Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 90 of 163
Found at i:25557212 original size:23 final size:24
Alignment explanation
Indices: 25557184--25557237 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
25557174 TTTAATACTA
* *
25557184 TAATTATATCTTTATTGTGTT-A-T
1 TAATTATAT-TTGATTGTCTTCATT
25557207 TAATTATATTTGATTGTCTTCATT
1 TAATTATATTTGATTGTCTTCATT
25557231 TAATTAT
1 TAATTAT
25557238 TTATATTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 9 0.33
23 10 0.37
24 8 0.30
ACGTcount: A:0.28, C:0.06, G:0.07, T:0.59
Consensus pattern (24 bp):
TAATTATATTTGATTGTCTTCATT
Found at i:25560763 original size:3 final size:3
Alignment explanation
Indices: 25560755--25560784 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
25560745 TCTCCATTTC
25560755 TCT TCT TC- TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
25560785 ATTATTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:25560789 original size:3 final size:3
Alignment explanation
Indices: 25560783--25560842 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
25560773 CTTCTTCTTC
25560783 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
25560831 TTA TTA TTA TTA
1 TTA TTA TTA TTA
25560843 AATTGGGTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:25562981 original size:15 final size:15
Alignment explanation
Indices: 25562957--25563004 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
25562947 ACCAAACAGC
*
25562957 TCACACATAAACAAT
1 TCACAGATAAACAAT
* * * *
25562972 TCGCATATAAAGAGT
1 TCACAGATAAACAAT
25562987 TCACAGATAAACAAT
1 TCACAGATAAACAAT
25563002 TCA
1 TCA
25563005 ATCTAGTGGT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.48, C:0.21, G:0.08, T:0.23
Consensus pattern (15 bp):
TCACAGATAAACAAT
Found at i:25564168 original size:75 final size:75
Alignment explanation
Indices: 25564050--25564211 Score: 234
Period size: 75 Copynumber: 2.2 Consensus size: 75
25564040 GTGTTATAAC
* *
25564050 GCTATGTGCCTACCAGGCTTCGTGCTGGTGATATCGAGATTTATGCCTAACAGGCCTTCATGTCG
1 GCTATGTGCCTACCAGGCTTCATGCTGGTGATATCGAGATTTATGCCTAACAAGCCTTCATGTCG
*
25564115 GTGTTATCGG
66 GTGATATCGG
* * * * *
25564125 GCTATGTGCCTATCAGGCTTTATGCTGGTGATATCGAGCTTTATGCCTAGCAAGCCTTCGTGTCG
1 GCTATGTGCCTACCAGGCTTCATGCTGGTGATATCGAGATTTATGCCTAACAAGCCTTCATGTCG
25564190 GTGATATCGG
66 GTGATATCGG
* *
25564200 GCTTTATGCCTA
1 GCTATGTGCCTA
25564212 GTAGGCCTTC
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.17, C:0.22, G:0.27, T:0.33
