Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 172 of 310
Found at i:56304858 original size:21 final size:21
Alignment explanation
Indices: 56304834--56304889 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
56304824 TACCAAAATG
56304834 ACACTAGTCTATACATGCCAT
1 ACACTAGTCTATACATGCCAT
56304855 ACACTAGTCTATACATGCCAT
1 ACACTAGTCTATACATGCCAT
*
56304876 ACACTA-TATATACA
1 ACACTAGTCTATACA
56304890 AAGCTTCAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 7 0.21
21 27 0.79
ACGTcount: A:0.38, C:0.27, G:0.07, T:0.29
Consensus pattern (21 bp):
ACACTAGTCTATACATGCCAT
Found at i:56307459 original size:48 final size:52
Alignment explanation
Indices: 56307400--56307526 Score: 154
Period size: 48 Copynumber: 2.4 Consensus size: 52
56307390 ATTTAATAGT
* *
56307400 TTTAATATTAAATTAAATTTAATAGTTATC-T-TA-AT-AGTATTTTATTAA
1 TTTAATATTAAATTAAATTTAATACTTATCATGTAGATAAATATTTTATTAA
* *
56307448 TTTAATGTTAAATTAAATTTAATACTTATCATGTAGATAAATGTTTTATTAA
1 TTTAATATTAAATTAAATTTAATACTTATCATGTAGATAAATATTTTATTAA
56307500 TTTAATAAATTTAATATTAAATTTAAT
1 TTTAAT--A-TTAA-ATTAAATTTAAT
56307527 GTAATATTTA
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
48 28 0.42
49 1 0.02
50 2 0.03
51 2 0.03
52 17 0.26
55 4 0.06
56 12 0.18
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (52 bp):
TTTAATATTAAATTAAATTTAATACTTATCATGTAGATAAATATTTTATTAA
Found at i:56307514 original size:61 final size:58
Alignment explanation
Indices: 56307446--56307564 Score: 148
Period size: 61 Copynumber: 2.0 Consensus size: 58
56307436 GTATTTTATT
* * * *
56307446 AATTTAATGTTAAATTAAATTTAATACTTATCATGTAGATAAATGTTTTATTAATTTAATA
1 AATTTAATATTAAATTAAATGTAATACTTATC-T-T-GATAAATATTATATTAATTTAATA
* * *
56307507 AATTTAATATTAAATTTAATGTAATATTTATCTTGATAATTATTATATTAATTTAATA
1 AATTTAATATTAAATTAAATGTAATACTTATCTTGATAAATATTATATTAATTTAATA
56307565 TTAAAGTGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
58 21 0.41
59 1 0.02
60 1 0.02
61 28 0.55
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.50
Consensus pattern (58 bp):
AATTTAATATTAAATTAAATGTAATACTTATCTTGATAAATATTATATTAATTTAATA
Found at i:56308275 original size:43 final size:43
Alignment explanation
Indices: 56308214--56308299 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
56308204 TATNAGGTAA
56308214 GAGTATCTGGTCTCTGTATCCCTAGGGATGCAAGAAGCAGTGG
1 GAGTATCTGGTCTCTGTATCCCTAGGGATGCAAGAAGCAGTGG
56308257 GAGTATCTGGTCTCTGTATCCCTAGGGATGCAAGAAGCAGTGG
1 GAGTATCTGGTCTCTGTATCCCTAGGGATGCAAGAAGCAGTGG
56308300 CGACATTAGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.26
Consensus pattern (43 bp):
GAGTATCTGGTCTCTGTATCCCTAGGGATGCAAGAAGCAGTGG
Found at i:56311094 original size:24 final size:24
Alignment explanation
Indices: 56311067--56311117 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
56311057 TAAAAATAAT
*
56311067 TATATTAAAAATATTATTAAATTA
1 TATATTAAAAATATTACTAAATTA
* * *
56311091 TATATTAATATTTTTACTAAATTA
1 TATATTAAAAATATTACTAAATTA
56311115 TAT
1 TAT
56311118 TCAATAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TATATTAAAAATATTACTAAATTA
Found at i:56324423 original size:32 final size:32
Alignment explanation
Indices: 56324377--56324456 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 32
56324367 TGTCAATCAT
* *
56324377 TTCAATAACCAACAAGCTT-AAAACATAATAAA
1 TTCAATATCCAACAA-ATTCAAAACATAATAAA
* * *
56324409 TTCAATATCTAACAAATTCAAGACATAATAAT
1 TTCAATATCCAACAAATTCAAAACATAATAAA
*
56324441 TTCAAAATCCAACAAA
1 TTCAATATCCAACAAA
56324457 CTAAAATTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 2 0.05
32 38 0.95
ACGTcount: A:0.54, C:0.19, G:0.03, T:0.25
Consensus pattern (32 bp):
TTCAATATCCAACAAATTCAAAACATAATAAA
Found at i:56327609 original size:852 final size:852
Alignment explanation
Indices: 56325966--56327669 Score: 3408
Period size: 852 Copynumber: 2.0 Consensus size: 852
56325956 ATTAAAAATC
56325966 TTTATTGATTTTGTAAAGAGACAATCAGACAAGTCATGTCAGATTAATAATGGGAAAAAAAATCT
1 TTTATTGATTTTGTAAAGAGACAATCAGACAAGTCATGTCAGATTAATAATGGGAAAAAAAATCT
56326031 TTTAAAGTTTTTCAAGCAATGATTTTTGTCGAAACCCAACACATTAGGGCACGATATCTCGAATT
66 TTTAAAGTTTTTCAAGCAATGATTTTTGTCGAAACCCAACACATTAGGGCACGATATCTCGAATT
56326096 ACCAAATACGAAATATTATCTTATTTTACGAAGTTTTTTAAATAGGAGCGATTATAAAAACAGAC
131 ACCAAATACGAAATATTATCTTATTTTACGAAGTTTTTTAAATAGGAGCGATTATAAAAACAGAC
56326161 TTGAAATATATTTATTCGATTTGTTTGAAGTAAAGAAAGTGGAATGAATAATTTCAGGAAAATAA
196 TTGAAATATATTTATTCGATTTGTTTGAAGTAAAGAAAGTGGAATGAATAATTTCAGGAAAATAA
56326226 GTTGGCAACTTCTGTAACAGTCTAATTTTCAGTGGTGTCGGAACAGTGATTCGAGATCACTAAAT
261 GTTGGCAACTTCTGTAACAGTCTAATTTTCAGTGGTGTCGGAACAGTGATTCGAGATCACTAAAT
56326291 CAGAAAAATGAGTAGGAAATATTATTAATTTAGTGAGTATAAGTTAAATGTGAAGTTAGGAAAAA
326 CAGAAAAATGAGTAGGAAATATTATTAATTTAGTGAGTATAAGTTAAATGTGAAGTTAGGAAAAA
56326356 TTTTGAAGTAGTGAATAGTGTACTAAAAATAAATATTAAAATAATTAGAATCGAAAACGAGGTAT
391 TTTTGAAGTAGTGAATAGTGTACTAAAAATAAATATTAAAATAATTAGAATCGAAAACGAGGTAT
56326421 CGAGACCTCAAGAATTTTAAATTGAGCCATAAATATTTTTATAAATATTTATGGAGTGTTAATAA
456 CGAGACCTCAAGAATTTTAAATTGAGCCATAAATATTTTTATAAATATTTATGGAGTGTTAATAA
56326486 GTCAGTATTAAAGTTTCATCAAGAAATTTTAAAGTTCTGATAGTTAATTGAACAAAAAGGACTAA
521 GTCAGTATTAAAGTTTCATCAAGAAATTTTAAAGTTCTGATAGTTAATTGAACAAAAAGGACTAA
56326551 ATTGTATTAAATGCAAAATTATGGGAAATGATTAAATAGCTTAAATGATAAAAGAAAGAGGGTTT
586 ATTGTATTAAATGCAAAATTATGGGAAATGATTAAATAGCTTAAATGATAAAAGAAAGAGGGTTT
56326616 AAAAGGAAAATAGACCCAAGGTCTCTTTGGGCTGGACGGCAATGGCATGAAATCAGCAAGAAAAT
651 AAAAGGAAAATAGACCCAAGGTCTCTTTGGGCTGGACGGCAATGGCATGAAATCAGCAAGAAAAT
56326681 AAGGAGAATTAAGGGCAAAATTGAAAAATTGCAAAATTTACTTAATAAAGCTAGGACCAAAGTGG
716 AAGGAGAATTAAGGGCAAAATTGAAAAATTGCAAAATTTACTTAATAAAGCTAGGACCAAAGTGG
56326746 AATTATCTAGATTTCTCTTTATTTTCTCTTCATATTCATCAGCTGAAAAACAGCCATGGAAGGGG
781 AATTATCTAGATTTCTCTTTATTTTCTCTTCATATTCATCAGCTGAAAAACAGCCATGGAAGGGG
56326811 GTTCAAA
846 GTTCAAA
56326818 TTTATTGATTTTGTAAAGAGACAATCAGACAAGTCATGTCAGATTAATAATGGGAAAAAAAATCT
1 TTTATTGATTTTGTAAAGAGACAATCAGACAAGTCATGTCAGATTAATAATGGGAAAAAAAATCT
56326883 TTTAAAGTTTTTCAAGCAATGATTTTTGTCGAAACCCAACACATTAGGGCACGATATCTCGAATT
66 TTTAAAGTTTTTCAAGCAATGATTTTTGTCGAAACCCAACACATTAGGGCACGATATCTCGAATT
56326948 ACCAAATACGAAATATTATCTTATTTTACGAAGTTTTTTAAATAGGAGCGATTATAAAAACAGAC
131 ACCAAATACGAAATATTATCTTATTTTACGAAGTTTTTTAAATAGGAGCGATTATAAAAACAGAC
56327013 TTGAAATATATTTATTCGATTTGTTTGAAGTAAAGAAAGTGGAATGAATAATTTCAGGAAAATAA
196 TTGAAATATATTTATTCGATTTGTTTGAAGTAAAGAAAGTGGAATGAATAATTTCAGGAAAATAA
56327078 GTTGGCAACTTCTGTAACAGTCTAATTTTCAGTGGTGTCGGAACAGTGATTCGAGATCACTAAAT
261 GTTGGCAACTTCTGTAACAGTCTAATTTTCAGTGGTGTCGGAACAGTGATTCGAGATCACTAAAT
56327143 CAGAAAAATGAGTAGGAAATATTATTAATTTAGTGAGTATAAGTTAAATGTGAAGTTAGGAAAAA
326 CAGAAAAATGAGTAGGAAATATTATTAATTTAGTGAGTATAAGTTAAATGTGAAGTTAGGAAAAA
56327208 TTTTGAAGTAGTGAATAGTGTACTAAAAATAAATATTAAAATAATTAGAATCGAAAACGAGGTAT
391 TTTTGAAGTAGTGAATAGTGTACTAAAAATAAATATTAAAATAATTAGAATCGAAAACGAGGTAT
56327273 CGAGACCTCAAGAATTTTAAATTGAGCCATAAATATTTTTATAAATATTTATGGAGTGTTAATAA
456 CGAGACCTCAAGAATTTTAAATTGAGCCATAAATATTTTTATAAATATTTATGGAGTGTTAATAA
56327338 GTCAGTATTAAAGTTTCATCAAGAAATTTTAAAGTTCTGATAGTTAATTGAACAAAAAGGACTAA
521 GTCAGTATTAAAGTTTCATCAAGAAATTTTAAAGTTCTGATAGTTAATTGAACAAAAAGGACTAA
56327403 ATTGTATTAAATGCAAAATTATGGGAAATGATTAAATAGCTTAAATGATAAAAGAAAGAGGGTTT
586 ATTGTATTAAATGCAAAATTATGGGAAATGATTAAATAGCTTAAATGATAAAAGAAAGAGGGTTT
56327468 AAAAGGAAAATAGACCCAAGGTCTCTTTGGGCTGGACGGCAATGGCATGAAATCAGCAAGAAAAT
651 AAAAGGAAAATAGACCCAAGGTCTCTTTGGGCTGGACGGCAATGGCATGAAATCAGCAAGAAAAT
56327533 AAGGAGAATTAAGGGCAAAATTGAAAAATTGCAAAATTTACTTAATAAAGCTAGGACCAAAGTGG
716 AAGGAGAATTAAGGGCAAAATTGAAAAATTGCAAAATTTACTTAATAAAGCTAGGACCAAAGTGG
56327598 AATTATCTAGATTTCTCTTTATTTTCTCTTCATATTCATCAGCTGAAAAACAGCCATGGAAGGGG
781 AATTATCTAGATTTCTCTTTATTTTCTCTTCATATTCATCAGCTGAAAAACAGCCATGGAAGGGG
56327663 GTTCAAA
846 GTTCAAA
56327670 CTGGTTTTCA
Statistics
Matches: 852, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
852 852 1.00
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (852 bp):
TTTATTGATTTTGTAAAGAGACAATCAGACAAGTCATGTCAGATTAATAATGGGAAAAAAAATCT
TTTAAAGTTTTTCAAGCAATGATTTTTGTCGAAACCCAACACATTAGGGCACGATATCTCGAATT
ACCAAATACGAAATATTATCTTATTTTACGAAGTTTTTTAAATAGGAGCGATTATAAAAACAGAC
TTGAAATATATTTATTCGATTTGTTTGAAGTAAAGAAAGTGGAATGAATAATTTCAGGAAAATAA
GTTGGCAACTTCTGTAACAGTCTAATTTTCAGTGGTGTCGGAACAGTGATTCGAGATCACTAAAT
CAGAAAAATGAGTAGGAAATATTATTAATTTAGTGAGTATAAGTTAAATGTGAAGTTAGGAAAAA
TTTTGAAGTAGTGAATAGTGTACTAAAAATAAATATTAAAATAATTAGAATCGAAAACGAGGTAT
CGAGACCTCAAGAATTTTAAATTGAGCCATAAATATTTTTATAAATATTTATGGAGTGTTAATAA
GTCAGTATTAAAGTTTCATCAAGAAATTTTAAAGTTCTGATAGTTAATTGAACAAAAAGGACTAA
ATTGTATTAAATGCAAAATTATGGGAAATGATTAAATAGCTTAAATGATAAAAGAAAGAGGGTTT
AAAAGGAAAATAGACCCAAGGTCTCTTTGGGCTGGACGGCAATGGCATGAAATCAGCAAGAAAAT
AAGGAGAATTAAGGGCAAAATTGAAAAATTGCAAAATTTACTTAATAAAGCTAGGACCAAAGTGG
AATTATCTAGATTTCTCTTTATTTTCTCTTCATATTCATCAGCTGAAAAACAGCCATGGAAGGGG
GTTCAAA
Found at i:56329054 original size:31 final size:30
Alignment explanation
Indices: 56329016--56329185 Score: 214
Period size: 31 Copynumber: 5.5 Consensus size: 30
56329006 TCCGGCTACA
56329016 GGTAGCTTCGACTACCTGATCAGTGAAAAGT
1 GGTAGCTTCG-CTACCTGATCAGTGAAAAGT
* *
56329047 GGTAGCTTCTGCTGCCTGATAAGTGAAAAGT
1 GGTAGCTTC-GCTACCTGATCAGTGAAAAGT
*
56329078 GGTAGCTTCTGCTACCTGATCAGTGAAAAAT
1 GGTAGCTTC-GCTACCTGATCAGTGAAAAGT
* * *
56329109 GGTAGCTCCGACTACCTGATCAATGAAAAAT
1 GGTAGCTTCG-CTACCTGATCAGTGAAAAGT
* *
56329140 GGTAGCTCCGGCTACCTGATCAGTGAATAGT
1 GGTAGCTTC-GCTACCTGATCAGTGAAAAGT
56329171 GGTAGCTTCGGCTAC
1 GGTAGCTTC-GCTAC
56329186 AAGTGACAAG
Statistics
Matches: 125, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
30 1 0.01
31 122 0.98
32 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (30 bp):
GGTAGCTTCGCTACCTGATCAGTGAAAAGT
Found at i:56329127 original size:93 final size:93
Alignment explanation
Indices: 56329016--56329185 Score: 259
Period size: 93 Copynumber: 1.8 Consensus size: 93
