Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 145 of 198
Found at i:46101559 original size:13 final size:14
Alignment explanation
Indices: 46101536--46101568 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
46101526 GTTGAGAGAG
46101536 GAAGAAAGAAAAAA
1 GAAGAAAGAAAAAA
46101550 GAAG-AAGAAAAAA
1 GAAGAAAGAAAAAA
46101563 G-AGAAA
1 GAAGAAA
46101569 TGGTGGAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 12 0.67
14 4 0.22
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
GAAGAAAGAAAAAA
Found at i:46101808 original size:29 final size:30
Alignment explanation
Indices: 46101756--46101832 Score: 93
Period size: 29 Copynumber: 2.5 Consensus size: 30
46101746 TGTTAAAAAA
* **
46101756 AAGTACCAAACTAGTTGACAAAAAAAAAGTTT
1 AAGTACCAATCTAG--GACAAAAAAAAACCTT
*
46101788 AGGTACCAATCTAGGAC-AAAAAAAACCTT
1 AAGTACCAATCTAGGACAAAAAAAAACCTT
46101817 AAGTACCAATCTAGGA
1 AAGTACCAATCTAGGA
46101833 GAAGTGGACA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
29 25 0.62
30 3 0.08
32 12 0.30
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.19
Consensus pattern (30 bp):
AAGTACCAATCTAGGACAAAAAAAAACCTT
Found at i:46112178 original size:2 final size:2
Alignment explanation
Indices: 46112171--46112207 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
46112161 GTAACCAGCA
46112171 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
46112208 AAAGAGGGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:46113069 original size:24 final size:24
Alignment explanation
Indices: 46113042--46113087 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
46113032 CAAATCTACA
* *
46113042 CATGAAAACAGACATGTGCAGACT
1 CATGAAAACACACATATGCAGACT
* *
46113066 CATGCATACACACATATGCAGA
1 CATGAAAACACACATATGCAGA
46113088 AGAATATCAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.17
Consensus pattern (24 bp):
CATGAAAACACACATATGCAGACT
Found at i:46114906 original size:17 final size:16
Alignment explanation
Indices: 46114890--46114936 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
46114880 ATAACCAAAT
46114890 TTATATATTTATTAAA
1 TTATATATTTATTAAA
*
46114906 TTAT-TATATAACTTAAAA
1 TTATATAT-TTA-TT-AAA
46114924 TTATATATTTATT
1 TTATATATTTATT
46114937 TTGTATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
15 3 0.12
16 6 0.24
17 4 0.16
18 9 0.36
19 3 0.12
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATATATTTATTAAA
Found at i:46115274 original size:60 final size:59
Alignment explanation
Indices: 46115200--46115324 Score: 196
Period size: 60 Copynumber: 2.1 Consensus size: 59
46115190 CATAAATCTA
** * *
46115200 AAAATTCAACAAATTTAGCCCTCAATGTTTACAAAATTTGTCATTTTAGTTCTAATTCTT
1 AAAATTCAACAAATTTAGCCCTCAACATTTACAAAATTTGTCAATTTAATTCTAATTC-T
*
46115260 AAAATTCAATAAATTTAGCCCTCAACATTTACAAAATTTGTCAATTTAATTCTAATTCT
1 AAAATTCAACAAATTTAGCCCTCAACATTTACAAAATTTGTCAATTTAATTCTAATTCT
46115319 AAAATT
1 AAAATT
46115325 TTAAAAAAAG
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
59 7 0.12
60 53 0.88
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.40
Consensus pattern (59 bp):
AAAATTCAACAAATTTAGCCCTCAACATTTACAAAATTTGTCAATTTAATTCTAATTCT
Found at i:46119935 original size:84 final size:84
Alignment explanation
Indices: 46119716--46119960 Score: 438
Period size: 83 Copynumber: 2.9 Consensus size: 84
46119706 ATACCATATT
* *
46119716 ATCCTAACCCAATCAAAACTAAGAATAATATGTTCAACAATCTCATCCTCAATACCACATAAACA
1 ATCCTATCCCAATCAAAACTAAGAATAATATGTTCAACAATCTCATCTTCAATACCACATAAACA
46119781 ACAAATTAGGTTCAAAAAA
66 ACAAATTAGGTTCAAAAAA
* * *
46119800 ATCCTGTCCCAATC-AAACTAAAAATAATATGTTCAACAATCACATCTTCAATACCACATAAACA
1 ATCCTATCCCAATCAAAACTAAGAATAATATGTTCAACAATCTCATCTTCAATACCACATAAACA
46119864 ACAAATTAGGTTCAAAAAA
66 ACAAATTAGGTTCAAAAAA
46119883 ATCCTATCCCAATCAAAACTAAGAATAATATGTTCAACAATCTCATCTTCAATACCACATAAACA
1 ATCCTATCCCAATCAAAACTAAGAATAATATGTTCAACAATCTCATCTTCAATACCACATAAACA
46119948 ACAAATTAGGTTC
66 ACAAATTAGGTTC
46119961 GAAACACACT
Statistics
Matches: 152, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
83 79 0.52
84 73 0.48
ACGTcount: A:0.47, C:0.24, G:0.05, T:0.24
Consensus pattern (84 bp):
ATCCTATCCCAATCAAAACTAAGAATAATATGTTCAACAATCTCATCTTCAATACCACATAAACA
ACAAATTAGGTTCAAAAAA
Found at i:46126333 original size:690 final size:690
Alignment explanation
Indices: 46124960--46126336 Score: 2093
Period size: 690 Copynumber: 2.0 Consensus size: 690
46124950 TACCAAAGAC
46124960 AAAAAGTATAGGCATAGCCGTTGTGTTGTAGGCGAGGTCTTTTGGTTAGAAAAAAAGTACACATT
1 AAAAAGTATAGGCATAGCCGTTGTGTTGTAGGCGAGGTCTTTTGGTTAGAAAAAAAGTACACATT
* * *
46125025 TCTTTCTGTAAAAACTGAAAAGGTAAACTGTATCACAAAGATAACTTGCAGAAGTAAAGTTGATA
66 TCTTTCTATAAAAACTGAAAAGGTAAACTATATCACAAAGATAACTTGCAGAAATAAAGTTGATA
*
46125090 TTATTCCTAATACACCATTTGTGAATGAAGGCATGTTGTATTGAACTTGTGAGACCTTGAAAGTA
131 TTATTCCTAATACACCATTTGTGAATGAAGGCATGTTGTATTGAACTTGCGAGACCTTGAAAGTA
* * * **
46125155 AAGTATGAACACAGAACGCGTAACTTTGAAGATAAAGTGTGAATGTAAAATTTGGTACTAAAGTT
196 AAGTATGAACACACAACGCGTAACTTTGAAGATAAAGTATGAATGCAAAAAGTGGTACTAAAGTT
* * *
46125220 TTGTTGAAAGGGTCGAAAAGGTGAAAAGTGAAATTATATGTAAGGAGGTTAAAATCTTGAAATCA
261 TTGTTGAAAGGCTCGAAAAGGTGAAAAGTGAAATTATATGTAAGAAGGTTAAAATCTTGAAATAA
* *
46125285 AAGTGACTAAAAAAGGTGCACAACTGAAGAAGGTGAAGACCTGAAAACATAAAGAGATCCTTGGA
326 AAGTGACTAAAAAAGGTGCACAACTGAAGAAGGTGAAGACCTGAAAACATAAAGAGATCCCTAGA
*
46125350 TCCATACTTCAAAAAGGATAAATATGTAGAAAATTACATGACCTGAAAAGATCAAGAGTTGGGTG
391 TCCATACTTCAAAAAGGATAAATAAGTAGAAAATTACATGACCTGAAAAGATCAAGAGTTGGGTG
** * * *
46125415 GCTTGATGCTTAGAAAATCTTAAGTAAGTGTTGACGAGTGATGTGAATTGTGGCTATATATGCCC
456 GCTTGATGCCCAGAAAAGCTTAAGTAAGTCTTGACGAGTGATGTGAATTGTGGCTATACATGCCC
* * **
46125480 AATAAGACAAATGGGAGAAAATAGTAAAATAAGTTTTGATAACCTTAATGCTTGCATCAATAGTG
521 AATAAGACAAATGGGAGAAAATAGTAAAATAAATTTCGATAACCTTAATGCTCACATCAATAGTG
* * *
46125545 GGTCAAGGACTACTAGTGCAATTGGGGAAATATTAGCTATTGCTAGCACATATATAATATATATA
586 GGCCAAGGACTACTAGTGCAATTGGGGAAATATTAACTATTGCTAGAACATATATAATATATATA
46125610 AATTGGGGCATTGTCAACCAATATATAAATATATATAATT
651 AATTGGGGCATTGTCAACCAATATATAAATATATATAATT
*
46125650 AAAAAGGTATAGGCATAGCCGTTGTGTTGTAGGCGAGGTCTTTTGGTTAGAAAAAAAAATTACAC
1 AAAAA-GTATAGGCATAGCCGTTGTGTTGTAGGCGAGGTCTTTTGGTTAG--AAAAAAAGTACAC
* ** *
46125715 ATTTCTTTTTATAAAAGTTGAAAAGGTAAACTATATCACAAAGATCACTTGC-GAAAATAAAGTT
63 ATTTCTTTCTATAAAAACTGAAAAGGTAAACTATATCACAAAGATAACTTGCAG-AAATAAAGTT
* ** *
46125779 GATATTATTCTTAATACACTGTTTGTGAATGAAGGCATGTTGTATTGAACTTGCGA-ACCTTGAG
127 GATATTATTCCTAATACACCATTTGTGAATGAAGGCATGTTGTATTGAACTTGCGAGACCTTGAA
*
46125843 AGTAAAGTATGAACACACAGCGCGTAACTTTGAAGATAAAGTATGAATGCAAAAAGTGGTACTAA
192 AGTAAAGTATGAACACACAACGCGTAACTTTGAAGATAAAGTATGAATGCAAAAAGTGGTACTAA
** * *
46125908 A-TTTT-TTTTAAGAGCT-GAAAAGGTGAAATGTGAAATTATATGTAAGAATGTTAAAATCTTGA
257 AGTTTTGTTGAAAG-GCTCGAAAAGGTGAAAAGTGAAATTATATGTAAGAAGGTTAAAATCTTGA
* * *
46125970 AATAAAAGTGACTAAAAAAGGTGCGCAACTTAAGAAGGTGAAGACCTGAAAATATAAAGAGATCC
321 AATAAAAGTGACTAAAAAAGGTGCACAACTGAAGAAGGTGAAGACCTGAAAACATAAAGAGATCC
* * * * * *
46126035 CTAGCTTCATGCTTCAAAATGGATAAATAAGTAGAAAATTACATGACTTGAAAAGATTAAGAGTT
386 CTAGATCCATACTTCAAAAAGGATAAATAAGTAGAAAATTACATGACCTGAAAAGATCAAGAGTT
* *
46126100 GGGTGGCTTGATGCCCGGAAAAGCTTAAGTAAGTACTT-ACGAG-GCATGTGAATTGTGGCTATG
451 GGGTGGCTTGATGCCCAGAAAAGCTTAAGTAAGT-CTTGACGAGTG-ATGTGAATTGTGGCTATA
* * * * *
46126163 CGTGCCCTATAAGACAAATTGGAGAGAATAGTAAAATAAATTTCGATAACCTTAATGCTCACATT
514 CATGCCCAATAAGACAAATGGGAGAAAATAGTAAAATAAATTTCGATAACCTTAATGCTCACATC
* * * *
46126228 AATAGTGGGCCAGGGACTATTAGTGCAATTGGGGAAATATTAATTATTGCTAGAACATATATAGT
579 AATAGTGGGCCAAGGACTACTAGTGCAATTGGGGAAATATTAACTATTGCTAGAACATATATAAT
46126293 ATATATAAATTGGGGCATTGTCAACCAATATATAAATATATATA
644 ATATATAAATTGGGGCATTGTCAACCAATATATAAATATATATA
46126337 TAACTTGCCA
Statistics
Matches: 619, Mismatches: 61, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
689 1 0.00
690 379 0.61
691 52 0.08
692 68 0.11
693 119 0.19
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (690 bp):
AAAAAGTATAGGCATAGCCGTTGTGTTGTAGGCGAGGTCTTTTGGTTAGAAAAAAAGTACACATT
TCTTTCTATAAAAACTGAAAAGGTAAACTATATCACAAAGATAACTTGCAGAAATAAAGTTGATA
TTATTCCTAATACACCATTTGTGAATGAAGGCATGTTGTATTGAACTTGCGAGACCTTGAAAGTA
AAGTATGAACACACAACGCGTAACTTTGAAGATAAAGTATGAATGCAAAAAGTGGTACTAAAGTT
TTGTTGAAAGGCTCGAAAAGGTGAAAAGTGAAATTATATGTAAGAAGGTTAAAATCTTGAAATAA
AAGTGACTAAAAAAGGTGCACAACTGAAGAAGGTGAAGACCTGAAAACATAAAGAGATCCCTAGA
TCCATACTTCAAAAAGGATAAATAAGTAGAAAATTACATGACCTGAAAAGATCAAGAGTTGGGTG
GCTTGATGCCCAGAAAAGCTTAAGTAAGTCTTGACGAGTGATGTGAATTGTGGCTATACATGCCC
AATAAGACAAATGGGAGAAAATAGTAAAATAAATTTCGATAACCTTAATGCTCACATCAATAGTG
GGCCAAGGACTACTAGTGCAATTGGGGAAATATTAACTATTGCTAGAACATATATAATATATATA
AATTGGGGCATTGTCAACCAATATATAAATATATATAATT
Found at i:46131463 original size:21 final size:20
Alignment explanation
Indices: 46131439--46131483 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
46131429 CACTCAGTAA
*
46131439 GAGAAGAACAACTCTCATTTT
1 GAGAAGAA-AACTCTCATTTC
*
46131460 GAG-AGAAAATTCTCATTTC
1 GAGAAGAAAACTCTCATTTC
46131479 GAGAA
1 GAGAA
46131484 ACAATACATG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 13 0.62
20 5 0.24
21 3 0.14
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.27
Consensus pattern (20 bp):
GAGAAGAAAACTCTCATTTC
Found at i:46134314 original size:30 final size:30
Alignment explanation
Indices: 46134278--46134334 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
46134268 TTGGAGTGGC
46134278 AAAAATTGAATATCAAATATTTAGTTTATA
1 AAAAATTGAATATCAAATATTTAGTTTATA
*
46134308 AAAAATTGAATATCAAATCTTTAGTTT
1 AAAAATTGAATATCAAATATTTAGTTT
46134335 TAACCACAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (30 bp):
AAAAATTGAATATCAAATATTTAGTTTATA
Found at i:46136920 original size:3 final size:3
Alignment explanation
Indices: 46136838--46136901 Score: 112
Period size: 3 Copynumber: 21.7 Consensus size: 3
46136828 AAGGAGTACT
*
46136838 ATA ATA ATA A-C 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
46136885 ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT
46136902 CTGATTACAA
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 1 0.02
3 57 0.98
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:46137023 original size:12 final size:12
Alignment explanation
Indices: 46137006--46137031 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
46136996 AAATGTCGAA
46137006 AAATAATAAAAT
1 AAATAATAAAAT
46137018 AAATAATAAAAT
1 AAATAATAAAAT
46137030 AA
1 AA
46137032 CGAGAAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATAATAAAAT
Found at i:46139754 original size:44 final size:43
Alignment explanation
Indices: 46139704--46139842 Score: 109
Period size: 44 Copynumber: 3.2 Consensus size: 43
46139694 CGGTGCAGAA
*
46139704 AGGCAAGATCTGCTATTTTTAGCCTGCTCCACTGCAACCCAGGG
1 AGGCAAGATCTGCTATTTTTA-CCTGCTCCGCTGCAACCCAGGG
* * * ** * * *** *
46139748 AGGCAAG-GCTGGTGACTTCGATCTGCTTCGCTGTCAGTGCAGGA
1 AGGCAAGATCTGCT-ATTTTTACCTGCTCCGCTG-CAACCCAGGG
* *
46139792 AGGCAAGATCTGTTATTTTTAACCTGCTCCGCTGTAACCCAGGG
1 AGGCAAGATCTGCTATTTTT-ACCTGCTCCGCTGCAACCCAGGG
46139836 AGGCAAG
1 AGGCAAG
46139843 GCTGGTGTCT
Statistics
Matches: 67, Mismatches: 24, Indels: 8
0.68 0.24 0.08
Matches are distributed among these distances:
43 13 0.19
44 39 0.58
45 15 0.22
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.25
Consensus pattern (43 bp):
AGGCAAGATCTGCTATTTTTACCTGCTCCGCTGCAACCCAGGG
