Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 80 of 427
Found at i:20090319 original size:21 final size:21
Alignment explanation
Indices: 20090293--20090333 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
20090283 TCATTAGCTA
20090293 TTTTTGATATTTTCATTACAT
1 TTTTTGATATTTTCATTACAT
20090314 TTTTTGATATTTTCATTACA
1 TTTTTGATATTTTCATTACA
20090334 CACCTATTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.10, G:0.05, T:0.61
Consensus pattern (21 bp):
TTTTTGATATTTTCATTACAT
Found at i:20091463 original size:915 final size:914
Alignment explanation
Indices: 20089395--20091677 Score: 2501
Period size: 926 Copynumber: 2.5 Consensus size: 914
20089385 TGTTTTTCGG
* * * * * *
20089395 GATTTTCTTTACACACCTGGTCGATTCTAAAATAGGAATTTACAGCACACTTTCAGACCCTAAAA
1 GATTTTCATGACACACCTAGTCGATTCT-AAACA-CAATTTACAGCACACTTCCAGACCCTAAAA
* * * * * *
20089460 TATTATTCAGAATAAACAAATTTACAAGGATTACCAATCTCAAGTTAATTGTTTTGC-A-ACAAA
64 TGTCATTCAAAATAAACAAATTAACAAGGATTACCAATCTCAAGTCAATTG--TTCCAACACAAA
* ** * * *
20089523 TGCTAAGGTATTCGACCCTTACCTAAGAAGAAACCAATTCCTAAAACACTTTGTTCGCTAGCAAA
127 TGCTAA-GTATT-G-CCCTTACCTAAAAAGAAACTGATTCCTAAGACACTCTGTTCACTAG-AAA
* * * * *
20089588 A-TGTTAGGTTCTTCTCAAACTTCACCTAAGAAATTCCCACACAAAAGAGGGCATCAAAATGCAA
188 AGTGTTGGGTGCTTCGCAAACTTCACCTAACAGATT-CCACACAAAAGAGGGCATCAAAATGCAA
*
20089652 TCAACTCTAATAAAAAAAATTCTCAAATAAGGTTATCTC-AAATCATCCATCTAAAAATAAGACG
252 TCAACTCTAA-CAAAAAAATTCTCAAATAAGGTTATCTCAAAAT-ATCCATCTAAAAA-AAGACG
* * * * * *
20089716 AACACCAATTACGCGAAACTTACGACAACTCTATTATTCTAGTTCGTACACCAATCACATACTCA
314 AACACCAATT--G-GAAAC-TATGACAACTCTA-TATTCCAATTCATACACCAATCACACACTCG
*
20089781 GAGACTATAGATGAAAATGGTCAGAACATCCATGAAGAAATCTTAAAAATGGTTAATAGAAAA-C
374 GAGACTATAGATGAAAAAGGTCAGAACATCCATGAAGAAATCTTAAAAATGGTTAATAGAAAACC
* * *
20089845 -AA-AAGA-A--T---ATACATAAATGAATCATGCTTATACATATTTCTCAAATTACAGATCAGA
439 AAAGAATATAGGTGAAATACATAAATGAATCATGCTTATACAGATTTCTCAAATTACAGATCAAA
* * *
20089902 AGTAGAGATTATACTACAAACATGCTCTTGAATGTTACACAAGCAATATTAGTGTTTAGATTTCA
504 AGTAAAGATTATACCACAAACATGCTCTTGAATGTTACACAAGCAATATCAG-G-TTA-ATTTCA
* * * *
20089967 GGTTTCACTTGCAAACATTAACCAGATAACAAATGTATTTATATATCATACATACCGTACATATT
566 GGTTTCACTTGCAAACACTAACAAGATAACAAATGTATTTATATATCATACATACCATACATATC
* * * * **
20090032 AGAACATACTATCACGCTTTTAGAAATCACATTAACGAAGGAAAAATACCATTTTTCATGTCCAT
631 AGAACATACTATCACGCGTTCAAAAATCACATTAACAAAGGAAAAATACCAAATTTCATGTCCAT
* * * *
20090097 AATACCTACATAACACATTTCACAACTTGCGAAGTGAGCAATTTTTGAATCGCACTTCAAATATG
696 AATACCTACATAACACATTTCACAACCTACAAAGTGAGCAATTTTCGAATCGCACTTCAAATATG
* * * *
20090162 ACCCTAACGAAATTTTATGAAAAACTAGGCCCACATGCCTGTGTGACCTACACGGCCCAACTTAC
761 ACCCTAACGAAATTTTATCAAAAAATAGGCCCACATGCCTGTGTGACCCACACGGCCCAACTAAC
* * * * * *
20090227 TTACCCCATGTGACCCACACGGCTGTGTGGCATAGACAGTGACCTTTAGCTTCACGTCATTAGCT
826 TCACCCCATGTAACCCACA--GCTGTCTGGCATA-ACAGTG--CTGTAGCGTCACGTCAGTAGCT
* **
20090292 ATTTTTGATATTTTCATTACATTTTTTGA
886 ATTTTGGATATTCGCATTACATTTTTTGA
* * * * *
20090321 TATTTTCATTACACACCTATTCGATTTTAAAACACGAATTTACAGCACACTTCTAGACCCTAAAA
1 GATTTTCATGACACACCTAGTCGATTCT-AAACAC-AATTTACAGCACACTTCCAGACCCTAAAA
* * * * * * *
20090386 TGTCATTCAAAATAAATAAATTAACAATGATTATCAATATCGAGTCAATTGTTCTACCACAAATG
64 TGTCATTCAAAATAAACAAATTAACAAGGATTACCAATCTCAAGTCAATTGTTCCAACACAAATG
* ** * *
20090451 C--CG-A---CCCTTACCTAAAAAGAAACTGATTCCTAAGACACTCTACTCACTGGCAAAGTGTT
129 CTAAGTATTGCCCTTACCTAAAAAGAAACTGATTCCTAAGACACTCTGTTCACTAGAAAAGTGTT
* * * * *
20090510 GGGTGCTTCGTGAAA-TTCACCTAACAGATTCC-CACAAAAAAGATGCATCAAAATGTAATCAAT
194 GGGTGCTTCG-CAAACTTCACCTAACAGATTCCACACAAAAGAG-GGCATCAAAATGCAATCAAC
*
20090573 TCTAACAAAAAAATTCTCAAATAAGGTTATCTCAAAATATCCATCTAAAAAAAAACCGAACACCA
257 TCTAACAAAAAAATTCTCAAATAAGGTTATCTCAAAATATCCATCTAAAAAAAGA-CGAACACCA
20090638 ATTGTGTGAAACGTATGACAACTCTATCATTCCAATTCATACACCAATCACACACTCGGAGACTA
321 A-T-TG-GAAAC-TATGACAACTCTAT-ATTCCAATTCATACACCAATCACACACTCGGAGACTA
20090703 TAGATGAAAAAGGTCAGAACATCCATGAAGAAATCTTAAAAATGGTTAATAGAAAACCAAAGAAT
381 TAGATGAAAAAGGTCAGAACATCCATGAAGAAATCTTAAAAATGGTTAATAGAAAACCAAAGAAT
* *
20090768 ATAGGGTGAAATCACATAAATGAATCGTGCTTATACAGATTTCTCAAATTACATATCAAAAGTAA
446 ATA-GGTGAAAT-ACATAAATGAATCATGCTTATACAGATTTCTCAAATTACAGATCAAAAGTAA
* *
20090833 AGATTATACCACAGACATGCTCTTGAATGTTACACATGCAATATCA-G-T-ATTTCAGGTTTCAC
509 AGATTATACCACAAACATGCTCTTGAATGTTACACAAGCAATATCAGGTTAATTTCAGGTTTCAC
* * *
20090895 TTGCAAACACTAATAAGATAACAGATGTATTTATATATCATACATACTATACATATCAGAACATA
574 TTGCAAACACTAACAAGATAACAAATGTATTTATATATCATACATACCATACATATCAGAACATA
* *
20090960 CTATCACGCGTTCAAAAATCACATTAACAAAGGCAAAATACCAAATTTCATGTCCATAGTACCTA
639 CTATCACGCGTTCAAAAATCACATTAACAAAGGAAAAATACCAAATTTCATGTCCATAATACCTA
* * *
20091025 CATAACACATTTCAGAACCTACAAAGTGA-CAAATTTTCGAATCGCACTTCAAATATGGCCCTGA
704 CATAACACATTTCACAACCTACAAAGTGAGC-AATTTTCGAATCGCACTTCAAATATGACCCTAA
* * * *
20091089 C-AAAGTTTTA-CAAAAAATGGGCCCACATGCCTGTGTGGCCCACATGGCCCAACTAAC-CCCTC
768 CGAAA-TTTTATCAAAAAATAGGCCCACATGCCTGTGTGACCCACACGGCCCAACTAACTCAC-C
* * * * * * *
20091151 CCGTGTAACCCACA-CTGTCTGGCAT-ACGGTTG-TGTGGCGTCGC-T-AGTGGC-CTTTTGGCT
831 CCATGTAACCCACAGCTGTCTGGCATAACAG-TGCTGTAGCGTCACGTCAGTAGCTATTTTGGAT
* *
20091210 -TTCGC-TGTTCGTTTTTTTCGA
895 ATTCGCAT-TAC-ATTTTTT-GA
* * * * *
20091231 GATTTTCGTGATACACCTGGTCTATTCT-AA-AC-A-TTATAGCACACTTCCAGACCCTAAAATG
1 GATTTTCATGACACACCTAGTCGATTCTAAACACAATTTACAGCACACTTCCAGACCCTAAAATG
* *
20091292 TCATTGAAAATAAACAAATTAACAAGGATTACCAATCTCAAATCAATTGTTCCAACACAAATGCT
66 TCATTCAAAATAAACAAATTAACAAGGATTACCAATCTCAAGTCAATTGTTCCAACACAAATGCT
* * *
20091357 AAGATATTTGGCCTTTACTTAAAAAGAAATTGATTCCTAAGACACTCTGTTCACTAGAAAAGTGT
131 AAG-TA-TT-GCCCTTACCTAAAAAGAAACTGATTCCTAAGACACTCTGTTCACTAGAAAAGTGT
*
20091422 TGGGTGCTTCGCAAACTTTACCTAACAGATTCTCACACAAAAGAGGGCATCAAAATGCAATCAAC
193 TGGGTGCTTCGCAAACTTCACCTAACAGATTC-CACACAAAAGAGGGCATCAAAATGCAATCAAC
* * *
20091487 TCTAAC-AAAAAATTCTCAAATAAAGTTATCTCAAAATATCCATATCAAAATAAGACGAACACC-
257 TCTAACAAAAAAATTCTCAAATAAGGTTATCTCAAAATATCCATCT-AAAAAAAGACGAACACCA
* * ** * * *
20091550 A----CAACT-TTATTATTCTAT-TT-C-A-T-ACACACCAATCACACACTTGGAGACTATAGAT
321 ATTGGAAACTATGACAACTCTATATTCCAATTCATACACCAATCACACACTCGGAGACTATAGAT
* * * * * *
20091605 GGAAAAGGTTAGAACATCCACGAAGAAATCTTAAAAATGGTCAATAGATAACAAAAGAATATAGG
386 GAAAAAGGTCAGAACATCCATGAAGAAATCTTAAAAATGGTTAATAGAAAACCAAAGAATATAGG
20091670 CTGAAATA
451 -TGAAATA
20091678 AAATAATAAT
Statistics
Matches: 1152, Mismatches: 162, Indels: 116
0.81 0.11 0.08
Matches are distributed among these distances:
896 3 0.00
897 93 0.08
898 1 0.00
899 1 0.00
900 1 0.00
901 2 0.00
903 8 0.01
904 82 0.07
905 4 0.00
906 1 0.00
907 3 0.00
908 8 0.01
909 12 0.01
910 26 0.02
911 1 0.00
912 11 0.01
913 118 0.10
914 38 0.03
915 175 0.15
916 43 0.04
917 64 0.06
918 7 0.01
919 58 0.05
920 190 0.16
922 3 0.00
923 1 0.00
924 3 0.00
925 2 0.00
926 193 0.17
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.28
Consensus pattern (914 bp):
GATTTTCATGACACACCTAGTCGATTCTAAACACAATTTACAGCACACTTCCAGACCCTAAAATG
TCATTCAAAATAAACAAATTAACAAGGATTACCAATCTCAAGTCAATTGTTCCAACACAAATGCT
AAGTATTGCCCTTACCTAAAAAGAAACTGATTCCTAAGACACTCTGTTCACTAGAAAAGTGTTGG
GTGCTTCGCAAACTTCACCTAACAGATTCCACACAAAAGAGGGCATCAAAATGCAATCAACTCTA
ACAAAAAAATTCTCAAATAAGGTTATCTCAAAATATCCATCTAAAAAAAGACGAACACCAATTGG
AAACTATGACAACTCTATATTCCAATTCATACACCAATCACACACTCGGAGACTATAGATGAAAA
AGGTCAGAACATCCATGAAGAAATCTTAAAAATGGTTAATAGAAAACCAAAGAATATAGGTGAAA
TACATAAATGAATCATGCTTATACAGATTTCTCAAATTACAGATCAAAAGTAAAGATTATACCAC
AAACATGCTCTTGAATGTTACACAAGCAATATCAGGTTAATTTCAGGTTTCACTTGCAAACACTA
ACAAGATAACAAATGTATTTATATATCATACATACCATACATATCAGAACATACTATCACGCGTT
CAAAAATCACATTAACAAAGGAAAAATACCAAATTTCATGTCCATAATACCTACATAACACATTT
CACAACCTACAAAGTGAGCAATTTTCGAATCGCACTTCAAATATGACCCTAACGAAATTTTATCA
AAAAATAGGCCCACATGCCTGTGTGACCCACACGGCCCAACTAACTCACCCCATGTAACCCACAG
CTGTCTGGCATAACAGTGCTGTAGCGTCACGTCAGTAGCTATTTTGGATATTCGCATTACATTTT
TTGA
Found at i:20093234 original size:24 final size:26
Alignment explanation
Indices: 20093207--20093254 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
20093197 ATAACTGAAA
*
20093207 ATAACATTATT-ATTTAA-TACATTG
1 ATAACATCATTGATTTAATTACATTG
*
20093231 ATAATATCATTGATTTAATTACAT
1 ATAACATCATTGATTTAATTACAT
20093255 CGATTTTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
25 6 0.30
26 5 0.25
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (26 bp):
ATAACATCATTGATTTAATTACATTG
Found at i:20100216 original size:19 final size:19
Alignment explanation
Indices: 20100192--20100232 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
20100182 TTGTTGTAGA
20100192 TCCTGGATCAATTTGAAGC
1 TCCTGGATCAATTTGAAGC
20100211 TCCTGGATCAATTTGAAGC
1 TCCTGGATCAATTTGAAGC
20100230 TCC
1 TCC
20100233 ACCTACTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (19 bp):
TCCTGGATCAATTTGAAGC
Found at i:20109318 original size:3 final size:3
Alignment explanation
Indices: 20109310--20109350 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
20109300 GGATGTATCA
20109310 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
20109351 ATATTTGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20111806 original size:23 final size:24
Alignment explanation
Indices: 20111761--20111825 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 24
20111751 TACTTTATTT
* * *
20111761 AAATAATAATAATAA-TAATAATA
1 AAATATTAATATTAATTAAAAATA
**
20111784 ATTTATTAA-ATTAATTAAAAATA
1 AAATATTAATATTAATTAAAAATA
20111807 AAATATTAATATTAATTAA
1 AAATATTAATATTAATTAA
20111826 CATGTAGCAC
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
22 4 0.12
23 20 0.61
24 9 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AAATATTAATATTAATTAAAAATA
Found at i:20116566 original size:27 final size:27
Alignment explanation
Indices: 20116514--20116566 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
20116504 AAAAAAAAAT
*
20116514 CACAATCCTAATTTTCTAGATGTTAAC
1 CACAATCCTAATTTTCTAGAAGTTAAC
*
20116541 CACAATTCTAATTTTCTA-AAGATTAA
1 CACAATCCTAATTTTCTAGAAG-TTAA
20116567 TCAATAAAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (27 bp):
CACAATCCTAATTTTCTAGAAGTTAAC
Found at i:20117155 original size:16 final size:16
Alignment explanation
Indices: 20117134--20117182 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 16
20117124 AAGAAAAAAT