56329006 TCCGGCTACA
* * * * * *
56329016 GGTAGCTTCGACTACCTGATCAGTGAAAAGTGGTAGCTTCTGCTGCCTGATAAGTGAAAAGTGGT
1 GGTAGCTCCGACTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATAAGTGAAAAGTGGT
*
56329081 AGCTTCTGCTACCTGATCAGTGAAAAAT
66 AGCTTCGGCTACCTGATCAGTGAAAAAT
* *
56329109 GGTAGCTCCGACTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCAGTGAATAGTGGT
1 GGTAGCTCCGACTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATAAGTGAAAAGTGGT
56329174 AGCTTCGGCTAC
66 AGCTTCGGCTAC
56329186 AAGTGACAAG
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 68 1.00
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (93 bp):
GGTAGCTCCGACTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATAAGTGAAAAGTGGT
AGCTTCGGCTACCTGATCAGTGAAAAAT
Found at i:56330301 original size:16 final size:18
Alignment explanation
Indices: 56330280--56330316 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
56330270 AATCATAAAG
56330280 AAATAA-AAATAAAA-AT
1 AAATAATAAATAAAATAT
*
56330296 AAATAATACATAAAATAT
1 AAATAATAAATAAAATAT
56330314 AAA
1 AAA
56330317 GTTTAACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 7 0.39
18 5 0.28
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (18 bp):
AAATAATAAATAAAATAT
Found at i:56346800 original size:18 final size:18
Alignment explanation
Indices: 56346777--56346869 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
56346767 CCCAACTACT
*
56346777 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
56346795 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
56346813 GTATACGTGAATAGTACT
1 GTATACGTGAATAGTACC
*
56346831 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
56346849 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
56346867 GTA
1 GTA
56346870 AACGGTCGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:56346829 original size:36 final size:36
Alignment explanation
Indices: 56346777--56346869 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
56346767 CCCAACTACT
*
56346777 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
*
56346813 GTATACGTGAATAGTACTGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
56346849 GTATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
56346870 AACGGTCGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
Found at i:56351334 original size:23 final size:23
Alignment explanation
Indices: 56351308--56351364 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
56351298 TTAGTATCAC
56351308 AACTTAATTGAACCGTAAACCGT
1 AACTTAATTGAACCGTAAACCGT
56351331 AACTTAATTGAACCGTAAACCGT
1 AACTTAATTGAACCGTAAACCGT
56351354 AACTTAATTGA
1 AACTTAATTGA
56351365 TGAAATTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.28
Consensus pattern (23 bp):
AACTTAATTGAACCGTAAACCGT
Found at i:56352082 original size:44 final size:44
Alignment explanation
Indices: 56352032--56352120 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
56352022 AGTTTCTAGA
* *
56352032 AGATGTTTTATTTTAACTCTTTATAACAACTTTTCACTTATAAT
1 AGATGTTTGATTTTAACCCTTTATAACAACTTTTCACTTATAAT
56352076 AGATGTTTGATTTTAACCCTTTATAACAACTTTTCACTTATAAT
1 AGATGTTTGATTTTAACCCTTTATAACAACTTTTCACTTATAAT
56352120 A
1 A
56352121 ATATCCATAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.47
Consensus pattern (44 bp):
AGATGTTTGATTTTAACCCTTTATAACAACTTTTCACTTATAAT
Found at i:56352242 original size:24 final size:20
Alignment explanation
Indices: 56352200--56352240 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
56352190 ACGTAAAATT
56352200 ATAGTTATTTCATATAAGCA
1 ATAGTTATTTCATATAAGCA
56352220 ATAGTTATTTCATATAAGCA
1 ATAGTTATTTCATATAAGCA
56352240 A
1 A
56352241 GCCTATCAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (20 bp):
ATAGTTATTTCATATAAGCA
Found at i:56354083 original size:10 final size:10
Alignment explanation
Indices: 56354068--56354092 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
56354058 ATAGAAGATA
56354068 TTATTTTGTT
1 TTATTTTGTT
56354078 TTATTTTGTT
1 TTATTTTGTT
56354088 TTATT
1 TTATT
56354093 ATTTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.00, G:0.08, T:0.80
Consensus pattern (10 bp):
TTATTTTGTT
Found at i:56354107 original size:18 final size:17
Alignment explanation
Indices: 56354077--56354114 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
56354067 ATTATTTTGT
*
56354077 TTTATTTTGTTTTATTA
1 TTTATTTTATTTTATTA
56354094 TTTATTTTTATTTTATTA
1 TTTA-TTTTATTTTATTA
56354112 TTT
1 TTT
56354115 TAGAATAGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTATTTTATTTTATTA
Found at i:56355330 original size:17 final size:18
Alignment explanation
Indices: 56355260--56355609 Score: 190
Period size: 18 Copynumber: 19.1 Consensus size: 18
56355250 TCATTAACAA
* *
56355260 TCAG-AACAATTATTTAT
1 TCAGTAACAATCAGTTAT
* *
56355277 TTAGTAACAGTCAGTTAT
1 TCAGTAACAATCAGTTAT
* *
56355295 TCGGTAACAATCAATTAT
1 TCAGTAACAATCAGTTAT
*
56355313 TCAGTAA-AATCAGGTAT
1 TCAGTAACAATCAGTTAT
*
56355330 TCAGTAACAATTAAGTTAT
1 TCAGTAACAA-TCAGTTAT
* *
56355349 TCAGTAGCAGTCA-TTCAT
1 TCAGTAACAATCAGTT-AT
* *
56355367 TCAGTGACAATCAATTAT
1 TCAGTAACAATCAGTTAT
* * *
56355385 TCAATAATAACCAGTTAT
1 TCAGTAACAATCAGTTAT
56355403 TCAGTATCGATCAATTGATCAGTTAT
1 TCAGTA---A-C-A---ATCAGTTAT
* * *
56355429 CCAGTAACAGTCAATTAT
1 TCAGTAACAATCAGTTAT
* *
56355447 TTAGTAA-AATCAGGTAT
1 TCAGTAACAATCAGTTAT
*
56355464 TCAGTAACAATTAAGTTAT
1 TCAGTAACAA-TCAGTTAT
* *
56355483 TCAGTAGCAGTCA-TTCAT
1 TCAGTAACAATCAGTT-AT
* *
56355501 TCAGTGACAATCAATTAT
1 TCAGTAACAATCAGTTAT
* *
56355519 TCAGTAATATTCAGTTAT
1 TCAGTAACAATCAGTTAT
* *
56355537 TCAGTAACAGTCTA-ATAT
1 TCAGTAACAATC-AGTTAT
* * *
56355555 CCAGTAACAGTCAATTAT
1 TCAGTAACAATCAGTTAT
* * * * *
56355573 CCGGTAACAGTTAATTAT
1 TCAGTAACAATCAGTTAT
* *
56355591 TCAGTAATAATCAATTAT
1 TCAGTAACAATCAGTTAT
56355609 T
1 T
56355610 TTATACCTTT
Statistics
Matches: 254, Mismatches: 60, Indels: 37
0.72 0.17 0.11
Matches are distributed among these distances:
17 36 0.14
18 167 0.66
19 33 0.13
21 2 0.01
22 1 0.00
23 2 0.01
26 13 0.05
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TCAGTAACAATCAGTTAT
Found at i:56355456 original size:134 final size:134
Alignment explanation
Indices: 56355287--56355542 Score: 449
Period size: 134 Copynumber: 1.9 Consensus size: 134
56355277 TTAGTAACAG
* *
56355287 TCAGTTATTCGGTAACAATCAATTATTCAGTAAAATCAGGTATTCAGTAACAATTAAGTTATTCA
1 TCAGTTATCCAGTAACAATCAATTATTCAGTAAAATCAGGTATTCAGTAACAATTAAGTTATTCA
56355352 GTAGCAGTCATTCATTCAGTGACAATCAATTATTCAATAATAACCAGTTATTCAGTATCGATCAA
66 GTAGCAGTCATTCATTCAGTGACAATCAATTATTCAATAATAACCAGTTATTCAGTATCGATCAA
56355417 TTGA
131 TTGA
* *
56355421 TCAGTTATCCAGTAACAGTCAATTATTTAGTAAAATCAGGTATTCAGTAACAATTAAGTTATTCA
1 TCAGTTATCCAGTAACAATCAATTATTCAGTAAAATCAGGTATTCAGTAACAATTAAGTTATTCA
* **
56355486 GTAGCAGTCATTCATTCAGTGACAATCAATTATTCAGTAATATTCAGTTATTCAGTA
66 GTAGCAGTCATTCATTCAGTGACAATCAATTATTCAATAATAACCAGTTATTCAGTA
56355543 ACAGTCTAAT
Statistics
Matches: 115, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
134 115 1.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (134 bp):
TCAGTTATCCAGTAACAATCAATTATTCAGTAAAATCAGGTATTCAGTAACAATTAAGTTATTCA
GTAGCAGTCATTCATTCAGTGACAATCAATTATTCAATAATAACCAGTTATTCAGTATCGATCAA
TTGA
Found at i:56355842 original size:45 final size:45
Alignment explanation
Indices: 56355785--56355894 Score: 150
Period size: 45 Copynumber: 2.4 Consensus size: 45
56355775 ACAGAAACAG
* * * *
56355785 TAACAGTAACAGTAATAGTATTCAACACACAAAGTGCTGAATTGA
1 TAACTGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCGA
* *
56355830 TAAC-GATAACAGTAACAGTATTCGACACACAAAGTGCCGAATCGG
1 TAACTG-TAACAGTAACAGTATTCAACACACAAAGTGCCGAATCGA
56355875 TAACTGTAACAGTAACAGTA
1 TAACTGTAACAGTAACAGTA
56355895 ACAGTAACAG
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
44 1 0.02
45 56 0.97
46 1 0.02
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.22
Consensus pattern (45 bp):
TAACTGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCGA
Found at i:56355889 original size:6 final size:6
Alignment explanation
Indices: 56355874--56355906 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
56355864 TGCCGAATCG
*
56355874 GTAACT GTAACA GTAACA GTAACA GTAACA GTA
1 GTAACA GTAACA GTAACA GTAACA GTAACA GTA
56355907 GTCGGCACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.21
Consensus pattern (6 bp):
GTAACA
Found at i:56357347 original size:26 final size:26
Alignment explanation
Indices: 56357301--56357353 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
56357291 TCAAACATGC
*
56357301 ATTTAGGTCAATTTAACCCTAGGGGT
1 ATTTAGGTCAATTTAACCCTAGAGGT
* *
56357327 ATTTCGGT-AATTTATCTCCTAGAGGT
1 ATTTAGGTCAATTTAAC-CCTAGAGGT
56357353 A
1 A
56357354 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACCCTAGAGGT
Found at i:56358874 original size:26 final size:26
Alignment explanation
Indices: 56358838--56358921 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
56358828 CATGAAATTC
56358838 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
56358864 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
56358890 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
56358916 TTATCA
1 TTATCA
56358922 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:56360175 original size:16 final size:16
Alignment explanation
Indices: 56360156--56360194 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
56360146 AATTTTTCCC
*
56360156 TTTTTCCTTCTTTCTT
1 TTTTTCCTTCCTTCTT
56360172 TTTTTCCTTCCTTCTT
1 TTTTTCCTTCCTTCTT
*
56360188 TCTTTCC
1 TTTTTCC
56360195 CCTGCTCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTTCCTTCCTTCTT
Found at i:56370613 original size:13 final size:13
Alignment explanation
Indices: 56370595--56370629 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
56370585 AAATAGAAGA
*
56370595 TATTATTTTGTTT
1 TATTATTTTATTT
56370608 TATTA-TTTATTT
1 TATTATTTTATTT
56370620 TATTATTTTA
