Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 191 of 218
Found at i:56711909 original size:86 final size:86
Alignment explanation
Indices: 56711733--56711945 Score: 234
Period size: 86 Copynumber: 2.5 Consensus size: 86
56711723 ACTTACACCA
** * * * *
56711733 GGTAAATGCATGAACTTGAACCATTTATTTTTGCTAATTTGTTGCATATAAGTTGTTATAAATAT
1 GGTAAATATATGAACTTGAACCATTGATTTTTGCTAATTTATTGCATATAAATCGTTATAAATAT
** ***
56711798 TGAAAAATTAGTTTGATTTTT
66 TGAAAAATTAGCCTGATTGCC
56711819 GGTAAATATATGAACTTGAACCATTGATTTTTGCTAATTTATTGCATATAAATCGTTATAGAA-A
1 GGTAAATATATGAACTTGAACCATTGATTTTTGCTAATTTATTGCATATAAATCGTTATA-AATA
* *
56711883 TTGAAGATTTAGCCCT-ATTGCC
65 TTGAAAAATTAG-CCTGATTGCC
* *
56711905 GGTAAATATATGAACTATGAA-TAGTTGATTTGTGCTAATTT
1 GGTAAATATATGAACT-TGAACCA-TTGATTTTTGCTAATTT
56711946 GTTTCACATA
Statistics
Matches: 108, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
86 85 0.79
87 23 0.21
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (86 bp):
GGTAAATATATGAACTTGAACCATTGATTTTTGCTAATTTATTGCATATAAATCGTTATAAATAT
TGAAAAATTAGCCTGATTGCC
Found at i:56711997 original size:40 final size:40
Alignment explanation
Indices: 56711928--56712024 Score: 97
Period size: 40 Copynumber: 2.4 Consensus size: 40
56711918 ACTATGAATA
* * * * *
56711928 GTTGATTTGTGCTAATTTGTTTCACATAAACAATTGTAA-
1 GTTGATTTTTGATAATTTCTTGCACATAAACAATTGAAAT
* * **
56711967 GATTGATTTTTGTTAATTTCTTGCATATAAATTATTGAAAT
1 G-TTGATTTTTGATAATTTCTTGCACATAAACAATTGAAAT
56712008 GTTGATTTTTGATAATT
1 GTTGATTTTTGATAATT
56712025 CTTTACATAT
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
39 1 0.02
40 45 0.96
41 1 0.02
ACGTcount: A:0.30, C:0.06, G:0.14, T:0.49
Consensus pattern (40 bp):
GTTGATTTTTGATAATTTCTTGCACATAAACAATTGAAAT
Found at i:56712034 original size:40 final size:40
Alignment explanation
Indices: 56711969--56712053 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 40
56711959 AATTGTAAGA
* *
56711969 TTGATTTTTGTTAATTTCTTGCATA-TAAATTATTGAAATG
1 TTGATTTTTGATAATTTCTTACATATTAAA-TATTGAAATG
*
56712009 TTGATTTTTGATAA-TTCTTTACATATTAAATATTGAAGTG
1 TTGATTTTTGATAATTTC-TTACATATTAAATATTGAAATG
56712049 TTGAT
1 TTGAT
56712054 ATTCAAGCTA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
39 3 0.08
40 33 0.82
41 4 0.10
ACGTcount: A:0.31, C:0.05, G:0.13, T:0.52
Consensus pattern (40 bp):
TTGATTTTTGATAATTTCTTACATATTAAATATTGAAATG
Found at i:56713147 original size:18 final size:18
Alignment explanation
Indices: 56713099--56713148 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
56713089 CTAAGGTTGT
* *
56713099 TTTATATTCTGTTATTTA
1 TTTATATACTATTATTTA
* * *
56713117 TTTATCTATTATTATTTC
1 TTTATATACTATTATTTA
56713135 TTTATATACTATTA
1 TTTATATACTATTA
56713149 GTAAATAAGG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTATATACTATTATTTA
Found at i:56718126 original size:43 final size:42
Alignment explanation
Indices: 56718039--56718270 Score: 261
Period size: 43 Copynumber: 5.4 Consensus size: 42
56718029 AAATATTTTT
* * * * *
56718039 TAAAAGTCATGTTTTTAGCGGCGTTTGT-GAAAAAGCGCCAC
1 TAAAAGTCATATCTTTAGCGGCGTTTGTGGTAGAAGCGCCGC
* * *
56718080 TAAAAGTCAT-TCTTTATAGTGGTGTTTGTGGTAGAAGCGTCGC
1 TAAAAGTCATATC-TT-TAGCGGCGTTTGTGGTAGAAGCGCCGC
* * *
56718123 TAAAAGTCATGATTTTTAGTGGTGTTTGTGGTAGAAGCGCCGC
1 TAAAAGTCAT-ATCTTTAGCGGCGTTTGTGGTAGAAGCGCCGC
* *
56718166 TAAAAGTCATGATCTTTAGCGGCGTTTTTGGTAGAAGCTCCGC
1 TAAAAGTCAT-ATCTTTAGCGGCGTTTGTGGTAGAAGCGCCGC
*
56718209 TAAAGGTCATGATCTTTAGCGGCGTTTGTGGTAGAAGCGCCGC
1 TAAAAGTCAT-ATCTTTAGCGGCGTTTGTGGTAGAAGCGCCGC
*
56718252 TAAAGGTCATGATCTTTAG
1 TAAAAGTCAT-ATCTTTAG
56718271 TGATGTTTTT
Statistics
Matches: 169, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
40 1 0.01
41 12 0.07
42 11 0.07
43 142 0.84
44 2 0.01
45 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (42 bp):
TAAAAGTCATATCTTTAGCGGCGTTTGTGGTAGAAGCGCCGC
Found at i:56718239 original size:129 final size:127
Alignment explanation
Indices: 56718039--56718278 Score: 313
Period size: 129 Copynumber: 1.9 Consensus size: 127
56718029 AAATATTTTT
* * *
56718039 TAAAAGTCATGTTTTTAGCGGCGTTTGTGAAAAAGCGCCACTAAAAGTCATTCTTTATAGTGGTG
1 TAAAAGTCATGTCTTTAGCGGCGTTTGTGAAAAAGCGCCACTAAAAGTCATTCTTTATAGCGGCG
* * *
56718104 TTTGTGGTAGAAGCGTCGCTAAAAGTCATGATTTTTAGTGGTGTTTGTGGTAGAAGCGCCGC
66 TTTGTGGTAGAAGCGCCGCTAAAAGTCATGATCTTTAGTGATGTTTGTGGTAGAAGCGCCGC
* * * * * *
56718166 TAAAAGTCATGATCTTTAGCGGCGTTTTTGGTAGAAGCTCCGCTAAAGGTCATGATC-TT-TAGC
1 TAAAAGTCATG-TCTTTAGCGGCGTTTGT-GAAAAAGCGCCACTAAAAGTCAT--TCTTTATAGC
*
56718229 GGCGTTTGTGGTAGAAGCGCCGCTAAAGGTCATGATCTTTAGTGATGTTT
62 GGCGTTTGTGGTAGAAGCGCCGCTAAAAGTCATGATCTTTAGTGATGTTT
56718279 TTCACATAAA
Statistics
Matches: 96, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
127 11 0.11
128 15 0.16
129 66 0.69
130 2 0.02
131 2 0.02
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.34
Consensus pattern (127 bp):
TAAAAGTCATGTCTTTAGCGGCGTTTGTGAAAAAGCGCCACTAAAAGTCATTCTTTATAGCGGCG
TTTGTGGTAGAAGCGCCGCTAAAAGTCATGATCTTTAGTGATGTTTGTGGTAGAAGCGCCGC
Found at i:56718279 original size:86 final size:86
Alignment explanation
Indices: 56718039--56718280 Score: 314
Period size: 86 Copynumber: 2.8 Consensus size: 86
56718029 AAATATTTTT
* * *
56718039 TAAAAGTCATG-TTTTTAGCGGCGTTTGT-GAAAAAGCGCCACTAAAAGTCAT--TCTTTATAGT
1 TAAAAGTCATGATTTTTAGCGGCGTTTGTGGTAGAAGCGCCGCTAAAAGTCATGATC-TT-TAGT
*
56718100 GGTGTTTGTGGTAGAAGCGTCGC
64 GGTGTTTTTGGTAGAAGCGTCGC
* * *
56718123 TAAAAGTCATGATTTTTAGTGGTGTTTGTGGTAGAAGCGCCGCTAAAAGTCATGATCTTTAGCGG
1 TAAAAGTCATGATTTTTAGCGGCGTTTGTGGTAGAAGCGCCGCTAAAAGTCATGATCTTTAGTGG
*
56718188 CGTTTTTGGTAGAAGC-TCCGC
66 TGTTTTTGGTAGAAGCGT-CGC
* * * *
56718209 TAAAGGTCATGATCTTTAGCGGCGTTTGTGGTAGAAGCGCCGCTAAAGGTCATGATCTTTAGTGA
1 TAAAAGTCATGATTTTTAGCGGCGTTTGTGGTAGAAGCGCCGCTAAAAGTCATGATCTTTAGTGG
56718274 TGTTTTT
66 TGTTTTT
56718281 CACATAAACG
Statistics
Matches: 137, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
84 11 0.08
85 16 0.12
86 106 0.77
87 2 0.01
88 2 0.01
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.34
Consensus pattern (86 bp):
TAAAAGTCATGATTTTTAGCGGCGTTTGTGGTAGAAGCGCCGCTAAAAGTCATGATCTTTAGTGG
TGTTTTTGGTAGAAGCGTCGC
Found at i:56718298 original size:86 final size:86
Alignment explanation
Indices: 56718122--56718299 Score: 221
Period size: 86 Copynumber: 2.1 Consensus size: 86
56718112 AGAAGCGTCG
* * *
56718122 CTAAAAGTCATGATTTTTAGTGGTGTTTGTGGTAGAAGCGCCGCTAAAAGTCATGATCTTTAGCG
1 CTAAAAGTCATGATCTTTAGCGGCGTTTGTGGTAGAAGCGCCGCTAAAAGTCATGATCTTTAGCG
* *** * * *
56718187 GCGTTTTTGGTAGAAGCTCCG
66 ACGTTTTTCACAGAAACGCCA
* * *
56718208 CTAAAGGTCATGATCTTTAGCGGCGTTTGTGGTAGAAGCGCCGCTAAAGGTCATGATCTTTAGTG
1 CTAAAAGTCATGATCTTTAGCGGCGTTTGTGGTAGAAGCGCCGCTAAAAGTCATGATCTTTAGCG
* *
56718273 ATGTTTTTCACATAAACGCCA
66 ACGTTTTTCACAGAAACGCCA
56718294 CTAAAA
1 CTAAAA
56718300 TTAGCGACGT
Statistics
Matches: 76, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
86 76 1.00
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (86 bp):
CTAAAAGTCATGATCTTTAGCGGCGTTTGTGGTAGAAGCGCCGCTAAAAGTCATGATCTTTAGCG
ACGTTTTTCACAGAAACGCCA
Found at i:56722018 original size:25 final size:25
Alignment explanation
Indices: 56721981--56722039 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 25
56721971 GGGAAAAAGT
56721981 AAGTTTCAGGAGATCTTCATTGTTTA
1 AAGTTT-AGGAGATCTTCATTGTTTA
*
56722007 AAGTTTAGGAGATCTTCGTTGTTTA
1 AAGTTTAGGAGATCTTCATTGTTTA
*
56722032 AAGCTTAG
1 AAGTTTAG
56722040 TGGTGAGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 25 0.81
26 6 0.19
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (25 bp):
AAGTTTAGGAGATCTTCATTGTTTA
Found at i:56722815 original size:14 final size:14
Alignment explanation
Indices: 56722793--56722832 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
56722783 TCAATCCGGC
*
56722793 CAAATCCAAAATGT
1 CAAAACCAAAATGT
*
56722807 CAAAACCAAAATTT
1 CAAAACCAAAATGT
*
56722821 CAAAATCAAAAT
1 CAAAACCAAAAT
56722833 CCAAATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.57, C:0.20, G:0.03, T:0.20
Consensus pattern (14 bp):
CAAAACCAAAATGT
Found at i:56723057 original size:89 final size:90
Alignment explanation
Indices: 56722906--56723086 Score: 328
Period size: 89 Copynumber: 2.0 Consensus size: 90
56722896 TGACCAAAAT
*
56722906 ATCATTTTTGACAAATATTACTAAATACTCATTTGATATTATGATGTTTCACCAACTGAATTGAT
1 ATCATTTTTGACAAATATTACTAAATACTCATTTGATATTACGATGTTTCACCAACTGAATTGAT
56722971 GGCTGA-GAGAGAGTTTATTACGAC
66 GGCTGAGGAGAGAGTTTATTACGAC
56722995 ATCATTTTTGACAAATATTACTAAATACTCATTTGATATTACGATGTTTCACCAACTGAATTGAT
1 ATCATTTTTGACAAATATTACTAAATACTCATTTGATATTACGATGTTTCACCAACTGAATTGAT
*
56723060 GGCTGAGTGAGAGAGTTTGTTACGAC
66 GGCTGAG-GAGAGAGTTTATTACGAC
56723086 A
1 A
56723087 CTCTAACACG
Statistics
Matches: 88, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
89 70 0.80
91 18 0.20
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (90 bp):
ATCATTTTTGACAAATATTACTAAATACTCATTTGATATTACGATGTTTCACCAACTGAATTGAT
GGCTGAGGAGAGAGTTTATTACGAC
Found at i:56723530 original size:20 final size:20
Alignment explanation
Indices: 56723492--56723532 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
56723482 TAAACACGAT
*
56723492 AATAATCTTTTATCCTAAAA
1 AATAATCTTTTATCATAAAA
56723512 AATAATCTTTTAAT-ATAAAA
1 AATAATCTTTT-ATCATAAAA
56723532 A
1 A
56723533 TGTTCTTCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (20 bp):
AATAATCTTTTATCATAAAA
Found at i:56724551 original size:44 final size:44
Alignment explanation
Indices: 56724492--56724582 Score: 146
Period size: 44 Copynumber: 2.1 Consensus size: 44
56724482 GCTAATAAAA
*
56724492 AATAGAATTTATGATAATTATACATTTAAAAATAATTATAATTT
1 AATAGAAGTTATGATAATTATACATTTAAAAATAATTATAATTT
* * *
56724536 AATAGAAGTTGTGATAATTTTACATTTAAAAATATTTATAATTT
1 AATAGAAGTTATGATAATTATACATTTAAAAATAATTATAATTT
56724580 AAT
1 AAT
56724583 TTACAATTAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (44 bp):
AATAGAAGTTATGATAATTATACATTTAAAAATAATTATAATTT
Found at i:56728864 original size:25 final size:25
Alignment explanation
Indices: 56728836--56728883 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
56728826 GTTTTAAGAG
*
56728836 ATCTTCGTTGTTTAAAGTTTAGTAT
1 ATCTTCGTTGTTTAAAGCTTAGTAT
56728861 ATCTTCGTTGTTTAAAGCTTAGT
1 ATCTTCGTTGTTTAAAGCTTAGT
56728884 GGTGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.23, C:0.10, G:0.17, T:0.50
Consensus pattern (25 bp):
ATCTTCGTTGTTTAAAGCTTAGTAT