20117134 AAAATTTTAATTTAAA
1 AAAATTTTAATTTAAA
20117150 AAAATTTTAATTTTTAAA
1 AAAATTTTAA--TTTAAA
20117168 AAGAATTTTTAATTT
1 AA-AA-TTTTAATTT
20117183 TTTTAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 10 0.34
18 11 0.38
19 2 0.07
20 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
AAAATTTTAATTTAAA
Found at i:20117179 original size:20 final size:18
Alignment explanation
Indices: 20117134--20117184 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 18
20117124 AAGAAAAAAT
20117134 AAAATTTTAA--TTTAAA
1 AAAATTTTAATTTTTAAA
20117150 AAAATTTTAATTTTTAAA
1 AAAATTTTAATTTTTAAA
20117168 AAGAATTTTTAATTTTT
1 AA-AA-TTTTAATTTTT
20117185 TTAATTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.32
18 8 0.26
19 2 0.06
20 11 0.35
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
AAAATTTTAATTTTTAAA
Found at i:20117233 original size:19 final size:21
Alignment explanation
Indices: 20117205--20117244 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
20117195 AAGATTTTGG
20117205 AAATATTTAT-TAATTTTTTA
1 AAATATTTATATAATTTTTTA
20117225 AAATA-TTATATAATTTTTTA
1 AAATATTTATATAATTTTTTA
20117245 TTTTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
AAATATTTATATAATTTTTTA
Found at i:20118150 original size:27 final size:23
Alignment explanation
Indices: 20118094--20118142 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
20118084 TTCAAATTTA
*
20118094 AATAATTAATATATTCTTTAAAG
1 AATAATTAATATATTCTATAAAG
*
20118117 AATAATTAATATATCTCTATACAG
1 AATAATTAATATAT-TCTATAAAG
20118141 AA
1 AA
20118143 ATGAAATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (23 bp):
AATAATTAATATATTCTATAAAG
Found at i:20119190 original size:14 final size:14
Alignment explanation
Indices: 20119173--20119209 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 14
20119163 TAGCCCGCTC
20119173 ATATTAATTTTTTT
1 ATATTAATTTTTTT
20119187 ATATT-A-TTTTTT
1 ATATTAATTTTTTT
20119199 ATA-TAATTTTT
1 ATATTAATTTTT
20119210 AAAAATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 1 0.05
12 10 0.48
13 5 0.24
14 5 0.24
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
ATATTAATTTTTTT
Found at i:20123369 original size:15 final size:15
Alignment explanation
Indices: 20123349--20123378 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20123339 GGCAAACCAC
20123349 ACTCGAACACTTTGT
1 ACTCGAACACTTTGT
*
20123364 ACTCGATCACTTTGT
1 ACTCGAACACTTTGT
20123379 GCAATCTACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.37
Consensus pattern (15 bp):
ACTCGAACACTTTGT
Found at i:20127110 original size:40 final size:39
Alignment explanation
Indices: 20127029--20127174 Score: 157
Period size: 40 Copynumber: 3.7 Consensus size: 39
20127019 CCGCACCAAG
* * * * * * *
20127029 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTAGCAC-AAT
* *
20127069 GCCTTCGGGTCTTAGCCCGGATTTAACAACTGGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTAGCAC-AAT
* *
20127109 GCCTTCGGGTCTTAGCCCGGATATAGCTACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTAGCACAA-T
*
20127149 GCCTTCGGGTCTTAACCCGGATATAA
1 GCCTTCGGGTCTTAGCCCGGATATAA
20127175 TTTTCAGCAT
Statistics
Matches: 90, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
39 2 0.02
40 88 0.98
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (39 bp):
GCCTTCGGGTCTTAGCCCGGATATAACAACTAGCACAAT
Found at i:20127189 original size:40 final size:40
Alignment explanation
Indices: 20127061--20127212 Score: 164
Period size: 40 Copynumber: 3.8 Consensus size: 40
20127051 ATCACGATTT
* * * * *
20127061 GCACAAATGCCTTCGGGTCTTAGCCCGGATTTAACAACTG
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
20127101 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
* * **
20127141 GCACAATTGCCTTCGGGTCTTAACCCGGATATA-ATTTTCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCTACT-A
* * *
20127181 GCATAATTGTCTTCGGGGCTTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
20127213 CATTCAATTT
Statistics
Matches: 97, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
39 4 0.04
40 91 0.94
41 2 0.02
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
Found at i:20143920 original size:2 final size:2
Alignment explanation
Indices: 20143913--20143950 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
20143903 ATAACTTCAA
20143913 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
20143951 TATCTTAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20144280 original size:18 final size:18
Alignment explanation
Indices: 20144243--20144300 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
20144233 AATAAAGTAA
*
20144243 TTTTCAAATTTTGAAAATAT
1 TTTTAAAATTTT--AAATAT
*
20144263 TTTTTAAATTTTAAATAT
1 TTTTAAAATTTTAAATAT
*
20144281 TTATAAAAATTTTAAA-AT
1 TT-TTAAAATTTTAAATAT
20144299 TT
1 TT
20144301 GTATTTTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 12 0.35
19 11 0.32
20 11 0.32
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
TTTTAAAATTTTAAATAT
Found at i:20147274 original size:22 final size:22
Alignment explanation
Indices: 20147247--20147293 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
20147237 GCTTGAATTA
* *
20147247 GTTGTTTCGCTATTGTTTTGTT
1 GTTGTTTCGCTACTATTTTGTT
*
20147269 GTTGTTTTGCTACTATTTTGTT
1 GTTGTTTCGCTACTATTTTGTT
20147291 GTT
1 GTT
20147294 ATTTTTTGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.06, C:0.09, G:0.21, T:0.64
Consensus pattern (22 bp):
GTTGTTTCGCTACTATTTTGTT
Found at i:20147537 original size:18 final size:18
Alignment explanation
Indices: 20147514--20147548 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20147504 CACAAACTCT
20147514 GAACATAAACAATAAAAC
1 GAACATAAACAATAAAAC
* *
20147532 GAACATGAAGAATAAAA
1 GAACATAAACAATAAAA
20147549 ATATATATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.11, G:0.11, T:0.11
Consensus pattern (18 bp):
GAACATAAACAATAAAAC
Found at i:20152659 original size:49 final size:48
Alignment explanation
Indices: 20152484--20152727 Score: 191
Period size: 49 Copynumber: 5.1 Consensus size: 48
20152474 CCATGGCAAC
* * * * * *
20152484 ATGTGATATGTGATCCGTATAAAACAATAGCTGGGCTATGGCATCGGTGT
1 ATGTGATATGTGATACGTGTAAGACCATAGCTGGGCTATGACATC-G-AT
** * * * *
20152534 GATGTGATTATGTTCTTCTGTGTAAGACCATATCTGGGATATTACATC-A-
1 -ATGTGA-TATGTGATAC-GTGTAAGACCATAGCTGGGCTATGACATCGAT
* * * * *
20152583 GTGAGATATGTGATCCGTGTAAGACCATAGTTGGGCTATGGCATCGAT
1 ATGTGATATGTGATACGTGTAAGACCATAGCTGGGCTATGACATCGAT
*
20152631 ATGTGATATGTGATTACGTGTAATACCATAGCTGGGCTATGACATCGAT
1 ATGTGATATGTGA-TACGTGTAAGACCATAGCTGGGCTATGACATCGAT
*
20152680 ATGTGA-A--T-AT--GTGTAAGACCATAGCTGGACTATGACATC-ATT
1 ATGTGATATGTGATACGTGTAAGACCATAGCTGGGCTATGACATCGA-T
20152722 ATGTGA
1 ATGTGA
20152728 AGATGTGTAA
Statistics
Matches: 158, Mismatches: 29, Indels: 21
0.76 0.14 0.10
Matches are distributed among these distances:
41 1 0.01
42 34 0.22
44 1 0.01
45 1 0.01
46 25 0.16
47 8 0.05
48 16 0.10
49 37 0.23
51 6 0.04
52 7 0.04
53 22 0.14
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.32
Consensus pattern (48 bp):
ATGTGATATGTGATACGTGTAAGACCATAGCTGGGCTATGACATCGAT
Found at i:20152694 original size:42 final size:42
Alignment explanation
Indices: 20152635--20152762 Score: 168
Period size: 42 Copynumber: 3.0 Consensus size: 42
20152625 ATCGATATGT
* * * *
20152635 GATATGTGATTACGTGTAATACCATAGCTGGGCTATGACATC
1 GATATGTGAATATGTGTAAGACCATAGCTGGACTATGACATC
20152677 GATATGTGAATATGTGTAAGACCATAGCTGGACTATGACATC
1 GATATGTGAATATGTGTAAGACCATAGCTGGACTATGACATC
* * * *
20152719 -ATTATGTGAAGATGTGTAAGACCATAGTTGAACTATGGCATC
1 GA-TATGTGAATATGTGTAAGACCATAGCTGGACTATGACATC
20152761 GA
1 GA
20152763 GAAAATGAAG
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
41 1 0.01
42 74 0.97
43 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (42 bp):
GATATGTGAATATGTGTAAGACCATAGCTGGACTATGACATC
Found at i:20153588 original size:22 final size:22
Alignment explanation
Indices: 20153563--20153606 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
20153553 GCACGTATGA
20153563 TTGATTGATTAGTCAATGTTGG
1 TTGATTGATTAGTCAATGTTGG
20153585 TTGATTGATTAGTCAATGTTGG
1 TTGATTGATTAGTCAATGTTGG
20153607 CTTATGAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.05, G:0.27, T:0.45
Consensus pattern (22 bp):
TTGATTGATTAGTCAATGTTGG
Found at i:20157837 original size:20 final size:19
Alignment explanation
Indices: 20157811--20157869 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
20157801 TAAGCAAAAA
*
20157811 TAAAAAAGTATCAATACCT
1 TAAAAAAATATCAATACCT
*
20157830 TAAAAAAA-AGTCGATACCT
1 TAAAAAAATA-TCAATACCT
**
20157849 TAAAAATTTTATCAATACCT
1 TAAAAA-AATATCAATACCT
20157869 T
1 T
20157870 GTCTGGTATC
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 1 0.03
19 21 0.66
20 9 0.28
21 1 0.03
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (19 bp):
TAAAAAAATATCAATACCT
Found at i:20162463 original size:46 final size:46
Alignment explanation
Indices: 20162413--20162588 Score: 210
Period size: 46 Copynumber: 3.8 Consensus size: 46
20162403 TGGTTGAGCA
*
20162413 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
*** * * ** *
20162459 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGC-AAACG
* *
20162506 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
20162552 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
20162589 GCGGTTACAT
Statistics
Matches: 107, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
46 72 0.67
47 35 0.33
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:20162569 original size:93 final size:93
Alignment explanation
Indices: 20162410--20162580 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
20162400 GGATGGTTGA
* *
20162410 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
20162475 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* * *
20162503 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
20162568 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
20162581 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:20165575 original size:14 final size:14
Alignment explanation
Indices: 20165496--20165575 Score: 54
Period size: 15 Copynumber: 5.4 Consensus size: 14
20165486 GTATCTTGGG
*
20165496 TTTCTTTATCCTGGA
1 TTTCTTTATTC-GGA
*
20165511 TCTT-TTTATTATGGA
1 T-TTCTTTATT-CGGA
*
20165526 TTTCTTTATTCCGGG
1 TTTCTTTATT-CGGA
* *