1 TATTATTTTA
56370630 GAATAGGCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (13 bp):
TATTATTTTATTT
Found at i:56374435 original size:25 final size:23
Alignment explanation
Indices: 56374378--56374435 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 23
56374368 AGAACAATAG
56374378 TAAA-ATAAT-GATATTAATACC
1 TAAATATAATAGATATTAATACC
*
56374399 TAAATACAAATAGATATATAATACC
1 TAAATA-TAATAGATAT-TAATACC
56374424 TAAAATATAATA
1 T-AAATATAATA
56374436 ATAACAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 4 0.13
22 1 0.03
23 3 0.10
24 5 0.17
25 12 0.40
26 5 0.17
ACGTcount: A:0.57, C:0.09, G:0.03, T:0.31
Consensus pattern (23 bp):
TAAATATAATAGATATTAATACC
Found at i:56374436 original size:17 final size:17
Alignment explanation
Indices: 56374412--56374450 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
56374402 ATACAAATAG
* *
56374412 ATAT-ATAATACCTAAA
1 ATATAATAATAACAAAA
56374428 ATATAATAATAACAAAA
1 ATATAATAATAACAAAA
56374445 ATATAA
1 ATATAA
56374451 ATAGATAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (17 bp):
ATATAATAATAACAAAA
Found at i:56374463 original size:17 final size:17
Alignment explanation
Indices: 56374443--56374481 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
56374433 ATAATAACAA
56374443 AAATATAAATAGATAAG
1 AAATATAAATAGATAAG
56374460 AAATATAAATAGATAAG
1 AAATATAAATAGATAAG
*
56374477 TAATA
1 AAATA
56374482 AGAAAATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.26
Consensus pattern (17 bp):
AAATATAAATAGATAAG
Found at i:56374642 original size:3 final size:3
Alignment explanation
Indices: 56374634--56374700 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
56374624 TAAGATGGCG
56374634 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
56374682 ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
56374701 CGACATAACA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:56375000 original size:18 final size:18
Alignment explanation
Indices: 56374920--56375000 Score: 60
Period size: 18 Copynumber: 4.5 Consensus size: 18
56374910 AAGACTAAGA
* *
56374920 TAATAATAATAGTAAT-G
1 TAATAATAACAGAAATAG
*
56374937 ATAATAAT-ACAAAAAATAG
1 -TAATAATAAC-AGAAATAG
**
56374956 TAATAACT-ACATTAATAG
1 TAATAA-TAACAGAAATAG
*
56374974 AAATAATAACAGAAATAG
1 TAATAATAACAGAAATAG
56374992 TAATAATAA
1 TAATAATAA
56375001 TAGTGCTTGA
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
17 2 0.04
18 44 0.88
19 4 0.08
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.27
Consensus pattern (18 bp):
TAATAATAACAGAAATAG
Found at i:56376580 original size:13 final size:14
Alignment explanation
Indices: 56376562--56376590 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
56376552 TTAAAATTGT
56376562 ATAAAAA-TTAAAA
1 ATAAAAACTTAAAA
56376575 ATAAAAACTTAAAA
1 ATAAAAACTTAAAA
56376589 AT
1 AT
56376591 GGAAAGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.24
Consensus pattern (14 bp):
ATAAAAACTTAAAA
Found at i:56377100 original size:24 final size:24
Alignment explanation
Indices: 56377037--56377088 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
56377027 TTTCTAGAAG
* * **
56377037 ATTTAGTATTTATGAGAATAATAT
1 ATTTAGCATTTATTAGCGTAATAT
56377061 ATTTAGCATTTATTAGCGTAATAT
1 ATTTAGCATTTATTAGCGTAATAT
56377085 ATTT
1 ATTT
56377089 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.48
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCGTAATAT
Found at i:56386778 original size:22 final size:22
Alignment explanation
Indices: 56386743--56386787 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
56386733 AAATAAGTTG
* *
56386743 TTTTGTTGTTATTTCACTATTA
1 TTTTGTTATCATTTCACTATTA
**
56386765 TTTTGTTATCATTTTGCTATTA
1 TTTTGTTATCATTTCACTATTA
56386787 T
1 T
56386788 ATTAATACTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.18, C:0.09, G:0.09, T:0.64
Consensus pattern (22 bp):
TTTTGTTATCATTTCACTATTA
Found at i:56389062 original size:22 final size:23
Alignment explanation
Indices: 56389037--56389107 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 23
56389027 TGGGTTTTTG
56389037 ATTTTTTTATTGCA-TTATATTA
1 ATTTTTTTATTGCAGTTATATTA
* * *
56389059 A-TTTGTTATTGTAGTTATATTG
1 ATTTTTTTATTGCAGTTATATTA
* * *
56389081 ATTTTTTTAGTGTAGTTAT-TAA
1 ATTTTTTTATTGCAGTTATATTA
56389103 ATTTT
1 ATTTT
56389108 GTATAGTTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 10 0.25
22 15 0.38
23 15 0.38
ACGTcount: A:0.25, C:0.01, G:0.11, T:0.62
Consensus pattern (23 bp):
ATTTTTTTATTGCAGTTATATTA
Found at i:56389098 original size:23 final size:23
Alignment explanation
Indices: 56389034--56389099 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
56389024 GATTGGGTTT
*
56389034 TTGATTTTTTTATTGCA-TTATA
1 TTGATTTTTTTATTGTAGTTATA
* *
56389056 TT-AATTTGTTATTGTAGTTATA
1 TTGATTTTTTTATTGTAGTTATA
*
56389078 TTGATTTTTTTAGTGTAGTTAT
1 TTGATTTTTTTATTGTAGTTAT
56389100 TAAATTTTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 11 0.31
22 9 0.25
23 16 0.44
ACGTcount: A:0.23, C:0.02, G:0.14, T:0.62
Consensus pattern (23 bp):
TTGATTTTTTTATTGTAGTTATA
Found at i:56392750 original size:2 final size:2
Alignment explanation
Indices: 56392743--56392769 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
56392733 ACAAATACAA
56392743 GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT G
56392770 CCTTAGTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:56395636 original size:25 final size:26
Alignment explanation
Indices: 56395606--56395657 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
56395596 TTTAAATTAA
*
56395606 TAAATGA-AAAATTAC-AGTTTACCCT
1 TAAATGATAAAATT-CTAGTTTAACCT
56395631 TAAATGATAAAATTCTAGTTTAACCT
1 TAAATGATAAAATTCTAGTTTAACCT
56395657 T
1 T
56395658 TTAAAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (26 bp):
TAAATGATAAAATTCTAGTTTAACCT
Found at i:56395875 original size:20 final size:21
Alignment explanation
Indices: 56395837--56395876 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
56395827 CTAAAGTCTA
*
56395837 ATTAAGTAACAAAACTATTAC
1 ATTAAGTAACAAAAATATTAC
*
56395858 ATTAA-TAATAAAAATATTA
1 ATTAAGTAACAAAAATATTA
56395877 TTAAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (21 bp):
ATTAAGTAACAAAAATATTAC
Found at i:56396046 original size:22 final size:22
Alignment explanation
Indices: 56396018--56396059 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
56396008 TTTATATATA
*
56396018 AAAATTATA-TTTATTTAATTAC
1 AAAATTAGATTTTA-TTAATTAC
56396040 AAAATTAGATTTTATTAATT
1 AAAATTAGATTTTATTAATT
56396060 TTAATTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
AAAATTAGATTTTATTAATTAC
Found at i:56405278 original size:30 final size:31
Alignment explanation
Indices: 56405237--56405296 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
56405227 GGTACCCATA
*
56405237 TAAAAATTTTAAA-ACAAAT-AATGTATATAT
1 TAAAAAGTTTAAATACAAATGAAT-TATATAT
*
56405267 TAAAAAGTTTAAATATAAATGAATTATATA
1 TAAAAAGTTTAAATACAAATGAATTATATA
56405297 AATAAAACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 12 0.46
31 11 0.42
32 3 0.12
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.37
Consensus pattern (31 bp):
TAAAAAGTTTAAATACAAATGAATTATATAT
Found at i:56416941 original size:17 final size:17
Alignment explanation
Indices: 56416896--56416941 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
56416886 CGACTTTATC
*
56416896 CGAATCGAGCAAGCTTT
1 CGAATCGAGCATGCTTT
56416913 CGAATCGAGCATGC-TT
1 CGAATCGAGCATGCTTT
56416929 CTGAATCGAGCAT
1 C-GAATCGAGCAT
56416942 TATAAACGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 3 0.11
17 24 0.89
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (17 bp):
CGAATCGAGCATGCTTT
Found at i:56417706 original size:27 final size:27
Alignment explanation
Indices: 56417668--56417723 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
56417658 ATTTAAATTT
56417668 AGATTCTAATTATACGAACTTACCTCG
1 AGATTCTAATTATACGAACTTACCTCG
56417695 AGATTCTAATTATACGAACTTACCTCG
1 AGATTCTAATTATACGAACTTACCTCG
56417722 AG
1 AG
56417724 TTGCTCGGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.32
Consensus pattern (27 bp):
AGATTCTAATTATACGAACTTACCTCG
Found at i:56420555 original size:34 final size:34
Alignment explanation
Indices: 56420495--56420589 Score: 131
Period size: 33 Copynumber: 2.8 Consensus size: 34
56420485 GTTCAGAGTT
56420495 TTTTAAA-AAATTAATTAAATTAGGTTTTAAGGG
1 TTTTAAATAAATTAATTAAATTAGGTTTTAAGGG
* *
56420528 TTTTAAATAAATAAATT-AATTAGGGTTTAAGGG
1 TTTTAAATAAATTAATTAAATTAGGTTTTAAGGG
* *
56420561 TTCTAAATAAATTAATTGAATTAAGGTTT
1 TTTTAAATAAATTAATTAAATT-AGGTTT
56420590 AGTTTTTTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
33 37 0.69
34 12 0.22
35 5 0.09
ACGTcount: A:0.42, C:0.01, G:0.15, T:0.42
Consensus pattern (34 bp):
TTTTAAATAAATTAATTAAATTAGGTTTTAAGGG
Found at i:56420912 original size:125 final size:124
Alignment explanation
Indices: 56420690--56421205 Score: 662
Period size: 125 Copynumber: 4.1 Consensus size: 124
56420680 AGGATTTTGT
* * * ** * *
56420690 TTTTTCTACAGTAGTT-TCAGAAAAATTAATTTTGAGAAGACGGTTCTGAAAAAATAATATAAAA
1 TTTTTCTACAGTAGTTCT-TGAAAAAATAATTTTGAGAAAACAATTCT-AAAAAATAGTATCAAA
* * *
56420754 AACGCTTCAAGCAAGATGCATTGTCAGCAAAATTACTGAAAAAGCT-TCCACGTGGACGCTC
64 AACGCTTTAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAGCTCT-CACGTGGACGCTC
* *
56420815 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGATAATTCTAAAAAAATAGTATCAAAA
1 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAAACAATTCT-AAAAAATAGTATCAAAA
* * * *
56420880 ACGCTTTAAGCAGGATTCACTGTCAGCAAAATTACTGAAAAAGCTCTAATGTAGACGCTC
65 ACGCTTTAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAGCTCTCACGTGGACGCTC
* * **
56420940 TTTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAGAAAATGATTCTCAAAAAATAGTATCAAAA
1 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAAACAATTCT-AAAAAATAGTATCAAAA
* *
56421005 ATGC-TTAAGGCAGTATGCACTGTCAGCAAAATTACTGAAAAAGGCTCTCACGT-GACGCTC
