAGGCTACTAATGATACCAGTTAACTAGATCACATGTGTAGTACTAAGTGCAAGCTACT
ACGCATACCAGAACGTTAAGTCACGTATGTAATACAAAGTGCAAGCTACTACGTGTACTAGATGG
ATAAG
Found at i:5160707 original size:16 final size:16
Alignment explanation
Indices: 5160686--5160717 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5160676 AAAATGGAGT
5160686 AAGTGAAATTATGTAA
1 AAGTGAAATTATGTAA
*
5160702 AAGTGAAATTTTGTAA
1 AAGTGAAATTATGTAA
5160718 TAAAATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (16 bp):
AAGTGAAATTATGTAA
Found at i:5165376 original size:6 final size:6
Alignment explanation
Indices: 5165358--5165455 Score: 115
Period size: 6 Copynumber: 16.3 Consensus size: 6
5165348 ATATGAAAAC
* * * * *
5165358 AAAATA AACATA AAAATA AAAATA AACATA AAAATA AACATA AAGAGA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
* * * *
5165406 AAAATA AAAATA AAAATA AACATA AAAATA AATATA AATATA AAGATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
5165454 AA
1 AA
5165456 TGGATTCAAT
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 79 1.00
ACGTcount: A:0.76, C:0.04, G:0.03, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:5166776 original size:27 final size:25
Alignment explanation
Indices: 5166713--5166778 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 25
5166703 CTTATTATTT
5166713 AAGAAATAATAATTATAATAAAAAA
1 AAGAAATAATAATTATAATAAAAAA
* *
5166738 ATATAATCTAATAA-TATAAATTAAAATAA
1 A-AGAA-ATAATAATTAT-AA-TAAAA-AA
5166767 AAGAAATAATAA
1 AAGAAATAATAA
5166779 AAAGAATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
25 1 0.03
26 6 0.19
27 14 0.44
28 8 0.25
29 3 0.09
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (25 bp):
AAGAAATAATAATTATAATAAAAAA
Found at i:5166843 original size:17 final size:18
Alignment explanation
Indices: 5166778--5166859 Score: 57
Period size: 17 Copynumber: 4.7 Consensus size: 18
5166768 AGAAATAATA
5166778 AAAAGAATAAAGAAA-CA-
1 AAAAGAA-AAAGAAAGCAG
5166795 ATAAAGAAAAAGAACAG-AG
1 A-AAAGAAAAAGAA-AGCAG
* * * *
5166814 AAATG-GAACGAAATCAG
1 AAAAGAAAAAGAAAGCAG
*
5166831 -AAAGAAAAAGAAAGGAG
1 AAAAGAAAAAGAAAGCAG
5166848 AAAAGAAAAAGA
1 AAAAGAAAAAGA
5166860 GAAAAATTAG
Statistics
Matches: 49, Mismatches: 9, Indels: 13
0.69 0.13 0.18
Matches are distributed among these distances:
16 4 0.08
17 22 0.45
18 22 0.45
19 1 0.02
ACGTcount: A:0.70, C:0.05, G:0.21, T:0.05
Consensus pattern (18 bp):
AAAAGAAAAAGAAAGCAG
Found at i:5167763 original size:6 final size:6
Alignment explanation
Indices: 5167741--5167775 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
5167731 TCTATGTACC
* *
5167741 GTTACT GCTATT GTTACT GTTACT GTTACT GTTAC
1 GTTACT GTTACT GTTACT GTTACT GTTACT GTTAC
5167776 GGTGTATTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (6 bp):
GTTACT
Found at i:5169666 original size:21 final size:23
Alignment explanation
Indices: 5169640--5169692 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 23
5169630 AAATAATAAT
*
5169640 TAAAGAAAGAAAAT-AA-AGAAA
1 TAAAGAAAGAAAATAAACAAAAA
*
5169661 TAAAGAATGAAAATGAAACAAAAA
1 TAAAGAAAGAAAAT-AAACAAAAA
5169685 TAAAGAAA
1 TAAAGAAA
5169693 AAGTTAAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 13 0.50
23 2 0.08
24 11 0.42
ACGTcount: A:0.74, C:0.02, G:0.13, T:0.11
Consensus pattern (23 bp):
TAAAGAAAGAAAATAAACAAAAA
Found at i:5175255 original size:25 final size:25
Alignment explanation
Indices: 5175213--5175316 Score: 86
Period size: 25 Copynumber: 4.2 Consensus size: 25
5175203 ACATGTAAAT
* * *
5175213 GGGAAGCTCTTCTTAGCCATATAAC
1 GGGAAGCTCATATGAGCCATATAAC
*
5175238 GGGAAGCTCATATGAGCCATGTAAC
1 GGGAAGCTCATATGAGCCATATAAC
** * *
5175263 GGGAAGCTCCGAAGAGCCAT-TAAT
1 GGGAAGCTCATATGAGCCATATAAC
* * * *
5175287 GGGAAGATCACACGAGCCA-ATATC
1 GGGAAGCTCATATGAGCCATATAAC
5175311 GGGAAG
1 GGGAAG
5175317 GTTCAAGCGA
Statistics
Matches: 64, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
24 26 0.41
25 38 0.59
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.18
Consensus pattern (25 bp):
GGGAAGCTCATATGAGCCATATAAC
Found at i:5175303 original size:24 final size:25
Alignment explanation
Indices: 5175227--5175316 Score: 87
Period size: 25 Copynumber: 3.7 Consensus size: 25
5175217 AGCTCTTCTT
* *
5175227 AGCCATATAACGGGAAGCTCATATG
1 AGCCATATAACGGGAAGCTCACAAG
*
5175252 AGCCATGTAACGGGAAGCTC-CGAAG
1 AGCCATATAACGGGAAGCTCAC-AAG
* * *
5175277 AGCCAT-TAATGGGAAGATCACACG
1 AGCCATATAACGGGAAGCTCACAAG
*
5175301 AGCCA-ATATCGGGAAG
1 AGCCATATAACGGGAAG
5175317 GTTCAAGCGA
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
24 26 0.48
25 28 0.52
ACGTcount: A:0.36, C:0.21, G:0.28, T:0.16
Consensus pattern (25 bp):
AGCCATATAACGGGAAGCTCACAAG
Found at i:5179697 original size:51 final size:51
Alignment explanation
Indices: 5179626--5179747 Score: 217
Period size: 51 Copynumber: 2.4 Consensus size: 51
5179616 CTGATCACAT
5179626 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
*
5179677 TTATCACTTGTCACTGATCAGATAAGTGTAGCTACAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
* *
5179728 TTGTCACTTGTCACTCATCA
1 TTATCACTTGTCACTGATCA
5179748 CTGATCAATA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 68 1.00
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
Found at i:5187378 original size:44 final size:45
Alignment explanation
Indices: 5187288--5187416 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
5187278 GACAGAACGA
*
5187288 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
5187334 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
5187378 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
5187417 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:5194759 original size:44 final size:45
Alignment explanation
Indices: 5194669--5194797 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
5194659 GACAGAACGA
*
5194669 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
5194715 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
5194759 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
5194798 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:5196386 original size:51 final size:51
Alignment explanation
Indices: 5196315--5196436 Score: 217
Period size: 51 Copynumber: 2.4 Consensus size: 51
5196305 CTGATCACAT
5196315 TTATCACTTGTCACTGATCAGATAAATGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAATGTAGCTAAAGCTACCACTTATCAC
*
5196366 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAATGTAGCTAAAGCTACCACTTATCAC
* *
5196417 TTGTCACTTGTCACTTATCA
1 TTATCACTTGTCACTGATCA
5196437 CTGATCACAT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 68 1.00
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAATGTAGCTAAAGCTACCACTTATCAC
Found at i:5196418 original size:58 final size:58
Alignment explanation
Indices: 5196356--5196487 Score: 192
Period size: 58 Copynumber: 2.3 Consensus size: 58
5196346 CTAAAGCTAC
* * *
5196356 CACTTATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTGTCACTTATCACTTATCACTGATCACATAAGTGTAGCTAAAGCTACCACTTAT
* * * *
5196414 CACTTGTCACTTGTCACTTATCACTGATCACATAAGTGTAGCTGAGGCTACTACTTAT
1 CACTTGTCACTTATCACTTATCACTGATCACATAAGTGTAGCTAAAGCTACCACTTAT
*
5196472 CACTTGTCACTGATCA
1 CACTTGTCACTTATCA
5196488 GAAGTACTCA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 65 1.00
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (58 bp):
