Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 268 of 333
Found at i:88624350 original size:23 final size:20
Alignment explanation
Indices: 88624313--88624364 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
88624303 ACAAAATAAT
* *
88624313 ATAAAATCAATAATATATATAC
1 ATAAAAT-AA-AAAATATTTAC
88624335 ATAATAATAAAAAATATTTAC
1 ATAA-AATAAAAAATATTTAC
88624356 ATAAAATAA
1 ATAAAATAA
88624365 TAGGAAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 5 0.19
21 13 0.48
22 6 0.22
23 3 0.11
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (20 bp):
ATAAAATAAAAAATATTTAC
Found at i:88624655 original size:18 final size:18
Alignment explanation
Indices: 88624634--88624673 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
88624624 AATAAGGAAT
88624634 AAAACATAAATTGAAGTAA
1 AAAAC-TAAATTGAAGTAA
*
88624653 AAAACTCAATTGAAGTAA
1 AAAACTAAATTGAAGTAA
88624671 AAA
1 AAA
88624674 TAAAACCCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.20
Consensus pattern (18 bp):
AAAACTAAATTGAAGTAA
Found at i:88625022 original size:40 final size:38
Alignment explanation
Indices: 88624978--88625083 Score: 115
Period size: 40 Copynumber: 2.7 Consensus size: 38
88624968 TAAATTGAGT
88624978 ATTAGCGGCGTTTTTTCAAAAACGCCGCTATAGATCGAGA
1 ATTAGCGGCGTTTTTT-AAAAACGCCGCTATAGATCGA-A
** * *
88625018 ATTAGCGGCG-TTTTTAAGGAAGTGCCGCTATAGGTCGAC
1 ATTAGCGGCGTTTTTTAA--AAACGCCGCTATAGATCGAA
88625057 ATATAGCGGCGTTTTTATAAAAACGCC
1 AT-TAGCGGCGTTTTT-TAAAAACGCC
88625084 ACTAAAAGAT
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
38 2 0.04
39 7 0.13
40 39 0.71
41 4 0.07
42 3 0.05
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (38 bp):
ATTAGCGGCGTTTTTTAAAAACGCCGCTATAGATCGAA
Found at i:88625220 original size:154 final size:154
Alignment explanation
Indices: 88624980--88625358 Score: 494
Period size: 154 Copynumber: 2.5 Consensus size: 154
88624970 AATTGAGTAT
* * * * * *
88624980 TAGCGGCGTTTTTTCAAAAACGCCGCTATAGATCGAGAATTAGCGGCGTTTTTAAGGAAGTGCCG
1 TAGCGGCGCTTTATCAAAAACGCCGCTATAGATTGAGTATTAGCGGCGTTTTTAAGAAAGCGCCG
* **
88625045 CTATAGGTCGACATATAGCGGCGTTTTTATAAAAACGCCACTAAAAGATT-AGGCGAACGGCGTC
66 CTATAGGTCGACATATAGCGGCGTTTTTATAAAAACGCCACTAAAAAATTAAACCGAACGGCGTC
88625109 GTTTATTGTGAGCTTCAGTGGCAA
131 GTTTATTGTGAGCTTCAGTGGCAA
* * *
88625133 TAGCGGCGCTTTATCAAAAACGCCGCTATAGGTTTGAGTATTAACGGCATTTTTTAA-AAAGCGC
1 TAGCGGCGCTTTATCAAAAACGCCGCTATA-GATTGAGTATTAGCGGC-GTTTTTAAGAAAGCGC
* * * *
88625197 CGCTATAGGTCGGCCTATAGCGGCGTTTTTATAGAAACGCCGCTAAAAAATTAAACCGAACGGCG
64 CGCTATAGGTCGACATATAGCGGCGTTTTTATAAAAACGCCACTAAAAAATTAAACCGAACGGCG
* *
88625262 TCGTTTATTTTGAGCTTCATTGGCAA
129 TCGTTTATTGTGAGCTTCAGTGGCAA
*** * *
88625288 TAGCGGCGCTTGCGCAAAAACGCCGCTATAGATTGAGTATTAGCGGCGCTTTCT-AGAAAACGCC
1 TAGCGGCGCTTTATCAAAAACGCCGCTATAGATTGAGTATTAGCGGCG-TTTTTAAGAAAGCGCC
*
88625352 GCAATAG
65 GCTATAG
88625359 ATATGAGTTT
Statistics
Matches: 194, Mismatches: 27, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
153 29 0.15
154 97 0.50
155 68 0.35
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (154 bp):
TAGCGGCGCTTTATCAAAAACGCCGCTATAGATTGAGTATTAGCGGCGTTTTTAAGAAAGCGCCG
CTATAGGTCGACATATAGCGGCGTTTTTATAAAAACGCCACTAAAAAATTAAACCGAACGGCGTC
GTTTATTGTGAGCTTCAGTGGCAA
Found at i:88625226 original size:40 final size:39
Alignment explanation
Indices: 88625132--88625241 Score: 103
Period size: 40 Copynumber: 2.7 Consensus size: 39
88625122 TTCAGTGGCA
* * ** *
88625132 ATAGCGGCGCTTTATCAAAAACGCCGCTATAGGTTTGAGT
1 ATAGCGGCG-TTTTTTAAAAACGCCGCTATAGGTCGGACT
* * *
88625172 ATTAACGGCATTTTTTAAAAAGCGCCGCTATAGGTCGGCCT
1 A-TAGCGGCGTTTTTTAAAAA-CGCCGCTATAGGTCGGACT
*
88625213 ATAGCGGCGTTTTTATAGAAACGCCGCTA
1 ATAGCGGCGTTTTT-TAAAAACGCCGCTA
88625242 AAAAATTAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
40 29 0.52
41 27 0.48
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (39 bp):
ATAGCGGCGTTTTTTAAAAACGCCGCTATAGGTCGGACT
Found at i:88625348 original size:40 final size:42
Alignment explanation
Indices: 88625303--88625402 Score: 125
Period size: 40 Copynumber: 2.4 Consensus size: 42
88625293 GCGCTTGCGC
*
88625303 AAAAACGCCGCTATAGAT-TGAGTATT-AGCGGCGCTTTCT-A
1 AAAAACGCCGCTATAGATATGAGT-TTCAGCGGCACTTTCTGA
* * *
88625343 GAAAACGCCGCAATAGATATGAGTTTCAGCGGCACTTTTTGA
1 AAAAACGCCGCTATAGATATGAGTTTCAGCGGCACTTTCTGA
*
88625385 AAAAACGCCGCTAAAGAT
1 AAAAACGCCGCTATAGAT
88625403 CTAAACTATT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 18 0.36
41 16 0.32
42 16 0.32
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (42 bp):
AAAAACGCCGCTATAGATATGAGTTTCAGCGGCACTTTCTGA
Found at i:88625374 original size:155 final size:154
Alignment explanation
Indices: 88625058--88625399 Score: 411
Period size: 155 Copynumber: 2.2 Consensus size: 154
88625048 TAGGTCGACA
* * **
88625058 TATAGCGGCGTTTTTATAAAAACGCCACTAAAAGATTAGGCGAACGGCGTCGTTTATTGTGAGCT
1 TATAGCGGCGTTTTTATAAAAACGCCGCTAAAAAATTAACCGAACGGCGTCGTTTATTGTGAGCT
* * * * *
88625123 TCAGTGGCAATAGCGGCGCTTTATCAAAAACGCCGCTATAGGTTTGAGTATTAACGGCATTTTTT
66 TCAGTGGCAATAGCGGCGCTTGAGCAAAAACGCCGCTATAGGATTGAGTATTAACGGCACTTTCT
* * * *
88625188 AAAAAGCGCCGCTATAGGTCGGCC
131 AAAAAGCGCCGCAATAGATAGGAC
* *
88625212 TATAGCGGCGTTTTTATAGAAACGCCGCTAAAAAATTAAACCGAACGGCGTCGTTTATTTTGAGC
1 TATAGCGGCGTTTTTATAAAAACGCCGCTAAAAAATT-AACCGAACGGCGTCGTTTATTGTGAGC
* * * *
88625277 TTCATTGGCAATAGCGGCGCTTGCGCAAAAACGCCGCTATA-GATTGAGTATTAGCGGCGCTTTC
65 TTCAGTGGCAATAGCGGCGCTTGAGCAAAAACGCCGCTATAGGATTGAGTATTAACGGCACTTTC
* *
88625341 TAGAAAA-CGCCGCAATAGATATGAG
130 TA-AAAAGCGCCGCAATAGATAGGAC
* *
88625366 TTTCAGCGGCACTTTTTGA-AAAAACGCCGCTAAA
1 TAT-AGCGGC-GTTTTT-ATAAAAACGCCGCTAAA
88625400 GATCTAAACT
Statistics
Matches: 159, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
154 68 0.43
155 71 0.45
156 19 0.12
157 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (154 bp):
TATAGCGGCGTTTTTATAAAAACGCCGCTAAAAAATTAACCGAACGGCGTCGTTTATTGTGAGCT
TCAGTGGCAATAGCGGCGCTTGAGCAAAAACGCCGCTATAGGATTGAGTATTAACGGCACTTTCT
AAAAAGCGCCGCAATAGATAGGAC
Found at i:88625711 original size:15 final size:15
Alignment explanation
Indices: 88625669--88625725 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
88625659 ACACCATGTT
* *
88625669 TTAAACCCTAACCCA
1 TTAAACCCTAAACTA
* *
88625684 CTAAACCCTTAAATTA
1 TTAAACCC-TAAACTA
* *
88625700 TTAAATCCTAAACTC
1 TTAAACCCTAAACTA
88625715 TTAAACCCTAA
1 TTAAACCCTAA
88625726 GTCTCAACCC
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
15 22 0.69
16 10 0.31
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (15 bp):
TTAAACCCTAAACTA
Found at i:88626489 original size:73 final size:72
Alignment explanation
Indices: 88626370--88626506 Score: 184
Period size: 73 Copynumber: 1.9 Consensus size: 72
88626360 TAAGGGGTTG
* * * *
88626370 AGGGGATATAGTTTAGGGTTTAGTGTTCAAAGTCTATGGATTAAGGGTTTAGGGTTTATGGGTTT
1 AGGGGACATAGTTTAAGGTTTAGTGTTCAAAGTCTAGGGATTAAGGGTTAAGGGTTTA-GGGTTT
88626435 GGAAGTTA
65 GGAAGTTA
* * * * *
88626443 AGGGGACATTGTTTAAGGTTTAGTGTTTAAATTTTAGGGATTAAGGGTTAATGGTTTAGGGTTT
1 AGGGGACATAGTTTAAGGTTTAGTGTTCAAAGTCTAGGGATTAAGGGTTAAGGGTTTAGGGTTT
88626507 AGGGGTTTAC
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
72 6 0.11
73 49 0.89
ACGTcount: A:0.25, C:0.02, G:0.33, T:0.40
Consensus pattern (72 bp):
AGGGGACATAGTTTAAGGTTTAGTGTTCAAAGTCTAGGGATTAAGGGTTAAGGGTTTAGGGTTTG
GAAGTTA
Found at i:88626684 original size:16 final size:16
Alignment explanation
Indices: 88626659--88626711 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 16
88626649 ACATATATTA
88626659 AATAATTTCAAATTTT
1 AATAATTTCAAATTTT
* *
88626675 AATGATTTCAAATTGTC
1 AATAATTTCAAATT-TT
88626692 AATAATTTTCAAGATTTT
1 AATAA-TTTCAA-ATTTT
88626710 AA
1 AA
88626712 ATTTTATGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
16 13 0.43
17 5 0.17
18 9 0.30
19 3 0.10
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.45
Consensus pattern (16 bp):
AATAATTTCAAATTTT
Found at i:88626862 original size:18 final size:17
Alignment explanation
Indices: 88626824--88626859 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
88626814 CTATATAACT
88626824 TATTGTTTTTTAATTTA
1 TATTGTTTTTTAATTTA
88626841 TATTGTTTTTT-ATTTA
1 TATTGTTTTTTAATTTA
88626857 TAT
1 TAT
88626860 ATTAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (17 bp):
TATTGTTTTTTAATTTA
Found at i:88628864 original size:15 final size:16
Alignment explanation
Indices: 88628838--88628867 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
88628828 GTAGTTATGA
88628838 ATGAGTTTTTCAGTGC
1 ATGAGTTTTTCAGTGC
88628854 ATGAG-TTTTCAGTG
1 ATGAGTTTTTCAGTG
88628868 TATAACCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.43
Consensus pattern (16 bp):
ATGAGTTTTTCAGTGC
Found at i:88630580 original size:14 final size:13
Alignment explanation
Indices: 88630557--88630593 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
88630547 ATTACTATAA
88630557 TAATTATATGAAG
1 TAATTATATGAAG
88630570 TAATATATATGAAG
1 TAAT-TATATGAAG
88630584 TAAATTATAT
1 T-AATTATAT
88630594 TGTATACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.18
14 15 0.68
15 3 0.14
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.41
Consensus pattern (13 bp):
TAATTATATGAAG
Found at i:88631062 original size:15 final size:15
Alignment explanation
Indices: 88631042--88631070 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
88631032 GGAGTAGACC
88631042 AGGTACGTTTTATTA
1 AGGTACGTTTTATTA
88631057 AGGTACGTTTTATT
1 AGGTACGTTTTATT
88631071 TCAAAATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.07, G:0.21, T:0.48
Consensus pattern (15 bp):
AGGTACGTTTTATTA
Found at i:88631949 original size:357 final size:358
Alignment explanation
Indices: 88631294--88631974 Score: 1285
Period size: 357 Copynumber: 1.9 Consensus size: 358
88631284 CTTGTCCATT
88631294 AAAATTACAACAATGGATGACCTTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTAT
1 AAAATTACAACAATGGATGACCTTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTAT
88631359 ATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAACTGCAAGATATAATGGATCCTCCCTAGGT
66 ATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAACTGCAAGATATAATGGATCCTCCCTAGGT
*
88631424 GTAACAACGCCATGTATGATAAATCTTAAAAATTCAAAAAGACTTGAAAAAAGTTCTATCGAGCT
131 GTAACAACGCCACGTATGATAAATCTTAAAAATTCAAAAAGACTTGAAAAAAGTTCTATCGAGCT