Found at i:46139895 original size:88 final size:88
Alignment explanation
Indices: 46139577--46139891 Score: 452
Period size: 88 Copynumber: 3.6 Consensus size: 88
46139567 AAAATCATAG
* *
46139577 AAGGCTGGTGACTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGAAAGATCTGCTA-TTTTAGCCT
1 AAGGCTGGTGACTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCT
* * *
46139641 GCTCTGCTGCAACCCAGTGAGGT
66 GCTCCGCTGCAACCCAGGGAGGC
* * *
46139664 AAGGCTGGTGACTTCGATCTGCTTCGTTGTCGGTGCAGAAAGGCAAGATCTGCTATTTTTAGCCT
1 AAGGCTGGTGACTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCT
*
46139729 GCTCCACTGCAACCCAGGGAGGC
66 GCTCCGCTGCAACCCAGGGAGGC
* *
46139752 AAGGCTGGTGACTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGTTATTTTTAACCT
1 AAGGCTGGTGACTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCT
*
46139817 GCTCCGCTGTAACCCAGGGAGGC
66 GCTCCGCTGCAACCCAGGGAGGC
* * * * * * *
46139840 AAGGCTGGTGTCTTTGATCTACTTCGCTGCCAGTACAGGAATGCAATATCTG
1 AAGGCTGGTGACTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTG
46139892 TTATCTTCAC
Statistics
Matches: 206, Mismatches: 21, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
87 52 0.25
88 154 0.75
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (88 bp):
AAGGCTGGTGACTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCT
GCTCCGCTGCAACCCAGGGAGGC
Found at i:46141214 original size:20 final size:21
Alignment explanation
Indices: 46141176--46141214 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
46141166 CACTTTCATT
* *
46141176 TTTTTATTTTGATTTTGAAAC
1 TTTTTATTTTGAATCTGAAAC
46141197 TTTTT-TTTTGAATCTGAA
1 TTTTTATTTTGAATCTGAA
46141215 CTCATAGGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.23, C:0.05, G:0.10, T:0.62
Consensus pattern (21 bp):
TTTTTATTTTGAATCTGAAAC
Found at i:46144709 original size:50 final size:50
Alignment explanation
Indices: 46144594--46144842 Score: 291
Period size: 50 Copynumber: 4.8 Consensus size: 50
46144584 GATAATAACA
* * ** * *
46144594 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGG
* *
46144645 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
46144695 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
46144745 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTC---TCATC-T-CGG
* *
46144800 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
46144843 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
50 92 0.54
51 33 0.19
53 4 0.02
54 1 0.01
55 2 0.01
56 38 0.22
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:46144780 original size:100 final size:104
Alignment explanation
Indices: 46144593--46144842 Score: 346
Period size: 100 Copynumber: 2.4 Consensus size: 104
46144583 TGATAATAAC
** * *
46144593 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCCATGCCATG
* *
46144658 TCCCAGACATGGTCTTATAGGGGACCTC-TCATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGG
* *
46144695 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCATGCCATGT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
*
46144759 CCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGG
66 CCCAGACATGGTCTTACAGGGGACCTC-T-TCATCTTAAGG
* *
46144800 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
46144843 TTACCCAAAT
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
100 48 0.37
101 36 0.27
103 4 0.03
104 1 0.01
105 2 0.02
106 40 0.31
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.27
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGG
Found at i:46144958 original size:13 final size:13
Alignment explanation
Indices: 46144937--46144968 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
46144927 GCTTGGATCA
*
46144937 TCATCAAATAAAT
1 TCATAAAATAAAT
46144950 TCATAAAATAAAT
1 TCATAAAATAAAT
46144963 TCATAA
1 TCATAA
46144969 TTGCTGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:46145214 original size:30 final size:30
Alignment explanation
Indices: 46145180--46145237 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
46145170 CCTCGACTCT
46145180 AACTTTTACAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
46145210 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
46145238 AAGGCTCGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.40
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:46148744 original size:52 final size:51
Alignment explanation
Indices: 46148646--46148750 Score: 122
Period size: 51 Copynumber: 2.0 Consensus size: 51
46148636 TTATAAAACT
* * *
46148646 TATATATATAAAATACATAATGCATTTATGAAAATAAGGAAAATATAAATA
1 TATACATATAAAATACATAATGCATTTATCAAAAAAAGGAAAATATAAATA
* * * *
46148697 TATACATATAAAATATATTCATGCATTTA-CAAAAAAATGAAATATATAAGTA
1 TATACATATAAAATACA-TAATGCATTTATCAAAAAAAGGAAA-ATATAAATA
46148749 TA
1 TA
46148751 ATATAAAAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
51 25 0.56
52 20 0.44
ACGTcount: A:0.55, C:0.06, G:0.07, T:0.32
Consensus pattern (51 bp):
TATACATATAAAATACATAATGCATTTATCAAAAAAAGGAAAATATAAATA
Found at i:46149529 original size:21 final size:21
Alignment explanation
Indices: 46149480--46149577 Score: 130
Period size: 21 Copynumber: 4.7 Consensus size: 21
46149470 AAATTAAATT
*
46149480 TCTAAGATTACA-AAATCATA
1 TCTAAGATTGCATAAATCATA
46149500 TCTTCTAAGATTGCATAAATCATA
1 ---TCTAAGATTGCATAAATCATA
*
46149524 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATAAATCATA
46149545 TCTAAGATTGCAT--ATCATA
1 TCTAAGATTGCATAAATCATA
46149564 TCTAAGATTGCATA
1 TCTAAGATTGCATA
46149578 TCCTCGAAGA
Statistics
Matches: 71, Mismatches: 2, Indels: 7
0.89 0.03 0.09
Matches are distributed among these distances:
19 19 0.27
21 33 0.46
23 11 0.15
24 8 0.11
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (21 bp):
TCTAAGATTGCATAAATCATA
Found at i:46149589 original size:17 final size:18
Alignment explanation
Indices: 46149506--46149589 Score: 62
Period size: 21 Copynumber: 4.3 Consensus size: 18
46149496 CATATCTTCT
*
46149506 AAGATTGCATAAATCATATCT
1 AAGATTGCAT--ATCA-ATCG
*
46149527 AAGATTGCATATATCATATCT
1 AAGATTGC--ATATCA-ATCG
*
46149548 AAGATTGCATATCATATCT
1 AAGATTGCATATCA-ATCG
*
46149567 AAGATTGCATATC-CTCG
1 AAGATTGCATATCAATCG
46149584 AAGATT
1 AAGATT
46149590 ATGTTTCCAT
Statistics
Matches: 59, Mismatches: 2, Indels: 8
0.86 0.03 0.12
Matches are distributed among these distances:
17 8 0.14
19 24 0.41
21 25 0.42
23 2 0.03
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
AAGATTGCATATCAATCG
Found at i:46149760 original size:21 final size:22
Alignment explanation
Indices: 46149730--46149771 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
46149720 TGTTTTCTCT
46149730 TTTTTCATTTGAGGTTGTAATA
1 TTTTTCATTTGAGGTTGTAATA
* *
46149752 TTTTT-ATTTTAGTTTGTAAT
1 TTTTTCATTTGAGGTTGTAAT
46149772 TTATTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.21, C:0.02, G:0.14, T:0.62
Consensus pattern (22 bp):
TTTTTCATTTGAGGTTGTAATA
Found at i:46156861 original size:98 final size:98
Alignment explanation
Indices: 46156692--46156888 Score: 322
Period size: 98 Copynumber: 2.0 Consensus size: 98
46156682 AAACAATAAA
*
46156692 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGGGCACAATC
*
46156757 CCTTTAGAATCCCAAACTCGGAATATTTCATTT
66 CCTTTAGAATCCCAAACTCGGAAAATTTCATTT
* * * *
46156790 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATATGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGGGCACAATC
* *
46156855 CCTTTAGAATCTCAAACTCGGAAAATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAAAATTTCATTT
46156888 A
1 A
46156889 TGATTTTTTT
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
98 91 1.00
ACGTcount: A:0.38, C:0.24, G:0.11, T:0.27
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGGGCACAATC
CCTTTAGAATCCCAAACTCGGAAAATTTCATTT
Found at i:46158984 original size:44 final size:44
Alignment explanation
Indices: 46158828--46159554 Score: 245
Period size: 44 Copynumber: 16.5 Consensus size: 44
46158818 TGGATGCGAC
* * *
46158828 CTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAA-
1 CTGCTCCACTACTGCTTAGGGAGATAAGATTTGCAGTCTTCAAT
* * * ** ** * *
46158871 CTTTCTCCGCTACTGCTTAGGGAGACAAGGCTTGGTGGC-TAAAT
1 C-TGCTCCACTACTGCTTAGGGAGATAAGATTTGCAGTCTTCAAT
* * *
46158915 CTGCTTCCCACTA-T-CTT-GGAAAGATAAGATTTGCCGTCTTCGAT
1 CTGC-T-CCACTACTGCTTAGG-GAGATAAGATTTGCAGTCTTCAAT
* ** * *
46158959 CTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAAC
1 CTGCTCCACTACTGCTTAGGGAGATAAGATTTGCAGTCTTCAAT
* * * * * ** ** * *
46159003 CTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAAT
1 CTGCTCCACTACTGCTTAGGGAGATAAGATTTGCAGTCTTCAAT
* * * *
46159047 CTGCTTTCCACTA-T-CTT-GGAAAGATAAGATTCGCCGTCTTCGAT
1 CTGC--TCCACTACTGCTTAGG-GAGATAAGATTTGCAGTCTTCAAT
* * ** * *
46159091 CTGCTCCACTACTGCTTAGGGAGATAAAATCTATAATCTTCAAC
1 CTGCTCCACTACTGCTTAGGGAGATAAGATTTGCAGTCTTCAAT
* * * * * ** ** * *
46159135 CTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAAT
1 CTGCTCCACTACTGCTTAGGGAGATAAGATTTGCAGTCTTCAAT
* *
46159179 CTGCTTCCCACTA-T-CTT-GGAAAGATAAGA-TT-CATCGTCTTCGAT
1 CTGC-T-CCACTACTGCTTAGG-GAGATAAGATTTGCA--GTCTTCAAT
* * * *
46159223 CTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAAC
1 CTGCTCCACTACTGCTTAGGGAGATAAGATTTGCAGTCTTCAAT
* * * * ** ** * *
46159267 CTTCTCCACTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAAT
1 CTGCTCCACTACTGCTTAGGGAGATAAGATTTGCAGTCTTCAAT
* * * *
46159311 CTGCTTCCCACTA-T-CTT-GGAAAGATAAGATTCGCCGTCTTCGAT
1 CTGC-T-CCACTACTGCTTAGG-GAGATAAGATTTGCAGTCTTCAAT
* * ** * *
46159355 CTGCTCCACTACTGCTTAGGGAGATAAAATCTATAATCTTCAAC
1 CTGCTCCACTACTGCTTAGGGAGATAAGATTTGCAGTCTTCAAT
* * * * * ** ** * *
46159399 CTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAAT
1 CTGCTCCACTACTGCTTAGGGAGATAAGATTTGCAGTCTTCAAT
* *
46159443 CTGCTTCCCACTA-T-CTT-GGAAAGATAAGA-TT-CATCGTCTTCGAT
1 CTGC-T-CCACTACTGCTTAGG-GAGATAAGATTTGCA--GTCTTCAAT
* * * *
46159487 CTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAAC
1 CTGCTCCACTACTGCTTAGGGAGATAAGATTTGCAGTCTTCAAT
* * *
46159531 CTTCTCCACTGCTGCTCAGGGAGA
1 CTGCTCCACTACTGCTTAGGGAGA
46159555 CAAGGCTTGG
Statistics
Matches: 467, Mismatches: 176, Indels: 81
0.65 0.24 0.11
Matches are distributed among these distances:
42 33 0.07
43 41 0.09
44 347 0.74
45 24 0.05
46 22 0.05
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (44 bp):
CTGCTCCACTACTGCTTAGGGAGATAAGATTTGCAGTCTTCAAT
Found at i:46159123 original size:132 final size:132
Alignment explanation
Indices: 46158828--46159628 Score: 1415
Period size: 132 Copynumber: 6.1 Consensus size: 132
46158818 TGGATGCGAC
* * * *
46158828 CTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACTTTCTCCGCTACTGCTTAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGG
**
46158893 AGACAAGGCTTGGTGGC-TAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCG
66 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCACCGTCTTCG
46158957 AT
131 AT
*
46158959 CTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTACTCCGCTGCTGCTCAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGG
* *
46159024 AGACAAGGCTTGGTGGCTTAAATCTGCTTTCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCG
66 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCACCGTCTTCG
46159089 AT
131 AT
* *
46159091 CTGCTCCACTACTGCTTAGGGAGATAAAATCTATAATCTTCAACCTACTCCGCTGCTGCTCAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGG
*
46159156 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCATCGTCTTCG
66 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCACCGTCTTCG
46159221 AT
131 AT
* *
46159223 CTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCACTGCTGCTCAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGG
*
46159288 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCG
66 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCACCGTCTTCG
46159353 AT
131 AT
* *
46159355 CTGCTCCACTACTGCTTAGGGAGATAAAATCTATAATCTTCAACCTACTCCGCTGCTGCTCAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGG
*
46159420 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCATCGTCTTCG
66 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCACCGTCTTCG
46159485 AT
131 AT
* *
46159487 CTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCACTGCTGCTCAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGG
46159552 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCACCGTCTTCG
66 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCACCGTCTTCG
46159617 AT
131 AT
46159619 CTGCTCCACT
1 CTGCTCCACT
46159629 GTCAATGCAG
Statistics
Matches: 641, Mismatches: 28, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
131 77 0.12
132 564 0.88
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (132 bp):
CTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGG
AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCACCGTCTTCG
AT
Found at i:46171212 original size:98 final size:98
Alignment explanation
Indices: 46171041--46171237 Score: 313
Period size: 98 Copynumber: 2.0 Consensus size: 98
46171031 AAACAATAAA
* *
46171041 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCCAATACATTAGGGCACAATC
* * *
46171106 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTATAGAATCCCAAACTCAGAAAATTTCCTTT
* * *
46171139 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACATTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCCAATACATTAGGGCACAATC
*
46171204 CCTATAGAATCTCAAACTCAGAAAATTTCCTTT
66 CCTATAGAATCCCAAACTCAGAAAATTTCCTTT
46171237 A
1 A
46171238 TGATTTTTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
98 90 1.00
ACGTcount: A:0.39, C:0.25, G:0.10, T:0.26
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCCAATACATTAGGGCACAATC
CCTATAGAATCCCAAACTCAGAAAATTTCCTTT
Found at i:46174262 original size:109 final size:108
Alignment explanation
Indices: 46174062--46174265 Score: 286
Period size: 109 Copynumber: 1.9 Consensus size: 108
46174052 GACACAAAGT
* * * ** *
46174062 CGTGTCCCAGCCCGTGTGTGCATTCAATGTTGGTCACACGACCGTGTCGTAGGTCATGTTTTAGA
1 CGTGTCCCAGCCCGTGTGTGCATTCAATGTTGGTCACACGACCATGTCGTAAGCCATGCCTCAGA
*
46174127 TCGTGTAACTAATCATTTTAAGACACACGGTCTTGTGGCAAGC
66 CCGTGTAACTAATCATTTTAAGACACACGGTCTTGTGGCAAGC
* *
46174170 CGTGTCCCAGCCCGTGTGTGCATTCAATGTTGGGTCACACGGCCATGTC-TCAAGCCGTGCCTCA
1 CGTGTCCCAGCCCGTGTGTGCATTCAATGTT-GGTCACACGACCATGTCGT-AAGCCATGCCTCA
46174234 GACCGTGTAACTAA-CTATTTTAAGACACACGG
64 GACCGTGTAACTAATC-ATTTTAAGACACACGG
46174266 CCGTGTCGCA
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
108 33 0.39
109 51 0.61
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.28
Consensus pattern (108 bp):
CGTGTCCCAGCCCGTGTGTGCATTCAATGTTGGTCACACGACCATGTCGTAAGCCATGCCTCAGA
CCGTGTAACTAATCATTTTAAGACACACGGTCTTGTGGCAAGC
Found at i:46175513 original size:34 final size:35
Alignment explanation
Indices: 46175439--46175513 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 35
46175429 GGATAAACCG
*
46175439 ACTAGTCGAATAAATCAACAAAGATTGTGCCCAAC
1 ACTAGTCGAATAAACCAACAAAGATTGTGCCCAAC
* * **
46175474 GCTAGTCGAAT-AACCGACAATAG-TTGTGCCCTGC
1 ACTAGTCGAATAAACCAACAA-AGATTGTGCCCAAC
46175508 ACTAGT
1 ACTAGT
46175514 TGGATGTGCC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
34 21 0.64
35 12 0.36
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.23
Consensus pattern (35 bp):
ACTAGTCGAATAAACCAACAAAGATTGTGCCCAAC
Found at i:46182536 original size:18 final size:16
Alignment explanation
Indices: 46182502--46182537 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
46182492 TAATATAATA
46182502 TATTTTTAATAACTTT
1 TATTTTTAATAACTTT
46182518 TATTTTGTAATATACTTT
1 TATTTT-TAATA-ACTTT
46182536 TA
1 TA
46182538 AAAACCCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.61
Consensus pattern (16 bp):
TATTTTTAATAACTTT
Found at i:46182614 original size:3 final size:3
Alignment explanation
Indices: 46182608--46182645 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
46182598 ATCATCATCT
*
46182608 TTA TTA TTA TTA TTA TTT TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
46182646 TTTCTTTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:46189328 original size:6 final size:6
Alignment explanation
Indices: 46189319--46189347 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
46189309 ATCCCTCCAT
46189319 CTCCTG CTCCTG CTCCTG CTCCTG CTCCT
1 CTCCTG CTCCTG CTCCTG CTCCTG CTCCT
46189348 TTCTCTCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.14, T:0.34
Consensus pattern (6 bp):
CTCCTG
Found at i:46197955 original size:17 final size:17
Alignment explanation
Indices: 46197933--46197996 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 17
46197923 CTTAGAGTTC
46197933 TAATTGTATACAGCTTT
1 TAATTGTATACAGCTTT
* * *
46197950 TAATTGTGTAATCTTAGAGTTC
1 TAATTGTAT-A-C--AG-CTTT
46197972 TAATTGTATACAGCTTT
1 TAATTGTATACAGCTTT
46197989 TAATTGTA
1 TAATTGTA
46197997 GCCATTGATG
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
17 18 0.50
18 3 0.08
19 1 0.03
20 1 0.03
21 3 0.08
22 10 0.28
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.47
Consensus pattern (17 bp):
TAATTGTATACAGCTTT
Found at i:46197974 original size:39 final size:39
Alignment explanation
Indices: 46197920--46197995 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
46197910 ATGATTATGC
46197920 AATCTTAGAGTTCTAATTGTATACAGCTTTTAATTGTGT
1 AATCTTAGAGTTCTAATTGTATACAGCTTTTAATTGTGT
46197959 AATCTTAGAGTTCTAATTGTATACAGCTTTTAATTGT
1 AATCTTAGAGTTCTAATTGTATACAGCTTTTAATTGT
46197996 AGCCATTGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (39 bp):
AATCTTAGAGTTCTAATTGTATACAGCTTTTAATTGTGT
Found at i:46203733 original size:35 final size:37
Alignment explanation
Indices: 46203661--46203734 Score: 116
Period size: 39 Copynumber: 2.0 Consensus size: 37
46203651 GAAAGATGGG
46203661 GTTTGTAACTGTTCTAACTGAAATGGAACCCTTTCTTCA
1 GTTTGTAACTGTTCTAACTGAAA--GAACCCTTTCTTCA
46203700 GTTTGTAACTGTTCTAACTG-AA-AACCCTTTCTTCA
1 GTTTGTAACTGTTCTAACTGAAAGAACCCTTTCTTCA
46203735 TAGACTGGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
35 13 0.37
38 2 0.06
39 20 0.57
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.39
Consensus pattern (37 bp):
GTTTGTAACTGTTCTAACTGAAAGAACCCTTTCTTCA
Found at i:46206124 original size:29 final size:29
Alignment explanation
Indices: 46206092--46206151 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
46206082 ATATAGGAAG
46206092 ACACATTTTAACAATAAAAAGAATATAAA
1 ACACATTTTAACAATAAAAAGAATATAAA
46206121 ACACATTTTAACAATAAAAAGAATATAAA
1 ACACATTTTAACAATAAAAAGAATATAAA
46206150 AC
1 AC
46206152 TTACAAGAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.62, C:0.12, G:0.03, T:0.23
Consensus pattern (29 bp):
ACACATTTTAACAATAAAAAGAATATAAA
Found at i:46206930 original size:16 final size:17
Alignment explanation
Indices: 46206904--46206938 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
46206894 TTGCTTTTTG
46206904 TTTTTAGTTTTTTATTT
1 TTTTTAGTTTTTTATTT
46206921 TTTTTA-TTTTTTATTT
1 TTTTTAGTTTTTTATTT
46206937 TT
1 TT
46206939 ATTTTGCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.11, C:0.00, G:0.03, T:0.86
Consensus pattern (17 bp):
TTTTTAGTTTTTTATTT
Found at i:46210444 original size:24 final size:24
Alignment explanation
Indices: 46210408--46210462 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
46210398 GAATGTTTAC
* *
46210408 ATTTTTTTATT-AATTTGATTC-TT
1 ATTTTTTAATTAAATTTG-GTCATT
46210431 ATTTTTTAAGTTAAATTTGGTCATT
1 ATTTTTTAA-TTAAATTTGGTCATT
46210456 ATTTTTT
1 ATTTTTT
46210463 TTAAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 8 0.30
24 4 0.15
25 15 0.56
ACGTcount: A:0.24, C:0.04, G:0.07, T:0.65
Consensus pattern (24 bp):
ATTTTTTAATTAAATTTGGTCATT
Found at i:46215545 original size:12 final size:12
Alignment explanation
Indices: 46215530--46215560 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
46215520 GTGTCGCAGT
46215530 CCGTGTCCATAC
1 CCGTGTCCATAC
*
46215542 CCGTGTTCATAC
1 CCGTGTCCATAC
46215554 CCGTGTC
1 CCGTGTC
46215561 ACTCTCTGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.39, G:0.19, T:0.29
Consensus pattern (12 bp):
CCGTGTCCATAC
Found at i:46215727 original size:42 final size:42
Alignment explanation
Indices: 46215649--46215729 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 42
46215639 GTGCAAGGAA
*
46215649 CACACGGCCAAACCACACGCCCGTGCGCATGGCCGTGTGTCG
1 CACACGGCCAAACCACACGCCCGTGCGCATGCCCGTGTGTCG
* *
46215691 CACACGGCTAAGA-CACACGCCCGTGTCTC-TGCCCGTGTG
1 CACACGGCCAA-ACCACACGCCCGTG-CGCATGCCCGTGTG
46215730 GACGAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 31 0.91
43 3 0.09
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.15
Consensus pattern (42 bp):
CACACGGCCAAACCACACGCCCGTGCGCATGCCCGTGTGTCG
Found at i:46219818 original size:25 final size:25
Alignment explanation
Indices: 46219790--46219851 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
46219780 TGTGCCTAGG
* **
46219790 AGGCTTTATGCCGGTGAATTTTATC
1 AGGCTTTATGCCAGTGAATTAGATC
* *
46219815 AGGCTTTATGCTAGTGTATTAGATC
1 AGGCTTTATGCCAGTGAATTAGATC
46219840 AGGCTTTATGCC
1 AGGCTTTATGCC
46219852 TAGCAGGCTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (25 bp):
AGGCTTTATGCCAGTGAATTAGATC
Found at i:46228671 original size:25 final size:25
Alignment explanation
Indices: 46228571--46228664 Score: 95
Period size: 25 Copynumber: 3.6 Consensus size: 25
46228561 TTCGTATTCG
*
46228571 GGAATGCTCATACGAGCACATA-AACA
1 GGAA-GCTCATTCGAGC-CATATAACA
*
46228597 GGAAGCTCTCTTTCGAGCCATATAAC-
1 GGAAG--CTCATTCGAGCCATATAACA
46228623 GTGAAGCTCATGT-GAGCCATATAACA
1 G-GAAGCTCAT-TCGAGCCATATAACA
46228649 GGAAGCTCATTCGAGC
1 GGAAGCTCATTCGAGC
46228665 TGTATAAAGG
Statistics
Matches: 58, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
24 1 0.02
25 30 0.52
26 11 0.19
27 16 0.28
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.21
Consensus pattern (25 bp):
GGAAGCTCATTCGAGCCATATAACA
Found at i:46239546 original size:50 final size:50
Alignment explanation
Indices: 46239492--46239598 Score: 112
Period size: 50 Copynumber: 2.1 Consensus size: 50
46239482 AGACTCATGT
* **
46239492 GAGCTGTATAA-CGGGAAGCTTATGA-GAGCCATAA-ATCAGGTAGCTCAAGA
1 GAGCTGT-TAATCGGGAAGCTCAT-ACGAGCCA-AATATCAGAAAGCTCAAGA
* * *
46239542 GAGCTATTAATCGGGAATCTCATACGAGCCAAATATCAGAAAGCTCATGA
1 GAGCTGTTAATCGGGAAGCTCATACGAGCCAAATATCAGAAAGCTCAAGA
46239592 GAGCTGT
1 GAGCTGT
46239599 GGTGTGTCCG
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
49 6 0.13
50 41 0.87
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (50 bp):
GAGCTGTTAATCGGGAAGCTCATACGAGCCAAATATCAGAAAGCTCAAGA
Found at i:46246503 original size:35 final size:35
Alignment explanation
Indices: 46246464--46246544 Score: 126
Period size: 35 Copynumber: 2.3 Consensus size: 35
46246454 TTTTAAAATG
*
46246464 GCTATAATAGTATATTCATTTGTGCTAGTTGATAA
1 GCTATAATAATATATTCATTTGTGCTAGTTGATAA