CACTTGTCACTTATCACTTATCACTGATCACATAAGTGTAGCTAAAGCTACCACTTAT
Found at i:5196475 original size:51 final size:51
Alignment explanation
Indices: 5196318--5196487 Score: 187
Period size: 51 Copynumber: 3.2 Consensus size: 51
5196308 ATCACATTTA
* * * *
5196318 TCACTTGTCACTGATCAGATAAATGTAGCTAAAGCTACCACTTATCACTTA
1 TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACTACTTATCACTTG
* *
5196369 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTG
1 TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCT---AC---T-ACTTATCACTTG
* * *
5196427 TCACTTATCACTGATCACATAAGTGTAGCTGAGGCTACTACTTATCACTTG
1 TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACTACTTATCACTTG
*
5196478 TCACTGATCA
1 TCACTTATCA
5196488 GAAGTACTCA
Statistics
Matches: 102, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
51 55 0.54
52 1 0.01
54 2 0.02
55 2 0.02
58 42 0.41
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.32
Consensus pattern (51 bp):
TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACTACTTATCACTTG
Found at i:5202076 original size:29 final size:29
Alignment explanation
Indices: 5202036--5202095 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
5202026 AAAAAAGTTA
5202036 AAAATATTTTTTTAATTTTTTATTCTTTT
1 AAAATATTTTTTTAATTTTTTATTCTTTT
5202065 AAAATATTTTTTTAATTTTTTATTCTTTT
1 AAAATATTTTTTTAATTTTTTATTCTTTT
5202094 AA
1 AA
5202096 CATTATTCGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (29 bp):
AAAATATTTTTTTAATTTTTTATTCTTTT
Found at i:5206710 original size:11 final size:11
Alignment explanation
Indices: 5206694--5206724 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
5206684 TTTTAAATGA
5206694 TATTTTATTAT
1 TATTTTATTAT
5206705 TATTTTATTAT
1 TATTTTATTAT
5206716 TATTTTATT
1 TATTTTATT
5206725 TAGTATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:5208930 original size:46 final size:46
Alignment explanation
Indices: 5208869--5209153 Score: 306
Period size: 46 Copynumber: 6.2 Consensus size: 46
5208859 ATGAAATGTG
* * *
5208869 TAAGACTATGGTTGAAAGATACCATGGCAGCGTGACATAAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATAAAATGAA
* * *
5208915 TAAGACCATGATTGAAAGATACCATGGCAATATGACGTGAAAA-GAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAT-AAAATGAA
* ***
5208961 TAAGACCATGGTTGAAAGATAACATGGCAACATGACAGGGAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATAAAATGAA
* * ***
5209007 TAAGATCATGGTTGAAAGATAACA-GGCAGTGTGACATAAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATAAAATGAA
* * *
5209052 TAAGACCATGGTTAAAAGATACCATGGCAACATGACAGAAAATGAG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATAAAATGAA
* * * * * * * *
5209098 TAACACCATAGTTGAAAGACACTATGGCATCATGTCA-AAGATAAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATAAAATGAA
5209143 TAAGACCATGG
1 TAAGACCATGG
5209154 ATGGGAGACG
Statistics
Matches: 196, Mismatches: 40, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
45 52 0.27
46 140 0.71
47 4 0.02
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.20
Consensus pattern (46 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACATAAAATGAA
Found at i:5209081 original size:91 final size:92
Alignment explanation
Indices: 5208869--5209116 Score: 320
Period size: 91 Copynumber: 2.7 Consensus size: 92
5208859 ATGAAATGTG
* * * * *
5208869 TAAGACTATGGTTGAAAGATACCATGGCAGCGTGACATAAAATGAATAAGACCATGATTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAATAAGACCATGGTTGAAAGA
* *
5208934 TACCATGGCAATATGACGTGAAAAGAA
66 TAACATGGCAATATGACATGAAAAGAA
* ** *
5208961 TAAGACCATGGTTGAAAGATAACATGGCAACATGACAGGGAATGAATAAGATCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAATAAGACCATGGTTGAAAGA
* *
5209026 TAACA-GGCAGTGTGACAT-AAAATGAA
66 TAACATGGCAATATGACATGAAAA-GAA
* * * *
5209052 TAAGACCATGGTTAAAAGATACCATGGCAACATGACAGAAAATGAGTAACACCATAGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAATAAGACCATGGTTGAAAGA
5209117 CACTATGGCA
Statistics
Matches: 134, Mismatches: 21, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
90 4 0.03
91 70 0.52
92 60 0.45
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.20
Consensus pattern (92 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAATAAGACCATGGTTGAAAGA
TAACATGGCAATATGACATGAAAAGAA
Found at i:5209145 original size:91 final size:87
Alignment explanation
Indices: 5208869--5209153 Score: 268
Period size: 91 Copynumber: 3.1 Consensus size: 87
5208859 ATGAAATGTG
* * * *
5208869 TAAGACTATGGTTGAAAGATACCATGGCAGCGTGACATAAAATGAATAAGACCATGATTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAATAAGACCATG-TTGAAAGA
* *
5208934 TACCATGGCAATATGACGTGAAAA-GAA
65 -AACATGGC-ATAT---GTCAAAATGAA
* ** *
5208961 TAAGACCATGGTTGAAAGATAACATGGCAACATGACAGGGAATGAATAAGATCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAATAAGACCAT-GTTGAAAGA
* *
5209026 TAACA-GGCAGTGTGACATAAAATGAA
65 -AACATGGCA-TATGTC--AAAATGAA
* * *
5209052 TAAGACCATGGTTAAAAGATACCATGGCAACATGACAGAAAATGAGTAACACCATAGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAATAAGACCAT-GTTGAAAGA
* *
5209117 CACTATGGCATCATGTCAAAGATAAA
65 AAC-ATGGCAT-ATGTCAAA-ATGAA
5209143 TAAGACCATGG
1 TAAGACCATGG
5209154 ATGGGAGACG
Statistics
Matches: 160, Mismatches: 24, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
88 1 0.01
90 10 0.06
91 82 0.51
92 66 0.41
93 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.20
Consensus pattern (87 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAATAAGACCATGTTGAAAGAA
ACATGGCATATGTCAAAATGAA
Found at i:5212237 original size:3 final size:3
Alignment explanation
Indices: 5212225--5212264 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
5212215 TTTTAAATGA
5212225 TAT T-T TAT TAT TAT TAT TAT TAT T-T TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5212265 TAGTATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 6 0.18
3 28 0.82
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TAT
Found at i:5212250 original size:20 final size:19
Alignment explanation
Indices: 5212225--5212264 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 19
5212215 TTTTAAATGA
5212225 TATTTTATTATTATTATTAT
1 TATTTTATTATTATT-TTAT
5212245 TATTTTATTATTATTTTAT
1 TATTTTATTATTATTTTAT
5212264 T
1 T
5212265 TAGTATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TATTTTATTATTATTTTAT
Found at i:5212252 original size:11 final size:11
Alignment explanation
Indices: 5212225--5212264 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
5212215 TTTTAAATGA
5212225 TATTTTATTAT
1 TATTTTATTAT
5212236 TA--TTATTAT
1 TATTTTATTAT
5212245 TATTTTATTAT
1 TATTTTATTAT
5212256 TATTTTATT
1 TATTTTATT
5212265 TAGTATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 9 0.33
11 18 0.67
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:5214469 original size:46 final size:46
Alignment explanation
Indices: 5214409--5214565 Score: 244
Period size: 46 Copynumber: 3.4 Consensus size: 46
5214399 ATGAAATGTG
* *
5214409 TAAGACCATGGTTGAAAGATACCATGGCAGCGTGACATAAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATAAAATGAA
*
5214455 TAAGACCATGGTTGAAAGATACCATGGCAATATGACATGAAAA-GAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAT-AAAATGAA
* *
5214501 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATAAAATGAA
*
5214547 TAAGACCATAGTTGAAAGA
1 TAAGACCATGGTTGAAAGA
5214566 CACTATGACA
Statistics