Found at i:56730581 original size:38 final size:38
Alignment explanation
Indices: 56730528--56730748 Score: 234
Period size: 38 Copynumber: 5.8 Consensus size: 38
56730518 AATGTATCGT
*
56730528 TATTCGGGCTCCGTGCCTAGCAGGCTTTGTGCCAGTGA
1 TATTCGGGCTTCGTGCCTAGCAGGCTTTGTGCCAGTGA
*
56730566 TATTCGGGATTCGTGCCTAGCAGGCTTTGTGCCAGTGA
1 TATTCGGGCTTCGTGCCTAGCAGGCTTTGTGCCAGTGA
** *
56730604 TATTTAGGCTGT-ATGCCTAGCAGGCTTTGTGCCAGTGA
1 TATTCGGGCT-TCGTGCCTAGCAGGCTTTGTGCCAGTGA
*
56730642 TATTCGGGC-TCTGTGCCTAGCAGGCTTTGTGCCGGTGA
1 TATTCGGGCTTC-GTGCCTAGCAGGCTTTGTGCCAGTGA
** * * *
56730680 TATTCTTG-TTCTATGCCTAGTAGCCTTTGTGCC-GATGA
1 TATTCGGGCTTC-GTGCCTAGCAGGCTTTGTGCCAG-TGA
** * * *
56730718 TATTTAGGCTTTGTGTCTAGTAGGCTTTGTG
1 TATTCGGGCTTCGTGCCTAGCAGGCTTTGTG
56730749 TCTAGTAGGC
Statistics
Matches: 155, Mismatches: 22, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
36 1 0.01
37 1 0.01
38 150 0.97
39 3 0.02
ACGTcount: A:0.14, C:0.20, G:0.29, T:0.36
Consensus pattern (38 bp):
TATTCGGGCTTCGTGCCTAGCAGGCTTTGTGCCAGTGA
Found at i:56730667 original size:76 final size:75
Alignment explanation
Indices: 56730541--56730748 Score: 258
Period size: 76 Copynumber: 2.7 Consensus size: 75
56730531 TCGGGCTCCG
*
56730541 TGCCTAGCAGGCTTTGTGCCAGTGATATTCGGGATTCGTGCCTAGCAGGCTTTGTGCCAGTGATA
1 TGCCTAGCAGGCTTTGTGCCAGTGATATTCGGGCTT-GTGCCTAGCAGGCTTTGTGCCAGTGATA
*
56730606 TT-TAGGCTGTA
65 TTCT-GGCTCTA
*
56730617 TGCCTAGCAGGCTTTGTGCCAGTGATATTCGGGCTCTGTGCCTAGCAGGCTTTGTGCCGGTGATA
1 TGCCTAGCAGGCTTTGTGCCAGTGATATTCGGGCT-TGTGCCTAGCAGGCTTTGTGCCAGTGATA
* *
56730682 TTCTTGTTCTA
65 TTCTGGCTCTA
* * ** * *
56730693 TGCCTAGTAGCCTTTGTGCC-GATGATATTTAGGCTTTGTGTCTAGTAGGCTTTGTG
1 TGCCTAGCAGGCTTTGTGCCAG-TGATATTCGGGC-TTGTGCCTAGCAGGCTTTGTG
56730749 TCTAGTAGGC
Statistics
Matches: 117, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
75 1 0.01
76 113 0.97
77 3 0.03
ACGTcount: A:0.15, C:0.20, G:0.29, T:0.36
Consensus pattern (75 bp):
TGCCTAGCAGGCTTTGTGCCAGTGATATTCGGGCTTGTGCCTAGCAGGCTTTGTGCCAGTGATAT
TCTGGCTCTA
Found at i:56730743 original size:16 final size:16
Alignment explanation
Indices: 56730722--56730764 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
56730712 CGATGATATT
56730722 TAGGCTTTGTGTCTAG
1 TAGGCTTTGTGTCTAG
56730738 TAGGCTTTGTGTCTAG
1 TAGGCTTTGTGTCTAG
56730754 TAGGCTTTGTG
1 TAGGCTTTGTG
56730765 CCGATGATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.12, C:0.12, G:0.33, T:0.44
Consensus pattern (16 bp):
TAGGCTTTGTGTCTAG
Found at i:56730743 original size:114 final size:114
Alignment explanation
Indices: 56730528--56730748 Score: 311
Period size: 114 Copynumber: 1.9 Consensus size: 114
56730518 AATGTATCGT
* *
56730528 TATTCGGGCTCCGTGCCTAGCAGGCTTTGTGCCAGTGATATTCGGGATTCGTGCCTAGCAGGCTT
1 TATTCGGGCTCCGTGCCTAGCAGGCTTTGTGCCAGTGATATTCGGGATTCATGCCTAGCAGCCTT
56730593 TGTGCCAGTGATATTTAGGCTGTATGCCTAGCAGGCTTTGTGCCAGTGA
66 TGTGCCAGTGATATTTAGGCTGTATGCCTAGCAGGCTTTGTGCCAGTGA
* * ** *
56730642 TATTCGGGCTCTGTGCCTAGCAGGCTTTGTGCCGGTGATATTCTTG-TTCTATGCCTAGTAGCCT
1 TATTCGGGCTCCGTGCCTAGCAGGCTTTGTGCCAGTGATATTCGGGATTC-ATGCCTAGCAGCCT
* * * *
56730706 TTGTGCC-GATGATATTTAGGCTTTGTGTCTAGTAGGCTTTGTG
65 TTGTGCCAG-TGATATTTAGGCTGTATGCCTAGCAGGCTTTGTG
56730749 TCTAGTAGGC
Statistics
Matches: 94, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
113 4 0.04
114 90 0.96
ACGTcount: A:0.14, C:0.20, G:0.29, T:0.36
Consensus pattern (114 bp):
TATTCGGGCTCCGTGCCTAGCAGGCTTTGTGCCAGTGATATTCGGGATTCATGCCTAGCAGCCTT
TGTGCCAGTGATATTTAGGCTGTATGCCTAGCAGGCTTTGTGCCAGTGA
Found at i:56730785 original size:130 final size:130
Alignment explanation
Indices: 56730620--56730864 Score: 343
Period size: 130 Copynumber: 1.9 Consensus size: 130
56730610 GGCTGTATGC
*
56730620 CTAGCAGGCTTTGTGCCAGTGATATTCGGGCTCTGTGCCTAGC-AGGCTTTGTGCCGGTGATATT
1 CTAGCAGGCTTTGTGCCAGTGATATTCGGGCTCTGTGCCTAGCTA-GCTCTGTGCCGGTGATATT
** * * *
56730684 CTTGTTCTATGCCTAGTAGCCTTTGTGCCGATGATATTTAGG-CTTTGTGTCTAGTAGGCTTTGT
65 CGGGCTCTATGCCTAGCAGCCTTTCTGCCGATGATA-TTAGGTCTTTGTGTCTAGTAGGCTTTGT
56730748 GT
129 GT
* *
56730750 CTAGTAGGCTTTGTGCC-GATGATATTCGGGTTCTGTGCCTAGCTAGCTCTGTGCCGGTGATATT
1 CTAGCAGGCTTTGTGCCAG-TGATATTCGGGCTCTGTGCCTAGCTAGCTCTGTGCCGGTGATATT
** *
56730814 CGGGCTCTATGCCTAGCAGGTTTTCTGCCGATGATATTCGGTCTTTGTGTC
65 CGGGCTCTATGCCTAGCAGCCTTTCTGCCGATGATATTAGGTCTTTGTGTC
56730865 AAAGTATTAT
Statistics
Matches: 101, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
129 5 0.05
130 95 0.94
131 1 0.01
ACGTcount: A:0.13, C:0.20, G:0.29, T:0.38
Consensus pattern (130 bp):
CTAGCAGGCTTTGTGCCAGTGATATTCGGGCTCTGTGCCTAGCTAGCTCTGTGCCGGTGATATTC
GGGCTCTATGCCTAGCAGCCTTTCTGCCGATGATATTAGGTCTTTGTGTCTAGTAGGCTTTGTGT
Found at i:56730843 original size:38 final size:38
Alignment explanation
Indices: 56730763--56730854 Score: 114
Period size: 38 Copynumber: 2.4 Consensus size: 38
56730753 GTAGGCTTTG
* * *
56730763 TGCCGATGATATTCGGGTTCTGTGCCTAGCTAGCTCTG
1 TGCCGATGATATTCGGGCTCTATGCCTAGCTAGCTCTC
* * *
56730801 TGCCGGTGATATTCGGGCTCTATGCCTAGC-AGGTTTTC
1 TGCCGATGATATTCGGGCTCTATGCCTAGCTA-GCTCTC
56730839 TGCCGATGATATTCGG
1 TGCCGATGATATTCGG
56730855 TCTTTGTGTC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
37 1 0.02
38 45 0.98
ACGTcount: A:0.14, C:0.23, G:0.29, T:0.34
Consensus pattern (38 bp):
TGCCGATGATATTCGGGCTCTATGCCTAGCTAGCTCTC
Found at i:56732879 original size:7 final size:6
Alignment explanation
Indices: 56732847--56732891 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
56732837 TTCTAGTTCC
* * *
56732847 TTTTCT TTCT-T TTTTCT TTTTCT TTTTCG TTTTCA TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
56732892 TTTAATCAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
5 4 0.12
6 29 0.88
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:56737676 original size:26 final size:25
Alignment explanation
Indices: 56737626--56737692 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 25
56737616 ACTGTCCTTA
* *
56737626 ATAGTATATCCTGAAATTGCTATAG
1 ATAGTATATACTGAAATTACTATAG
*
56737651 GTAGTATATACTGAGAATTACTATAG
1 ATAGTATATACTGA-AATTACTATAG
56737677 ATAG-ACTATACTGAAA
1 ATAGTA-TATACTGAAA
56737693 ACACTTCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 15 0.42
26 21 0.58
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.33
Consensus pattern (25 bp):
ATAGTATATACTGAAATTACTATAG
Found at i:56749951 original size:17 final size:17
Alignment explanation
Indices: 56749929--56749961 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
56749919 CTCTCTCAAC
56749929 TGAAAA-TCGGTAAAAGT
1 TGAAAAGTCGG-AAAAGT
56749946 TGAAAAGTCGGAAAAG
1 TGAAAAGTCGGAAAAG
56749962 ATGACACCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.48, C:0.06, G:0.27, T:0.18
Consensus pattern (17 bp):
TGAAAAGTCGGAAAAGT
Found at i:56750116 original size:27 final size:26
Alignment explanation
Indices: 56750086--56750334 Score: 309
Period size: 27 Copynumber: 9.3 Consensus size: 26
56750076 ATCAGGCCTT
*
56750086 AAATGACCGAAATACTCCCGAAGGGTA
1 AAATGACCGAATTAC-CCCGAAGGGTA
*
56750113 AAATGATCGAATTACCCTCGAAGGGTA
1 AAATGACCGAATTACCC-CGAAGGGTA
*
56750140 AAATGACCGAAATACCCCCGAAGGGTA
1 AAATGACCGAATTA-CCCCGAAGGGTA
**
56750167 AAATGATTGAATTACCCCTGAAGGGTA
1 AAATGACCGAATTACCCC-GAAGGGTA
* *
56750194 AAATGACTGAAATACCCCTGAAGGGTA
1 AAATGACCGAATTACCCC-GAAGGGTA
56750221 AAATGACCGAATTACCCCTGAAGGGTA
1 AAATGACCGAATTACCCC-GAAGGGTA
*
56750248 AAATGATCGAATTACCCCCGAAGGGTA
1 AAATGACCGAATTA-CCCCGAAGGGTA
* * * *
56750275 AAATGATCGAAATACCCCCAAGGGCA
1 AAATGACCGAATTACCCCGAAGGGTA
*
56750301 AAATGACCGAATTACCCTCAAAGGGTA
1 AAATGACCGAATTACCC-CGAAGGGTA
56750328 AAATGAC
1 AAATGAC
56750335 TGTTATACCC
Statistics
Matches: 198, Mismatches: 19, Indels: 10
0.87 0.08 0.04
Matches are distributed among these distances:
26 31 0.16
27 160 0.81
28 7 0.04
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.18
Consensus pattern (26 bp):
AAATGACCGAATTACCCCGAAGGGTA
Found at i:56750168 original size:54 final size:54
Alignment explanation
Indices: 56750086--56750333 Score: 356
Period size: 54 Copynumber: 4.6 Consensus size: 54
56750076 ATCAGGCCTT
*
56750086 AAATGACCGAAATACTCCCGAAGGGTAAAATGATCGAATTA-CCCTCGAAGGGTA
1 AAATGACCGAAATACCCCCGAAGGGTAAAATGATCGAATTACCCCT-GAAGGGTA
*
56750140 AAATGACCGAAATACCCCCGAAGGGTAAAATGATTGAATTACCCCTGAAGGGTA
1 AAATGACCGAAATACCCCCGAAGGGTAAAATGATCGAATTACCCCTGAAGGGTA
* * *
56750194 AAATGACTGAAATACCCCTGAAGGGTAAAATGACCGAATTACCCCTGAAGGGTA
1 AAATGACCGAAATACCCCCGAAGGGTAAAATGATCGAATTACCCCTGAAGGGTA
* * * * *
56750248 AAATGATCGAATTACCCCCGAAGGGTAAAATGATCGAAATACCCC-CAAGGGCA
1 AAATGACCGAAATACCCCCGAAGGGTAAAATGATCGAATTACCCCTGAAGGGTA
* * *
56750301 AAATGACCGAATTACCCTCAAAGGGTAAAATGA
1 AAATGACCGAAATACCCCCGAAGGGTAAAATGA
56750334 CTGTTATACC
Statistics
Matches: 176, Mismatches: 17, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
53 36 0.20
54 136 0.77
55 4 0.02
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.18
Consensus pattern (54 bp):
AAATGACCGAAATACCCCCGAAGGGTAAAATGATCGAATTACCCCTGAAGGGTA
Found at i:56750221 original size:81 final size:81
Alignment explanation
Indices: 56750086--56750333 Score: 349
Period size: 81 Copynumber: 3.1 Consensus size: 81
56750076 ATCAGGCCTT
* * * *
56750086 AAATGACCGAAATACTCCCGAAGGGTAAAATGATCGAATTA-CCCTCGAAGGGTAAAATGACCGA
1 AAATGATCGAATTACCCCCGAAGGGTAAAATGATCGAAATACCCCT-GAAGGGTAAAATGACCGA
*
56750150 AATACCCCCGAAGGGTA
65 ATTACCCCCGAAGGGTA
* *
56750167 AAATGATTGAATTACCCCTGAAGGGTAAAATGA-CTGAAATACCCCTGAAGGGTAAAATGACCGA
1 AAATGATCGAATTACCCCCGAAGGGTAAAATGATC-GAAATACCCCTGAAGGGTAAAATGACCGA
*
56750231 ATTACCCCTGAAGGGTA
65 ATTACCCCCGAAGGGTA
* *
56750248 AAATGATCGAATTACCCCCGAAGGGTAAAATGATCGAAATACCCC-CAAGGGCAAAATGACCGAA
1 AAATGATCGAATTACCCCCGAAGGGTAAAATGATCGAAATACCCCTGAAGGGTAAAATGACCGAA
* *
56750312 TTACCCTCAAAGGGTA
66 TTACCCCCGAAGGGTA
56750328 AAATGA
1 AAATGA
56750334 CTGTTATACC
Statistics
Matches: 149, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
80 37 0.25
81 107 0.72
82 5 0.03
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.18
Consensus pattern (81 bp):
AAATGATCGAATTACCCCCGAAGGGTAAAATGATCGAAATACCCCTGAAGGGTAAAATGACCGAA
TTACCCCCGAAGGGTA
Found at i:56750526 original size:27 final size:26
Alignment explanation
Indices: 56750483--56750581 Score: 67
Period size: 26 Copynumber: 3.8 Consensus size: 26
56750473 AGGGGAAGTA
**
56750483 TACTG-TACTGGTGGCTTTGCCACAT
1 TACTGTTACTGGCAGCTTTGCCACAT