Consensus pattern (75 bp):
GCTATGTGCCTACCAGGCTTCATGCTGGTGATATCGAGATTTATGCCTAACAAGCCTTCATGTCG
GTGATATCGG
Found at i:25564172 original size:37 final size:37
Alignment explanation
Indices: 25564056--25564211 Score: 145
Period size: 38 Copynumber: 4.2 Consensus size: 37
25564046 TAACGCTATG
* * *
25564056 TGCCTACCAGGCTTCGTG-CTGGTGATATCGAGATTTA
1 TGCCTAACAGGCTTCATGTC-GGTGATATCGAGCTTTA
* * * *
25564093 TGCCTAACAGGCCTTCATGTCGGTGTTATCGGGCTATG
1 TGCCTAACAGG-CTTCATGTCGGTGATATCGAGCTTTA
* *
25564131 TGCCTATCAGGCTTTATG-CTGGTGATATCGAGCTTTA
1 TGCCTAACAGGCTTCATGTC-GGTGATATCGAGCTTTA
* * * *
25564168 TGCCTAGCAAGCCTTCGTGTCGGTGATATCGGGCTTTA
1 TGCCTAAC-AGGCTTCATGTCGGTGATATCGAGCTTTA
25564206 TGCCTA
1 TGCCTA
25564212 GTAGGCCTTC
Statistics
Matches: 96, Mismatches: 18, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
36 1 0.01
37 36 0.38
38 57 0.59
39 2 0.02
ACGTcount: A:0.17, C:0.22, G:0.27, T:0.33
Consensus pattern (37 bp):
TGCCTAACAGGCTTCATGTCGGTGATATCGAGCTTTA
Found at i:25564256 original size:75 final size:74
Alignment explanation
Indices: 25564093--25564438 Score: 268
Period size: 75 Copynumber: 4.6 Consensus size: 74
25564083 TCGAGATTTA
* * * * * * * *
25564093 TGCCTAACAGGCCTTCATGTCGGTGTTATCGGGCTATGTGCCTA-TCAGG-CTTTATGCTGGTGA
1 TGCCTAGCA-GCCTTCGTGTCGGTGATATCGGGCTTTATGCCTAGT-AGGCCTTTGTGC-CGTGT
* *
25564156 TATCGAGCTTTA
63 TATCGAGCTATG
*
25564168 TGCCTAGCAAGCCTTCGTGTCGGTGATATCGGGCTTTATGCCTAGTAGGCCTTCGTGCCAGTGTT
1 TGCCTAGC-AGCCTTCGTGTCGGTGATATCGGGCTTTATGCCTAGTAGGCCTTTGTGCC-GTGTT
*
25564233 ATCGAACTATG
64 ATCGAGCTATG
* * * * * *
25564244 TGCCTAGCAGCCTTCGTG-CTAGTGATATCAGGCTCTATGCCTAGTAGCCCTTTGTGTCGAAGTT
1 TGCCTAGCAGCCTTCGTGTC-GGTGATATCGGGCTTTATGCCTAGTAGGCCTTTGTGCCG-TGTT
* *
25564308 ATTGGGCTATG
64 ATCGAGCTATG
* * * * * * *
25564319 TGCCTAGCAGGCTTCGTGCCGATGATATCGGGCTTTATGCCTAGCAAGCCTTTGTTCCGATGATA
1 TGCCTAGCAGCCTTCGTGTCGGTGATATCGGGCTTTATGCCTAGTAGGCCTTTGTGCCG-TGTTA
* * * *
25564384 TTGAGTTTTA
65 TCGAGCTATG
* * *
25564394 TGCCTAGCAGGCCTTCGTG-CTGGTGTTATCGGGCTATGTGCCTAG
1 TGCCTAGCA-GCCTTCGTGTC-GGTGATATCGGGCTTTATGCCTAG
25564439 CAGGTTTCAT
Statistics
Matches: 219, Mismatches: 43, Indels: 17
0.78 0.15 0.06
Matches are distributed among these distances:
74 2 0.01
75 160 0.73
76 57 0.26
ACGTcount: A:0.17, C:0.23, G:0.27, T:0.33
Consensus pattern (74 bp):
TGCCTAGCAGCCTTCGTGTCGGTGATATCGGGCTTTATGCCTAGTAGGCCTTTGTGCCGTGTTAT
CGAGCTATG
Found at i:25564269 original size:113 final size:112
Alignment explanation
