Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 217 of 292
Found at i:63770778 original size:38 final size:38
Alignment explanation
Indices: 63770717--63770789 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
63770707 AAGTTCAGAT
*
63770717 TCTACATTTAGATTTTATAGTTTTCGGGTTTAGTTAAAA
1 TCTACATTTAGATTTTATAGTTTT-GGATTTAGTTAAAA
* *
63770756 TCTACA-TTAGTTTTTATGGTTTTGGATTTAGTTA
1 TCTACATTTAGATTTTATAGTTTTGGATTTAGTTA
63770790 TTGTATTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 10 0.32
38 15 0.48
39 6 0.19
ACGTcount: A:0.25, C:0.07, G:0.16, T:0.52
Consensus pattern (38 bp):
TCTACATTTAGATTTTATAGTTTTGGATTTAGTTAAAA
Found at i:63771518 original size:18 final size:18
Alignment explanation
Indices: 63771483--63771520 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
63771473 AACTGACCGA
*
63771483 TTAACCGAATTCAGTCGG
1 TTAACCGAATTAAGTCGG
*
63771501 TTAACCGAATTAATTCGG
1 TTAACCGAATTAAGTCGG
63771519 TT
1 TT
63771521 TTATCGGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (18 bp):
TTAACCGAATTAAGTCGG
Found at i:63773237 original size:30 final size:29
Alignment explanation
Indices: 63773201--63773257 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
63773191 TTTTATTTTA
*
63773201 AAAAAAGTTAAAAATTCTAAAAAATATATT
1 AAAAAAGTTAAAAAAT-TAAAAAATATATT
*
63773231 AAAAAAGTTAAAAAATTATAAAATATA
1 AAAAAAGTTAAAAAATTAAAAAATATA
63773258 ATTTTGGGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.28
Consensus pattern (29 bp):
AAAAAAGTTAAAAAATTAAAAAATATATT
Found at i:63774852 original size:3 final size:3
Alignment explanation
Indices: 63774844--63775395 Score: 295
Period size: 3 Copynumber: 183.3 Consensus size: 3
63774834 GATGAAAACG
* * * * * * * *
63774844 ATA ATA ATA ATA ATA TTG TTG ATA ATA ATA ATA GTA GTA GTA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
63774892 ATA ATA CTA ATG ATA ATA ATA A-A AGTA ATA ATA AGA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA
* * *
63774937 TTA GTA TTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
63774985 ATA ATA ATA ATA ATA ATA ATA ATA GTA CATTA ATA ATG ATA GTA TATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -A-TA ATA ATA ATA ATA -ATA
* * * * *
63775033 TTA ATA ACA ATA ATA ATA TATA AAA ATA GGA-A ATA ATA TATG GTA ATA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA --ATA ATA ATA -ATA ATA ATA
* * * * * *
63775081 ATA ATA ATA ATA ATA ATA ACA AAA ATA GTA ATA ATA GTA TGTG A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
* * * * * *
63775126 ATA ATA ATT GTA A-A A-A ACTA ATA GTA ATA ATT ATA TTG ATA ATA
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
63775170 CTA ATA ATA ATA GTA GTA A-A AAA ATA AAA AT- ATA AAA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
63775216 ATA ATA GTA AAA ATG ACA ATA A-A ATA A-G ATA ATA ATA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * **
63775262 ATA A-A AAA ATA A-A A-A AGTA ATA ATG GCA ATA ATA ATA ATA CCATA
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA --ATA
* * * * * *
63775307 ATA A-A AGA AAA AGAA ATA ATA ACA TGTAA ATA ATA ATA ACA ATA ATA
1 ATA ATA ATA ATA A-TA ATA ATA ATA -AT-A ATA ATA ATA ATA ATA ATA
* * * * *
63775354 AAA ATA AT- ATA TTT ATA ATA ATA ATA ATA GTA AAA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
63775396 AATTAACTAA
Statistics
Matches: 416, Mismatches: 105, Indels: 56
0.72 0.18 0.10
Matches are distributed among these distances:
2 25 0.06
3 364 0.88
4 20 0.05
5 7 0.02
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:63775240 original size:40 final size:38
Alignment explanation
Indices: 63775171--63775276 Score: 112
Period size: 40 Copynumber: 2.8 Consensus size: 38
63775161 TTGATAATAC
*
63775171 TAATAATAATAGTAGT-AAAAAAATAAAAATATA-AAAA
1 TAATAATAATAATAGTAAAAAAAATAAAAATA-AGAAAA
*
63775208 TAATAATAATAATAGTAAAAATGACAAT-AAAATAAGATAA
1 TAATAATAATAATAGTAAAAA--A-AATAAAAATAAGAAAA
* *
63775248 TAATAATGATAATAAT-AAAAAAATAAAAA
1 TAATAATAATAATAGTAAAAAAAATAAAAA
63775277 AGTAATAATG
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
36 3 0.05
37 20 0.34
38 4 0.07
39 5 0.08
40 24 0.41
41 3 0.05
ACGTcount: A:0.69, C:0.01, G:0.06, T:0.25
Consensus pattern (38 bp):
TAATAATAATAATAGTAAAAAAAATAAAAATAAGAAAA
Found at i:63775271 original size:31 final size:30
Alignment explanation
Indices: 63775193--63775286 Score: 93
Period size: 34 Copynumber: 3.0 Consensus size: 30
63775183 TAGTAAAAAA
*
63775193 ATAAAAATATAAAAAT-AATAATAATAAT-
1 ATAAAAATAAAAAAATAAATAATAATAATG
63775221 AGTAAAAATGACAATAAAATAAGATAATAATAATG
1 A-TAAAAAT-A-AA-AAAATAA-ATAATAATAATG
* *
63775256 ATAATAATAAAAAAATAAAAAAGTAATAATG
1 ATAAAAATAAAAAAATAAATAA-TAATAATG
63775287 GCAATAATAA
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
28 1 0.02
29 7 0.13
30 4 0.07
31 16 0.29
32 7 0.13
33 2 0.04
34 17 0.31
35 1 0.02
ACGTcount: A:0.68, C:0.01, G:0.06, T:0.24
Consensus pattern (30 bp):
ATAAAAATAAAAAAATAAATAATAATAATG
Found at i:63775360 original size:32 final size:32
Alignment explanation
Indices: 63775324--63775392 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
63775314 AAAAAGAAAT
*
63775324 AATAACATGTAAATAATAATAACAATAATAAA
1 AATAACATATAAATAATAATAACAATAATAAA
* ** * *
63775356 AATAATATATTTATAATAATAATAATAGTAAA
1 AATAACATATAAATAATAATAACAATAATAAA
63775388 AATAA
1 AATAA
63775393 TAAAATTAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (32 bp):
AATAACATATAAATAATAATAACAATAATAAA
Found at i:63776039 original size:5 final size:5
Alignment explanation
Indices: 63776029--63776062 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
63776019 AAATAGGTTC
* *
63776029 AAAAG AAAAG AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
63776063 AAACAAAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (5 bp):
AAAAT
Found at i:63776812 original size:44 final size:44
Alignment explanation
Indices: 63776753--63777006 Score: 181
Period size: 44 Copynumber: 5.6 Consensus size: 44
63776743 TTTATTTTTG
** *
63776753 ATCTGCTCTGCTGCAACTTTAGGGAGATAAGACTTGTAACTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCA
* * ** **
63776797 ACCTGCTCTACTGCAACTTCAGGGAGATAAGGTTTGT---TTTG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCA
** * *
63776838 ATCTGCTTTACTGCAACTTCAGAGAGATAAGATCTGTTTATTCATAGCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA-C---TT-GT-A-A-CTTCA
* * * *
63776890 ATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-TAACTTCA
* * *
63776935 GTTTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTGACTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCA
* * * * *
63776979 ATCTACTCCGCTGAAACTTTAAGGAGAT
1 ATCTGCTCCACTGCAACTTCAGGGAGAT
63777007 CTGCTGTGGC
Statistics
Matches: 161, Mismatches: 37, Indels: 24
0.73 0.17 0.11
Matches are distributed among these distances:
41 30 0.19
44 59 0.37
45 38 0.24
46 1 0.01
47 1 0.01
48 3 0.02
52 29 0.18
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCA
Found at i:63776876 original size:41 final size:41
Alignment explanation
Indices: 63776748--63776876 Score: 125
Period size: 41 Copynumber: 3.1 Consensus size: 41
63776738 TAGAATTTAT
* * *
63776748 TTTTGATCTGCTCTGCTGCAACTTTAGGGAGATAAGA-CTTG
1 TTTTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATC-TG
** * * * *
63776789 TAACTTCAACCTGCTCTACTGCAACTTCAGGGAGATAAGGTTTG
1 T---TTTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTG
*
63776833 TTTTGATCTGCTTTACTGCAACTTCAGAGAGATAAGATCTG
1 TTTTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTG
63776874 TTT
1 TTT
63776877 ATTCATAGCT
Statistics
Matches: 70, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
41 37 0.53
44 33 0.47
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.36
Consensus pattern (41 bp):
TTTTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTG
Found at i:63777105 original size:68 final size:68
Alignment explanation
Indices: 63776985--63777391 Score: 589
Period size: 68 Copynumber: 6.0 Consensus size: 68
63776975 TTCAATCTAC
* * * * * *
63776985 TCCGCTGAAACTTTAAGGAGATCTGCTGTGGCTTCGAGCCGTTCTAATGCCATTTCAGGGAGAAG
1 TCCGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAACGCCATTTCAGGGAGAAA
63777050 AGA
66 AGA
* * * *
63777053 TCCGCTGAAACTTCAAGGAGATTTGCTGTGGCTTCTAGCTGCTCCAACGCCATTTTAAGGAGAAA
1 TCCGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAACGCCATTTCAGGGAGAAA
63777118 AGAA
66 AG-A
* *
63777122 TCCGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCTAGTCGCTCCAACGCCATTTTAGGGAGAAA
1 TCCGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAACGCCATTTCAGGGAGAAA
*
63777187 AAA
66 AGA
** * * * *
63777190 TCCGCTGAAACTTCAAGGAGATCTATTATGGCTTTTAGCCGCTCCAACGCCATTTCAAGGAGAAG
1 TCCGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAACGCCATTTCAGGGAGAAA
63777255 AGA
66 AGA
* * * *
63777258 TTCGCTGAAACTTTAAGGAGATCTGTTGTGGCTTCTAGCCGTTCCAACGCCATTTCAGGGAGAAA
1 TCCGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAACGCCATTTCAGGGAGAAA
63777323 AGA
66 AGA
*
63777326 TCCGTTGAAACTTCAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAACGCCATTTCAGGGAGAAA
1 TCCGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAACGCCATTTCAGGGAGAAA
63777391 A
66 A
63777392 AATCTATAAT
Statistics
Matches: 301, Mismatches: 37, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
68 238 0.79
69 63 0.21
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (68 bp):
TCCGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAACGCCATTTCAGGGAGAAA
AGA
Found at i:63777472 original size:44 final size:42
Alignment explanation
Indices: 63777409--63777560 Score: 117
Period size: 44 Copynumber: 3.5 Consensus size: 42
63777399 AATTTTCAGC
63777409 CTGTTACCCTACTGCTTAGGGGGTCAAGGCTCATTGCCTTCAAT
1 CTGTTACCCTACTGCTTAGGGGGT-AA-GCTCATTGCCTTCAAT
* * * *** * **
63777453 CTGTTTCCCTACTGCTTAGGGTGATAAGATC-TGTAAATTTAGC
1 CTGTTACCCTACTGCTTAGGG-GGTAAGCTCAT-TGCCTTCAAT
* * *
63777496 CTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCGCCTTCGAT
1 CTGTTACCCTACTGCTTAGGGGG-T-AAGCTCATTGCCTTCAAT
* *
63777540 CTATTTCCCTACTGCTTAGGG
1 CTGTTACCCTACTGCTTAGGG
63777561 TGATAAGATC
Statistics
Matches: 80, Mismatches: 23, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