* ****
56750508 ATATTGTTACTGGCAGCTTTGTTGGAT
1 -TACTGTTACTGGCAGCTTTGCCACAT
**
56750535 TACTGTTACTGGCAGCTTTGCTGCAT
1 TACTGTTACTGGCAGCTTTGCCACAT
* *
56750561 CACTATTACTGGC-GCCTTTGC
1 TACTGTTACTGGCAG-CTTTGC
56750582 TGTGATATTG
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
25 1 0.02
26 44 0.75
27 14 0.24
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.38
Consensus pattern (26 bp):
TACTGTTACTGGCAGCTTTGCCACAT
Found at i:56750547 original size:26 final size:26
Alignment explanation
Indices: 56750512--56750583 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 26
56750502 CCACATATAT
* * *
56750512 TGTTACTGGCAGCTTTGTTGGATTAC
1 TGTTACTGGCAGCTTTGCTGCATCAC
56750538 TGTTACTGGCAGCTTTGCTGCATCAC
1 TGTTACTGGCAGCTTTGCTGCATCAC
*
56750564 TATTACTGGC-GCCTTTGCTG
1 TGTTACTGGCAG-CTTTGCTG
56750584 TGATATTGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 1 0.02
26 40 0.98
ACGTcount: A:0.14, C:0.22, G:0.25, T:0.39
Consensus pattern (26 bp):
TGTTACTGGCAGCTTTGCTGCATCAC
Found at i:56761208 original size:15 final size:16
Alignment explanation
Indices: 56761188--56761222 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
56761178 ATATGAAGAA
56761188 TATTTTTAAAA-TTAT
1 TATTTTTAAAATTTAT
56761203 TATTTTTAAAATTTAT
1 TATTTTTAAAATTTAT
56761219 TATT
1 TATT
56761223 AACATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTTTAAAATTTAT
Found at i:56761283 original size:16 final size:16
Alignment explanation
Indices: 56761237--56761286 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
56761227 TAAAATTAAA
56761237 ATATTAAATAATTTATT
1 ATATT-AATAATTTATT
**
56761254 A-A--AATAATAAATT
1 ATATTAATAATTTATT
56761267 ATATTAATAATTTATT
1 ATATTAATAATTTATT
56761283 ATAT
1 ATAT
56761287 GATTAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
13 10 0.38
14 1 0.04
16 14 0.54
17 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATTAATAATTTATT
Found at i:56761303 original size:26 final size:26
Alignment explanation
Indices: 56761227--56761304 Score: 70
Period size: 29 Copynumber: 2.9 Consensus size: 26
56761217 ATTATTAACA
*
56761227 TAAAATTA-AAATATTAAATAATTTAT
1 TAAAATAATAAATA-TAAATAATTTAT
56761253 TAAAATAATAAATTATATTAATAATTTAT
1 TAAAATAATAAA-TATA--AATAATTTAT
* *
56761282 T-ATATGATTAAATATAAATAATT
1 TAAAAT-AATAAATATAAATAATT
56761305 AAAGATGTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
26 14 0.32
27 5 0.11
28 9 0.20
29 16 0.36
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (26 bp):
TAAAATAATAAATATAAATAATTTAT
Found at i:56771024 original size:27 final size:27
Alignment explanation
Indices: 56770974--56771025 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
56770964 TGTCGTATAA
**
56770974 CATATAATGCATTAAAATTTCCAATAT
1 CATATAATGCATTAAAATCGCCAATAT
56771001 CATATAATGCGA-TAAAATCGCCAAT
1 CATATAATGC-ATTAAAATCGCCAAT
56771026 TCTCTTGGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (27 bp):
CATATAATGCATTAAAATCGCCAATAT
Found at i:56799252 original size:22 final size:22
Alignment explanation
Indices: 56799227--56799269 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
56799217 CTTCTTTGCC
56799227 CTCGATTGTTCTTAACTTTACA
1 CTCGATTGTTCTTAACTTTACA
*
56799249 CTCGGTTGTTCTTAACTTTAC
1 CTCGATTGTTCTTAACTTTAC
56799270 TATCTTTGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.23, G:0.12, T:0.47
Consensus pattern (22 bp):
CTCGATTGTTCTTAACTTTACA
Found at i:56802454 original size:22 final size:22
Alignment explanation
Indices: 56802411--56802454 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
56802401 GGGCATTGAG
**
56802411 GGAAATCAAAAGCTTATAGTTT
1 GGAAATCAAAAGCAAATAGTTT
* *
56802433 GGAAATCAAAATCAAATGGTTT
1 GGAAATCAAAAGCAAATAGTTT
56802455 AGTGTTGGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.09, G:0.18, T:0.30
Consensus pattern (22 bp):
GGAAATCAAAAGCAAATAGTTT
Found at i:56808676 original size:3 final size:3
Alignment explanation
Indices: 56808668--56808759 Score: 51
Period size: 3 Copynumber: 29.3 Consensus size: 3
56808658 ATTTTAACAA
* * * * * *
56808668 TAT TAT TAT TTT TAC TAT TAT TAT TAT TTT TAAA TGT TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT
* * *
56808714 TAT T-G TATT TAT TGT TAT TACT TAT CTCAT TAT TAT TAT AAT TAT T
1 TAT TAT TA-T TAT TAT TAT TA-T TAT -T-AT TAT TAT TAT TAT TAT T
56808760 TATTCATTCA
Statistics
Matches: 65, Mismatches: 18, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
2 1 0.02
3 54 0.83
4 8 0.12
5 2 0.03
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:56808680 original size:18 final size:19
Alignment explanation
Indices: 56808632--56808700 Score: 63
Period size: 18 Copynumber: 3.7 Consensus size: 19
56808622 TTAGTCCTTT
* *
56808632 TTATTATTTTT-GCTATTAA
1 TTATTATTTTTAACTAAT-A
*
56808651 TTGATTAATTTTAAC-AATA
1 TT-ATTATTTTTAACTAATA
*
56808670 TTATTATTTTT-ACTATTA
1 TTATTATTTTTAACTAATA
56808688 TTATTATTTTTAA
1 TTATTATTTTTAA
56808701 ATGTTATTAC
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
17 2 0.05
18 22 0.54
19 6 0.15
20 10 0.24
21 1 0.02
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (19 bp):
TTATTATTTTTAACTAATA
Found at i:56812399 original size:14 final size:14
Alignment explanation
Indices: 56812380--56812409 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
56812370 TTGTATATTT
56812380 TACATACATATCTA
1 TACATACATATCTA
*
56812394 TACATATATATCTA
1 TACATACATATCTA
56812408 TA
1 TA
56812410 TACATATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (14 bp):
TACATACATATCTA
Found at i:56815307 original size:26 final size:26
Alignment explanation
Indices: 56815269--56815330 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
56815259 GCTCACCCCC
56815269 AATATAGCCTAGCCATTTCAGTGGCT
1 AATATAGCCTAGCCATTTCAGTGGCT
* *
56815295 AATATAGCTTAGCCATTTCGGTGGCT
1 AATATAGCCTAGCCATTTCAGTGGCT
*
56815321 AATGTAGCCT
1 AATATAGCCT
56815331 TCTCAATCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (26 bp):
AATATAGCCTAGCCATTTCAGTGGCT
Found at i:56822261 original size:23 final size:23
Alignment explanation
Indices: 56822232--56822422 Score: 303
Period size: 23 Copynumber: 8.3 Consensus size: 23
56822222 ATAAGTGCCA
56822232 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
56822255 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
56822278 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
56822301 CACTGAAATGT-GCCCGAAGCTAC
1 CACTGATATGTAG-CCGAAGCTAC
*
56822324 CACTGATATTTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
56822347 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
56822370 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
56822393 CACTGATATGTAGCCGAGGCTAC
1 CACTGATATGTAGCCGAAGCTAC
56822416 CACTGAT
1 CACTGAT
56822423 CAATAACACT
Statistics
Matches: 155, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
22 1 0.01
23 153 0.99
24 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:56825458 original size:22 final size:23
Alignment explanation
Indices: 56825428--56825476 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
56825418 CCTTCCCTCC
56825428 TTTTCTTATTTTTAT-TTTAAAA
1 TTTTCTTATTTTTATATTTAAAA
* *
56825450 TTTTTTTATTTTTATATTTCAAA
1 TTTTCTTATTTTTATATTTAAAA
56825473 TTTT
1 TTTT
56825477 AAAATTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTTCTTATTTTTATATTTAAAA
Found at i:56841032 original size:27 final size:27
Alignment explanation
Indices: 56840994--56841047 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
56840984 GACCCTAAGA
*
56840994 AAAATCACCAAATTTCACAAACAAATC
1 AAAATCACCAAACTTCACAAACAAATC
56841021 AAAATCACCAAACTTCACAAACAAATC
1 AAAATCACCAAACTTCACAAACAAATC
56841048 TTCATCGCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.17
Consensus pattern (27 bp):
AAAATCACCAAACTTCACAAACAAATC
Found at i:56845635 original size:2 final size:2
Alignment explanation
Indices: 56845630--56845667 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
56845620 AAGAGAGAGA
56845630 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56845668 TTATTTATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56849457 original size:8 final size:8
Alignment explanation
Indices: 56849446--56849493 Score: 52
Period size: 8 Copynumber: 6.6 Consensus size: 8
56849436 TAAATAAAAA
*
56849446 TAAAATTC
1 TAAAAGTC
56849454 TAAAA--C
1 TAAAAGTC
56849460 TAAAA--C
1 TAAAAGTC
56849466 TAA-AGTC
1 TAAAAGTC
56849473 TAAAAGTC
1 TAAAAGTC
56849481 TAAAAGTC
1 TAAAAGTC
56849489 TAAAA
1 TAAAA
56849494 ATAATTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
5 1 0.03
6 10 0.27
7 4 0.11
8 22 0.59
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.25
Consensus pattern (8 bp):
TAAAAGTC
Found at i:56849531 original size:9 final size:9
Alignment explanation
Indices: 56849517--56849601 Score: 127
Period size: 9 Copynumber: 9.4 Consensus size: 9
56849507 GTAGTGATTC
56849517 AATTCGGTT
1 AATTCGGTT
56849526 AATTCGGTT
1 AATTCGGTT
56849535 AATTCGAG-T
1 AATTCG-GTT
*
56849544 AATCCGGTT
1 AATTCGGTT
56849553 AATTCGGTT
1 AATTCGGTT
56849562 AATTCGGTT
1 AATTCGGTT
*
56849571 AATTCGGGT
1 AATTCGGTT
*
56849580 AATTTGGTT
1 AATTCGGTT
56849589 AATTCGGTT
1 AATTCGGTT
56849598 AATT
1 AATT
56849602 TTTAACCAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
8 1 0.01
9 66 0.97
10 1 0.01
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:56850186 original size:12 final size:12
Alignment explanation
Indices: 56850170--56850203 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
56850160 GGCGCTTCTT
56850170 AAAGCGCCGCAA
1 AAAGCGCCGCAA
*
56850182 GAAGCGCCGCAA
1 AAAGCGCCGCAA
*
56850194 AAAACGCCGC
1 AAAGCGCCGC
56850204 TATTGAACAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.38, C:0.35, G:0.26, T:0.00
Consensus pattern (12 bp):
AAAGCGCCGCAA
Found at i:56850313 original size:43 final size:43
Alignment explanation
Indices: 56850264--56850551 Score: 210
Period size: 43 Copynumber: 6.7 Consensus size: 43
56850254 AAAAGTCATG
* * * *
56850264 ACCTTTAGTGGCGCTTTTCCCACAAATGTCACTAAAGACCAGA
1 ACCTTTAGCGGCGCTTTTCCCACAAACGCCACTATAGACCAGA
* * *
56850307 ACCTTTAACGGCGC-TGTCCTCACAAACGCCACTATAGACCATA
1 ACCTTTAGCGGCGCTTTTCC-CACAAACGCCACTATAGACCAGA
* ** *
56850350 ACCTTTAGCTGCGCTTTTGTCACAAACGCCGCTATAGACCATG-
1 ACCTTTAGCGGCGCTTTTCCCACAAACGCCACTATAGACCA-GA
* * * *
56850393 GCCTTTAGCGACGCTTTTCCCACAAACACCGCTATAGACCATG-
1 ACCTTTAGCGGCGCTTTTCCCACAAACGCCACTATAGACCA-GA
* ** * * *