*
46246499 GCTATAATAATATATTCATTTGTGTTAGTTGATAA
1 GCTATAATAATATATTCATTTGTGCTAGTTGATAA
**
46246534 TATATAATAAT
1 GCTATAATAAT
46246545 GTATGTTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (35 bp):
GCTATAATAATATATTCATTTGTGCTAGTTGATAA
Found at i:46262251 original size:7 final size:7
Alignment explanation
Indices: 46262239--46262274 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
46262229 CTTTGATCGT
46262239 ACTGCTC
1 ACTGCTC
46262246 ACTGCTC
1 ACTGCTC
46262253 ACTGCTC
1 ACTGCTC
46262260 ACTGCTC
1 ACTGCTC
46262267 ACTGCTC
1 ACTGCTC
46262274 A
1 A
46262275 GTTTTCTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.17, C:0.42, G:0.14, T:0.28
Consensus pattern (7 bp):
ACTGCTC
Found at i:46271778 original size:18 final size:18
Alignment explanation
Indices: 46271755--46271790 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
46271745 CCTTGGTCTC
46271755 CAAGTAAAAAGATAAGGA
1 CAAGTAAAAAGATAAGGA
*
46271773 CAAGTATAAAGATAAGGA
1 CAAGTAAAAAGATAAGGA
46271791 TAGAATAAAG
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:0.58, C:0.06, G:0.22, T:0.14
Consensus pattern (18 bp):
CAAGTAAAAAGATAAGGA
Found at i:46276728 original size:69 final size:68
Alignment explanation
Indices: 46276610--46276980 Score: 284
Period size: 69 Copynumber: 5.4 Consensus size: 68
46276600 TCTTATAATG
* * * * * *
46276610 TCAACTGGGAGCATAGGTCTGCGAGCTGCTTTAGAAGTTGTGATTTTAAATCGTCAAACCTTTAA
1 TCAACTGGGAGCGTAGGTCCGCTAGCTGCTTTAG-AGTTGTGATATTAAACCGTCAAACCTTTAT
46276675 GACA
65 GACA
* * * *
46276679 TCAACTGGGAGCGTATGACCGCTAGCTGCTTTAGAGTTTGCGATATTAAACCGTTAAACCTTTAT
1 TCAACTGGGAGCGTAGGTCCGCTAGCTGCTTTAGAG-TTGTGATATTAAACCGTCAAACCTTTAT
46276744 GACA
65 GACA
* * * * * * * *
46276748 TCAACTAGGAACGTAGGTTCGCTAGTTGCTTTGGAGGTTATGATCTTAAACCGTCAAACCTCTAT
1 TCAACTGGGAGCGTAGGTCCGCTAGCTGCTTTAGA-GTTGTGATATTAAACCGTCAAACCTTTAT
46276813 GACA
65 GACA
* * * * * ** * * * *
46276817 TCAACTGGGAGCGTAGGTCTGCTAGTTG-TATTGGAGCTGCGAGCTT-AACTCTTCGAGCTTTTA
1 TCAACTGGGAGCGTAGGTCCGCTAGCTGCT-TTAGAGTTGTGATATTAAAC-CGTCAAACCTTTA
46276880 T-A-A
64 TGACA
* * * * ** **
46276883 TGCCAGCTGGGAGCGTGGGTCCGCTAGCTACTTTGGAGGTTACGACCTTAAACCGTCAAACCTTT
1 T--CAACTGGGAGCGTAGGTCCGCTAGCTGCTTTAGA-GTTGTGATATTAAACCGTCAAACCTTT
46276948 ATGACA
63 ATGACA
* *
46276954 TC-AGTTGGAGCGTAGGTCCGCTAGCTG
1 TCAACTGGGAGCGTAGGTCCGCTAGCTG
46276981 TGCTGGAGCT
Statistics
Matches: 239, Mismatches: 52, Indels: 23
0.76 0.17 0.07
Matches are distributed among these distances:
66 2 0.01
67 4 0.02
68 66 0.28
69 160 0.67
70 5 0.02
71 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (68 bp):
TCAACTGGGAGCGTAGGTCCGCTAGCTGCTTTAGAGTTGTGATATTAAACCGTCAAACCTTTATG
ACA
Found at i:46280902 original size:21 final size:21
Alignment explanation
Indices: 46280878--46281055 Score: 144
Period size: 21 Copynumber: 8.5 Consensus size: 21
46280868 GTGTTTTACT
* *
46280878 TTCTGTTTAGCTATTACGAGC
1 TTCTGTTTAGCTCTTATGAGC
* * * *
46280899 TTCTATTTAACTCATATGAGT
1 TTCTGTTTAGCTCTTATGAGC
*
46280920 TTCTATTTAGCTCTTATGAGC
1 TTCTGTTTAGCTCTTATGAGC
* *
46280941 TTCTGTTAAACTCTTATGAG-
1 TTCTGTTTAGCTCTTATGAGC
* * *
46280961 TTTTTTTTCAGCTCTTACGAGC
1 TTCTGTTT-AGCTCTTATGAGC
* * * *
46280983 TTCTGTTCAACTCTAATCG-GT
1 TTCTGTTTAGCTCTTAT-GAGC
*
46281004 TTTTGTTTAGCTCTTATGAGC
1 TTCTGTTTAGCTCTTATGAGC
* *
46281025 TTCTATTTAGCTCTCATGAGC
1 TTCTGTTTAGCTCTTATGAGC
*
46281046 TTTTGTTTAG
1 TTCTGTTTAG
46281056 TTTTCGGGAT
Statistics
Matches: 119, Mismatches: 34, Indels: 8
0.74 0.21 0.05
Matches are distributed among these distances:
20 6 0.05
21 107 0.90
22 6 0.05
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTGTTTAGCTCTTATGAGC
Found at i:46280929 original size:42 final size:41
Alignment explanation
Indices: 46280877--46281055 Score: 175
Period size: 42 Copynumber: 4.3 Consensus size: 41
46280867 CGTGTTTTAC
*
46280877 TTTCTGTTTAGCTATTACGAGCTTCTATTTAACTCATATGAG
1 TTTCTGTTTAGCTCTTACGAGCTTCTATTTAACTC-TATGAG
* * * *
46280919 TTTCTATTTAGCTCTTATGAGCTTCTGTTAAACTCTTATGAG
1 TTTCTGTTTAGCTCTTACGAGCTTCTATTTAACTC-TATGAG
* * *
46280961 TTT-TTTTTCAGCTCTTACGAGCTTCTGTTCAACTCTAATCG-G
1 TTTCTGTTT-AGCTCTTACGAGCTTCTATTTAACTCT-AT-GAG
* * *
46281003 TTTTTGTTTAGCTCTTATGAGCTTCTATTTAGCTCTCATGAG
1 TTTCTGTTTAGCTCTTACGAGCTTCTATTTAACTCT-ATGAG
46281045 CTTT-TGTTTAG
1 -TTTCTGTTTAG
46281056 TTTTCGGGAT
Statistics
Matches: 116, Mismatches: 15, Indels: 12
0.81 0.10 0.08
Matches are distributed among these distances:
41 6 0.05
42 102 0.88
43 8 0.07
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.48
Consensus pattern (41 bp):
TTTCTGTTTAGCTCTTACGAGCTTCTATTTAACTCTATGAG
Found at i:46281044 original size:84 final size:84
Alignment explanation
Indices: 46280886--46281049 Score: 206
Period size: 84 Copynumber: 2.0 Consensus size: 84
46280876 CTTTCTGTTT
* *
46280886 AGCTATTACGAGCTTCTATTTAACTCATATGAGTTTCTATTTAGCTCTTATGAGCTTCTGTTAAA
1 AGCTATTACGAGCTTCTATTCAACTCATATGAGTTTCTATTTAGCTCTTATGAGCTTCTATTAAA
* *
46280951 CTCTTATGAGTTTTTTTTC
66 CTCTCATGAGCTTTTTTTC
* * * * *
46280970 AGCTCTTACGAGCTTCTGTTCAACTC-TAATCG-GTTTTTGTTTAGCTCTTATGAGCTTCTATTT
1 AGCTATTACGAGCTTCTATTCAACTCAT-AT-GAGTTTCTATTTAGCTCTTATGAGCTTCTATTA
*
46281033 AGCTCTCATGAGCTTTT
64 AACTCTCATGAGCTTTT
46281050 GTTTAGTTTT
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
83 1 0.01
84 66 0.97
85 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.15, T:0.46
Consensus pattern (84 bp):
AGCTATTACGAGCTTCTATTCAACTCATATGAGTTTCTATTTAGCTCTTATGAGCTTCTATTAAA
CTCTCATGAGCTTTTTTTC
Found at i:46288564 original size:21 final size:21
Alignment explanation
Indices: 46288540--46288617 Score: 95
Period size: 21 Copynumber: 3.7 Consensus size: 21
46288530 TTTTTAGCTT
46288540 TTATGAGCTTCTGTTAAACCC
1 TTATGAGCTTCTGTTAAACCC
*
46288561 TTATGAGCTTCTGTTCAACCC
1 TTATGAGCTTCTGTTAAACCC
* * * *
46288582 TTATCG-GATTCTGTTTAGCTC
1 TTAT-GAGCTTCTGTTAAACCC
46288603 TTATGAGCTTCTGTT
1 TTATGAGCTTCTGTT
46288618 CAGCTTTCGG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 1 0.02
21 47 0.96
22 1 0.02
ACGTcount: A:0.18, C:0.22, G:0.17, T:0.44
Consensus pattern (21 bp):
TTATGAGCTTCTGTTAAACCC
Found at i:46288622 original size:21 final size:21
Alignment explanation
Indices: 46288535--46288622 Score: 88
Period size: 21 Copynumber: 4.2 Consensus size: 21
46288525 CTTTCTTTTT
* *
46288535 AGCTTTTATGAGCTTCTGTTA
1 AGCTCTTATGAGCTTCTGTTC
* *
46288556 AACCCTTATGAGCTTCTGTTC
1 AGCTCTTATGAGCTTCTGTTC
* * * *
46288577 AACCCTTATCG-GATTCTGTTT
1 AGCTCTTAT-GAGCTTCTGTTC
46288598 AGCTCTTATGAGCTTCTGTTC
1 AGCTCTTATGAGCTTCTGTTC
46288619 AGCT
1 AGCT
46288623 TTCGGGCTTC
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
20 1 0.02
21 53 0.96
22 1 0.02
ACGTcount: A:0.18, C:0.23, G:0.17, T:0.42
Consensus pattern (21 bp):
AGCTCTTATGAGCTTCTGTTC
Found at i:46309949 original size:37 final size:37
Alignment explanation
Indices: 46309908--46310056 Score: 253
Period size: 37 Copynumber: 4.0 Consensus size: 37
46309898 GCTGAAGCTA
*
46309908 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
* *
46309945 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
**
46309982 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
46310019 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
46310056 C
1 C
46310057 TAAAACTACC
Statistics
Matches: 105, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 105 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (37 bp):
CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
Found at i:46318289 original size:17 final size:17
Alignment explanation
Indices: 46318259--46318292 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
46318249 AAAACGGGTC
**
46318259 ATATTTTTGTCCAAACT
1 ATATTTTTACCCAAACT
46318276 ATATTTTTACCCAAACT
1 ATATTTTTACCCAAACT
46318293 CTCCCACTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.21, G:0.03, T:0.44
Consensus pattern (17 bp):
ATATTTTTACCCAAACT
Found at i:46319052 original size:20 final size:21
Alignment explanation
Indices: 46319027--46319074 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
46319017 TTGCAAAAAC
46319027 TATAAAAGCTATTTAAAAATT
1 TATAAAAGCTATTTAAAAATT
***
46319048 T-TAAATTTTATTTAAAAATT
1 TATAAAAGCTATTTAAAAATT
46319068 TATAAAA
1 TATAAAA
46319075 ATATAAACTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
TATAAAAGCTATTTAAAAATT
Found at i:46319244 original size:20 final size:20
Alignment explanation
Indices: 46319194--46319235 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
46319184 AAAACATTTT
46319194 TTTTACAAA--TTTTAATAA
1 TTTTACAAATTTTTTAATAA
*
46319212 TTTTACAACTTTTTTAAT-A
1 TTTTACAAATTTTTTAATAA
46319231 TTTTA
1 TTTTA
46319236 ATAAATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 8 0.38
19 6 0.29
20 7 0.33
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTACAAATTTTTTAATAA
Found at i:46322312 original size:33 final size:33
Alignment explanation
Indices: 46322270--46322337 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
46322260 TTTCATAAGT
46322270 AAGACAAGATGAGTACCTTCAAGTGTACTTTGC
1 AAGACAAGATGAGTACCTTCAAGTGTACTTTGC
46322303 AAGACAAGATGAGTACCTTCAAGTGTACTTTGC
1 AAGACAAGATGAGTACCTTCAAGTGTACTTTGC
46322336 AA
1 AA
46322338 CCAGTTGTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (33 bp):
AAGACAAGATGAGTACCTTCAAGTGTACTTTGC
Found at i:46330689 original size:3 final size:3
Alignment explanation
Indices: 46330671--46330725 Score: 67
Period size: 3 Copynumber: 18.3 Consensus size: 3
46330661 TGTTTAATTA
* * *
46330671 ATT ATT -TT AGT ATT ATT ATT ATT ATT AAT ATT ATT ATT ACT ATT AATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT
46330719 ATT ATT A
1 ATT ATT A
46330726 GTTTTGTTTC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:46330914 original size:2 final size:2
Alignment explanation
Indices: 46330909--46330939 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
46330899 CTATATATCC
46330909 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46330940 CTTTACATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46337170 original size:22 final size:22
Alignment explanation
Indices: 46337108--46337193 Score: 118
Period size: 22 Copynumber: 3.9 Consensus size: 22
46337098 ATTGTTCAAA
* **
46337108 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
46337130 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
46337152 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
* * *
46337174 CATGAGGGTTTAGTTCGTTA
1 CATGAGAGCTTAGTACGTTA
46337194 AACATATCAC
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:46343419 original size:50 final size:50
Alignment explanation
Indices: 46343341--46343898 Score: 362
Period size: 50 Copynumber: 11.2 Consensus size: 50
46343331 TTTGCAATTA
* * * * * *
46343341 AAAAGATTAAAGCCACAACGACGAATCTTACTTCCCAAGTAGTGCAGTGG
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCACGCATTGCAGTGG
* * * ** * **
46343391 AACAGATTGAAGCTACAACGGTGAATCTTGC-TCCTTCGACATTGCAATTA
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCACG-CATTGCAGTGG
* * * * * *
46343441 AAAAGATTGAGGCCACAACAGCGAATCTTACTTCCCAGGTAGTGCAGTGG
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCACGCATTGCAGTGG
* * * * * **
46343491 AACAGATTGAAGCTCCAACGGCGAATCTTGC-TCCCCCGACATTGCAATTA
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCACG-CATTGCAGTGG
* * * ** * *
46343541 AAAAGATTGAGGCCACAACGGTGAATCTTACTTCTTAGGCAATGCAGTGG