Matches: 102, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
45 4 0.04
46 94 0.92
47 4 0.04
ACGTcount: A:0.44, C:0.14, G:0.23, T:0.19
Consensus pattern (46 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACATAAAATGAA
Found at i:5216259 original size:54 final size:54
Alignment explanation
Indices: 5216174--5216283 Score: 202
Period size: 54 Copynumber: 2.0 Consensus size: 54
5216164 TTTTTCAAAG
5216174 CATTGGTGCATAGGAATCAACCAAATATCATCCAAAATGGGGAAGAAAAGTGAT
1 CATTGGTGCATAGGAATCAACCAAATATCATCCAAAATGGGGAAGAAAAGTGAT
* *
5216228 CATTGGTGCATAGGTATCAACCAAATTTCATCCAAAATGGGGAAGAAAAGTGAT
1 CATTGGTGCATAGGAATCAACCAAATATCATCCAAAATGGGGAAGAAAAGTGAT
5216282 CA
1 CA
5216284 CTATGGAAAG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (54 bp):
CATTGGTGCATAGGAATCAACCAAATATCATCCAAAATGGGGAAGAAAAGTGAT
Found at i:5220823 original size:1 final size:1
Alignment explanation
Indices: 5220817--5220854 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
5220807 TTTGTAAGTT
5220817 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5220855 CAATGACTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5226836 original size:16 final size:16
Alignment explanation
Indices: 5226815--5226854 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
5226805 GTCCCACCAA
5226815 TACCAAACCCTCCCGT
1 TACCAAACCCTCCCGT
*
5226831 TACC-AACCCTCCTGT
1 TACCAAACCCTCCCGT
5226846 TA-CAAACCC
1 TACCAAACCC
5226855 ACCACCTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 17 0.77
16 4 0.18
ACGTcount: A:0.28, C:0.47, G:0.05, T:0.20
Consensus pattern (16 bp):
TACCAAACCCTCCCGT
Found at i:5226916 original size:15 final size:15
Alignment explanation
Indices: 5226892--5226938 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
5226882 TGGTGGAGGG
*
5226892 GGAGGCGGCGGTGGA
1 GGAGGTGGCGGTGGA
*
5226907 GGAGGTGGCGGTGGC
1 GGAGGTGGCGGTGGA
* *
5226922 GGTGGTGGAGGTGGA
1 GGAGGTGGCGGTGGA
5226937 GG
1 GG
5226939 TGGAGGTGGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.11, C:0.09, G:0.68, T:0.13
Consensus pattern (15 bp):
GGAGGTGGCGGTGGA
Found at i:5226922 original size:21 final size:21
Alignment explanation
Indices: 5226882--5226962 Score: 99
Period size: 21 Copynumber: 3.9 Consensus size: 21
5226872 ACCCACCTTC
* *
5226882 TGGTGGAGGGGGAGGCGGCGG
1 TGGTGGAGGTGGAGGTGGCGG
* *
5226903 TGGAGGAGGTGGCGGTGGCGG
1 TGGTGGAGGTGGAGGTGGCGG
*
5226924 TGGTGGAGGTGGAGGTGGAGG
1 TGGTGGAGGTGGAGGTGGCGG
* *
5226945 TGGTGGCGGTGGTGGTGG
1 TGGTGGAGGTGGAGGTGG
5226963 TGGGGGTAGC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.09, C:0.06, G:0.68, T:0.17
Consensus pattern (21 bp):
TGGTGGAGGTGGAGGTGGCGG
Found at i:5226928 original size:9 final size:9
Alignment explanation
Indices: 5226910--5226965 Score: 58
Period size: 9 Copynumber: 6.2 Consensus size: 9
5226900 CGGTGGAGGA
*
5226910 GGTGGCGGT
1 GGTGGTGGT
*
5226919 GGCGGTGGT
1 GGTGGTGGT
* *
5226928 GGAGGTGGA
1 GGTGGTGGT
*
5226937 GGTGGAGGT
1 GGTGGTGGT
*
5226946 GGTGGCGGT
1 GGTGGTGGT
5226955 GGTGGTGGT
1 GGTGGTGGT
5226964 GG
1 GG
5226966 GGGTAGCACT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.05, C:0.05, G:0.68, T:0.21
Consensus pattern (9 bp):
GGTGGTGGT
Found at i:5226940 original size:15 final size:15
Alignment explanation
Indices: 5226901--5226965 Score: 76
Period size: 15 Copynumber: 4.3 Consensus size: 15
5226891 GGGAGGCGGC
* *
5226901 GGTGGAGGAGGTGGC
1 GGTGGAGGTGGTGGT
* *
5226916 GGTGGCGGTGGTGGA
1 GGTGGAGGTGGTGGT
*
5226931 GGTGGAGGTGGAGGT
1 GGTGGAGGTGGTGGT
*
5226946 GGTGGCGGTGGTGGT
1 GGTGGAGGTGGTGGT
5226961 GGTGG
1 GGTGG
5226966 GGGTAGCACT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.08, C:0.05, G:0.68, T:0.20
Consensus pattern (15 bp):
GGTGGAGGTGGTGGT
Found at i:5226958 original size:12 final size:12
Alignment explanation
Indices: 5226904--5226962 Score: 55
Period size: 12 Copynumber: 4.9 Consensus size: 12
5226894 AGGCGGCGGT
*
5226904 GGAGGAGGTGGC
1 GGAGGTGGTGGC
* * *
5226916 GGTGGCGGTGGT
1 GGAGGTGGTGGC
* *
5226928 GGAGGTGGAGGT
1 GGAGGTGGTGGC
5226940 GGAGGTGGTGGC
1 GGAGGTGGTGGC
*
5226952 GGTGGTGGTGG
1 GGAGGTGGTGG
5226963 TGGGGGTAGC
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.08, C:0.05, G:0.68, T:0.19
Consensus pattern (12 bp):
GGAGGTGGTGGC
Found at i:5226963 original size:6 final size:6
Alignment explanation
Indices: 5226910--5226965 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
5226900 CGGTGGAGGA
* * * * * *
5226910 GGTGGC GGTGGC GGTGGT GGAGGT GGAGGT GGAGGT GGTGGC GGTGGT
1 GGTGGT GGTGGT GGTGGT GGTGGT GGTGGT GGTGGT GGTGGT GGTGGT
5226958 GGTGGT GG
1 GGTGGT GG
5226966 GGGTAGCACT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.05, C:0.05, G:0.68, T:0.21
Consensus pattern (6 bp):
GGTGGT
Found at i:5232972 original size:29 final size:30
Alignment explanation
Indices: 5232940--5233000 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 30
5232930 ACTTAACAAG
5232940 CAAATG-CTTCTAAAATAATAA-AAAATTAA
1 CAAATGCCTT-TAAAATAATAAGAAAATTAA
5232969 CAAATGCCTTTAAAATAATAAGAAAATTAA
1 CAAATGCCTTTAAAATAATAAGAAAATTAA
5232999 CA
1 CA
5233001 GTAAAATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 17 0.57
30 13 0.43
ACGTcount: A:0.57, C:0.11, G:0.05, T:0.26
Consensus pattern (30 bp):
CAAATGCCTTTAAAATAATAAGAAAATTAA
Found at i:5233056 original size:11 final size:11
Alignment explanation
Indices: 5233038--5233078 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
5233028 ACAATATCAA
5233038 CAAAATAATAG
1 CAAAATAATAG
*
5233049 CAACATAATAG
1 CAAAATAATAG
* *
5233060 TAAAATAGTAG
1 CAAAATAATAG
5233071 CAAAATAA
1 CAAAATAA
5233079 GGAGAAAACA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.20
Consensus pattern (11 bp):
CAAAATAATAG
Found at i:5233086 original size:22 final size:22
Alignment explanation
Indices: 5233039--5233100 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 22
5233029 CAATATCAAC
* *
5233039 AAAATAATAGCAACATAATAGT
1 AAAATAATAGCAAAATAAGAGT
*
5233061 AAAATAGTAGCAAAATAAGGAG-
1 AAAATAATAGCAAAATAA-GAGT
*
5233083 AAAACAATAAG-AAAATAA
1 AAAATAAT-AGCAAAATAA
5233101 CATTCAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.65, C:0.06, G:0.13, T:0.16
Consensus pattern (22 bp):
AAAATAATAGCAAAATAAGAGT
Found at i:5249154 original size:87 final size:86
Alignment explanation
Indices: 5249059--5249288 Score: 221
Period size: 87 Copynumber: 2.8 Consensus size: 86
5249049 AAAGACTATT
* * *
5249059 TAAATTAGGGTTAATAGTTTTTAAATAAATTAAATTAGGGTCTT-AAATAAATTAGAGCTTAGGG
1 TAAATTAGGGTTAATAGATTTTAAATAAATTAAATTAGGAT-TTAAAATAAATTA-A-ATTAGGG
5249123 TTTAT-GGTTTTAAATAGATTAAG
63 TTTATAGGTTTTAAATAGATTAAG
** * * * **
5249146 TAAATTAGGGTTCTTGGATTTTAATTAAATTAAGTTATTATTTAAAATAAATTAAATTAGGGTTT
1 TAAATTAGGGTTAATAGATTTTAAATAAATTAAATTAGGATTTAAAATAAATTAAATTAGGGTTT
**
5249211 ATATTTTTTAAATAGATTAAG
66 ATAGGTTTTAAATAGATTAAG
* *
5249232 TAAATTAGGGTT--T--A----AAATGAATTAAATTAAGG-TTTAAAATAAATTAAATTAGTGTT
1 TAAATTAGGGTTAATAGATTTTAAATAAATTAAATT-AGGATTTAAAATAAATTAAATTAGGGTT
5249288 T
65 T
5249289 TGGGTTTATT
Statistics
Matches: 122, Mismatches: 18, Indels: 15
0.79 0.12 0.10
Matches are distributed among these distances:
78 35 0.29
79 1 0.01
82 1 0.01
84 1 0.01
85 11 0.09
86 31 0.25
87 42 0.34
ACGTcount: A:0.41, C:0.01, G:0.15, T:0.43
Consensus pattern (86 bp):
TAAATTAGGGTTAATAGATTTTAAATAAATTAAATTAGGATTTAAAATAAATTAAATTAGGGTTT
ATAGGTTTTAAATAGATTAAG