88631489 CATTTACTATTGAATATTTATTTCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTTATA
196 CATTTACTATTGAATATTTATTTCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTTATA
*
88631554 TTATTATATTCAAATTACTATTTTTTTGCATTAATAATGTTTGATTTTAATATTT-AATATTTTT
261 TTATTATATTCAAATTACTATTTTTTTACATTAATAATGTTTGATTTTAATATTTAAATATTTTT
88631618 AAATGTCTTTAAAAGTTATAACTAATTTTTATC
326 AAATGTCTTTAAAAGTTATAACTAATTTTTATC
*
88631651 AAAATTACAACAATGGCTGACCTTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTAT
1 AAAATTACAACAATGGATGACCTTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTAT
*
88631716 ATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAGGT
66 ATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAACTGCAAGATATAATGGATCCTCCCTAGGT
*
88631781 GTAACAACGCCACGTATGATGAATCTTAAAAAATTCAAAAAGACTTGAAAAAAGTTCTATCGAGC
131 GTAACAACGCCACGTATGATAAATCTT-AAAAATTCAAAAAGACTTGAAAAAAGTTCTATCGAGC
88631846 TCATTTACTATTGAATATTTATTTCCAATTTACTTATAAAAATTAAACTACGATTC-TTTTTTAT
195 TCATTTACTATTGAATATTTATTTCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTTAT
*
88631910 ATTATTATATTCAAATTACTATTTTTTTATATTAATAATGTTTGATTTTAATATTTAAATATTTT
260 ATTATTATATTCAAATTACTATTTTTTTACATTAATAATGTTTGATTTTAATATTTAAATATTTT
88631975 AAAGATTCAA
Statistics
Matches: 316, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
357 215 0.68
358 101 0.32
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (358 bp):
AAAATTACAACAATGGATGACCTTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTAT
ATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAACTGCAAGATATAATGGATCCTCCCTAGGT
GTAACAACGCCACGTATGATAAATCTTAAAAATTCAAAAAGACTTGAAAAAAGTTCTATCGAGCT
CATTTACTATTGAATATTTATTTCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTTATA
TTATTATATTCAAATTACTATTTTTTTACATTAATAATGTTTGATTTTAATATTTAAATATTTTT
AAATGTCTTTAAAAGTTATAACTAATTTTTATC
Found at i:88633877 original size:13 final size:14
Alignment explanation
Indices: 88633861--88633889 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
88633851 TTCTAAATAT
88633861 TTATAA-TGTTTAA
1 TTATAATTGTTTAA
88633874 TTATAATTGTTTAA
1 TTATAATTGTTTAA
88633888 TT
1 TT
88633890 CAATTCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTATAATTGTTTAA
Found at i:88634326 original size:21 final size:21
Alignment explanation
Indices: 88634301--88634341 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
88634291 TTAGAGCGGA
88634301 GGCAGCAGAGAGGGAGGCAGC
1 GGCAGCAGAGAGGGAGGCAGC
*
88634322 GGCAGCAGCGAGGGAGGCAG
1 GGCAGCAGAGAGGGAGGCAG
88634342 AGCATAGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.20, G:0.54, T:0.00
Consensus pattern (21 bp):
GGCAGCAGAGAGGGAGGCAGC
Found at i:88634761 original size:43 final size:43
Alignment explanation
Indices: 88634695--88634965 Score: 429
Period size: 43 Copynumber: 6.3 Consensus size: 43
88634685 TCTGCCAAAA
88634695 TTAGCGGCGCTTTTTCTTCAAACGCCGCTAAAGGCCACGACTT
1 TTAGCGGCGCTTTTTCTTCAAACGCCGCTAAAGGCCACGACTT
* *
88634738 TTAGCGGCGTTTTTTCTTTAAACGCCGCTAAAGGCCACGACTT
1 TTAGCGGCGCTTTTTCTTCAAACGCCGCTAAAGGCCACGACTT
*
88634781 TTAGCGGTGC-TTTTCTTCAAACGCCGCTAAAGGCCACGACTT
1 TTAGCGGCGCTTTTTCTTCAAACGCCGCTAAAGGCCACGACTT
* * *
88634823 TTAGTGGCGTTTTTTCTTCAAACGCCGCTAAAGGCCATGACTT
1 TTAGCGGCGCTTTTTCTTCAAACGCCGCTAAAGGCCACGACTT
*
88634866 TTAGCGGCGCTTTTT-TTCAAACGCCGCTAAAGGCCACGATTT
1 TTAGCGGCGCTTTTTCTTCAAACGCCGCTAAAGGCCACGACTT
** * *
88634908 TTAGCTACGTTTTTTCTTCAAACGCCGCTAAAGGCCATGACTT
1 TTAGCGGCGCTTTTTCTTCAAACGCCGCTAAAGGCCACGACTT
88634951 TTAGCGGCGCTTTTT
1 TTAGCGGCGCTTTTT
88634966 TTTAATAAAT
Statistics
Matches: 205, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
42 75 0.37
43 130 0.63
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (43 bp):
TTAGCGGCGCTTTTTCTTCAAACGCCGCTAAAGGCCACGACTT
Found at i:88634932 original size:128 final size:128
Alignment explanation
Indices: 88634695--88634966 Score: 422
Period size: 128 Copynumber: 2.1 Consensus size: 128
88634685 TCTGCCAAAA
* * *
88634695 TTAGCGGCGCTTTTTCTTCAAACGCCGCTAAAGGCCACGACTTTTAGCGGCGTTTTTTCTTTAAA
1 TTAGCGGCGTTTTTTCTTCAAACGCCGCTAAAGGCCACGACTTTTAGCGGCGCTTTTTCTTCAAA
*
88634760 CGCCGCTAAAGGCCACGACTTTTAGCGGTGCTTTTCTTCAAACGCCGCTAAAGGCCACGACTT
66 CGCCGCTAAAGGCCACGACTTTTAGCCGTGCTTTTCTTCAAACGCCGCTAAAGGCCACGACTT
* *
88634823 TTAGTGGCGTTTTTTCTTCAAACGCCGCTAAAGGCCATGACTTTTAGCGGCGCTTTTT-TTCAAA
1 TTAGCGGCGTTTTTTCTTCAAACGCCGCTAAAGGCCACGACTTTTAGCGGCGCTTTTTCTTCAAA
* * *
88634887 CGCCGCTAAAGGCCACGATTTTTAGCTACGT-TTTTTCTTCAAACGCCGCTAAAGGCCATGACTT
66 CGCCGCTAAAGGCCACGACTTTTAGC--CGTGCTTTTCTTCAAACGCCGCTAAAGGCCACGACTT
88634951 TTAGCGGCGCTTTTTT
1 TTAGCGGCG-TTTTTT
88634967 TTAATAAATG
Statistics
Matches: 131, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
127 30 0.23
128 93 0.71
129 8 0.06
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.33
Consensus pattern (128 bp):
TTAGCGGCGTTTTTTCTTCAAACGCCGCTAAAGGCCACGACTTTTAGCGGCGCTTTTTCTTCAAA
CGCCGCTAAAGGCCACGACTTTTAGCCGTGCTTTTCTTCAAACGCCGCTAAAGGCCACGACTT
Found at i:88634965 original size:85 final size:85
Alignment explanation
Indices: 88634695--88634967 Score: 458
Period size: 85 Copynumber: 3.2 Consensus size: 85
88634685 TCTGCCAAAA
* *
88634695 TTAGCGGCGCTTTTTCTTCAAACGCCGCTAAAGGCCACGACTTTTAGCGGCGTTTTTTCTTTAAA
1 TTAGCGGCGCTTTTT-TTCAAACGCCGCTAAAGGCCACGACTTTTAGCTGCGTTTTTTCTTCAAA
*
88634760 CGCCGCTAAAGGCCACGACTT
65 CGCCGCTAAAGGCCATGACTT
* *
88634781 TTAGCGGTGCTTTTCTTCAAACGCCGCTAAAGGCCACGACTTTTAG-TGGCGTTTTTTCTTCAAA
1 TTAGCGGCGCTTTTTTTCAAACGCCGCTAAAGGCCACGACTTTTAGCT-GCGTTTTTTCTTCAAA
88634845 CGCCGCTAAAGGCCATGACTT
65 CGCCGCTAAAGGCCATGACTT
* *
88634866 TTAGCGGCGCTTTTTTTCAAACGCCGCTAAAGGCCACGATTTTTAGCTACGTTTTTTCTTCAAAC
1 TTAGCGGCGCTTTTTTTCAAACGCCGCTAAAGGCCACGACTTTTAGCTGCGTTTTTTCTTCAAAC
88634931 GCCGCTAAAGGCCATGACTT
66 GCCGCTAAAGGCCATGACTT
88634951 TTAGCGGCGCTTTTTTT
1 TTAGCGGCGCTTTTTTT
88634968 TAATAAATGC
Statistics
Matches: 176, Mismatches: 9, Indels: 5
0.93 0.05 0.03
Matches are distributed among these distances:
85 162 0.92
86 14 0.08
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.33
Consensus pattern (85 bp):
TTAGCGGCGCTTTTTTTCAAACGCCGCTAAAGGCCACGACTTTTAGCTGCGTTTTTTCTTCAAAC
GCCGCTAAAGGCCATGACTT
Found at i:88635867 original size:19 final size:19
Alignment explanation
Indices: 88635843--88635879 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
88635833 ATTTATGTAA
* *
88635843 TTGGGCTGTAATTGGGTAT
1 TTGGGCTGAAATTAGGTAT
88635862 TTGGGCTGAAATTAGGTA
1 TTGGGCTGAAATTAGGTA
88635880 GCCCGGGCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.05, G:0.35, T:0.38
Consensus pattern (19 bp):
TTGGGCTGAAATTAGGTAT
Found at i:88636234 original size:88 final size:87
Alignment explanation
Indices: 88636115--88636540 Score: 509
Period size: 88 Copynumber: 4.8 Consensus size: 87
88636105 CGTTTCAATT
* * * * * *
88636115 TGCTCCACTACTGTTTAGGGAGATATGATTTGTAATCTTCAGCC-ATCT-CCACTGCTGGTCAG-
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAAT-TTCAGCCTAT-TACC-CTACTGCTTAGA
* *
88636177 GGAGATAAGGCTCACTGTCTTCGATC
63 GG-GTTAAGGCTCACCGTCTTCGATC
* * * * *
88636203 TGCTCCGCTATTGCTTAGGGAGATAAGATTTGTAGTTTCCAGCCTGTTACCCTACTGCTTAGAGG
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTT-CAGCCTATTACCCTACTGCTTAGAGG
* *
88636268 GTTAAGACTCACCGTCCTCGATC
65 GTTAAGGCTCACCGTCTTCGATC
* * *
88636291 TGTTCCACTACTGCTTAGAGAGATAAGATCTGTAATTTTCAGCCTATTACCCTACCGCTTAG-GA
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA-TTTCAGCCTATTACCCTACTGCTTAGAG-
88636355 GGTTAAGGCTCACCGTCTTCGATC
64 GGTTAAGGCTCACCGTCTTCGATC
* * *
88636379 TACTCCACTACTACTTAGGGAGATAAGATCTGTAATTTCCAGCCTATTACCCTAATGCTTAGAGG
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTT-CAGCCTATTACCCTACTGCTTAGAGG
* **
88636444 GTTAAGGCTCACCGTTTTTTATC
65 GTTAAGGCTCACCGTCTTCGATC
* *
88636467 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGG
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA-TTTCAGCCTATTACCCTACTGCTTAGAGG
88636532 GTTAAGGCT
65 GTTAAGGCT
88636541 GGTCGAGATT
Statistics
Matches: 292, Mismatches: 37, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
87 6 0.02
88 274 0.94
89 12 0.04
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.32
Consensus pattern (87 bp):
TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTCAGCCTATTACCCTACTGCTTAGAGGG
TTAAGGCTCACCGTCTTCGATC
Found at i:88636522 original size:44 final size:44
Alignment explanation
Indices: 88636214--88636530 Score: 124
Period size: 44 Copynumber: 7.2 Consensus size: 44
88636204 GCTCCGCTAT
* * *
88636214 TGCTTAGGGAGATAAGATTTGTAGTTTCCAGCCTGTTACCCTAC
1 TGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTAC
* * * ** *
88636258 TGCTTAGAGG-GTTAAGA-CT-CACCGTCCTC-GATCTGTT-CCACTAC
1 TGCTTAG-GGAGATAAGATCTGTA--ATTTTCAG-CCTGTTACC-CTAC
* *
88636302 TGCTTAGAGAGATAAGATCTGTAATTTTCAGCCTATTACCCTAC
1 TGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTAC
* * * * * * * **
88636346 CGCTTA-GGAGGTTAAG-GCT-CACCGTCTTC-GATCTACT-CCACTAC
1 TGCTTAGGGA-GATAAGATCTGTA--ATTTTCAG-CCTGTTACC-CTAC
* * * *
88636390 TACTTAGGGAGATAAGATCTGTAATTTCCAGCCTATTACCCTAA
1 TGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTAC
* * * * * *
88636434 TGCTTAGAGG-GTTAAGGCTCACCGT--TTTTTA-TCTGCT-CCACTAC
1 TGCTTAG-GGAGATAA-GAT--CTGTAATTTTCAGCCTGTTACC-CTAC
88636478 TGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTAC
1 TGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTAC
88636522 TGCTTAGGG
1 TGCTTAGGG
88636531 GGTTAAGGCT
Statistics
Matches: 192, Mismatches: 51, Indels: 60
0.63 0.17 0.20
Matches are distributed among these distances:
41 3 0.02
42 2 0.01
43 23 0.12
44 134 0.70
45 25 0.13
46 2 0.01
47 3 0.02
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (44 bp):
TGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTAC
Found at i:88640599 original size:19 final size:20
Alignment explanation
Indices: 88640575--88640621 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
88640565 TTGTGAAGTT
*
88640575 TAATGCACATG-ATGCAATG
1 TAATGCAAATGCATGCAATG
*
88640594 TAATGCAAATGCATGGAATG
1 TAATGCAAATGCATGCAATG
88640614 -AATGCAAA
1 TAATGCAAA
88640622 AGAAAGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (20 bp):
TAATGCAAATGCATGCAATG
Found at i:88642689 original size:15 final size:14
Alignment explanation
Indices: 88642655--88642699 Score: 58
Period size: 15 Copynumber: 3.3 Consensus size: 14