20165541 TTTCTCTATCTTGGA
1 TTTCTTTAT-TCGGA
*
20165556 TTTCTTTATTCGGT
1 TTTCTTTATTCGGA
20165570 TTTCTT
1 TTTCTT
20165576 GTTATCTTTG
Statistics
Matches: 50, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
14 11 0.22
15 36 0.72
16 3 0.06
ACGTcount: A:0.11, C:0.16, G:0.14, T:0.59
Consensus pattern (14 bp):
TTTCTTTATTCGGA
Found at i:20168016 original size:46 final size:45
Alignment explanation
Indices: 20167966--20168141 Score: 174
Period size: 46 Copynumber: 3.8 Consensus size: 45
20167956 TGGTTGAGCA
*
20167966 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGTTGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGTTGC-AACG
* *** ** * *
20168012 TCCGAACTCGTTGAGTTGAGTCTGAGTTCGAGAGAT-GTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGTTGC-A-ACG
* *
20168059 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGTTGC-AACG
* * *
20168105 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
20168142 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 23, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
46 71 0.68
47 33 0.32
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGTTGCAACG
Found at i:20168122 original size:93 final size:93
Alignment explanation
Indices: 20167963--20168134 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
20167953 GGATGGTTGA
* * *
20167963 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGTTGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
*
20168028 TGAGTCTGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* * *
20168056 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
20168121 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
20168135 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:20171396 original size:3 final size:3
Alignment explanation
Indices: 20171383--20171507 Score: 53
Period size: 3 Copynumber: 39.3 Consensus size: 3
20171373 TATATAAACA
* * *
20171383 AAT AA- AAT AAT AAT AAC AAT AAT AAT AAT AAT AGA- AAT CAG AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
**
20171427 AAT -AT ATAT AAGT GCAA- AAT GGGT AAT AAAT AAAT AAAT GAAT AAAT
1 AAT AAT A-AT AA-T --AAT AAT -AAT AAT -AAT -AAT -AAT -AAT -AAT
*
20171474 AAT AAT AAT AAT GAT AAT AAT AGAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT A
20171508 CCAATGATAA
Statistics
Matches: 95, Mismatches: 14, Indels: 26
0.70 0.10 0.19
Matches are distributed among these distances:
2 9 0.09
3 58 0.61
4 26 0.27
6 2 0.02
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:20173286 original size:44 final size:44
Alignment explanation
Indices: 20173236--20173330 Score: 154
Period size: 44 Copynumber: 2.2 Consensus size: 44
20173226 TACTGTAATT
*
20173236 TAAGATTTGTGGCTTCAATTTGCTCCACTGCACCTTCAAGGAGA
1 TAAGATTTGTGGCTTCAATCTGCTCCACTGCACCTTCAAGGAGA
* *
20173280 TAAGATTTGTGGCTTCAATCTGCTCCACTGCACTTTCAGGGAGA
1 TAAGATTTGTGGCTTCAATCTGCTCCACTGCACCTTCAAGGAGA
*
20173324 CAAGATT
1 TAAGATT
20173331 CGCCATGGTA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (44 bp):
TAAGATTTGTGGCTTCAATCTGCTCCACTGCACCTTCAAGGAGA
Found at i:20173541 original size:35 final size:36
Alignment explanation
Indices: 20173502--20173584 Score: 98
Period size: 38 Copynumber: 2.3 Consensus size: 36
20173492 ATAACTTGAA
*
20173502 GGAGATAAGA-TCAATTTGCTCCACTGCT-ACTTCAG
1 GGAGATAAGATTCAATCTGCTCCACTG-TGACTTCAG
* *
20173537 GGAGATAAGATTTTTAGTCTGCTCCACTGTGACTTCAG
1 GGAGATAAGA--TTCAATCTGCTCCACTGTGACTTCAG
20173575 GGAGATAAGA
1 GGAGATAAGA
20173585 CTTATAACTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
35 10 0.24
37 1 0.02
38 30 0.73
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (36 bp):
GGAGATAAGATTCAATCTGCTCCACTGTGACTTCAG
Found at i:20173704 original size:45 final size:44
Alignment explanation
Indices: 20173568--20173733 Score: 172
Period size: 44 Copynumber: 3.8 Consensus size: 44
20173558 CTCCACTGTG
* * * * *
20173568 ACTTCAGGGAGATAAGACTTATAACTTCAACCTACTTTACTGCA
1 ACTTCAGAGAGATAAGATTTATAACTTCAATCTACTCTACTACA
* * *
20173612 ACTTCAGAGAGATAATG-TTTATAGCTTTAATCTACTCTACTAGA
1 ACTTCAGAGAGATAA-GATTTATAACTTCAATCTACTCTACTACA
* * *
20173656 ACTTCAGAGAGATAAGATTTGCTATCATCAATCTACTCTACTACA
1 ACTTCAGAGAGATAAGATTT-ATAACTTCAATCTACTCTACTACA
* * * *
20173701 ACTTCAGGGAGATAAGATCTATAGCTTTAATCT
1 ACTTCAGAGAGATAAGATTTATAACTTCAATCT
20173734 GCTCCACAAT
Statistics
Matches: 100, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
43 1 0.01
44 61 0.61
45 38 0.38
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (44 bp):
ACTTCAGAGAGATAAGATTTATAACTTCAATCTACTCTACTACA
Found at i:20173724 original size:89 final size:88
Alignment explanation
Indices: 20173568--20173733 Score: 217
Period size: 89 Copynumber: 1.9 Consensus size: 88
20173558 CTCCACTGTG
* * * * *
20173568 ACTTCAGGGAGATAAGACTTATAACTTCAACCTACTTTACTGCAACTTCAGAGAGATAATGTTTA
1 ACTTCAGAGAGATAAGACTTATAACATCAACCTACTCTACTACAACTTCAGAGAGATAATGTCTA
20173633 TAGCTTTAATCTACTCTACTAGA
66 TAGCTTTAATCTACTCTACTAGA
* * * * *
20173656 ACTTCAGAGAGATAAGATTTGCTATCATCAATCTACTCTACTACAACTTCAGGGAGATAA-GATC
1 ACTTCAGAGAGATAAGACTT-ATAACATCAACCTACTCTACTACAACTTCAGAGAGATAATG-TC
20173720 TATAGCTTTAATCT
64 TATAGCTTTAATCT
20173734 GCTCCACAAT
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
88 19 0.29
89 47 0.71
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (88 bp):
ACTTCAGAGAGATAAGACTTATAACATCAACCTACTCTACTACAACTTCAGAGAGATAATGTCTA
TAGCTTTAATCTACTCTACTAGA
Found at i:20186288 original size:3 final size:3
Alignment explanation
Indices: 20186275--20186391 Score: 96
Period size: 3 Copynumber: 39.0 Consensus size: 3
20186265 TAAAGAAAGA
* * * *
20186275 AAT ATAT AAT AAT AAT AAT AAT AAT AGT AA- AAA AAT AGT AAT AGT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
20186320 AAT AAT AACG AA- AAT AGT AGT AAT AAT AGT AAT AAA AAT AAT AGT
1 AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20186365 AAT AAT AAT AAAT AAT AAT -AT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT
20186392 GTTAAAATTA
Statistics
Matches: 92, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
2 6 0.07
3 78 0.85
4 8 0.09
ACGTcount: A:0.62, C:0.01, G:0.07, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:20186338 original size:24 final size:23
Alignment explanation
Indices: 20186285--20186391 Score: 87
Period size: 23 Copynumber: 4.8 Consensus size: 23
20186275 AATATATAAT
* * * *
20186285 AATAATAATAATAATAGTAAAAA
1 AATAGTAATAGTAATAATAAGAA
20186308 AATAGTAATAGTAATAATAACGAA
1 AATAGTAATAGTAATAATAA-GAA
* * * *
20186332 AATAGTAGTAATAATAGTAATAA
1 AATAGTAATAGTAATAATAAGAA
*
20186355 AA-A-TAATAGTAATAATAA-TA
1 AATAGTAATAGTAATAATAAGAA
*
20186375 AATAATAATA-TAATAAT
1 AATAGTAATAGTAATAAT
20186392 GTTAAAATTA
Statistics
Matches: 69, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
20 3 0.04
21 20 0.29
22 6 0.09
23 21 0.30
24 19 0.28
ACGTcount: A:0.63, C:0.01, G:0.07, T:0.29
Consensus pattern (23 bp):
AATAGTAATAGTAATAATAAGAA
Found at i:20186793 original size:35 final size:35
Alignment explanation
Indices: 20186745--20186830 Score: 145
Period size: 35 Copynumber: 2.5 Consensus size: 35
20186735 CCTAGGGGTG
*
20186745 AAACGACGTCGTTTTGCGCTTGGTGTTTTAAATCA
1 AAACGACGCCGTTTTGCGCTTGGTGTTTTAAATCA
20186780 AAACGACGCCGTTTTGCGCTTGGTGTTTTAAATCA
1 AAACGACGCCGTTTTGCGCTTGGTGTTTTAAATCA
* *
20186815 AAATGACGCTGTTTTG
1 AAACGACGCCGTTTTG
20186831 ATAAGCTTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (35 bp):
AAACGACGCCGTTTTGCGCTTGGTGTTTTAAATCA
Found at i:20196072 original size:38 final size:40
Alignment explanation
Indices: 20196018--20196134 Score: 166
Period size: 38 Copynumber: 2.8 Consensus size: 40
20196008 TCTGATATGA
20196018 AATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 AATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
20196058 -A-GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 AATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
20196096 ATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGG
1 ------AATGTGTAAGACCATGGTTGAAAGATACCATGG
20196135 TTGAAAGATA
Statistics
Matches: 69, Mismatches: 0, Indels: 10
0.87 0.00 0.13
Matches are distributed among these distances:
38 37 0.54
39 1 0.01
45 1 0.01
46 30 0.43
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (40 bp):
AATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
Found at i:20196133 original size:16 final size:16
Alignment explanation
Indices: 20196112--20196150 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
20196102 AATGTGTAAG
20196112 ACCATGGTTGAAAGAT
1 ACCATGGTTGAAAGAT
20196128 ACCATGGTTGAAAGAT
1 ACCATGGTTGAAAGAT
20196144 ACCATGG
1 ACCATGG
20196151 CAACCTGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (16 bp):
ACCATGGTTGAAAGAT
Found at i:20196167 original size:62 final size:62
Alignment explanation
Indices: 20196066--20196196 Score: 253
Period size: 62 Copynumber: 2.1 Consensus size: 62
20196056 TGAGTGTAAG
20196066 ACCATGGTTGAAAGATACCATGGCAACCTGATATAAAATGTGTAAGACCATGGTTGAAAGAT
1 ACCATGGTTGAAAGATACCATGGCAACCTGATATAAAATGTGTAAGACCATGGTTGAAAGAT
*
20196128 ACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGAT
1 ACCATGGTTGAAAGATACCATGGCAACCTGATATAAAATGTGTAAGACCATGGTTGAAAGAT
20196190 ACCATGG
1 ACCATGG
20196197 CAACGTGATA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 68 1.00
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (62 bp):
ACCATGGTTGAAAGATACCATGGCAACCTGATATAAAATGTGTAAGACCATGGTTGAAAGAT
Found at i:20196178 original size:46 final size:46
Alignment explanation
Indices: 20196128--20196295 Score: 230
Period size: 46 Copynumber: 3.7 Consensus size: 46
20196118 GTTGAAAGAT
* *
20196128 ACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAG
1 ACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGAGTAAG
* **
20196174 ACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAACAAG
1 ACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGAGTAAG
*
20196220 ACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAGTAAG
1 ACCATGGTTGAAAGATACCATGGCAACATGATATG-AAATGAGTAAG
* * * *
20196266 ACCATAGTTGAAAGACACTATGGCATCATG
1 ACCATGGTTGAAAGATACCATGGCAACATG
20196296 TCAAAGATAA
Statistics
Matches: 109, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
45 1 0.01
46 108 0.99
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (46 bp):
ACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGAGTAAG
Found at i:20199632 original size:40 final size:38
Alignment explanation
Indices: 20199487--20199635 Score: 226
Period size: 38 Copynumber: 3.9 Consensus size: 38
20199477 CACTCGATAC
* *
20199487 ATCCGGGTTAAGTCCCGCAGGCTTCGTACTGGTAATAT
1 ATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATAT
20199525 ATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATAT
1 ATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATAT
* *
20199563 ATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTACTAT
1 ATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATAT
* *
20199601 ATCCGAGCTTAAAGTCCCGCAGGCTTTGTGCTGGT
1 ATCCG-GGTTAAA-TCCCGCAGGCTTCGTGCTGGT
20199636 GACTGGATTC
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
38 77 0.75
39 6 0.06
40 20 0.19
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (38 bp):
ATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATAT
Found at i:20205529 original size:26 final size:24
Alignment explanation
Indices: 20205488--20205546 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
20205478 TTATTTTATT
* *
20205488 AAATAAA-AAATTTAAAAATATAA
1 AAATAAATATATTTAAAAACATAA
20205511 TAAATCAAATATATTTAAAAACATAA
1 -AAAT-AAATATATTTAAAAACATAA
20205537 AAATAAATAT
1 AAATAAATAT
20205547 TAAAACAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 10 0.32
25 7 0.23
26 14 0.45
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (24 bp):
AAATAAATATATTTAAAAACATAA
Found at i:20205558 original size:22 final size:22
Alignment explanation
Indices: 20205517--20205575 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
20205507 ATAATAAATC
* *
20205517 AAATATAT-TTAAAA-ACATAA
1 AAATAAATATTAAAACAAATAA
20205537 AAATAAATATTAAAACAAATAA
1 AAATAAATATTAAAACAAATAA
*
20205559 AAAT-AATACTAAAACAA
1 AAATAAATATTAAAACAA
20205576 TTCTTAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 18 0.53
22 9 0.26
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (22 bp):
AAATAAATATTAAAACAAATAA
Found at i:20214638 original size:19 final size:19
Alignment explanation
Indices: 20214590--20214639 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
20214580 TAATATTTTC
* *
20214590 TTATTTATTTTTAAGATTC
1 TTATTAATTTTTAAGATTA
20214609 TT-TTAACTTTTT-AGAATTA
1 TTATTAA-TTTTTAAG-ATTA
20214628 TTATTAATTTTT
1 TTATTAATTTTT
20214640 TTAAAAGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 5 0.19
19 17 0.65
20 4 0.15
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (19 bp):
TTATTAATTTTTAAGATTA
Found at i:20214640 original size:20 final size:19
Alignment explanation
Indices: 20214590--20214640 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
20214580 TAATATTTTC
* * *
20214590 TTATTTATTTTTAAGATTC
1 TTATTAATTTTTTAGATTA
*
20214609 TT-TTAACTTTTTAGAATTA
1 TTATTAATTTTTTAG-ATTA
20214628 TTATTAATTTTTT
1 TTATTAATTTTTT
20214641 TAAAAGTATC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 9 0.36
19 7 0.28
20 9 0.36
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (19 bp):
TTATTAATTTTTTAGATTA
Found at i:20224626 original size:67 final size:67
Alignment explanation
Indices: 20224524--20224670 Score: 267
Period size: 67 Copynumber: 2.2 Consensus size: 67
20224514 AAAATCATGC
20224524 CAAAACAATATGCCATAACCTTAACTTCTATATGTATTTTCTCACCATTTTATTAACTATTTCAT
1 CAAAAC-ATAT-CCATAACCTTAACTTCTATATGTATTTTCTCACCATTTTATTAACTATTTCAT
20224589 GTCT
64 GTCT
*
20224593 CAAAACATATCCATAACCTTAACTTCTATATGTATTTTCTCACTATTTTATTAACTATTTCATGT
1 CAAAACATATCCATAACCTTAACTTCTATATGTATTTTCTCACCATTTTATTAACTATTTCATGT
20224658 CT
66 CT
20224660 CAAAACATATC
1 CAAAACATATC
20224671 AATTCATCAT
Statistics
Matches: 77, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
67 67 0.87
68 4 0.05
69 6 0.08
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.41
Consensus pattern (67 bp):
CAAAACATATCCATAACCTTAACTTCTATATGTATTTTCTCACCATTTTATTAACTATTTCATGT
CT
Found at i:20225428 original size:43 final size:43
Alignment explanation
Indices: 20225373--20225520 Score: 199
Period size: 43 Copynumber: 3.4 Consensus size: 43
20225363 CAATGTCATA
* * * *
20225373 TCCCAGATATGGTCTTACATGTTATCATATATCGATGTCAATG
1 TCCCAGACATGGTCTTACACGTAATCATATATCGATGCCAATG
* *
20225416 TCCCAGACATGGTCTTACACGAAATCATATAACGATGCCAATG
1 TCCCAGACATGGTCTTACACGTAATCATATATCGATGCCAATG
* * *
20225459 TCTCAGACATGGTCTTACACGTAATCACA-ATACAATGCCAATG
1 TCCCAGACATGGTCTTACACGTAATCATATAT-CGATGCCAATG
20225502 TCCCAGACATGGTCTTACA
1 TCCCAGACATGGTCTTACA
20225521 TATAATTACA
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 1 0.01
43 91 0.99
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACACGTAATCATATATCGATGCCAATG
Found at i:20227355 original size:59 final size:59
Alignment explanation
Indices: 20227233--20227356 Score: 146
Period size: 59 Copynumber: 2.1 Consensus size: 59
20227223 TGCATTGATT
* * * *
20227233 TTTTTAATATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAACAGAAATTG
1 TTTTGAATATATTTGTACAAACTATTTTTATATAGTTTCATTTAATAAAACAGAAACTA
* *
20227292 TTTTGAATATTTTTGTACAAATTATTTTT-TCATAGTTTCATTTAATAAATTA-AG-AACTA
1 TTTTGAATATATTTGTACAAACTATTTTTAT-ATAGTTTCATTTAATAAA--ACAGAAACTA
20227351 TTTTGA
1 TTTTGA
20227357 TTTGGACATG
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
58 1 0.02
59 52 0.93
60 2 0.04
61 1 0.02
ACGTcount: A:0.35, C:0.06, G:0.07, T:0.51
Consensus pattern (59 bp):
TTTTGAATATATTTGTACAAACTATTTTTATATAGTTTCATTTAATAAAACAGAAACTA
Found at i:20231916 original size:27 final size:28
Alignment explanation
Indices: 20231886--20231956 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 28
20231876 AAAATATCTT
20231886 AAAACCCTAAACCTTAA-TTTATTTTAA
1 AAAACCCTAAACCTTAATTTTATTTTAA
* * * *
20231913 AAAATCATAAACCTTAATTTTTTTTTCA
1 AAAACCCTAAACCTTAATTTTATTTTAA
20231941 AAAACCCT-AACCTTAA
1 AAAACCCTAAACCTTAA
20231957 ACCCATAAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
27 23 0.62
28 14 0.38
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.37
Consensus pattern (28 bp):
AAAACCCTAAACCTTAATTTTATTTTAA
Found at i:20234666 original size:21 final size:21
Alignment explanation
Indices: 20234640--20234681 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
20234630 CTGCAAATTG
20234640 AGGTATACAGACATAGTTGCA
1 AGGTATACAGACATAGTTGCA
20234661 AGGTATACAGACATAGTTGCA
1 AGGTATACAGACATAGTTGCA
20234682 TGAAAAAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (21 bp):
AGGTATACAGACATAGTTGCA
Found at i:20235811 original size:11 final size:12
Alignment explanation
Indices: 20235781--20235820 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
20235771 GGTAAATCTG
*
20235781 TTTCTCTTTTCC
1 TTTCTTTTTTCC
20235793 TTTCTTTTTTCC
1 TTTCTTTTTTCC
*
20235805 TTTTTTTTTTACC
1 TTTCTTTTTT-CC
20235818 TTT
1 TTT
20235821 TAAATTGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 20 0.80
13 5 0.20
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTCTTTTTTCC
Found at i:20256350 original size:125 final size:124
Alignment explanation
Indices: 20256128--20256482 Score: 438
Period size: 125 Copynumber: 2.9 Consensus size: 124
20256118 AAGGCCAAAC
*
20256128 AAGAACTATTGTAGAAAAAGAGCATCCATGTGGGAGCTTTTTTCA-TCAATTTTGCTGACAGTGC
1 AAGAACTATTGTAGAAAAAGAGCGTCCA-GTGGGAGCTTTTTTCAGT-AATTTTGCTGACAGTGC
* * * * * * *
20256192 ATCCTATTTAAAGCGTTTTTAACATTATTTGTTCAGGACTGTTTTCTCAAAATTA-TTTTTT
64 ATCCTCTTGAAA-CGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTT
20256253 AAGAACTATTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCA
1 AAGAACTATTGTAGAAAAAGAGCGTCCA-GTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCA
20256318 TCCTGCTTGAAACGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTT
65 TCCT-CTTGAAACGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTT
* * * * *
20256379 AGGAATTACTGTAGAAAAAGAGCGTCCA----AAGCTTTTTTCAGTAATTTTTG-TGATAGTGCA
1 AAGAACTATTGTAGAAAAAGAGCGTCCAGTGGGAGCTTTTTTCAGTAA-TTTTGCTGACAGTGCA
* * *
20256439 TACTACTTGAAGCGTTTTTGACATTATCTT-TTCAGAACCGTCTT
65 TCCT-CTTGAAACGTTTTTGACACTAT-TTGTTCAGAACCGTCTT
20256483 TTCACTGTAG
Statistics
Matches: 207, Mismatches: 18, Indels: 14
0.87 0.08 0.06
Matches are distributed among these distances:
121 61 0.29
122 7 0.03
125 102 0.49
126 37 0.18
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (124 bp):
AAGAACTATTGTAGAAAAAGAGCGTCCAGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCAT
CCTCTTGAAACGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTT
Found at i:20256602 original size:34 final size:33
Alignment explanation
Indices: 20256553--20256654 Score: 129
Period size: 34 Copynumber: 3.1 Consensus size: 33
20256543 ACAAATTTAT
20256553 TTTTTTAAAAA--CTAAACCCTAATTTAATTAA
1 TTTTTTAAAAACTCTAAACCCTAATTTAATTAA
* *
20256584 TTTTCTTAAAAACTCTAAACTCTAATTTAATTAC
1 TTTT-TTAAAAACTCTAAACCCTAATTTAATTAA
*
20256618 TTTATTTAAAATCAT-TAAACCCTAATTTAATTAA
1 TTT-TTTAAAAAC-TCTAAACCCTAATTTAATTAA
20256652 TTT
1 TTT
20256655 AAAAAAATAC
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
31 4 0.07
32 7 0.11
34 48 0.79
35 2 0.03
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (33 bp):
TTTTTTAAAAACTCTAAACCCTAATTTAATTAA
Found at i:20256786 original size:6 final size:6
Alignment explanation
Indices: 20256776--20256810 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
20256766 CATAAACAAT
*
20256776 TAACCT TAACCC TAACCC TAACCC TAACCC TAACC
1 TAACCC TAACCC TAACCC TAACCC TAACCC TAACC
20256811 TTAAACCTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.34, C:0.46, G:0.00, T:0.20
Consensus pattern (6 bp):
TAACCC
Found at i:20258887 original size:14 final size:14
Alignment explanation
Indices: 20258868--20258905 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
20258858 TACTGATTTT
20258868 ATTCTATACCTGCA
1 ATTCTATACCTGCA
20258882 ATTCTATACCTGCA
1 ATTCTATACCTGCA
20258896 ATTCTATACC
1 ATTCTATACC
20258906 ATGAAAGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.05, T:0.37
Consensus pattern (14 bp):
ATTCTATACCTGCA
Found at i:20259062 original size:43 final size:43
Alignment explanation
Indices: 20258998--20259096 Score: 171
Period size: 43 Copynumber: 2.3 Consensus size: 43
20258988 AGTTATCTAA
* *
20258998 TGAGTAAGTATAGCCCTTCAAAGATTAGTTTAAATATACTGTTT
1 TGAGTAAGT-TATCCCTTCAAAGATTAGTTTAAATATACTATTT