Indices: 25564067--25564442 Score: 332
Period size: 113 Copynumber: 3.3 Consensus size: 112
25564057 GCCTACCAGG
* * * * * *
25564067 CTTCGTGCTGGTGATATCGAGATTTATGCCTAACAGGCCTTCATGTCGGTGTTATCGGGCTATGT
1 CTTCGTGCTGGTGATATCGGGCTATATGCCTAGCAGGCCTTCGTG-CCGTGTTATCGGGCTATGT
* * * *
25564132 GCCTATCAGGCTTTATGCTGGTGATATCGAGCTTTATGCCTAGCAAGC
65 GCCTAGCAGCCTTTGTGCTAGTGATATCGAGCTTTATGCCTAGCAAGC
* * **
25564180 CTTCGTG-TCGGTGATATCGGGCTTTATGCCTAGTAGGCCTTCGTGCCAGTGTTATCGAACTATG
1 CTTCGTGCT-GGTGATATCGGGCTATATGCCTAGCAGGCCTTCGTGCC-GTGTTATCGGGCTATG
* * *
25564244 TGCCTAGCAGCCTTCGTGCTAGTGATATC-AGGCTCTATGCCTAG-TAGCC
64 TGCCTAGCAGCCTTTGTGCTAGTGATATCGA-GCTTTATGCCTAGCAAG-C
* ** * * * * * *
25564293 CTTTGTG-TCGAAGTTATTGGGCTATGTGCCTAGCAGG-CTTCGTGCCGATGATATCGGGCTTTA
1 CTTCGTGCT-GGTGATATCGGGCTATATGCCTAGCAGGCCTTCGTGCCG-TGTTATCGGGCTATG
* * * * *
25564356 TGCCTAGCAAGCCTTTGTTC-CGATGATATTGAGTTTTATGCCTAGCAGGC
64 TGCCTAGC-AGCCTTTGTGCTAG-TGATATCGAGCTTTATGCCTAGCAAGC
* *
25564406 CTTCGTGCTGGTGTTATCGGGCTATGTGCCTAGCAGG
1 CTTCGTGCTGGTGATATCGGGCTATATGCCTAGCAGG
25564443 TTTCATGCTG
Statistics
Matches: 213, Mismatches: 40, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
111 1 0.00
112 33 0.15
113 176 0.83
114 3 0.01
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (112 bp):
CTTCGTGCTGGTGATATCGGGCTATATGCCTAGCAGGCCTTCGTGCCGTGTTATCGGGCTATGTG
CCTAGCAGCCTTTGTGCTAGTGATATCGAGCTTTATGCCTAGCAAGC
Found at i:25564356 original size:188 final size:187
Alignment explanation
Indices: 25564051--25564483 Score: 535
Period size: 188 Copynumber: 2.3 Consensus size: 187
25564041 TGTTATAACG
* ** *
25564051 CTATGTGCCTACCAGGCTTCGTGCTGGTGATATCGAGATTTATGCCTAACAGGCCTTCATGTCGG
1 CTATGTGCCTAGCAGGCTTCGTGCTGGTGATATCG-GATTTATGCCTAGTAGGCCTTCATGTCGA
* * * * *
25564116 TGTTATCGGGCTATGTGCCTATCAGGCTTTATGCTGGTGATATCGAGCTTTATGCCTAGCAAGCC
65 AGTTATCGGGCTATGTGCCTAGCAGGCTTCATGCCGATGATATCGAGCTTTATGCCTAGCAAGCC
* * *
25564181 TTCGTGT-CGGTGATATCGGGCTTTATGCCTAGTAGGCCTTCGTGCCAGTGTTATCGAA
130 TTCGT-TCCGATGATATCGAGCTTTATGCCTAGCAGGCCTTCGTGCCAGTGTTATCGAA
* * * * * **
25564239 CTATGTGCCTAGCAGCCTTCGTGCTAGTGATATCAGGCTCTATGCCTAGTAGCCCTTTGTGTCGA
1 CTATGTGCCTAGCAGGCTTCGTGCTGGTGATATC-GGATTTATGCCTAGTAGGCCTTCATGTCGA
* * *
25564304 AGTTATTGGGCTATGTGCCTAGCAGGCTTCGTGCCGATGATATCGGGCTTTATGCCTAGCAAGCC
65 AGTTATCGGGCTATGTGCCTAGCAGGCTTCATGCCGATGATATCGAGCTTTATGCCTAGCAAGCC
* * * ** **
25564369 TTTGTTCCGATGATATTGAGTTTTATGCCTAGCAGGCCTTCGTGCTGGTGTTATCGGG