88642645 AAATAAATCA
*
88642655 AAATAATAAGA-AT
1 AAATAATAATATAT
88642668 AAA-AATAATATAT
1 AAATAATAATATAT
88642681 GAAATAATAATATAT
1 -AAATAATAATATAT
88642696 AAAT
1 AAAT
88642700 GAAATTTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 6 0.21
13 5 0.18
14 7 0.25
15 10 0.36
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (14 bp):
AAATAATAATATAT
Found at i:88642703 original size:19 final size:18
Alignment explanation
Indices: 88642645--88642704 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 18
88642635 TTAAAGTTCG
*
88642645 AAAT-AAATCAAAATAAT
1 AAATGAAATAAAAATAAT
88642662 -AA-G-AATAAAAATAAT
1 AAATGAAATAAAAATAAT
* *
88642677 ATATGAAATAATAATATAT
1 AAATGAAATAAAAATA-AT
88642696 AAATGAAAT
1 AAATGAAAT
88642705 TTCAAAATAC
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 11 0.32
16 3 0.09
17 1 0.03
18 9 0.26
19 10 0.29
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.27
Consensus pattern (18 bp):
AAATGAAATAAAAATAAT
Found at i:88642919 original size:30 final size:29
Alignment explanation
Indices: 88642885--88642976 Score: 86
Period size: 30 Copynumber: 3.3 Consensus size: 29
88642875 AAAAGAAAAT
88642885 ATATATACACAAAATAATATAAAATCAATA
1 ATATATACACAAAATAATA-AAAATCAATA
* *
88642915 ATATATATACATAATAATAAAAA--AAT-
1 ATATATACACAAAATAATAAAAATCAATA
* *
88642941 AT-T-TACATAAAATAATAGGAAATCAATA
1 ATATATACACAAAATAATA-AAAATCAATA
*
88642969 ATGTATAC
1 ATATATAC
88642977 TTAGAATAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
24 11 0.22
25 4 0.08
26 2 0.04
27 6 0.12
28 2 0.04
29 5 0.10
30 20 0.40
ACGTcount: A:0.60, C:0.08, G:0.03, T:0.29
Consensus pattern (29 bp):
ATATATACACAAAATAATAAAAATCAATA
Found at i:88642930 original size:16 final size:16
Alignment explanation
Indices: 88642882--88642933 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
88642872 CTTAAAAGAA
*
88642882 AATATATATACACAA-
1 AATATATATACATAAT
*
88642897 AATA-ATATAAAATCAAT
1 AATATATAT-ACAT-AAT
88642914 AATATATATACATAAT
1 AATATATATACATAAT
88642930 AATA
1 AATA
88642934 AAAAAATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
14 4 0.13
15 6 0.20
16 9 0.30
17 7 0.23
18 4 0.13
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (16 bp):
AATATATATACATAAT
Found at i:88643247 original size:18 final size:18
Alignment explanation
Indices: 88643226--88643265 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
88643216 AATAAGGAAT
88643226 AAAACATAAATTGAAGTAA
1 AAAAC-TAAATTGAAGTAA
*
88643245 AAAACTCAATTGAAGTAA
1 AAAACTAAATTGAAGTAA
88643263 AAA
1 AAA
88643266 TAAAACCGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.20
Consensus pattern (18 bp):
AAAACTAAATTGAAGTAA
Found at i:88648472 original size:25 final size:25
Alignment explanation
Indices: 88648405--88648475 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 25
88648395 AATACAAACA
* *
88648405 CAACCCAATTACAAAACCCAAAACCTAT
1 CAACCCAATTAC--AACCC-AAACCAAG
* *
88648433 CAACCTAATTA-AACCCAAATCAAG
1 CAACCCAATTACAACCCAAACCAAG
88648457 CAACCCAATTACAACCCAA
1 CAACCCAATTACAACCCAA
88648476 CCTACCCCAG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
24 15 0.41
25 12 0.32
28 10 0.27
ACGTcount: A:0.49, C:0.35, G:0.01, T:0.14
Consensus pattern (25 bp):
CAACCCAATTACAACCCAAACCAAG
Found at i:88649485 original size:3 final size:3
Alignment explanation
Indices: 88649477--88649702 Score: 141
Period size: 3 Copynumber: 74.7 Consensus size: 3
88649467 TTTAACTACT
* * * *
88649477 TTA TTA TTA -AA TTA GTTAA TT- TTA TTA TTA TTA CTA TTA TTT TTT
1 TTA TTA TTA TTA TTA -TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * ** *
88649522 TTCA CTA TTA TTA GTCA TTA TCA TTA CTA CCA TTA TTA TTA CTA TTA
1 TT-A TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * * * * *
88649569 TTT TTA TTT TTA TCA CTA TTA CTC TCA CTA TTA TTA TTT TTA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
88649617 TTA CTA TTA TCA TTA TTA TTA TTC TTA TTA TTA GTA TTA TTA TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** *
88649665 TGC TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
88649703 TTGTTTTATT
Statistics
Matches: 164, Mismatches: 53, Indels: 12
0.72 0.23 0.05
Matches are distributed among these distances:
2 3 0.02
3 153 0.93
4 7 0.04
5 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:88649721 original size:17 final size:17
Alignment explanation
Indices: 88649699--88649748 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
88649689 TTATTATTAT
88649699 TATTTTGTTTTATTTAA
1 TATTTTGTTTTATTTAA
*
88649716 TATTTT-TATTTAATTTTA
1 TATTTTGT-TTT-ATTTAA
88649734 T-TTTTAGTTTTATTT
1 TATTTT-GTTTTATTT
88649749 TTATTTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
16 1 0.04
17 17 0.61
18 9 0.32
19 1 0.04
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (17 bp):
TATTTTGTTTTATTTAA
Found at i:88649724 original size:23 final size:22
Alignment explanation
Indices: 88649680--88649760 Score: 65
Period size: 23 Copynumber: 3.5 Consensus size: 22
88649670 ATTATTACTA
*
88649680 TTATTATTA-TTATTATTATTATT
1 TTATT-TTATTTA-TATTTTTATT
*
88649703 TTGTTTTATTTAATATTTTTATT
1 TTATTTTATTT-ATATTTTTATT
* * *
88649726 TAATTTTATTTTTAGTTTTATTT
1 TTATTTTATTTATATTTTTA-TT
88649749 TTATTTTTATTT
1 TTA-TTTTATTT
88649761 TACAATTAGC
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
22 10 0.21
23 28 0.60
24 9 0.19
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (22 bp):
TTATTTTATTTATATTTTTATT
Found at i:88649731 original size:28 final size:28
Alignment explanation
Indices: 88649686--88649754 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 28
88649676 ACTATTATTA
* *
88649686 TTATTATTATTATTATTTT-GTTTTA-TT
1 TTATTTTTATT-TAATTTTAGTTTTAGTT
*
88649713 TAATATTTTTATTTAATTTTATTTTTAGTT
1 T--TATTTTTATTTAATTTTAGTTTTAGTT
88649743 TTATTTTTATTT
1 TTATTTTTATTT
88649755 TTATTTTACA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
27 1 0.03
28 17 0.49
29 14 0.40
30 3 0.09
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (28 bp):
TTATTTTTATTTAATTTTAGTTTTAGTT
Found at i:88649739 original size:12 final size:12
Alignment explanation
Indices: 88649711--88649761 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
88649701 TTTTGTTTTA
88649711 TTTAATATTT-TT
1 TTTAAT-TTTATT
88649723 ATTTAATTTTATT
1 -TTTAATTTTATT
*
88649736 TTTAGTTTTATT
1 TTTAATTTTATT
*
88649748 TTTATTTTTATT
1 TTTAATTTTATT
88649760 TT
1 TT
88649762 ACAATTAGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
12 27 0.77
13 8 0.23
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (12 bp):
TTTAATTTTATT
Found at i:88649819 original size:21 final size:22
Alignment explanation
Indices: 88649778--88649819 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
88649768 AGCTTGCTTT
88649778 TCATTTATTCATTTACTTTATCG
1 TCATTTATT-ATTTACTTTATCG
*
88649801 TCATTTATT-TTTGCTTTAT
1 TCATTTATTATTTACTTTAT
88649820 TGTCGCTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
23 9 0.50
ACGTcount: A:0.19, C:0.14, G:0.05, T:0.62
Consensus pattern (22 bp):
TCATTTATTATTTACTTTATCG
Found at i:88653412 original size:50 final size:50
Alignment explanation
Indices: 88653337--88653613 Score: 464
Period size: 50 Copynumber: 5.5 Consensus size: 50
88653327 CCATGGTAAC
88653337 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
88653387 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
88653437 AAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
88653487 AAGTGATAAGTAATAGCTTCGACTACACTTATCTGATCAAGGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
88653537 AAGTGATAAGTGATAGCTTCGGTTACACTTATCTGATCAATGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
88653587 CAAGTGAAAAGTGGTAGCTTTGGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
88653614 CTGATCAGTG
Statistics
Matches: 214, Mismatches: 12, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
50 192 0.90
51 22 0.10
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.27
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:88653627 original size:31 final size:31
Alignment explanation
Indices: 88653589--88653768 Score: 270
Period size: 31 Copynumber: 5.8 Consensus size: 31
88653579 ACAAATGACA
**
88653589 AGTGAAAAGTGGTAGCTTTGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
* *
88653620 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
*
88653651 AGTGAAAAGTGGTAGCTCCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
*
88653682 AGTGAAAAGTGGTAGCTCCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
* *
88653713 AGTGAAAAATGGTAGCTCCGACTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
* *
88653744 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTCCGGCTAC
88653769 AAGTGACAAG
Statistics
Matches: 138, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 138 1.00
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
Found at i:88653941 original size:42 final size:43
Alignment explanation
Indices: 88653881--88653994 Score: 151
Period size: 42 Copynumber: 2.7 Consensus size: 43
88653871 ATGTGATTCG
* *
88653881 TGTAAGACTATAGTTGGGCTATGGCATCGA-TATATGAATATA
1 TGTAAGACCATAGTTGGGCTATGGCATCGATTATATGAAGATA
* * *
88653923 TGTAAGACCATAGCTGGGCTATGGCATC-ATTATGTGAAGATG
1 TGTAAGACCATAGTTGGGCTATGGCATCGATTATATGAAGATA
**
88653965 TGTAAGACCATAGTTGAACTATGGCATCGA
1 TGTAAGACCATAGTTGGGCTATGGCATCGA
88653995 GAAAACGAAG
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
41 1 0.02
42 60 0.97
43 1 0.02
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (43 bp):
TGTAAGACCATAGTTGGGCTATGGCATCGATTATATGAAGATA
Found at i:88657594 original size:38 final size:38
Alignment explanation
Indices: 88657547--88657619 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
88657537 TAGAGGGATA
88657547 TCAAAACTTTGAAGATGGTAGAGATTGTAGCCTATATC
1 TCAAAACTTTGAAGATGGTAGAGATTGTAGCCTATATC
88657585 TCAAAACTTTGAAGATGGTAGAGATTGTAGCCTAT
1 TCAAAACTTTGAAGATGGTAGAGATTGTAGCCTAT
88657620 CTCCTGGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (38 bp):
TCAAAACTTTGAAGATGGTAGAGATTGTAGCCTATATC
Found at i:88658878 original size:21 final size:21
Alignment explanation
Indices: 88658833--88658878 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
88658823 AAAGTTTTCC
*
88658833 AAAAAAAAAGAATAATAAAAT
1 AAAAAAAAAGAATAAGAAAAT
* *
88658854 AAAAAAAAAGAA-AAGACAAG
1 AAAAAAAAAGAATAAGAAAAT