20259042 TGAGTAAGTTATCCCTTCAAAGATTAGTTTAAATATACTATTT
1 TGAGTAAGTTATCCCTTCAAAGATTAGTTTAAATATACTATTT
20259085 TGAGTAAGTTAT
1 TGAGTAAGTTAT
20259097 GTCAGCAGAA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
43 44 0.83
44 9 0.17
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.40
Consensus pattern (43 bp):
TGAGTAAGTTATCCCTTCAAAGATTAGTTTAAATATACTATTT
Found at i:20259149 original size:6 final size:6
Alignment explanation
Indices: 20259138--20259177 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
20259128 ATATGCACTT
*
20259138 AAAACC AAAACC AAAACC AAAACC AAAACC AAATCC AAAA
1 AAAACC AAAACC AAAACC AAAACC AAAACC AAAACC AAAA
20259178 TCCAGCAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.68, C:0.30, G:0.00, T:0.03
Consensus pattern (6 bp):
AAAACC
Found at i:20260485 original size:30 final size:28
Alignment explanation
Indices: 20260445--20260512 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
20260435 TAAAGGATTT
*
20260445 TTATGAAAATAA-TATTAAAAAATTAATTAA
1 TTATGAAAATAAGT-TT--AAAATAAATTAA
*
20260475 TTATAAAAATAAGTTTAAAATAAATTAA
1 TTATGAAAATAAGTTTAAAATAAATTAA
20260503 TTATGAAAAT
1 TTATGAAAAT
20260513 GGAGTATTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 20 0.59
30 13 0.38
31 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (28 bp):
TTATGAAAATAAGTTTAAAATAAATTAA
Found at i:20260734 original size:20 final size:20
Alignment explanation
Indices: 20260698--20260743 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
20260688 TAGTTTTAGA
* *
20260698 CATTAAATGCAGAGAAAATG
1 CATTAAATGAAGAGAAAAAG
20260718 CATTAAATGTAAG-GAAAAAG
1 CATTAAATG-AAGAGAAAAAG
20260738 CATTAA
1 CATTAA
20260744 GATATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.52, C:0.09, G:0.17, T:0.22
Consensus pattern (20 bp):
CATTAAATGAAGAGAAAAAG
Found at i:20266009 original size:16 final size:16
Alignment explanation
Indices: 20265988--20266045 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
20265978 AATGTGTAAG
20265988 ACCATGGTTGAAAGAT
1 ACCATGGTTGAAAGAT
* ** *
20266004 ACCATGGCCTGAGTGTAAG
1 ACCATGG-TTGAAAG--AT
20266023 ACCATGGTTGAAAGAT
1 ACCATGGTTGAAAGAT
20266039 ACCATGG
1 ACCATGG
20266046 CAACCTGATA
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 15 0.48
17 4 0.13
18 4 0.13
19 8 0.26
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (16 bp):
ACCATGGTTGAAAGAT
Found at i:20266083 original size:46 final size:46
Alignment explanation
Indices: 20266016--20266231 Score: 315
Period size: 46 Copynumber: 4.7 Consensus size: 46
20266006 CATGGCCTGA
20266016 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
*
20266062 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
* *
20266108 GTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
*** * * *
20266154 GAACAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
* * * *
20266200 GAGTAAGACCATAGTTGAAAGACACTATGGCA
1 GTGTAAGACCATGGTTGAAAGATACCATGGCA
20266232 TCATGTCAAA
Statistics
Matches: 156, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 156 1.00
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
Found at i:20268388 original size:2 final size:2
Alignment explanation
Indices: 20268375--20268406 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
20268365 AAACACATGC
*
20268375 AT AT AA 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
20268407 GTAGAATAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:20270605 original size:11 final size:11
Alignment explanation
Indices: 20270557--20270608 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
20270547 ATTAGATAAA
20270557 TATTATTTTAT
1 TATTATTTTAT
*
20270568 TAATATTTTAAT
1 TATTATTTT-AT
* *
20270580 AAGATATTTTAT
1 TA-TTATTTTAT
20270592 TATTATTTTAT
1 TATTATTTTAT
20270603 TATTAT
1 TATTAT
20270609 ATAAAGAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
11 22 0.63
12 6 0.17
13 7 0.20
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:20272458 original size:45 final size:45
Alignment explanation
Indices: 20272352--20272465 Score: 158
Period size: 45 Copynumber: 2.5 Consensus size: 45
20272342 CATACCAGAA
* * * **
20272352 ATGAGTAAGACCATAGCTAAAAGACGTTATGGCATCGTGATTCAG
1 ATGAGCAAGACCATAGTTGAAAGACGTTATGGCATCACGATTCAG
*
20272397 ATGAGTAAGACCATAGTTGAAAGACGTTATGGCATCACGATTCAG
1 ATGAGCAAGACCATAGTTGAAAGACGTTATGGCATCACGATTCAG
20272442 AT-ATGCAAGACCATAGTTGAAAGA
1 ATGA-GCAAGACCATAGTTGAAAGA
20272466 TACTATGACA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
44 1 0.02
45 62 0.98
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.24
Consensus pattern (45 bp):
ATGAGCAAGACCATAGTTGAAAGACGTTATGGCATCACGATTCAG
Found at i:20272536 original size:46 final size:46
Alignment explanation
Indices: 20272448--20272613 Score: 235
Period size: 46 Copynumber: 3.6 Consensus size: 46
20272438 TCAGATATGC
* * * *
20272448 AAGACCATAGTTGAAAGATACTATGACAATAAGAC-GAGAAATGAAT
1 AAGACCATAGTTGAAAGATACCATGGCAACATGACAGA-AAATGAAT
*
20272494 AAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAAT
1 AAGACCATAGTTGAAAGATACCATGGCAACATGACAGAAAATGAAT
*
20272540 AAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAAT
1 AAGACCATAGTTGAAAGATACCATGGCAACATGACAGAAAATGAAT
* * *
20272586 AAGACCATAGTTGGAAGACACTATGGCA
1 AAGACCATAGTTGAAAGATACCATGGCA
20272614 TCCTGTCCAA
Statistics
Matches: 110, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
46 108 0.98
47 2 0.02
ACGTcount: A:0.46, C:0.14, G:0.22, T:0.18
Consensus pattern (46 bp):
AAGACCATAGTTGAAAGATACCATGGCAACATGACAGAAAATGAAT
Found at i:20277691 original size:18 final size:19
Alignment explanation
Indices: 20277668--20277710 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
20277658 TAGTTAAAAC
20277668 TATTTTTTATATA-TTATT
1 TATTTTTTATATATTTATT
* *
20277686 TATTTTTTATGTATTTTTT
1 TATTTTTTATATATTTATT
20277705 TATTTT
1 TATTTT
20277711 AAAAATTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (19 bp):
TATTTTTTATATATTTATT
Found at i:20284571 original size:64 final size:64
Alignment explanation
Indices: 20284498--20284625 Score: 204
Period size: 64 Copynumber: 2.0 Consensus size: 64
20284488 TCATTCATAA
*
20284498 CACATCTAGTTAGGAGCATTGGATTCATTTCGATCATAGCATCCTAACTATTT-GACATAAGCAT
1 CACATCTAGTTAGGAGCATTGGATTCATTTCAATCATAGCATCCTAACTATTTAG-CATAAGCAT
* * *
20284562 CACATCTAGTTAGGAGCATTTGATTCATTTCAATCATAGTATCCTAATTATTTAGCATAAGCAT
1 CACATCTAGTTAGGAGCATTGGATTCATTTCAATCATAGCATCCTAACTATTTAGCATAAGCAT
20284626 AGATACATGA
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
64 58 0.98
65 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (64 bp):
CACATCTAGTTAGGAGCATTGGATTCATTTCAATCATAGCATCCTAACTATTTAGCATAAGCAT
Found at i:20284930 original size:44 final size:44
Alignment explanation
Indices: 20284792--20285022 Score: 115
Period size: 44 Copynumber: 5.3 Consensus size: 44
20284782 AGCCTTAACC
* *
20284792 CCCTAAGTAGTAGAGAAATAGGCTAGAAATTACAGATCTTATCT
1 CCCTAAGCAGTAGGGAAATAGGCTAGAAATTACAGATCTTATCT
** * * * * * *
20284836 CCCTAAGCAGTAGTGG-AGCA-GATCG-AA-GACGGTGAGCCTTAAC-
1 CCCTAAGCAGTAG-GGAAATAGGCTAGAAATTAC--AGA-TCTTATCT
*
20284879 CCTCTAAGCAGTAGGGAAATAGGCTGGAAATTACAGATCTTATCT
1 CC-CTAAGCAGTAGGGAAATAGGCTAGAAATTACAGATCTTATCT
* ** * * * *
20284924 CCCTAAGCAGTAGTGAAGCA-GATCA-AAGATGGT-GAG-CCTTAAC-
1 CCCTAAGCAGTAGGGAAATAGGCT-AGAA-AT--TACAGATCTTATCT
* *
20284967 CCCTTAAGCAGTAGGAAAACAGGCTAGAAATTACAGATCTTATCT
1 CCC-TAAGCAGTAGGGAAATAGGCTAGAAATTACAGATCTTATCT
20285012 -CCTAAGCAGTA
1 CCCTAAGCAGTA
20285023 ATGGAGCAGA
Statistics
Matches: 134, Mismatches: 33, Indels: 41
0.64 0.16 0.20
Matches are distributed among these distances:
41 2 0.01
42 3 0.02
43 27 0.20
44 83 0.62
45 14 0.10
46 3 0.02
47 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.23
Consensus pattern (44 bp):
CCCTAAGCAGTAGGGAAATAGGCTAGAAATTACAGATCTTATCT
Found at i:20285240 original size:263 final size:263
Alignment explanation
Indices: 20284694--20285262 Score: 768
Period size: 263 Copynumber: 2.2 Consensus size: 263
20284684 TGAATTCACT
* * * * *
20284694 AGCCTTAACCCCCTAAGTAGTAGGGAAATAGGCTGGCAATTATAGATCTTATCTCCCTAAGTAGT
1 AGCCTCAACCCCCTAAGCAGTAGGGAAATAGGCT-GAAATTACAGATCTTATCTCCCTAAGCAGT
* ** *
20284759 AGTCGAGTGGATCAAAGACGGTGAGCCTTAACCCCCTAAGTAGTAGAGAAATAGGCTAGAAATTA
65 AATCGAGCAGATCAAAGACGGTGAGCCTTAACCCCCTAAGCAGTAGAGAAATAGGCTAGAAATTA
* * * *
20284824 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACCCTCTAAGCA
130 CAGATATTATCTCCCTAAGCAGTAATGGAGCAGATCGAAGACGGTAAGCCTTAACCCCCTAAGCA
* * * *
20284889 GTAGGGAAATAGGCTGGAAATTACAGATCTTATCTCCCTAAGCAGTAGTGAAGCAGATCAAAGAT
195 GTAGGGAAACAGACTGGAAATTACAGATCTCATCACCCTAAGCAGTAGTGAAGCAGATCAAAGAT
20284954 GGTG
260 GGTG
* * * *
20284958 AGCCTTAACCCCTTAAGCAGTAGGAAAACAGGCTAGAAATTACAGATCTTATCT-CCTAAGCAGT
1 AGCCTCAACCCCCTAAGCAGTAGGGAAATAGGCT-GAAATTACAGATCTTATCTCCCTAAGCAGT
* *
20285022 AATGGAGCAGATCAAAGACGGTGAGCCTTAACCCCCTAAGCAGTAG-GAAAATAGGCTGGAAATT
65 AATCGAGCAGATCAAAGACGGTGAGCCTTAACCCCCTAAGCAGTAGAG-AAATAGGCTAGAAATT
* * * *
20285086 ACAGATATTATCTCCTTAAGCGGTAATGGAGCGGATCGAAGACGGTAAGCCTTATCCCCCTAAGC
129 ACAGATATTATCTCCCTAAGCAGTAATGGAGCAGATCGAAGACGGTAAGCCTTAACCCCCTAAGC
* ** *
20285151 AGTAGGGAAACAGACT-GAAGATTATAGATCTCATCACCCTAAGCAGTAGT-AGAGTGGATCGAA
194 AGTAGGGAAACAGACTGGAA-ATTACAGATCTCATCACCCTAAGCAGTAGTGA-AGCAGATCAAA
20285214 GATGGTG
257 GATGGTG
*
20285221 AGCCTCATCCCCCTAAGCAGTAGGGAAATAGGCTGAAGATTA
1 AGCCTCAACCCCCTAAGCAGTAGGGAAATAGGCTGAA-ATTA
20285263 GAAGTTTTAT
Statistics
Matches: 266, Mismatches: 35, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
262 8 0.03
263 211 0.79
264 47 0.18
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (263 bp):
AGCCTCAACCCCCTAAGCAGTAGGGAAATAGGCTGAAATTACAGATCTTATCTCCCTAAGCAGTA
ATCGAGCAGATCAAAGACGGTGAGCCTTAACCCCCTAAGCAGTAGAGAAATAGGCTAGAAATTAC
AGATATTATCTCCCTAAGCAGTAATGGAGCAGATCGAAGACGGTAAGCCTTAACCCCCTAAGCAG
TAGGGAAACAGACTGGAAATTACAGATCTCATCACCCTAAGCAGTAGTGAAGCAGATCAAAGATG
GTG
Found at i:20285259 original size:44 final size:43
Alignment explanation
Indices: 20285123--20285260 Score: 118
Period size: 44 Copynumber: 3.1 Consensus size: 43
20285113 GGAGCGGATC
* * * *
20285123 GAAGACGGTAAGCCTTATCCCCCTAAGCAGTAGGGAAACAGACT
1 GAAGATGGT-AGCCTCATCCCCCTAAGCAGTAGGGAAATAGGCT
** * * * * *
20285167 GAAGATTATAGATCTCATCACCCTAAGCAGTA-GTAGAGT-GGAT
1 GAAGATGGTAG-CCTCATCCCCCTAAGCAGTAGGGA-AATAGGCT