42 2 0.03
43 28 0.35
44 47 0.59
45 3 0.04
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.34
Consensus pattern (42 bp):
CTGTTACCCTACTGCTTAGGGGGTAAGCTCATTGCCTTCAAT
Found at i:63777707 original size:86 final size:86
Alignment explanation
Indices: 63777403--63777753 Score: 434
Period size: 87 Copynumber: 4.0 Consensus size: 86
63777393 ATCTATAATT
* * * * *
63777403 TTCAGCCTGTTACCCTACTGCTTAGGGGGTCAAGGCTCATTGCCTTCAATCTGTTTCCCTACTGC
1 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGCCTTCGATCTG-CTCCCTACTGC
*
63777468 TTAGGGTGATAAGATCTGTAAA
65 TTAGGGAGATAAGATCTGTAAA
* * **
63777490 TTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCGCCTTCGATCTATTTCCCTACTGC
1 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGCCTTCGATCT-GCTCCCTACTGC
* *
63777555 TTAGGGTGATAAGATCTGTAAT
65 TTAGGGAGATAAGATCTGTAAA
* * * * * *
63777577 TTCAACCTGTTACCCTACTACTTAGGAGGTTAAGGCCCATCGTCTTCGATCTGCTCCACCACTAC
1 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGCCTTCGATCTGCTCC-CTACTGC
*
63777642 TTAGGGAGACAAGATCTGT-AA
65 TTAGGGAGATAAGATCTGTAAA
* * * * *
63777663 TTCGGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACCGC
1 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGCCTTCGATCTGCTCC-CTACTGC
*
63777728 TTAGGGAGATAAGATCTGTGAA
65 TTAGGGAGATAAGATCTGTAAA
63777750 TTCA
1 TTCA
63777754 CCGATGTTGC
Statistics
Matches: 229, Mismatches: 32, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
86 78 0.34
87 151 0.66
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.31
Consensus pattern (86 bp):
TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGCCTTCGATCTGCTCCCTACTGCT
TAGGGAGATAAGATCTGTAAA
Found at i:63777972 original size:66 final size:66
Alignment explanation
Indices: 63777811--63778010 Score: 334
Period size: 66 Copynumber: 3.1 Consensus size: 66
63777801 TTCATGTATC
* * *
63777811 TATGCTTATGCCAAATAATTAGGATACTATGATC-AGAATGAATCAAATGCTCCTAACTAGATGT
1 TATGCTTGTGTCAAATAATTAGGATGCTATGATCGA-AATGAATCAAATGCTCCTAACTAGATGT
63777875 G-
65 GT
63777876 -ATGCTTGTGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
1 TATGCTTGTGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
63777940 T
66 T
*
63777941 TATGCTTGTGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAATTAGATGTG
1 TATGCTTGTGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
63778006 T
66 T
63778007 TATG
1 TATG
63778011 AATGATATAT
Statistics
Matches: 128, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
64 59 0.46
65 1 0.01
66 68 0.53
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (66 bp):
TATGCTTGTGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
T
Found at i:63783074 original size:3 final size:3
Alignment explanation
Indices: 63783068--63783251 Score: 90
Period size: 3 Copynumber: 61.3 Consensus size: 3
63783058 GAAGAAAACG
* * * * * * *
63783068 ATA ATA ATA ATA ATA ATG TTG ATA ATA ATA ATA GTA GTA GTA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
63783116 ATA ATA CTA ATG ATA ATA ATA A-A AGTA ATA ATA AGA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA
* * * * * * * *
63783161 TTA GTA TTA ATA ATA ATG ATA ATA GTA ATA GAAA AAA ATA A-A AAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
* * *
63783206 ATA A-A AAA AGTA ATA GTA ATA A-A AGTGA AT- ATA ATA GTA ATA ATA
1 ATA ATA ATA A-TA ATA ATA ATA ATA A-T-A ATA ATA ATA ATA ATA ATA
63783251 A
1 A
63783252 CGGTAAATAC
Statistics
Matches: 139, Mismatches: 32, Indels: 20
0.73 0.17 0.10
Matches are distributed among these distances:
2 10 0.07
3 120 0.86
4 7 0.05
5 2 0.01
ACGTcount: A:0.60, C:0.01, G:0.09, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:63783260 original size:24 final size:22
Alignment explanation
Indices: 63783216--63783270 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 22
63783206 ATAAAAAAAG
*
63783216 TAATAGTAATAAAAGTGAATA-
1 TAATAGTAATAAAAGTAAATAC
63783237 TAATAGTAATAATAACGGTAAATAC
1 TAATAGTAATAA-AA--GTAAATAC
*
63783262 AAATAGTAA
1 TAATAGTAA
63783271 CAACAATGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 12 0.43
22 2 0.07
24 6 0.21
25 8 0.29
ACGTcount: A:0.56, C:0.04, G:0.13, T:0.27
Consensus pattern (22 bp):
TAATAGTAATAAAAGTAAATAC
Found at i:63783463 original size:3 final size:3
Alignment explanation
Indices: 63783457--63783941 Score: 246
Period size: 3 Copynumber: 162.3 Consensus size: 3
63783447 AAAAAAAAAT
63783457 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
63783505 ATA ATA ATA ATA ATA TTA GTA ATA ATA ATA ATA AGA AGA AGA AGAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA
* * * * * * *
63783551 ATA AGA GTA CATTA ATA ATG ATA GTA TATG TTA ATA ACA ATA ATA ATA
1 ATA ATA ATA -A-TA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA
* * *
63783599 TATA AAA ATA GGA-A ATA ATA AT- ATG GTA ATA ATA ATA ATA ATA ATA
1 -ATA ATA ATA --ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * * *
63783645 ACA AAA ATA GTA ATA ATA GTA TGTG A-A ATA ATA ATT GTA A-A A-A
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * *
63783688 ATA ATA GTA ATA ATT ATA TTG ATA ATA CTA ATA ATA ATA GTA GTA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
63783735 AAA ATA A-A A-A AT- ATA A-A ATA ATA ATA ATA ATA GTA AAA ATG ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
63783779 ATA A-A ATA A-G ATA ATA ATA ATG ATA ATA ATA A-A AAA ATA A-A AAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* ** * * *
63783823 AGTA ATA ATG GCA ATA ATA ATA ATA CCATA ATA A-A AGA AAA AGAA ATA
1 A-TA ATA ATA ATA ATA ATA ATA ATA --ATA ATA ATA ATA ATA A-TA ATA
* * * * * *
63783871 ATA ACA TGTAA ATA ATA ATA ACA ATA ATA ACA ATA AT- ATA TTT ATA
1 ATA ATA -AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
63783917 ATA ATA ATA ATA GTA AAA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
63783942 AATTAACTAA
Statistics
Matches: 365, Mismatches: 89, Indels: 56
0.72 0.17 0.11
Matches are distributed among these distances:
2 29 0.08
3 313 0.86
4 16 0.04
5 7 0.02
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:63783762 original size:37 final size:38
Alignment explanation
Indices: 63783716--63783943 Score: 135
Period size: 40 Copynumber: 5.7 Consensus size: 38
63783706 TTGATAATAC
*
63783716 TAATAATAATAGTAGTAAAAAAATAAAAAATATA-A-AA
1 TAATAATAATAATAGTAAAAAAATAAAAAATA-AGATAA
* *
63783753 TAATAATAATAATAGTAAAAATGACAATAAAATAAGATAA
1 TAATAATAATAATAGTAAAAA-AATAA-AAAATAAGATAA
* *
63783793 TAATAATGATAATAATAAAAAAAT-AAAAA-AAG-TAA
1 TAATAATAATAATAGTAAAAAAATAAAAAATAAGATAA
* ** * *
63783828 TAATGGCAATAATAATAATACCATAATAAAAGAAAAAGA-AA
1 TAAT---AATAATAATAGTAAAAAAATAAAA-AATAAGATAA
* * * * *
63783869 TAATAACATGTAAATAATAATAACAATAATAACAATAATATATTTA
1 TAATAATA-AT-AATAGTAA-AAAAATAA-AA-AATAAGATA---A
63783915 TAATAATAATAATAGTAAAAATAATAAAA
1 TAATAATAATAATAGTAAAAA-AATAAAA
63783944 TTAACTAATT
Statistics
Matches: 148, Mismatches: 23, Indels: 34
0.72 0.11 0.17
Matches are distributed among these distances:
35 7 0.05
36 3 0.02
37 24 0.16
38 24 0.16
39 12 0.08
40 30 0.20
41 15 0.10
42 7 0.05
43 5 0.03
44 12 0.08
45 1 0.01
46 8 0.05
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.25
Consensus pattern (38 bp):
TAATAATAATAATAGTAAAAAAATAAAAAATAAGATAA
Found at i:63783839 original size:41 final size:43
Alignment explanation
Indices: 63783794--63783874 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
63783784 ATAAGATAAT
* * *
63783794 AATAATGATAATA-ATAAAAAAATAAAAA-AAGTAATAATGGC
1 AATAATAATAATACATAAAAAAAGAAAAAGAAATAATAATGGC
*
63783835 AATAATAATAATACCATAATAAAAGAAAAAGAAATAATAA
1 AATAATAATAATA-CATAAAAAAAGAAAAAGAAATAATAA
63783875 CATGTAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 12 0.36
43 13 0.39
44 8 0.24
ACGTcount: A:0.68, C:0.04, G:0.07, T:0.21
Consensus pattern (43 bp):
AATAATAATAATACATAAAAAAAGAAAAAGAAATAATAATGGC
Found at i:63784186 original size:23 final size:23
Alignment explanation
Indices: 63784160--63784204 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
63784150 AATTGCAGGG
*
63784160 TAAAATTAAAAATAATAAAAAAA
1 TAAAATTAAAAACAATAAAAAAA
* *
63784183 TAAATTTCAAAACAATAAAAAA
1 TAAAATTAAAAACAATAAAAAA
63784205 GCAGAAGGGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (23 bp):
TAAAATTAAAAACAATAAAAAAA
Found at i:63788342 original size:14 final size:13
Alignment explanation
Indices: 63788310--63788345 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
63788300 AAAGTCTCAT
63788310 TTATTTATTTTTA
1 TTATTTATTTTTA
*
63788323 TCATTTATTTTTA
1 TTATTTATTTTTA
63788336 TATATTTATT
1 T-TATTTATT
63788346 ATATAAATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (13 bp):
TTATTTATTTTTA
Found at i:63788465 original size:19 final size:18
Alignment explanation
Indices: 63788441--63788490 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
63788431 TTCACTTAAA
* *
63788441 TTAATTATTTGTTTTAATT
1 TTAATTATTT-TTTGAAAT
63788460 TTAATTTATTTTTTGAAAT
1 TTAA-TTATTTTTTGAAAT
*
63788479 ATAATTATTTTT
1 TTAATTATTTTT
63788491 AATGAATACT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 8 0.30
19 13 0.48
20 6 0.22
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (18 bp):
TTAATTATTTTTTGAAAT
Found at i:63788713 original size:24 final size:24
Alignment explanation
Indices: 63788686--63788731 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
63788676 ATATAATCTA
63788686 TAATATAATAATA-ATTATATATAG
1 TAATA-AATAATATATTATATATAG
* *
63788710 TAATACATTATATATTATATAT
1 TAATAAATAATATATTATATAT
63788732 TAATTATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (24 bp):
TAATAAATAATATATTATATATAG
Found at i:63788722 original size:17 final size:16
Alignment explanation
Indices: 63788674--63788738 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 16
63788664 CTATATCTTT
63788674 TAAT-ATAATCTATAATA
1 TAATAATAAT-TAT-ATA
63788691 TAATAATAATTATATA
1 TAATAATAATTATATA
*
63788707 TAGTAATACATTATATA
1 TAATAATA-ATTATATA
*
63788724 TTATATATTAATTAT
1 -TA-ATAATAATTAT
63788739 TATTGTTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
16 10 0.24
17 15 0.37
18 12 0.29
19 4 0.10