130 TTCGTTCCGATGATATCGAGCTTTATGCCTAGCAGGCCTTCGTGCCAGTGTTATCGAA
* * * *
25564427 CTATGTGCCTAGCAGGTTTCATGCTGGTGATATTGGGTTTATGCCTAGTAGGCCTTC
1 CTATGTGCCTAGCAGGCTTCGTGCTGGTGATATCGGATTTATGCCTAGTAGGCCTTC
25564484 GTGCCAGTGT
Statistics
Matches: 205, Mismatches: 38, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
187 20 0.10
188 184 0.90
189 1 0.00
ACGTcount: A:0.17, C:0.22, G:0.27, T:0.34
Consensus pattern (187 bp):
CTATGTGCCTAGCAGGCTTCGTGCTGGTGATATCGGATTTATGCCTAGTAGGCCTTCATGTCGAA
GTTATCGGGCTATGTGCCTAGCAGGCTTCATGCCGATGATATCGAGCTTTATGCCTAGCAAGCCT
TCGTTCCGATGATATCGAGCTTTATGCCTAGCAGGCCTTCGTGCCAGTGTTATCGAA
Found at i:25569617 original size:75 final size:75
Alignment explanation
Indices: 25569486--25569918 Score: 311
Period size: 75 Copynumber: 5.8 Consensus size: 75
25569476 TACATACAAG
* ** * * *
25569486 TGTTATCGGACTATGTGCTTAGCAGGCTTCGTGCTGGTGATATCAGCCTTTGTGCCTAACAAACT
1 TGTTATCGGGCTATGTGCTTAGCAGGCTTCGTGCCAGTGATATCAGGCTTTATGCCTAACAAACC
25569551 TTCATGCCGA
66 TTCATGCCGA
* * * * * ** *
25569561 TGTTATCGGGTTATGCGCCTAGTAGGCTTTGTGCCAGTGATATCAGGCTTTATGCCTAGTAACCC
1 TGTTATCGGGCTATGTGCTTAGCAGGCTTCGTGCCAGTGATATCAGGCTTTATGCCTAACAAACC
*
25569626 TTCGTGCCGA
66 TTCATGCCGA
* * **
25569636 TGTTATCGAGCTATGTGCTTAGCAGGCCTTCGTGCCAGTGATATC-GAGCTTTATGCCTAGCAGG
1 TGTTATCGGGCTATGTGCTTAGCAGG-CTTCGTGCCAGTGATATCAG-GCTTTATGCCTAACAAA
** * *
25569700 CCTTTGTGTCGG
64 CCTTCATGCCGA
** * * ** * * ** **
25569712 TGTTATCAAGCTATATGCCTAGTGGGCTTCGTACC-GATGATATCGGGCTTTATGCCTAGTAGGC
1 TGTTATCGGGCTATGTGCTTAGCAGGCTTCGTGCCAG-TGATATCAGGCTTTATGCCTAACAAAC
*
25569776 CTTCGTGCCGA
65 CTTCATGCCGA
* * * * **
25569787 TGTTATCGGGCTATGTGCTTAGCAGGTTTCGTACC-GATGATATC-GAACTTTATGCCTAGCAGG
1 TGTTATCGGGCTATGTGCTTAGCAGGCTTCGTGCCAG-TGATATCAG-GCTTTATGCCTAACAAA
* * *
25569850 CCTTCGTGTCGG
64 CCTTCATGCCGA
* * *** *
25569862 TGTTATCGGGCTATGTGAC-TAGCATGCTTCAT-ATGGTGATATCGGGCTTTATGCCTA
1 TGTTATCGGGCTATGTG-CTTAGCAGGCTTCGTGCCAGTGATATCAGGCTTTATGCCTA
25569919 CTGGTGTTAT
Statistics
Matches: 296, Mismatches: 54, Indels: 17
0.81 0.15 0.05
Matches are distributed among these distances:
74 20 0.07
75 213 0.72
76 63 0.21
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (75 bp):
TGTTATCGGGCTATGTGCTTAGCAGGCTTCGTGCCAGTGATATCAGGCTTTATGCCTAACAAACC
TTCATGCCGA
Found at i:25569666 original size:38 final size:38
Alignment explanation
Indices: 25569555--25569885 Score: 242
Period size: 38 Copynumber: 8.8 Consensus size: 38
25569545 CAAACTTTCA
* * ** * *