20285210 CGAAGATGGTGAGCCTCATCCCCCTAAGCAGTAGGGAAATAGGCT
1 -GAAGATGGT-AGCCTCATCCCCCTAAGCAGTAGGGAAATAGGCT
20285255 GAAGAT
1 GAAGAT
20285261 TAGAAGTTTT
Statistics
Matches: 70, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
43 6 0.09
44 57 0.81
45 7 0.10
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.20
Consensus pattern (43 bp):
GAAGATGGTAGCCTCATCCCCCTAAGCAGTAGGGAAATAGGCT
Found at i:20285262 original size:88 final size:88
Alignment explanation
Indices: 20284694--20285255 Score: 741
Period size: 88 Copynumber: 6.4 Consensus size: 88
20284684 TGAATTCACT
* * * *
20284694 AGCCTTAACCCCCTAAGTAGTAGGGAAATAGGCTGGCAATTATAGATCTTATCTCCCTAAGTAGT
1 AGCCTTAACCCCCTAAGCAGTAGGGAAATAGGCTGGAAATTACAGATCTTATCTCCCTAAGCAGT
* **
20284759 AGTCGAGTGGATCAAAGACGGTG
66 AGTGGAGCAGATCAAAGACGGTG
* * *
20284782 AGCCTTAACCCCCTAAGTAGTAGAGAAATAGGCTAGAAATTACAGATCTTATCTCCCTAAGCAGT
1 AGCCTTAACCCCCTAAGCAGTAGGGAAATAGGCTGGAAATTACAGATCTTATCTCCCTAAGCAGT
*
20284847 AGTGGAGCAGATCGAAGACGGTG
66 AGTGGAGCAGATCAAAGACGGTG
*
20284870 AGCCTTAACCCTCTAAGCAGTAGGGAAATAGGCTGGAAATTACAGATCTTATCTCCCTAAGCAGT
1 AGCCTTAACCCCCTAAGCAGTAGGGAAATAGGCTGGAAATTACAGATCTTATCTCCCTAAGCAGT
* *
20284935 AGTGAAGCAGATCAAAGATGGTG
66 AGTGGAGCAGATCAAAGACGGTG
* * * *
20284958 AGCCTTAACCCCTTAAGCAGTAGGAAAACAGGCTAGAAATTACAGATCTTATCT-CCTAAGCAGT
1 AGCCTTAACCCCCTAAGCAGTAGGGAAATAGGCTGGAAATTACAGATCTTATCTCCCTAAGCAGT
*
20285022 AATGGAGCAGATCAAAGACGGTG
66 AGTGGAGCAGATCAAAGACGGTG
* * * *
20285045 AGCCTTAACCCCCTAAGCAGTAGGAAAATAGGCTGGAAATTACAGATATTATCTCCTTAAGCGGT
1 AGCCTTAACCCCCTAAGCAGTAGGGAAATAGGCTGGAAATTACAGATCTTATCTCCCTAAGCAGT
* * * *
20285110 AATGGAGCGGATCGAAGACGGTA
66 AGTGGAGCAGATCAAAGACGGTG
* * * * * *
20285133 AGCCTTATCCCCCTAAGCAGTAGGGAAACAGACT-GAAGATTATAGATCTCATCACCCTAAGCAG
1 AGCCTTAACCCCCTAAGCAGTAGGGAAATAGGCTGGAA-ATTACAGATCTTATCTCCCTAAGCAG
* ** * *
20285197 TAGTAGAGTGGATCGAAGATGGTG
65 TAGTGGAGCAGATCAAAGACGGTG
* *
20285221 AGCCTCATCCCCCTAAGCAGTAGGGAAATAGGCTG
1 AGCCTTAACCCCCTAAGCAGTAGGGAAATAGGCTG
20285256 AAGATTAGAA
Statistics
Matches: 420, Mismatches: 51, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
87 83 0.20
88 337 0.80
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.22
Consensus pattern (88 bp):
AGCCTTAACCCCCTAAGCAGTAGGGAAATAGGCTGGAAATTACAGATCTTATCTCCCTAAGCAGT
AGTGGAGCAGATCAAAGACGGTG
Found at i:20289150 original size:46 final size:44
Alignment explanation
Indices: 20289091--20289205 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
20289081 ACAGGACAGA
* *
20289091 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
20289137 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
20289181 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
20289206 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:20289186 original size:44 final size:45
Alignment explanation
Indices: 20289091--20289224 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
20289081 ACAGGACAGA
* *
20289091 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
20289137 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
20289181 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
20289225 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:20305865 original size:17 final size:17
Alignment explanation
Indices: 20305843--20305876 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
20305833 TAGTAATAAA
20305843 AAATTGAGATTAGCGTT
1 AAATTGAGATTAGCGTT
20305860 AAATTGAGATTAGCGTT
1 AAATTGAGATTAGCGTT
20305877 TTCAAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (17 bp):
AAATTGAGATTAGCGTT
Found at i:20312291 original size:15 final size:16
Alignment explanation
Indices: 20312271--20312300 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20312261 GGAATATTAC
20312271 TTAAAA-TTATTATTT
1 TTAAAATTTATTATTT
20312286 TTAAAATTTATTATT
1 TTAAAATTTATTATT
20312301 AAATAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTAAAATTTATTATTT
Found at i:20319347 original size:2 final size:2
Alignment explanation
Indices: 20319340--20319365 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20319330 TTTTGTTTCC
20319340 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
20319366 GAAGATCATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20332458 original size:16 final size:16
Alignment explanation
Indices: 20332437--20332467 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20332427 AATTTAAATT
*
20332437 AATTAATTAATTTTTC
1 AATTAAATAATTTTTC
20332453 AATTAAATAATTTTT
1 AATTAAATAATTTTT
20332468 TTAACTTGAT
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:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
AATTAAATAATTTTTC
Found at i:20335808 original size:30 final size:30
Alignment explanation
Indices: 20335772--20335832 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
20335762 ACCTTCCCTC
20335772 ACACTAGATTTTCGGCTGACAATATAGTTA
1 ACACTAGATTTTCGGCTGACAATATAGTTA
20335802 ACACTAGATTTTCGGCTGACAATATAGTTA
1 ACACTAGATTTTCGGCTGACAATATAGTTA
20335832 A
1 A
20335833 ACAGAGGTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (30 bp):
ACACTAGATTTTCGGCTGACAATATAGTTA
Found at i:20345877 original size:46 final size:46
Alignment explanation
Indices: 20345817--20345939 Score: 133
Period size: 46 Copynumber: 2.6 Consensus size: 46
20345807 ATAGCTGATG
** * *
20345817 CATGTCCCAAACATGTCTTACACTGGCT-TACGTCTCGAGGCCGATA
1 CATGTCCCTGACATGTCTTACACTAGCTCT-CGTCTCAAGGCCGATA
* *
20345863 CATGTCCCTGACATGTCTTACACTAGCTCTCGTCTCAATGCCGATG
1 CATGTCCCTGACATGTCTTACACTAGCTCTCGTCTCAAGGCCGATA
*
20345909 CTATG-CCCTAGACATGGTCTAACACTAGCTC
1 C-ATGTCCCT-GACAT-GTCTTACACTAGCTC
20345940 CCATAATATG
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
46 43 0.65
47 9 0.14
48 14 0.21
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.28
Consensus pattern (46 bp):
CATGTCCCTGACATGTCTTACACTAGCTCTCGTCTCAAGGCCGATA
Found at i:20355063 original size:27 final size:27
Alignment explanation
Indices: 20354991--20355067 Score: 136
Period size: 27 Copynumber: 2.9 Consensus size: 27
20354981 CCAGATTGAT
* *
20354991 AAATGACTATTTTGCCCTCATATGGTA
1 AAATGACTATTTTGCCCTTATGTGGTA
20355018 AAATGACTATTTTGCCCTTATGTGGTA
1 AAATGACTATTTTGCCCTTATGTGGTA
20355045 AAATGACTATTTTGCCCTTATGT
1 AAATGACTATTTTGCCCTTATGT
20355068 TATGTATGCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (27 bp):
AAATGACTATTTTGCCCTTATGTGGTA
Found at i:20377025 original size:88 final size:88
Alignment explanation
Indices: 20376852--20377029 Score: 329
Period size: 88 Copynumber: 2.0 Consensus size: 88
20376842 GGGGGTCTCA
20376852 TTTACAGATTTGAACTCCATGGAAGCTTTAACTTCTTTGTAAATGGAAGGATAAAAAACGAACGT
1 TTTACAGATTTGAACTCCATGGAAGCTTTAACTTCTTTGTAAATGGAAGGATAAAAAACGAACGT
20376917 CATTTGAGCAGATGTAAAAAAGT
66 CATTTGAGCAGATGTAAAAAAGT
* *
20376940 TTTACAGATTTGAACTCCGTGGAAGCTTTAACTTCTTTGTAAATGGAAGGATAAAAAAACGGACG
1 TTTACAGATTTGAACTCCATGGAAGCTTTAACTTCTTTGTAAATGGAAGGAT-AAAAAACGAACG
20377005 TCATTTGAGCAGATGTAAAAAAGT
65 TCATTTGAGCAGATGTAAAAAAGT
20377029 T
1 T
20377030 AACACATTGC
Statistics
Matches: 87, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
88 51 0.59
89 36 0.41
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (88 bp):
TTTACAGATTTGAACTCCATGGAAGCTTTAACTTCTTTGTAAATGGAAGGATAAAAAACGAACGT
CATTTGAGCAGATGTAAAAAAGT
Found at i:20378421 original size:24 final size:24
Alignment explanation
Indices: 20378394--20378439 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
20378384 CATGGATTTG
20378394 TTGACTGTCAAGAAAATGGTTCTT
1 TTGACTGTCAAGAAAATGGTTCTT
20378418 TTGACTGTCAAGAAAATGGTTC
1 TTGACTGTCAAGAAAATGGTTC
20378440 AGCTGGTGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (24 bp):
TTGACTGTCAAGAAAATGGTTCTT
Found at i:20379804 original size:18 final size:19
Alignment explanation
Indices: 20379781--20379820 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
20379771 GAAAAAAATA
20379781 TTTAAAAAAATATATA-AT
1 TTTAAAAAAATATATATAT
**
20379799 TTTAAATTAATATATATAT
1 TTTAAAAAAATATATATAT
20379818 TTT
1 TTT
20379821 TCTCTTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTAAAAAAATATATATAT
Found at i:20387971 original size:18 final size:18
Alignment explanation
Indices: 20387944--20387990 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
20387934 TTCAAATTTT
* *
20387944 TTTTATATTTTGATAT-TC
1 TTTTAAATTTT-ATATATA
*
20387962 TTTTAGATTTTATATATA
1 TTTTAAATTTTATATATA
20387980 TTTTAAATTTT
1 TTTTAAATTTT
20387991 TTTAGTGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (18 bp):
TTTTAAATTTTATATATA
Found at i:20394494 original size:40 final size:40
Alignment explanation
Indices: 20394440--20394572 Score: 133
Period size: 40 Copynumber: 3.3 Consensus size: 40
20394430 CGAAGGCTTT
* *
20394440 GTGCTAAGTGACTAAATCCGGACTAAGATCCGACGGCATAC
1 GTGC-AAGTTACTAAATCCGGACTAAGATCCGAAGGCATAC
* *
20394481 GTGCAAGTTACTAAATCCGGACTAAGATCCGAAGGCTTTC
1 GTGCAAGTTACTAAATCCGGACTAAGATCCGAAGGCATAC
** * ** * *
20394521 AAGCAAGCTACTAAATCCGGGTTGAG-TCCCGAAGGCATTC
1 GTGCAAGTTACTAAATCCGGACTAAGAT-CCGAAGGCATAC
*
20394561 GTGCGAGTTACT
1 GTGCAAGTTACT
20394573 GTAACCGGGC
Statistics
Matches: 76, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
39 1 0.01
40 71 0.93
41 4 0.05
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (40 bp):
GTGCAAGTTACTAAATCCGGACTAAGATCCGAAGGCATAC
Found at i:20415061 original size:16 final size:17
Alignment explanation
Indices: 20415030--20415062 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
20415020 TTCATAAGTA
20415030 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
20415047 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
20415063 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:20415245 original size:13 final size:13
Alignment explanation
Indices: 20415227--20415262 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
20415217 CGATTCTTAT
20415227 AAACATTTCACAC
1 AAACATTTCACAC
20415240 AAACATTTCACAC
1 AAACATTTCACAC
*
20415253 AACCATTTCA
1 AAACATTTCA
20415263 TGTAACCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (13 bp):
AAACATTTCACAC
Found at i:20415680 original size:46 final size:46
Alignment explanation
Indices: 20415361--20415680 Score: 426
Period size: 46 Copynumber: 7.0 Consensus size: 46
20415351 TTTGACATGA
* * * * *
20415361 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATATCAGGT
* * * *
20415407 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
* *** *
20415453 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
* * * *
20415499 TGCCATGGTATCTTTCAACCATGATCTTATTCATTTGATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
* *
20415545 TGCCACGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
*
20415591 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
*
20415637 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAG
20415681 AGAGCACACT
Statistics
Matches: 252, Mismatches: 21, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
45 4 0.02
46 248 0.98
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
Found at i:20419823 original size:21 final size:21
Alignment explanation
Indices: 20419783--20420036 Score: 183
Period size: 21 Copynumber: 12.2 Consensus size: 21
20419773 TAAATATGCC
*
20419783 AACAGAAACTC-GAA-AGCTG
1 AACAGAAACTCATAAGAGCTG
* *
20419802 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAACTCATAAGAGCTG
* *
20419823 AATAGAAACTCATAAGAGTTG
1 AACAGAAACTCATAAGAGCTG
* *
20419844 AA-AAAAAGCTCGTAAGAGCTG
1 AACAGAAA-CTCATAAGAGCTG
* *
20419865 AACAGAAACTCATAAGAGTTA
1 AACAGAAACTCATAAGAGCTG
*
20419886 AACA-AAAGCTCGTAAGAGCTG
1 AACAGAAA-CTCATAAGAGCTG
* * * * *
20419907 AACAAAAACCCAAAAAAGTTG
1 AACAGAAACTCATAAGAGCTG
* * *
20419928 AACAGAAGCTCATAAAAGCTT
1 AACAGAAACTCATAAGAGCTG
* *
20419949 AACAGAAACTCATAAAAGTTG
1 AACAGAAACTCATAAGAGCTG
* ** * *
20419970 AACAGATACTTGTAAGAGTTA
1 AACAGAAACTCATAAGAGCTG
* * *
20419991 AATAGAAACTCATAAGGGTTG
1 AACAGAAACTCATAAGAGCTG
* * *
20420012 AACAGAAGCTCTTAAGAGCTT
1 AACAGAAACTCATAAGAGCTG
20420033 AACA
1 AACA
20420037 TAAGCTTGAA
Statistics
Matches: 182, Mismatches: 47, Indels: 10
0.76 0.20 0.04
Matches are distributed among these distances:
19 10 0.05
20 9 0.05
21 156 0.86
22 7 0.04
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.18
Consensus pattern (21 bp):
AACAGAAACTCATAAGAGCTG
Found at i:20419856 original size:42 final size:42
Alignment explanation
Indices: 20419807--20420036 Score: 230
Period size: 42 Copynumber: 5.5 Consensus size: 42
20419797 AGCTGAACAG
*
20419807 AAGCTCGTAAGAGCTGAATAGAAACTCATAAGAGTTGAAAAA
1 AAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTGAAAAA
20419849 AAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTT-AAACAA
1 AAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTGAAA-AA
* * * * * *
20419891 AAGCTCGTAAGAGCTGAACAAAAACCCAAAAAAGTTGAACAG
1 AAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTGAAAAA
* * * * *
20419933 AAGCTCATAAAAGCTTAACAGAAACTCATAAAAGTTGAACAGA
1 AAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTGAA-AAA
* * * * * * * *
20419976 TA-CTTGTAAGAGTTAAATAGAAACTCATAAGGGTTGAACAG
1 AAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTGAAAAA
* *
20420017 AAGCTCTTAAGAGCTTAACA
1 AAGCTCGTAAGAGCTGAACA
20420037 TAAGCTTGAA
Statistics
Matches: 150, Mismatches: 34, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
41 4 0.03
42 143 0.95
43 3 0.02
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (42 bp):
AAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTGAAAAA
Found at i:20419901 original size:84 final size:84
Alignment explanation
Indices: 20419802--20420036 Score: 283
Period size: 84 Copynumber: 2.8 Consensus size: 84
20419792 TCGAAAGCTG
* * * * *
20419802 AACAGAAGCTCGTAAGAGCTGAATAGAAACTCATAAGAGTTGAAAAAAAGCTCGTAAGAGCTGAA
1 AACAAAAGCTCGTAAGAGCTGAATAGAAACTCATAAGAGTTGAACAGAAGCTCATAAGAGCTTAA
*
20419867 CAGAAACTCATAAGAGTTA
66 CAGAAACTCATAAAAGTTA
* * * * * *
20419886 AACAAAAGCTCGTAAGAGCTGAACAAAAACCCAAAAAAGTTGAACAGAAGCTCATAAAAGCTTAA
1 AACAAAAGCTCGTAAGAGCTGAATAGAAACTCATAAGAGTTGAACAGAAGCTCATAAGAGCTTAA
*
20419951 CAGAAACTCATAAAAGTTG
66 CAGAAACTCATAAAAGTTA
* * * * * *
20419970 AACAGATA-CTTGTAAGAGTTAAATAGAAACTCATAAGGGTTGAACAGAAGCTCTTAAGAGCTTA
1 AACA-AAAGCTCGTAAGAGCTGAATAGAAACTCATAAGAGTTGAACAGAAGCTCATAAGAGCTTA
20420034 ACA
65 ACA
20420037 TAAGCTTGAA
Statistics
Matches: 125, Mismatches: 25, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
84 123 0.98
85 2 0.02
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (84 bp):
AACAAAAGCTCGTAAGAGCTGAATAGAAACTCATAAGAGTTGAACAGAAGCTCATAAGAGCTTAA
CAGAAACTCATAAAAGTTA
Found at i:20423309 original size:38 final size:35
Alignment explanation
Indices: 20423250--20423367 Score: 135
Period size: 31 Copynumber: 3.5 Consensus size: 35
20423240 TCAATCATGC
*
20423250 ACTGGGCCGTAGCCCTTTTCATATTTCATATTTCATAAT
1 ACTGGGCCGAAG-CCTTTTCATATTTCATATTT-AT--T
20423289 ACTGGGCCGAAGCCTTTTCATATTTC--A--TATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
20423320 ACTGGGCCGAAGCCTTTTCATATTTC--A--TATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
20423351 ACTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
20423368 ACTGTAAACG
Statistics
Matches: 78, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
31 49 0.63
33 2 0.03
34 1 0.01
36 1 0.01
38 14 0.18
39 11 0.14
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (35 bp):
ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
Found at i:20423311 original size:31 final size:31
Alignment explanation
Indices: 20423273--20423367 Score: 181
Period size: 31 Copynumber: 3.1 Consensus size: 31
20423263 CCTTTTCATA
*
20423273 TTTCATATTTCATAATACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
20423304 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
20423335 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
20423366 TT
1 TT
20423368 ACTGTAAACG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATATTACTGGGCCGAAGCCT
Found at i:20423610 original size:24 final size:24
Alignment explanation
Indices: 20423559--20423677 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
20423549 GCTTTATCAT
*
20423559 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
20423584 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
20423608 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
20423631 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
20423655 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
20423678 TCACTTCCTC
Statistics
Matches: 87, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
23 23 0.26
24 52 0.60
25 12 0.14
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:20423638 original size:47 final size:48
Alignment explanation
Indices: 20423559--20423677 Score: 170
Period size: 47 Copynumber: 2.5 Consensus size: 48
20423549 GCTTTATCAT
*
20423559 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAAGCCCTTTCA
* **
20423608 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCA
20423655 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
20423678 TCACTTCCTC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
47 44 0.68
48 9 0.14
49 12 0.18
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCA
Found at i:20423753 original size:20 final size:20
Alignment explanation
Indices: 20423728--20423787 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
20423718 TATGATTACC
20423728 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
*
20423748 TCATGTGCATATCATACATT
1 TCATGTGCATATCATACATA
20423768 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
20423788 CTATATTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:20423758 original size:11 final size:11
Alignment explanation
Indices: 20423728--20423782 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
20423718 TATGATTACC
20423728 TCATGTGCATA
1 TCATGTGCATA
*
20423739 TCA--TACATA
1 TCATGTGCATA
20423748 TCATGTGCATA
1 TCATGTGCATA
* *
20423759 TCA--TACATT
1 TCATGTGCATA
20423768 TCATGTGCATA
1 TCATGTGCATA
20423779 TCAT
1 TCAT
20423783 ACATACTATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:20423858 original size:25 final size:25
Alignment explanation
Indices: 20423830--20423877 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
20423820 ATACATAAAC
* * *
20423830 CCTAGGGGTAGAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
20423855 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
20423878 CATGGTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:20427056 original size:21 final size:23
Alignment explanation
Indices: 20427032--20427089 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
20427022 CAGAATATGT
20427032 CACATAAAGTGCCT-AAA-ACGA
1 CACATAAAGTGCCTAAAATACGA
** *
20427053 CACACGAGGTGCCTAAAATACGA
1 CACATAAAGTGCCTAAAATACGA
20427076 CACATAAAGTGCCT
1 CACATAAAGTGCCT
20427090 GATCAGTAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
21 11 0.38
22 3 0.10
23 15 0.52
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.16
Consensus pattern (23 bp):
CACATAAAGTGCCTAAAATACGA
Found at i:20428260 original size:23 final size:23
Alignment explanation
Indices: 20428228--20428287 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 23
20428218 GTAAATTAAT
*
20428228 TATTTTTATTACAAGTGTA-C-A
1 TATTTTTATTACAAATGTACCAA
20428249 TATCTATTTATTACAAATGTACCAA
1 TAT-T-TTTATTACAAATGTACCAA
20428274 TATTTTTATTACAA
1 TATTTTTATTACAA
20428288 TTATTATTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
21 3 0.09
22 1 0.03
23 24 0.71
24 2 0.06
25 4 0.12
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.47
Consensus pattern (23 bp):
TATTTTTATTACAAATGTACCAA
Found at i:20432684 original size:16 final size:16
Alignment explanation
Indices: 20432659--20432720 Score: 97
Period size: 16 Copynumber: 3.9 Consensus size: 16
20432649 TTCACTGTAA
20432659 AATAGAGCTGTAATGG
1 AATAGAGCTGTAATGG
* *
20432675 AATAGGGCTGTAATTG
1 AATAGAGCTGTAATGG
20432691 AATAGAGCTGTAATGG
1 AATAGAGCTGTAATGG
*
20432707 AATAGGGCTGTAAT
1 AATAGAGCTGTAAT
20432721 CAGTAATTCA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.35, C:0.06, G:0.31, T:0.27
Consensus pattern (16 bp):
AATAGAGCTGTAATGG
Found at i:20432700 original size:32 final size:32
Alignment explanation
Indices: 20432659--20432720 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
20432649 TTCACTGTAA
20432659 AATAGAGCTGTAATGGAATAGGGCTGTAATTG
1 AATAGAGCTGTAATGGAATAGGGCTGTAATTG
20432691 AATAGAGCTGTAATGGAATAGGGCTGTAAT
1 AATAGAGCTGTAATGGAATAGGGCTGTAAT
20432721 CAGTAATTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.06, G:0.31, T:0.27
Consensus pattern (32 bp):
AATAGAGCTGTAATGGAATAGGGCTGTAATTG