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (16 bp):
TAATAATAATTATATA
Found at i:63788978 original size:17 final size:17
Alignment explanation
Indices: 63788956--63788990 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
63788946 ATAGTAGTAC
63788956 ATTATATATTACATATT
1 ATTATATATTACATATT
*
63788973 ATTATATATTATATATT
1 ATTATATATTACATATT
63788990 A
1 A
63788991 CTGTTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTATATATTACATATT
Found at i:63788984 original size:24 final size:25
Alignment explanation
Indices: 63788956--63789008 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
63788946 ATAGTAGTAC
63788956 ATTATATATTACAT-ATTATTA-TAT
1 ATTATATATTAC-TGATTATTATTAT
*
63788980 ATTATATATTACTGTTTATTATTAT
1 ATTATATATTACTGATTATTATTAT
63789005 ATTA
1 ATTA
63789009 GTTGAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 1 0.04
24 18 0.69
25 7 0.27
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (25 bp):
ATTATATATTACTGATTATTATTAT
Found at i:63789195 original size:16 final size:16
Alignment explanation
Indices: 63789174--63789226 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
63789164 TAATCCATAT
63789174 TATAATAATAGTTATA
1 TATAATAATAGTTATA
*
63789190 TATAATAGTAGTATATTA
1 TATAATAATAGT-TA-TA
* * *
63789208 TATATTACTTGTTATA
1 TATAATAATAGTTATA
63789224 TAT
1 TAT
63789227 TATTATTTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
16 16 0.52
17 4 0.13
18 11 0.35
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.49
Consensus pattern (16 bp):
TATAATAATAGTTATA
Found at i:63789212 original size:248 final size:246
Alignment explanation
Indices: 63788713--63789370 Score: 673
Period size: 248 Copynumber: 2.7 Consensus size: 246
63788703 TATATAGTAA
* * * * *
63788713 TACATTATATATTATATATTA-ATTATTATTGTTTATAAATGTATTGGTTGAAATATACTCTAAA
1 TACA-TAT-TATTATATATTATA-TATTA-TGTTTATTATTATATTAGTTGAAATATACTCTAAG
* * * * * *
63788777 TCCCTATA-TTTTCCATGCGTATATGAAAGTTAGCCCTCTTATCATATTATATAATACTATAT--
62 TCCATATACTTTT-CATAC--ATTTGAAAGATAGCCCTC--CT-ATATTATATAATGCTATATCA
** * * * *
63788839 TATACCATATTAGTAGTTTATATATATACATAAATGGA-TAAACATTATAATGTTATGTAATATT
121 TATAATATATTAATAGTTTATATATATGCATAAAT-GATTAAACATTATAATATCATGTAATATT
*
63788903 ATATCTTTTATTATAATATATAATATAATAATAGTTATATATAATAGTAGTACATTATATAT
185 ATATCTTTTATTATAATACATAATATAATAATAGTTATATATAATAGTAGTACATTATATAT
63788965 TACATATTATTATATATTATATATTACTGTTTATTATTATATTAGTTGAAATATACTCTAAGTCC
1 TACATATTATTATATATTATATATTA-TGTTTATTATTATATTAGTTGAAATATACTCTAAGTCC
* *
63789030 ATATACTTTTCATACATTTGGAAGATAGCACTCCTATATTATATAATGCTATATCATATAATATA
65 ATATACTTTTCATACATTTGAAAGATAGCCCTCCTATATTATATAATGCTATATCATATAATATA
63789095 TTAATAGTTTATATATATGCATAAATGATTAAACATTATAATATCATGTAATACTATATAT-TTT
130 TTAATAGTTTATATATATGCATAAATGATTAAACATTATAATATCATGTAATA-T-TATATCTTT
* * *
63789159 TATTATAATCCATATTATAATAATAGTTATATATAATAGTAGTATATTATATAT
193 TATTATAATACATAATATAATAATAGTTATATATAATAGTAGTACATTATATAT
* * ** ** **
63789213 TAC---TT-GT-TATA-TAT-TATTA--TTTACTATTATGCTAGTTGAAATATGTTCTAAGTCTT
1 TACATATTATTATATATTATATATTATGTTTATTATTATATTAGTTGAAATATACTCTAAGTCCA
* * * * * *
63789269 TATACTTCTCATACATTT-AAAAATTAGCCCTCCTACTACATTTTATAAGGTTATATCATATCAT
66 TATACTTTTCATACATTTGAAAGA-TAGCCCTCCTA-T--ATTATATAATGCTATATCATATAAT
**
63789333 ATATTAATAGTTTATACATATATGCATTGATGATTAAA
127 ATATTAATAGTTTAT--ATATATGCATAAATGATTAAA
63789371 GTCGAGCTTT
Statistics
Matches: 351, Mismatches: 42, Indels: 35
0.82 0.10 0.08
Matches are distributed among these distances:
237 3 0.01
238 57 0.16
239 1 0.00
241 41 0.12
242 3 0.01
243 23 0.07
244 1 0.00
245 20 0.06
246 3 0.01
247 53 0.15
248 71 0.20
249 5 0.01
250 58 0.17
251 8 0.02
252 4 0.01
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.45
Consensus pattern (246 bp):
TACATATTATTATATATTATATATTATGTTTATTATTATATTAGTTGAAATATACTCTAAGTCCA
TATACTTTTCATACATTTGAAAGATAGCCCTCCTATATTATATAATGCTATATCATATAATATAT
TAATAGTTTATATATATGCATAAATGATTAAACATTATAATATCATGTAATATTATATCTTTTAT
TATAATACATAATATAATAATAGTTATATATAATAGTAGTACATTATATAT
Found at i:63789631 original size:20 final size:20
Alignment explanation
Indices: 63789591--63789643 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
63789581 TTTAGATTTT
**
63789591 TTTAAATTAAAAATATTAAA
1 TTTAAATTAAAAATAGAAAA
63789611 TTTAAATTAAAAATAGAAAA
1 TTTAAATTAAAAATAGAAAA
63789631 TTATAATATTAAA
1 TT-TAA-ATTAAA
63789644 CATTTCAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 20 0.69
21 3 0.10
22 6 0.21
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
TTTAAATTAAAAATAGAAAA
Found at i:63790205 original size:19 final size:19
Alignment explanation
Indices: 63790140--63790205 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
63790130 TTTTGTAAAT
63790140 TTTAT-TTTTATATATTT-
1 TTTATATTTTATATATTTA
* *
63790157 TTAATAATTTATATATATATA
1 TTTAT-ATTT-TATATATTTA
*
63790178 TTTAGATTTTATATATTTA
1 TTTATATTTTATATATTTA
*
63790197 TTTCTATTT
1 TTTATATTT
63790206 CCATTTTTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
17 4 0.11
19 19 0.50
20 12 0.32
21 3 0.08
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTATATTTTATATATTTA
Found at i:63804954 original size:23 final size:24
Alignment explanation
Indices: 63804922--63804976 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 24
63804912 TGCATTTTGG
*
63804922 TTTTG-TTGCTTCTCTGCTT-ATT
1 TTTTGATTGCTTCTCTACTTGATT
*
63804944 TTTTGATTGCTTCTCTACTTGTTT
1 TTTTGATTGCTTCTCTACTTGATT
63804968 TTTTGATTG
1 TTTTGATTG
63804977 GTTTTTATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 5 0.17
23 13 0.45
24 11 0.38
ACGTcount: A:0.07, C:0.15, G:0.15, T:0.64
Consensus pattern (24 bp):
TTTTGATTGCTTCTCTACTTGATT
Found at i:63808395 original size:12 final size:11
Alignment explanation
Indices: 63808376--63808407 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
63808366 AACATAAATG
63808376 CATTTTTTTTT
1 CATTTTTTTTT
63808387 CACTTTTTTTTT
1 CA-TTTTTTTTT
63808399 CATTTTTTT
1 CATTTTTTT
63808408 GAGAACAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.78
Consensus pattern (11 bp):
CATTTTTTTTT
Found at i:63809541 original size:5 final size:5
Alignment explanation
Indices: 63809531--63809582 Score: 59
Period size: 5 Copynumber: 9.6 Consensus size: 5
63809521 TAAGAATAAT
*
63809531 AAATA AAATA AAATA AATTAGTA AAATA AAAAA TAAATA AAATA AAATA
1 AAATA AAATA AAATA AA--A-TA AAATA AAATA -AAATA AAATA AAATA
63809580 AAA
1 AAA
63809583 ATAGGGTGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 31 0.76
6 5 0.12
7 1 0.02
8 4 0.10
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:63813686 original size:132 final size:131
Alignment explanation
Indices: 63813407--63813736 Score: 387
Period size: 132 Copynumber: 2.5 Consensus size: 131
63813397 ACTTAAAACT
* * * *
63813407 TCTTGAAAACGAAGGCGAGATTTGATATTTGGCAACTCGCGGAATCGTGCCCTAACGTGCTGGAT
1 TCTTGAAAACAAAGGCGAGACTTGATATTTGGCAATTCG-GGAATCGTGCCCTAACGTGCTGGGT
* *
63813472 TGCAAATTCGCGTTTGCTTAAAATAATCAAATGTCCCTTCAAAATTTCATCCATGTCTTCTAAAA
65 TGCAAATTCGCGTTTGCTCAAAATAATCAAATATCCCTTCAAAATTTCATCCATGTCTTCTAAAA
63813537 AG
130 AG
* * * *
63813539 TCTTGAAAACGAAGGCGAGGCTTGATATTTGGCAATTCGTAGAATCGTGCCCTAACGTGTTGGGT
1 TCTTGAAAACAAAGGCGAGACTTGATATTTGGCAATTCG-GGAATCGTGCCCTAACGTGCTGGGT
* ** *
63813604 TGC-AATTCCTCGTTTGCTCAAAATGTTCAAATATCCCTTCAAAATTTTA-CTCATGTCTTCTAA
65 TGCAAATT-CGCGTTTGCTCAAAATAATCAAATATCCCTTCAAAATTTCATC-CATGTCTTCTAA
63813667 AAA-
128 AAAG
* * * * * * * * *
63813670 TCCTTTAAGACAAAGGCAATACTCGGTATTTGACAATTCGGGAATCATGCCCTATCGTGCTGGGT
1 T-CTTGAAAACAAAGGCGAGACTTGATATTTGGCAATTCGGGAATCGTGCCCTAACGTGCTGGGT
63813735 TG
65 TG
63813737 TGATTTCTTG
Statistics
Matches: 169, Mismatches: 26, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
131 29 0.17
132 140 0.83
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (131 bp):
TCTTGAAAACAAAGGCGAGACTTGATATTTGGCAATTCGGGAATCGTGCCCTAACGTGCTGGGTT
GCAAATTCGCGTTTGCTCAAAATAATCAAATATCCCTTCAAAATTTCATCCATGTCTTCTAAAAA
G
Found at i:63813817 original size:131 final size:131
Alignment explanation
Indices: 63813516--63813893 Score: 282
Period size: 131 Copynumber: 2.9 Consensus size: 131
63813506 CCCTTCAAAA
* * * * ** * *
63813516 TTTCATCCATGTCTTCTAAAAAGT-CTTGAAAACGAAGGCGAGGCTTGATATTTGGCAATTCGTA
1 TTTCATTCATGTCTTCTAAAAA-TCCTTTAAAACAAAGGCAATACTCGATATTTGACAATTCG-A
* * * * ** * *** * *
63813580 GAATC-GTGCCCTAACGTGTTGGGTTGCAATTCCTCGTTTGCTCAAAATGTTCAAATATCCCTTC
64 GAATCAG-GCCCTATCGTGCTGGGTTGCACTTTCTTATTTGTTCAAAACAATCGAATATTCCTT-
* **
63813644 AAAAT
127 TAGGT
* * * *
63813649 TTT-ACTCATGTCTTCTAAAAATCCTTTAAGACAAAGGCAATACTCGGTATTTGACAATTCGGGA
1 TTTCATTCATGTCTTCTAAAAATCCTTTAAAACAAAGGCAATACTCGATATTTGACAATTCGAGA
* * *
63813713 ATCATGCCCTATCGTGCTGGGTTGTGA-TTTCTTGTTTGTTCAAAACAATCGAATATTCCTTTAG
66 ATCAGGCCCTATCGTGCTGGGTTG-CACTTTCTTATTTGTTCAAAACAATCGAATATTCCTTTAG
63813777 GT
130 GT
* * ** * * * *
63813779 TTTCATTCATGT-TTACTAAAAA-CCTTTCAAAACGAAGGCGATGTTCGATGTTTGGCGATTTGA
1 TTTCATTCATGTCTT-CTAAAAATCCTTT-AAAACAAAGGCAATACTCGATATTTGACAATTCGA
* * *
63813842 GAATCGGGCCCTATCGTGCTGGGTTGCACTTTTTTATTTTTTCAAAACAATC
64 GAATCAGGCCCTATCGTGCTGGGTTGCACTTTCTTATTTGTTCAAAACAATC
63813894 AAAGATCCCT
Statistics
Matches: 193, Mismatches: 45, Indels: 16
0.76 0.18 0.06
Matches are distributed among these distances:
130 13 0.07
131 131 0.68
132 46 0.24
133 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (131 bp):
TTTCATTCATGTCTTCTAAAAATCCTTTAAAACAAAGGCAATACTCGATATTTGACAATTCGAGA
ATCAGGCCCTATCGTGCTGGGTTGCACTTTCTTATTTGTTCAAAACAATCGAATATTCCTTTAGG
T
Found at i:63817459 original size:44 final size:41
Alignment explanation
Indices: 63817409--63817559 Score: 133
Period size: 42 Copynumber: 3.5 Consensus size: 41
63817399 TATGTGATTT
63817409 CGTGTAAGACCACGTCTGGGACACTGGCATCGATTTGAGAATTA
1 CGTGTAAGACCACGTCTGGGACA-TGGCATCGATTT--GAATTA
* * ** *
63817453 CGTGTAAGACCATGTTTGGGACATCAACATCGTATTTG-ATTT
1 CGTGTAAGACCACGTCTGGGACAT-GGCATCG-ATTTGAATTA
** * *
63817495 CGTGTAAGACCTTGTCTGGGATAGTGGCATCGATATTTAATTA
1 CGTGTAAGACCACGTCTGGGACA-TGGCATCGAT-TTGAATTA
* *
63817538 CATGTAAGACCACATCTGGGAC
1 CGTGTAAGACCACGTCTGGGAC
63817560 GTTAACATTG
Statistics