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCACGCATTGCAGTGG
* * * * * *
46343591 AATAGATTGAAGCTACAACGACGAATCTTGCTACCC-CGACATTGCAACT-A
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCACG-CATTGC-AGTGG
* * * * **
46343641 AAAAGATTGAGGCCACAACGACGAATCTTACTTCCCAGGCGGTGCAGTGG
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCACGCATTGCAGTGG
* * * * **
46343691 AATAGATTGAAGCTATAACGGCGAATCTT-CTTCCCCCGACATTGCAATCA
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCACG-CATTGCAGTGG
* * * ** *
46343741 AAAAGATTG-AGACCACAACGACAAATCTTACTTCCCTA-GCGGTACAGTGG
1 AAAAGATTGAAG-CTACAACGGCGAATCTTACTTCCC-ACGCATTGCAGTGG
* * * * *
46343791 AACAGATTGAAGCTACAACGGCGAATATTGCTTCCC-CGACATTGCGGT-T
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCACG-CATTGCAGTGG
* * *
46343840 AATAGATTGAAGCTACAACAGCGAATCTTACTTCCC-CGACATTGCAGTTG
1 AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCACG-CATTGCAGTGG
*
46343890 AACAGATTG
1 AAAAGATTG
46343899 GAGATGACAG
Statistics
Matches: 372, Mismatches: 120, Indels: 32
0.71 0.23 0.06
Matches are distributed among these distances:
49 65 0.17
50 288 0.77
51 19 0.05
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.23
Consensus pattern (50 bp):
AAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCACGCATTGCAGTGG
Found at i:46343510 original size:100 final size:99
Alignment explanation
Indices: 46343332--46343898 Score: 712
Period size: 100 Copynumber: 5.7 Consensus size: 99
46343322 AAACCATAGT
* * * *
46343332 TTGCAATTAAAAAGATTAAAGCCACAACGACGAATCTTACTTCCCAAGTAGTGCAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAGGCCACAACGACGAATCTTACTTCCCAGGCAGTGCAGTGGAACAGA
* *
46343397 TTGAAGCTACAACGGTGAATCTTGCTCCTTCGACA
66 TTGAAGCTACAACGGCGAATCTTGCTCC-CCGACA
*
46343432 TTGCAATTAAAAAGATTGAGGCCACAAC-AGCGAATCTTACTTCCCAGGTAGTGCAGTGGAACAG
1 TTGCAATTAAAAAGATTGAGGCCACAACGA-CGAATCTTACTTCCCAGGCAGTGCAGTGGAACAG
*
46343496 ATTGAAGCTCCAACGGCGAATCTTGCTCCCCCGACA
65 ATTGAAGCTACAACGGCGAATCTTGCT-CCCCGACA
** ** * *
46343532 TTGCAATTAAAAAGATTGAGGCCACAACGGTGAATCTTACTTCTTAGGCAATGCAGTGGAATAGA
1 TTGCAATTAAAAAGATTGAGGCCACAACGACGAATCTTACTTCCCAGGCAGTGCAGTGGAACAGA
*
46343597 TTGAAGCTACAACGACGAATCTTGCTACCCCGACA
66 TTGAAGCTACAACGGCGAATCTTGCT-CCCCGACA
* * *
46343632 TTGCAACTAAAAAGATTGAGGCCACAACGACGAATCTTACTTCCCAGGCGGTGCAGTGGAATAGA
1 TTGCAATTAAAAAGATTGAGGCCACAACGACGAATCTTACTTCCCAGGCAGTGCAGTGGAACAGA
*
46343697 TTGAAGCTATAACGGCGAATCTT-CTTCCCCCGACA
66 TTGAAGCTACAACGGCGAATCTTGC-T-CCCCGACA
* * * * *
46343732 TTGCAATCAAAAAGATTGAGACCACAACGACAAATCTTACTTCCCTA-GCGGTACAGTGGAACAG
1 TTGCAATTAAAAAGATTGAGGCCACAACGACGAATCTTACTTCCC-AGGCAGTGCAGTGGAACAG
*
46343796 ATTGAAGCTACAACGGCGAATATTGCTTCCCCGACA
65 ATTGAAGCTACAACGGCGAATCTTGC-TCCCCGACA
** * * * * * * *
46343832 TTGCGGTT-AATAGATTGAAGCTACAAC-AGCGAATCTTACTTCCCCGACATTGCAGTTGAACAG
1 TTGCAATTAAAAAGATTGAGGCCACAACGA-CGAATCTTACTTCCCAGGCAGTGCAGTGGAACAG
46343895 ATTG
65 ATTG
46343899 GAGATGACAG
Statistics
Matches: 411, Mismatches: 48, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
98 1 0.00
99 47 0.11
100 357 0.87
101 6 0.01
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (99 bp):
TTGCAATTAAAAAGATTGAGGCCACAACGACGAATCTTACTTCCCAGGCAGTGCAGTGGAACAGA
TTGAAGCTACAACGGCGAATCTTGCTCCCCGACA
Found at i:46345582 original size:3 final size:3
Alignment explanation
Indices: 46345564--46345621 Score: 82
Period size: 3 Copynumber: 19.3 Consensus size: 3
46345554 TGTTTAATTA
* *
46345564 ATT ATT -TT AGT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
46345611 AATT ATT ATT A
1 -ATT ATT ATT A
46345622 GTTTTGTTTC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:46345731 original size:2 final size:2
Alignment explanation
Indices: 46345720--46345754 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
46345710 TATACCTCCG
*
46345720 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46345755 GCATACACGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:46348651 original size:91 final size:91
Alignment explanation
Indices: 46348445--46348654 Score: 257
Period size: 91 Copynumber: 2.3 Consensus size: 91
46348435 CGGACACTCC
* **
46348445 AGTTTGAGGATAAACCACAAGTG-TTGCAAGTTAATACGCTGCCAATAGTTGTGAATACACAATT
1 AGTTTGTGGATAAACCACAAGTGTTTGCAAGTTAATACGCTGCCAATAGTTGTGAATACACAACG
*
46348509 GGTTTACAGATAAAAGCTGCTAGTAAA
66 GGTTTACAGATAAAAGCTACTAGT-AA
* * * * *
46348536 AG-TTGTGGATAAACCACGAA-TGTTTGTAGGTTAATACGTTGCCAATAGGTTGTGAATGCACAG
1 AGTTTGTGGATAAACCAC-AAGTGTTTGCAAGTTAATACGCTGCCAATA-GTTGTGAATACACAA
*
46348599 CGGGTTTGCAGATAAAAGCTACTAGT-A
64 CGGGTTTACAGATAAAAGCTACTAGTAA
* *
46348626 AGTTTGTGGATGAACCACTAGTGTTTGCA
1 AGTTTGTGGATAAACCACAAGTGTTTGCA
46348655 GATAAACTGC
Statistics
Matches: 101, Mismatches: 13, Indels: 10
0.81 0.10 0.08
Matches are distributed among these distances:
90 20 0.20
91 46 0.46
92 35 0.35
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (91 bp):
AGTTTGTGGATAAACCACAAGTGTTTGCAAGTTAATACGCTGCCAATAGTTGTGAATACACAACG
GGTTTACAGATAAAAGCTACTAGTAA
Found at i:46350282 original size:37 final size:37
Alignment explanation
Indices: 46350204--46350282 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 37
46350194 AAATAATAAT
** *
46350204 AAATAATATTCAAATAATTAAATATAATGATATTTGT
1 AAATAATATTCAAATAATTAAATATAATGATACATGA
* * *
46350241 AAATAATATTTAAATAGTTTAATATTAATGATACAT-A
1 AAATAATATTCAAATAATTAAATA-TAATGATACATGA
46350278 AAATA
1 AAATA
46350283 TAAATTAACC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
37 26 0.74
38 9 0.26
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (37 bp):
AAATAATATTCAAATAATTAAATATAATGATACATGA
Found at i:46353684 original size:18 final size:18
Alignment explanation
Indices: 46353656--46353709 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 18
46353646 TTCAAAATAA
*
46353656 TATAAAT-TTTTAATTTT
1 TATAAATATTTTGATTTT
46353673 TATAAATATTTTGATTTT
1 TATAAATATTTTGATTTT
46353691 TGA-AAATTATTTTGATTTT
1 T-ATAAA-TATTTTGATTTT
46353710 ATTTTAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
17 7 0.21
18 13 0.39
19 13 0.39
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (18 bp):
TATAAATATTTTGATTTT
Found at i:46353691 original size:19 final size:19
Alignment explanation
Indices: 46353656--46353709 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
46353646 TTCAAAATAA
*
46353656 TATAAAT-TTTT-AATTTT
1 TATAAATATTTTGATTTTT
46353673 TATAAATATTTTGATTTTT
1 TATAAATATTTTGATTTTT
*
46353692 GA-AAATTATTTTGATTTT
1 TATAAA-TATTTTGATTTT
46353710 ATTTTAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 7 0.22
18 7 0.22
19 18 0.56
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (19 bp):
TATAAATATTTTGATTTTT
Found at i:46354206 original size:29 final size:30
Alignment explanation
Indices: 46354150--46354206 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
46354140 TGATATATCA
*
46354150 TTGAGAGTTTAAGAATGTAATTATAATATT
1 TTGAGAGTTTAAGAATGTAATTAAAATATT
*
46354180 TTGA-AGTTTAATAA-GTAATTTAAAATA
1 TTGAGAGTTTAAGAATGTAA-TTAAAATA
46354207 ATTATCATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.17
29 16 0.67
30 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (30 bp):
TTGAGAGTTTAAGAATGTAATTAAAATATT
Found at i:46355532 original size:2 final size:2
Alignment explanation
Indices: 46355525--46355557 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
46355515 AATTAAGAAA
*
46355525 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
46355558 AATCTGAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46356196 original size:4 final size:4
Alignment explanation
Indices: 46356187--46356213 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
46356177 TTTTAAGTTC
46356187 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
46356214 ATTTGGTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:46359427 original size:14 final size:14
Alignment explanation
Indices: 46359408--46359437 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
46359398 TGTCCATGCC
*
46359408 TTTTTTTTTTCTCT
1 TTTTTTTTTTCACT
46359422 TTTTTTTTTTCACT
1 TTTTTTTTTTCACT
46359436 TT
1 TT
46359438 AAAACTATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTTTTTCACT
Found at i:46362562 original size:22 final size:20
Alignment explanation
Indices: 46362535--46362577 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
46362525 CCGGTCCAAT
46362535 TTTTAATAAACACAAAAAAATA
1 TTTTAA-AAACA-AAAAAAATA
*
46362557 TTTTAAAAATAAAAAAAATA
1 TTTTAAAAACAAAAAAAATA
46362577 T
1 T
46362578 ATTTTTAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 4 0.20
22 6 0.30
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (20 bp):
TTTTAAAAACAAAAAAAATA
Found at i:46377790 original size:43 final size:43
Alignment explanation
Indices: 46377742--46377829 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
46377732 TGGTTCTATG
46377742 TATGCCTTTGTTCATTCCATTTTTAGTTTCATCCTTAAATACT
1 TATGCCTTTGTTCATTCCATTTTTAGTTTCATCCTTAAATACT
46377785 TATGCCTTTGTTCATTCCATTTTTAGTTTCATCCTTAAATACT
1 TATGCCTTTGTTCATTCCATTTTTAGTTTCATCCTTAAATACT
46377828 TA
1 TA
46377830 CATATCGCCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.22, C:0.20, G:0.07, T:0.51
Consensus pattern (43 bp):
TATGCCTTTGTTCATTCCATTTTTAGTTTCATCCTTAAATACT
Found at i:46384532 original size:5 final size:5
Alignment explanation
Indices: 46384522--46384553 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
46384512 TGAGCATTCG
46384522 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA AT
1 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA AT
46384554 AAAAAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (5 bp):
ATCGA
Found at i:46385507 original size:30 final size:31
Alignment explanation
Indices: 46385465--46385525 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
46385455 GGGCTGGGAG
*
46385465 GGGAAGGGAGTAAAAGTTTTGGGGGAAAAGT
1 GGGAAGGGAGTAAAAGTTTTGAGGGAAAAGT
46385496 GGGAA-GGAGTAAAAGTTTTGAGGGAAAAGT
1 GGGAAGGGAGTAAAAGTTTTGAGGGAAAAGT
46385526 AAAAAGGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 24 0.83
31 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.43, T:0.20
Consensus pattern (31 bp):
GGGAAGGGAGTAAAAGTTTTGAGGGAAAAGT
Found at i:46385588 original size:9 final size:9
Alignment explanation
Indices: 46385574--46385610 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
46385564 TATAGTTTGA
46385574 TATTCGAAT
1 TATTCGAAT
46385583 TATTCGAAT
1 TATTCGAAT
*
46385592 TATTCGAGT
1 TATTCGAAT
46385601 TATTCGAAT
1 TATTCGAAT
46385610 T
1 T
46385611 CGAAAATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:46385680 original size:9 final size:9
Alignment explanation
Indices: 46385663--46385693 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
46385653 TCGAGTTGAT
46385663 TCGAATAAC
1 TCGAATAAC
*
46385672 TCGATTAAC
1 TCGAATAAC
46385681 TCGAATAAC
1 TCGAATAAC
46385690 TCGA
1 TCGA
46385694 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:46386880 original size:9 final size:9
Alignment explanation
Indices: 46386866--46386926 Score: 77
Period size: 9 Copynumber: 6.6 Consensus size: 9
46386856 TGTAGTGATT
*
46386866 TAATTCTGG
1 TAATTCGGG
46386875 TAATTCGGG
1 TAATTCGGG
*
46386884 TAATTTGGG
1 TAATTCGGG
*
46386893 TAATTTTCGGA
1 TAA--TTCGGG
46386904 TAATTCGGG
1 TAATTCGGG
46386913 TAATTCGGG
1 TAATTCGGG
46386922 TAATT
1 TAATT