Found at i:5249156 original size:33 final size:34
Alignment explanation
Indices: 5249101--5249180 Score: 87
Period size: 34 Copynumber: 2.4 Consensus size: 34
5249091 AATTAGGGTC
**
5249101 TTAAATAAATT-AG-AGCTTAGGGTT-TATGG-TT
1 TTAAATAAATTAAGTAAATTAGGGTTCT-TGGATT
*
5249132 TTAAATAGATTAAGTAAATTAGGGTTCTTGGATT
1 TTAAATAAATTAAGTAAATTAGGGTTCTTGGATT
*
5249166 TTAATTAAATTAAGT
1 TTAAATAAATTAAGT
5249181 TATTATTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
31 10 0.25
32 2 0.05
33 12 0.30
34 16 0.40
ACGTcount: A:0.36, C:0.03, G:0.19, T:0.42
Consensus pattern (34 bp):
TTAAATAAATTAAGTAAATTAGGGTTCTTGGATT
Found at i:5249259 original size:22 final size:22
Alignment explanation
Indices: 5249232--5249288 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
5249222 ATAGATTAAG
*
5249232 TAAATTAGGGTTTAAAATGAAT
1 TAAATTAGGGTTTAAAATAAAT
*
5249254 TAAATTAAGGTTTAAAATAAAT
1 TAAATTAGGGTTTAAAATAAAT
*
5249276 TAAATTAGTGTTT
1 TAAATTAGGGTTT
5249289 TGGGTTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.40
Consensus pattern (22 bp):
TAAATTAGGGTTTAAAATAAAT
Found at i:5255864 original size:26 final size:25
Alignment explanation
Indices: 5255835--5255920 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 25
5255825 ATACAAATTA
5255835 ATTAAAATTACGTAAATGAAAAAAAT
1 ATTAAAATTACGTAAATG-AAAAAAT
* ** ** *
5255861 ATTAAATAATATTTAAAATTTAAAATT
1 ATTAAA-ATTACGT-AAATGAAAAAAT
5255888 AATTAAAATTACGTAAATGAAAAAAT
1 -ATTAAAATTACGTAAATGAAAAAAT
5255914 ATTAAAA
1 ATTAAAA
5255921 AATTCAAAAT
Statistics
Matches: 45, Mismatches: 12, Indels: 7
0.70 0.19 0.11
Matches are distributed among these distances:
25 7 0.16
26 15 0.33
27 13 0.29
28 10 0.22
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (25 bp):
ATTAAAATTACGTAAATGAAAAAAT
Found at i:5255902 original size:54 final size:51
Alignment explanation
Indices: 5255829--5255936 Score: 180
Period size: 54 Copynumber: 2.1 Consensus size: 51
5255819 TATAAAATAC
*
5255829 AAATTAATTAAAATTACGTAAATGAAAAAAATATTAAATAATATTTAAAATTTA
1 AAATTAATTAAAATTACGTAAATG-AAAAAATATTAAA-AA-ATTCAAAATTTA
5255883 AAATTAATTAAAATTACGTAAATGAAAAAATATTAAAAAATTCAAAATTTA
1 AAATTAATTAAAATTACGTAAATGAAAAAATATTAAAAAATTCAAAATTTA
5255934 AAA
1 AAA
5255937 CAAACTGTTA
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
51 14 0.26
52 2 0.04
53 13 0.25
54 24 0.45
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.32
Consensus pattern (51 bp):
AAATTAATTAAAATTACGTAAATGAAAAAATATTAAAAAATTCAAAATTTA
Found at i:5259341 original size:6 final size:6
Alignment explanation
Indices: 5259330--5259355 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5259320 AAGTGTCGCC
5259330 TTACTG TTACTG TTACTG TTACTG TT
1 TTACTG TTACTG TTACTG TTACTG TT
5259356 TCAGACTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (6 bp):
TTACTG
Found at i:5272912 original size:27 final size:28
Alignment explanation
Indices: 5272844--5272915 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 28
5272834 ACCAACTCTG
5272844 AAAGAATAACCTTTGTGGCAAACTTTGA
1 AAAGAATAACCTTTGTGGCAAACTTTGA
*
5272872 ATAAG--TAGCCTTTGTGGCAAA-TTCT-A
1 A-AAGAATAACCTTTGTGGCAAACTT-TGA
*
5272898 AAAGAATAACATTTGTGG
1 AAAGAATAACCTTTGTGG
5272916 TGTATTCTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
25 3 0.08
26 4 0.11
27 26 0.70
28 1 0.03
29 3 0.08
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (28 bp):
AAAGAATAACCTTTGTGGCAAACTTTGA
Found at i:5272951 original size:16 final size:16
Alignment explanation
Indices: 5272930--5272964 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
5272920 TTCTAAATGA
5272930 ACTGCCTTTCAGGTGT
1 ACTGCCTTTCAGGTGT
5272946 ACTGCCTTTCAGGTGT
1 ACTGCCTTTCAGGTGT
5272962 ACT
1 ACT
5272965 CTGAAAGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.14, C:0.26, G:0.23, T:0.37
Consensus pattern (16 bp):
ACTGCCTTTCAGGTGT
Found at i:5282552 original size:32 final size:32
Alignment explanation
Indices: 5282511--5282576 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
5282501 AAAATTACTT
5282511 TACAAAATAGTTCTATTTTAACATCAAGCTTA
1 TACAAAATAGTTCTATTTTAACATCAAGCTTA
5282543 TACAAAATAGTTCTATTTTAACATCAAGCTTA
1 TACAAAATAGTTCTATTTTAACATCAAGCTTA
5282575 TA
1 TA
5282577 ATCTATCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (32 bp):
TACAAAATAGTTCTATTTTAACATCAAGCTTA
Found at i:5283506 original size:25 final size:25
Alignment explanation
Indices: 5283472--5283523 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
5283462 AAGCACCAAT
*
5283472 GTCACCTTACTCAATTTATTACTTA
1 GTCACCTTACTCAATTTATCACTTA
5283497 GTCACCTTACTCAATTTATCACTTA
1 GTCACCTTACTCAATTTATCACTTA
5283522 GT
1 GT
5283524 TAAAATATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.25, G:0.06, T:0.42
Consensus pattern (25 bp):
GTCACCTTACTCAATTTATCACTTA
Found at i:5286268 original size:13 final size:13
Alignment explanation
Indices: 5286252--5286285 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
5286242 AATAAAATAA
5286252 TAAAATATCTTAT
1 TAAAATATCTTAT
5286265 TAAAATATCTTAT
1 TAAAATATCTTAT
5286278 TAAAATAT
1 TAAAATAT
5286286 TAAATAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (13 bp):
TAAAATATCTTAT
Found at i:5290961 original size:6 final size:6
Alignment explanation
Indices: 5290950--5290979 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
5290940 GTACCTAACC
*
5290950 CTTTTG CTTTTG CTTTTG CTTTTT CTTTTG
1 CTTTTG CTTTTG CTTTTG CTTTTG CTTTTG
5290980 TATTTAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.17, G:0.13, T:0.70
Consensus pattern (6 bp):
CTTTTG
Found at i:5291723 original size:2 final size:2
Alignment explanation
Indices: 5291716--5291746 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5291706 ATATTGTAGA
5291716 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5291747 AAGTGAAGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5296116 original size:21 final size:21
Alignment explanation
Indices: 5296092--5296132 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5296082 TTTAATCATT
5296092 CTTAAAAGTTTCTTAAAAAAC
1 CTTAAAAGTTTCTTAAAAAAC
* *
5296113 CTTAAAATTTTGTTAAAAAA
1 CTTAAAAGTTTCTTAAAAAA
5296133 TAAAAGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.37
Consensus pattern (21 bp):
CTTAAAAGTTTCTTAAAAAAC
Found at i:5299278 original size:12 final size:12
Alignment explanation
Indices: 5299264--5299320 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
5299254 TAAGCTTTGC
*
5299264 AATAATTTAAAC
1 AATAATTTAAAA
*
5299276 AATACTTTAAAA
1 AATAATTTAAAA
* *
5299288 AAT-ATATAATA
1 AATAATTTAAAA
5299299 AA-AATTTGAAAA
1 AATAATTT-AAAA
5299311 AATAATTTAA
1 AATAATTTAA
5299321 TTATGAAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
11 10 0.29
12 20 0.57
13 5 0.14
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (12 bp):
AATAATTTAAAA
Found at i:5304552 original size:21 final size:22
Alignment explanation
Indices: 5304505--5304553 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
5304495 TATTTCTTGA
*
5304505 AATTTTGATATTTAATTATTGT
1 AATTTTGATATTTAATAATTGT
*
5304527 AATTTT-ATTTTTAATAATT-T
1 AATTTTGATATTTAATAATTGT
5304547 AGATTTT
1 A-ATTTT
5304554 TTTACTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 16 0.67
22 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (22 bp):
AATTTTGATATTTAATAATTGT
Found at i:5306709 original size:9 final size:9