Matches: 85, Mismatches: 17, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
41 2 0.02
42 30 0.35
43 23 0.27
44 26 0.31
45 4 0.05
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.30
Consensus pattern (41 bp):
CGTGTAAGACCACGTCTGGGACATGGCATCGATTTGAATTA
Found at i:63817515 original size:42 final size:41
Alignment explanation
Indices: 63817403--63817515 Score: 120
Period size: 44 Copynumber: 2.7 Consensus size: 41
63817393 TTTCGATATG
* **
63817403 TGATTTCGTGTAAGACCACGTCTGGGACACTGGCATCGATT
1 TGATTTCGTGTAAGACCATGTCTGGGACACTAACATCGATT
* *
63817444 TGAGAATTACGTGTAAGACCATGTTTGGGACA-TCAACATCGTATT
1 T--G-ATTTCGTGTAAGACCATGTCTGGGACACT-AACATCG-ATT
*
63817489 TGATTTCGTGTAAGACCTTGTCTGGGA
1 TGATTTCGTGTAAGACCATGTCTGGGA
63817516 TAGTGGCATC
Statistics
Matches: 59, Mismatches: 8, Indels: 9
0.78 0.11 0.12
Matches are distributed among these distances:
41 1 0.02
42 22 0.37
43 3 0.05
44 29 0.49
45 4 0.07
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.32
Consensus pattern (41 bp):
TGATTTCGTGTAAGACCATGTCTGGGACACTAACATCGATT
Found at i:63817526 original size:42 final size:41
Alignment explanation
Indices: 63817403--63817559 Score: 136
Period size: 43 Copynumber: 3.7 Consensus size: 41
63817393 TTTCGATATG
* *
63817403 TGATTTCGTGTAAGACCACGTCTGGGACACTGGCATCG-ATT
1 TGATTACGTGTAAGACCATGTCTGGGACA-TGGCATCGTATT
* **
63817444 TGAGAATTACGTGTAAGACCATGTTTGGGACATCAACATCGTATT
1 T--G-ATTACGTGTAAGACCATGTCTGGGACAT-GGCATCGTATT
* * *
63817489 TGATTTCGTGTAAGACCTTGTCTGGGATAGTGGCATCGATATT
1 TGATTACGTGTAAGACCATGTCTGGGACA-TGGCATCG-TATT
* * **
63817532 TAATTACATGTAAGACCACATCTGGGAC
1 TGATTACGTGTAAGACCATGTCTGGGAC
63817560 GTTAACATTG
Statistics
Matches: 91, Mismatches: 18, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
41 1 0.01
42 28 0.31
43 29 0.32
44 29 0.32
45 4 0.04
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (41 bp):
TGATTACGTGTAAGACCATGTCTGGGACATGGCATCGTATT
Found at i:63819191 original size:16 final size:17
Alignment explanation
Indices: 63819170--63819202 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
63819160 GAAAAGAGCG
63819170 AAAG-AAGAGAAAAGTT
1 AAAGAAAGAGAAAAGTT
*
63819186 AAAGAAAGAGCAAAGTT
1 AAAGAAAGAGAAAAGTT
63819203 TCGGCAAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.61, C:0.03, G:0.24, T:0.12
Consensus pattern (17 bp):
AAAGAAAGAGAAAAGTT
Found at i:63829422 original size:19 final size:20
Alignment explanation
Indices: 63829398--63829436 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
63829388 TCTTATTTTT
63829398 TATTTGTTTTT-TGTTTTAA
1 TATTTGTTTTTATGTTTTAA
63829417 TATTTGTTTTTATGTTTTAA
1 TATTTGTTTTTATGTTTTAA
63829437 ATGTATTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.18, C:0.00, G:0.10, T:0.72
Consensus pattern (20 bp):
TATTTGTTTTTATGTTTTAA
Found at i:63829454 original size:25 final size:23
Alignment explanation
Indices: 63829398--63829462 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 23
63829388 TCTTATTTTT
*
63829398 TATTTGTTTTT-TGTTTT-AA--
1 TATTTGTTTTTATATTTTAAATG
*
63829417 TATTTGTTTTTATGTTTTAAATG
1 TATTTGTTTTTATATTTTAAATG
63829440 TATTTGATTTATTATATTTTAAA
1 TATTTG-TTT-TTATATTTTAAA
63829463 GTTTTTTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
19 11 0.28
20 6 0.15
21 2 0.05
23 6 0.15
24 3 0.08
25 11 0.28
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (23 bp):
TATTTGTTTTTATATTTTAAATG
Found at i:63829854 original size:13 final size:13
Alignment explanation
Indices: 63829836--63829862 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
63829826 CGAGGGAATA
63829836 ACGTCTGATATGC
1 ACGTCTGATATGC
63829849 ACGTCTGATATGC
1 ACGTCTGATATGC
63829862 A
1 A
63829863 TAACTTTATT
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:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (13 bp):
ACGTCTGATATGC
Found at i:63838403 original size:23 final size:23
Alignment explanation
Indices: 63838361--63838411 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
63838351 CTTTGAGAGT
* *
63838361 TTTTCCTCTGCTACTGTAGCTCG
1 TTTTCCTCTGCTACTATAGCACG
63838384 TTTTCCTCTGCTTA-TATAGCACG
1 TTTTCCTCTGC-TACTATAGCACG
63838407 TTTTC
1 TTTTC
63838412 TAGGTTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.12, C:0.27, G:0.14, T:0.47
Consensus pattern (23 bp):
TTTTCCTCTGCTACTATAGCACG
Found at i:63842596 original size:21 final size:21
Alignment explanation
Indices: 63842570--63842615 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
63842560 GGGATTTGAT
63842570 TGACTTACTTTTTATAGCTGC
1 TGACTTACTTTTTATAGCTGC
63842591 TGACTTACTTTTTATAGCTGC
1 TGACTTACTTTTTATAGCTGC
63842612 TGAC
1 TGAC
63842616 GCAATCCTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.46
Consensus pattern (21 bp):
TGACTTACTTTTTATAGCTGC
Found at i:63846520 original size:17 final size:17
Alignment explanation
Indices: 63846500--63846532 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
63846490 ATTATTTTAA
63846500 TATT-TATATTATAGTAG
1 TATTATATATT-TAGTAG
63846517 TATTATATATTTAGTA
1 TATTATATATTTAGTA
63846533 TATGTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (17 bp):
TATTATATATTTAGTAG
Found at i:63857078 original size:5 final size:5
Alignment explanation
Indices: 63857068--63857107 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
63857058 AATAATTAAG
63857068 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
63857108 ATAAAAGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:63858198 original size:12 final size:12
Alignment explanation
Indices: 63858181--63858205 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
63858171 GCCGACTACT
63858181 GTTACTGTTACC
1 GTTACTGTTACC
63858193 GTTACTGTTACC
1 GTTACTGTTACC
63858205 G
1 G
63858206 ATTTGACACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:63858247 original size:6 final size:6
Alignment explanation
Indices: 63858228--63858258 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
63858218 GTGTGTCGAA
*
63858228 TACTGT TACCGT TACTGT TACTGT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT T
63858259 TCGGATTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:63858500 original size:2 final size:2
Alignment explanation
Indices: 63858493--63858529 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
63858483 AATAAGAATG
*
63858493 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
63858530 ATCGAATGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:63859082 original size:15 final size:15
Alignment explanation
Indices: 63859064--63859111 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 15
63859054 AAATTTATAA
63859064 AAATAAAATAAAATT
1 AAATAAAATAAAATT
*
63859079 AAATAAAATAATAATA
1 AAATAAAATAA-AATT
63859095 ATAATAATAATAAAATT
1 A-AATAA-AATAAAATT
63859112 GGAATACTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 11 0.39
16 4 0.14
17 8 0.29
18 5 0.18
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATAAAATAAAATT
Found at i:63859093 original size:3 final size:3
Alignment explanation
Indices: 63859060--63859107 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
63859050 GTCGAAATTT
* *
63859060 ATA AAA ATA A-A ATA A-A ATT A-A ATA A-A ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
63859104 ATA A
1 ATA A
63859108 AATTGGAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 7 0.19
3 30 0.81
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:63860491 original size:17 final size:17
Alignment explanation
Indices: 63860447--63860482 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
63860437 CTTGATTATT
* *
63860447 AAAATTTTAAAATTAAA
1 AAAAATTTAAAAATAAA
63860464 AAAAATTTAAAAATAAA
1 AAAAATTTAAAAATAAA
63860481 AA
1 AA
63860483 TTATTTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAAATTTAAAAATAAA
Found at i:63861152 original size:24 final size:24
Alignment explanation
Indices: 63861122--63861170 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
63861112 AATTTGGAAA
63861122 AATACCCATAGGTGAAATTTGTGT
1 AATACCCATAGGTGAAATTTGTGT
63861146 AATACCCATAGGTGAAATTTGTGT
1 AATACCCATAGGTGAAATTTGTGT
63861170 A
1 A
63861171 TTTTGATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (24 bp):
AATACCCATAGGTGAAATTTGTGT
Found at i:63861838 original size:46 final size:44
Alignment explanation
Indices: 63861784--63861893 Score: 139
Period size: 44 Copynumber: 2.5 Consensus size: 44
63861774 GACAGAACGA
*
63861784 AATGAGCCATGTAAGTCCATATTAGAAATATAGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATT--AAATATAGCATTGGAGACAGG
* * *
63861830 ATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAATATAGCATTGGAGACAGG
* **
63861874 AATAATTCATGTAAGTCCAT
1 AATGAGCCATGTAAGTCCAT
63861894 GTCAAAGACA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 34 0.61
46 22 0.39
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (44 bp):
AATGAGCCATGTAAGTCCATATTAAATATAGCATTGGAGACAGG
Found at i:63863869 original size:19 final size:19
Alignment explanation
Indices: 63863847--63863886 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
63863837 AAAAATAAAC
63863847 TTTTAAATAAATT-TTTATT
1 TTTTAAA-AAATTGTTTATT
*
63863866 TTTTAAAAATTTGTTTATT
1 TTTTAAAAAATTGTTTATT
63863885 TT
1 TT
63863887 GAATGCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTAAAAAATTGTTTATT
Found at i:63883091 original size:32 final size:32
Alignment explanation
Indices: 63883050--63883173 Score: 221
Period size: 32 Copynumber: 3.9 Consensus size: 32
63883040 AAAATTAACA
*
63883050 AATATGTAAAACTCATATCAAGCAAGAGTGTT
1 AATATGTAAAACTCACATCAAGCAAGAGTGTT
*
63883082 AATATGTAAAACTCACATCAAGCAAGCGTGTT
1 AATATGTAAAACTCACATCAAGCAAGAGTGTT
63883114 AATATGTAAAACTCACATCAAGCAAGAGTGTT
1 AATATGTAAAACTCACATCAAGCAAGAGTGTT
*
63883146 AATATTTAAAACTCACATCAAGCAAGAG
1 AATATGTAAAACTCACATCAAGCAAGAG
63883174 GACTTTGATT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 88 1.00
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.25
Consensus pattern (32 bp):
AATATGTAAAACTCACATCAAGCAAGAGTGTT
Found at i:63887789 original size:21 final size:21
Alignment explanation
Indices: 63887765--63887805 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
63887755 TTTTTTTCTA