88658874 AAAAA
1 AAAAA
88658879 TGAGAAGCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.83, C:0.02, G:0.09, T:0.07
Consensus pattern (21 bp):
AAAAAAAAAGAATAAGAAAAT
Found at i:88660132 original size:92 final size:91
Alignment explanation
Indices: 88660017--88660313 Score: 284
Period size: 92 Copynumber: 3.3 Consensus size: 91
88660007 CATTTCTTTA
* * *
88660017 AAGTTGCAGTGGAACAGATTGAAGCTATAAATTGCAGACCTTATCTCTCTGAAGTTGTAGTAGAG
1 AAGTTGCAGTGGAGCAGATTGAAGCTATAAATT-CAGATCTTATCTCTCTGAAGTTGCAGTAGAG
* *
88660082 CAGATCAGAGCAAACCTTATCTCCCTG
65 CAGATAAGAACAAACCTTATCTCCCTG
* * * *
88660109 AAGTTGCAGTAGAGCACG-TTGAAG-T-T--A-TAAG-TCTTATCTCCCTGAAGTTGCAGTGGAG
1 AAGTTGCAGTGGAGCA-GATTGAAGCTATAAATTCAGATCTTATCTCTCTGAAGTTGCAGTAGAG
* * * * *
88660167 CAAACTGAAGATATCGAATCTTATTTCCTTG
65 CAGA-T-AAGA-A-CAAACCTTATCTCCCTG
* ** * *
88660198 AAGTTACAGTGGAAAAGATTGAAACTATAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAAAG
1 AAGTTGCAGTGGAGCAGATTGAAGCTATAAATT-CAGATCTTATCTCTCTGAAGTTGCAGTAGAG
*
88660263 CAGATAAAAACAAACCTTATCTCCCTG
65 CAGATAAGAACAAACCTTATCTCCCTG
* *
88660290 AAGTTGTAGTGGAGCAGGTTGAAG
1 AAGTTGCAGTGGAGCAGATTGAAG
88660314 TCACTAGTCT
Statistics
Matches: 157, Mismatches: 35, Indels: 26
0.72 0.16 0.12
Matches are distributed among these distances:
85 26 0.17
86 3 0.02
87 4 0.03
88 2 0.01
89 30 0.19
90 2 0.01
91 2 0.01
92 51 0.32
93 3 0.02
94 4 0.03
95 3 0.02
96 27 0.17
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (91 bp):
AAGTTGCAGTGGAGCAGATTGAAGCTATAAATTCAGATCTTATCTCTCTGAAGTTGCAGTAGAGC
AGATAAGAACAAACCTTATCTCCCTG
Found at i:88660155 original size:44 final size:43
Alignment explanation
Indices: 88660097--88660516 Score: 242
Period size: 44 Copynumber: 9.4 Consensus size: 43
88660087 CAGAGCAAAC
* * *
88660097 CTTATCTCCCTGAAGTTGCAGTAGAGCACGTTGAAGTTATAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCA-GTTGAAGATACAAGT
**
88660141 CTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATATCGAA-T
1 CTTATCTCCCTGAAGTTGCAGTGGAGC-AGTTGAAGATA-C-AAGT
* * * ** * *
88660186 CTTATTTCCTTGAAGTTACAGTGGAAAAGATTGAAACTATAAATTACAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAG-TTG-AA-GAT--A-CA-AG-T
* ** * * **
88660237 CTTATCTCTCTGAAGTTGCAGTAAAGCAGAT-AA-AAACAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGTTGAAGATACAAGT
* *
88660278 CTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTGAAG-TCACTAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCA-GTTGAAGAT-ACAAGT
* *
88660322 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGACA-ATAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAG-TTGAAGATACA-AG-T
* ** * * **
88660367 CTTATCTCCTTGAAGTTATAGTGGAGTAGATCGAAGATAGCAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAG-TTGAAGATA-CAAGT
** * * * *
88660412 CTTATCTATCTAAAGTAGCAGTAGAGCGGGTTGAA-ATTACAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGC-AGTTGAAGA-TACAAGT
*
88660456 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATACCAA-T
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAG-TTGAAGATA-CAAGT
*
88660500 CTTATTTCCCTGAAGTT
1 CTTATCTCCCTGAAGTT
88660517 ACAGCAGAGC
Statistics
Matches: 280, Mismatches: 70, Indels: 52
0.70 0.17 0.13
Matches are distributed among these distances:
41 24 0.09
42 3 0.01
43 5 0.02
44 122 0.44
45 87 0.31
46 7 0.03
47 3 0.01
48 3 0.01
49 3 0.01
50 1 0.00
51 22 0.08
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (43 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGTTGAAGATACAAGT
Found at i:88660166 original size:181 final size:180
Alignment explanation
Indices: 88659834--88660358 Score: 655
Period size: 181 Copynumber: 2.9 Consensus size: 180
88659824 CATACCCCTG
* * * * * *
88659834 AAGTTGCAGTGGGACGGATTGAAGTTAT-AATGGC-GAATCTTATCTCCCTGTAGTTGCAGTAGA
1 AAGTTGCAGTGGAACAGATTGAAGCTATAAATTGCAG-ATCTTATCTCTCTGAAGTTGCAGTAGA
* * *
88659897 GCAGATTGAAGCCACTAAACCTTATCTCCCTGAAATAGCAGTGGAGCAGGTTGAAGTTA-AAGTC
65 GCAGATAG-AG---C-AAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTATAAGTC
** * * *
88659961 TTATCTCCCTGAAGTTATAGTGGAGTAGATTGAAGATAGT-GAATCTCATTTCTTTA
125 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATA-TCGAATCTCATTTCCTTA
* *
88660017 AAGTTGCAGTGGAACAGATTGAAGCTATAAATTGCAGACCTTATCTCTCTGAAGTTGTAGTAGAG
1 AAGTTGCAGTGGAACAGATTGAAGCTATAAATTGCAGATCTTATCTCTCTGAAGTTGCAGTAGAG
* *
88660082 CAGATCAGAGCAAACCTTATCTCCCTGAAGTTGCAGTAGAGCACGTTGAAGTTATAAGTCTTATC
66 CAGAT-AGAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTATAAGTCTTATC
* * *
88660147 TCCCTGAAGTTGCAGTGGAGCAAACTGAAGATATCGAATCTTATTTCCTTG
130 TCCCTGAAGTTGCAGTGGAGCAGACTGAAGATATCGAATCTCATTTCCTTA
* * * * *
88660198 AAGTTACAGTGGAAAAGATTGAAACTATAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAAAG
1 AAGTTGCAGTGGAACAGATTGAAGCTATAAATTGCAGATCTTATCTCTCTGAAGTTGCAGTAGAG
* * * *
88660263 CAGATAAAAACAAACCTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTGAAGTCACT-AGTCTTAT
66 CAGAT-AGAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTA-TAAGTCTTAT
88660327 CTCCCTGAAGTTGCAGTGGAGCAGACTGAAGA
129 CTCCCTGAAGTTGCAGTGGAGCAGACTGAAGA
88660359 CAATAGATCT
Statistics
Matches: 300, Mismatches: 36, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
180 40 0.13
181 196 0.65
182 1 0.00
183 25 0.08
184 36 0.12
185 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (180 bp):
AAGTTGCAGTGGAACAGATTGAAGCTATAAATTGCAGATCTTATCTCTCTGAAGTTGCAGTAGAG
CAGATAGAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTATAAGTCTTATCT
CCCTGAAGTTGCAGTGGAGCAGACTGAAGATATCGAATCTCATTTCCTTA
Found at i:88662076 original size:3 final size:3
Alignment explanation
Indices: 88662068--88662385 Score: 218
Period size: 3 Copynumber: 106.3 Consensus size: 3
88662058 TTTAGCTACT
* * * * *
88662068 TTA TTA TTA -AA TTA GTTAA TT- TTA TTA TTC TTA CTA TTA TTT TTT
1 TTA TTA TTA TTA TTA -TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * ** *
88662113 TTCA CTA TTA TTA TTCA TTA TCA TTA TTA CCA TTA TTA TTA CTA TTA
1 TT-A TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * * * *
88662160 TTT TTA TTT TTA TCA CTA TTA CTC TTA CTA TTT TTA TT- TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
88662207 CTA TTA TCA TTA TTA TTA TTA CTA TTA TTA TT- TTC TT- TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
88662253 TTTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TCA TTA TTC TTA TTA
1 -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * ** * *
88662299 TTG GTA TTA TTA TCA TGC TTA TTA TTA CTA TTA TTA TTA -TG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
88662346 TTCT TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
88662386 CATCATCATT
Statistics
Matches: 238, Mismatches: 64, Indels: 26
0.73 0.20 0.08
Matches are distributed among these distances:
2 12 0.05
3 212 0.89
4 13 0.05
5 1 0.00
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:88662427 original size:6 final size:6
Alignment explanation
Indices: 88662406--88662459 Score: 53
Period size: 5 Copynumber: 9.5 Consensus size: 6
88662396 TCTTATTTTG
* *
88662406 TTTTAT TTAATAT TTTTA- TTTT-G TTTTAT TTTTAT TTTTA- TTTTA-
1 TTTTAT TT-TTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
88662451 TTTTAT TTT
1 TTTTAT TTT
88662460 ACAATTAGCT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
5 18 0.44
6 18 0.44
7 5 0.12
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:88662437 original size:16 final size:16
Alignment explanation
Indices: 88662343--88662460 Score: 69
Period size: 18 Copynumber: 6.9 Consensus size: 16
88662333 TATTATGTTA
88662343 TTATTCTTTATTTTATT
1 TTATT-TTTATTTTATT
*
88662360 ATTATTATTATTATTATT
1 -TTATTTTTATT-TTATT
* * * *
88662378 ATTATTATCATCATCATT
1 -TTATTTTTAT-TTTATT
*
88662396 TCT-TATTTTGTTTTATT
1 T-TAT-TTTTATTTTATT
*
88662413 TAATATTTTTATTTTGTT
1 T--TATTTTTATTTTATT
88662431 TTATTTTTATTTTTATT
1 TTATTTTTA-TTTTATT
88662448 TTA-TTTTATTTTA
1 TTATTTTTATTTTA
88662461 CAATTAGCTT
Statistics
Matches: 80, Mismatches: 13, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
15 5 0.06
16 13 0.16
17 21 0.26
18 40 0.50
19 1 0.01
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (16 bp):
TTATTTTTATTTTATT
Found at i:88662444 original size:22 final size:22
Alignment explanation
Indices: 88662393--88662459 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
88662383 TATCATCATC
*
88662393 ATTTCTTATTTTGTTTTATTTAAT
1 ATTT-TTATTTTGTTTTATTT-TT
88662417 ATTTTTATTTTGTTTTATTTTT
1 ATTTTTATTTTGTTTTATTTTT
*
88662439 ATTTTTATTTTATTTTATTTT
1 ATTTTTATTTTGTTTTATTTT
88662460 ACAATTAGCT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
22 21 0.51
23 16 0.39
24 4 0.10
ACGTcount: A:0.18, C:0.01, G:0.03, T:0.78
Consensus pattern (22 bp):
ATTTTTATTTTGTTTTATTTTT
Found at i:88674428 original size:6 final size:6
Alignment explanation
Indices: 88674414--88674450 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
88674404 TTATATTGTA
88674414 TTTATAT TTTAAT TTTAAT TTTAAT TTT-AT TTTAAT T
1 TTTA-AT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT T
88674451 ATTTTCATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 5 0.17
6 20 0.69
7 4 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTAAT
Found at i:88674891 original size:6 final size:6
Alignment explanation
Indices: 88674880--88674907 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
88674870 TCGCTCTTGT
88674880 TATTTA TATTTA TATTTA TATTTA TATT
1 TATTTA TATTTA TATTTA TATTTA TATT
88674908 AAGTTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATTTA
Found at i:88675229 original size:31 final size:32
Alignment explanation
Indices: 88675194--88675262 Score: 113
Period size: 31 Copynumber: 2.2 Consensus size: 32
88675184 ATGGGCATTA
*
88675194 TCATTACATACTTTTATTATTTTAGTCA-ATG
1 TCATTACATACTTTTATCATTTTAGTCACATG
*
88675225 TCATTACATACTTTTATCATTTTAGTCACCTG
1 TCATTACATACTTTTATCATTTTAGTCACATG
88675257 TCATTA
1 TCATTA
88675263 ATTTCTCATT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 27 0.77
32 8 0.23
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.49
Consensus pattern (32 bp):
TCATTACATACTTTTATCATTTTAGTCACATG
Found at i:88675434 original size:14 final size:14
Alignment explanation
Indices: 88675415--88675441 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
88675405 TTTTACAGAG
88675415 GAAAATCTGAGTTA
1 GAAAATCTGAGTTA