65 ACGCTTTAA-GCAGGATGCACTGTCAGCAAAATTACTGAAAAA-GCTCTCACGTGGACGCTC
* *
56421065 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAAACAATTCTGAAAAATAGTGTCAAAAA
1 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAAACAATTCTAAAAAATAGTATCAAAAA
* * * * * *
56421130 CGCTTTAAGCATGATGCACTATCAGTAAAATTACTGAAAAAAGCTCCCACGTGAACGCTA
66 CGCTTTAAGCAGGATGCACTGTCAGCAAAATTACTG-AAAAAGCTCTCACGTGGACGCTC
56421190 TTTTTCTACAGTAGTT
1 TTTTTCTACAGTAGTT
56421206 TCTGCTTGGC
Statistics
Matches: 345, Mismatches: 39, Indels: 14
0.87 0.10 0.04
Matches are distributed among these distances:
124 55 0.16
125 280 0.81
126 10 0.03
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (124 bp):
TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAAACAATTCTAAAAAATAGTATCAAAAA
CGCTTTAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAGCTCTCACGTGGACGCTC
Found at i:56423294 original size:21 final size:20
Alignment explanation
Indices: 56423265--56423311 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
56423255 ATATAATAAT
56423265 ATAATAACATAAAATAAAAGAA
1 ATAA-AACATAAAAT-AAAGAA
* *
56423287 ATAAAACATGAAATAAATAA
1 ATAAAACATAAAATAAAGAA
56423307 ATAAA
1 ATAAA
56423312 GAATGAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.43
21 9 0.39
22 4 0.17
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.19
Consensus pattern (20 bp):
ATAAAACATAAAATAAAGAA
Found at i:56423346 original size:17 final size:15
Alignment explanation
Indices: 56423309--56423347 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
56423299 ATAAATAAAT
*
56423309 AAAGAATGAAAACAA
1 AAAGAATGAAAAAAA
56423324 AAAGAATGAAAAAAGA
1 AAAGAATGAAAAAA-A
56423340 AACAGAAT
1 AA-AGAAT
56423348 AGCAAATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 3 0.14
17 5 0.24
ACGTcount: A:0.72, C:0.05, G:0.15, T:0.08
Consensus pattern (15 bp):
AAAGAATGAAAAAAA
Found at i:56424546 original size:22 final size:23
Alignment explanation
Indices: 56424503--56424547 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
56424493 ATATAGTGAA
56424503 TTGAAAATAGAATGTGAAATATG
1 TTGAAAATAGAATGTGAAATATG
56424526 TTGAAAATA-AATG-GAATATATG
1 TTGAAAATAGAATGTGAA-ATATG
56424548 AGTTATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 3 0.14
22 9 0.43
23 9 0.43
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.31
Consensus pattern (23 bp):
TTGAAAATAGAATGTGAAATATG
Found at i:56426938 original size:18 final size:18
Alignment explanation
Indices: 56426915--56426955 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
56426905 CTGAGAAAAT
*
56426915 GATACATATAAGGGTTAG
1 GATACATATAAGGGCTAG
56426933 GATACATATAAGGGCTAG
1 GATACATATAAGGGCTAG
56426951 GATAC
1 GATAC
56426956 GCACCTGGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.39, C:0.10, G:0.27, T:0.24
Consensus pattern (18 bp):
GATACATATAAGGGCTAG
Found at i:56440423 original size:23 final size:23
Alignment explanation
Indices: 56440396--56440440 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
56440386 GTAATAAATT
56440396 TGAAAAGGCAACAACTGTTTATC
1 TGAAAAGGCAACAACTGTTTATC
56440419 TGAAAAGGCAACAACTGTTTAT
1 TGAAAAGGCAACAACTGTTTAT
56440441 GAATATATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.27
Consensus pattern (23 bp):
TGAAAAGGCAACAACTGTTTATC
Found at i:56447187 original size:27 final size:28
Alignment explanation
Indices: 56447157--56447267 Score: 104
Period size: 27 Copynumber: 4.1 Consensus size: 28
56447147 AGACTATCCC
* *
56447157 TTCATGATT-AGCCATAAAGGCGTTCCT
1 TTCATGATTGCGCCACAAAGGCGTTCCT
* *
56447184 TTCAT-ATTGCGCCACAAAGGCTTTCTT
1 TTCATGATTGCGCCACAAAGGCGTTCCT
* * ** *
56447211 TTTATG-TTGTGCCACAAAGATGTTCAT
1 TTCATGATTGCGCCACAAAGGCGTTCCT
*
56447238 TTCATAATT-CGCCACAAAGGCGTTCCT
1 TTCATGATTGCGCCACAAAGGCGTTCCT
56447265 TTC
1 TTC
56447268 CTAATGTGTT
Statistics
Matches: 65, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
26 3 0.05
27 60 0.92
28 2 0.03
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.36
Consensus pattern (28 bp):
TTCATGATTGCGCCACAAAGGCGTTCCT
Found at i:56449080 original size:40 final size:40
Alignment explanation
Indices: 56449035--56449169 Score: 146
Period size: 40 Copynumber: 3.4 Consensus size: 40
56449025 TGGTTATTTG
* *
56449035 TGGCACTTTGTGTGCGATACGACATAGCTTCGGCTATATA
1 TGGCACTTAGTGTGCGATTCGACATAGCTTCGGCTATATA
** *** *
56449075 TGGCACTTAGTGTGCGATTCGACATAATTTCAAATATTTA
1 TGGCACTTAGTGTGCGATTCGACATAGCTTCGGCTATATA
* * *
56449115 TGGCACTTAGTGT-CTGATTTGAGATAGCTTCGGCTATGTA
1 TGGCACTTAGTGTGC-GATTCGACATAGCTTCGGCTATATA
*
56449155 TGACACTTAGTGTGC
1 TGGCACTTAGTGTGC
56449170 TAGATATTGA
Statistics
Matches: 76, Mismatches: 17, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
39 1 0.01
40 74 0.97
41 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (40 bp):
TGGCACTTAGTGTGCGATTCGACATAGCTTCGGCTATATA
Found at i:56449206 original size:28 final size:28
Alignment explanation
Indices: 56449152--56449211 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
56449142 CTTCGGCTAT
*
56449152 GTATGACACTTAGTGTGCTAGATATTGA
1 GTATGACACTTAGTGTGCTAGACATTGA
*
56449180 GTATGACACTTAGTGTG-TAAGGCATTGA
1 GTATGACACTTAGTGTGCT-AGACATTGA
56449208 GTAT
1 GTAT
56449212 TCAACGACAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 1 0.03
28 28 0.97
ACGTcount: A:0.28, C:0.10, G:0.27, T:0.35
Consensus pattern (28 bp):
GTATGACACTTAGTGTGCTAGACATTGA
Found at i:56456669 original size:40 final size:40
Alignment explanation
Indices: 56456598--56456685 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
56456588 TGGCACTTAG
* *
56456598 TGTGCGATACGACATAGCTTCGGCTAGATATGACACTTGA
1 TGTGCGATACGACATAGCTTCAGATAGATATGACACTTGA
* * * * *
56456638 TGTGTGATTCGACATAGTTTCAGATATATATGGCACTT-A
1 TGTGCGATACGACATAGCTTCAGATAGATATGACACTTGA
56456677 GTGTGCGAT
1 -TGTGCGAT
56456686 TTGAGATGGC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
39 1 0.03
40 38 0.97
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (40 bp):
TGTGCGATACGACATAGCTTCAGATAGATATGACACTTGA
Found at i:56458370 original size:35 final size:35
Alignment explanation
Indices: 56458308--56458415 Score: 85
Period size: 40 Copynumber: 2.9 Consensus size: 35
56458298 TTTCCTCATT
*
56458308 GAAATACCATACCTACATTTTGCAACTCGGTATCG
1 GAAATACCATACCTACATTTTGCAACTCAGTATCG
* * * *
56458343 GAAATGCCATACCTACGTTTCT-TAACTCAGTATGG
1 GAAATACCATACCTACATTT-TGCAACTCAGTATCG
*
56458378 ATTTGATAATACCATACCTACGTTTCT-CAACTCAGTAT
1 ----GA-AATACCATACCTACATTT-TGCAACTCAGTAT
56458416 AGATGATATC
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
35 28 0.47
36 1 0.02
39 2 0.03
40 29 0.48
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (35 bp):
GAAATACCATACCTACATTTTGCAACTCAGTATCG
Found at i:56458430 original size:35 final size:38
Alignment explanation
Indices: 56458350--56458438 Score: 121
Period size: 40 Copynumber: 2.4 Consensus size: 38
56458340 TCGGAAATGC
* *
56458350 CATACCTACGTTTCTTAACTCAGTATGGATTTGATAATA
1 CATACCTACGTTTCTCAACTCAGTATAGA-TTGATAATA
56458389 CCATACCTACGTTTCTCAACTCAGTATAGA-TGAT-AT-
1 -CATACCTACGTTTCTCAACTCAGTATAGATTGATAATA
56458425 CATACCTACGTTTC
1 CATACCTACGTTTC
56458439 ACACTTTTCC
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
35 14 0.30
37 2 0.04
38 4 0.09
40 27 0.57
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (38 bp):
CATACCTACGTTTCTCAACTCAGTATAGATTGATAATA
Found at i:56461859 original size:21 final size:21
Alignment explanation
Indices: 56461818--56461864 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
56461808 TAACAAATTT
*
56461818 AGTTAATTACATATTATATAA
1 AGTTAATTAAATATTATATAA
*
56461839 AGTTAATTATAATTTTA-ATAA
1 AGTTAATTA-AATATTATATAA
56461860 A-TTAA
1 AGTTAA
56461865 CCCTAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.17
21 14 0.61
22 5 0.22
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (21 bp):
AGTTAATTAAATATTATATAA
Found at i:56464074 original size:3 final size:3
Alignment explanation
Indices: 56464066--56464093 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
56464056 CTTTCTTTCT
56464066 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
56464094 GTTTTATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:56464155 original size:17 final size:18
Alignment explanation
Indices: 56464134--56464176 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
56464124 AAATTATATA
56464134 ATATAATA-TATTTTACTT
1 ATATAATACTA-TTTACTT
*
56464152 -TATATTACTATTTACTT
1 ATATAATACTATTTACTT
56464169 ATATAATA
1 ATATAATA
56464177 AGTAAAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATAATACTATTTACTT
Found at i:56465862 original size:17 final size:17
Alignment explanation
Indices: 56465840--56465872 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
56465830 AAACTTCACA
56465840 AATTTTTAAGATTTTTC
1 AATTTTTAAGATTTTTC
56465857 AATTTTTAAGATTTTT
1 AATTTTTAAGATTTTT
56465873 TTTAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.61
Consensus pattern (17 bp):
AATTTTTAAGATTTTTC
Found at i:56465902 original size:14 final size:15
Alignment explanation
Indices: 56465869--56465902 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
56465859 TTTTTAAGAT
56465869 TTTTTTTAAAATTAA
1 TTTTTTTAAAATTAA
*
56465884 ATTTTTTAAAA-TAA
1 TTTTTTTAAAATTAA
56465898 TTTTT
1 TTTTT
56465903 ACTAATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTTTAAAATTAA
Found at i:56471334 original size:6 final size:6
Alignment explanation
Indices: 56471267--56471331 Score: 121
Period size: 6 Copynumber: 10.8 Consensus size: 6
56471257 AGGCATGGAC
56471267 GATGAA GATGAA GATGAA GATGAA GATGAA GATGAA GATGAA GATGAA
1 GATGAA GATGAA GATGAA GATGAA GATGAA GATGAA GATGAA GATGAA
*
56471315 GATGAA GATGAT GATGA
1 GATGAA GATGAA GATGA
56471332 TGAGGAGGAG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.48, C:0.00, G:0.34, T:0.18
Consensus pattern (6 bp):
GATGAA
Found at i:56480321 original size:12 final size:12
Alignment explanation