Alignment explanation
Indices: 5306695--5306737 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
5306685 TTACTTGACT
5306695 TTAAAAAAA
1 TTAAAAAAA
*
5306704 TTAAAAATA
1 TTAAAAAAA
5306713 TTAAAAATAA
1 TTAAAAA-AA
* *
5306723 GTAACAAAA
1 TTAAAAAAA
5306732 TTAAAA
1 TTAAAA
5306738 TTGAAGCGGA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
9 21 0.78
10 6 0.22
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:5306734 original size:19 final size:18
Alignment explanation
Indices: 5306695--5306737 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
5306685 TTACTTGACT
*
5306695 TTAAAAAAATTAAAAATA
1 TTAAAAAAAGTAAAAATA
5306713 TTAAAAATAAGTAACAAA-A
1 TTAAAAA-AAGTAA-AAATA
5306732 TTAAAA
1 TTAAAA
5306738 TTGAAGCGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
19 12 0.55
20 3 0.14
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (18 bp):
TTAAAAAAAGTAAAAATA
Found at i:5311630 original size:16 final size:16
Alignment explanation
Indices: 5311611--5311643 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5311601 GCACCACTTT
*
5311611 AAATTGTTTGCCATTA
1 AAATTGTTTACCATTA
5311627 AAATTGTTTACCATTA
1 AAATTGTTTACCATTA
5311643 A
1 A
5311644 TCATAATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.42
Consensus pattern (16 bp):
AAATTGTTTACCATTA
Found at i:5312347 original size:16 final size:16
Alignment explanation
Indices: 5312311--5312357 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
5312301 ATAATTACTC
* *
5312311 TTAATTTAAATCT-AT
1 TTAATTTAAATTTGAA
5312326 TTAATTTAAATTTGAA
1 TTAATTTAAATTTGAA
*
5312342 TTAATTTTAATTTGAA
1 TTAATTTAAATTTGAA
5312358 GGAAGTTACT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (16 bp):
TTAATTTAAATTTGAA
Found at i:5313374 original size:22 final size:22
Alignment explanation
Indices: 5313347--5313391 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
5313337 ACCTTCTAAT
5313347 TTAAATT-TTAAAATATAAAAAA
1 TTAAATTGTTAAAA-ATAAAAAA
*
5313369 TTAAATTGTTACAAATAAAAAA
1 TTAAATTGTTAAAAATAAAAAA
5313391 T
1 T
5313392 AATATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
TTAAATTGTTAAAAATAAAAAA
Found at i:5320404 original size:34 final size:34
Alignment explanation
Indices: 5320361--5320430 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
5320351 CGGTGATAAG
5320361 ATAATGACTACCACTAGTAATCAATAAGGTTGCC
1 ATAATGACTACCACTAGTAATCAATAAGGTTGCC
5320395 ATAATGACTACCACTAGTAATCAATAAGGTTGCC
1 ATAATGACTACCACTAGTAATCAATAAGGTTGCC
5320429 AT
1 AT
5320431 TCAGGGAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (34 bp):
ATAATGACTACCACTAGTAATCAATAAGGTTGCC
Found at i:5323658 original size:18 final size:16
Alignment explanation
Indices: 5323608--5323665 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 16
5323598 TAGGCAAATA
5323608 AATTAATT-AATTTTT
1 AATTAATTAAATTTTT
*
5323623 AATTAAATAAA--TTT
1 AATTAATTAAATTTTT
5323637 AATTAATTAAATTTTCT
1 AATTAATTAAATTTT-T
5323654 AAATTAATTAAA
1 -AATTAATTAAA
5323666 GGAAAATGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
14 13 0.36
15 7 0.19
16 4 0.11
17 1 0.03
18 11 0.31
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTAATTAAATTTTT
Found at i:5323665 original size:9 final size:9
Alignment explanation
Indices: 5323606--5323665 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
5323596 TCTAGGCAAA
5323606 TAAATTAAT
1 TAAATTAAT
*
5323615 TAATTTTTAAT
1 TAA--ATTAAT
*
5323626 TAAATAAAT
1 TAAATTAAT
*
5323635 TTAATTAAT
1 TAAATTAAT
*
5323644 TAAATT-TT
1 TAAATTAAT
5323652 CTAAATTAAT
1 -TAAATTAAT
5323662 TAAA
1 TAAA
5323666 GGAAAATGTT
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
8 1 0.03
9 29 0.74
10 1 0.03
11 8 0.21
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (9 bp):
TAAATTAAT
Found at i:5325550 original size:19 final size:20
Alignment explanation
Indices: 5325522--5325567 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
5325512 TTATAATTTT
*
5325522 AAAATAATTATTATTAT-AAA
1 AAAAT-ATTATTAGTATGAAA
*
5325542 AAAATATTATTAGTATGATA
1 AAAATATTATTAGTATGAAA
5325562 AAAATA
1 AAAATA
5325568 ATTTTTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (20 bp):
AAAATATTATTAGTATGAAA
Found at i:5325933 original size:41 final size:41
Alignment explanation
Indices: 5325885--5325965 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
5325875 TTTATAATCT
5325885 ATAACA-TTTATAAAAAAAATATAAATTATTCAATAACTTTC
1 ATAACATTTTATAAAAAAAATAT-AATTATTCAATAACTTTC
* * * * *
5325926 ATAACATTTTTTATAAATAATATAATTTTTCCATAACTTT
1 ATAACATTTTATAAAAAAAATATAATTATTCAATAACTTT
5325966 AAAAAATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 21 0.62
42 13 0.38
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (41 bp):
ATAACATTTTATAAAAAAAATATAATTATTCAATAACTTTC
Found at i:5332748 original size:17 final size:18
Alignment explanation
Indices: 5332715--5332761 Score: 78
Period size: 17 Copynumber: 2.7 Consensus size: 18
5332705 AAAATGTGAG
*
5332715 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTC
5332733 AAATGATGTT-ACATTTC
1 AAATGATGTTCACATTTC
5332750 AAATGATGTTCA
1 AAATGATGTTCA
5332762 AATTGATGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 16 0.59
18 11 0.41
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:5335389 original size:13 final size:13
Alignment explanation
Indices: 5335371--5335403 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
5335361 CTTAAAATTT
5335371 TCAAAAGTACTTC
1 TCAAAAGTACTTC
5335384 TCAAAAGTACTTC
1 TCAAAAGTACTTC
5335397 TCAAAAG
1 TCAAAAG
5335404 CATTATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.27
Consensus pattern (13 bp):
TCAAAAGTACTTC
Found at i:5335721 original size:26 final size:27
Alignment explanation
Indices: 5335692--5335757 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 27
5335682 GTCATAAATC
* *
5335692 AAAATTATAATTATT-ATATTTTATTT
1 AAAATTATAATTATTAATATATTAATT
5335718 AAAATGTAT--TTATTAATATATTAATT
1 AAAAT-TATAATTATTAATATATTAATT
5335744 ATAAATTATAATTA
1 A-AAATTATAATTA
5335758 GTGTTGCAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
25 5 0.15
26 18 0.55
27 7 0.21
28 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (27 bp):
AAAATTATAATTATTAATATATTAATT
Found at i:5339094 original size:14 final size:15
Alignment explanation
Indices: 5339068--5339096 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5339058 CCCTTTGATA
5339068 AAATTTATATATTAT
1 AAATTTATATATTAT
5339083 AAATTT-TATATTAT
1 AAATTTATATATTAT
5339097 TTTGATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AAATTTATATATTAT
Found at i:5342187 original size:29 final size:30
Alignment explanation
Indices: 5342143--5342200 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
5342133 GTAGATTCCC
*
5342143 TGCAAAAGTATCTAAAATTGTAATAATGTA
1 TGCAAAACTATCTAAAATTGTAATAATGTA
* *
5342173 TGCAAAACTAT-TAAAATTTTAATGATGT
1 TGCAAAACTATCTAAAATTGTAATAATGT
5342201 GTGGAAATAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (30 bp):
TGCAAAACTATCTAAAATTGTAATAATGTA
Found at i:5353769 original size:17 final size:17
Alignment explanation
Indices: 5353747--5353795 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
5353737 TTTGTTCTAC
*
5353747 TTATTTTTATTTCATTT
1 TTATTTTTATTTAATTT
5353764 TTATTTTTATTTAATTT
1 TTATTTTTATTTAATTT
*
5353781 CTATTATTTATTTAA
1 TTATT-TTTATTTAA
5353796 GATTTATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 20 0.69