56850436 GCCTTTAGCGGCGCTTTTGTCACAAACGCCGCTAAAGAACATG-
1 ACCTTTAGCGGCGCTTTTCCCACAAACGCCACTATAGACCA-GA
* * ** * * *
56850479 ACCTTTAGCAGTGCTTTTTTTCAAAAACGCCGCTATAGAACA-A
1 ACCTTTAGCGGCGC-TTTTCCCACAAACGCCACTATAGACCAGA
* *
56850522 ACCTTTAACGGCGCTTCTCGCCA-AAACGCC
1 ACCTTTAGCGGCGCTTTTC-CCACAAACGCC
56850552 GCTAAAAACA
Statistics
Matches: 201, Mismatches: 38, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
42 14 0.07
43 161 0.80
44 26 0.13
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (43 bp):
ACCTTTAGCGGCGCTTTTCCCACAAACGCCACTATAGACCAGA
Found at i:56850486 original size:86 final size:86
Alignment explanation
Indices: 56850260--56850487 Score: 271
Period size: 86 Copynumber: 2.7 Consensus size: 86
56850250 CGCTAAAAGT
* ** * * * * *
56850260 CATGACCTTTAGTGGCGCTTTTCCCACAAATGTCACTAAAGACCA-GAACCTTTAACGGCGCTGT
1 CATGACCTTTAGCGGCGCTTTTGTCACAAACGCCGCTAAAGACCATG-ACCTTTAGCGACGCTGT
*
56850324 CCTCACAAACGCCACTATAGAC
65 CCTCACAAACACCACTATAGAC
* * * * *
56850346 CATAACCTTTAGCTGCGCTTTTGTCACAAACGCCGCTATAGACCATGGCCTTTAGCGACGCTTTT
1 CATGACCTTTAGCGGCGCTTTTGTCACAAACGCCGCTAAAGACCATGACCTTTAGCGACGC-TGT
*
56850411 CC-CACAAACACCGCTATAGAC
65 CCTCACAAACACCACTATAGAC
* *
56850432 CATGGCCTTTAGCGGCGCTTTTGTCACAAACGCCGCTAAAGAACATGACCTTTAGC
1 CATGACCTTTAGCGGCGCTTTTGTCACAAACGCCGCTAAAGACCATGACCTTTAGC
56850488 AGTGCTTTTT
Statistics
Matches: 119, Mismatches: 21, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
86 114 0.96
87 5 0.04
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.25
Consensus pattern (86 bp):
CATGACCTTTAGCGGCGCTTTTGTCACAAACGCCGCTAAAGACCATGACCTTTAGCGACGCTGTC
CTCACAAACACCACTATAGAC
Found at i:56850495 original size:86 final size:87
Alignment explanation
Indices: 56850327--56850562 Score: 275
Period size: 86 Copynumber: 2.7 Consensus size: 87
56850317 GCGCTGTCCT
* * * *
56850327 CACAAACGCCACTATAGACCATAACCTTTAGCTGCGCTTTTGTCACAAACGCCGCTATAGACCAT
1 CACAAACGCCGCTATAGACCATAACCTTTAGCGGCGCTTTTGTCACAAACGCCGCTAAAGAACAT
*
56850392 GGCCTTTAGCGACGC-TTTTCC
66 GACCTTTAGCGACGCTTTTTCC
* **
56850413 CACAAACACCGCTATAGACCATGGCCTTTAGCGGCGCTTTTGTCACAAACGCCGCTAAAGAACAT
1 CACAAACGCCGCTATAGACCATAACCTTTAGCGGCGCTTTTGTCACAAACGCCGCTAAAGAACAT
* **
56850478 GACCTTTAGC-AGTGCTTTTTTT
66 GACCTTTAGCGA-CGCTTTTTCC
* * * * *
56850500 CAAAAACGCCGCTATAGAACA-AACCTTTAACGGCGCTTCTCGCCA-AAACGCCGCTAAA-AACA
1 CACAAACGCCGCTATAGACCATAACCTTTAGCGGCGCTT-TTGTCACAAACGCCGCTAAAGAACA
56850562 T
65 T
56850563 ATCATGCAAA
Statistics
Matches: 128, Mismatches: 19, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
85 6 0.05
86 96 0.75
87 26 0.20
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.24
Consensus pattern (87 bp):
CACAAACGCCGCTATAGACCATAACCTTTAGCGGCGCTTTTGTCACAAACGCCGCTAAAGAACAT
GACCTTTAGCGACGCTTTTTCC
Found at i:56850527 original size:129 final size:129
Alignment explanation
Indices: 56850264--56850557 Score: 315
Period size: 129 Copynumber: 2.3 Consensus size: 129
56850254 AAAAGTCATG
* * * *
56850264 ACCTTTAGTGGCGCTTTTCCCACAAATGTCACTAAAGACCAGAACCTTTAACGGCGCTGTCCTCA
1 ACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAGAACCTTTAACGGCGCTGTCCTCA
* * * * * *
56850329 CAAACGCCACTATAGACCATAACCTTTAGCTGCGCTTTTGTCACAAACGCCGCTATAGACCATG
66 CAAACGCCACTAAAGAACATAACCTTTAGCAGCGCTTTTGTCAAAAACGCCGCTATAGAACATA
* * * * * * * **
56850393 GCCTTTAGCGACGCTTTTCCCACAAACACCGCTATAGACCATG-GCCTTTAGCGGCGCTTTTGTC
1 ACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCA-GAACCTTTAACGGCGCTGTCCTC
* * * *
56850457 ACAAACGCCGCTAAAGAACATGACCTTTAGCAGTGCTTTTTTTCAAAAACGCCGCTATAGAACA-
65 ACAAACGCCACTAAAGAACATAACCTTTAGCAGCGC-TTTTGTCAAAAACGCCGCTATAGAACAT
56850521 A
129 A
* *
56850522 ACCTTTAACGGCGCTTCTCGCCA-AAACGCCGCTAAA
1 ACCTTTAGCGGCGCTTTTC-CCACAAACGCCGCTAAA
56850558 AACATATCAT
Statistics
Matches: 133, Mismatches: 29, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
129 105 0.79
130 28 0.21
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (129 bp):
ACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAGAACCTTTAACGGCGCTGTCCTCA
CAAACGCCACTAAAGAACATAACCTTTAGCAGCGCTTTTGTCAAAAACGCCGCTATAGAACATA
Found at i:56850801 original size:27 final size:27
Alignment explanation
Indices: 56850744--56850802 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
56850734 TTAAATAATA
*
56850744 ATAAA-AATTAATAAAAGTGAGAAAAT
1 ATAAATAATTAATAAAAATGAGAAAAT
* * * *
56850770 GTAAATAATTAATAAAAATTATAAATT
1 ATAAATAATTAATAAAAATGAGAAAAT
56850797 ATAAAT
1 ATAAAT
56850803 TATAAACCTC
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.31
Consensus pattern (27 bp):
ATAAATAATTAATAAAAATGAGAAAAT
Found at i:56855520 original size:30 final size:28
Alignment explanation
Indices: 56855450--56855521 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 28
56855440 ATTATAAAAA
*
56855450 TAAAAGTTTAAAATCTTTTTCAATTTTT
1 TAAAAATTTAAAATCTTTTTCAATTTTT
56855478 TAAAAAAATTTAAAATC-TTTTCAAATTCATTT
1 T--AAAAATTTAAAATCTTTTTC-AATT--TTT
*
56855510 TAAAATTTTAAA
1 TAAAAATTTAAA
56855522 TCACGAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
28 1 0.03
29 5 0.14
30 27 0.73
32 4 0.11
ACGTcount: A:0.44, C:0.07, G:0.01, T:0.47
Consensus pattern (28 bp):
TAAAAATTTAAAATCTTTTTCAATTTTT
Found at i:56857003 original size:40 final size:39
Alignment explanation
Indices: 56856890--56857040 Score: 132
Period size: 40 Copynumber: 3.9 Consensus size: 39
56856880 TGGGCTTAGG
* * *
56856890 TTTTTTGCGGCGCTTTTTG-AAAAACGCCGCTAATGCTT
1 TTTTTAGCGGCGCTTTTTGTAAAAGCGCCGCTAATGCTA
** *
56856928 TTTTTAGCGGCG--TTTTCCAAATGCGCCGCTAATGCTCAA
1 TTTTTAGCGGCGCTTTTTGTAAAAGCGCCGCTAATGCT--A
*
56856967 TCTTTAGCGGCG-TTTTTGTAAAAGCGCCGCTAATGCTTGA
1 TTTTTAGCGGCGCTTTTTGTAAAAGCGCCGCTAATGC-T-A
* * *
56857007 TTTTTAGTGGCGTTTTTTGTCCAAA-CGCCGCTAA
1 TTTTTAGCGGCGCTTTTTGT-AAAAGCGCCGCTAA
56857041 AAGTGCCGCC
Statistics
Matches: 93, Mismatches: 13, Indels: 11
0.79 0.11 0.09
Matches are distributed among these distances:
36 4 0.04
37 16 0.17
38 11 0.12
39 11 0.12
40 31 0.33
41 17 0.18
42 3 0.03
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (39 bp):
TTTTTAGCGGCGCTTTTTGTAAAAGCGCCGCTAATGCTA
Found at i:56857036 original size:41 final size:40
Alignment explanation
Indices: 56856914--56857040 Score: 140
Period size: 40 Copynumber: 3.2 Consensus size: 40
56856904 TTTTGAAAAA
56856914 CGCCGCTAATGCTT-TTTTTAGCGGCG--TTT-TCCAAATG
1 CGCCGCTAATGCTTATTTTTAGCGGCGTTTTTGTCCAAA-G
* * *
56856951 CGCCGCTAATGCTCAATCTTTAGCGGCGTTTTTGT-AAAAG
1 CGCCGCTAATGCT-TATTTTTAGCGGCGTTTTTGTCCAAAG
*
56856991 CGCCGCTAATGCTTGATTTTTAGTGGCGTTTTTTGTCCAAA-
1 CGCCGCTAATGCTT-ATTTTTAGCGGCG-TTTTTGTCCAAAG
56857032 CGCCGCTAA
1 CGCCGCTAA
56857041 AAGTGCCGCC
Statistics
Matches: 75, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
37 13 0.17
39 11 0.15
40 25 0.33
41 22 0.29
42 4 0.05
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (40 bp):
CGCCGCTAATGCTTATTTTTAGCGGCGTTTTTGTCCAAAG
Found at i:56861052 original size:23 final size:23
Alignment explanation
Indices: 56861020--56861099 Score: 65
Period size: 24 Copynumber: 3.5 Consensus size: 23
56861010 CTACCCTGTT
*
56861020 TTGGATAGCATTTATACATCAAA
1 TTGGACAGCATTTATACATCAAA
* *
56861043 TTGGACAGCATCGATATGC-TCAAA
1 TTGGACAGCAT--TTATACATCAAA
* * *
56861067 CTGGACAACA-TTATACATTAAA
1 TTGGACAGCATTTATACATCAAA
*
56861089 GTGGACAGCAT
1 TTGGACAGCAT
56861100 CAATATGCTC
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
21 4 0.09
22 12 0.28
23 10 0.23
24 13 0.30
25 4 0.09
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (23 bp):
TTGGACAGCATTTATACATCAAA
Found at i:56861071 original size:24 final size:23
Alignment explanation
Indices: 56861038--56861147 Score: 109
Period size: 24 Copynumber: 4.7 Consensus size: 23
56861028 CATTTATACA
*
56861038 TCAAATTGGACAGCATCGATATGC
1 TCAAA-TGGACAGCATCAATATGC
* *
56861062 TCAAACTGGACA--A-CATTATAC
1 TCAAA-TGGACAGCATCAATATGC
*
56861083 ATTAAAGTGGACAGCATCAATATGC
1 -TCAAA-TGGACAGCATCAATATGC
56861108 TCTAAATGGACAGCATCAATATGC
1 TC-AAATGGACAGCATCAATATGC
56861132 TCAAAATGGACAGCAT
1 TC-AAATGGACAGCAT
56861148 TATACATCTA
Statistics
Matches: 71, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
21 5 0.07
22 11 0.15
24 46 0.65
25 9 0.13
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (23 bp):
TCAAATGGACAGCATCAATATGC
Found at i:56861098 original size:46 final size:46
Alignment explanation
Indices: 56861031--56861119 Score: 135
Period size: 46 Copynumber: 1.9 Consensus size: 46
56861021 TGGATAGCAT
* *
56861031 TTATACATCAAATTGGACAGCATCGATATGCTC-AAACTGGACAACA
1 TTATACATCAAAGTGGACAGCATCAATATGCTCTAAA-TGGACAACA
*
56861077 TTATACATTAAAGTGGACAGCATCAATATGCTCTAAATGGACA
1 TTATACATCAAAGTGGACAGCATCAATATGCTCTAAATGGACA
56861120 GCATCAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
46 36 0.92
47 3 0.08
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (46 bp):
TTATACATCAAAGTGGACAGCATCAATATGCTCTAAATGGACAACA
Found at i:56861889 original size:41 final size:40
Alignment explanation
Indices: 56861837--56861972 Score: 132
Period size: 41 Copynumber: 3.4 Consensus size: 40
56861827 TTGCCATCGT
* * * *
56861837 ATAGTCGAAGCTATTATAATCTCTCACACTAAGTGCCTTAC
1 ATAGCCGAAGCTATTA-AATCTCGCACACTAAGTGCCATAA
* * * *
56861878 ATAGCCGAAGCTATCTCAGTCTCGCACACTAAGTGTCATAT
1 ATAGCCGAAGCTAT-TAAATCTCGCACACTAAGTGCCATAA
* *
56861919 ATAGCTGAATCTATTCCAAAT-T-GCACACTAAGTGCCATAA
1 ATAGCCGAAGCTATT--AAATCTCGCACACTAAGTGCCATAA
56861959 ATAGCCGAAGCTAT
1 ATAGCCGAAGCTAT
56861973 CTCGAATTTC
Statistics
Matches: 77, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
40 29 0.38
41 45 0.58
42 3 0.04
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (40 bp):
ATAGCCGAAGCTATTAAATCTCGCACACTAAGTGCCATAA
Found at i:56862946 original size:14 final size:13
Alignment explanation
Indices: 56862923--56862952 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
56862913 TGTATTTTTA
56862923 TTTCTTTTTTATT
1 TTTCTTTTTTATT
56862936 TTTCGTTTTTTATT
1 TTTC-TTTTTTATT
56862950 TTT
1 TTT
56862953 AGCCTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.07, C:0.07, G:0.03, T:0.83
Consensus pattern (13 bp):
TTTCTTTTTTATT
Found at i:56864288 original size:14 final size:16
Alignment explanation
Indices: 56864253--56864289 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
56864243 CTTATTTCAA
56864253 CTTATATATATATTAT
1 CTTATATATATATTAT
*
56864269 CATATATAT-TATTAT
1 CTTATATATATATTAT
56864284 -TTATAT
1 CTTATAT