88675429 GAAAATCTGAGTT
1 GAAAATCTGAGTT
88675442 CTTACACTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (14 bp):
GAAAATCTGAGTTA
Found at i:88675635 original size:13 final size:13
Alignment explanation
Indices: 88675603--88675629 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
88675593 AGACATTTCA
88675603 TATTATCTAGTAT
1 TATTATCTAGTAT
88675616 TATTATCTAGTAT
1 TATTATCTAGTAT
88675629 T
1 T
88675630 CATATCAGAA
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:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (13 bp):
TATTATCTAGTAT
Found at i:88678506 original size:25 final size:25
Alignment explanation
Indices: 88678478--88678548 Score: 115
Period size: 25 Copynumber: 2.8 Consensus size: 25
88678468 ATGCTTATAA
88678478 GAGCTATGAATCAGTATGCTCTCGC
1 GAGCTATGAATCAGTATGCTCTCGC
88678503 GAGCTATGAATCAGTATGCTCTCGC
1 GAGCTATGAATCAGTATGCTCTCGC
* * *
88678528 GAGCTGTGAATCGGTAAGCTC
1 GAGCTATGAATCAGTATGCTC
88678549 ATAAGAGCTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.27
Consensus pattern (25 bp):
GAGCTATGAATCAGTATGCTCTCGC
Found at i:88681373 original size:25 final size:26
Alignment explanation
Indices: 88681313--88681374 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 26
88681303 TTCAGGAATG
*
88681313 CTCATACGAG-CATGTAAACGGGAAC
1 CTCATAAGAGCCATGTAAACGGGAAC
** *
88681338 CTCATGTGAGCCATGT-AACGGGAAG
1 CTCATAAGAGCCATGTAAACGGGAAC
*
88681363 TTCATAAGAGCC
1 CTCATAAGAGCC
88681375 GTAATCAGGA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
25 25 0.83
26 5 0.17
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (26 bp):
CTCATAAGAGCCATGTAAACGGGAAC
Found at i:88681496 original size:27 final size:25
Alignment explanation
Indices: 88681356--88681497 Score: 96
Period size: 24 Copynumber: 5.7 Consensus size: 25
88681346 AGCCATGTAA
* * *
88681356 CGGGAAGTTCATAAGAGCC-GTAAT
1 CGGGAAGCTCATAAGAGCCAATTAT
* ** *
88681380 CAGGAAGCTCATGCGAGCTAA-TAT
1 CGGGAAGCTCATAAGAGCCAATTAT
* * *
88681404 CGAGAAGCTTA-AAAAGCC-ATTAAT
1 CGGGAAGCTCATAAGAGCCAATT-AT
*
88681428 CAGGAAGCTCATAAGAGCCAATTAT
1 CGGGAAGCTCATAAGAGCCAATTAT
* *
88681453 CGGGAAGCTCGTGAGAGCCATATATAT
1 CGGGAAGCTCATAAGAGCCA-AT-TAT
88681480 CGGGACA-CTCATAAGAGC
1 CGGGA-AGCTCATAAGAGC
88681498 TGTAGTGAGT
Statistics
Matches: 87, Mismatches: 23, Indels: 13
0.71 0.19 0.11
Matches are distributed among these distances:
22 1 0.01
23 4 0.05
24 34 0.39
25 25 0.29
26 5 0.06
27 17 0.20
28 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.20
Consensus pattern (25 bp):
CGGGAAGCTCATAAGAGCCAATTAT
Found at i:88682408 original size:32 final size:31
Alignment explanation
Indices: 88682367--88682434 Score: 75
Period size: 32 Copynumber: 2.2 Consensus size: 31
88682357 GAAAGCTTTA
**
88682367 AATTAAATTTGTTTCATT-TTAATTTTTATTT
1 AATTAAATTT-TGCCATTATTAATTTTTATTT
*
88682398 AATTACAATTTTGCCATTATTTATTTTTATTT
1 AATTA-AATTTTGCCATTATTAATTTTTATTT
*
88682430 TATTA
1 AATTA
88682435 TTTTTTATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
31 10 0.32
32 21 0.68
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (31 bp):
AATTAAATTTTGCCATTATTAATTTTTATTT
Found at i:88687213 original size:36 final size:34
Alignment explanation
Indices: 88687133--88687213 Score: 85
Period size: 34 Copynumber: 2.3 Consensus size: 34
88687123 TACTAAACAT
*
88687133 TATAAAATATTATATAAAATCAAACAAAGATGGAA
1 TATAAAA-ATTATATAAAATAAAACAAAGATGGAA
* *
88687168 T-CAATAATTATTATAAAATAAAAGCACAAGAT-GAA
1 TATAAAAATTA-TATAAAATAAAA-CA-AAGATGGAA
88687203 TATAAAAATTA
1 TATAAAAATTA
88687214 ATGAACATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
33 4 0.11
34 14 0.38
35 7 0.19
36 12 0.32
ACGTcount: A:0.59, C:0.06, G:0.07, T:0.27
Consensus pattern (34 bp):
TATAAAAATTATATAAAATAAAACAAAGATGGAA
Found at i:88690087 original size:50 final size:50
Alignment explanation
Indices: 88689974--88690088 Score: 112
Period size: 50 Copynumber: 2.3 Consensus size: 50
88689964 AATCATCCAT
*
88689974 ATTTCAGAATCAAATACAGATGCAGAAATAAAGAATTTCAGATACAAATAC
1 ATTT-AGATTCAAATACAGATGCAGAAATAAAGAATTTCAGATACAAATAC
* * * *
88690025 A-TAATATATCAAATACAGATGCAGAACATATCAG-A-TTCAGATATAGAATA-
1 ATTTAGAT-TCAAATACAGATGCAGAA-ATA-AAGAATTTCAGATACA-AATAC
88690075 ATTTAGATTCAAAT
1 ATTTAGATTCAAAT
88690089 GCAGGTTCTT
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
49 2 0.04
50 35 0.67
51 13 0.25
52 2 0.04
ACGTcount: A:0.50, C:0.12, G:0.11, T:0.27
Consensus pattern (50 bp):
ATTTAGATTCAAATACAGATGCAGAAATAAAGAATTTCAGATACAAATAC
Found at i:88695313 original size:32 final size:32
Alignment explanation
Indices: 88695277--88695339 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
88695267 TACATGAATA
* * *
88695277 ATGAATTTAGATAAATCTACATCCAAATTCAC
1 ATGAATCTAGACAAATATACATCCAAATTCAC
**
88695309 ATGAATCTAGACAAATATTTATCCAAATTCA
1 ATGAATCTAGACAAATATACATCCAAATTCA
88695340 TTTTGGATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.32
Consensus pattern (32 bp):
ATGAATCTAGACAAATATACATCCAAATTCAC
Found at i:88695722 original size:17 final size:19
Alignment explanation
Indices: 88695699--88695735 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
88695689 TATGTGTCTT
*
88695699 TTTTTTATA-AAATATATA
1 TTTTTAATATAAATATATA
88695717 TTTTTAATATAAATATATA
1 TTTTTAATATAAATATATA
88695736 AATATATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTTAATATAAATATATA
Found at i:88698371 original size:14 final size:14
Alignment explanation
Indices: 88698338--88698383 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
88698328 AGGAATAGGA
*
88698338 AATTTTATTAGATT
1 AATTTAATTAGATT
*
88698352 ATTTTAAGTTA-ATT
1 AATTTAA-TTAGATT
88698366 AATTTAATTAGATT
1 AATTTAATTAGATT
88698380 AATT
1 AATT
88698384 AATATTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 3 0.11
14 21 0.78
15 3 0.11
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (14 bp):
AATTTAATTAGATT
Found at i:88700664 original size:17 final size:16
Alignment explanation
Indices: 88700644--88700676 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
88700634 TATTTTATAT
88700644 TAATTAAATAAAGTAAA
1 TAATTAAATAAA-TAAA
88700661 TAATTAAATAAATAAA
1 TAATTAAATAAATAAA
88700677 AGAAAGACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
TAATTAAATAAATAAA
Found at i:88700842 original size:16 final size:16
Alignment explanation
Indices: 88700795--88700843 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
88700785 TTAAATGAAG
* *
88700795 AAAGAAAAGAAAGAAA
1 AAAGAATAGAAAGAAC
*
88700811 AAAGAATACAAAGAAC
1 AAAGAATAGAAAGAAC
88700827 AAAGAATAGAAAGAAC
1 AAAGAATAGAAAGAAC
88700843 A
1 A
88700844 GAAGGTGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.73, C:0.06, G:0.16, T:0.04
Consensus pattern (16 bp):
AAAGAATAGAAAGAAC
Found at i:88700846 original size:5 final size:4
Alignment explanation
Indices: 88700792--88700896 Score: 63
Period size: 4 Copynumber: 24.5 Consensus size: 4
88700782 TAGTTAAATG
* *
88700792 AAGA AAGAA AAGA AAGA AA-A AAGA ATACA AAG- AACA AAGA ATAGA AAGA
1 AAGA AAG-A AAGA AAGA AAGA AAGA A-AGA AAGA AAGA AAGA A-AGA AAGA
* *
88700841 ACAGA AGGTGA AACGA AA-A ACAGA GAAGGA AAGA AGGA AAGA AAGA AAGA
1 A-AGA A--AGA AA-GA AAGA A-AGA -AA-GA AAGA AAGA AAGA AAGA AAGA
88700891 AAGA AA
1 AAGA AA
88700897 AGGGAAAATT
Statistics
Matches: 80, Mismatches: 9, Indels: 24
0.71 0.08 0.21
Matches are distributed among these distances:
3 7 0.09
4 44 0.55
5 23 0.29
6 6 0.08
ACGTcount: A:0.69, C:0.05, G:0.24, T:0.03
Consensus pattern (4 bp):
AAGA
Found at i:88703289 original size:22 final size:20
Alignment explanation
Indices: 88703243--88703298 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 20
88703233 CATGGTGTGC
*
88703243 CCACACGGGTGTGTTATGGA
1 CCACACGGGTGTGTTATAGA
* *
88703263 ACACACGGGTGTGTCATCTAGA
1 CCACACGGGTGTGT--TATAGA
88703285 CCACACGGGTGTGT
1 CCACACGGGTGTGT
88703299 GAAACTATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 13 0.43
22 17 0.57
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.23
Consensus pattern (20 bp):
CCACACGGGTGTGTTATAGA
Found at i:88704620 original size:16 final size:16
Alignment explanation
Indices: 88704601--88704647 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 16
88704591 TAAAAGATAT
88704601 AAATATTTTTATAATA
1 AAATATTTTTATAATA
88704617 AAATTTATTTTTATAA-A
1 AAA--TATTTTTATAATA
*
88704634 AAACATTTTT-TAAT
1 AAATATTTTTATAAT
88704648 TTTTTTTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 3 0.11
15 6 0.22
16 3 0.11
17 4 0.15
18 11 0.41
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
AAATATTTTTATAATA
Found at i:88706053 original size:10 final size:9
Alignment explanation
Indices: 88706039--88706123 Score: 64
Period size: 10 Copynumber: 8.9 Consensus size: 9
88706029 TATTTAAGCT
88706039 TAAAAATTA
1 TAAAAATTA
88706048 TTAAAATATTA
1 -TAAAA-ATTA
88706059 TAATAAATT-
1 TAA-AAATTA
*
88706068 TAAAATTTA
1 TAAAAATTA
88706077 TAAAAATTA
1 TAAAAATTA
* *
88706086 AAGAAAACTA
1 TA-AAAATTA
*
88706096 TAAAAAATA
1 TAAAAATTA
*
88706105 TTAAAATGTTA
1 -TAAAA-ATTA
88706116 TAAAAATT
1 TAAAAATT
88706124 TACATGATTA
Statistics
Matches: 60, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
8 4 0.07
9 20 0.33
10 28 0.47
11 8 0.13
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.35
Consensus pattern (9 bp):
TAAAAATTA
Found at i:88706072 original size:19 final size:18
Alignment explanation
Indices: 88706048--88706125 Score: 77
Period size: 19 Copynumber: 4.2 Consensus size: 18
88706038 TTAAAAATTA
88706048 TTAAAATATTATAATAAAT
1 TTAAAATATTATAA-AAAT
88706067 TTAAAAT-TTATAAAAAT
1 TTAAAATATTATAAAAAT
* * *
88706084 TAAAGAAAACTATAAAAAAT
1 TTAA-AATATTAT-AAAAAT
*
88706104 ATTAAAATGTTATAAAAAT
1 -TTAAAATATTATAAAAAT
88706123 TTA
1 TTA
88706126 CATGATTAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
17 7 0.15
18 11 0.23
19 16 0.33
20 11 0.23
21 3 0.06
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (18 bp):
TTAAAATATTATAAAAAT
Found at i:88706159 original size:21 final size:20
Alignment explanation
Indices: 88706135--88706187 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
88706125 ACATGATTAA
* **
88706135 ATATTATAAAAGATTATCGAT
1 ATATTATAAAA-AATATAAAT
88706156 ATATTATGAAAAAATATAAAT
1 ATATTAT-AAAAAATATAAAT
88706177 ATATTATAAAA
1 ATATTATAAAA
88706188 TTTGTAGATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.14