25569555 TGCCGATGTTATCGGGTTATGCGCCTAGTAGG-CTTTG
1 TGCCGATGTTATCGAGCTATATGCCTAGCAGGCCTTCG
* * * **
25569592 TGCC-AGTGATATC-AGGCTTTATGCCTAGTAACCCTTCG
1 TGCCGA-TGTTATCGA-GCTATATGCCTAGCAGGCCTTCG
* *
25569630 TGCCGATGTTATCGAGCTATGTGCTTAGCAGGCCTTCG
1 TGCCGATGTTATCGAGCTATATGCCTAGCAGGCCTTCG
* * *
25569668 TGCC-AGTGATATCGAGCTTTATGCCTAGCAGGCCTTTG
1 TGCCGA-TGTTATCGAGCTATATGCCTAGCAGGCCTTCG
* * * * *
25569706 TGTCGGTGTTATCAAGCTATATGCCTAG-TGGGCTTCG
1 TGCCGATGTTATCGAGCTATATGCCTAGCAGGCCTTCG
* * * * *
25569743 TACCGATGATATCGGGCTTTATGCCTAGTAGGCCTTCG
1 TGCCGATGTTATCGAGCTATATGCCTAGCAGGCCTTCG
* * * *
25569781 TGCCGATGTTATCGGGCTATGTGCTTAGCAGG-TTTCG
1 TGCCGATGTTATCGAGCTATATGCCTAGCAGGCCTTCG
* * * *
25569818 TACCGATGATATCGAACTTTATGCCTAGCAGGCCTTCG
1 TGCCGATGTTATCGAGCTATATGCCTAGCAGGCCTTCG
* * * * *
25569856 TGTCGGTGTTATCGGGCTATGTGACTAGCA
1 TGCCGATGTTATCGAGCTATATGCCTAGCA
25569886 TGCTTCATAT
Statistics
Matches: 223, Mismatches: 62, Indels: 17
0.74 0.21 0.06
Matches are distributed among these distances:
36 1 0.00
37 78 0.35
38 142 0.64
39 2 0.01
ACGTcount: A:0.18, C:0.22, G:0.28, T:0.33
Consensus pattern (38 bp):
TGCCGATGTTATCGAGCTATATGCCTAGCAGGCCTTCG
Found at i:25569770 original size:37 final size:37
Alignment explanation
Indices: 25569725--25569845 Score: 134
Period size: 37 Copynumber: 3.2 Consensus size: 37
25569715 TATCAAGCTA
25569725 TATGCCTAGTGGGCTTCGTACCGATGATATCGGGCTT
1 TATGCCTAGTGGGCTTCGTACCGATGATATCGGGCTT
* * * *
25569762 TATGCCTAGTAGGCCTTCGTGCCGATGTTATCGGGCTA
1 TATGCCTAGT-GGGCTTCGTACCGATGATATCGGGCTT
* * ** * **
25569800 TGTGCTTAGCAGGTTTCGTACCGATGATATCGAACTT
1 TATGCCTAGTGGGCTTCGTACCGATGATATCGGGCTT
25569837 TATGCCTAG
1 TATGCCTAG
25569846 CAGGCCTTCG
Statistics
Matches: 66, Mismatches: 17, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
37 36 0.55
38 30 0.45
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.33
Consensus pattern (37 bp):
TATGCCTAGTGGGCTTCGTACCGATGATATCGGGCTT
Found at i:25571888 original size:22 final size:22
Alignment explanation
Indices: 25571862--25571919 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
25571852 GACACCTCTA
25571862 TTTTCTATTT-CTTTTAATTCTG
1 TTTTCT-TTTACTTTTAATTCTG
*
25571884 TTTTCTTTTATTTTTAATTCTG
1 TTTTCTTTTACTTTTAATTCTG
*
25571906 TTTT-TTTTATTTTT
1 TTTTCTTTTACTTTT
25571920 CTTCAGATCG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 13 0.38
22 21 0.62
ACGTcount: A:0.12, C:0.09, G:0.03, T:0.76
Consensus pattern (22 bp):