18 9 0.31
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTTTTATTTAATTT
Found at i:5353800 original size:20 final size:17
Alignment explanation
Indices: 5353748--5353806 Score: 64
Period size: 17 Copynumber: 3.3 Consensus size: 17
5353738 TTGTTCTACT
* *
5353748 TATTTTTATTTCATTTT
1 TATTTTTATTTAATTTA
*
5353765 TATTTTTATTTAATTTC
1 TATTTTTATTTAATTTA
5353782 TATTATTTATTTAAGATTTA
1 TATT-TTTATTT-A-ATTTA
5353802 TATTT
1 TATTT
5353807 AATCCTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 19 0.53
18 7 0.19
19 2 0.06
20 8 0.22
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.69
Consensus pattern (17 bp):
TATTTTTATTTAATTTA
Found at i:5355105 original size:21 final size:22
Alignment explanation
Indices: 5355081--5355131 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
5355071 ACTAATTTAC
5355081 TATTTTATTAATGG-TTATTAT
1 TATTTTATTAATGGTTTATTAT
* * *
5355102 TATTATT-TTGATGGTTTTTTTT
1 TATT-TTATTAATGGTTTATTAT
5355124 TATTTTAT
1 TATTTTAT
5355132 CTTTTCATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.22, C:0.00, G:0.10, T:0.69
Consensus pattern (22 bp):
TATTTTATTAATGGTTTATTAT
Found at i:5360549 original size:2 final size:2
Alignment explanation
Indices: 5360542--5360566 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5360532 TGTCCAACAT
5360542 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5360567 TTGCATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5372055 original size:1 final size:1
Alignment explanation
Indices: 5372049--5372074 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
5372039 TCCCCTATGC
5372049 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
5372075 ACTGTAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5379671 original size:32 final size:31
Alignment explanation
Indices: 5379557--5379681 Score: 134
Period size: 32 Copynumber: 4.2 Consensus size: 31
5379547 TCGGTACTTG
*
5379557 AACTTGATATTTTTTCTTAATTTGGTACCTA
1 AACTTGATATTTTTTCTCAATTTGGTACCTA
* *
5379588 AA-TT--T-TTTTGTC-CAATTTGGTACCCA
1 AACTTGATATTTTTTCTCAATTTGGTACCTA
* * *
5379614 AACTTGACAATTTTTCTTAATTTGGTACCTA
1 AACTTGATATTTTTTCTCAATTTGGTACCTA
* *
5379645 AACTTGATATTTTTTTCTCAAGTTGGTACTTA
1 AACTTGATA-TTTTTTCTCAATTTGGTACCTA
5379677 AACTT
1 AACTT
5379682 TTGGGGGGTC
Statistics
Matches: 75, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
26 14 0.19
27 8 0.11
28 1 0.01
30 7 0.09
31 22 0.29
32 23 0.31
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.48
Consensus pattern (31 bp):
AACTTGATATTTTTTCTCAATTTGGTACCTA
Found at i:5379680 original size:63 final size:57
Alignment explanation
Indices: 5379549--5379681 Score: 149
Period size: 57 Copynumber: 2.2 Consensus size: 57
5379539 TATAATATTC
* * * *
5379549 GGTACTTGAACTTGATATTTTTTCTTAATTTGGTACCTAAATTTTTTTGTCCAATTT
1 GGTACTTAAACTTGACAATTTTTCTTAATTTGGTACCTAAATTTTTTTGTCCAAGTT
** *
5379606 GGTACCCAAACTTGACAATTTTTCTTAATTTGGTACCTAAACTTGATATTTTTTTCTCAAGTT
1 GGTACTTAAACTTGACAATTTTTCTTAATTTGGTACCTAAA--T--T-TTTTTGTC-CAAGTT
5379669 GGTACTTAAACTT
1 GGTACTTAAACTT
5379682 TTGGGGGGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
57 36 0.59
59 1 0.02
61 1 0.02
62 7 0.11
63 16 0.26
ACGTcount: A:0.26, C:0.15, G:0.12, T:0.47
Consensus pattern (57 bp):
GGTACTTAAACTTGACAATTTTTCTTAATTTGGTACCTAAATTTTTTTGTCCAAGTT
Found at i:5382412 original size:20 final size:20
Alignment explanation
Indices: 5382387--5382440 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
5382377 AGGGGCACAT
* *
5382387 GCCCGTGTAGCCTGGGACAC
1 GCCCGTGTGGCCTGGAACAC
* *
5382407 GCCCGTATGGCCTGGAACAT
1 GCCCGTGTGGCCTGGAACAC
5382427 GCCCGTGTGGCCTG
1 GCCCGTGTGGCCTG
5382441 CCCGTGGGCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.13, C:0.33, G:0.35, T:0.19
Consensus pattern (20 bp):
GCCCGTGTGGCCTGGAACAC
Found at i:5382989 original size:13 final size:14
Alignment explanation
Indices: 5382971--5383003 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
5382961 AATTAGCAAC
5382971 TCATACATACAAA-
1 TCATACATACAAAT
*
5382984 TCATACATATAAAT
1 TCATACATACAAAT
5382998 TCATAC
1 TCATAC
5383004 CAAACTATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.30
Consensus pattern (14 bp):
TCATACATACAAAT
Found at i:5383393 original size:40 final size:40
Alignment explanation
Indices: 5383336--5383432 Score: 112
Period size: 40 Copynumber: 2.5 Consensus size: 40
5383326 CACACCAGAA
*
5383336 TGACGACCAACGCCTCATTGGAT-AGTTCGAAGCAAATAAG
1 TGACGACCAACGCCTCATCGGATAAG-TCGAAGCAAATAAG
* *
5383376 TGACGACCAACGTCTCATCGGCTAAGTCGAAGC--A-AAG
1 TGACGACCAACGCCTCATCGGATAAGTCGAAGCAAATAAG
* *
5383413 TGGCGACCAATGCCTCATCG
1 TGACGACCAACGCCTCATCG
5383433 AATCTATCCG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
37 20 0.40
38 1 0.02
40 27 0.54
41 2 0.04
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.19
Consensus pattern (40 bp):
TGACGACCAACGCCTCATCGGATAAGTCGAAGCAAATAAG
Found at i:5384462 original size:16 final size:16
Alignment explanation
Indices: 5384441--5384471 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5384431 TTTCTTTTGT
*
5384441 TTCTTTATTTTATTTA
1 TTCTTTATTTCATTTA
5384457 TTCTTTATTTCATTT
1 TTCTTTATTTCATTT
5384472 TATTTACTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (16 bp):
TTCTTTATTTCATTTA
Found at i:5384612 original size:3 final size:3
Alignment explanation
Indices: 5384598--5384675 Score: 138
Period size: 3 Copynumber: 25.7 Consensus size: 3
5384588 TTATCTCATT
5384598 TAA TAGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
5384644 TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5384676 TCTTTTACTT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
3 69 0.96
4 3 0.04
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5388696 original size:6 final size:6
Alignment explanation
Indices: 5388676--5388724 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
5388666 ATTGAGTCCA
* *
5388676 TTTA-T TTTA-T TTTATT TTTATT TTTAGT TTTATT TCTATT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
5388722 TTT
1 TTT
5388725 TAGACTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
5 9 0.23
6 30 0.77
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTATT
Found at i:5393309 original size:6 final size:6
Alignment explanation
Indices: 5393298--5393329 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
5393288 ACAAATCTGG
5393298 AACAGT AACAGT AACAGT AACAGT AACAGT AA
1 AACAGT AACAGT AACAGT AACAGT AACAGT AA
5393330 GGCGACACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.53, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
AACAGT
Found at i:5394179 original size:4 final size:4
Alignment explanation
Indices: 5394170--5394201 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
5394160 GCCTTTTCTT
5394170 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
5394202 CTTCAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:5394262 original size:13 final size:13
Alignment explanation
Indices: 5394228--5394265 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
5394218 TTCTCTGTTA
5394228 TGTTTC-TTACTTT
1 TGTTTCTTTA-TTT
*
5394241 TTTTTCTTTATTT
1 TGTTTCTTTATTT
5394254 TGTTTCTTTATT
1 TGTTTCTTTATT
5394266 CTTTTAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 19 0.86
14 3 0.14
ACGTcount: A:0.08, C:0.11, G:0.05, T:0.76