46386927 TTTAACCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
9 38 0.84
11 7 0.16
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (9 bp):
TAATTCGGG
Found at i:46386907 original size:20 final size:20
Alignment explanation
Indices: 46386866--46386917 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
46386856 TGTAGTGATT
* *
46386866 TAATTCTGGTAA--TTCGGG
1 TAATTCGGGTAATTTTCGGA
*
46386884 TAATTTGGGTAATTTTCGGA
1 TAATTCGGGTAATTTTCGGA
46386904 TAATTCGGGTAATT
1 TAATTCGGGTAATT
46386918 CGGGTAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 10 0.36
20 18 0.64
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.42
Consensus pattern (20 bp):
TAATTCGGGTAATTTTCGGA
Found at i:46388303 original size:3 final size:3
Alignment explanation
Indices: 46388295--46388325 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
46388285 GAAAGTATGA
46388295 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
46388326 GCAAATGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:46388395 original size:3 final size:3
Alignment explanation
Indices: 46388387--46388423 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
46388377 GAAAGTATGA
46388387 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
46388424 GGAATAAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:46390246 original size:129 final size:127
Alignment explanation
Indices: 46390022--46390276 Score: 314
Period size: 129 Copynumber: 2.0 Consensus size: 127
46390012 GAAATAAAGT
* * *** * *
46390022 CTGATTCGATCTGTTCTACTGCAACTTCAGAGATAAGATCCATCATTTTAATTTGCTCCGCTGTA
1 CTGATGCGATCTGCTCTACTGCAACTTCAGAGATAAGATCCATCATTTTAATCCACTCCACTGCA
* * * ** *
46390087 ACTTCAGGGAGATACAATTGGTTTATTCAATCTGTTCCACTGTAACTTCAGGGAGATAAGAC
66 ACTTCAGGGAGATACAATTAGTTTACTCAATCTGCTCCACTACAACTTCAAGGAGATAAGAC
* *
46390149 CTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAGGATCCATCATTTTAATCCACTCTACTG
1 CTGATGCGATCTGCTCTACTGCAACTTC--AGAGATAAGATCCATCATTTTAATCCACTCCACTG
* * *
46390214 CAACTTCAGGGAGATA-AGATTAGTTTCCTCAATTTGCTCCACTACAACTTTAAGGAGATAAGA
64 CAACTTCAGGGAGATACA-ATTAGTTTACTCAATCTGCTCCACTACAACTTCAAGGAGATAAGA
46390277 TTGGTTTATT
Statistics
Matches: 107, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
127 26 0.24
128 1 0.01
129 80 0.75
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (127 bp):
CTGATGCGATCTGCTCTACTGCAACTTCAGAGATAAGATCCATCATTTTAATCCACTCCACTGCA
ACTTCAGGGAGATACAATTAGTTTACTCAATCTGCTCCACTACAACTTCAAGGAGATAAGAC
Found at i:46390262 original size:44 final size:41
Alignment explanation
Indices: 46390067--46390450 Score: 242
Period size: 44 Copynumber: 9.0 Consensus size: 41
46390057 AGATCCATCA
* * *
46390067 TTTT-AATTTGCTCCGCTGTAACTTCAGGGAGATACA-ATTGG
1 TTTTCAATCTGCTCCACTGCAACTTCAGGGAGATA-AGATT-G
* * *
46390108 TTTATTCAATCTGTTCCACTGTAACTTCAGGGAGATAAGACCTG
1 -TT-TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTG
* * * * * * *
46390152 -ATGCGATCTGCTCTACTGCAACTTCAGAGAGATAGGATCCATCA
1 TTTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT---T-G
** *
46390196 TTTT-AATCCACTCTACTGCAACTTCAGGGAGATAAGATTAG
1 TTTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-G
* * * *
46390237 TTTCCTCAATTTGCTCCACTACAACTTTAAGGAGATAAGATTGG
1 TTT--TCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-G
*
46390281 TTTATTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG
1 -TT-TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTG
* * * * *
46390325 -ATGCGATATGCT-CTCTGCAACTTCAGGGAGATAAGATCTG
1 TTTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG
* * *
46390365 TGATTTTAATCTGCTCCACAGCAACTTCAGGGAGATAGGATTATTTG
1 T--TTTCAATCTGCTCCACTGCAACTTCAGGGAGATA--A-GA-TTG
*
46390412 TTTT-AATCTGGTCCACTGCAACTTCAGGGAGATAAGATT
1 TTTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
46390451 CGCCATCTTC
Statistics
Matches: 265, Mismatches: 53, Indels: 50
0.72 0.14 0.14
Matches are distributed among these distances:
39 1 0.00
40 27 0.10
41 41 0.15
42 3 0.01
43 12 0.05
44 165 0.62
45 9 0.03
46 2 0.01
47 4 0.02
48 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (41 bp):
TTTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTG
Found at i:46390329 original size:173 final size:172
Alignment explanation
Indices: 46390071--46390407 Score: 469
Period size: 173 Copynumber: 2.0 Consensus size: 172
46390061 CCATCATTTT
* ** * * *
46390071 AATTTGCTCCGCTGTAACTTCAGGGAGATACAATTGGTTTATTCAATCTGTTCCACTGTAACTTC
1 AATTTGCTCCACTACAACTTCAAGGAGATACAATTGGTTTATTCAATCTGCTCCACTGCAACTTC
* *
46390136 AGGGAGATAAGACCTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAGGATCCATCATTTTA
66 AGGGAGATAAGACCTGATGCGATATGCTCT-CTGCAACTTCAGAGAGATAAGATCCATCATTTTA
* *
46390201 ATCCACTCTACTGCAACTTCAGGGAGATAAGATTAGTTTCCTC
130 ATCCACTCCACAGCAACTTCAGGGAGATAAGATTAGTTTCCTC
* *
46390244 AATTTGCTCCACTACAACTTTAAGGAGATA-AGATTGGTTTATTCAGTCTGCTCCACTGCAACTT
1 AATTTGCTCCACTACAACTTCAAGGAGATACA-ATTGGTTTATTCAATCTGCTCCACTGCAACTT
* * ** *
46390308 CAGGGAGATAAGACTTGATGCGATATGCTCTCTGCAACTTCAGGGAGATAAGATCTGTGATTTTA
65 CAGGGAGATAAGACCTGATGCGATATGCTCTCTGCAACTTCAGAGAGATAAGATCCATCATTTTA
** *
46390373 ATCTGCTCCACAGCAACTTCAGGGAGATAGGATTA
130 ATCCACTCCACAGCAACTTCAGGGAGATAAGATTA
46390408 TTTGTTTTAA
Statistics
Matches: 143, Mismatches: 20, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
172 60 0.42
173 83 0.58
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (172 bp):
AATTTGCTCCACTACAACTTCAAGGAGATACAATTGGTTTATTCAATCTGCTCCACTGCAACTTC
AGGGAGATAAGACCTGATGCGATATGCTCTCTGCAACTTCAGAGAGATAAGATCCATCATTTTAA
TCCACTCCACAGCAACTTCAGGGAGATAAGATTAGTTTCCTC
Found at i:46390379 original size:84 final size:84
Alignment explanation
Indices: 46390086--46390401 Score: 282
Period size: 85 Copynumber: 3.7 Consensus size: 84
46390076 GCTCCGCTGT
* * * *
46390086 AACTTCAGGGAGATACA-ATTGGTTTATTCAATCTGTTCCACTGTAACTTCAGGGAGATAAGACC
1 AACTTCAGGGAGATA-AGATTGGATTATTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACT
*
46390150 TGATGCGATCTGCTCTACTGC
65 TGATGCGATATGCTCT-CTGC
* * ** * * ** *
46390171 AACTTCAGAGAGATAGGA-TCCATCATTTTAATCCACTCTACTGCAACTTCAGGGAGATAAGA-T
1 AACTTCAGGGAGATAAGATTGGATTA-TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACT
* * * * * *
46390234 TAGTTTCCTCAATTTGCTCCACTAC
65 T-G-AT--GCGATATGCT-CTCTGC
* * * *
46390259 AACTTTAAGGAGATAAGATTGGTTTATTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTT
1 AACTTCAGGGAGATAAGATTGGATTATTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT
46390324 GATGCGATATGCTCTCTGC
66 GATGCGATATGCTCTCTGC
*
46390343 AACTTCAGGGAGATAAGATCTGTGATT-TT-AATCTGCTCCACAGCAACTTCAGGGAGATA
1 AACTTCAGGGAGATAAGAT-TG-GATTATTCAATCTGCTCCACTGCAACTTCAGGGAGATA
46390402 GGATTATTTG
Statistics
Matches: 177, Mismatches: 43, Indels: 23
0.73 0.18 0.09
Matches are distributed among these distances:
84 53 0.30
85 57 0.32
86 4 0.02
87 1 0.01
88 56 0.32
89 6 0.03
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (84 bp):
AACTTCAGGGAGATAAGATTGGATTATTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT
GATGCGATATGCTCTCTGC
Found at i:46390380 original size:128 final size:128
Alignment explanation
Indices: 46390206--46390448 Score: 307
Period size: 128 Copynumber: 1.9 Consensus size: 128
46390196 TTTTAATCCA
* *
46390206 CTCTACTGCAACTTCAGGGAGATAAGATTAGTTTCCTCAATTTGCTCCACTA-CAACTTTAAGGA
1 CTCTACTGCAACTTCAGGGAGATAAGATTAGTTT-CTCAATCTGCTCCAC-AGCAACTTCAAGGA
* *
46390270 GATAAGATTGGTTT-ATTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGATGCGATAT
64 GATAAGATT-ATTTGATTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGATGCGATAT
46390334 G
128 G
* *
46390335 CTCT-CTGCAACTTCAGGGAGATAAGATCT-GTGATT-TTAATCTGCTCCACAGCAACTTCAGGG
1 CTCTACTGCAACTTCAGGGAGATAAGAT-TAGT--TTCTCAATCTGCTCCACAGCAACTTCAAGG
* * * *
46390397 AGATAGGATTATTTGTTTTAATCTGGTCCACTGCAACTTCAGGGAGATAAGA
63 AGATAAGATTATTTGATTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA
46390449 TTCGCCATCT
Statistics
Matches: 99, Mismatches: 10, Indels: 11
0.82 0.08 0.09
Matches are distributed among these distances:
127 4 0.04
128 88 0.89
129 5 0.05
130 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (128 bp):
CTCTACTGCAACTTCAGGGAGATAAGATTAGTTTCTCAATCTGCTCCACAGCAACTTCAAGGAGA
TAAGATTATTTGATTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGATGCGATATG
Found at i:46390448 original size:172 final size:173
Alignment explanation
Indices: 46390067--46390450 Score: 504
Period size: 172 Copynumber: 2.2 Consensus size: 173
46390057 AGATCCATCA
* * * *
46390067 TTTTAATTTGCTCCGCTGTAACTTCAGGGAGATACA-ATTGGTTTATTCAATCTGTTCCACTGTA
1 TTTTAATTTGCTCCACTGCAACTTCAGGGAGATA-AGATTGGTTTATTCAATCTGCTCCACTGCA
* *
46390131 ACTTCAGGGAGATAAGACCTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAGGATCCATCA
65 ACTTCAGGGAGATAAGACCTGATGCGATATGCTCTACTGCAACTTCAGAGAGATAAGATCCATCA
* *
46390196 TTTTAATCCACTCTACTGCAACTTCAGGGAGATAAGATTAGTTT
130 TTTTAATCCACTCCACAGCAACTTCAGGGAGATAAGATTAGTTT
** * * * * *
46390240 CCTCAATTTGCTCCACTACAACTTTAAGGAGATAAGATTGGTTTATTCAGTCTGCTCCACTGCAA
1 TTTTAATTTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTATTCAATCTGCTCCACTGCAA
* * ** *
46390305 CTTCAGGGAGATAAGACTTGATGCGATATGCTCT-CTGCAACTTCAGGGAGATAAGATCTGTGAT
66 CTTCAGGGAGATAAGACCTGATGCGATATGCTCTACTGCAACTTCAGAGAGATAAGATCCATCAT
** *
46390369 TTTAATCTGCTCCACAGCAACTTCAGGGAGATAGGATTA-TTT
131 TTTAATCCACTCCACAGCAACTTCAGGGAGATAAGATTAGTTT
* *
46390411 GTTTTAATCTGGTCCACTGCAACTTCAGGGAGATAAGATT
1 -TTTTAATTTGCTCCACTGCAACTTCAGGGAGATAAGATT
46390451 CGCCATCTTC
Statistics
Matches: 178, Mismatches: 31, Indels: 5
0.83 0.14 0.02
Matches are distributed among these distances:
171 3 0.02
172 91 0.51
173 84 0.47
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (173 bp):
TTTTAATTTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTATTCAATCTGCTCCACTGCAA
CTTCAGGGAGATAAGACCTGATGCGATATGCTCTACTGCAACTTCAGAGAGATAAGATCCATCAT
TTTAATCCACTCCACAGCAACTTCAGGGAGATAAGATTAGTTT
Found at i:46390707 original size:210 final size:210
Alignment explanation
Indices: 46390467--46390988 Score: 818
Period size: 210 Copynumber: 2.5 Consensus size: 210
46390457 CTTCAGTCTG
* * *
46390467 CGCCAGGGAGATAAGATTCACTGCCTTCAGCTTTAATCTGCTTCGCTGCAACGTCAGGGAAACAA
1 CGCCAGAGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCTGCAACGTCAGGGAAACAA
*
46390532 GATTCGTTAACTTTAGCTTTAATCTGTTCCATTGTAACACTTAAGAGATAAGATCTGCTGCCTTC
66 GATTCGTTAACTTTAGCTTTAATCTGTTCCATTGTAACACCTAAGAGATAAGATCTGCTGCCTTC
* *
46390597 AGCTTTAATCCGCTCCACTTTAGCTTTAATCTATT-CTATTGTAACGCTAGGGAAAAAAGATTTG
131 AGCTTTAATCCGCTCCACTTCAGCTTTAATCTATTAC-ATTGCAACGCTAGGGAAAAAAGATTTG
46390661 CTGCCTTCAGTCTTAA
195 CTGCCTTCAGTCTTAA
* *
46390677 TGCCAGAGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCCGCAACGTCAGGGAAACAA
1 CGCCAGAGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCTGCAACGTCAGGGAAACAA
* *
46390742 GATTCGTTAACTTTAGCTTTAATCTGTTCCATTGTAACGCCTAAGAGATAAGATTTGCTGCCTTC
66 GATTCGTTAACTTTAGCTTTAATCTGTTCCATTGTAACACCTAAGAGATAAGATCTGCTGCCTTC
* *
46390807 AGCTTTAATCCGCTCCACTTCAGCTTTAATCTATTACATTGCAATGCTAGGGAAATAAGATTTGC
131 AGCTTTAATCCGCTCCACTTCAGCTTTAATCTATTACATTGCAACGCTAGGGAAAAAAGATTTGC
*
46390872 TGCCTTTAGTCTTAA
196 TGCCTTCAGTCTTAA
* *
46390887 CGCCAGAGTGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCACTGCAACG-CTAGGGAAACA
1 CGCCAGAGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCTGCAACGTC-AGGGAAACA
* * *
46390951 AGATTTGGTT--CTTTTAGCTTTAATCTGTTTCGTTGTAA