56864290 CAAGTTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
14 5 0.26
15 6 0.32
16 8 0.42
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (16 bp):
CTTATATATATATTAT
Found at i:56868328 original size:18 final size:18
Alignment explanation
Indices: 56868300--56868350 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
56868290 TATTATGGCG
* *
56868300 AACTGTGTTAATTTGGTA
1 AACTGTATTAATTTGGAA
* *
56868318 ATCTGTATTAATATGGAA
1 AACTGTATTAATTTGGAA
*
56868336 AACTGCATTAATTTG
1 AACTGTATTAATTTG
56868351 TCAAACTGTG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (18 bp):
AACTGTATTAATTTGGAA
Found at i:56868340 original size:36 final size:36
Alignment explanation
Indices: 56868269--56868350 Score: 85
Period size: 36 Copynumber: 2.3 Consensus size: 36
56868259 TTGTGAACCA
* * **
56868269 TGTTAACTTGGTGAATTATATTATTATGGCGAACTG
1 TGTTAATTTGGTGAATTATATTAATATGGAAAACTG
*
56868305 TGTTAATTTGGT-AATCTGTATTAATATGGAAAACTG
1 TGTTAATTTGGTGAAT-TATATTAATATGGAAAACTG
**
56868341 CATTAATTTG
1 TGTTAATTTG
56868351 TCAAACTGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
35 3 0.08
36 35 0.92
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (36 bp):
TGTTAATTTGGTGAATTATATTAATATGGAAAACTG
Found at i:56869055 original size:51 final size:51
Alignment explanation
Indices: 56868992--56869099 Score: 146
Period size: 51 Copynumber: 2.1 Consensus size: 51
56868982 CTGATAGAGC
* * *
56868992 ATGAACTTTTATTTCGCATGAAG-TGTTATTCGGTATGAACTGATATTTCAT
1 ATGAACTATTATTTCGCATG-AGTTGTCATTCGGTAAGAACTGATATTTCAT
* * *
56869043 ATGAACTATTATTTTGCATGAGTTGTCATTTGGTAAGAACTGTTATTTCAT
1 ATGAACTATTATTTCGCATGAGTTGTCATTCGGTAAGAACTGATATTTCAT
56869094 ATGAAC
1 ATGAAC
56869100 AGATGTTTGG
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
50 2 0.04
51 48 0.96
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.43
Consensus pattern (51 bp):
ATGAACTATTATTTCGCATGAGTTGTCATTCGGTAAGAACTGATATTTCAT
Found at i:56869099 original size:17 final size:17
Alignment explanation
Indices: 56868992--56869099 Score: 74
Period size: 17 Copynumber: 6.4 Consensus size: 17
56868982 CTGATAGAGC
* *
56868992 ATGAACTTTTATTTCGC
1 ATGAACTGTTATTTCGT
*
56869009 ATGAAGTGTTA-TTCGGT
1 ATGAACTGTTATTTC-GT
* *
56869026 ATGAACTGATATTTCAT
1 ATGAACTGTTATTTCGT
* * *
56869043 ATGAACTATTATTTTGC
1 ATGAACTGTTATTTCGT
** * *
56869060 ATGAGTTGTCATTTGGT
1 ATGAACTGTTATTTCGT
* *
56869077 AAGAACTGTTATTTCAT
1 ATGAACTGTTATTTCGT
56869094 ATGAAC
1 ATGAAC
56869100 AGATGTTTGG
Statistics
Matches: 65, Mismatches: 24, Indels: 4
0.70 0.26 0.04
Matches are distributed among these distances:
16 3 0.05
17 59 0.91
18 3 0.05
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.43
Consensus pattern (17 bp):
ATGAACTGTTATTTCGT
Found at i:56871965 original size:123 final size:126
Alignment explanation
Indices: 56871745--56872025 Score: 437
Period size: 123 Copynumber: 2.3 Consensus size: 126
56871735 ATTATTTTGA
*
56871745 TTTGACGTTTCTG-GTCAAATAGTAGAAAATCG-TATCTACCAGGATGCTATTTGAGAAGAAATT
1 TTTGACGTTTCTGAG-CAAATAGTATAAAATCGCTATCTACCAGGATGCTATTTGAGAAGAAATT
* *
56871808 GTGAAATCGTGCCCTCGTGGATGCGATTTTGCTACAGTTAGTCATGTAAGAAATA-A-ATTT
65 GTGAAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTAGTCATGTAAGAAATACATATTT
* *
56871868 TTTGACGTTTCTGAGCAAATAGTATAAAATCGCT-TCTACCAGGATGCTATTTTAGAAGGAATTG
1 TTTGACGTTTCTGAGCAAATAGTATAAAATCGCTATCTACCAGGATGCTATTTGAGAAGAAATTG
* *
56871932 TGAAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATACATTTTT
66 TGAAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTAGTCATGTAAGAAATACATATTT
* *
56871993 TTTGACGTTTCTGAACAAATAATATAAAATCGC
1 TTTGACGTTTCTGAGCAAATAGTATAAAATCGC
56872026 GCCCTCGTGG
Statistics
Matches: 145, Mismatches: 9, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
123 108 0.74
124 3 0.02
125 34 0.23
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (126 bp):
TTTGACGTTTCTGAGCAAATAGTATAAAATCGCTATCTACCAGGATGCTATTTGAGAAGAAATTG
TGAAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTAGTCATGTAAGAAATACATATTT
Found at i:56873266 original size:15 final size:15
Alignment explanation
Indices: 56873229--56873260 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
56873219 TACAAAGGTC
*
56873229 CACATACATGTGCTG
1 CACATACATGTACTG
56873244 CACATACATGTACTG
1 CACATACATGTACTG
56873259 CA
1 CA
56873261 GGTACAGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (15 bp):
CACATACATGTACTG
Found at i:56875140 original size:23 final size:23
Alignment explanation
Indices: 56875114--56875220 Score: 79
Period size: 23 Copynumber: 4.2 Consensus size: 23
56875104 TTTGTTAATG
56875114 GTTAGAGTTTTTAATTAAATTAA
1 GTTAGAGTTTTTAATTAAATTAA
*
56875137 GTTAGGGTTTAGGGTTTTTAATTAAATTAGGTT
1 GTTA--G---A--GTTTTTAATTAAATTA---A
*
56875170 GTTAGGGTTTTTAATTAAATTAA
1 GTTAGAGTTTTTAATTAAATTAA
* * *
56875193 GTTAGGGTTTTTAAATAAATTAG
1 GTTAGAGTTTTTAATTAAATTAA
56875216 GTTAG
1 GTTAG
56875221 GGTTAGGGTT
Statistics
Matches: 69, Mismatches: 5, Indels: 20
0.73 0.05 0.21
Matches are distributed among these distances:
23 30 0.43
25 1 0.01
26 16 0.23
28 1 0.01
30 16 0.23
31 1 0.01
33 4 0.06
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (23 bp):
GTTAGAGTTTTTAATTAAATTAA
Found at i:56875226 original size:29 final size:29
Alignment explanation
Indices: 56875113--56875304 Score: 267
Period size: 29 Copynumber: 6.9 Consensus size: 29
56875103 TTTTGTTAAT
* *
56875113 GGTTAGAGTTTTTAATTAAATTAAGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
56875142 GGTTTAGGGTTTTTAATTAAATTAGGTT--
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
56875170 -GTTAGGGTTTTTAATTAAATTA----A-
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
56875193 -GTTAGGGTTTTTAAATAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
56875221 GGTTAGGGTTTTTAATTAAATTAGGGTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
56875250 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
56875279 GGTTTAGGGTTTTTAATTAAATTAGG
1 GG-TTAGGGTTTTTAATTAAATTAGG
56875305 ATTTTTATTA
Statistics
Matches: 148, Mismatches: 6, Indels: 17
0.87 0.04 0.10
Matches are distributed among these distances:
23 21 0.14
26 21 0.14
27 2 0.01
29 58 0.39
30 46 0.31
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (29 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:56875340 original size:21 final size:22
Alignment explanation
Indices: 56875290--56875340 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
56875280 GTTTAGGGTT
* * *
56875290 TTTAATTAAATTAGGATTTTTA
1 TTTAATTAAATTAGAACTTATA
56875312 -TTACATTAAA-TAGAACTTATA
1 TTTA-ATTAAATTAGAACTTATA
56875333 TTTAATTA
1 TTTAATTA
56875341 TATCAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (22 bp):
TTTAATTAAATTAGAACTTATA
Found at i:56877533 original size:26 final size:25
Alignment explanation
Indices: 56877478--56877533 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
56877468 CTTTTATAAC
*
56877478 AAATAATAAATTAATAATTCTCTAA
1 AAATAATAAATTAAAAATTCTCTAA
56877503 AAATACATAAA-TAAAAATATCT-TAA
1 AAATA-ATAAATTAAAAAT-TCTCTAA
56877528 ATAATA
1 A-AATA
56877534 TTTAAGATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 15 0.56
26 12 0.44
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (25 bp):
AAATAATAAATTAAAAATTCTCTAA
Found at i:56877668 original size:30 final size:31
Alignment explanation
Indices: 56877624--56877690 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
56877614 GTCATTGATG
* *
56877624 AAAATATAAAAAAAATTAAAGTTATTTTTAA
1 AAAATATAAAAAAAATTAAAATTATTTTAAA
56877655 AAAATATAAAAAAAATTAAAATTATTTTAAA
1 AAAATATAAAAAAAATTAAAATTATTTTAAA
56877686 AAAAT
1 AAAAT
56877691 GAAATTGAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (31 bp):
AAAATATAAAAAAAATTAAAATTATTTTAAA
Found at i:56877749 original size:22 final size:22
Alignment explanation
Indices: 56877724--56877773 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
56877714 TAATATGGAT
56877724 TTGAGA-GATTTTTGGAAGGAAA
1 TTGAGAGGA-TTTTGGAAGGAAA
56877746 TTGAGAGGATTTTGGAAGGAAA
1 TTGAGAGGATTTTGGAAGGAAA
56877768 TTGAGA
1 TTGAGA
56877774 TAGGATTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 25 0.93
23 2 0.07
ACGTcount: A:0.36, C:0.00, G:0.34, T:0.30
Consensus pattern (22 bp):
TTGAGAGGATTTTGGAAGGAAA
Found at i:56884360 original size:20 final size:20
Alignment explanation
Indices: 56884335--56884372 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
56884325 ACTCCCATCA
56884335 GTAGTAATAGTAAATGAGTT
1 GTAGTAATAGTAAATGAGTT
*
56884355 GTAGTATTAGTAAATGAG
1 GTAGTAATAGTAAATGAG
56884373 CCCAACGCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.26, T:0.34
Consensus pattern (20 bp):
GTAGTAATAGTAAATGAGTT
Found at i:56890115 original size:21 final size:21
Alignment explanation
Indices: 56890077--56890116 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
56890067 TAAAAATGAT
* *
56890077 ATATTTATATTATTGATTGTG
1 ATATTAATATTATCGATTGTG
*
56890098 ATATTAATATTGTCGATTG
1 ATATTAATATTATCGATTG
56890117 CAAAATATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.03, G:0.15, T:0.53
Consensus pattern (21 bp):
ATATTAATATTATCGATTGTG
Found at i:56892609 original size:4 final size:4
Alignment explanation
Indices: 56892600--56892634 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
56892590 ATTTTTATTT
56892600 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
56892635 TCTTTAAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
TTAA
Found at i:56893600 original size:61 final size:61
Alignment explanation
Indices: 56893530--56893655 Score: 182
Period size: 61 Copynumber: 2.1 Consensus size: 61
56893520 CACACGAGCG
* * *
56893530 TGTGCAAGGCCATGTGGACCACACAGGCCAGCTACCTA-AGTCGTGTTAATCCACATGGGCA
1 TGTGCAAGGCCATGTGGACCACACAGACCAGCAACCTAGA-CCGTGTTAATCCACATGGGCA
* * *
56893591 TGTGTAAGGCCATGTGGATCACACAGACCAGCAACCTAGACCGTGTTAATCCACATGGGCG
1 TGTGCAAGGCCATGTGGACCACACAGACCAGCAACCTAGACCGTGTTAATCCACATGGGCA
56893652 TGTG
1 TGTG
56893656 GGCCAAAAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
61 57 0.98
62 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.27, T:0.21
Consensus pattern (61 bp):
TGTGCAAGGCCATGTGGACCACACAGACCAGCAACCTAGACCGTGTTAATCCACATGGGCA
Found at i:56895567 original size:170 final size:170
Alignment explanation
Indices: 56895285--56895626 Score: 675
Period size: 170 Copynumber: 2.0 Consensus size: 170
56895275 GTGCAGTGTC