Indices: 56480304--56480328 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56480294 TATTAAAATA
56480304 TATTAATTATTT
1 TATTAATTATTT
56480316 TATTAATTATTT
1 TATTAATTATTT
56480328 T
1 T
56480329 GATAACGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTAATTATTT
Found at i:56480994 original size:44 final size:43
Alignment explanation
Indices: 56480869--56480999 Score: 97
Period size: 44 Copynumber: 3.0 Consensus size: 43
56480859 CTTTTATTTC
* * * * *
56480869 AATTATAATTATTTTAATTA-AAAAATATAATAAATGTAAATTA
1 AATTATAATTATTTTAAATATATAATTATTATAAAT-TATATTA
* * *
56480912 AATTAATAATTATTTTTAAATAT-TCAATTATCT-CAAATTCTATTG
1 AATT-ATAATTA-TTTTAAATATAT-AATTAT-TATAAATTATATTA
* *
56480957 AATTATAATTATTGTTAAGTATATAATTATTATAAATTTTATT
1 AATTATAATTATT-TTAAATATATAATTATTATAAATTATATT
56481000 TTATGTCAAT
Statistics
Matches: 69, Mismatches: 11, Indels: 15
0.73 0.12 0.16
Matches are distributed among these distances:
43 7 0.10
44 36 0.52
45 17 0.25
46 9 0.13
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (43 bp):
AATTATAATTATTTTAAATATATAATTATTATAAATTATATTA
Found at i:56483459 original size:20 final size:21
Alignment explanation
Indices: 56483425--56483478 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
56483415 TGATGATATT
*
56483425 TTATGATTA-TTTAATTAGATA
1 TTAT-ATTATTTTAATGAGATA
56483446 -TATATTATTTTAATGAGATA
1 TTATATTATTTTAATGAGATA
*
56483466 TTTTATTATTTTA
1 TTATATTATTTTA
56483479 TTATTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.14
20 14 0.48
21 11 0.38
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
TTATATTATTTTAATGAGATA
Found at i:56483484 original size:11 final size:11
Alignment explanation
Indices: 56483468--56483495 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
56483458 ATGAGATATT
56483468 TTATTATTTTA
1 TTATTATTTTA
56483479 TTATTATTTTA
1 TTATTATTTTA
56483490 TTATTA
1 TTATTA
56483496 ATTATTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:56485780 original size:24 final size:23
Alignment explanation
Indices: 56485651--56485780 Score: 111
Period size: 23 Copynumber: 5.5 Consensus size: 23
56485641 CCCGATATAT
*
56485651 GGCTCTTCGTGAGCTTCCCGATA
1 GGCTCTTTGTGAGCTTCCCGATA
*
56485674 GGCTCTTTGTGAGCTTTCCGATA
1 GGCTCTTTGTGAGCTTCCCGATA
** * *
56485697 GTGCTCGCT-TGAACTTCCTGATATA
1 G-GCTCTTTGTGAGCTTCCCG--ATA
* **
56485722 TGGCTATCCG-GAGCTTCCCGATA
1 -GGCTCTTTGTGAGCTTCCCGATA
56485745 GGCTCTTTGTGAGCTTCCCGATA
1 GGCTCTTTGTGAGCTTCCCGATA
*
56485768 TGGTTCTTTGTGA
1 -GGCTCTTTGTGA
56485781 ACTACCTAAT
Statistics
Matches: 84, Mismatches: 16, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
22 6 0.07
23 46 0.55
24 16 0.19
25 15 0.18
26 1 0.01
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (23 bp):
GGCTCTTTGTGAGCTTCCCGATA
Found at i:56485807 original size:71 final size:71
Alignment explanation
Indices: 56485645--56485811 Score: 176
Period size: 71 Copynumber: 2.3 Consensus size: 71
56485635 GAGTGTCCCG
* * *
56485645 ATATATGGCTCTTCGTGAGCTTCCCGATAGGCTCTTTGTGAGCTTTCCGATAGTGCTCGCTTGAA
1 ATATATGGCTATAC-TGAGCTTCCCGATAGGCTCTTTGTGAGCTTCCCGATAGTGCTCGCTTGAA
* *
56485710 CTTCCTG
65 CTACCTA
* * * **
56485717 ATATATGGCTATCCGGAGCTTCCCGATAGGCTCTTTGTGAGCTTCCCGATA-TGGTTCTTTGTGA
1 ATATATGGCTATACTGAGCTTCCCGATAGGCTCTTTGTGAGCTTCCCGATAGT-GCTCGCT-TGA
56485781 ACTACCTA
64 ACTACCTA
* * *
56485789 AT-TTTGGCTCTATTGAGCTTCCC
1 ATATATGGCTATACTGAGCTTCCC
56485812 ATTATAGCCC
Statistics
Matches: 79, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
70 1 0.01
71 55 0.70
72 23 0.29
ACGTcount: A:0.17, C:0.25, G:0.22, T:0.37
Consensus pattern (71 bp):
ATATATGGCTATACTGAGCTTCCCGATAGGCTCTTTGTGAGCTTCCCGATAGTGCTCGCTTGAAC
TACCTA
Found at i:56490531 original size:3 final size:3
Alignment explanation
Indices: 56490525--56490563 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
56490515 ACACTACTAT
56490525 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
56490564 TAGAAATGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:56490733 original size:38 final size:37
Alignment explanation
Indices: 56490662--56490739 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 37
56490652 GATATACACT
* *
56490662 AATATATAATAATAGTAATAATAATAAAGTAGTAAAA
1 AATATATAATAATAGTAAAAATAACAAAGTAGTAAAA
*
56490699 AATATAATTATAATAGTAAAATATAACAAATAGTAGTAAAA
1 AATAT-ATAATAATAGTAAAA-ATAAC-AA-AGTAGTAAAA
56490740 GAAAATAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 5 0.15
38 13 0.38
39 4 0.12
40 2 0.06
41 10 0.29
ACGTcount: A:0.62, C:0.01, G:0.08, T:0.29
Consensus pattern (37 bp):
AATATATAATAATAGTAAAAATAACAAAGTAGTAAAA
Found at i:56492479 original size:45 final size:43
Alignment explanation
Indices: 56492373--56492582 Score: 134
Period size: 44 Copynumber: 4.8 Consensus size: 43
56492363 ATTTGTAATT
* * *
56492373 TTCAGCCTGTTACCCTACTGCATAGGGGTTTAAGGCCCATCAA
1 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGACCCATCAA
* * * * **
56492416 TTCTGCTATGTTTCCCTACTACTTAGGGGGTTAAGATTCATCAA
1 TTCAGC-CTGTTACCCTACTGCTTAGGGGGTTAAGACCCATCAA
* * * * *** *
56492460 TGTTCAGCCTGTTACCCTACTGTTTAGGGGTTTAGGGCTTGTCACC
1 --TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGACCCATCA-A
* * * * * *
56492506 TT-TGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTATGAA
1 TTCAG-CCTGTTACCCTACTGCTTAGGGGGTTAAGACCCATCAA
* * *
56492549 TTCAACCTGTTACCCTACTGTTTAGGGGGGTAAG
1 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
56492583 GTTTGTCAAT
Statistics
Matches: 122, Mismatches: 39, Indels: 12
0.71 0.23 0.07
Matches are distributed among these distances:
43 33 0.27
44 58 0.48
45 26 0.21
46 5 0.04
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (43 bp):
TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGACCCATCAA
Found at i:56492524 original size:89 final size:87
Alignment explanation
Indices: 56492373--56492576 Score: 250
Period size: 89 Copynumber: 2.3 Consensus size: 87
56492363 ATTTGTAATT
** *
56492373 TTCAGCCTGTTACCCTACTGCATAGGGGTTTAAGGCCCATCAATTCTGCTATGTTTCCCTACTAC
1 TTCAGCCTGTTACCCTACTGTTTAGGGGTTTAAGGCCCATCAATTCTGATATGTTTCCCTACTAC
56492438 TTAGGGGGTTAAGAT-TCATCAA
66 TTAGGGGGTTAAGATCT-ATCAA
* *** * *
56492460 TGTTCAGCCTGTTACCCTACTGTTTAGGGGTTTAGGGCTTGTCACCTT-TGATCTGTTTCCCTAC
1 --TTCAGCCTGTTACCCTACTGTTTAGGGGTTTAAGGCCCATCA-ATTCTGATATGTTTCCCTAC
* *
56492524 TGCTTAGGGGGTTAAGATCTATGAA
63 TACTTAGGGGGTTAAGATCTATCAA
*
56492549 TTCAACCTGTTACCCTACTGTTTAGGGG
1 TTCAGCCTGTTACCCTACTGTTTAGGGG
56492577 GGTAAGGTTT
Statistics
Matches: 101, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
87 27 0.27
89 71 0.70
90 3 0.03
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.36
Consensus pattern (87 bp):
TTCAGCCTGTTACCCTACTGTTTAGGGGTTTAAGGCCCATCAATTCTGATATGTTTCCCTACTAC
TTAGGGGGTTAAGATCTATCAA
Found at i:56492658 original size:42 final size:42
Alignment explanation
Indices: 56492608--56492841 Score: 147
Period size: 42 Copynumber: 5.5 Consensus size: 42
56492598 ACCTGCTCCA
*
56492608 CTACTGCTTAGGGAGATAAGATCTCCAATTTGGTCTGTTACC
1 CTACTGCTTAGGGAGATAAGATCTGCAATTTGGTCTGTTACC
* * * * * **
56492650 CTACTGCTTAGGG-GTTTAAGACCCTTC-GTCTTCGATCTACT-CC
1 CTACTGCTTAGGGAG-ATAAGA-TCTGCAAT-TT-GGTCTGTTACC
* * *
56492693 ACTACGGCTTAGGGAGATCAGGTCTGCAATTTGGTCTGTTACC
1 -CTACTGCTTAGGGAGATAAGATCTGCAATTTGGTCTGTTACC
* * * * * **
56492736 CTACTGCTTAGGG-GTTTAAGACCCTTC-GTCTTCGATCTACT-CC
1 CTACTGCTTAGGGAG-ATAAGA-TCTGCAAT-TT-GGTCTGTTACC
* * *
56492779 ACTACGGCTTAGGGAGATCAGGTCTGCAATTTGGTCTGTTACC
1 -CTACTGCTTAGGGAGATAAGATCTGCAATTTGGTCTGTTACC
56492822 CTACTGCTTAGGGAGATAAG
1 CTACTGCTTAGGGAGATAAG
56492842 GCTCGTGGAT
Statistics
Matches: 137, Mismatches: 39, Indels: 32
0.66 0.19 0.15
Matches are distributed among these distances:
41 2 0.01
42 63 0.46
43 28 0.20
44 42 0.31
45 2 0.01
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.32
Consensus pattern (42 bp):
CTACTGCTTAGGGAGATAAGATCTGCAATTTGGTCTGTTACC
Found at i:56492703 original size:86 final size:86
Alignment explanation
Indices: 56492592--56492834 Score: 432
Period size: 86 Copynumber: 2.8 Consensus size: 86
56492582 GGTTTGTCAA
* * * * * *
56492592 TCTTCGACCTGCTCCACTACTGCTTAGGGAGATAAGATCTCCAATTTGGTCTGTTACCCTACTGC
1 TCTTCGATCTACTCCACTACGGCTTAGGGAGATCAGGTCTGCAATTTGGTCTGTTACCCTACTGC
56492657 TTAGGGGTTTAAGACCCTTCG
66 TTAGGGGTTTAAGACCCTTCG
56492678 TCTTCGATCTACTCCACTACGGCTTAGGGAGATCAGGTCTGCAATTTGGTCTGTTACCCTACTGC
1 TCTTCGATCTACTCCACTACGGCTTAGGGAGATCAGGTCTGCAATTTGGTCTGTTACCCTACTGC
56492743 TTAGGGGTTTAAGACCCTTCG
66 TTAGGGGTTTAAGACCCTTCG
56492764 TCTTCGATCTACTCCACTACGGCTTAGGGAGATCAGGTCTGCAATTTGGTCTGTTACCCTACTGC
1 TCTTCGATCTACTCCACTACGGCTTAGGGAGATCAGGTCTGCAATTTGGTCTGTTACCCTACTGC
56492829 TTAGGG
66 TTAGGG
56492835 AGATAAGGCT
Statistics
Matches: 151, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
86 151 1.00
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.33
Consensus pattern (86 bp):
TCTTCGATCTACTCCACTACGGCTTAGGGAGATCAGGTCTGCAATTTGGTCTGTTACCCTACTGC
TTAGGGGTTTAAGACCCTTCG
Found at i:56492705 original size:44 final size:44
Alignment explanation
Indices: 56492650--56492792 Score: 125
Period size: 44 Copynumber: 3.3 Consensus size: 44
56492640 GTCTGTTACC
*
56492650 CTACTGCTTAGGGGTTTAAGACCCTTCGTCTTCGATCTACTCCA
1 CTACGGCTTAGGGGTTTAAGACCCTTCGTCTTCGATCTACTCCA
* * ** * * * **
56492694 CTACGGCTTAGGGAG-ATCAG-GTCTGCAAT-TT-GGTCTGTTACC-
1 CTACGGCTTAGGG-GTTTAAGACCCTTC-GTCTTCGATCTACT-CCA
*
56492736 CTACTGCTTAGGGGTTTAAGACCCTTCGTCTTCGATCTACTCCA
1 CTACGGCTTAGGGGTTTAAGACCCTTCGTCTTCGATCTACTCCA
56492780 CTACGGCTTAGGG
1 CTACGGCTTAGGG
56492793 AGATCAGGTC
Statistics
Matches: 70, Mismatches: 21, Indels: 16
0.65 0.20 0.15
Matches are distributed among these distances:
41 1 0.01
42 21 0.30
43 14 0.20
44 33 0.47
45 1 0.01
ACGTcount: A:0.18, C:0.27, G:0.23, T:0.32
Consensus pattern (44 bp):
CTACGGCTTAGGGGTTTAAGACCCTTCGTCTTCGATCTACTCCA
Found at i:56502079 original size:3 final size:3
Alignment explanation