65 AGA-TTCGTTAAC-TTTAGCTTTAATCTGTTCCATTGTAA
46390989 GGCCAAGGAG
Statistics
Matches: 288, Mismatches: 20, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
209 2 0.01
210 280 0.97
211 6 0.02
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.33
Consensus pattern (210 bp):
CGCCAGAGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCTGCAACGTCAGGGAAACAA
GATTCGTTAACTTTAGCTTTAATCTGTTCCATTGTAACACCTAAGAGATAAGATCTGCTGCCTTC
AGCTTTAATCCGCTCCACTTCAGCTTTAATCTATTACATTGCAACGCTAGGGAAAAAAGATTTGC
TGCCTTCAGTCTTAA
Found at i:46390809 original size:102 final size:102
Alignment explanation
Indices: 46390474--46390822 Score: 268
Period size: 102 Copynumber: 3.4 Consensus size: 102
46390464 CTGCGCCAGG
* * * *
46390474 GAGATAAGATTCACTGCCTTCAGCTTTAATCTGCTTCGCTGCAACGTCAGGGAAACAAGATTCGT
1 GAGATAAGATTCGCTGCCTTCAGCTTTAATCCGCTCCGCAGCAACGTCAGGGAAACAAGATTCGT
* *
46390539 TAACTTTAGCTTTAATCTGTTCCATTGTAACACTTAA
66 TAACTTTAGCTTTAATCTGTTCCATTGTAACGCCTAA
* * ** *
46390576 GAGATAAGA-TCTGCTGCCTTCAGCTTTAATCCGCTCCACTTTAGCTTTAATCTATTCTATTGTA
1 GAGATAAGATTC-GCTGCCTTCAGCTTTAATCCGCTCCGC---AGC---AA-C--GTC-AGGGAA
* * ** *** * * *
46390640 AC--G-CTAGGGAA-AAAAGATTT--GCTGCCTT-CAGTCT-TAATGCC-AGA
55 ACAAGATTCGTTAACTTTAGCTTTAATCTG--TTCCA-T-TGTAACGCCTA-A
* *
46390684 GAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCCGCAACGTCAGGGAAACAAGATTCGT
1 GAGATAAGATTCGCTGCCTTCAGCTTTAATCCGCTCCGCAGCAACGTCAGGGAAACAAGATTCGT
46390749 TAACTTTAGCTTTAATCTGTTCCATTGTAACGCCTAA
66 TAACTTTAGCTTTAATCTGTTCCATTGTAACGCCTAA
*
46390786 GAGATAAGATTTGCTGCCTTCAGCTTTAATCCGCTCC
1 GAGATAAGATTCGCTGCCTTCAGCTTTAATCCGCTCC
46390823 ACTTCAGCTT
Statistics
Matches: 181, Mismatches: 40, Indels: 52
0.66 0.15 0.19
Matches are distributed among these distances:
98 5 0.03
99 2 0.01
100 1 0.01
101 8 0.04
102 84 0.46
103 3 0.02
104 3 0.02
105 4 0.02
106 3 0.02
107 3 0.02
108 49 0.27
109 8 0.04
110 1 0.01
111 2 0.01
112 5 0.03
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (102 bp):
GAGATAAGATTCGCTGCCTTCAGCTTTAATCCGCTCCGCAGCAACGTCAGGGAAACAAGATTCGT
TAACTTTAGCTTTAATCTGTTCCATTGTAACGCCTAA
Found at i:46397238 original size:3 final size:3
Alignment explanation
Indices: 46397230--46397281 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
46397220 GAAAGTATGA
46397230 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
46397278 AAT A
1 AAT A
46397282 GCAAATGAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:46397361 original size:3 final size:3
Alignment explanation
Indices: 46397355--46397403 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
46397345 TAAAGTATGA
*
46397355 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
46397403 A
1 A
46397404 GGAATAAAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:46397438 original size:20 final size:20
Alignment explanation
Indices: 46397415--46397473 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
46397405 GAATAAAGTA
46397415 AAATACAAAGAAATATGAAC
1 AAATACAAAGAAATATGAAC
*
46397435 AAAT--AAAG-AA-GT-AA-
1 AAATACAAAGAAATATGAAC
46397449 AAATACAAAGAAATATGAAC
1 AAATACAAAGAAATATGAAC
46397469 AAATA
1 AAATA
46397474 AAGAAGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
14 4 0.13
15 2 0.06
16 5 0.16
17 4 0.13
18 5 0.16
19 2 0.06
20 9 0.29
ACGTcount: A:0.68, C:0.07, G:0.10, T:0.15
Consensus pattern (20 bp):
AAATACAAAGAAATATGAAC
Found at i:46397455 original size:34 final size:34
Alignment explanation
Indices: 46397410--46397487 Score: 149
Period size: 34 Copynumber: 2.3 Consensus size: 34
46397400 AATAGGAATA
46397410 AAGT-AAAATACAAAGAAATATGAACAAATAAAG
1 AAGTAAAAATACAAAGAAATATGAACAAATAAAG
46397443 AAGTAAAAATACAAAGAAATATGAACAAATAAAG
1 AAGTAAAAATACAAAGAAATATGAACAAATAAAG
46397477 AAGTAAAAATA
1 AAGTAAAAATA
46397488 TACATAATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 4 0.09
34 40 0.91
ACGTcount: A:0.68, C:0.05, G:0.12, T:0.15
Consensus pattern (34 bp):
AAGTAAAAATACAAAGAAATATGAACAAATAAAG
Found at i:46399920 original size:20 final size:19
Alignment explanation
Indices: 46399872--46399921 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
46399862 ATATCTAATA
*
46399872 ATTTATTATTTATTTATGT
1 ATTTTTTATTTATTTATGT
*
46399891 ATTTTCTATTTATTTTAT-T
1 ATTTTTTATTTA-TTTATGT
46399910 CATTTTTTATTT
1 -ATTTTTTATTT
46399922 TAATTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (19 bp):
ATTTTTTATTTATTTATGT
Found at i:46400176 original size:2 final size:2
Alignment explanation
Indices: 46400169--46400193 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
46400159 CTCAAAATTG
46400169 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
46400194 ATTAAACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46400306 original size:2 final size:2
Alignment explanation
Indices: 46400294--46400332 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
46400284 AAGTATCATT
46400294 TA TA CTA TA TA TA 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 TA TA TA TA TA TA
46400333 AACTTACAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:46406724 original size:10 final size:10
Alignment explanation
Indices: 46406709--46406733 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
46406699 CACTTTAACC
46406709 TAAAATTAAA
1 TAAAATTAAA
46406719 TAAAATTAAA
1 TAAAATTAAA
46406729 TAAAA
1 TAAAA
46406734 AATAAAATAA
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
TAAAATTAAA
Found at i:46408313 original size:25 final size:25
Alignment explanation
Indices: 46408265--46408313 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
46408255 CATAATTGAA
* * *
46408265 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
46408290 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
46408314 ATGTGTATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:46408323 original size:17 final size:17
Alignment explanation
Indices: 46408286--46408328 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
46408276 TGATTTTGTA
46408286 TATTATGAAATATATTG
1 TATTATGAAATATATTG
46408303 -ATTATG-AATATATGTG
1 TATTATGAAATATAT-TG
*
46408319 TATTAAGAAA
1 TATTATGAAA
46408329 AAATGTGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 7 0.32
16 8 0.36
17 5 0.23
18 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (17 bp):
TATTATGAAATATATTG
Found at i:46408758 original size:43 final size:43
Alignment explanation
Indices: 46408710--46408795 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 43
46408700 TATGTGATTG
46408710 ATATTGAAATGGA-AAATATGAGAAATGAA-TATGAGATGAGAAA
1 ATATTGAAAT-GACAAATATGAGAAAT-AATTATGAGATGAGAAA
* *
46408753 ATATTGAAATGACAAATATGATAAATAATTATGATATGAGAAA
1 ATATTGAAATGACAAATATGAGAAATAATTATGAGATGAGAAA
46408796 TGAGATATGA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
42 4 0.10
43 35 0.90
ACGTcount: A:0.53, C:0.01, G:0.19, T:0.27
Consensus pattern (43 bp):
ATATTGAAATGACAAATATGAGAAATAATTATGAGATGAGAAA
Found at i:46409378 original size:13 final size:13
Alignment explanation
Indices: 46409360--46409386 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
46409350 TAAAGTTTGG
46409360 TAGCTTAGCATAA
1 TAGCTTAGCATAA
46409373 TAGCTTAGCATAA
1 TAGCTTAGCATAA
46409386 T
1 T
46409387 GATTGGTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
TAGCTTAGCATAA
Found at i:46412774 original size:21 final size:20
Alignment explanation
Indices: 46412749--46412789 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
46412739 ATCATATATT
*
46412749 AATATTTAATTATTATTAAAA
1 AATATTTAATTAATA-TAAAA
*
46412770 AATATTTTATTAATATAAAA
1 AATATTTAATTAATATAAAA
46412790 TATAAGTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATATTTAATTAATATAAAA
Found at i:46412781 original size:18 final size:18
Alignment explanation
Indices: 46412758--46412792 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
46412748 TAATATTTAA
*
46412758 TTATTATTAAAAAATATT
1 TTATTAATAAAAAATATT
*
46412776 TTATTAATATAAAATAT
1 TTATTAATAAAAAATAT
46412793 AAGTTTATAG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTATTAATAAAAAATATT
Found at i:46415629 original size:7 final size:7
Alignment explanation
Indices: 46415617--46415643 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
46415607 TTGATATTAG
46415617 GTGTAAC
1 GTGTAAC
46415624 GTGTAAC
1 GTGTAAC
46415631 GTGTAAC
1 GTGTAAC
46415638 GTGTAA
1 GTGTAA
46415644 GTGCTTTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.30
Consensus pattern (7 bp):
GTGTAAC
Found at i:46421388 original size:7 final size:7
Alignment explanation
Indices: 46421376--46421400 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
46421366 CCACTTCCTT
46421376 CAACCTC
1 CAACCTC
46421383 CAACCTC
1 CAACCTC
46421390 CAACCTC
1 CAACCTC
46421397 CAAC
1 CAAC
46421401 TTGTTTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.56, G:0.00, T:0.12
Consensus pattern (7 bp):
CAACCTC
Found at i:46434249 original size:43 final size:43
Alignment explanation
Indices: 46434161--46434766 Score: 676
Period size: 43 Copynumber: 14.0 Consensus size: 43
46434151 AAGAATTATA
* * *
46434161 TTTAAGTTAAGGGTTAGTGTTTTTAAGTTAAGAG-ATAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* *
46434203 TTTAAGTTAAGGGTTTAGGGTTTTTAGGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
*
46434247 TTAAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* *
46434290 TTTAAGTTAAGGGTTTAGGGTTTTAAAGTTAAGGG-TTAAGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* *
46434333 TTTAAGTTAAGAGTTTAGAGTTTTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAG-GGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * * *
46434377 TTTAGGTTAAGGGTTTATGGTTTTAAAGTCAA-GGATTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
46434420 TTTAAGTTAAGGGTTATGATTTTTAAGTTAAGGGTTTAGTGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
*
46434463 TTTAA-TTCAAGGGTTAGGGTTTTAAAGTTAAGGG-TTAGGGTT
1 TTTAAGTT-AAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
46434505 TTTAAGTTAAGGGTTAGTGTTTTTTATTTAAGGG-TTA-GGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
**** * *
46434546 TAGGGGTT-AGGGTTAGGGCTTTTAAGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
46434588 TTAAAGTCAAGAGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * *
46434631 TTTAGGTTAAGGGTTTAGAGTTTTTAGGTTAAGGGTTTATGG-T
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* *
46434674 TTTAAGTCAAGGGTTTAGGGTTTTTAA-TTCAAGGG-TTAGAGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTT-AAGGGTTTAGGGTT
46434717 TTTAAGTTAAGGGTTAGGGTTAGGATTTTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTA--G---GG-TTTTTAAGTTAAGGGTTTAGGGTT
46434766 T
1 T
46434767 GTCAATTAAA
Statistics
Matches: 474, Mismatches: 67, Indels: 39
0.82 0.12 0.07
Matches are distributed among these distances:
40 21 0.04
41 11 0.02
42 83 0.18
43 239 0.50
44 96 0.20
47 2 0.00
48 12 0.03
49 10 0.02
ACGTcount: A:0.25, C:0.01, G:0.30, T:0.44
Consensus pattern (43 bp):
TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
Found at i:46434577 original size:61 final size:63
Alignment explanation
Indices: 46434164--46434737 Score: 467
Period size: 65 Copynumber: 9.0 Consensus size: 63
46434154 AATTATATTT
* * * * * *
46434164 AAGTTAAGGGTTAGTGTTTTTAAGTTAAGAGATAGGGTTTTTAAGTT-AAGGGTTTAGGGTTTTT
1 AAGTTAAGGGTTAGGGCTTTTAAGTTAAGGGTTAGTGTTTTTAA-TTCAAGGG-TTAGGGTTTTA
* * *
46434228 AGGTTAAGGGTTTATGG-TTTTAAAGTTAAGGGTTAGGGTTTTTAAGTT-AAGGGTTTAGGGTTT