63887765 TTTTTGAAT-AAATTTAAAATG
1 TTTTT-AATGAAATTTAAAATG
*
63887786 TTTTTAATGAAATTTTAAAT
1 TTTTTAATGAAATTTAAAAT
63887806 TATTATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (21 bp):
TTTTTAATGAAATTTAAAATG
Found at i:63893972 original size:26 final size:26
Alignment explanation
Indices: 63893936--63894066 Score: 217
Period size: 26 Copynumber: 5.0 Consensus size: 26
63893926 AATTCCCATT
*
63893936 ATGGAACATTTACCTAAACCATTATC
1 ATGGAACATTTACCTAACCCATTATC
*
63893962 ATGAAACATTTACCTAACCCATTATC
1 ATGGAACATTTACCTAACCCATTATC
*
63893988 ATGGAATATTTACCTAACCCATTATC
1 ATGGAACATTTACCTAACCCATTATC
* *
63894014 ATGGAATATTTACCTAATCCATTATC
1 ATGGAACATTTACCTAACCCATTATC
63894040 ATGGAACATTTACCTAACCCATTATC
1 ATGGAACATTTACCTAACCCATTATC
63894066 A
1 A
63894067 ATTTGTATCA
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 98 1.00
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.33
Consensus pattern (26 bp):
ATGGAACATTTACCTAACCCATTATC
Found at i:63901425 original size:87 final size:88
Alignment explanation
Indices: 63901316--63901504 Score: 281
Period size: 87 Copynumber: 2.2 Consensus size: 88
63901306 TTTATGATCA
* * * *
63901316 ATGAATTTGATATTAATGAAAAAGTATTATGCCTTTAGGAGGATTTGATTTTAGGCTTTTAGCAT
1 ATGAATTTGATAATAATAAAAAAGTATTATGACTTTAGGAGGATTTGATTTTAGGCTTTTAGCAC
63901381 ACATATTTTTT-CATATGTTCTT
66 ACATATTTTTTCCATATGTTCTT
* * *
63901403 ATGAATTTGATAATAATAAAAAAGTCTTGTGACTTTTGGAGGATTTGATTTTAGGCTTTTAGCAC
1 ATGAATTTGATAATAATAAAAAAGTATTATGACTTTAGGAGGATTTGATTTTAGGCTTTTAGCAC
*
63901468 ATATATTTTTTCCATATGTTCTT
66 ACATATTTTTTCCATATGTTCTT
* *
63901491 ATGAAGTCGATAAT
1 ATGAATTTGATAAT
63901505 TATTGCAATT
Statistics
Matches: 91, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
87 68 0.75
88 23 0.25
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.44
Consensus pattern (88 bp):
ATGAATTTGATAATAATAAAAAAGTATTATGACTTTAGGAGGATTTGATTTTAGGCTTTTAGCAC
ACATATTTTTTCCATATGTTCTT
Found at i:63910013 original size:31 final size:31
Alignment explanation
Indices: 63909973--63910031 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
63909963 AAATGGTAAT
63909973 TAAACTATTTAA-ATATTTTTATTTAAGTTAA
1 TAAACTATTTAATA-ATTTTTATTTAAGTTAA
* *
63910004 TAAATTATTTGATAATTTTTATTTAAGT
1 TAAACTATTTAATAATTTTTATTTAAGT
63910032 CATTGGGCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (31 bp):
TAAACTATTTAATAATTTTTATTTAAGTTAA
Found at i:63912127 original size:2 final size:2
Alignment explanation
Indices: 63912120--63912153 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
63912110 TTAACTAATG
*
63912120 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
63912154 GAAAATGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:63912279 original size:2 final size:2
Alignment explanation
Indices: 63912272--63912302 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
63912262 TAAAAGAAAA
*
63912272 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
63912303 ATAAATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:63915706 original size:33 final size:34
Alignment explanation
Indices: 63915669--63915747 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 34
63915659 TAGTCCGTTG
* *
63915669 GGATAGTAAACATGGAACAGAGAT-GGTCCACTA
1 GGATAGTAAACATAGAACAGAGATACGTCCACTA
** * *
63915702 GGATAGTAAGTATAGAACATAGATACGTCCGCTA
1 GGATAGTAAACATAGAACAGAGATACGTCCACTA
63915736 GGATAGTAAACA
1 GGATAGTAAACA
63915748 CAAGACAAAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
33 20 0.54
34 17 0.46
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (34 bp):
GGATAGTAAACATAGAACAGAGATACGTCCACTA
Found at i:63917311 original size:46 final size:46
Alignment explanation
Indices: 63917244--63917416 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 46
63917234 TGCAACCCGC
* *
63917244 CCATAAGCGAACTCGGACTCAAATCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
* * *
63917290 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * *
63917340 --ATCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
*
63917383 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC
63917417 AGATGCCCAA
Statistics
Matches: 105, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 1 0.01
45 3 0.03
46 58 0.55
47 27 0.26
48 4 0.04
49 1 0.01
50 3 0.03
51 3 0.03
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:63917364 original size:93 final size:93
Alignment explanation
Indices: 63917251--63917423 Score: 292
Period size: 93 Copynumber: 1.9 Consensus size: 93
63917241 CGCCCATAAG
* *
63917251 CGAACTCGGACTCAAATCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAAATCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
*
63917316 ACGAGTTCGGATGCCTAGTTACATATCA
66 ACGAGTTCAGATGCCTAGTTACATATCA
* * *
63917344 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAAATCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
63917409 ACGAGTTCAGATGCC
66 ACGAGTTCAGATGCC
63917424 CAAATATCCG
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAAATCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
ACGAGTTCAGATGCCTAGTTACATATCA
Found at i:63920394 original size:2 final size:2
Alignment explanation
Indices: 63920336--63920375 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
63920326 CATTACATAA
*
63920336 AT AT AT ACT -T AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
63920376 TAAAGATATG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.94
3 1 0.03
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:63920803 original size:3 final size:3
Alignment explanation
Indices: 63920783--63920874 Score: 159
Period size: 3 Copynumber: 31.0 Consensus size: 3
63920773 GTATATGCAT
* *
63920783 ATA ATA AAA AT- ATT 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
63920830 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
63920875 TGAAAATACA
Statistics
Matches: 85, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
2 2 0.02
3 83 0.98
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:63921378 original size:14 final size:16
Alignment explanation
Indices: 63921352--63921386 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
63921342 AAAAAAAGGA
63921352 GAGAAAGGGAGA-GGG
1 GAGAAAGGGAGAGGGG
63921367 GAGAAA-GGAGAGGGG
1 GAGAAAGGGAGAGGGG
63921382 GAGAA
1 GAGAA
63921387 GAGAAGGCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (16 bp):
GAGAAAGGGAGAGGGG
Found at i:63925113 original size:21 final size:21
Alignment explanation
Indices: 63925067--63925113 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
63925057 ATTGTCCTTT
*
63925067 CAACAAAGGATATATGAGGAA
1 CAACAAAGGATATATGAGAAA
*
63925088 GAACAAAGGATATATGAGAAA
1 CAACAAAGGATATATGAGAAA
63925109 CAACA
1 CAACA
63925114 GAAGTTTAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.55, C:0.11, G:0.21, T:0.13
Consensus pattern (21 bp):
CAACAAAGGATATATGAGAAA
Found at i:63925335 original size:20 final size:21
Alignment explanation
Indices: 63925307--63925346 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
63925297 ATGAATATAT
* *
63925307 ATTTGAGG-AGAAGATGCAAC
1 ATTTAAGGAAGAAAATGCAAC
63925327 ATTTAAGGAAGAAAATGCAA
1 ATTTAAGGAAGAAAATGCAA
63925347 GACTATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.47, C:0.07, G:0.25, T:0.20
Consensus pattern (21 bp):
ATTTAAGGAAGAAAATGCAAC
Found at i:63927487 original size:85 final size:84
Alignment explanation
Indices: 63927398--63927555 Score: 203
Period size: 85 Copynumber: 1.9 Consensus size: 84
63927388 TATTGGAGTA
* * * * * * *
63927398 AAAATATAATTTTATTATTTTAATAGTTT-ATATCTTTATAAATTTTAAAAGA-TTATATTAAAA
1 AAAATATAATTTTATT-TTTTAATAATTTAAAAT-TTTAAAAAATTTAAAAAATTTAAATAAAAA
63927461 TTTTATTATTTTTAAGGAAGTT
64 TTTT-TTATTTTTAAGGAAGTT
*
63927483 AAAATATAATTTTATTTTTTATTAATTTAAAATTTTAAAAAATTTAAAAAATTTAAATAAAAATT
1 AAAATATAATTTTATTTTTTAATAATTTAAAATTTTAAAAAATTTAAAAAATTTAAATAAAAATT
63927548 TTTTATTT
66 TTTTATTT
63927556 GAAAGAGGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
84 31 0.49
85 32 0.51
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (84 bp):
AAAATATAATTTTATTTTTTAATAATTTAAAATTTTAAAAAATTTAAAAAATTTAAATAAAAATT
TTTTATTTTTAAGGAAGTT
Found at i:63927531 original size:8 final size:9
Alignment explanation
Indices: 63927506--63927539 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
63927496 ATTTTTTATT
63927506 AATTT-AAA
1 AATTTAAAA
*
63927514 ATTTTAAAA
1 AATTTAAAA
63927523 AATTTAAAA
1 AATTTAAAA
63927532 AATTTAAA
1 AATTTAAA
63927540 TAAAAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 4 0.17
9 19 0.83
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
AATTTAAAA
Found at i:63928212 original size:26 final size:26
Alignment explanation
Indices: 63928182--63928232 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
63928172 TATATTATGA
63928182 TAAATAATATTAATCTTTATGATAAT
1 TAAATAATATTAATCTTTATGATAAT
* * *
63928208 TAAATAATATTTATTTTTGTGATAA
1 TAAATAATATTAATCTTTATGATAA
63928233 AATTATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (26 bp):
TAAATAATATTAATCTTTATGATAAT
Found at i:63928625 original size:2 final size:2
Alignment explanation
Indices: 63928618--63928650 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
63928608 AAAAATGTGA
63928618 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
63928651 AAAGGATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:63930741 original size:26 final size:26
Alignment explanation
Indices: 63930705--63930814 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
63930695 TGATACAAAT
63930705 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
63930731 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
63930757 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
63930783 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
63930809 TGATAA
1 TGATAA
63930815 GAATTTCATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:63932468 original size:27 final size:27
Alignment explanation
Indices: 63932427--63932538 Score: 161
Period size: 27 Copynumber: 4.1 Consensus size: 27
63932417 GAGGAAGCGT
*
63932427 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