Indices: 56502073--56502111 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
56502063 ACACTACTAT
56502073 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
56502112 TAGAAATGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:56502281 original size:38 final size:37
Alignment explanation
Indices: 56502210--56502287 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 37
56502200 GATATACACT
* *
56502210 AATATATAATAATAGTAATAATAATAAAGTAGTAAAA
1 AATATATAATAATAGTAAAAATAACAAAGTAGTAAAA
*
56502247 AATATAATTATAATAGTAAAATATAACAAATAGTAGTAAAA
1 AATAT-ATAATAATAGTAAAA-ATAAC-AA-AGTAGTAAAA
56502288 GAAAATAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 5 0.15
38 13 0.38
39 4 0.12
40 2 0.06
41 10 0.29
ACGTcount: A:0.62, C:0.01, G:0.08, T:0.29
Consensus pattern (37 bp):
AATATATAATAATAGTAAAAATAACAAAGTAGTAAAA
Found at i:56503719 original size:45 final size:45
Alignment explanation
Indices: 56503668--56503793 Score: 121
Period size: 49 Copynumber: 2.7 Consensus size: 45
56503658 ACTCAATTGC
56503668 AACTTCAGAGAAATAATATTTGCTATCTTCAGTCTGTTCCACTGA
1 AACTTCAGAGAAATAATATTTGCTATCTTCAGTCTGTTCCACTGA
* * * *
56503713 AACTTCAGAGAGATAGGATCTATAATT--TAGCTTCAATCTGTTCCACTGC
1 AACTTCAGAGAAATA--A--TAT--TTGCTATCTTCAGTCTGTTCCACTGA
* * *
56503762 AACTTCAGGGAAATAAGATTTGCTATTTTCAG
1 AACTTCAGAGAAATAATATTTGCTATCTTCAG
56503794 CCTACTCCAC
Statistics
Matches: 63, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
43 2 0.03
45 22 0.35
47 2 0.03
49 35 0.56
51 2 0.03
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (45 bp):
AACTTCAGAGAAATAATATTTGCTATCTTCAGTCTGTTCCACTGA
Found at i:56504027 original size:45 final size:46
Alignment explanation
Indices: 56503908--56504384 Score: 242
Period size: 44 Copynumber: 10.9 Consensus size: 46
56503898 TCAGGGATAA
* * * *
56503908 AAGATTTGT-AATTTTCAGCT-TGTTACCCTACTGCATAGGGGTTT
1 AAGATTCGTCAATCTTCAGCTCTGTTACCCTACTGCTTAGGGGGTT
*** * * * *
56503952 AAGGCCCATC-A-CTTCTGCTATGTTTCCCTACTGCTTAGGGGGTT
1 AAGATTCGTCAATCTTCAGCTCTGTTACCCTACTGCTTAGGGGGTT
* *
56503996 AAGATTCGTCAATCTTCAGCT-TGTTACCCTACTGTTTAGGGGTTT
1 AAGATTCGTCAATCTTCAGCTCTGTTACCCTACTGCTTAGGGGGTT
* * * * *
56504041 AAGGCTT-GTC-ACCTT-TGATCTGTTTCCCTACTGCTTAGGGGGTT
1 AA-GATTCGTCAATCTTCAGCTCTGTTACCCTACTGCTTAGGGGGTT
* *
56504085 AAGATTCGTCAATCTTCAGCT-TGTTACCCTACTGTTTAGGGGGGT
1 AAGATTCGTCAATCTTCAGCTCTGTTACCCTACTGCTTAGGGGGTT
* * * * * *
56504130 AAGGTTTGTCAATCTTC-GATCTGCT-CCACTACTGCTTAGGGTGAT
1 AAGATTCGTCAATCTTCAGCTCTGTTACC-CTACTGCTTAGGGGGTT
* *
56504175 AAGA-TC-TGCAAT-TT--GGTCTGTTACCCTACTGCTTAGGGGTTT
1 AAGATTCGT-CAATCTTCAGCTCTGTTACCCTACTGCTTAGGGGGTT
** * * * * * *
56504217 AAGACCCTTC-GTCTTC-GATCTGCT-CCACTACTGCTTAGGGAGAT
1 AAGATTCGTCAATCTTCAGCTCTGTTACC-CTACTGCTTAGGGGGTT
* * *
56504261 AAGA-TC-TGCAAT-TT-AGCT-TGTTACCTTACTGCTTAGGTGTTT
1 AAGATTCGT-CAATCTTCAGCTCTGTTACCCTACTGCTTAGGGGGTT
** * * ** * * *
56504303 AAGACCCTTC-GT-TTTTGATCTGTTTCCCTACTGCATAGGGGGTT
1 AAGATTCGTCAATCTTCAGCTCTGTTACCCTACTGCTTAGGGGGTT
*
56504347 AAGA-TCTGT-AAT-TT--GGTCTGTTACCCTACTGCTTAGGG
1 AAGATTC-GTCAATCTTCAGCTCTGTTACCCTACTGCTTAGGG
56504385 AGATAAGGCT
Statistics
Matches: 328, Mismatches: 77, Indels: 58
0.71 0.17 0.13
Matches are distributed among these distances:
42 69 0.21
43 35 0.11
44 125 0.38
45 87 0.27
46 12 0.04
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.37
Consensus pattern (46 bp):
AAGATTCGTCAATCTTCAGCTCTGTTACCCTACTGCTTAGGGGGTT
Found at i:56504072 original size:89 final size:87
Alignment explanation
Indices: 56503920--56504384 Score: 418
Period size: 86 Copynumber: 5.3 Consensus size: 87
56503910 GATTTGTAAT
* * * *
56503920 TTTCAGCTTGTTACCCTACTGCATAGGGGTTTAAGGCCCATCA-CTTCTGCTATGTTTCCCTACT
1 TTTCAGCTTGTTACCCTACTGCTTAGGGGTTTAAGG-CCTTCATCTT-TGATCTGTTTCCCTACT
56503984 GCTTAGGGGGTTAAGATTCGTCAA
64 GCTTAGGGGGTTAAGATTCGTCAA
* * *
56504008 TCTTCAGCTTGTTACCCTACTGTTTAGGGGTTTAAGGCTTGTCACCTTTGATCTGTTTCCCTACT
1 T-TTCAGCTTGTTACCCTACTGCTTAGGGGTTTAAGGCCT-TCATCTTTGATCTGTTTCCCTACT
56504073 GCTTAGGGGGTTAAGATTCGTCAA
64 GCTTAGGGGGTTAAGATTCGTCAA
* ** ** * *
56504097 TCTTCAGCTTGTTACCCTACTGTTTAGGGGGGTAAGGTTTGTCAATCTTCGATCTG-CTCCACTA
1 T-TTCAGCTTGTTACCCTACTGCTTAGGGGTTTAAGGCCT-TC-ATCTTTGATCTGTTTCC-CTA
* *
56504161 CTGCTTAGGGTGATAAGA-TC-TGCAA
62 CTGCTTAGGGGGTTAAGATTCGT-CAA
* * * * *
56504186 TTT--GGTCTGTTACCCTACTGCTTAGGGGTTTAAGACCCTTCGTCTTCGATCTG-CTCCACTAC
1 TTTCAGCT-TGTTACCCTACTGCTTAGGGGTTTAAG-GCCTTCATCTTTGATCTGTTTCC-CTAC
* *
56504248 TGCTTAGGGAGATAAGA-TC-TGCAA
63 TGCTTAGGGGGTTAAGATTCGT-CAA
* * * * *
56504272 TTT-AGCTTGTTACCTTACTGCTTAGGTGTTTAAGACCCTTCGTTTTTGATCTGTTTCCCTACTG
1 TTTCAGCTTGTTACCCTACTGCTTAGGGGTTTAAG-GCCTTCATCTTTGATCTGTTTCCCTACTG
*
56504336 CATAGGGGGTTAAGA-TCTGT-AA
65 CTTAGGGGGTTAAGATTC-GTCAA
*
56504358 TTT--GGTCTGTTACCCTACTGCTTAGGG
1 TTTCAGCT-TGTTACCCTACTGCTTAGGG
56504385 AGATAAGGCT
Statistics
Matches: 329, Mismatches: 35, Indels: 28
0.84 0.09 0.07
Matches are distributed among these distances:
85 2 0.01
86 133 0.40
87 31 0.09
88 7 0.02
89 124 0.38
90 32 0.10
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.37
Consensus pattern (87 bp):
TTTCAGCTTGTTACCCTACTGCTTAGGGGTTTAAGGCCTTCATCTTTGATCTGTTTCCCTACTGC
TTAGGGGGTTAAGATTCGTCAA
Found at i:56504208 original size:42 final size:42
Alignment explanation
Indices: 56504158--56504391 Score: 163
Period size: 42 Copynumber: 5.5 Consensus size: 42
56504148 ATCTGCTCCA
*
56504158 CTACTGCTTAGGGTGATAAGATCTGCAATTTGGTCTGTTACC
1 CTACTGCTTAGGGAGATAAGATCTGCAATTTGGTCTGTTACC
* * * * * *
56504200 CTACTGCTTAGGG-GTTTAAGACCCTTC-GTCTTCGATCTGCT-CC
1 CTACTGCTTAGGGAG-ATAAGA-TCTGCAAT-TT-GGTCTGTTACC
*
56504243 ACTACTGCTTAGGGAGATAAGATCTGCAATTTAG-CTTGTTACC
1 -CTACTGCTTAGGGAGATAAGATCTGCAATTTGGTC-TGTTACC
* ** * * ** * *
56504286 TTACTGCTTAGGTG-TTTAAGACCCTTCGTTTTTGATCTGTTTCC
1 CTACTGCTTAGG-GAGATAAGA-TCTGC-AATTTGGTCTGTTACC
* * * *
56504330 CTACTGCATAGGGGGTTAAGATCTGTAATTTGGTCTGTTACC
1 CTACTGCTTAGGGAGATAAGATCTGCAATTTGGTCTGTTACC
56504372 CTACTGCTTAGGGAGATAAG
1 CTACTGCTTAGGGAGATAAG
56504392 GCTCGTGGAT
Statistics
Matches: 142, Mismatches: 36, Indels: 28
0.69 0.17 0.14
Matches are distributed among these distances:
41 2 0.01
42 67 0.47
43 21 0.15
44 50 0.35
45 2 0.01
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.36
Consensus pattern (42 bp):
CTACTGCTTAGGGAGATAAGATCTGCAATTTGGTCTGTTACC
Found at i:56512355 original size:43 final size:43
Alignment explanation
Indices: 56512262--56512358 Score: 106
Period size: 43 Copynumber: 2.3 Consensus size: 43
56512252 AGATGTGATT
* * * * * *
56512262 ACATGTAAGACCATGTTTGGGATATTGGCATTGTATTGTGATT
1 ACATGTAAGACCATGTCTGAGACATTGGCATCGTATTGTAATA
* *
56512305 GCGTGTAAGACCATGTCTGAGACATTGGCATCG-ATATGTAATA
1 ACATGTAAGACCATGTCTGAGACATTGGCATCGTAT-TGTAATA
56512348 ACATGTAAGAC
1 ACATGTAAGAC
56512359 TATATCTGGG
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
42 2 0.05
43 41 0.95
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (43 bp):
ACATGTAAGACCATGTCTGAGACATTGGCATCGTATTGTAATA
Found at i:56515715 original size:43 final size:43
Alignment explanation
Indices: 56515622--56515718 Score: 106
Period size: 43 Copynumber: 2.3 Consensus size: 43
56515612 AGATGTGATT
* * * * * *
56515622 ACATGTAAGACCATGTTTGGGATATTGGCATTGTATTGTGATT
1 ACATGTAAGACCATGTCTGAGACATTGGCATCGTATTGTAATA
* *
56515665 GCGTGTAAGACCATGTCTGAGACATTGGCATCG-ATATGTAATA
1 ACATGTAAGACCATGTCTGAGACATTGGCATCGTAT-TGTAATA
56515708 ACATGTAAGAC
1 ACATGTAAGAC
56515719 TATATCTGGG
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
42 2 0.05
43 41 0.95
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (43 bp):
ACATGTAAGACCATGTCTGAGACATTGGCATCGTATTGTAATA
Found at i:56519469 original size:18 final size:19
Alignment explanation
Indices: 56519442--56519477 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
56519432 GAATGTACTA
56519442 TTCATATACA-CATATATT
1 TTCATATACATCATATATT
*
56519460 TTCATTTACATCATATAT
1 TTCATATACATCATATAT
56519478 AAATTGCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.36, C:0.17, G:0.00, T:0.47
Consensus pattern (19 bp):
TTCATATACATCATATATT
Found at i:56519768 original size:56 final size:56
Alignment explanation
Indices: 56519707--56519898 Score: 339
Period size: 56 Copynumber: 3.4 Consensus size: 56
56519697 TCCCAGACAG
* *
56519707 GGTCTTACTCGCACACATAAATTGGAATCACATATCGATGCCAACGTATTAAACTT
1 GGTCTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAACTT
56519763 GGTCTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAACTT
1 GGTCTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAACTT
* *
56519819 GGTCTTACTCGCACACATATATCGGAATCACATATCGATGCCAACATATTAAACAT
1 GGTCTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAACTT
*
56519875 AGTCTTACTCGCACACATATATCG
1 GGTCTTACTCGCACACATATATCG
56519899 ATGCCATGGT
Statistics
Matches: 131, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 131 1.00
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (56 bp):
GGTCTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAACTT
Found at i:56520827 original size:16 final size:18
Alignment explanation
Indices: 56520796--56520828 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
56520786 GAATTTTAGT
56520796 ATAACATATATTATTATA
1 ATAACATATATTATTATA
56520814 ATAACAT-T-TTATTAT
1 ATAACATATATTATTAT
56520829 TCATTTACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (18 bp):
ATAACATATATTATTATA
Found at i:56532645 original size:26 final size:26
Alignment explanation
Indices: 56532616--56532803 Score: 367
Period size: 26 Copynumber: 7.2 Consensus size: 26
56532606 TGATACAAAT
56532616 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
56532642 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
56532668 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
56532694 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
56532720 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