Consensus pattern (13 bp):
TGTTTCTTTATTT
Found at i:5394312 original size:23 final size:23
Alignment explanation
Indices: 5394286--5394338 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
5394276 TTTCTTTTAT
5394286 TTATTTTACTTTATATTATAA-TA
1 TTATTTTACTTTA-ATTATAATTA
**
5394309 TTATATTTTTTTTAATTATAATTA
1 TTAT-TTTACTTTAATTATAATTA
5394333 TTATTT
1 TTATTT
5394339 CTTAAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (23 bp):
TTATTTTACTTTAATTATAATTA
Found at i:5395368 original size:51 final size:51
Alignment explanation
Indices: 5395297--5395410 Score: 201
Period size: 51 Copynumber: 2.2 Consensus size: 51
5395287 CTGATCACAT
5395297 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
*
5395348 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
* *
5395399 TTGTCGCTTGTC
1 TTATCACTTGTC
5395411 GCTTGTCGCT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
Found at i:5395432 original size:7 final size:7
Alignment explanation
Indices: 5395389--5395441 Score: 61
Period size: 7 Copynumber: 7.6 Consensus size: 7
5395379 CTAAAGCTAC
*
5395389 CACTTAT
1 CACTTGT
5395396 CACTTGT
1 CACTTGT
*
5395403 CGCTTGT
1 CACTTGT
*
5395410 CGCTTGT
1 CACTTGT
*
5395417 CGCTTGT
1 CACTTGT
5395424 CACTTGT
1 CACTTGT
*
5395431 CACTTAT
1 CACTTGT
5395438 CACT
1 CACT
5395442 GATCAGATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 42 1.00
ACGTcount: A:0.13, C:0.30, G:0.15, T:0.42
Consensus pattern (7 bp):
CACTTGT
Found at i:5395793 original size:83 final size:83
Alignment explanation
Indices: 5395662--5395819 Score: 289
Period size: 83 Copynumber: 1.9 Consensus size: 83
5395652 ACCTGGGTTG
* *
5395662 ATTTGCAAAATTTGTGAAAGTTCAGGGACTAATTAGCTACTTTTTCTTTTCCTCGACTTGTTTCG
1 ATTTGCAAAATTTGTGAAAGTTCAGGGACTAATCAGCTACTTTTTCTTTTCCTCGACTTGCTTCG
5395727 GGTTCTCGATCTGGGTCA
66 GGTTCTCGATCTGGGTCA
*
5395745 ATTTGCAAAATTTGTGAAAGTTTAGGGACTAATCAGCTACTTTTTCTTTTCCTCGACTTGCTTCG
1 ATTTGCAAAATTTGTGAAAGTTCAGGGACTAATCAGCTACTTTTTCTTTTCCTCGACTTGCTTCG
5395810 GGTTCTCGAT
66 GGTTCTCGAT
5395820 TTGCAGTAAA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 72 1.00
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (83 bp):
ATTTGCAAAATTTGTGAAAGTTCAGGGACTAATCAGCTACTTTTTCTTTTCCTCGACTTGCTTCG
GGTTCTCGATCTGGGTCA
Found at i:5397306 original size:21 final size:21
Alignment explanation
Indices: 5397253--5397316 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
5397243 CGAACACGCC
** *
5397253 AACAGAAGCTCAAAATAGCTG
1 AACAGAAGCTCGTAAGAGCTG
*
5397274 AACAGAAGCTCGTAAGAGTTG
1 AACAGAAGCTCGTAAGAGCTG
*
5397295 AACAGAAGCTCGTAAGGGCTG
1 AACAGAAGCTCGTAAGAGCTG
5397316 A
1 A
5397317 TCCACCCAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.41, C:0.17, G:0.27, T:0.16
Consensus pattern (21 bp):
AACAGAAGCTCGTAAGAGCTG
Found at i:5402475 original size:182 final size:182
Alignment explanation
Indices: 5402168--5402528 Score: 652
Period size: 182 Copynumber: 2.0 Consensus size: 182
5402158 TTCCCTAATG
*
5402168 GAGACATTACAATTTTGATTGGTGATTGGTACACTCGCAACCACACGGTTAGAACTTTGTTGAGT
1 GAGACATTACAATTTTGATTGGTGATTGGTACACTCGCAACCACACGGTTAGAACTTTGTCGAGT
*
5402233 TACAGGATTTATGGCCATGTTTTACTTTTCAGGGTAGTATATATAGTGTGTTCAATAATGAAACC
66 TACAGGATTTATAGCCATGTTTTACTTTTCAGGGTAGTATATATAGTGTGTTCAATAATGAAACC
5402298 TTCCTTTTGATTCTAGGCTTTGAGAAAGGCACTTGATGCTAGAAAAGATATA
131 TTCCTTTTGATTCTAGGCTTTGAGAAAGGCACTTGATGCTAGAAAAGATATA
5402350 GAGACATTACAATTTTGATTGGTGATTGGTACACTCGCAACCACACGGTTAGAACTTTGTCGAGT
1 GAGACATTACAATTTTGATTGGTGATTGGTACACTCGCAACCACACGGTTAGAACTTTGTCGAGT
**
5402415 TATTGGATTTATAGCCATGTTTTACTTTTCAGGGTAGTATATATCA-TGTGTTCAATAATGAAAC
66 TACAGGATTTATAGCCATGTTTTACTTTTCAGGGTAGTATATAT-AGTGTGTTCAATAATGAAAC
* *
5402479 CTTCCTTTTGATTCTAGGTTTTGAGAAAGGCACTTGATGCTGGAAAAGAT
130 CTTCCTTTTGATTCTAGGCTTTGAGAAAGGCACTTGATGCTAGAAAAGAT
5402529 CTTGGGATGC
Statistics
Matches: 172, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
182 171 0.99
183 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (182 bp):
GAGACATTACAATTTTGATTGGTGATTGGTACACTCGCAACCACACGGTTAGAACTTTGTCGAGT
TACAGGATTTATAGCCATGTTTTACTTTTCAGGGTAGTATATATAGTGTGTTCAATAATGAAACC
TTCCTTTTGATTCTAGGCTTTGAGAAAGGCACTTGATGCTAGAAAAGATATA
Found at i:5403576 original size:25 final size:24
Alignment explanation
Indices: 5403534--5403655 Score: 174
Period size: 25 Copynumber: 5.0 Consensus size: 24
5403524 GCTTTATCAT
*
5403534 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
5403559 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
5403583 ATAACTGGGGCATAAGCCCTTTTTA
1 ATAACTGGGGCATAAGCCC-TTTTA
*
5403608 ATAACTGGGGCGTAAGCCCTTTTTA
1 ATAACTGGGGCATAAGCCC-TTTTA
5403633 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
5403656 GCACTTCCTC
Statistics
Matches: 90, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
24 32 0.36
25 58 0.64
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.31
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:5403730 original size:20 final size:20
Alignment explanation
Indices: 5403705--5403771 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
5403695 TTATGAAAAC
5403705 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
5403725 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
5403745 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
5403765 ACCATGT
1 ATCATGT
5403772 TTATTAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:5403736 original size:11 final size:11
Alignment explanation
Indices: 5403705--5403760 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
5403695 TTATGAAAAC
5403705 ATCATGTGCAT
1 ATCATGTGCAT
*
5403716 ATCA--TACAT
1 ATCATGTGCAT
5403725 ATCATGTGCAT
1 ATCATGTGCAT
*
5403736 ATCA--TACAT
1 ATCATGTGCAT
*
5403745 GTCATGTGCAT
1 ATCATGTGCAT
5403756 ATCAT
1 ATCAT
5403761 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:5414209 original size:2 final size:2
Alignment explanation
Indices: 5414202--5414243 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5414192 ATTTTAATGA
5414202 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5414244 GGTTGTTTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5415800 original size:34 final size:36
Alignment explanation
Indices: 5415759--5415840 Score: 118
Period size: 37 Copynumber: 2.4 Consensus size: 36
5415749 ACTAGATTAG
5415759 TATATTATTAATACATA-A-AA-TAATATTATAATA
1 TATATTATTAATACATATATAACTAATATTATAATA
*
5415792 TATAATTATTAATACATATATAACTATTATTATAATA
1 TAT-ATTATTAATACATATATAACTAATATTATAATA
5415829 TATATTA-TAATA
1 TATATTATTAATA
5415841 AAAGATATAG
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
33 3 0.07
34 14 0.32
35 6 0.14
36 6 0.14
37 15 0.34
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (36 bp):
TATATTATTAATACATATATAACTAATATTATAATA
Found at i:5415812 original size:18 final size:17
Alignment explanation
Indices: 5415762--5415841 Score: 69
Period size: 18 Copynumber: 4.6 Consensus size: 17
5415752 AGATTAGTAT
*
5415762 ATTATTAATACATAAAATA
1 ATTATTAATA-AT-ATATA
5415781 A-TATT-ATAATATATA
1 ATTATTAATAATATATA
5415796 ATTATTAATACATATATA
1 ATTATTAATA-ATATATA
*
5415814 ACTATTATTATAATATAT-
1 ATTATTA--ATAATATATA
5415832 ATTA-TAATAA
1 ATTATTAATAA
5415842 AAGATATAGT
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
15 9 0.17
16 6 0.11
17 8 0.15
18 20 0.38
19 7 0.13
20 3 0.06
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTATTAATAATATATA
Found at i:5415834 original size:12 final size:12
Alignment explanation
Indices: 5415777--5415840 Score: 71
Period size: 12 Copynumber: 5.3 Consensus size: 12
5415767 TAATACATAA
5415777 AATA-ATATTAT
1 AATATATATTAT
5415788 AATATATAATTATT
1 AATATAT-ATTA-T
*
5415802 AATACATA-TAT
1 AATATATATTAT
5415813 AACTAT-TATTAT
1 AA-TATATATTAT
5415825 AATATATATTAT
1 AATATATATTAT
5415837 AATA
1 AATA
5415841 AAAGATATAG
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
11 12 0.27
12 21 0.47
13 5 0.11
14 7 0.16
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (12 bp):
AATATATATTAT
Found at i:5416074 original size:234 final size:239
Alignment explanation
Indices: 5415789--5416286 Score: 585
Period size: 234 Copynumber: 2.1 Consensus size: 239
5415779 TAATATTATA
* * * * *
5415789 ATAT-ATAATTATTAATACATATATAACTATTATTATAATATATATTATAATAAAAGATATAGTA
1 ATATGATAATAATTAATATATATATAACTACTATTATAATATACAATATAATAAAAGATATAGTA
* *
5415853 TCACATGATATTAAAATGTTTTATCATTGATACACATATATAAAAACTGGTAATATA-T-TATA-
66 TCACATGATATTAAAATGTTTAATCATTGAT--ACATATATAAAAACTAGTAATATATTATATAG
* * * *
5415915 TA-CT-ATACGATATGATAT-A-AC-AT-T-ATAGTAGGAGGGTTAACTTTCAAATGTA-AG-AA
129 TATATAATACGATATGATATAACACTATATAATAGTAAGAGGATTAACTTT-AAA-ATACAGAAA
* *
5415971 AAGTATAGAGACTTGGAACATATTTCAACCAATATAATATTAAATAATAAT
192 AAGTATAGAGACTTAGAACATATTTCAACCAATAT-A-A-TAAACAATAAT
* * *
5416022 ATATGATAATAATTAATATATA-ATGTACTACTATTATATTATACAATATAATAAAAGGTATAGT
1 ATATGATAATAATTAATATATATAT-AACTACTATTATAATATACAATATAATAAAAGATATAGT
* * * * *
5416086 ATTACATGATATTATAATGTTTAATCATTGATGCATATATATAAACTATTAATATATTATATAGT
65 ATCACATGATATTAAAATGTTTAATCATTGATACATATATAAAAACTAGTAATATATTATATAGT
*
5416151 ATATAATATGATATGATATAACACTATATAACATAGTAAGAGGATTAACTTTAAAATACAGAAAA
130 ATATAATACGATATGATATAACACTATAT-A-ATAGTAAGAGGATTAACTTTAAAATACAGAAAA
* *
5416216 AGTATAGGGACTTAGAACATATTTCAACCAGTATAATAAACAATAAT
193 AGTATAGAGACTTAGAACATATTTCAACCAATATAATAAACAATAAT
5416263 ATATGATAATAATTAATATA-ATAT
1 ATATGATAATAATTAATATATATAT
5416287 GTATTACTCT
Statistics
Matches: 224, Mismatches: 24, Indels: 26
0.82 0.09 0.09
Matches are distributed among these distances:
232 20 0.09
233 7 0.03
234 81 0.36
235 2 0.01
236 1 0.00
237 13 0.06
238 1 0.00
239 2 0.01
240 3 0.01
241 33 0.15
242 3 0.01
243 6 0.03
244 52 0.23
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.36
Consensus pattern (239 bp):
ATATGATAATAATTAATATATATATAACTACTATTATAATATACAATATAATAAAAGATATAGTA
TCACATGATATTAAAATGTTTAATCATTGATACATATATAAAAACTAGTAATATATTATATAGTA
TATAATACGATATGATATAACACTATATAATAGTAAGAGGATTAACTTTAAAATACAGAAAAAGT
ATAGAGACTTAGAACATATTTCAACCAATATAATAAACAATAAT
Found at i:5416323 original size:234 final size:229
Alignment explanation
Indices: 5415829--5416282 Score: 521
Period size: 244 Copynumber: 1.9 Consensus size: 229
5415819 TATTATAATA
* *
5415829 TATATTAT-AATA-AA-AGATATAGTATCACATGATATTAAAATGTTTTATCATTGATACACATA
1 TATATTATAAATATAATAGATATAGTATTACATGATATTAAAATGTTTAATCATTGATA-ACATA
* * * *
5415891 TATAAAAACTGGTAATATATTATATACTATACGATATGATATAACATTATAGTAGGAGGGTTAAC
65 TATAAAAACTAGTAATATATTATATAATATACGATATGATATAACATTATAGTAAGAGGATTAAC
* * *
5415956 TTTCAAATGTAAGAAAAGTATAGAGACTTGGAACATATTTCAACCAATATAATATTAAATAATAA
130 TTTCAAATATAAGAAAAGTATAGAGACTTAGAACATATTTCAACCAATATAATATTAAACAATAA
5416021 TATATGATAATAATTAATATATAATGTACTACTAT
195 TATATGATAATAATTAATATATAATGTACTACTAT
* * *
5416056 TATATTATACAATATAATAAAAGGTATAGTATTACATGATATTATAATGTTTAATCATTGAT-GC
1 TATATTATA-AATATAAT---AGATATAGTATTACATGATATTAAAATGTTTAATCATTGATAAC
* * *
5416120 ATATATATAAACTATTAATATATTATATAGTATATAATATGATATGATATAACACTATATAACAT
62 ATATATAAAAACTAGTAATATA-T-TATA-TA-AT-ATACGATATGATAT-A-AC-AT-T---AT
* *
5416185 AGTAAGAGGATTAACTTT-AAA-ATACAGAAAAAGTATAGGGACTTAGAACATATTTCAACCAGT
115 AGTAAGAGGATTAACTTTCAAATATA-AG-AAAAGTATAGAGACTTAGAACATATTTCAACCAAT
5416248 AT-A-A-TAAACAATAATATATGATAATAATTAATATA
178 ATAATATTAAACAATAATATATGATAATAATTAATATA
5416283 ATATGTATTA
Statistics
Matches: 189, Mismatches: 17, Indels: 28
0.81 0.07 0.12
Matches are distributed among these distances:
227 8 0.04
229 4 0.02
230 2 0.01
232 20 0.11
233 1 0.01
234 41 0.22
235 2 0.01
236 1 0.01
237 13 0.07
238 1 0.01
239 2 0.01
240 2 0.01
241 31 0.16
242 3 0.02
243 6 0.03
244 52 0.28
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.35
Consensus pattern (229 bp):
TATATTATAAATATAATAGATATAGTATTACATGATATTAAAATGTTTAATCATTGATAACATAT
ATAAAAACTAGTAATATATTATATAATATACGATATGATATAACATTATAGTAAGAGGATTAACT
TTCAAATATAAGAAAAGTATAGAGACTTAGAACATATTTCAACCAATATAATATTAAACAATAAT
ATATGATAATAATTAATATATAATGTACTACTAT
Found at i:5424812 original size:84 final size:81
Alignment explanation
Indices: 5424697--5424923 Score: 256
Period size: 84 Copynumber: 2.7 Consensus size: 81
5424687 CTATTTAGTC
* * * * *
5424697 CTTTATTATTTTTTACACCATTGTTTCTATTATTCATGTACCTTTTAAACCCTTAAATAGAAAGG
1 CTTTATTA-TTTTTATACCATT-TTTTTATTATTCATATACCTTTCAAACCCTTAAATAGAAAGA
* *
5424762 CTAGTGTTTCTATTTGATT
64 CTAATATTTCTATTTGA-T
* ** * * *
5424781 CTTTATTATTATTTATACAATTTTTGTTATTATTCATATGTCTTTCAAACCTTTAAGTCGAAAGA
1 CTTTATTATT-TTTATACCATTTTT-TTATTATTCATATACCTTTCAAACCCTTAAATAGAAAGA
5424846 CTAATATTTCTATTTGAT
64 CTAATATTTCTATTTGAT
*
5424864 CTTTTATTATTTATTATACCATTTTTATTATTATTCATATAGCTTTCAAACCCTTAAATA
1 C-TTTATTATTT-TTATACCATTTTT-TTATTATTCATATACCTTTCAAACCCTTAAATA
5424924 CGTGGATTGG
Statistics
Matches: 119, Mismatches: 20, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
83 8 0.07
84 111 0.93
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (81 bp):
CTTTATTATTTTTATACCATTTTTTTATTATTCATATACCTTTCAAACCCTTAAATAGAAAGACT
AATATTTCTATTTGAT
Found at i:5435228 original size:53 final size:53
Alignment explanation
Indices: 5435087--5435237 Score: 205
Period size: 53 Copynumber: 2.8 Consensus size: 53
5435077 ATAAGTGCGC
* * **
5435087 CCGTTTAAGACCATAGCTGGGTTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGATATGGCATCGGTATAATGTGATAATGTGACT
* *
5435140 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGATATGGCATCGGTATAATGTGATAATGTGACT
*
5435193 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGATATGGCATCGGTAT-A-ATGTGA
5435238 ACCGTGTAAG
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
52 1 0.01
53 80 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGATATGGCATCGGTATAATGTGATAATGTGACT
Found at i:5442738 original size:53 final size:53
Alignment explanation
Indices: 5442582--5442747 Score: 221
Period size: 53 Copynumber: 3.1 Consensus size: 53
5442572 TGACGAAAAT
* **
5442582 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
5442634 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
* * *
5442687 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGA
1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A
5442741 TATGTGA
1 -ATGTGA
5442748 ACCGTGTAAG
Statistics
Matches: 103, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
51 4 0.04
52 11 0.11
53 81 0.79
54 1 0.01
55 6 0.06
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
Found at i:5444799 original size:2 final size:2
Alignment explanation
Indices: 5444792--5444834 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5444782 AACTGAGCAA
5444792 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5444834 A
1 A
5444835 AATGTTTAGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.