63932454 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
63932481 TTTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
63932508 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
63932536 TCT
1 TCT
63932539 TTGTCACATT
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
27 72 0.96
28 3 0.04
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:63932645 original size:19 final size:22
Alignment explanation
Indices: 63932621--63932660 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
63932611 CTCCCCACAC
63932621 GGTGTA-A-GGTTGG-TATGGG
1 GGTGTATACGGTTGGATATGGG
63932640 GGTGTATACGGTTGGATATGG
1 GGTGTATACGGTTGGATATGG
63932661 TTGGGTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 6 0.33
22 5 0.28
ACGTcount: A:0.17, C:0.03, G:0.47, T:0.33
Consensus pattern (22 bp):
GGTGTATACGGTTGGATATGGG
Found at i:63933934 original size:46 final size:46
Alignment explanation
Indices: 63933809--63934118 Score: 417
Period size: 46 Copynumber: 7.0 Consensus size: 46
63933799 TTTGACATGA
* * * * * *
63933809 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
*** **
63933855 TGCCATGGTA--TTTCAACCATGGTCTTGTTCATTTCATATCACAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
63933899 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
63933945 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
63933991 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
63934037 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C---TCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
63934075 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
63934119 AGAGCACACT
Statistics
Matches: 238, Mismatches: 15, Indels: 22
0.87 0.05 0.08
Matches are distributed among these distances:
38 34 0.14
40 3 0.01
43 5 0.02
44 36 0.15
46 160 0.67
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:63934082 original size:38 final size:38
Alignment explanation
Indices: 63934031--63934106 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
63934021 ACATTTTATA
63934031 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
63934069 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
63934107 ATTTCATATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (38 bp):
TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
Found at i:63936270 original size:11 final size:11
Alignment explanation
Indices: 63936254--63936305 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
63936244 TATACTAAAT
63936254 AAATAATAATA
1 AAATAATAATA
*
63936265 AAATAAT-ATT
1 AAATAATAATA
* *
63936275 AAATATCTCATA
1 AAATA-ATAATA
*
63936287 AAATATTAATA
1 AAATAATAATA
63936298 AAATAATA
1 AAATAATA
63936306 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:63938242 original size:4 final size:4
Alignment explanation
Indices: 63938233--63938273 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
63938223 AAAAAGAAAA
63938233 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
63938274 GTTAGAATAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:63941304 original size:30 final size:30
Alignment explanation
Indices: 63941239--63941314 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
63941229 GGTAACCTTG
* * * *
63941239 ATATAATGTCAACTTGAGTGAGCAGCCCTG
1 ATATAATGTCAACTTGAGTAAACAACCCTA
*
63941269 TTATAATGTCAACTTGTA-TAAACAACCCTA
1 ATATAATGTCAACTTG-AGTAAACAACCCTA
*
63941299 ATATAATGTCAGCTTG
1 ATATAATGTCAACTTG
63941315 CGTATGCAAC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 37 0.97
31 1 0.03
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (30 bp):
ATATAATGTCAACTTGAGTAAACAACCCTA
Found at i:63944284 original size:26 final size:26
Alignment explanation
Indices: 63944248--63944357 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
63944238 CATGAAATTC
63944248 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
63944274 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
63944300 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
*
63944326 TTGTCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
63944352 TTATCA
1 TTATCA
63944358 ATTTGTATCA
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:63949167 original size:12 final size:12
Alignment explanation
Indices: 63949150--63949204 Score: 110
Period size: 12 Copynumber: 4.6 Consensus size: 12
63949140 AGTACTACCT
63949150 CGGCCTCGACCA
1 CGGCCTCGACCA
63949162 CGGCCTCGACCA
1 CGGCCTCGACCA
63949174 CGGCCTCGACCA
1 CGGCCTCGACCA
63949186 CGGCCTCGACCA
1 CGGCCTCGACCA
63949198 CGGCCTC
1 CGGCCTC
63949205 TTCCCCGAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.15, C:0.51, G:0.25, T:0.09
Consensus pattern (12 bp):
CGGCCTCGACCA
Found at i:63949508 original size:20 final size:21
Alignment explanation
Indices: 63949463--63949511 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 21
63949453 ACTATTATAT
*
63949463 TTATTATTATCCTATTTCACTG
1 TTATTATTAT-CTATTTCACTA
63949485 TTATTATTAT-TATTTCA-TCA
1 TTATTATTATCTATTTCACT-A
63949505 TTATTAT
1 TTATTAT
63949512 ACATATATGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 1 0.04
20 14 0.56
22 10 0.40
ACGTcount: A:0.27, C:0.12, G:0.02, T:0.59
Consensus pattern (21 bp):
TTATTATTATCTATTTCACTA
Found at i:63962003 original size:71 final size:71
Alignment explanation
Indices: 63961882--63962282 Score: 317
Period size: 71 Copynumber: 5.5 Consensus size: 71
63961872 GTTTTCCAAG
* * * * *
63961882 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGAGGCACGCTGAGGTAATTTCAATTTAT
63961947 GTTTCA
66 GTTTCA
* * * *
63961953 AAAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGGCACGCTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGAGGCACGCTGAGGTAATTTCAATTTAT
63962018 GCTTTTTAATTCA
66 G-----T--TTCA
* * * * *
63962031 TGAAAATCAGCTCATATTGCGAG-AGATGAGTTGAGCCTCAAGACACGTTGGGGTAATTTCAATT
1 --AAAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCGAGGCACGCTGAGGTAATTTCAATT
*
63962095 CATGTTTCA
63 TATGTTTCA
* * *
63962104 AAAATCAACTCATATTGCGAGAAGTGAGTTGAACC-CTGGGGTACGCTGAGGTAATTTCAATTCC
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GAGGCACGCTGAGGTAATTTCAATT--
* * *
63962168 CAT-TAAATCT
63 TATGT--TTCA
* * * * * *
63962178 AAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTTGCGGCACGCTAAGGTATTTTCAAATTCT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGAGGCACGCTGAGGTAATTTC-AATT-T
*
63962243 AT-CTT-A
64 ATGTTTCA
* * * *
63962249 AAGAGTCAATTCATATTACGAGAGGTGAGTTGAG
1 AA-AATCAACTCATATTGCGAGAAGTGAGTTGAG
63962283 TCTTTTAATT
Statistics
Matches: 266, Mismatches: 45, Indels: 37
0.76 0.13 0.11
Matches are distributed among these distances:
70 1 0.00
71 108 0.41
72 31 0.12
73 7 0.03
74 54 0.20
75 5 0.02
76 1 0.00
78 4 0.02
79 2 0.01
80 53 0.20
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (71 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGAGGCACGCTGAGGTAATTTCAATTTAT
GTTTCA
Found at i:63962155 original size:151 final size:146
Alignment explanation
Indices: 63961881--63962213 Score: 510
Period size: 151 Copynumber: 2.3 Consensus size: 146
63961871 TGTTTTCCAA
*
63961881 GAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTA
1 GAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTCA
*
63961946 TGTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGGCACGCTGAGGTATTTTC
66 TGTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGGCACGCTGAGGTAATTTC
** *
63962011 AATTTCTGCTTTTTAATTCAT
131 AA-TTC--C-CATTAAATC-T
* *
63962032 GAAAATCAGCTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGGGGTAATTTCAATTCA
1 GAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTCA
*
63962097 TGTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAACC-CTGGGGTACGCTGAGGTAATTT
66 TGTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAACCTC-GGGGCACGCTGAGGTAATTT
63962161 CAATTCCCATTAAATCT
130 CAATTCCCATTAAATCT
63962178 -AAAATC-GACTCATATTGCGAGAGGTGAGTTGAGCCT
1 GAAAATCAG-CTCATATTGCGAGAGGTGAGTTGAGCCT
63962214 TGCGGCACGC
Statistics
Matches: 171, Mismatches: 9, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
144 1 0.01
145 33 0.19
146 1 0.01
147 6 0.04
148 1 0.01
150 4 0.02
151 125 0.73
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (146 bp):
GAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTCA
TGTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGGCACGCTGAGGTAATTTC
AATTCCCATTAAATCT
Found at i:63962457 original size:219 final size:218
Alignment explanation
Indices: 63962185--63962651 Score: 898
Period size: 219 Copynumber: 2.1 Consensus size: 218
63962175 TCTAAAATCG
*
63962185 ACTCATATTGCGAGAGGTGAGTTGAGCCTTGCGGCACGCTAAGGTATTTTCAAATTCTATCTTAA
1 ACTCATGTTGCGAGAGGTGAGTTGAGCCTTGCGGCACGCTAAGGTATTTTCAAATTCTATCTTAA
63962250 AGAGTCAATTCATATTACGAGAGGTGAGTTGAGTCTTTTAATTTCTATTTTCAATTTCTGTCTTT
66 AGAGTCAATTCATATTACGAGAGGTGAGTTGAGTCTTTTAATTTCTATTTTCAATTTCTGTC-TT
*
63962315 TTTTGTTTTTTTCAAAGATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTTCGTTTTT
130 TTTTGTTTTTTTCAAAGATCAACTCATATTGCGAGAGGTGAGTTCAGCCTTTAATTTTCGTTTTT
63962380 CGAAATCTAATTTTCGAATTATTA
195 CGAAATCTAATTTTCGAATTATTA
63962404 ACTCATGTTGCGAGAGGTGAGTTGAGCCTTGCGGCACGCTAAGGTATTTTCAAATTCTATCTTAA
1 ACTCATGTTGCGAGAGGTGAGTTGAGCCTTGCGGCACGCTAAGGTATTTTCAAATTCTATCTTAA
63962469 AGAGTCAATTCATATTACGAGAGGTGAGTTGAGTCTTTTAATTTCTATTTTCAATTTCTGTCTTT
66 AGAGTCAATTCATATTACGAGAGGTGAGTTGAGTCTTTTAATTTCTATTTTCAATTTCTGTCTTT
63962534 TTTGTTTTTTTCAAAGATCAACTCATATTGCGAGAGGTGAGTTCAGCCTTTAATTTTCGTTTTTC
131 TTTGTTTTTTTCAAAGATCAACTCATATTGCGAGAGGTGAGTTCAGCCTTTAATTTTCGTTTTTC
*
63962599 GAAATCTACTTTTCGAATTATTA
196 GAAATCTAATTTTCGAATTATTA
63962622 ACTCATGTTGCGAGAGGTGAGTTGAGCCTT
1 ACTCATGTTGCGAGAGGTGAGTTGAGCCTT
63962652 TTAATTTCTA
Statistics
Matches: 245, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
218 119 0.49
219 126 0.51
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (218 bp):
ACTCATGTTGCGAGAGGTGAGTTGAGCCTTGCGGCACGCTAAGGTATTTTCAAATTCTATCTTAA
AGAGTCAATTCATATTACGAGAGGTGAGTTGAGTCTTTTAATTTCTATTTTCAATTTCTGTCTTT
TTTGTTTTTTTCAAAGATCAACTCATATTGCGAGAGGTGAGTTCAGCCTTTAATTTTCGTTTTTC
GAAATCTAATTTTCGAATTATTA
Found at i:63963408 original size:14 final size:14