56895285 TCTGTTGCAAGATGAGGCTTACCATTGGTGGCTAACCATCTAGGAGGGCACTCAACCCAAACACA
1 TCTGTTGCAAGATGAGGCTTACCATTGGTGGCTAACCATCTAGGAGGGCACTCAACCCAAACACA
56895350 TCACTTGGAATTTCTTCAGGAACACCTTTCAGAGTAAGTATGTGGGGGTGAGTTATGTGGAGGCC
66 TCACTTGGAATTTCTTCAGGAACACCTTTCAGAGTAAGTATGTGGGGGTGAGTTATGTGGAGGCC
56895415 CGTAGACTCGAGTTTGTGAGCCTTGTTAAAGGTGAGAGGA
131 CGTAGACTCGAGTTTGTGAGCCTTGTTAAAGGTGAGAGGA
56895455 TCTGTTGCAAGATGAGGCTTACCATTGGTGGCTAACCATCTAGGAGGGCACTCAACCCAAACACA
1 TCTGTTGCAAGATGAGGCTTACCATTGGTGGCTAACCATCTAGGAGGGCACTCAACCCAAACACA
*
56895520 TCACTTGGGATTTCTTCAGGAACACCTTTCAGAGTAAGTATGTGGGGGTGAGTTATGTGGAGGCC
66 TCACTTGGAATTTCTTCAGGAACACCTTTCAGAGTAAGTATGTGGGGGTGAGTTATGTGGAGGCC
56895585 CGTAGACTCGAGTTTGTGAGCCTTGTTAAAGGTGAGAGGA
131 CGTAGACTCGAGTTTGTGAGCCTTGTTAAAGGTGAGAGGA
56895625 TC
1 TC
56895627 GTGTCCGAGT
Statistics
Matches: 171, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
170 171 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (170 bp):
TCTGTTGCAAGATGAGGCTTACCATTGGTGGCTAACCATCTAGGAGGGCACTCAACCCAAACACA
TCACTTGGAATTTCTTCAGGAACACCTTTCAGAGTAAGTATGTGGGGGTGAGTTATGTGGAGGCC
CGTAGACTCGAGTTTGTGAGCCTTGTTAAAGGTGAGAGGA
Found at i:56901793 original size:6 final size:6
Alignment explanation
Indices: 56901782--56901809 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
56901772 GAGGTGTTAC
56901782 AAATTA AAATTA AAATTA AAATTA AAAT
1 AAATTA AAATTA AAATTA AAATTA AAAT
56901810 AGTGTAAGAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATTA
Found at i:56908158 original size:19 final size:18
Alignment explanation
Indices: 56908121--56908168 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
56908111 TACTATGTTA
56908121 CAAAATACAAAAATATTTT
1 CAAAATA-AAAAATATTTT
*
56908140 CAAAATAAAAATATTTTTT
1 CAAAATAAAAA-ATATTTT
*
56908159 CAATATAAAA
1 CAAAATAAAA
56908169 TGCTCATGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (18 bp):
CAAAATAAAAAATATTTT
Found at i:56910231 original size:17 final size:17
Alignment explanation
Indices: 56910198--56910242 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
56910188 CGCGTAAGAC
* *
56910198 AACAGTCCATATGAAAT
1 AACAGTTCATATAAAAT
*
56910215 AATAGTTCATATAAAAT
1 AACAGTTCATATAAAAT
*
56910232 AGCAGTTCATA
1 AACAGTTCATA
56910243 CAACATCATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (17 bp):
AACAGTTCATATAAAAT
Found at i:56911143 original size:23 final size:23
Alignment explanation
Indices: 56911077--56911256 Score: 175
Period size: 24 Copynumber: 7.7 Consensus size: 23
56911067 ACATATACCA
**
56911077 AGTGATAAGGGTTCATACATGTCT
1 AGTGAT-AGGGTTCGCACATGTCT
* *
56911101 GGTGATAGGGGTTCGTACATGTCT
1 AGTGATA-GGGTTCGCACATGTCT
*
56911125 GGTGATAGGGTTCGCACATGTCT
1 AGTGATAGGGTTCGCACATGTCT
*
56911148 AGTGATATGGTTCGCACATGT-T
1 AGTGATAGGGTTCGCACATGTCT
* **
56911170 TGTGATAGGGGTT-ATACATGTCT
1 AGTGATA-GGGTTCGCACATGTCT
* *
56911193 AGTGATAGGTGTTCACACATTTCT
1 AGTGATAGG-GTTCGCACATGTCT
* *
56911217 GGTGATAGGGATTCGCGCATGTCT
1 AGTGATAGGG-TTCGCACATGTCT
*
56911241 AGTGATACGGTTCGCA
1 AGTGATAGGGTTCGCA
56911257 GTTATCACAC
Statistics
Matches: 131, Mismatches: 19, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
22 15 0.11
23 55 0.42
24 61 0.47
ACGTcount: A:0.22, C:0.14, G:0.31, T:0.33
Consensus pattern (23 bp):
AGTGATAGGGTTCGCACATGTCT
Found at i:56914831 original size:25 final size:24
Alignment explanation
Indices: 56914786--56914832 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
56914776 TTTCTTCTTC
* *
56914786 TTTCTTTTTTTTTATTTTTTTATT
1 TTTCCTTTTCTTTATTTTTTTATT
*
56914810 TTTCCTTTTCTTTCTTTGTTTTA
1 TTTCCTTTTCTTTATTT-TTTTA
56914833 CTTCTTTGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.06, C:0.11, G:0.02, T:0.81
Consensus pattern (24 bp):
TTTCCTTTTCTTTATTTTTTTATT
Found at i:56919362 original size:19 final size:18
Alignment explanation
Indices: 56919325--56919372 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
56919315 TGCTATGTTA
56919325 CAAAATACAAAAATATTTT
1 CAAAATA-AAAAATATTTT
*
56919344 CAAAATAAAAATATTTTTT
1 CAAAATAAAAA-ATATTTT
*
56919363 CAATATAAAA
1 CAAAATAAAA
56919373 TTCTCATGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (18 bp):
CAAAATAAAAAATATTTT
Found at i:56931183 original size:21 final size:21
Alignment explanation
Indices: 56931140--56931188 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
56931130 AATAGAAAAT
*
56931140 ATATCAAAAAATTAAAAAGTAC
1 ATAT-AAAAAATAAAAAAGTAC
*
56931162 A-ATAAAAAATAAAAAATTTAC
1 ATATAAAAAATAAAAAA-GTAC
56931183 ATATAA
1 ATATAA
56931189 TTTGAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 12 0.52
21 6 0.26
22 5 0.22
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.24
Consensus pattern (21 bp):
ATATAAAAAATAAAAAAGTAC
Found at i:56932114 original size:22 final size:22
Alignment explanation
Indices: 56932084--56932127 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
56932074 AACACTCTTT
* *
56932084 TAAATAATAAATAAGAAATAAG
1 TAAACAATAAAAAAGAAATAAG
56932106 TAAACAATAAAAAAGAAATAAG
1 TAAACAATAAAAAAGAAATAAG
56932128 GGGCTCCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.18
Consensus pattern (22 bp):
TAAACAATAAAAAAGAAATAAG
Found at i:56933686 original size:14 final size:15
Alignment explanation
Indices: 56933661--56933695 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
56933651 TTTAATTTTC
56933661 AAAATTTCAAAAAAA
1 AAAATTTCAAAAAAA
*
56933676 AAAATTT-AAAAATA
1 AAAATTTCAAAAAAA
56933690 AAAATT
1 AAAATT
56933696 GCATTTTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATTTCAAAAAAA
Found at i:56933725 original size:30 final size:31
Alignment explanation
Indices: 56933691--56933792 Score: 122
Period size: 30 Copynumber: 3.4 Consensus size: 31
56933681 TTAAAAATAA
*
56933691 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
56933721 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
56933751 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
56933781 AAATTTCATTTT
1 AAATTTCATTTT
56933793 AATCCTAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 4 0.06
30 57 0.92
31 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:56934187 original size:3 final size:3
Alignment explanation
Indices: 56934179--56934250 Score: 53
Period size: 3 Copynumber: 24.0 Consensus size: 3
56934169 GCTAGACTTT
* *
56934179 GAA GAA GAA AAA GGAA GAA GAAA GAA GAA GAA -AA GAG GAA GAA GAAA
1 GAA GAA GAA GAA -GAA GAA G-AA GAA GAA GAA GAA GAA GAA GAA G-AA
*
56934226 GAAA GAA -AA -AA GAA AAA GAA -AA GAA
1 G-AA GAA GAA GAA GAA GAA GAA GAA GAA
56934251 ATAATAAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
2 8 0.14
3 37 0.65
4 12 0.21
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:56934205 original size:7 final size:7
Alignment explanation
Indices: 56934180--56934246 Score: 57
Period size: 7 Copynumber: 9.3 Consensus size: 7
56934170 CTAGACTTTG
56934180 AAGAAGA
1 AAGAAGA
*
56934187 AA-AAGG
1 AAGAAGA
56934193 AAGAAGA
1 AAGAAGA
56934200 AAGAAGA
1 AAGAAGA
*
56934207 AGAAAAGA
1 A-AGAAGA
56934215 GGAAGAAGA
1 --AAGAAGA
56934224 AAGAAAGA
1 AAG-AAGA
*
56934232 AAAAAGA
1 AAGAAGA
56934239 AA-AAGA
1 AAGAAGA
56934245 AA
1 AA
56934247 AGAAATAATA
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
6 11 0.22
7 22 0.44
8 11 0.22
9 5 0.10
10 1 0.02
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (7 bp):
AAGAAGA
Found at i:56934213 original size:11 final size:11
Alignment explanation
Indices: 56934180--56934250 Score: 67
Period size: 10 Copynumber: 6.5 Consensus size: 11
56934170 CTAGACTTTG
56934180 AAGAAGAA-AA
1 AAGAAGAAGAA
*
56934190 AGGAAGAAG-A
1 AAGAAGAAGAA
56934200 AAGAAGAAGAA
1 AAGAAGAAGAA
*
56934211 AAGAGGAAGAAGA
1 AAGAAGAAG-A-A
56934224 AAGAAAGAA-AA
1 AAG-AAGAAGAA
*
56934235 AAGAAAAAGAA
1 AAGAAGAAGAA
56934246 AAGAA
1 AAGAA
56934251 ATAATAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
10 20 0.40
11 20 0.40
12 2 0.04
13 4 0.08
14 4 0.08
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (11 bp):
AAGAAGAAGAA
Found at i:56934222 original size:24 final size:24
Alignment explanation
Indices: 56934179--56934238 Score: 97
Period size: 24 Copynumber: 2.5 Consensus size: 24
56934169 GCTAGACTTT
56934179 GAAGAAGAAAA-AGGAAGAAGAAA
1 GAAGAAGAAAAGAGGAAGAAGAAA
56934202 GAAGAAGAAAAGAGGAAGAAGAAA
1 GAAGAAGAAAAGAGGAAGAAGAAA
56934226 GAAAGAA-AAAAGA
1 G-AAGAAGAAAAGA
56934239 AAAAGAAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
23 11 0.31
24 19 0.54
25 5 0.14
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (24 bp):
GAAGAAGAAAAGAGGAAGAAGAAA
Found at i:56934244 original size:24 final size:24
Alignment explanation
Indices: 56934179--56934245 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
56934169 GCTAGACTTT
**
56934179 GAAGAAGAAAA-AGGAAGAAGAAA
1 GAAGAAGAAAAGAAAAAGAAGAAA
**
56934202 GAAGAAGAAAAGAGGAAGAAGAAA
1 GAAGAAGAAAAGAAAAAGAAGAAA
56934226 GAAAGAA-AAAAGAAAAAGAA
1 G-AAGAAGAAAAGAAAAAGAA
56934246 AAGAAATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
23 11 0.28
24 24 0.60
25 5 0.12
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (24 bp):
GAAGAAGAAAAGAAAAAGAAGAAA
Found at i:56934251 original size:11 final size:12
Alignment explanation
Indices: 56934180--56934251 Score: 73
Period size: 11 Copynumber: 6.2 Consensus size: 12
56934170 CTAGACTTTG
*
56934180 AAGAAGAAAAAGG
1 AAGAAG-AAAAGA
56934193 AAGAAG-AAAG-
1 AAGAAGAAAAGA
56934203 AAGAAGAAAAGA
1 AAGAAGAAAAGA
56934215 GGAAGAAG-AAAGA
1 --AAGAAGAAAAGA
56934228 AAGAA-AAAAGA
1 AAGAAGAAAAGA
56934239 AA-AAGAAAAGA
1 AAGAAGAAAAGA
56934250 AA
1 AA
56934252 TAATAAAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
10 8 0.15
11 28 0.53
13 11 0.21
14 6 0.11
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AAGAAGAAAAGA
Found at i:56934260 original size:18 final size:17
Alignment explanation
Indices: 56934183--56934251 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
56934173 GACTTTGAAG
* *
56934183 AAGAAAAAGGAAGAAGA
1 AAGAAAAAGAAAGAAAA
* **
56934200 AAGAAGAAGAAA-AGAGG
1 AAGAAAAAGAAAGA-AAA
56934217 AAGAAGAAAGAAAGAAAA
1 AAGAA-AAAGAAAGAAAA
56934235 AAGAAAAAGAAAAGAAA
1 AAGAAAAAG-AAAGAAA
56934252 TAATAAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
16 1 0.02
17 21 0.50
18 19 0.45
19 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (17 bp):
AAGAAAAAGAAAGAAAA
Found at i:56934350 original size:15 final size:13
Alignment explanation
Indices: 56934328--56934366 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