56532746 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
56532772 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
56532798 TGATAA
1 TGATAA
56532804 GAATTTCATG
Statistics
Matches: 161, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
26 161 1.00
ACGTcount: A:0.31, C:0.07, G:0.27, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:56533528 original size:22 final size:21
Alignment explanation
Indices: 56533501--56533541 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
56533491 CATGTTTGAC
*
56533501 TGTTGTTATTTACTGCATGCTA
1 TGTTGTTATTAACTG-ATGCTA
56533523 TGTTGTTATTAACTGATGC
1 TGTTGTTATTAACTGATGC
56533542 ATGGGACTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.49
Consensus pattern (21 bp):
TGTTGTTATTAACTGATGCTA
Found at i:56535994 original size:23 final size:23
Alignment explanation
Indices: 56535925--56535994 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 23
56535915 ATTATGGGAA
*
56535925 TTGAAAAAGCTAAAATAGAAA-T
1 TTGAAAAAGCTAAAGTAGAAATT
* **
56535947 TTGAAAAAGC-ATAAGGAGGTGATT
1 TTGAAAAAGCTA-AAGTA-GAAATT
*
56535971 TTGAAAAGGCTAAAGTAGAAATT
1 TTGAAAAAGCTAAAGTAGAAATT
56535994 T
1 T
56535995 GGTGTACATT
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
21 1 0.03
22 13 0.36
23 7 0.19
24 14 0.39
25 1 0.03
ACGTcount: A:0.49, C:0.04, G:0.21, T:0.26
Consensus pattern (23 bp):
TTGAAAAAGCTAAAGTAGAAATT
Found at i:56539419 original size:13 final size:13
Alignment explanation
Indices: 56539403--56539427 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56539393 TGATTAGTTT
56539403 TATTAATTAATTC
1 TATTAATTAATTC
56539416 TATTAATTAATT
1 TATTAATTAATT
56539428 ATTTAAAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTAATTAATTC
Found at i:56541078 original size:16 final size:16
Alignment explanation
Indices: 56541057--56541087 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56541047 TTTGGCCCCT
56541057 GAACTTGGATTATGTC
1 GAACTTGGATTATGTC
*
56541073 GAACTTTGATTATGT
1 GAACTTGGATTATGT
56541088 GACTAATTAG
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:0.26, C:0.10, G:0.23, T:0.42
Consensus pattern (16 bp):
GAACTTGGATTATGTC
Found at i:56542028 original size:18 final size:18
Alignment explanation
Indices: 56541988--56542034 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
56541978 ATATCTAATA
*
56541988 AGTAATCAGTAACGGTAGC
1 AGTAA-CAGTAACAGTAGC
*
56542007 AGTAGCAGTAACAGTAAG-
1 AGTAACAGTAACAGT-AGC
56542025 AGTAACAGTA
1 AGTAACAGTA
56542035 TTCAACACAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.43, C:0.13, G:0.26, T:0.19
Consensus pattern (18 bp):
AGTAACAGTAACAGTAGC
Found at i:56542088 original size:45 final size:45
Alignment explanation
Indices: 56542014--56542121 Score: 146
Period size: 45 Copynumber: 2.4 Consensus size: 45
56542004 AGCAGTAGCA
* *
56542014 GTAACAGTAAGAGTAACAGTATTCAACACACAAAGTG-CTAAATCT
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTC-AAATCG
* * * *
56542059 GTAATAGTAACGGTAACAGTATTCGACACACAAAGTGTCGAATCG
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTCAAATCG
56542104 GTAACAGTAACAGTAACA
1 GTAACAGTAACAGTAACA
56542122 ATAGTCGGCA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
45 53 0.98
46 1 0.02
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.21
Consensus pattern (45 bp):
GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTCAAATCG
Found at i:56542924 original size:3 final size:3
Alignment explanation
Indices: 56542916--56542970 Score: 83
Period size: 3 Copynumber: 18.3 Consensus size: 3
56542906 TATTAACTTT
* *
56542916 ATA ATA ATA ATA AAA ATA ATA ATA ATA ATA AAA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
56542964 ATT ATA A
1 ATA ATA A
56542971 ATATCTTATT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:56542939 original size:18 final size:18
Alignment explanation
Indices: 56542916--56542964 Score: 98
Period size: 18 Copynumber: 2.7 Consensus size: 18
56542906 TATTAACTTT
56542916 ATAATAATAATAAAAATA
1 ATAATAATAATAAAAATA
56542934 ATAATAATAATAAAAATA
1 ATAATAATAATAAAAATA
56542952 ATAATAATAATAA
1 ATAATAATAATAA
56542965 TTATAAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAATAATAATAAAAATA
Found at i:56543243 original size:20 final size:20
Alignment explanation
Indices: 56543220--56543274 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 20
56543210 TTATTTTTAA
56543220 TAATAATAATAATCATAATT
1 TAATAATAATAATCATAATT
*
56543240 TAATAAT-ATAAATTATAATT
1 TAATAATAAT-AATCATAATT
56543260 TAATAGAATAATAAT
1 TAAT--AATAATAAT
56543275 AAATAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.07
20 20 0.67
22 6 0.20
23 2 0.07
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
TAATAATAATAATCATAATT
Found at i:56545922 original size:40 final size:40
Alignment explanation
Indices: 56545885--56546109 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
56545875 GCTACTCGTT
* *
56545885 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
56545925 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
56545965 CAAATGCCTTCGGGCCTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
56546005 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
56546044 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
56546085 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
56546110 CATCATTCAA
Statistics
Matches: 166, Mismatches: 14, Indels: 10
0.87 0.07 0.05
Matches are distributed among these distances:
38 2 0.01
39 33 0.20
40 118 0.71
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:56546069 original size:119 final size:120
Alignment explanation
Indices: 56545885--56546109 Score: 296
Period size: 119 Copynumber: 1.9 Consensus size: 120
56545875 GCTACTCGTT
*
56545885 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* * *
56545950 ATTTAGTAAC-TCGCACAAATGCCTTCGGGCCTTAACCCGGATTTAGTAACTCGCA
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * **
56546005 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* * *
56546067 GGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 GGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
56546110 CATCATTCAA
Statistics
Matches: 91, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
118 4 0.04
119 65 0.71
120 22 0.24
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:56553997 original size:79 final size:81
Alignment explanation
Indices: 56553895--56554079 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
56553885 GCTCCTCGTT
* *
56553895 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
56553958 GGATTTAGTAAC-TCGCA
64 GGATATAGTAACTTAGCA
* **
56553975 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
56554039 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
56554055 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
56554080 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:56554079 original size:40 final size:40
Alignment explanation
Indices: 56553895--56554079 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
56553885 GCTCCTCGTT
* *
56553895 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
56553935 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
56553975 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
56554014 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
56554055 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
56554080 CATCATTCAA
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.02
39 32 0.25
40 80 0.63
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:56561905 original size:3 final size:3
Alignment explanation
Indices: 56561897--56561940 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
56561887 TTTATATCAT
56561897 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
56561941 CTGCTAAGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:56562046 original size:23 final size:20
Alignment explanation
Indices: 56562020--56562079 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 20
56562010 TAGTTTTATG
56562020 TTTTATTTTTTTTCTATTTGT
1 TTTTATTTTTTTT-TATTTGT
56562041 ACTTTTATTTTTCTTGTTATTTGT
1 --TTTTATTTTT-TT-TTATTTGT
56562065 TTTTATTTTATTTTT
1 TTTTATTTT-TTTTT
56562080 CGGACTTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
21 2 0.06
22 11 0.32
23 11 0.32
24 9 0.26
25 1 0.03
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTTATTTTTTTTTATTTGT
Found at i:56567117 original size:25 final size:26
Alignment explanation
Indices: 56567089--56567139 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
56567079 CTTATTTCAT
*
56567089 TAAATAAAAAAT-TTTAAAAATATAA
1 TAAATAAAAAATATTTAAAAACATAA
* *
56567114 TAAATCAAATATATTTAAAAACATAA
1 TAAATAAAAAATATTTAAAAACATAA
56567140 AAACAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (26 bp):
TAAATAAAAAATATTTAAAAACATAA
Found at i:56567131 original size:26 final size:24
Alignment explanation
Indices: 56567101--56567149 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
56567091 AATAAAAAAT
*
56567101 TTTAAAAATATAATAAATCAAATATA
1 TTTAAAAACATAA-AAA-CAAATATA
56567127 TTTAAAAACATAAAAACAAATAT
1 TTTAAAAACATAAAAACAAATAT
56567150 TAATACAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (24 bp):
TTTAAAAACATAAAAACAAATATA
Found at i:56569813 original size:47 final size:47
Alignment explanation
Indices: 56569743--56569838 Score: 183
Period size: 47 Copynumber: 2.0 Consensus size: 47
56569733 TAATAAATAC
*
56569743 TTAGTTTCTTGTTCTCAATTATGTGTACTTAATTTTTGATGTAAGAT
1 TTAGTTTCTTGTTCTCAAGTATGTGTACTTAATTTTTGATGTAAGAT
56569790 TTAGTTTCTTGTTCTCAAGTATGTGTACTTAATTTTTGATGTAAGAT
1 TTAGTTTCTTGTTCTCAAGTATGTGTACTTAATTTTTGATGTAAGAT
56569837 TT
1 TT
56569839 CTAAATTATT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.23, C:0.08, G:0.16, T:0.53
Consensus pattern (47 bp):
TTAGTTTCTTGTTCTCAAGTATGTGTACTTAATTTTTGATGTAAGAT
Found at i:56572317 original size:18 final size:18
Alignment explanation