TTTTCTTTTACTTTTAATTCTG
Found at i:25571913 original size:21 final size:22
Alignment explanation
Indices: 25571873--25571919 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
25571863 TTTCTATTTC
25571873 TTTTAATTCTGTTTTCTTTTAT
1 TTTTAATTCTGTTTTCTTTTAT
25571895 TTTTAATTCTGTTTT-TTTTAT
1 TTTTAATTCTGTTTTCTTTTAT
25571916 TTTT
1 TTTT
25571920 CTTCAGATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.13, C:0.06, G:0.04, T:0.77
Consensus pattern (22 bp):
TTTTAATTCTGTTTTCTTTTAT
Found at i:25572667 original size:24 final size:24
Alignment explanation
Indices: 25572640--25572686 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
25572630 CAATTCGAAA
*
25572640 GAGCACGCAATGCACAGTTCACAT
1 GAGCACGCAATACACAGTTCACAT
*
25572664 GAGCTCGCAATACACAGTTCACA
1 GAGCACGCAATACACAGTTCACA
25572687 ACACATGATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.30, G:0.19, T:0.17
Consensus pattern (24 bp):
GAGCACGCAATACACAGTTCACAT
Found at i:25572934 original size:17 final size:18
Alignment explanation
Indices: 25572897--25572935 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
25572887 CGCATGCAAT
*
25572897 ATAGGTTCGCATAATATC
1 ATAGGTTCGCATAACATC
*
25572915 ATAGGTTCGCA-CACATC
1 ATAGGTTCGCATAACATC
25572932 ATAG
1 ATAG
25572936 CAAATCCCGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (18 bp):
ATAGGTTCGCATAACATC
Found at i:25573088 original size:21 final size:21
Alignment explanation
Indices: 25573058--25573108 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
25573048 ATGTTTGCAC
*
25573058 AACATCTAAAAGAGTTCACAT
1 AACATATAAAAGAGTTCACAT
* *
25573079 AGCATATAAAAGAGTTCGCAT
1 AACATATAAAAGAGTTCACAT
25573100 AACATATAA
1 AACATATAA
25573109 CTAGCTCGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.24
Consensus pattern (21 bp):
AACATATAAAAGAGTTCACAT
Found at i:25574560 original size:20 final size:21
Alignment explanation
Indices: 25574537--25574586 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
25574527 AATAAAAGTT
25574537 ATAAAAATTA-TTAAATTTTA
1 ATAAAAATTATTTAAATTTTA
*
25574557 ATAAAAA-TATTTAGATTTTA
1 ATAAAAATTATTTAAATTTTA
*
25574577 TTAAAAATTA
1 ATAAAAATTA
25574587 GGGAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
ATAAAAATTATTTAAATTTTA
Found at i:25574615 original size:20 final size:19
Alignment explanation
Indices: 25574590--25574760 Score: 89
Period size: 20 Copynumber: 8.7 Consensus size: 19
25574580 AAAATTAGGG
*
25574590 AAAAAATTATATAAATCGTAA
1 AAAAAATTATA-AAATTGT-A