56934318 GCAGCCCAAG
56934328 AAAAAAACAACAAA
1 AAAAAAACAA-AAA
56934342 AACAAAAACAAAAA
1 AA-AAAAACAAAAA
56934356 AAAAGAAACAA
1 AAAA-AAACAA
56934367 GCCCAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.09
14 13 0.57
15 8 0.35
ACGTcount: A:0.85, C:0.13, G:0.03, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAA
Found at i:56934532 original size:11 final size:11
Alignment explanation
Indices: 56934516--56934582 Score: 71
Period size: 11 Copynumber: 6.0 Consensus size: 11
56934506 GGCCCAGCAG
56934516 AGAAAAAAAAA
1 AGAAAAAAAAA
*
56934527 AGAAAAGAAAA
1 AGAAAAAAAAA
* *
56934538 AGAAGAAAAAG
1 AGAAAAAAAAA
**
56934549 AGAAGGAAAAA
1 AGAAAAAAAAA
*
56934560 AGAAGGAAAAAA
1 AGAA-AAAAAAA
56934572 AGAAAAAAAAA
1 AGAAAAAAAAA
56934583 GAGGTTCAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
11 37 0.79
12 10 0.21
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:56934546 original size:22 final size:22
Alignment explanation
Indices: 56934516--56934584 Score: 79
Period size: 22 Copynumber: 3.1 Consensus size: 22
56934506 GGCCCAGCAG
*
56934516 AGAAAAAAAAAAGAAAAGAAAA
1 AGAAGAAAAAAAGAAAAGAAAA
* *
56934538 AGAAGAAAAAGAG-AAGGAAAAA
1 AGAAGAAAAAAAGAAAAG-AAAA
56934560 AGAAGGAAAAAAAGAAAA-AAAA
1 AGAA-GAAAAAAAGAAAAGAAAA
56934582 AGA
1 AGA
56934585 GGTTCAATTC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 3 0.08
22 26 0.67
23 8 0.21
24 2 0.05
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (22 bp):
AGAAGAAAAAAAGAAAAGAAAA
Found at i:56934952 original size:18 final size:18
Alignment explanation
Indices: 56934931--56935283 Score: 157
Period size: 17 Copynumber: 19.6 Consensus size: 18
56934921 AATTCTCATG
56934931 TTTCAAAAATCTTCGTGT
1 TTTCAAAAATCTTCGTGT
* *
56934949 TTTCAAAATTC-TAGTG-
1 TTTCAAAAATCTTCGTGT
* *
56934965 TTTCAAAAATTTTCTTGT
1 TTTCAAAAATCTTCGTGT
56934983 TTTCAGAAAAAAAT-TTCGTGT
1 TTTC----AAAAATCTTCGTGT
* *
56935004 TTT-ATAAAT-TTCCGTAT
1 TTTCAAAAATCTT-CGTGT
* *
56935021 TTTCAAAAAAAC--CATGT
1 TTTC-AAAAATCTTCGTGT
*
56935038 CTTTCAAAAATTTTCGTGT
1 -TTTCAAAAATCTTCGTGT
***
56935057 TTTCAAAAAAAAATGACCGTG-
1 TTTC----AAAAATCTTCGTGT
56935078 TTTCAAAAAT-TTCCGTGT
1 TTTCAAAAATCTT-CGTGT
*** *
56935096 TAAAAAAAAATCTTCGTAT
1 T-TTCAAAAATCTTCGTGT
*
56935115 TTTCAAAAAATTTTCGTG-
1 TTTC-AAAAATCTTCGTGT
56935133 TTTCAAAAATCTTCGTGT
1 TTTCAAAAATCTTCGTGT
56935151 TTTCAAAAAT-TTCG-GT
1 TTTCAAAAATCTTCGTGT
* *
56935167 GTTTCAAAGATTTTCGTGT
1 -TTTCAAAAATCTTCGTGT
*
56935186 TTTCAAAAA-CTCCGGTGAT
1 TTTCAAAAATCTTC-GTG-T
*** *
56935205 TTT-AAAAAAAATAGT-T
1 TTTCAAAAATCTTCGTGT
*
56935221 TTCTAAAAAAT-TTCCGTG-
1 TT-TCAAAAATCTT-CGTGT
*
56935239 TTTCAAAAATTTTCGTGT
1 TTTCAAAAATCTTCGTGT
*
56935257 TTT-AAAAATTTTCGTGT
1 TTTCAAAAATCTTCGTGT
*
56935274 TTTTAAAAAT
1 TTTCAAAAAT
56935284 TCTCGTATTT
Statistics
Matches: 256, Mismatches: 43, Indels: 72
0.69 0.12 0.19
Matches are distributed among these distances:
16 21 0.08
17 89 0.35
18 79 0.31
19 36 0.14
20 2 0.01
21 13 0.05
22 16 0.06
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (18 bp):
TTTCAAAAATCTTCGTGT
Found at i:56934967 original size:34 final size:34
Alignment explanation
Indices: 56934909--56934987 Score: 106
Period size: 34 Copynumber: 2.3 Consensus size: 34
56934899 CTATAATCCC
*
56934909 CGTGCTTTTAAAAATTCTCATGTTTCAAAAATCTT
1 CGTG-TTTTCAAAATTCTCATGTTTCAAAAATCTT
*
56934944 CGTGTTTTCAAAATTCT-AGTGTTTCAAAAATTTT
1 CGTGTTTTCAAAATTCTCA-TGTTTCAAAAATCTT
*
56934978 CTTGTTTTCA
1 CGTGTTTTCA
56934988 GAAAAAAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
33 1 0.03
34 35 0.88
35 4 0.10
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.47
Consensus pattern (34 bp):
CGTGTTTTCAAAATTCTCATGTTTCAAAAATCTT
Found at i:56934970 original size:16 final size:16
Alignment explanation
Indices: 56934919--56934972 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
56934909 CGTGCTTTTA
56934919 AAAATTCTCA-TGTTTC
1 AAAATTCT-AGTGTTTC
* *
56934935 AAAAATCTTCGTGTTTTC
1 AAAATTC-TAGTG-TTTC
56934953 AAAATTCTAGTGTTTC
1 AAAATTCTAGTGTTTC
56934969 AAAA
1 AAAA
56934973 ATTTTCTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 14 0.45
17 7 0.23
18 10 0.32
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (16 bp):
AAAATTCTAGTGTTTC
Found at i:56934983 original size:17 final size:17
Alignment explanation
Indices: 56934918--56935430 Score: 148
Period size: 17 Copynumber: 29.3 Consensus size: 17
56934908 CCGTGCTTTT
*
56934918 AAAAATTCTCATGTTTC
1 AAAAATTCTCGTGTTTC
56934935 AAAAA-TCTTCGTGTTTTC
1 AAAAATTC-TCGTG-TTTC
*
56934953 -AAAATTCTAGTGTTTC
1 AAAAATTCTCGTGTTTC
* *
56934969 AAAAATTTTCTTGTTTTC
1 AAAAATTCTCGTG-TTTC
*
56934987 AGAAAAAAATT-TCGTGTTTT
1 ----AAAAATTCTCGTGTTTC
* *
56935007 ATAAATT-TCCGTATTTTC
1 AAAAATTCT-CGT-GTTTC
** *
56935025 AAAAAAAC-CATGTCTTTC
1 AAAAATTCTC--GTGTTTC
*
56935043 AAAAATTTTCGTGTTTTC
1 AAAAATTCTCGTG-TTTC
*
56935061 AAAAAAAAATGAC-CGTGTTTC
1 ----AAAAAT-TCTCGTGTTTC
**
56935082 AAAAATT-TCCGTGTTAAA
1 AAAAATTCT-CGTGTT-TC
* *
56935100 AAAAAATCTTCGTATTTTC
1 AAAAATTC-TCGT-GTTTC
*
56935119 AAAAAATTTTCGTGTTTC
1 -AAAAATTCTCGTGTTTC
56935137 AAAAA-TCTTCGTGTTTTC
1 AAAAATTC-TCGTG-TTTC
56935155 AAAAATT-TCGGTGTTTC
1 AAAAATTCTC-GTGTTTC
* *
56935172 AAAGATTTTCGTGTTTTC
1 AAAAATTCTCGTG-TTTC
* *
56935190 AAAAACTC-CGGTGATTTT
1 AAAAATTCTC-GTG-TTTC
*** *
56935208 AAAAAAAATAGT-TTTC
1 AAAAATTCTCGTGTTTC
56935224 TAAAAAATT-TCCGTGTTTC
1 --AAAAATTCT-CGTGTTTC
* *
56935243 AAAAATTTTCGTGTTTT
1 AAAAATTCTCGTGTTTC
* *
56935260 AAAAATTTTCGTGTTTTT
1 AAAAATTCTCGTG-TTTC
*
56935278 AAAAATTCTCGTATTT-
1 AAAAATTCTCGTGTTTC
* *
56935294 -TAAATT-T--T-TTTA
1 AAAAATTCTCGTGTTTC
*** *
56935306 AGAAAAAAATTGTGTTTC
1 A-AAAATTCTCGTGTTTC
* * * *
56935324 AAAAAAATGTCTTGTTTT
1 -AAAAATTCTCGTGTTTC
56935342 AAAAATTCTCGTGTTTC
1 AAAAATTCTCGTGTTTC
* * *
56935359 AAAAAATGTCGTGTTTT
1 AAAAATTCTCGTGTTTC
*
56935376 AAAAATTTTCGTGTTTC
1 AAAAATTCTCGTGTTTC
**
56935393 TGAAATT-TCCGTGTTT-
1 AAAAATTCT-CGTGTTTC
*
56935409 AAAAATTCTCGTGTTTT
1 AAAAATTCTCGTGTTTC
56935426 AAAAA
1 AAAAA
56935431 AAACTTTCAT
Statistics
Matches: 371, Mismatches: 72, Indels: 106
0.68 0.13 0.19
Matches are distributed among these distances:
11 3 0.01
12 1 0.00
14 4 0.01
15 6 0.02
16 30 0.08
17 161 0.43
18 113 0.30
19 16 0.04
20 12 0.03
21 8 0.02
22 17 0.05
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.43
Consensus pattern (17 bp):
AAAAATTCTCGTGTTTC
Found at i:56935169 original size:35 final size:34
Alignment explanation
Indices: 56935074--56935275 Score: 158
Period size: 35 Copynumber: 5.7 Consensus size: 34
56935064 AAAAAATGAC
**
56935074 CGTG-TTTCAAAAATTTCCGTGTTAAAAAAAAATCTT
1 CGTGTTTTCAAAAATTT-CGTGTT--TCAAAAATCTT
*
56935110 CGTATTTTCAAAAAATTTTCGTGTTTCAAAAATCTT
1 CGTGTTTTC-AAAAA-TTTCGTGTTTCAAAAATCTT
* *
56935146 CGTGTTTTCAAAAATTTCGGTGTTTCAAAGATTTT
1 CGTGTTTTCAAAAATTTC-GTGTTTCAAAAATCTT
* * * ***
56935181 CGTGTTTTCAAAAACTCCGGTGATTTTAAAAAAAAT
1 CGTGTTTTCAAAAATTTC-GTG-TTTCAAAAATCTT
* * *
56935217 AGT-TTTCTAAAAAATTTCCGTGTTTCAAAAATTTT
1 CGTGTTT-TCAAAAATTT-CGTGTTTCAAAAATCTT
56935252 CGTGTTTT-AAAAATTTTCGTGTTT
1 CGTGTTTTCAAAAA-TTTCGTGTTT
56935276 TTAAAAATTC
Statistics
Matches: 135, Mismatches: 22, Indels: 20
0.76 0.12 0.11
Matches are distributed among these distances:
34 16 0.12
35 57 0.42
36 43 0.32
37 5 0.04
38 11 0.08
39 3 0.02
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (34 bp):
CGTGTTTTCAAAAATTTCGTGTTTCAAAAATCTT
Found at i:56935469 original size:20 final size:20
Alignment explanation
Indices: 56935409--56935461 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
56935399 TTCCGTGTTT
56935409 AAAAATTCTCGTGTTTTAAAA
1 AAAAATT-TCGTGTTTTAAAA
* * *
56935430 AAAACTTTCATTTTTTAAAA
1 AAAAATTTCGTGTTTTAAAA
56935450 AAAAATTTCGTG
1 AAAAATTTCGTG
56935462 CTTCAAAATT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 20 0.77
21 6 0.23
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (20 bp):
AAAAATTTCGTGTTTTAAAA
Found at i:56944606 original size:30 final size:30
Alignment explanation
Indices: 56944566--56944666 Score: 102
Period size: 30 Copynumber: 3.4 Consensus size: 30
56944556 TTTAAAAATA
*
56944566 AAATTGCATTTTGACCCCTAAACTTT-TCCT
1 AAATTTCATTTTGACCCCTAAACTTTCT-CT
* *
56944596 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCTCT
* *
56944626 AAATTTCACTTAGACCCCT-AAC-TTCAAT-T
1 AAATTTCATTTTGACCCCTAAACTTTC--TCT
56944655 AAATTTCATTTT
1 AAATTTCATTTT
56944667 AATCCTAAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
28 3 0.05
29 14 0.23
30 42 0.70
31 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.04, T:0.44
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCTCT
Found at i:56945048 original size:3 final size:3
Alignment explanation
Indices: 56945040--56945111 Score: 62
Period size: 3 Copynumber: 24.0 Consensus size: 3
56945030 GCTAGACTTT
*
56945040 GAA GAA GAA GAA GGAA GAA GAA GGAA GAA GAA -AA GAG GAA GAA GAAA
1 GAA GAA GAA GAA -GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA G-AA
*
56945087 GAAA GAA -AA -AA GAA AAA GAA -AA GAA
1 G-AA GAA GAA GAA GAA GAA GAA GAA GAA
56945112 ATAATAAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
2 8 0.14
3 38 0.64
4 13 0.22
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:56945058 original size:10 final size:10
Alignment explanation
Indices: 56945043--56945071 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
56945033 AGACTTTGAA
56945043 GAAGAAGAAG
1 GAAGAAGAAG
56945053 GAAGAAGAAG
1 GAAGAAGAAG
56945063 GAAGAAGAA
1 GAAGAAGAA
56945072 AAGAGGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAG
Found at i:56945058 original size:13 final size:13
Alignment explanation
Indices: 56945040--56945085 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
56945030 GCTAGACTTT
56945040 GAAGAAGAAGAAG
1 GAAGAAGAAGAAG
56945053 GAAGAAGAAGGAA-
1 GAAGAAGAA-GAAG
56945066 GAAGAA-AAG-AG
1 GAAGAAGAAGAAG
56945077 GAAGAAGAA
1 GAAGAAGAA
56945086 AGAAAGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 7 0.23
12 4 0.13
13 15 0.50
14 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAGAAG
Found at i:56945381 original size:9 final size:9
Alignment explanation
Indices: 56945369--56945419 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
56945359 CCCAGCAGAG
56945369 AAAAA-AAA
1 AAAAAGAAA
*
56945377 GAAAAGAAA
1 AAAAAGAAA
*
56945386 AAGAAGAAA
1 AAAAAGAAA
*
56945395 AAGAGAAGGAA
1 AA-A-AAGAAA