Alignment explanation
Indices: 63963389--63963422 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
63963379 CTAAACCCGA
63963389 AGCCCAACTACCCC
1 AGCCCAACTACCCC
63963403 AGCCCAACTACCCC
1 AGCCCAACTACCCC
63963417 AGCCCA
1 AGCCCA
63963423 TCTGCAACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.29, C:0.56, G:0.09, T:0.06
Consensus pattern (14 bp):
AGCCCAACTACCCC
Found at i:63964019 original size:22 final size:23
Alignment explanation
Indices: 63963994--63964036 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
63963984 CCGGAGCTCC
63963994 CTCCCTCTC-CCCTTTCTTTTCT
1 CTCCCTCTCTCCCTTTCTTTTCT
* *
63964016 CTCCCTTTCTCTCTTTCTTTT
1 CTCCCTCTCTCCCTTTCTTTT
63964037 TTTTCTTTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (23 bp):
CTCCCTCTCTCCCTTTCTTTTCT
Found at i:63964477 original size:3 final size:3
Alignment explanation
Indices: 63964471--63964531 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
63964461 TTTTTCTTAT
** *
63964471 TTA TTA TTA TTA TTA TTA TTA GGA TTA TTA TTA TTA TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
63964519 TTA CTA TGTA TTA
1 TTA TTA T-TA TTA
63964532 GTATACGTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:63964746 original size:26 final size:29
Alignment explanation
Indices: 63964715--63964773 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
63964705 TTTAATATAG
63964715 TATTAT-CT-TTTT-ACTATTA-TATTTAT
1 TATTATCCTATTTTCACTATTATTA-TTAT
*
63964741 TATTATCCTATTTTCACTGTTATTATTAT
1 TATTATCCTATTTTCACTATTATTATTAT
63964770 TATT
1 TATT
63964774 TTCATCATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 6 0.21
27 2 0.07
28 4 0.14
29 14 0.50
30 2 0.07
ACGTcount: A:0.25, C:0.10, G:0.02, T:0.63
Consensus pattern (29 bp):
TATTATCCTATTTTCACTATTATTATTAT
Found at i:63964784 original size:21 final size:22
Alignment explanation
Indices: 63964737--63964787 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
63964727 ACTATTATAT
*
63964737 TTATTATTATCCTATTTTCACTG
1 TTATTATTAT-CTATTTTCACTA
63964760 TTATTATTAT-TATTTTCA-TCA
1 TTATTATTATCTATTTTCACT-A
63964781 TTATTAT
1 TTATTAT
63964788 ACATATATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 1 0.04
21 15 0.58
23 10 0.38
ACGTcount: A:0.25, C:0.12, G:0.02, T:0.61
Consensus pattern (22 bp):
TTATTATTATCTATTTTCACTA
Found at i:63967748 original size:26 final size:26
Alignment explanation
Indices: 63967712--63967821 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
63967702 CATGAAATTC
63967712 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
63967738 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
63967764 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
*
63967790 TTGTCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
63967816 TTATCA
1 TTATCA
63967822 ATTTGTATCA
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:63970359 original size:22 final size:22
Alignment explanation
Indices: 63970329--63970446 Score: 87
Period size: 22 Copynumber: 5.2 Consensus size: 22
63970319 GTGACTTATC
* *
63970329 GCAATTTACTGGCAGCTTGTCT
1 GCAACTTACTAGCAGCTTGTCT
63970351 GCAACTTACTAGCAGCTTGTCT
1 GCAACTTACTAGCAGCTTGTCT
* *
63970373 ACAAAC-TATTAGCAG-TTGTACT
1 GC-AACTTACTAGCAGCTTGT-CT
* * *
63970395 GCATACTATTACTAGCGGTTTATCT
1 GCA-AC--TTACTAGCAGCTTGTCT
* *
63970420 GCAACTTACTGGCAACTTGTCT
1 GCAACTTACTAGCAGCTTGTCT
*
63970442 ACAAC
1 GCAAC
63970447 CCATTGACAG
Statistics
Matches: 75, Mismatches: 14, Indels: 14
0.73 0.14 0.14
Matches are distributed among these distances:
21 5 0.07
22 50 0.67
23 3 0.04
24 2 0.03
25 12 0.16
26 3 0.04
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (22 bp):
GCAACTTACTAGCAGCTTGTCT
Found at i:63970485 original size:69 final size:69
Alignment explanation
Indices: 63970334--63970487 Score: 184
Period size: 69 Copynumber: 2.2 Consensus size: 69
63970324 TTATCGCAAT
* * * * *
63970334 TTACTGGCAGCTTGTCTGCAACTTACTAGCAGCTTGTCTACAAACTATTAGCAGTTGTACTGCAT
1 TTACTGGCAGTTTATCTGCAACTTACTAGCAACTTGTCTACAAACCATTAGCAGTTGTACAGCAT
63970399 ACTA
66 ACTA
* * * * *
63970403 TTACTAGCGGTTTATCTGCAACTTACTGGCAACTTGTCTACAACCCATT-GACAGTTTTACAGCA
1 TTACTGGCAGTTTATCTGCAACTTACTAGCAACTTGTCTACAAACCATTAG-CAGTTGTACAGCA
*
63970467 TACTG
65 TACTA
*
63970472 TTACTGGTAGTTTATC
1 TTACTGGCAGTTTATC
63970488 AACAACGAGC
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
68 1 0.01
69 69 0.99
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (69 bp):
TTACTGGCAGTTTATCTGCAACTTACTAGCAACTTGTCTACAAACCATTAGCAGTTGTACAGCAT
ACTA
Found at i:63973075 original size:10 final size:10
Alignment explanation
Indices: 63973060--63973085 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
63973050 TTGCCCATCC
63973060 CCTTCATCGA
1 CCTTCATCGA
63973070 CCTTCATCGA
1 CCTTCATCGA
63973080 CCTTCA
1 CCTTCA
63973086 AAGGCTCTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.42, G:0.08, T:0.31
Consensus pattern (10 bp):
CCTTCATCGA
Found at i:63974405 original size:21 final size:22
Alignment explanation
Indices: 63974363--63974406 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
63974353 TGACTTAGTG
*
63974363 ATTAATTTAATTTCTTTGAATT
1 ATTAATTTAATTTCATTGAATT
63974385 ATTAA-TTAA-TTCATTGTAATT
1 ATTAATTTAATTTCATTG-AATT
63974406 A
1 A
63974407 AATAATTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 9 0.45
22 5 0.25
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (22 bp):
ATTAATTTAATTTCATTGAATT
Found at i:63975645 original size:24 final size:24
Alignment explanation
Indices: 63975617--63975662 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
63975607 ACAAAATTTT
*
63975617 TTAAAAAATAGTTTTTAAATTACA
1 TTAAAAAATACTTTTTAAATTACA
*
63975641 TTAAAAAGTACTTTTTAAATTA
1 TTAAAAAATACTTTTTAAATTA
63975663 TTTTGTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (24 bp):
TTAAAAAATACTTTTTAAATTACA
Found at i:63976092 original size:19 final size:19
Alignment explanation
Indices: 63976036--63976092 Score: 61
Period size: 17 Copynumber: 3.2 Consensus size: 19
63976026 GGATATTTTT
63976036 TTAATTATATGGATTTATA
1 TTAATTATATGGATTTATA
*
63976055 TTAAATTCTA---ATTT-T-
1 TT-AATTATATGGATTTATA
63976070 TTAATTATATGGATTTATA
1 TTAATTATATGGATTTATA
63976089 TTAA
1 TTAA
63976093 ATTCTAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
14 6 0.20
15 2 0.07
16 1 0.03
17 8 0.27
18 1 0.03
19 6 0.20
20 6 0.20
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (19 bp):
TTAATTATATGGATTTATA
Found at i:63976102 original size:17 final size:17
Alignment explanation
Indices: 63976048--63976102 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
63976038 AATTATATGG
63976048 ATTTATATTAAATTCTA
1 ATTTATATTAAATTCTA
*
63976065 ATTT-T-TT-AATTATA
1 ATTTATATTAAATTCTA
63976079 TGGATTTATATTAAATTCTA
1 ---ATTTATATTAAATTCTA
63976099 ATTT
1 ATTT
63976103 TAATTTTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
14 6 0.20
15 2 0.07
16 1 0.03
17 12 0.40
18 1 0.03
19 2 0.07
20 6 0.20
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (17 bp):
ATTTATATTAAATTCTA
Found at i:63976111 original size:40 final size:34
Alignment explanation
Indices: 63976032--63976103 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
63976022 ATTTGGATAT
63976032 TTTTTTAATTATATGGATTTATATTAAATTCTAA
1 TTTTTTAATTATATGGATTTATATTAAATTCTAA
63976066 TTTTTTAATTATATGGATTTATATTAAATTCTAA
1 TTTTTTAATTATATGGATTTATATTAAATTCTAA
63976100 TTTT
1 TTTT
63976104 AATTTTTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (34 bp):
TTTTTTAATTATATGGATTTATATTAAATTCTAA
Found at i:63976228 original size:2 final size:2
Alignment explanation
Indices: 63976223--63976267 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
63976213 TATATACGTG
63976223 TA TA TA TA TA 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 TA TA
63976265 TA T
1 TA T
63976268 TTGCCTCGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:63980401 original size:31 final size:31
Alignment explanation
Indices: 63980366--63980428 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
63980356 TTTTTGTTTA
63980366 TTTCTTCATATAGATTTAAATTATCAAATTT
1 TTTCTTCATATAGATTTAAATTATCAAATTT
*
63980397 TTTCTTCATATAGATTTAAATTATTAAATTT
1 TTTCTTCATATAGATTTAAATTATCAAATTT
63980428 T
1 T
63980429 CTTTTAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.08, G:0.03, T:0.54
Consensus pattern (31 bp):
TTTCTTCATATAGATTTAAATTATCAAATTT
Found at i:63989872 original size:3 final size:3
Alignment explanation
Indices: 63989866--63989958 Score: 147
Period size: 3 Copynumber: 32.0 Consensus size: 3
63989856 TTAGTTAATT
* *
63989866 TTA TTA TTA TT- TTC TT- TTA CTA -TA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
63989911 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
63989959 AACCATTTCA
Statistics
Matches: 86, Mismatches: 1, Indels: 6
0.92 0.01 0.06
Matches are distributed among these distances:
2 6 0.07
3 80 0.93
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:63990262 original size:20 final size:20
Alignment explanation
Indices: 63990225--63990263 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
63990215 TTTCACCCCT
*
63990225 TTTACTTTTTTTTCTATTTA
1 TTTACTTTTTATTCTATTTA
63990245 TTTACCTTTTTATT-TATTT
1 TTTA-CTTTTTATTCTATTT
63990264 TGTTTTATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTACTTTTTATTCTATTTA
Found at i:63994681 original size:21 final size:20
Alignment explanation
Indices: 63994657--63994722 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 20
63994647 TCGAAACCAA
*
63994657 TAAATTATTATTATTTTTATT
1 TAAATTATAATTATTTTT-TT
63994678 TAAATTA-AATTATCTTTCTTT
1 TAAATTATAATTAT-TTT-TTT
* *
63994699 CAAAATATAATTATTTTTTT
1 TAAATTATAATTATTTTTTT
63994719 TAAA
1 TAAA
63994723 AAAATTCACT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
20 11 0.29
21 20 0.53
22 7 0.18
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.58
Consensus pattern (20 bp):
TAAATTATAATTATTTTTTT
Found at i:63998186 original size:6 final size:6
Alignment explanation
Indices: 63998177--63998201 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
63998167 TTTTTTTTTT
63998177 CCTTTG CCTTTG CCTTTG CCTTTG C