21 20 0.71
22 4 0.14
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.36
Consensus pattern (20 bp):
ATATTATAAAAAATATAAAT
Found at i:88709554 original size:21 final size:21
Alignment explanation
Indices: 88709529--88709581 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
88709519 CGCTATTTCT
* *
88709529 AATCTCATCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
88709550 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
88709571 AATCTCACCGC
1 AATCTCACCGC
88709582 CACCGCTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.36, G:0.09, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:88709796 original size:87 final size:87
Alignment explanation
Indices: 88709650--88709823 Score: 348
Period size: 87 Copynumber: 2.0 Consensus size: 87
88709640 GTCTAATAAG
88709650 GAGTGTTACATTAATCGTCCAAACAATTCTGGTTAATCTATCTTACAAGCATTTCCATCATCAAA
1 GAGTGTTACATTAATCGTCCAAACAATTCTGGTTAATCTATCTTACAAGCATTTCCATCATCAAA
88709715 CTTGAATTTTTAACATTCAAAT
66 CTTGAATTTTTAACATTCAAAT
88709737 GAGTGTTACATTAATCGTCCAAACAATTCTGGTTAATCTATCTTACAAGCATTTCCATCATCAAA
1 GAGTGTTACATTAATCGTCCAAACAATTCTGGTTAATCTATCTTACAAGCATTTCCATCATCAAA
88709802 CTTGAATTTTTAACATTCAAAT
66 CTTGAATTTTTAACATTCAAAT
88709824 AACATTTCAT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (87 bp):
GAGTGTTACATTAATCGTCCAAACAATTCTGGTTAATCTATCTTACAAGCATTTCCATCATCAAA
CTTGAATTTTTAACATTCAAAT
Found at i:88710105 original size:20 final size:20
Alignment explanation
Indices: 88710080--88710122 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
88710070 ATTGGGATTG
88710080 AAGTAAGGAAAGGAGAA-GGA
1 AAGTAAGGAAA-GAGAAGGGA
*
88710100 AAGTAAGGGAAGAGAAGGGA
1 AAGTAAGGAAAGAGAAGGGA
88710120 AAG
1 AAG
88710123 GAATGCGAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.53, C:0.00, G:0.42, T:0.05
Consensus pattern (20 bp):
AAGTAAGGAAAGAGAAGGGA
Found at i:88711916 original size:17 final size:17
Alignment explanation
Indices: 88711891--88711923 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
88711881 ATTATGATAT
88711891 ATATATATATATAGACA
1 ATATATATATATAGACA
*
88711908 ATATGTATATATAGAC
1 ATATATATATATAGAC
88711924 TCATGAATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (17 bp):
ATATATATATATAGACA
Found at i:88714222 original size:62 final size:63
Alignment explanation
Indices: 88714125--88714262 Score: 149
Period size: 62 Copynumber: 2.2 Consensus size: 63
88714115 AATCCTAAAT
* * *
88714125 AATGAGTTACACGGCTTGGATACACGTCCATGTCCTTGGC-CTGTGTGAC-CTAA-AATACAAAA
1 AATGAGTTACACGGCTTGGACACACCTCCATGTCCTTAGCTC-GTGTGACTCTAATAATA-AAAA
** * *
88714187 AATGAGTTACACGGCTTGGACACACACTTGA-GTCCTTAGCTCGTGTGCCTCTAATTCATAAAAA
1 AATGAGTTACACGGCTTGGACACAC-CTCCATGTCCTTAGCTCGTGTGACTCTAA-TAATAAAAA
88714251 AATGAGTTACAC
1 AATGAGTTACAC
88714263 AACCTACCAC
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
62 38 0.59
63 7 0.11
64 16 0.25
65 3 0.05
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (63 bp):
AATGAGTTACACGGCTTGGACACACCTCCATGTCCTTAGCTCGTGTGACTCTAATAATAAAAA
Found at i:88721997 original size:16 final size:16
Alignment explanation
Indices: 88721976--88722006 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
88721966 AATCGAAAGT
88721976 AAAGAAAAAGAAAAAC
1 AAAGAAAAAGAAAAAC
*
88721992 AAAGAAAATGAAAAA
1 AAAGAAAAAGAAAAA
88722007 GAAATAAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.03, G:0.13, T:0.03
Consensus pattern (16 bp):
AAAGAAAAAGAAAAAC
Found at i:88722006 original size:7 final size:6
Alignment explanation
Indices: 88721976--88722036 Score: 54
Period size: 6 Copynumber: 10.0 Consensus size: 6
88721966 AATCGAAAGT
* *
88721976 AAAGAA AAAG-A AAA-AC AAAGAA AATGAA AAAGAA ATAAGAA ACAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA A-AAGAA A-AAGAA
*
88722024 AAATAGA AAAGAA
1 AAAGA-A AAAGAA
88722037 GAAGGAACGT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
5 7 0.16
6 20 0.45
7 17 0.39
ACGTcount: A:0.77, C:0.03, G:0.15, T:0.05
Consensus pattern (6 bp):
AAAGAA
Found at i:88730877 original size:29 final size:29
Alignment explanation
Indices: 88730820--88730877 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
88730810 CCACTTTGAA
* * * * *
88730820 ACGAATTCTCAACGAATAAGTTGTTCACC
1 ACGAACTCTCAACAAACAAGTTCTCCACC
88730849 ACGAACTCTCAACAAACAAGTTCTCCACC
1 ACGAACTCTCAACAAACAAGTTCTCCACC
88730878 TCTTCCACGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.36, C:0.31, G:0.10, T:0.22
Consensus pattern (29 bp):
ACGAACTCTCAACAAACAAGTTCTCCACC
Found at i:88735732 original size:5 final size:5
Alignment explanation
Indices: 88735722--88735753 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
88735712 CAATTTGAGA
88735722 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
88735754 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:88735747 original size:9 final size:9
Alignment explanation
Indices: 88735723--88735753 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
88735713 AATTTGAGAA
88735723 AAATAAAAT
1 AAATAAAAT
88735732 AAAATAAAAT
1 -AAATAAAAT
88735742 AAATAAAAT
1 AAATAAAAT
88735751 AAA
1 AAA
88735754 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:88740663 original size:17 final size:17
Alignment explanation
Indices: 88740643--88740749 Score: 108
Period size: 17 Copynumber: 6.3 Consensus size: 17
88740633 AAGTCTACTC
*
88740643 AAGTTCAGAATTTGCTT
1 AAGTTCAAAATTTGCTT
88740660 AAGTTCAAAATTCT-CTT
1 AAGTTCAAAATT-TGCTT
** *
88740677 AAGCCCAAAATTTGTTT
1 AAGTTCAAAATTTGCTT
* *
88740694 AAGTTCAAAATGTGTTT
1 AAGTTCAAAATTTGCTT
* *
88740711 AAGTTCAAGATTTGATT
1 AAGTTCAAAATTTGCTT
*
88740728 AAATTCAAAATTTGCTT
1 AAGTTCAAAATTTGCTT
*
88740745 GAGTT
1 AAGTT
88740750 TACAGAAAGA
Statistics
Matches: 73, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
16 1 0.01
17 71 0.97
18 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (17 bp):
AAGTTCAAAATTTGCTT
Found at i:88743705 original size:45 final size:45
Alignment explanation
Indices: 88743644--88743729 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
88743634 GTCAAGAAAG
88743644 GGAGCTCGCGGTCTCAGTTCAG-ACATGCCAAGGGGTGCTCGCAAA
1 GGAGCTCGCGGTCTCAGTTC-GTACATGCCAAGGGGTGCTCGCAAA
*
88743689 GGAGCTCGCGGTCTCAGTTCGTACATGTCAAGGGGTGCTCG
1 GGAGCTCGCGGTCTCAGTTCGTACATGCCAAGGGGTGCTCG
88743730 TAAGGGGAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 1 0.03
45 38 0.97
ACGTcount: A:0.19, C:0.26, G:0.35, T:0.21
Consensus pattern (45 bp):
GGAGCTCGCGGTCTCAGTTCGTACATGCCAAGGGGTGCTCGCAAA
Found at i:88748912 original size:16 final size:17
Alignment explanation
Indices: 88748891--88748923 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
88748881 AATCGATGTC
88748891 ACCCCT-AAAGTATCGG
1 ACCCCTAAAAGTATCGG
88748907 ACCCCTAAAAGTATCGG
1 ACCCCTAAAAGTATCGG
88748924 GTAAGGAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.33, C:0.30, G:0.18, T:0.18
Consensus pattern (17 bp):
ACCCCTAAAAGTATCGG
Found at i:88752513 original size:16 final size:16
Alignment explanation
Indices: 88752492--88752523 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
88752482 TCAGGAGCTA
88752492 CAGGAGTACATGGCTG
1 CAGGAGTACATGGCTG
88752508 CAGGAGTACATGGCTG
1 CAGGAGTACATGGCTG
88752524 TGATTTCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.38, T:0.19
Consensus pattern (16 bp):
CAGGAGTACATGGCTG
Found at i:88753276 original size:16 final size:17
Alignment explanation
Indices: 88753241--88753278 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
88753231 ATTATTTTAA
*
88753241 ATTTTTATTAAATCATAT
1 ATTTTAATTAAA-CATAT
88753259 ATTTTAATTAAA-ATAT
1 ATTTTAATTAAACATAT
88753275 ATTT
1 ATTT
88753279 AATATTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTAATTAAACATAT
Found at i:88753367 original size:120 final size:120
Alignment explanation
Indices: 88753243--88753530 Score: 481
Period size: 120 Copynumber: 2.4 Consensus size: 120
88753233 TATTTTAAAT
* *
88753243 TTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTT-TCTTTTA
1 TTTTATTAAATTATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTTATATTTTA
* *
88753307 TAGTATCATATATTATGATTTGAGTAAATTCATATAAGACTATTAATTATTAAGAA
65 CAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAA
* *
88753363 TTTTATTAAATTATATATTTTAATTATAATATATTTAATAATT-ATTATTTTAATTTATATTTTA
1 TTTTATTAAATTATATATTTTAATTAAAATATATTTAAT-ATTAATTATTTAAATTTATATTTTA
88753427 CAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAA
65 CAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAA
*
88753483 TTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTAT
1 TTTTATTAAATTATATATTTTAATTAAAATATATTTAATATTAATTAT
88753531 GTTTAAATAT
Statistics
Matches: 157, Mismatches: 8, Indels: 6
0.92 0.05 0.04
Matches are distributed among these distances:
119 7 0.04
120 147 0.94
121 3 0.02
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (120 bp):
TTTTATTAAATTATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTTATATTTTAC
AGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAA
Found at i:88753423 original size:15 final size:14
Alignment explanation
Indices: 88753371--88753426 Score: 55
Period size: 15 Copynumber: 4.1 Consensus size: 14
88753361 AATTTTATTA
88753371 AATTATA-TATTTT
1 AATTATATTATTTT
*
88753384 AATTATAATATATTT
1 AATTATATTAT-TTT
*
88753399 AATAATTATTATTTT
1 AATTA-TATTATTTT
88753414 AATT-TA-TATTTT
1 AATTATATTATTTT
88753426 A
1 A
88753427 CAGTATCATA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
12 7 0.19
13 9 0.24
14 3 0.08
15 13 0.35
16 5 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
AATTATATTATTTT
Found at i:88753487 original size:61 final size:61
Alignment explanation
Indices: 88753302--88753488 Score: 183
Period size: 61 Copynumber: 3.1 Consensus size: 61
88753292 TCAAATTTTC
*
88753302 TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGACTATTAATTATTAAGAA
1 TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAA
* * * * * * *
88753363 TTTTATTA-AATTATATATT-TTAATT-A-T-AATAT-ATTTAATAATTATT-ATT-TTAATTTA
1 TTTTA-TAGTATCATATATTATGATTTGAGTAAAT-TCATATAAGAA-TATTAATTATTAA--GA
88753420 TA
61 -A
*
88753422 TTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAA
1 TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAA
88753483 TTTTAT
1 TTTTAT
88753489 TAAATTATAT
Statistics
Matches: 95, Mismatches: 17, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