Found at i:20443774 original size:29 final size:29
Alignment explanation
Indices: 20443741--20443798 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
20443731 TCCACAAACA
20443741 AGCTGGTCGGTTCTAGGCTTCTGGCTAAG
1 AGCTGGTCGGTTCTAGGCTTCTGGCTAAG
20443770 AGCTGGTCGGTTCTAGGCTTCTGGCTAAG
1 AGCTGGTCGGTTCTAGGCTTCTGGCTAAG
20443799 GTTCATTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.14, C:0.21, G:0.34, T:0.31
Consensus pattern (29 bp):
AGCTGGTCGGTTCTAGGCTTCTGGCTAAG
Found at i:20454263 original size:45 final size:45
Alignment explanation
Indices: 20454199--20454287 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
20454189 CATGATCACT
* *
20454199 GACTCTCCCAGCTGGTGAAATGAAGGGATGATGGTTTAATGGTAC
1 GACTCCCCCAGCTGGTGAAATGAAAGGATGATGGTTTAATGGTAC
20454244 GACTCCCCCAGCTGGTGAAATGAAAGGATGATGGTTTAATGGTA
1 GACTCCCCCAGCTGGTGAAATGAAAGGATGATGGTTTAATGGTA
20454288 GAATATAAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (45 bp):
GACTCCCCCAGCTGGTGAAATGAAAGGATGATGGTTTAATGGTAC
Found at i:20454729 original size:183 final size:183
Alignment explanation
Indices: 20454415--20454784 Score: 695
Period size: 183 Copynumber: 2.0 Consensus size: 183
20454405 TGTTTTTAGA
20454415 TGAAAAATCCAACATCCTACACCACCTTTCATCACCGGAAATCTCAACCACGCCATCATTTGCGT
1 TGAAAAATCCAACATCCTACACCACCTTTCATCACCGGAAATCTCAACCACGCCATCATTTGCGT
*
20454480 TATCCTTAGTTTTTTCAGTCGTCACTTCTGAAGCATTGAAACAAGCACCACGTGTTTCATCATGT
66 TATCCTTAGTTTTTTCAGTCGTCACTTCTGAAGCATTGAAACAAGCACCACGTGTTTCACCATGT
20454545 GGAGCCCAGTATTCACCATTTTTTATCATAGAATCGCCTTGGTTGTGACCATT
131 GGAGCCCAGTATTCACCATTTTTTATCATAGAATCGCCTTGGTTGTGACCATT
*
20454598 TGAAAAATCCAACATCCTACGCCACCTTTCATCACCGGAAATCTCAACCACGCCATCATTTGCGT
1 TGAAAAATCCAACATCCTACACCACCTTTCATCACCGGAAATCTCAACCACGCCATCATTTGCGT
*
20454663 TATCCTTAGTTTTTTCAGTCGTCACTTCTGAAGTATTGAAACAAGCACCACGTGTTTCACCATGT
66 TATCCTTAGTTTTTTCAGTCGTCACTTCTGAAGCATTGAAACAAGCACCACGTGTTTCACCATGT
* *
20454728 GGAGCCCAGTATTTACCATTTTTTATCATAGAATCGTCTTGGTTGTGACCATT
131 GGAGCCCAGTATTCACCATTTTTTATCATAGAATCGCCTTGGTTGTGACCATT
20454781 TGAA
1 TGAA
20454785 CTTGACCCAC
Statistics
Matches: 182, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
183 182 1.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (183 bp):
TGAAAAATCCAACATCCTACACCACCTTTCATCACCGGAAATCTCAACCACGCCATCATTTGCGT
TATCCTTAGTTTTTTCAGTCGTCACTTCTGAAGCATTGAAACAAGCACCACGTGTTTCACCATGT
GGAGCCCAGTATTCACCATTTTTTATCATAGAATCGCCTTGGTTGTGACCATT
Found at i:20455214 original size:33 final size:33
Alignment explanation
Indices: 20455169--20455543 Score: 417
Period size: 33 Copynumber: 11.0 Consensus size: 33
20455159 CTTTTTCAGA
*
20455169 AGTCGTTACTTTTTCCGAAGGAGAGGTAGCAGG
1 AGTCGTTACTTTTTCCGGAGGAGAGGTAGCAGG
* *
20455202 AGTCGTTTCTTTTGCCGGAGGAGAGGTAGCAGG
1 AGTCGTTACTTTTTCCGGAGGAGAGGTAGCAGG
* **
20455235 AGTCGTTTCTTTCGCCGGAGGAGAGGTGGCAGTAGCAGG
1 AGTCGTTACTTTTTCCGGAGGAGA----G--GTAGCAGG
*
20455274 AGTGGTTACTTTTTCCGGAGGAGAGGTAGCAGTAGCAGG
1 AGTCGTTACTTTTTCCGGA-G-GA-G-AG--GTAGCAGG
* * * * *
20455313 AGTTGTTACTTTTTCCAGAGGAGAGGTCGAAGA
1 AGTCGTTACTTTTTCCGGAGGAGAGGTAGCAGG
* * *
20455346 AGTCGTTACCTTTTCCGGAGGAAAGGTAACAGG
1 AGTCGTTACTTTTTCCGGAGGAGAGGTAGCAGG
* *
20455379 AGTCGTTTCTTTTTCCGAAGGAGAGGTAGCAGG
1 AGTCGTTACTTTTTCCGGAGGAGAGGTAGCAGG
* *
20455412 AGTCGTTTCATTTTCCGGAGGAGAGGTAGCAGG
1 AGTCGTTACTTTTTCCGGAGGAGAGGTAGCAGG
* *
20455445 AGTCGTTCCTTTTTCCGGAGGAGAGGTAGCTGG
1 AGTCGTTACTTTTTCCGGAGGAGAGGTAGCAGG
*
20455478 AGTCGTTACCTTTTCCGGAGGAGAGGTAGCAGG
1 AGTCGTTACTTTTTCCGGAGGAGAGGTAGCAGG
* * *
20455511 TGTCGTTTCTTTTTCCAGAGGAGAGGTAGCAGG
1 AGTCGTTACTTTTTCCGGAGGAGAGGTAGCAGG
20455544 GGATGATGCC
Statistics
Matches: 294, Mismatches: 38, Indels: 20
0.84 0.11 0.06
Matches are distributed among these distances:
33 231 0.79
35 2 0.01
36 1 0.00
37 3 0.01
38 1 0.00
39 51 0.17
40 1 0.00
41 2 0.01
42 1 0.00
43 1 0.00
ACGTcount: A:0.21, C:0.16, G:0.35, T:0.27
Consensus pattern (33 bp):
AGTCGTTACTTTTTCCGGAGGAGAGGTAGCAGG
Found at i:20456693 original size:33 final size:33
Alignment explanation
Indices: 20456656--20456719 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
20456646 TTTAAAAATC
20456656 AAATATTATTTATCCTTTCATAAAATTTTAAAA
1 AAATATTATTTATCCTTTCATAAAATTTTAAAA
*
20456689 AAATATTATTTATTCTTTCATAAAATTTTAA
1 AAATATTATTTATCCTTTCATAAAATTTTAA
20456720 TTGCTTAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (33 bp):
AAATATTATTTATCCTTTCATAAAATTTTAAAA
Found at i:20461964 original size:15 final size:15
Alignment explanation
Indices: 20461940--20461970 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20461930 TCTAGAAAAC
20461940 AAATAAAAATAAATA
1 AAATAAAAATAAATA
*
20461955 AAATAGAAATAAATA
1 AAATAAAAATAAATA
20461970 A
1 A
20461971 GCAAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (15 bp):
AAATAAAAATAAATA
Found at i:20463965 original size:21 final size:22
Alignment explanation
Indices: 20463934--20463974 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
20463924 GAATGTATTG
*
20463934 TGATGTATGTGGAAATGAAATA
1 TGATGTATGTGCAAATGAAATA
*
20463956 TGAT-TATGTGCCAATGAAA
1 TGATGTATGTGCAAATGAAA
20463975 CATAAATGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (22 bp):
TGATGTATGTGCAAATGAAATA
Found at i:20474448 original size:18 final size:18
Alignment explanation
Indices: 20474425--20474460 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
20474415 CACTTTAGTT
*
20474425 ACCTCATACATCGGATGA
1 ACCTCATACATCCGATGA
20474443 ACCTCATACATCCGATGA
1 ACCTCATACATCCGATGA
20474461 TTGTGGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.31, G:0.14, T:0.22
Consensus pattern (18 bp):
ACCTCATACATCCGATGA
Found at i:20479559 original size:21 final size:21
Alignment explanation
Indices: 20479533--20479573 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
20479523 ATATGTTCAA
*
20479533 TATGTAAATAATATATTTAGT
1 TATGTAAATAACATATTTAGT
20479554 TATGTAAATAACATATTTAG
1 TATGTAAATAACATATTTAG
20479574 GAGAGAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (21 bp):
TATGTAAATAACATATTTAGT
Found at i:20489404 original size:18 final size:19
Alignment explanation
Indices: 20489376--20489420 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
20489366 GGCCACCACA
*
20489376 TCTCTCTCCCCTTTTC-CTT
1 TCTC-CTCCCCCTTTCTCTT
*
20489395 TTTCCTCCCCCTTTCTCTT
1 TCTCCTCCCCCTTTCTCTT
20489414 TCTCCTC
1 TCTCCTC
20489421 TTCTTTCTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (19 bp):
TCTCCTCCCCCTTTCTCTT
Found at i:20491526 original size:6 final size:6
Alignment explanation
Indices: 20491512--20491562 Score: 75
Period size: 6 Copynumber: 8.3 Consensus size: 6
20491502 TTGAGTTCGA
* *
20491512 TTATTT TTATGT TTATGT TTATTT TTATTT TTATCTT TTATTT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTAT-TT TTATTT TTATTT
20491561 TT
1 TT
20491563 GTAACGAGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
6 36 0.86
7 6 0.14
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (6 bp):
TTATTT
Found at i:20495846 original size:20 final size:20
Alignment explanation
Indices: 20495802--20495858 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
20495792 ATCAATGAAA
20495802 ATATTAAGATATGTAAATAT
1 ATATTAAGATATGTAAATAT
* *
20495822 CTATTAA-ATATGTAAATGCT
1 ATATTAAGATATGTAAAT-AT
* *
20495842 ATATTTAGTTATGTAAA
1 ATATTAAGATATGTAAA
20495859 AAATATGTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 10 0.33
20 12 0.40
21 8 0.27
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.42
Consensus pattern (20 bp):
ATATTAAGATATGTAAATAT
Found at i:20501278 original size:11 final size:11
Alignment explanation
Indices: 20501262--20501290 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
20501252 TTAAAAAGGA
20501262 TCGGGCCGAGC
1 TCGGGCCGAGC
20501273 TCGGGCCGAGC
1 TCGGGCCGAGC
20501284 TCGGGCC
1 TCGGGCC
20501291 TTGAATGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.38, G:0.45, T:0.10
Consensus pattern (11 bp):
TCGGGCCGAGC
Found at i:20502546 original size:18 final size:18
Alignment explanation
Indices: 20502523--20502557 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20502513 ATGCAATGGC
*
20502523 AGCATGGTGAATGGTGGT
1 AGCATGGTGAACGGTGGT
20502541 AGCATGGTGAACGGTGG
1 AGCATGGTGAACGGTGG
20502558 CTCTGTATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.09, G:0.46, T:0.23
Consensus pattern (18 bp):
AGCATGGTGAACGGTGGT
Found at i:20508347 original size:42 final size:42
Alignment explanation
Indices: 20508293--20508412 Score: 116
Period size: 42 Copynumber: 2.9 Consensus size: 42
20508283 CTTACATGGG
* *
20508293 ATCTCACATCGATGCCATATCCCAGATATGGTCTTATACGAAA
1 ATCTCATATCGATGCCATATCCCAGATATGGTCTTAGACG-AA
* * * * * ** *
20508336 ATTTTAT-TCGATGACATGTCCTAGACGTGATCTTAGACGAA
1 ATCTCATATCGATGCCATATCCCAGATATGGTCTTAGACGAA
* *
20508377 ATCTCATATCAACGCCATATCCCAGATATGGTCTTA
1 ATCTCATATCGATGCCATATCCCAGATATGGTCTTA
20508413 CATGGTAACA
Statistics
Matches: 56, Mismatches: 20, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
41 7 0.12
42 45 0.80
43 4 0.07
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (42 bp):
ATCTCATATCGATGCCATATCCCAGATATGGTCTTAGACGAA
Found at i:20510620 original size:13 final size:13
Alignment explanation
Indices: 20510602--20510635 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
20510592 ATTCGTTTAA
* *
20510602 CATTTCACATTTT
1 CATTTCAAATATT
20510615 CATTTCAAATATT
1 CATTTCAAATATT
20510628 CATTTCAA
1 CATTTCAA
20510636 TTCTCCCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (13 bp):
CATTTCAAATATT
Found at i:20510789 original size:6 final size:6
Alignment explanation
Indices: 20510778--20510832 Score: 101
Period size: 6 Copynumber: 9.2 Consensus size: 6
20510768 ACAAAGTGTG
*
20510778 ACTGTA ACTGTA ACTGTA ACTGTA ACTGTA ACTGTA ACTGTA ACCGTA
1 ACTGTA ACTGTA ACTGTA ACTGTA ACTGTA ACTGTA ACTGTA ACTGTA
20510826 ACTGTA A
1 ACTGTA A
20510833 ATACTCACAC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (6 bp):
ACTGTA
Found at i:20511233 original size:9 final size:9
Alignment explanation
Indices: 20511219--20511243 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
20511209 CATATCTATA
20511219 ATTAAATTC
1 ATTAAATTC
20511228 ATTAAATTC
1 ATTAAATTC
20511237 ATTAAAT
1 ATTAAAT
20511244 ATATATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (9 bp):
ATTAAATTC
Done.