Indices: 56572296--56572337 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
56572286 AAAGATAAAA
56572296 ATAATAACA-ATAATAATG
1 ATAATAA-ATATAATAATG
*
56572314 ATAATAAATATAGTAATG
1 ATAATAAATATAATAATG
56572332 ATAATA
1 ATAATA
56572338 GTAAGAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (18 bp):
ATAATAAATATAATAATG
Found at i:56572792 original size:2 final size:2
Alignment explanation
Indices: 56572778--56572862 Score: 50
Period size: 2 Copynumber: 43.5 Consensus size: 2
56572768 AATATGCATA
* * * * *
56572778 AT AT AT -T AA AT AT AT AT AT AT AC AT AT A- AT AT TT AT AA AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
56572818 AT AT AT AC AT A- AT AT AC AT AA AGT AT AC AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
56572860 AT A
1 AT A
56572863 ATACTTAAAA
Statistics
Matches: 61, Mismatches: 18, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
1 3 0.05
2 57 0.93
3 1 0.02
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (2 bp):
AT
Found at i:56572838 original size:23 final size:24
Alignment explanation
Indices: 56572793--56572839 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
56572783 TTAAATATAT
**
56572793 ATATATACATATAATATTTATAAAA
1 ATATATACA-ATAATATACATAAAA
56572818 ATATATAC-ATAATATACATAAA
1 ATATATACAATAATATACATAAA
56572840 GTATACATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
25 8 0.40
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36
Consensus pattern (24 bp):
ATATATACAATAATATACATAAAA
Found at i:56575065 original size:205 final size:204
Alignment explanation
Indices: 56574696--56575178 Score: 682
Period size: 205 Copynumber: 2.4 Consensus size: 204
56574686 GGGAACATCC
* * * * *
56574696 GAAAGTCAAATCTGCTATGTCTTTGATTTGTTCCTTGTAAGCACAAGGATGCCGGATCC-TCTTG
1 GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCC-AAACCATCTTG
* * * ** * *
56574760 GATCTTGCTTCAGTATAAACATCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATTGACGTGG
65 GATC-TGCTTCAGCATAAACATCCGAAGGTCAGATCTGCTATGTATCTACTCTCCATCAAAGTGA
* *
56574825 AGATGCCAAACTTCGATTTGTTCTCTGAAAATACAGAGACGACAAATCATCTTAGATTTGTTTCA
129 AGATGCCAAACTTCGATTCGTTCTCTGAAAATACAGAGACGACAAATCATCTTAGA-TTGCTTCA
56574890 GAGTAAACACGT
193 GAGTAAACACGT
*
56574902 GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTTGG
1 GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGG
* *
56574967 ATCCGCTTCAGCATAAACATCCGAAGG-CAAGATCTGCTATGTGTCTACTCTCCATCAAAGTGAA
66 ATCTGCTTCAGCATAAACATCCGAAGGTC-AGATCTGCTATGTATCTACTCTCCATCAAAGTGAA
* * * **
56575031 GATGCCATACTTTGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTGCTTCATC
130 GATGCCAAACTTCGATTCGTTCTCTGAAAATACAGAGACGACAAATCATCTTAGATTGCTTCAGA
*
56575096 GTAAGCACGT
195 GTAAACACGT
* * *
56575106 GAAAGCCAAATCGGCTATGTCTTCAATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGG
1 GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGG
56575171 ATCTGCTT
66 ATCTGCTT
56575179 TAGCCAGATC
Statistics
Matches: 247, Mismatches: 28, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
204 85 0.34
205 104 0.42
206 58 0.23
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (204 bp):
GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGG
ATCTGCTTCAGCATAAACATCCGAAGGTCAGATCTGCTATGTATCTACTCTCCATCAAAGTGAAG
ATGCCAAACTTCGATTCGTTCTCTGAAAATACAGAGACGACAAATCATCTTAGATTGCTTCAGAG
TAAACACGT
Found at i:56585120 original size:23 final size:23
Alignment explanation
Indices: 56585088--56585133 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
56585078 TGCTTGATCT
56585088 GGGTTATCACCCACTGTTCGCTC
1 GGGTTATCACCCACTGTTCGCTC
*
56585111 GGGTTGTCACCCACTGTTCGCTC
1 GGGTTATCACCCACTGTTCGCTC
56585134 ATCCCTGTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.11, C:0.35, G:0.24, T:0.30
Consensus pattern (23 bp):
GGGTTATCACCCACTGTTCGCTC
Found at i:56587444 original size:18 final size:18
Alignment explanation
Indices: 56587423--56587464 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
56587413 AAAGATAAAA
56587423 ATAATAACA-ATAATAATG
1 ATAATAA-ATATAATAATG
*
56587441 ATAATAAATATAGTAATG
1 ATAATAAATATAATAATG
56587459 ATAATA
1 ATAATA
56587465 GTAAGAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (18 bp):
ATAATAAATATAATAATG
Found at i:56587919 original size:2 final size:2
Alignment explanation
Indices: 56587905--56587989 Score: 50
Period size: 2 Copynumber: 43.5 Consensus size: 2
56587895 AATATGCATA
* * * * *
56587905 AT AT AT -T AA AT AT AT AT AT AT AC AT AT A- AT AT TT AT AA AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
56587945 AT AT AT AC AT A- AT AT AC AT AA AGT AT AC AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
56587987 AT A
1 AT A
56587990 ATACTTAAAA
Statistics
Matches: 61, Mismatches: 18, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
1 3 0.05
2 57 0.93
3 1 0.02
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (2 bp):
AT
Found at i:56587965 original size:23 final size:24
Alignment explanation
Indices: 56587920--56587966 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
56587910 TTAAATATAT
**
56587920 ATATATACATATAATATTTATAAAA
1 ATATATACA-ATAATATACATAAAA
56587945 ATATATAC-ATAATATACATAAA
1 ATATATACAATAATATACATAAA
56587967 GTATACATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
25 8 0.40
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36
Consensus pattern (24 bp):
ATATATACAATAATATACATAAAA
Found at i:56591167 original size:16 final size:16
Alignment explanation
Indices: 56591145--56591213 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
56591135 TTTGGTTCGC
56591145 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
56591161 CGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
56591177 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
56591194 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
56591210 TGTA
1 TGTA
56591214 ATAGCTAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:56591191 original size:33 final size:32
Alignment explanation
Indices: 56591145--56591213 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
56591135 TTTGGTTCGC
56591145 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
*
56591177 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGCGTATTGGATTAGAGG
56591210 TGTA
1 TGTA
56591214 ATAGCTAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 6 0.17
33 29 0.83
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (32 bp):
TGTATTGGATTAGAGGCGTATTGGATTAGAGG
Found at i:56591278 original size:44 final size:45
Alignment explanation
Indices: 56591194--56591284 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
56591184 GGATTAGAGG
* * *
56591194 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
56591239 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
56591283 TG
1 TG
56591285 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:56591470 original size:18 final size:17
Alignment explanation
Indices: 56591449--56591483 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
56591439 TTATTATTAA
*
56591449 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
56591467 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
56591484 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:56595188 original size:16 final size:16
Alignment explanation
Indices: 56595151--56595192 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
56595141 TTAATCATAT
*
56595151 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
56595167 TT-AAATATATTATAA
1 TTAAAATATATTATAA
56595182 TTAAAATATAT
1 TTAAAATATAT
56595193 GATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:56595297 original size:120 final size:121
Alignment explanation
Indices: 56595149--56595439 Score: 482
Period size: 120 Copynumber: 2.4 Consensus size: 121
56595139 ATTTAATCAT
* *
56595149 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATGATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATA
*
56595214 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAAT-ATAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAATGA-AA
*
56595271 A-TT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATA
56595334 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
* *
56595390 ATTTGAA-ATAATTAATATTAAATATATTTTAATTATAATATATGATTTAA
1 ATTTGAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAA
56595440 AATAATTTAA
Statistics
Matches: 160, Mismatches: 6, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
119 7 0.04
120 148 0.93
121 4 0.03
122 1 0.01
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
Found at i:56595312 original size:18 final size:17
Alignment explanation
Indices: 56595291--56595325 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
56595281 TTATTATTAA
*
56595291 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
56595309 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
56595326 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:56595371 original size:61 final size:61
Alignment explanation
Indices: 56595186--56595376 Score: 198
Period size: 61 Copynumber: 3.2 Consensus size: 61
56595176 TTATAATTAA
56595186 AATATATGATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATGATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * *
56595247 AATATATGATACT-GTAAAA-TATAAATTAACATAATTATTATTAAAT-ATATTT--T--AATTA
1 AATATATGAT-TTAATAAAATTCTTAA-TAA-TTAA-TATTCTTATATGA-ATTTACTCAAATCA
*
56595305 A
61 T
*
56595306 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATGATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
56595367 AATATATGAT
1 AATATATGAT
56595377 ACTATAAATG
Statistics
Matches: 98, Mismatches: 20, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
57 13 0.13
58 5 0.05
59 22 0.22
60 8 0.08
61 32 0.33
62 5 0.05
63 13 0.13
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.43
Consensus pattern (61 bp):
AATATATGATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
Done.