56 4 0.04
57 12 0.13
58 8 0.08
59 16 0.17
60 8 0.08
61 21 0.22
62 9 0.09
63 13 0.14
64 4 0.04
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (61 bp):
TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAA
Found at i:88753510 original size:18 final size:17
Alignment explanation
Indices: 88753482--88753516 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
88753472 ATTATTAAGA
*
88753482 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
88753499 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
88753517 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:88753630 original size:147 final size:149
Alignment explanation
Indices: 88753470--88753744 Score: 509
Period size: 147 Copynumber: 1.9 Consensus size: 149
88753460 ATAAGAATAT
*
88753470 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
88753535 AAATATGATTAAATTATTTATTATTGAT-ATTAATAATCTTATTAAAATTTAAATAA-AATAATT
66 AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
88753598 TACCAAAACAAATTTCTGC
131 TACCAAAACAAATTTCTGC
88753617 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
88753682 AAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
88753745 CAATAATCAT
Statistics
Matches: 123, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
147 91 0.74
148 27 0.22
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (149 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
TACCAAAACAAATTTCTGC
Found at i:88753657 original size:18 final size:17
Alignment explanation
Indices: 88753629--88753663 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
88753619 ATTATTAAGA
*
88753629 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
88753646 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
88753664 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:88753874 original size:44 final size:45
Alignment explanation
Indices: 88753825--88753919 Score: 129
Period size: 45 Copynumber: 2.1 Consensus size: 45
88753815 TTACACCTCT
* * *
88753825 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
** *
88753869 ATTACATTCAACCAAACAGTTGATTTGCTATTACACATCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
88753914 ATTACA
1 ATTACA
88753920 CCTCTAATCC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 18 0.41
45 26 0.59
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
Found at i:88755754 original size:21 final size:23
Alignment explanation
Indices: 88755715--88755756 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
88755705 TCACTGTCTA
*
88755715 AACACCAAACCAAACAAAATCAC
1 AACACCAAACCAAAAAAAATCAC
88755738 AACA-CAAA-CAAAAAAAATC
1 AACACCAAACCAAAAAAAATC
88755757 TCTAAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 4 0.22
23 4 0.22
ACGTcount: A:0.67, C:0.29, G:0.00, T:0.05
Consensus pattern (23 bp):
AACACCAAACCAAAAAAAATCAC
Found at i:88759248 original size:30 final size:30
Alignment explanation
Indices: 88759212--88759276 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
88759202 CAACTTAACA
88759212 AACAAATGTCTCTAAAATAATAACAAAATT
1 AACAAATGTCTCTAAAATAATAACAAAATT
*
88759242 AACAAATGTCTTTAAAATAATAACAAAATT
1 AACAAATGTCTCTAAAATAATAACAAAATT
88759272 AACAA
1 AACAA
88759277 TAAAATAAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.58, C:0.12, G:0.03, T:0.26
Consensus pattern (30 bp):
AACAAATGTCTCTAAAATAATAACAAAATT
Found at i:88765965 original size:19 final size:21
Alignment explanation
Indices: 88765941--88765979 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
88765931 ATTTATGCAT
88765941 ATGACA-TTAAAATA-ATTAC
1 ATGACATTTAAAATATATTAC
88765960 ATGACATTTAAAATATATTA
1 ATGACATTTAAAATATATTA
88765980 ATCATAGGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 8 0.44
21 4 0.22
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (21 bp):
ATGACATTTAAAATATATTAC
Found at i:88766982 original size:40 final size:40
Alignment explanation
Indices: 88766926--88767166 Score: 259
Period size: 40 Copynumber: 6.0 Consensus size: 40
88766916 ATAACTGTTC
*
88766926 AGGGTTACCGAAGTACAAAGAGGGGCACGTATGTGCATTCA
1 AGGG-TACCGAAGTACAAACAGGGGCACGTATGTGCATTCA
* * * *
88766967 AGGGTACCGAAGTACAAACAAGAGCATGTATGTGTATTCA
1 AGGGTACCGAAGTACAAACAGGGGCACGTATGTGCATTCA
* * * * *
88767007 GGGGTAACAAAGTACAAACAAGGGCACGTATGTGTATTCA
1 AGGGTACCGAAGTACAAACAGGGGCACGTATGTGCATTCA
* * * * * *
88767047 GGGGTACCAAAGTACAAACAGGAGCTCATATGTGCATTTA
1 AGGGTACCGAAGTACAAACAGGGGCACGTATGTGCATTCA
*
88767087 GGGGTACCGAAGTACAAACAGGGGCACGTATGTGCATTC-
1 AGGGTACCGAAGTACAAACAGGGGCACGTATGTGCATTCA
* * ***
88767126 AGAGGTATCGAAGTACAAATAGGGGCATAAATGTGCATTCA
1 AG-GGTACCGAAGTACAAACAGGGGCACGTATGTGCATTCA
88767167 TACAATAGTT
Statistics
Matches: 170, Mismatches: 28, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
39 1 0.01
40 165 0.97
41 4 0.02
ACGTcount: A:0.35, C:0.16, G:0.28, T:0.21
Consensus pattern (40 bp):
AGGGTACCGAAGTACAAACAGGGGCACGTATGTGCATTCA
Found at i:88767152 original size:120 final size:120
Alignment explanation
Indices: 88766923--88767144 Score: 309
Period size: 120 Copynumber: 1.9 Consensus size: 120
88766913 TGTATAACTG
* * * * *
88766923 TTCAGGGTTACCGAAGTACAAAGAGGGGCACGTATGTGCATTCAAGGGTACCGAAGTACAAACAA
1 TTCAGGGGTACCAAAGTACAAACAGGAGCACATATGTGCATTCAAGGGTACCGAAGTACAAACAA
* * *
88766988 GAGCATGTATGTGTATTCAGGGGTAACAAAGTACAAACAAGGGCACGTATGTGTA
66 GAGCACGTATGTGCATTCAGAGGTAACAAAGTACAAACAAGGGCACGTATGTGTA
* * * *
88767043 TTCAGGGGTACCAAAGTACAAACAGGAGCTCATATGTGCATTTAGGGGTACCGAAGTACAAACAG
1 TTCAGGGGTACCAAAGTACAAACAGGAGCACATATGTGCATTCAAGGGTACCGAAGTACAAACAA
* * *
88767108 GGGCACGTATGTGCATTCAGAGGTATCGAAGTACAAA
66 GAGCACGTATGTGCATTCAGAGGTAACAAAGTACAAA
88767145 TAGGGGCATA
Statistics
Matches: 87, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
120 87 1.00
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.21
Consensus pattern (120 bp):
TTCAGGGGTACCAAAGTACAAACAGGAGCACATATGTGCATTCAAGGGTACCGAAGTACAAACAA
GAGCACGTATGTGCATTCAGAGGTAACAAAGTACAAACAAGGGCACGTATGTGTA
Found at i:88767160 original size:80 final size:80
Alignment explanation
Indices: 88766923--88767166 Score: 312
Period size: 80 Copynumber: 3.0 Consensus size: 80
88766913 TGTATAACTG
* *
88766923 TTCAGGGTTACCGAAGTACAAAGAGGGGCACGTATGTGCATTCA-AGGGTACCGAAGTACAAACA
1 TTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCATTCAGA-GGTACCGAAGTACAAACA
* * *
88766987 AGAGCATGTATGTGTA
65 GGAGCATATATGTGCA
* * * * * *
88767003 TTCAGGGGTAACAAAGTACAAACAAGGGCACGTATGTGTATTCAGGGGTACCAAAGTACAAACAG
1 TTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCATTCAGAGGTACCGAAGTACAAACAG
88767068 GAGC-TCATATGTGCA
66 GAGCAT-ATATGTGCA
* * *
88767083 TTTAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCATTCAGAGGTATCGAAGTACAAATAG
1 TTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCATTCAGAGGTACCGAAGTACAAACAG
* *
88767148 GGGCATAAATGTGCA
66 GAGCATATATGTGCA
88767163 TTCA
1 TTCA
88767167 TACAATAGTT
Statistics
Matches: 138, Mismatches: 23, Indels: 6
0.83 0.14 0.04
Matches are distributed among these distances:
79 1 0.01
80 136 0.99
81 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.21
Consensus pattern (80 bp):
TTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCATTCAGAGGTACCGAAGTACAAACAG
GAGCATATATGTGCA
Found at i:88774118 original size:72 final size:72
Alignment explanation
Indices: 88773958--88774135 Score: 205
Period size: 72 Copynumber: 2.5 Consensus size: 72
88773948 GCCCGCATTT
* * * * *
88773958 GAGCTACTCACGGGTCTATACACAAAGTCAGCACCCGGACCCTAAAGCATTATCATGTAATACCC
1 GAGCTACTCACGGGTTTATACACAAAGTCAGTACCCGAACCCCAAAGCATTAACATGTAATACCC
**
88774023 GCTCATT
66 GCTCAGC
* * * * *
88774030 GAGCTGCTTACAGGTTTATACACAAAGTCAGTACCCGAACCCCAAAGCATTAACATG-ATATGCT
1 GAGCTACTCACGGGTTTATACACAAAGTCAGTACCCGAACCCCAAAGCATTAACATGTA-ATACC
*
88774094 CTCTCAGC
65 CGCTCAGC
* *
88774102 GAGTTACTCACGGGTTTATACACAAAGTCTGTAC
1 GAGCTACTCACGGGTTTATACACAAAGTCAGTAC
88774136 TCGGACCCAC
Statistics
Matches: 87, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
71 1 0.01
72 86 0.99
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (72 bp):
GAGCTACTCACGGGTTTATACACAAAGTCAGTACCCGAACCCCAAAGCATTAACATGTAATACCC
GCTCAGC
Found at i:88780167 original size:22 final size:22
Alignment explanation
Indices: 88780142--88780185 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
88780132 AAATGCTATA
88780142 CAGAGAGCA-CAGATGTGCTAAT
1 CAGAGAGCACCA-ATGTGCTAAT
88780164 CAGAGAGCACCAATGTGCTAAT
1 CAGAGAGCACCAATGTGCTAAT
88780186 AATTAGAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.18
Consensus pattern (22 bp):
CAGAGAGCACCAATGTGCTAAT
Found at i:88780194 original size:25 final size:25
Alignment explanation
Indices: 88780160--88780221 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
88780150 ACAGATGTGC
*
88780160 TAATCAGAGAGCACCAATGTGCTAA
1 TAATCAGAGAGCACCAACGTGCTAA
* **
88780185 TAATTAGAGAGCACTGACGTGCTAA
1 TAATCAGAGAGCACCAACGTGCTAA
88780210 TAATCAGAGAGC
1 TAATCAGAGAGC
88780222 GCGCTAAGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.21
Consensus pattern (25 bp):
TAATCAGAGAGCACCAACGTGCTAA
Found at i:88781268 original size:13 final size:13
Alignment explanation
Indices: 88781250--88781274 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
88781240 CCCAAATTTT
88781250 CTTTTTTCTTTCC
1 CTTTTTTCTTTCC
88781263 CTTTTTTCTTTC
1 CTTTTTTCTTTC
88781275 TTTCTCTCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (13 bp):
CTTTTTTCTTTCC
Found at i:88781341 original size:5 final size:5
Alignment explanation
Indices: 88781325--88781400 Score: 61
Period size: 5 Copynumber: 15.0 Consensus size: 5
88781315 TTCTTTTGTT
* *
88781325 ATATA TATATA ATATA ATATT ATAATA ATATA ATATA ATA-A CATACTT
1 ATATA -ATATA ATATA ATATA AT-ATA ATATA ATATA ATATA -ATA-TA
88781373 AT-TA AT-TA ACTA-A ATATA ATATA ATATA
1 ATATA ATATA A-TATA ATATA ATATA ATATA
88781401 TATTTTAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
4 9 0.15
5 39 0.66
6 11 0.19
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:88781355 original size:21 final size:21
Alignment explanation
Indices: 88781323--88781364 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
88781313 CTTTCTTTTG
88781323 TTATATATATATAATATAATA
1 TTATATATATATAATATAATA
88781344 TTATA-ATAATATAATATAATA
1 TTATATAT-ATATAATATAATA
88781365 ACATACTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTATATATATATAATATAATA
Found at i:88781404 original size:29 final size:27
Alignment explanation
Indices: 88781325--88781404 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 27
88781315 TTCTTTTGTT
88781325 ATATATATATAATATAATATTA-TAATA
1 ATATA-ATATAATATAATATTATTAATA
88781352 ATATAATATAATA-ACATACTTATTAATTA
1 ATATAATATAATATA-ATA-TTATTAA-TA
88781381 ACTA-AATATAATATAATATATATT
1 A-TATAATATAATATAATAT-TATT
88781405 TTAAATTAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
25 1 0.02
26 11 0.24
27 8 0.17
28 4 0.09
29 19 0.41
30 3 0.07
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (27 bp):
ATATAATATAATATAATATTATTAATA
Found at i:88782156 original size:85 final size:85
Alignment explanation
Indices: 88782013--88782182 Score: 243
Period size: 85 Copynumber: 2.0 Consensus size: 85
88782003 GAACTTCATG
* * *
88782013 TACTTGTGTTGTTGTAGGTACATCATAGGAGCATCTAAAATTGGATTCTAACTTGATCTCTGACA
1 TACTTGTGTTGTTGTAGGTACATCACAAGAGCATCTAAAATTGGATTCTAACATGATCTCTGACA
*
88782078 TTGTCTTACATATGGTGAAA
66 TTATCTTACATATGGTGAAA
** * *
88782098 TACTTGTGTTGTTGTAGGTATGTCACAAGATCAT-TCAAAATTGGATTCTGACATGATCTCTGAC
1 TACTTGTGTTGTTGTAGGTACATCACAAGAGCATCT-AAAATTGGATTCTAACATGATCTCTGAC
*
88782162 ATTATCTTACCTATGGTGAAA
65 ATTATCTTACATATGGTGAAA
88782183 GCGAGTTCTA
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
84 1 0.01
85 74 0.99
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (85 bp):
TACTTGTGTTGTTGTAGGTACATCACAAGAGCATCTAAAATTGGATTCTAACATGATCTCTGACA
TTATCTTACATATGGTGAAA
Found at i:88785193 original size:48 final size:48
Alignment explanation
Indices: 88785090--88785314 Score: 169
Period size: 48 Copynumber: 4.8 Consensus size: 48
88785080 AAGAGGGTAA
* * * * *
88785090 AATGCCGATGCCATGTCCTAAACATGGTCTTACACTGGTTCACATGTT
1 AATGCCGATGCCATGTCCTAAACATGGTCTTACACTAGCTCTCATCTC
* * * *
88785138 GAGGCCGATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCGTCTC
1 AATGCCGATGCCATGTCCTAAACATGGTCTTACACTAGCTCTCATCTC
* * * * * *
88785186 AATGCCGATTCTATGTCCCAAACATGATCTTACACTAGCTCTCATAATG
1 AATGCCGATGCCATGTCCTAAACATGGTCTTACACTAGCTCTCAT-CTC
* * * *
88785235 TA-GCCGATGCCATGT-CTCAAATATGGTCTTGCAC-A-----CATATC
1 AATGCCGATGCCATGTCCT-AAACATGGTCTTACACTAGCTCTCATCTC
* * * *
88785276 AATACTGATGCCATGTCCCAGACATGGTCTTACACTAGC
1 AATGCCGATGCCATGTCCTAAACATGGTCTTACACTAGC
88785315 ACACATATCA
Statistics
Matches: 136, Mismatches: 34, Indels: 17
0.73 0.18 0.09
Matches are distributed among these distances:
41 3 0.02
42 27 0.20
43 2 0.01
47 2 0.01
48 100 0.74
49 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.29
Consensus pattern (48 bp):
AATGCCGATGCCATGTCCTAAACATGGTCTTACACTAGCTCTCATCTC
Found at i:88785261 original size:96 final size:96
Alignment explanation
Indices: 88785090--88785321 Score: 219
Period size: 96 Copynumber: 2.5 Consensus size: 96
88785080 AAGAGGGTAA
* * * * **
88785090 AATGCCGATGCCATGTCCTAAACATGGTCTTACACTGGTTCACATGTTGAGGCCGATGCCATGTC
1 AATGCCGATGCCATGTCCCAAACATGATCTTACACTAGCTCACATAATGAGGCCGATGCCATGTC
*
88785155 CTAGACATGGTCTTACACTAGCTCTCGTCTC
66 CTAAACATGGTCTTACACTAGCTCTCGTCTC
* * *
88785186 AATGCCGATTCTATGTCCCAAACATGATCTTACACTAGCTCTCATAATGTA-GCCGATGCCATGT
1 AATGCCGATGCCATGTCCCAAACATGATCTTACACTAGCTCACATAATG-AGGCCGATGCCATGT
* * * *
88785250 -CTCAAATATGGTCTTGCAC-A-----CATATC
65 CCT-AAACATGGTCTTACACTAGCTCTCGTCTC
* * * * *
88785276 AATACTGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATA
1 AATGCCGATGCCATGTCCCAAACATGATCTTACACTAGCTCACATA
88785322 TCACATGTTC
Statistics
Matches: 112, Mismatches: 22, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
90 42 0.38
95 3 0.03
96 66 0.59
97 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (96 bp):
AATGCCGATGCCATGTCCCAAACATGATCTTACACTAGCTCACATAATGAGGCCGATGCCATGTC
CTAAACATGGTCTTACACTAGCTCTCGTCTC
Found at i:88787283 original size:75 final size:70
Alignment explanation
Indices: 88787160--88787354 Score: 228
Period size: 75 Copynumber: 2.7 Consensus size: 70
88787150 TTATTCATTT
** *
88787160 TTTCCATTTTTGGGTAAATTGTAAATAAGTATATTATTTATGTAAAAATACAATATAATACAATA
1 TTTCCATTTTTTCGTAAATTGTAAATAAGTATATTATTGATGTAAAAATAC---AT--TACAATA
88787225 AAAAAAATTG
61 AAAAAAATTG
* * * * *
88787235 TTTCCATTTTTTTGTAAATTATAAATAAGTATATTATTGATGTAAAAATACATTGCAATACAAAT
1 TTTCCATTTTTTCGTAAATTGTAAATAAGTATATTATTGATGTAAAAATACATTACAATAAAAAA
*
88787300 AATTT
66 AATTG
* *
88787305 TTTTCATTTTCTTCATAAATTGTAAATAAGTATATTATTGATGTAGAAAA
1 TTTCCATTTT-TTCGTAAATTGTAAATAAGTATATTATTGATGTA-AAAA
88787355 ATAAACAAAC
Statistics
Matches: 106, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
70 22 0.21
71 31 0.29
72 6 0.06
75 47 0.44
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (70 bp):
TTTCCATTTTTTCGTAAATTGTAAATAAGTATATTATTGATGTAAAAATACATTACAATAAAAAA
AATTG
Found at i:88789497 original size:13 final size:13
Alignment explanation
Indices: 88789479--88789509 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
88789469 AGAACAACTT
88789479 ATTAATTATATTA
1 ATTAATTATATTA
88789492 ATTAATTATATTA
1 ATTAATTATATTA
88789505 ATTAA
1 ATTAA
88789510 AAGAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTAATTATATTA
Found at i:88789995 original size:22 final size:22
Alignment explanation
Indices: 88789970--88790014 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
88789960 CTAAAATGTT
88789970 AGTCCAAATTAAAAGTAATCTA
1 AGTCCAAATTAAAAGTAATCTA
88789992 AGTCCAAATTAAAAGTAATCTA
1 AGTCCAAATTAAAAGTAATCTA
88790014 A
1 A
88790015 TTCGGTTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.51, C:0.13, G:0.09, T:0.27
Consensus pattern (22 bp):
AGTCCAAATTAAAAGTAATCTA
Found at i:88793733 original size:6 final size:5
Alignment explanation
Indices: 88793704--88793771 Score: 50
Period size: 6 Copynumber: 12.8 Consensus size: 5
88793694 TATGTCTTGC
* *
88793704 AAAAT AAAAT --AAT AAAATT GAAAT GAAAAT AAAAAT CAAAAT CAAAAGA
1 AAAAT AAAAT AAAAT AAAA-T AAAAT -AAAAT -AAAAT -AAAAT -AAAA-T
88793753 AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAA
88793772 ATAAGACTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
3 3 0.06
5 22 0.42
6 27 0.52
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:88793739 original size:12 final size:12
Alignment explanation
Indices: 88793724--88793773 Score: 52
Period size: 11 Copynumber: 4.3 Consensus size: 12
88793714 AATAAAATTG
88793724 AAATGAAAATAA
1 AAATGAAAATAA
* *
88793736 AAATCAAAATCA
1 AAATGAAAATAA
88793748 AAA-GAAAA-ATA
1 AAATGAAAATA-A
88793759 AAAT-AAAATAA
1 AAATGAAAATAA
88793770 AAAT
1 AAAT
88793774 AAGACTAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
11 17 0.55
12 14 0.45
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (12 bp):
AAATGAAAATAA
Found at i:88793772 original size:6 final size:6
Alignment explanation
Indices: 88793724--88793775 Score: 54
Period size: 6 Copynumber: 9.0 Consensus size: 6
88793714 AATAAAATTG
* * * *
88793724 AAATGA AAATAA AAATCA AAATCA AAAGAA AAAT-A AAAT-A AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
88793770 AAATAA
1 AAATAA
88793776 GACTAAATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
5 10 0.25
6 30 0.75
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:88800551 original size:16 final size:16
Alignment explanation
Indices: 88800530--88800576 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
88800520 AATAGTATTC
*
88800530 CTTTCCTTCTTTTGTT
1 CTTTCCTTCTTTTCTT
88800546 CTTTCCTTCTTTTCTT
1 CTTTCCTTCTTTTCTT
88800562 C-TT-CTTCTTCTTCTT
1 CTTTCCTTCTT-TTCTT
88800577 TTTTTTTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 6 0.21
15 7 0.24
16 16 0.55
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.68
Consensus pattern (16 bp):
CTTTCCTTCTTTTCTT
Found at i:88806284 original size:28 final size:28
Alignment explanation
Indices: 88806207--88806291 Score: 98
Period size: 28 Copynumber: 3.0 Consensus size: 28
88806197 ATTATGAAAG
*
88806207 ATGTAAAAGTCCGTCAAGACTATCTTAT
1 ATGTGAAAGTCCGTCAAGACTATCTTAT
* * * **
88806235 ATATGGAAGTCCATCGGGACTATCTTAT
1 ATGTGAAAGTCCGTCAAGACTATCTTAT
* *
88806263 ATGTGAAAGTGCGTCAAAACTATCTTAT
1 ATGTGAAAGTCCGTCAAGACTATCTTAT
88806291 A
1 A
88806292 AGTGGAAATC
Statistics
Matches: 44, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (28 bp):
ATGTGAAAGTCCGTCAAGACTATCTTAT
Found at i:88808519 original size:24 final size:24
Alignment explanation
Indices: 88808487--88808534 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
88808477 AGATACCGAC
**
88808487 CTTTTCATTGTTATCCTTTTCGAA
1 CTTTTCATTGACATCCTTTTCGAA
*
88808511 CTTTTCATTGACATCTTTTTCGAA
1 CTTTTCATTGACATCCTTTTCGAA
88808535 TAACATCCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.19, C:0.21, G:0.08, T:0.52
Consensus pattern (24 bp):
CTTTTCATTGACATCCTTTTCGAA
Found at i:88808579 original size:41 final size:40
Alignment explanation
Indices: 88808499--88808603 Score: 156
Period size: 41 Copynumber: 2.6 Consensus size: 40
88808489 TTTCATTGTT
* *
88808499 ATCCTTTTCGAACTTTTCATTGACATCTTTTTCGAATAAC
1 ATCCTTTTCAAACTTTTCATTGATATCTTTTTCGAATAAC
* *
88808539 ATCCTTTTCAAAATTTTCACTTGATATCTTTTTCGGATAAC
1 ATCCTTTTCAAACTTTTCA-TTGATATCTTTTTCGAATAAC
*
88808580 ATCCTTTTCAACCTTTTCATTGAT
1 ATCCTTTTCAAACTTTTCATTGAT
88808604 TAAAAAATAC
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
40 22 0.38
41 36 0.62
ACGTcount: A:0.25, C:0.22, G:0.07, T:0.47
Consensus pattern (40 bp):
ATCCTTTTCAAACTTTTCATTGATATCTTTTTCGAATAAC
Found at i:88810412 original size:15 final size:15
Alignment explanation
Indices: 88810392--88810422 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
88810382 AGAGAAAGAA
88810392 AAAAACTTGTTTCTT
1 AAAAACTTGTTTCTT
88810407 AAAAACTTGTTTCTT
1 AAAAACTTGTTTCTT
88810422 A
1 A
88810423 TTACGCTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.45
Consensus pattern (15 bp):
AAAAACTTGTTTCTT
Found at i:88818443 original size:10 final size:9
Alignment explanation
Indices: 88818411--88818454 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
88818401 ACAATCAAAA
88818411 TGAGAGAGT
1 TGAGAGAGT
* *
88818420 TAAGAGACT
1 TGAGAGAGT
*
88818429 TGAGAGGGTT
1 TGAGAGAG-T
88818439 TGAGAGAGT
1 TGAGAGAGT
88818448 TGAGAGA
1 TGAGAGA
88818455 AACATGTGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
9 20 0.71
10 8 0.29
ACGTcount: A:0.34, C:0.02, G:0.41, T:0.23
Consensus pattern (9 bp):
TGAGAGAGT
Done.