1 AAGTTAAGGG-TTAGGGCTTTT-AAGTTAAGGGTTAGTGTTTTTAA-TTCAAGGG-TTAGGGTTT
*
46434291 TT
62 TA
* *
46434293 AAGTTAAGGGTTTAGGG-TTTTAAAGTTAAGGGTTAAG-GTTTTTAAGTT-AAGAGTTTAGAGTT
1 AAGTTAAGGG-TTAGGGCTTTT-AAGTTAAGGGTT-AGTGTTTTTAA-TTCAAG-GGTTAGGGTT
*
46434355 TTT
61 TTA
* * * * *
46434358 AAGTTAAGGGTTTAGGGTTTTTAGGTTAAGGGTTTA-TGGTTTTAAAGTCAAGGATTAGGGTTTT
1 AAGTTAAGGG-TTAGGGCTTTTAAGTTAAGGG-TTAGT-GTTTTTAATTCAAGGGTTAGGGTTTT
*
46434422 T
63 A
* **
46434423 AAGTTAAGGGTTATGATTTTTAAGTTAAGGGTTTAGTGTTTTTAATTCAAGGGTTAGGGTTTTA
1 AAGTTAAGGGTTAGGGCTTTTAAGTTAAGGG-TTAGTGTTTTTAATTCAAGGGTTAGGGTTTTA
* * *
46434487 AAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGTGTTTTTTATTTAAGGGTTA-GG-TTTA
1 AAGTTAAGGGTTAGGGCTTTTAAGTTAAGGGTTAGTGTTTTTAATTCAAGGGTTAGGGTTTTA
** * * *
46434548 GGGGTT-AGGGTTAGGGCTTTTAAGTTAAGGGTTTAAG-GTTTTAAAGTCAAGAGTTAGGGTTTT
1 -AAGTTAAGGGTTAGGGCTTTTAAGTTAAGGG-TT-AGTGTTTTTAATTCAAGGGTTAGGGTTTT
*
46434611 T
63 A
* * * * *
46434612 AAGTTAAGGGTTTAGGGTTTTTAGGTTAAGGGTTTAGAGTTTTTAGGTT-AAGGGTTTATGGTTT
1 AAGTTAAGGG-TTAGGGCTTTTAAGTTAAGGG-TTAGTGTTTTTA-ATTCAAGGG-TTAGGGTTT
46434676 T-
62 TA
* * *
46434677 AAGTCAAGGGTTTAGGGTTTTTAA-TTCAAGGGTTAGAGTTTTTAAGTT-AAGGGTTAGGGTT
1 AAGTTAAGGG-TTAGGGCTTTTAAGTT-AAGGGTTAGTGTTTTTAA-TTCAAGGGTTAGGGTT
46434738 AGGATTTTTA
Statistics
Matches: 441, Mismatches: 47, Indels: 45
0.83 0.09 0.08
Matches are distributed among these distances:
61 28 0.06
62 21 0.05
63 36 0.08
64 117 0.27
65 210 0.48
66 29 0.07
ACGTcount: A:0.25, C:0.01, G:0.30, T:0.43
Consensus pattern (63 bp):
AAGTTAAGGGTTAGGGCTTTTAAGTTAAGGGTTAGTGTTTTTAATTCAAGGGTTAGGGTTTTA
Found at i:46434758 original size:21 final size:21
Alignment explanation
Indices: 46434161--46434737 Score: 651
Period size: 21 Copynumber: 27.0 Consensus size: 21
46434151 AAGAATTATA
*
46434161 TTTAAGTTAAGGGTTAGTGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
46434182 TTTAAGTTAAGAGATAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
46434203 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* *
46434225 TTTAGGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
*
46434247 TTAAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
46434268 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
46434290 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* *
46434312 TTAAAGTTAAGGGTTAAGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
46434333 TTTAAGTTAAGAGTTTAGAGTT
1 TTTAAGTTAAG-GGTTAGGGTT
46434355 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* *
46434377 TTTAGGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* * *
46434399 TTAAAGTCAAGGATTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
46434420 TTTAAGTTAAGGGTTATGATT
1 TTTAAGTTAAGGGTTAGGGTT
*
46434441 TTTAAGTTAAGGGTTTAGTGTT
1 TTTAAGTTAAGGG-TTAGGGTT
46434463 TTTAA-TTCAAGGGTTAGGGTT
1 TTTAAGTT-AAGGGTTAGGGTT
*
46434484 TTAAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
46434505 TTTAAGTTAAGGGTTAGTGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
46434526 TTTTATTTAAGGGTTA-GGTT
1 TTTAAGTTAAGGGTTAGGGTT
**** *
46434546 TAGGGGTT-AGGGTTAGGGCT
1 TTTAAGTTAAGGGTTAGGGTT
*
46434566 TTTAAGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* * *
46434588 TTAAAGTCAAGAGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
46434609 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* *
46434631 TTTAGGTTAAGGGTTTAGAGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* *
46434653 TTTAGGTTAAGGGTTTATGG-T
1 TTTAAGTTAAGGG-TTAGGGTT
*
46434674 TTTAAGTCAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
*
46434696 TTTAA-TTCAAGGGTTAGAGTT
1 TTTAAGTT-AAGGGTTAGGGTT
46434717 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
46434738 AGGATTTTTA
Statistics
Matches: 472, Mismatches: 70, Indels: 28
0.83 0.12 0.05
Matches are distributed among these distances:
19 7 0.01
20 13 0.03
21 226 0.48
22 226 0.48
ACGTcount: A:0.25, C:0.01, G:0.30, T:0.44
Consensus pattern (21 bp):
TTTAAGTTAAGGGTTAGGGTT
Found at i:46434775 original size:22 final size:22
Alignment explanation
Indices: 46434161--46434766 Score: 681
Period size: 22 Copynumber: 28.0 Consensus size: 22
46434151 AAGAATTATA
*
46434161 TTTAAGTTAAGGG-TTAGTGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
46434182 TTTAAGTTAAGAG-ATAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
46434203 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
46434225 TTTAGGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
46434247 TTAAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
46434268 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
46434290 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
46434312 TTAAAGTTAAGGG-TTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
46434333 TTTAAGTTAAGAGTTTAGAGTT
1 TTTAAGTTAAGGGTTTAGGGTT
46434355 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
46434377 TTTAGGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
46434399 TTAAAGTCAA-GGATTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
46434420 TTTAAGTTAAGGG-TTATGATT
1 TTTAAGTTAAGGGTTTAGGGTT
*
46434441 TTTAAGTTAAGGGTTTAGTGTT
1 TTTAAGTTAAGGGTTTAGGGTT
46434463 TTTAA-TTCAAGGG-TTAGGGTT
1 TTTAAGTT-AAGGGTTTAGGGTT
*
46434484 TTAAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
46434505 TTTAAGTTAAGGG-TTAGTGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
46434526 TTTTATTTAAGGG-TTA-GGTT
1 TTTAAGTTAAGGGTTTAGGGTT
**** *
46434546 TAGGGGTT-AGGG-TTAGGGCT
1 TTTAAGTTAAGGGTTTAGGGTT
*
46434566 TTTAAGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
46434588 TTAAAGTCAAGAG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
46434609 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
46434631 TTTAGGTTAAGGGTTTAGAGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
46434653 TTTAGGTTAAGGGTTTATGG-T
1 TTTAAGTTAAGGGTTTAGGGTT
*
46434674 TTTAAGTCAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
46434696 TTTAA-TTCAAGGG-TTAGAGTT
1 TTTAAGTT-AAGGGTTTAGGGTT
*
46434717 TTTAAGTTAAGGGTTAGGGTTAGGATT
1 TTTAAGTTAAGGG-T----TTAGGGTT
46434744 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
46434766 T
1 T
46434767 GTCAATTAAA
Statistics
Matches: 494, Mismatches: 71, Indels: 39
0.82 0.12 0.06
Matches are distributed among these distances:
19 7 0.01
20 13 0.03
21 219 0.44
22 235 0.48
26 1 0.00
27 19 0.04
ACGTcount: A:0.25, C:0.01, G:0.30, T:0.44
Consensus pattern (22 bp):
TTTAAGTTAAGGGTTTAGGGTT
Found at i:46437207 original size:51 final size:51
Alignment explanation
Indices: 46437139--46437238 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
46437129 ATTTATTTAA
46437139 AAATAGGGATTTAAGAGAAATTTA-AGAGGAAATTGAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGGAAATTGAGAGCAAATTGAGATT
* * * *
46437190 AAATATGGATTTCAGAGAAATTTGGAAGGAATTTGAGAGCAAATTGAGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGA
46437239 GGAAATTGAG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 43 0.98
52 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.26, T:0.26
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGATT
Found at i:46437236 original size:11 final size:11
Alignment explanation
Indices: 46437216--46437262 Score: 67
Period size: 11 Copynumber: 4.2 Consensus size: 11
46437206 GAAATTTGGA
*
46437216 AGGAATTTGAG
1 AGGAAATTGAG
*
46437227 AGCAAATTGAG
1 AGGAAATTGAG
46437238 AGGAAATTGAG
1 AGGAAATTGAG
46437249 AGGAAATTTGAG
1 AGGAAA-TTGAG
46437261 AG
1 AG
46437263 ATGATTAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
11 25 0.78
12 7 0.22
ACGTcount: A:0.43, C:0.02, G:0.34, T:0.21
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:46437241 original size:22 final size:23
Alignment explanation
Indices: 46437203--46437262 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
46437193 TATGGATTTC
*
46437203 AGAG-AAATTTG-GAAGGAATTTG
1 AGAGCAAATTTGAG-AGGAAATTG
46437225 AGAGCAAA-TTGAGAGGAAATTG
1 AGAGCAAATTTGAGAGGAAATTG
*
46437247 AGAGGAAATTTGAGAG
1 AGAGCAAATTTGAGAG
46437263 ATGATTAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 22 0.67
23 11 0.33
ACGTcount: A:0.43, C:0.02, G:0.33, T:0.22
Consensus pattern (23 bp):
AGAGCAAATTTGAGAGGAAATTG
Found at i:46451774 original size:8 final size:7
Alignment explanation
Indices: 46451757--46451787 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
46451747 AAATAGAATT
46451757 AAAAAGA
1 AAAAAGA
46451764 AAAAAGA
1 AAAAAGA
46451771 AAAAAGAA
1 AAAAAG-A
46451779 AAAAAGA
1 AAAAAGA
46451786 AA
1 AA
46451788 GCCAAATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:46451776 original size:14 final size:15
Alignment explanation
Indices: 46451757--46451787 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
46451747 AAATAGAATT
46451757 AAAAAG-AAAAAAGA
1 AAAAAGAAAAAAAGA
46451771 AAAAAGAAAAAAAGA
1 AAAAAGAAAAAAAGA
46451786 AA
1 AA
46451788 GCCAAATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAGA
Found at i:46452610 original size:17 final size:19
Alignment explanation
Indices: 46452583--46452617 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
46452573 GTAACTTTTA
46452583 AAAGTTAAAACT-AAAAAT
1 AAAGTTAAAACTGAAAAAT
46452601 AAAG-TAAAACTGAAAAA
1 AAAGTTAAAACTGAAAAA
46452618 CAGAGGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.69, C:0.06, G:0.09, T:0.17
Consensus pattern (19 bp):
AAAGTTAAAACTGAAAAAT
Found at i:46452975 original size:38 final size:38
Alignment explanation
Indices: 46452932--46453007 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
46452922 TCCCTCTGTT
*
46452932 CCTCTGTTTATTTTCTTTTCTTTTCTGCCGATTTGCTC
1 CCTCTGTTTATTTTCCTTTCTTTTCTGCCGATTTGCTC
*
46452970 CCTCTGTTTCTTTTCCTTTCTTTTCTGCCGATTTGCTC
1 CCTCTGTTTATTTTCCTTTCTTTTCTGCCGATTTGCTC
46453008 AGTTTCTGCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.04, C:0.29, G:0.11, T:0.57
Consensus pattern (38 bp):
CCTCTGTTTATTTTCCTTTCTTTTCTGCCGATTTGCTC
Found at i:46455605 original size:16 final size:16
Alignment explanation
Indices: 46455584--46455616 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
46455574 TTGATTTGCT
46455584 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
46455600 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
46455616 A
1 A
46455617 ATACAGCGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.36, G:0.06, T:0.36
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:46456532 original size:22 final size:22
Alignment explanation
Indices: 46456481--46456536 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
46456471 TCACATTCAG
* *
46456481 CACCAATCCACCTCCAGTCCGG
1 CACCGATCCACCTCCAGTCCGC
* *
46456503 CACCGATCCACCTCCAGTTCTC
1 CACCGATCCACCTCCAGTCCGC
*
46456525 CACGGATCCACC
1 CACCGATCCACC
46456537 CATTTCCCCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.21, C:0.50, G:0.12, T:0.16
Consensus pattern (22 bp):
CACCGATCCACCTCCAGTCCGC
Found at i:46456651 original size:22 final size:22
Alignment explanation
Indices: 46456625--46456671 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
46456615 AACCTTTACC
46456625 TCCGGCACCAATCCACCTCCGG
1 TCCGGCACCAATCCACCTCCGG
*
46456647 TCCGGCACCGATCCACCTCCGG
1 TCCGGCACCAATCCACCTCCGG
46456669 TCC
1 TCC
46456672 TCCACGGCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.15, C:0.51, G:0.19, T:0.15
Consensus pattern (22 bp):
TCCGGCACCAATCCACCTCCGG
Done.