1 CCTTTG CCTTTG CCTTTG CCTTTG C
63998202 AATATAGCGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.36, G:0.16, T:0.48
Consensus pattern (6 bp):
CCTTTG
Found at i:64000318 original size:19 final size:19
Alignment explanation
Indices: 64000294--64000339 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
64000284 ACGAAAGTTT
64000294 AATGCAAAT-GAT-GCAATG
1 AATGCAAATGGATAG-AATG
64000312 CAATGCAAATGGATAGAATG
1 -AATGCAAATGGATAGAATG
64000332 AATGCAAA
1 AATGCAAA
64000340 AAGAAAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 17 0.68
20 7 0.28
21 1 0.04
ACGTcount: A:0.48, C:0.11, G:0.22, T:0.20
Consensus pattern (19 bp):
AATGCAAATGGATAGAATG
Found at i:64002982 original size:3 final size:3
Alignment explanation
Indices: 64002974--64003008 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
64002964 CAAAAAGAGA
64002974 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
64003009 ACTAATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:64005247 original size:14 final size:15
Alignment explanation
Indices: 64005228--64005256 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
64005218 TCTTTATGCG
64005228 AAAAAAGAAA-AAAA
1 AAAAAAGAAAGAAAA
64005242 AAAAAAGAAAGAAAA
1 AAAAAAGAAAGAAAA
64005257 GAAGATCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAGAAAA
Found at i:64006245 original size:19 final size:20
Alignment explanation
Indices: 64006215--64006260 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
64006205 CGAAAAATAA
*
64006215 TTTCTAGAAAATGATTTACT
1 TTTCTAGAAAATGATCTACT
*
64006235 TTTCT-GAAAATGATCTATT
1 TTTCTAGAAAATGATCTACT
64006254 TTTCTAG
1 TTTCTAG
64006261 TGTTTTGATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (20 bp):
TTTCTAGAAAATGATCTACT
Found at i:64007397 original size:93 final size:91
Alignment explanation
Indices: 64007228--64007398 Score: 209
Period size: 93 Copynumber: 1.9 Consensus size: 91
64007218 CTTTATATTC
* * *
64007228 TCATAAAATGTTTAATATGATACATATATTTTAAAATATTTAATATAATACTTAAACTATTAATA
1 TCATAAAATGTTTAATACGATACATATATTTTAAAATATCTAACATAATACTTAAACTATTAATA
64007293 TATGTTTTATTATTATATATATTTTT
66 TATGTTTTATTATTATATATATTTTT
* * * * * * *
64007319 TCATAAAATGTTTAATACGATACTTGTATTTCTGAAAATGTCTAACGTGATACTTGAACTA-TCA
1 TCATAAAATGTTTAATACGATACATATATTT-T-AAAATATCTAACATAATACTTAAACTATTAA
*
64007383 TGATGTGTTTTATTAT
64 T-ATATGTTTTATTAT
64007399 GGTATCTAGT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
91 28 0.42
92 4 0.06
93 34 0.52
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (91 bp):
TCATAAAATGTTTAATACGATACATATATTTTAAAATATCTAACATAATACTTAAACTATTAATA
TATGTTTTATTATTATATATATTTTT
Found at i:64012165 original size:2 final size:2
Alignment explanation
Indices: 64012108--64012146 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
64012098 GGTATTTAAA
*
64012108 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
64012147 ATAGTATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:64013489 original size:88 final size:83
Alignment explanation
Indices: 64013382--64013958 Score: 290
Period size: 88 Copynumber: 7.0 Consensus size: 83
64013372 AACAGACATT
** * *
64013382 AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
64013447 TTGATTTTTTGAAACTTAACTTG
65 TTGATTTTTTGAAA---AA-TTG
* * * ** *
64013470 AAAAGCAGATTTTGAAAATACCTCGATATGTGA-CTGGAGGTTCAACTCACCTCTCGCAATATGA
1 AAAAACAGATTTTGAAAATACCTCG-CACGTGAGC-CAAGGCTCAACTCACCTCTCGCAATATGA
*
64013534 GTTGA-TTTTTGAAAAATAG
64 GTTGATTTTTTGAAAAATTG
* * * * ** *** *
64013553 AAATTAAAAGA--CT-CAACTCAACTCTCGCA-GAAATTAAAAAGCTCAACTCACCTCTCGCAAT
1 AAA--AACAGATTTTGAAAAT--AC-CTCGCACGTGA-GCCAAGGCTCAACTCACCTCTCGCAAT
64013614 ATGAGTTGAATTTTTTTG-AAAA---
60 ATGAGTTG-A-TTTTTTGAAAAATTG
** * *
64013636 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACTTCTCGCAATATGAG
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
64013701 TTGA-TTTTTGAAAACAGAATTTG
65 TTGATTTTTTG--AA-A-AA-TTG
* * * * * *
64013724 AAAAACAGATTTTGAAAATACCTCGACATGTAACCCGAGGCTCAACTCACATCTCGCAATGTGAG
1 AAAAACAGATTTTGAAAATACCTCG-CACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
64013789 TTGATTTTTTTGAAAAA-T-
65 TTGA-TTTTTTGAAAAATTG
* *** *** * *
64013807 --ATA-A-ATTGAAAAAATACCTCAGTGTGTGATCTGAA-GCTCAACTCACCTCTCGCAATATGA
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGAGC-CAAGGCTCAACTCACCTCTCGCAATATGA
64013867 GTTGATTTTTTTG--AAA--G
64 GTTGA-TTTTTTGAAAAATTG
* * * * * * *
64013884 ATAGA-A-A--TTGAAAATAGCTCAGCGCATGAGCCAAGGGTCAACTCACCTCT-GCAATATAAG
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
*
64013944 TTGATTTTTGGAAAA
65 TTGATTTTTTGAAAA
64013959 CAGAAATTGA
Statistics
Matches: 382, Mismatches: 70, Indels: 85
0.71 0.13 0.16
Matches are distributed among these distances:
75 6 0.02
76 15 0.04
77 35 0.09
79 64 0.17
80 3 0.01
81 11 0.03
82 38 0.10
83 15 0.04
84 40 0.10
85 9 0.02
86 6 0.02
87 19 0.05
88 115 0.30
90 6 0.02
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (83 bp):
AAAAACAGATTTTGAAAATACCTCGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTTTGAAAAATTG
Found at i:64013587 original size:30 final size:30
Alignment explanation
Indices: 64013551--64013611 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
64013541 TTTGAAAAAT
64013551 AGAAATT-AAAAGACTCAACTCAACTCTCGC
1 AGAAATTAAAAAG-CTCAACTCAACTCTCGC
*
64013581 AGAAATTAAAAAGCTCAACTCACCTCTCGC
1 AGAAATTAAAAAGCTCAACTCAACTCTCGC
64013611 A
1 A
64013612 ATATGAGTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 24 0.83
31 5 0.17
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.20
Consensus pattern (30 bp):
AGAAATTAAAAAGCTCAACTCAACTCTCGC
Found at i:64013730 original size:14 final size:14
Alignment explanation
Indices: 64013707--64013741 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
64013697 TGAGTTGATT
64013707 TTTG-AAAACAGAA
1 TTTGAAAAACAGAA
*
64013720 TTTGAAAAACAGAT
1 TTTGAAAAACAGAA
64013734 TTTGAAAA
1 TTTGAAAA
64013742 TACCTCGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (14 bp):
TTTGAAAAACAGAA
Found at i:64014037 original size:72 final size:72
Alignment explanation
Indices: 64013759--64014097 Score: 358
Period size: 72 Copynumber: 4.5 Consensus size: 72
64013749 ACATGTAACC
* * *
64013759 CGAGGCTCAACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATAC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTG-AAAATAGAAATTG--AAAATAC
* *
64013824 CTCAGTGTGTGAT
61 CTCAGCGTGT-CT
* *
64013837 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGATAGAAATTGAAAATAGC
1 C-GAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAA-ATAGAAATTGAAAATACC
*
64013902 TCAGCGCATGAGC-
62 TCAGCG--TG-TCT
* * * *
64013915 CAAGGGTCAACTCACCTCT-GCAATATAAGTTGATTTTTGGAAAACAGAAATTGAAAATACCTCA
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-GAAAATAGAAATTGAAAATACCTCA
*
64013979 ACGTGTCT
65 GCGTGTCT
* ** * * *
64013987 TGAGGCTCAACTCATTTCTCACAATATGAGTTGAATTTTGAAAATAGAAATTGAAATTACCTCAG
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAATAGAAATTGAAAATACCTCAG
*
64014052 CGTGTCC
66 CGTGTCT
64014059 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
64014098 TTTTTTTTTT
Statistics
Matches: 220, Mismatches: 33, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
71 1 0.00
72 79 0.36
73 16 0.07
74 26 0.12
75 4 0.02
76 13 0.06
77 27 0.12
78 5 0.02
79 49 0.22
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (72 bp):
CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAATAGAAATTGAAAATACCTCAG
CGTGTCT
Found at i:64014246 original size:173 final size:168
Alignment explanation
Indices: 64013955--64014434 Score: 695
Period size: 165 Copynumber: 2.9 Consensus size: 168
64013945 TGATTTTTGG
* * * ** * *
64013955 AAAACAGAAATTGAAAATACCTCAACGTGT-CT-TGAGGCTCAACTCATTTCTCACAATATGAGT
1 AAAACGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGT
* * *
64014018 TGA-ATTTTGAAAATAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCA
66 TGATTTTTTGACAATAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCA
* *
64014082 ATATGAGTTGATTTTTTTTTTTTTTTGAAATGCAGAAATTGA
131 ATATGAGTTGA----TTTTTTTTTTTGAAAGGCAAAAATTGA
*
64014124 AAAATGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGT
1 AAAACGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGT
64014189 TGACTTTTTTGACAATAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
66 TGA-TTTTTTGACAATAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
64014254 AATATGAGTTGA----TTTTTTTGAAAGGCAAAAATTGA
130 AATATGAGTTGATTTTTTTTTTTGAAAGGCAAAAATTGA
* * * *
64014289 AAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATACGAGT
1 AAAACGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGT
*
64014354 TGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
66 TGA-TTTTTTGACAATAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
64014419 AATATGAGTTGATTTT
130 AATATGAGTTGATTTT
64014435 GAAAAAGTAG
Statistics
Matches: 283, Mismatches: 20, Indels: 16
0.89 0.06 0.05
Matches are distributed among these distances:
165 156 0.55
169 27 0.10
170 1 0.00
171 30 0.11
173 69 0.24
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (168 bp):
AAAACGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGT
TGATTTTTTGACAATAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCA
ATATGAGTTGATTTTTTTTTTTGAAAGGCAAAAATTGA
Found at i:64014253 original size:74 final size:75
Alignment explanation
Indices: 64014130--64014274 Score: 222
Period size: 74 Copynumber: 1.9 Consensus size: 75
64014120 TTGAAAAATG
*
64014130 GAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTT
1 GAAATTGAAAATACCTCGACGTGT-ACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTT
64014195 TTTTGACAATA
65 TTTTGACAATA
* * *
64014206 GAAATTGAAATTACCTC-AGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 GAAATTGAAAATACCTCGA-CGTGTACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTT
64014269 TTTTGA
65 TTTTGA
64014275 AAGGCAAAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
74 42 0.66
75 1 0.02
76 21 0.33
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (75 bp):
GAAATTGAAAATACCTCGACGTGTACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTT
TTTGACAATA
Done.