56945406 AAAAAGAAA
1 AAAAAGAAA
56945415 AAAAA
1 AAAAA
56945420 AAGAGGTTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
8 4 0.12
9 22 0.65
10 1 0.03
11 7 0.21
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:56945395 original size:20 final size:20
Alignment explanation
Indices: 56945367--56945423 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
56945357 GGCCCAGCAG
*
56945367 AGAAAAAAAAGAAAAGAAAA
1 AGAAGAAAAAGAAAAGAAAA
*
56945387 AGAAGAAAAAGAGAAGGAAAA
1 AGAAGAAAAAGA-AAAGAAAA
*
56945408 A-AAGAAAAAAAAAAGA
1 AGAAGAAAAAGAAAAGA
56945424 GGTTCAATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 4 0.12
20 20 0.62
21 8 0.25
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (20 bp):
AGAAGAAAAAGAAAAGAAAA
Found at i:56945406 original size:12 final size:10
Alignment explanation
Indices: 56945367--56945417 Score: 52
Period size: 11 Copynumber: 5.1 Consensus size: 10
56945357 GGCCCAGCAG
56945367 AGAA-AAAAA
1 AGAAGAAAAA
*
56945376 AGAAAAGAAAA
1 AGAAGA-AAAA
56945387 AGAAGAAAAA
1 AGAAGAAAAA
*
56945397 GAGAAGGAAAA
1 -AGAAGAAAAA
56945408 A-AAGAAAAA
1 AGAAGAAAAA
56945417 A
1 A
56945418 AAAAGAGGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
9 12 0.33
10 6 0.17
11 18 0.50
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
AGAAGAAAAA
Found at i:56945421 original size:14 final size:14
Alignment explanation
Indices: 56945367--56945421 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
56945357 GGCCCAGCAG
*
56945367 AGAAAAAAAAGAAA
1 AGAAAAAAAAAAAA
*
56945381 AGAAAAAGAAGAAAA
1 AGAAAAA-AAAAAAA
* **
56945396 AGAGAAGGAAAAAA
1 AGAAAAAAAAAAAA
56945410 AGAAAAAAAAAA
1 AGAAAAAAAAAA
56945422 GAGGTTCAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
14 21 0.68
15 10 0.32
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AGAAAAAAAAAAAA
Found at i:56945581 original size:16 final size:17
Alignment explanation
Indices: 56945555--56945592 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
56945545 TTATATTTAT
56945555 ATTTTTAATTTAATTTG
1 ATTTTTAATTTAATTTG
* *
56945572 ATTTTT-ATTTTATTTT
1 ATTTTTAATTTAATTTG
56945588 ATTTT
1 ATTTT
56945593 AAATAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTTTAATTTAATTTG
Found at i:56945788 original size:18 final size:18
Alignment explanation
Indices: 56945744--56946263 Score: 276
Period size: 17 Copynumber: 29.8 Consensus size: 18
56945734 TCTATAATCC
*
56945744 TCGTGCTTTT-AAAAATTC
1 TCGTG-TTTTCAAAAATTT
* *
56945762 TCATG-TTTCAAAAATCT
1 TCGTGTTTTCAAAAATTT
*
56945779 TCGTGTTTTC-AAAATTC
1 TCGTGTTTTCAAAAATTT
*
56945796 TAGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
*
56945813 TCTTGTTTTCAGAAAAAATTT
1 TCGTGTTTTC---AAAAATTT
*
56945834 TCGTG-TTTCATAAATTT
1 TCGTGTTTTCAAAAATTT
* * **
56945851 CCGTATTTTCAAAAA-AA
1 TCGTGTTTTCAAAAATTT
*
56945868 TCATGTCTTTCAAAAATTT
1 TCGTGT-TTTCAAAAATTT
**
56945887 TCGTGTTTTCAAAAAAAATGA
1 TCGTGTTTTC---AAAAATTT
*
56945908 CCGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
* *** *
56945925 CCGTGTTAAAAAAAATCT
1 TCGTGTTTTCAAAAATTT
*
56945943 TCGTCTTTTCAAAAAATTT
1 TCGTGTTTTC-AAAAATTT
*
56945962 TCGTG-TTTCAAAAATCT
1 TCGTGTTTTCAAAAATTT
56945979 TCGTGTTTTCAAAAA-TT
1 TCGTGTTTTCAAAAATTT
*
56945996 TCG-GTGTTTCAAAGATTT
1 TCGTGT-TTTCAAAAATTT
*
56946014 TCGTGTTTTCAAAAA-CT
1 TCGTGTTTTCAAAAATTT
* **
56946031 CCGGTGATTTT-AAAAA-AA
1 TC-GTG-TTTTCAAAAATTT
*
56946049 TCGT-TTTCTAAAAAATTT
1 TCGTGTTT-TCAAAAATTT
*
56946067 CCGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
56946084 TCGTGTTTT-AAAAATTT
1 TCGTGTTTTCAAAAATTT
* *
56946101 TCGTGTTTTTAAAAATTC
1 TCGTGTTTTCAAAAATTT
*
56946119 TCGTATTTT---AAATTT
1 TCGTGTTTTCAAAAATTT
*** **
56946134 T--T-TTAAGAAAAAAAT
1 TCGTGTTTTCAAAAATTT
* *
56946149 T-GTG-TTTCAAAAAAATG
1 TCGTGTTTTC-AAAAATTT
* *
56946166 TCTTGTTTT-AAAAATTC
1 TCGTGTTTTCAAAAATTT
* *
56946183 TCGTG-TTTCAAAAAATG
1 TCGTGTTTTCAAAAATTT
56946200 TCGTGTTTT-AAAAATTT
1 TCGTGTTTTCAAAAATTT
**
56946217 TCGTG-TTTCTGAAATTT
1 TCGTGTTTTCAAAAATTT
56946234 TCGTG-TTT-AAAAATTCT
1 TCGTGTTTTCAAAAATT-T
56946251 T-GTGTTTT-AAAAA
1 TCGTGTTTTCAAAAA
56946264 AAAACTTTCA
Statistics
Matches: 385, Mismatches: 77, Indels: 81
0.71 0.14 0.15
Matches are distributed among these distances:
12 2 0.01
13 1 0.00
15 14 0.04
16 26 0.07
17 178 0.46
18 109 0.28
19 25 0.06
20 8 0.02
21 22 0.06
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTT
Found at i:56945806 original size:16 final size:16
Alignment explanation
Indices: 56945755--56945808 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
56945745 CGTGCTTTTA
56945755 AAAATTCTCA-TGTTTC
1 AAAATTCT-AGTGTTTC
* *
56945771 AAAAATCTTCGTGTTTTC
1 AAAATTC-TAGTG-TTTC
56945789 AAAATTCTAGTGTTTC
1 AAAATTCTAGTGTTTC
56945805 AAAA
1 AAAA
56945809 ATTTTCTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 14 0.45
17 7 0.23
18 10 0.32
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (16 bp):
AAAATTCTAGTGTTTC
Found at i:56945904 original size:74 final size:74
Alignment explanation
Indices: 56945801--56945975 Score: 221
Period size: 74 Copynumber: 2.4 Consensus size: 74
56945791 AATTCTAGTG
* * *** * * *
56945801 TTTCAAAAATTTTCTTGTTTTCAGAAAAAATTTTCGTGTTTCATAAATTTCCGTATTTTCAAAAA
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAAATGACCGTGTTTCAAAAATTTCCG--TGTTAAAAAA
56945866 AATCAT-GTC-
64 AATCATCGTCT
56945875 TTTCAAAAATTTTCGTGTTTTCAAAAAAAATGACCGTGTTTCAAAAATTTCCGTGTTAAAAAAAA
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAAATGACCGTGTTTCAAAAATTTCCGTGTTAAAAAAAA
*
56945940 TCTTCGTCT
66 TCATCGTCT
56945949 TTTCAAAAAATTTTCGTG-TTTCAAAAA
1 TTTC-AAAAATTTTCGTGTTTTCAAAAA
56945976 TCTTCGTGTT
Statistics
Matches: 89, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
72 13 0.15
73 3 0.03
74 60 0.67
75 13 0.15
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (74 bp):
TTTCAAAAATTTTCGTGTTTTCAAAAAAAATGACCGTGTTTCAAAAATTTCCGTGTTAAAAAAAA
TCATCGTCT
Found at i:56945937 original size:36 final size:35
Alignment explanation
Indices: 56945835--56945939 Score: 93
Period size: 36 Copynumber: 2.9 Consensus size: 35
56945825 AAAAAATTTT
* * **
56945835 CGTGTTTCATAAATTTCCGTATTTTCAAAAAAATCA
1 CGTGTTTCAAAAATTTCCGT-GTTAAAAAAAAATCA
* * * * *
56945871 TGTCTTTCAAAAATTTTCGTGTTTTCAAAAAAAATGA
1 CGTGTTTCAAAAATTTCCGTG--TTAAAAAAAAATCA
56945908 CCGTGTTTCAAAAATTTCCGTGTTAAAAAAAA
1 -CGTGTTTCAAAAATTTCCGTGTTAAAAAAAA
56945940 TCTTCGTCTT
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
36 25 0.46
37 11 0.20
38 18 0.33
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.37
Consensus pattern (35 bp):
CGTGTTTCAAAAATTTCCGTGTTAAAAAAAAATCA
Found at i:56945959 original size:54 final size:55
Alignment explanation
Indices: 56945879--56945985 Score: 137
Period size: 54 Copynumber: 1.9 Consensus size: 55
56945869 CATGTCTTTC
* *
56945879 AAAAATTTTCGTGTTTTCAAAAAAAATGACCGTGTTTCAAAAAT-TTCCGTGTTAAA
1 AAAAATCTTCGTCTTTTC-AAAAAAATGACCGTGTTTCAAAAATCTT-CGTGTTAAA
***
56945935 AAAAATCTTCGTCTTTTC-AAAAAATTTTCGTGTTTCAAAAATCTTCGTGTT
1 AAAAATCTTCGTCTTTTCAAAAAAATGACCGTGTTTCAAAAATCTTCGTGTT
56945986 TTCAAAAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
54 27 0.60
55 2 0.04
56 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (55 bp):
AAAAATCTTCGTCTTTTCAAAAAAATGACCGTGTTTCAAAAATCTTCGTGTTAAA
Found at i:56946003 original size:35 final size:34
Alignment explanation
Indices: 56945767--56946108 Score: 187
Period size: 35 Copynumber: 9.6 Consensus size: 34
56945757 AATTCTCATG
* *
56945767 TTTCAAAAATCTTCGTGTTTTCAAAATTC-TAGTG-
1 TTTCAAAAAT-TTCGTG-TTTCAAAAATCTTCGTGT
* *
56945801 TTTCAAAAATTTTCTTGTTTTCAGAAAAAATTTTCGTG-
1 TTTCAAAAA-TTTCGTG-TTTC---AAAAATCTTCGTGT
* * ** *
56945839 TTTCATAAATTTCCGTATTTTCAAAAA-AATCATGT
1 TTTCAAAAATTT-CGT-GTTTCAAAAATCTTCGTGT
***
56945874 CTTTCAAAAATTTTCGTGTTTTCAAAAAAAATGACCGTG-
1 -TTTCAAAAA-TTTCGTG-TTTC---AAAAATCTTCGTGT
** *
56945913 TTTCAAAAATTTCCGTGTTAAAAAAAATCTTCGTCT
1 TTTCAAAAATTT-CGTGTT-TCAAAAATCTTCGTGT
56945949 TTTCAAAAAATTTTCGTGTTTCAAAAATCTTCGTGT
1 TTTC-AAAAA-TTTCGTGTTTCAAAAATCTTCGTGT
* *
56945985 TTTCAAAAATTTCGGTGTTTCAAAGATTTTCGTGT
1 TTTCAAAAATTTC-GTGTTTCAAAAATCTTCGTGT
* * * **
56946020 TTTCAAAAACTCCGGTGATTTTAAAAA-AATCGT-T
1 TTTCAAAAATTTC-GTG-TTTCAAAAATCTTCGTGT
* *
56946054 TTCTAAAAAATTTCCGTGTTTCAAAAATTTTCGTGT
1 TT-TCAAAAATTT-CGTGTTTCAAAAATCTTCGTGT
56946090 TTT-AAAAATTTTCGTGTTT
1 TTTCAAAAA-TTTCGTGTTT
56946109 TTAAAAATTC
Statistics
Matches: 243, Mismatches: 38, Indels: 54
0.73 0.11 0.16
Matches are distributed among these distances:
34 50 0.21
35 76 0.31
36 47 0.19
37 27 0.11
38 34 0.14
39 5 0.02
40 4 0.02
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.43
Consensus pattern (34 bp):
TTTCAAAAATTTCGTGTTTCAAAAATCTTCGTGT
Found at i:56946255 original size:16 final size:16
Alignment explanation
Indices: 56946159--56946263 Score: 74
Period size: 16 Copynumber: 6.3 Consensus size: 16
56946149 TGTGTTTCAA
56946159 AAAAATGTCTTGT-TTT
1 AAAAAT-TCTTGTGTTT
*
56946175 AAAAATTCTCGTGTTT
1 AAAAATTCTTGTGTTT
*
56946191 CAAAAAATGTCGTGT-TTT
1 --AAAAAT-TCTTGTGTTT
56946209 AAAAATT-TTCGTGTTT
1 AAAAATTCTT-GTGTTT
**
56946225 CTGAAATT-TTCGTGTTT
1 -AAAAATTCTT-GTGTTT
56946242 AAAAATTCTTGTGTTTT
1 AAAAATTCTTGTG-TTT
56946259 AAAAA
1 AAAAA
56946264 AAAACTTTCA
Statistics
Matches: 72, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
14 1 0.01
15 8 0.11
16 26 0.36
17 24 0.33
18 9 0.12
19 4 0.06
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.46
Consensus pattern (16 bp):
AAAAATTCTTGTGTTT
Found at i:56947177 original size:20 final size:21
Alignment explanation
Indices: 56947152--56947190 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
56947142 GAAGTTGTGA
56947152 TTTCCTTTGG-AGTTTCTTCT
1 TTTCCTTTGGTAGTTTCTTCT
56947172 TTTCCTTTGGTAGTTTCTT
1 TTTCCTTTGGTAGTTTCTT
56947191 AAATATCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.05, C:0.18, G:0.15, T:0.62
Consensus pattern (21 bp):
TTTCCTTTGGTAGTTTCTTCT
Found at i:56948608 original size:17 final size:19
Alignment explanation
Indices: 56948570--56948608 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
56948560 TTCAAGGATA
*
56948570 ATGCAATCTTAGGTATGAT
1 ATGCAATCTTAGGTAAGAT
56948589 ATGCAATCTTA-G-AAGAT
1 ATGCAATCTTAGGTAAGAT
56948606 ATG
1 ATG
56948609 ATTTTGTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 1 0.05
19 11 0.58
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (19 bp):
ATGCAATCTTAGGTAAGAT
Done.