25574611 AAAAAATTATTAAAAATTGT-
1 AAAAAATTA-T-AAAATTGTA
*
25574631 AAAAATTTATAAAAGTTGTA
1 AAAAAATTATAAAA-TTGTA
*
25574651 AAAAAATTATAAAATATATA
1 AAAAAATTATAAAAT-TGTA
* * * * *
25574671 GAAATATAGAAAAAATTAT-
1 AAAAAAT-TATAAAATTGTA
** *
25574690 AAAATTTTATAAATTTGTA
1 AAAAAATTATAAAATTGTA
* **
25574709 ATAAAATTATAAAAAAAGTA
1 AAAAAATTAT-AAAATTGTA
**
25574729 AAGGAA-TATAAAATTCGT-
1 AAAAAATTATAAAATT-GTA
25574747 AAAAAATTATAAAA
1 AAAAAATTATAAAA
25574761 ACTATCCTAC
Statistics
Matches: 113, Mismatches: 27, Indels: 22
0.70 0.17 0.14
Matches are distributed among these distances:
18 19 0.17
19 30 0.27
20 41 0.36
21 15 0.13
22 7 0.06
23 1 0.01
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.31
Consensus pattern (19 bp):
AAAAAATTATAAAATTGTA
Found at i:25574615 original size:22 final size:22
Alignment explanation
Indices: 25574590--25574635 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
25574580 AAAATTAGGG
*
25574590 AAAAAATTA-TATAAATCGTAA
1 AAAAAATTATTAAAAATCGTAA
*
25574611 AAAAAATTATTAAAAATTGTAA
1 AAAAAATTATTAAAAATCGTAA
25574633 AAA
1 AAA
25574636 TTTATAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.28
Consensus pattern (22 bp):
AAAAAATTATTAAAAATCGTAA
Found at i:25574654 original size:29 final size:28
Alignment explanation
Indices: 25574613--25574723 Score: 100
Period size: 29 Copynumber: 3.8 Consensus size: 28
25574603 AATCGTAAAA
* * *
25574613 AAAATTATTAAAAATTGTAAAAATTTAT
1 AAAATTGTAAAAAATTATAAAAATTTAT
*
25574641 AAAAGTTGTAAAAAAATTAT-AAAATATAT
1 AAAA-TTGT-AAAAAATTATAAAAATTTAT
*
25574670 AGAAATATAG-AAAAAATTATAAAATTTTAT
1 A-AAAT-T-GTAAAAAATTATAAAAATTTAT
*
25574700 AAATTTGTAATAAAATTATAAAAA
1 AAAATTGTAA-AAAATTATAAAAA
25574724 AAGTAAAGGA
Statistics
Matches: 67, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
27 1 0.01
28 7 0.10
29 38 0.57
30 20 0.30
31 1 0.01
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.34
Consensus pattern (28 bp):
AAAATTGTAAAAAATTATAAAAATTTAT
Found at i:25574664 original size:10 final size:10
Alignment explanation
Indices: 25574611--25574724 Score: 58
Period size: 10 Copynumber: 11.6 Consensus size: 10
25574601 TAAATCGTAA
25574611 AAAAAATTAT
1 AAAAAATTAT
* *
25574621 TAAAAATTGT
1 AAAAAATTAT
*
25574631 AAAAATTTAT
1 AAAAAATTAT
* *
25574641 -AAAAGTTGT
1 AAAAAATTAT
25574650 AAAAAAATTAT
1 -AAAAAATTAT
*
25574661 AAAATA-TAT
1 AAAAAATTAT
* *
25574670 -AGAAATATAG
1 AAAAAAT-TAT
25574680 AAAAAATTAT
1 AAAAAATTAT
*
25574690 --AAAATTTT
1 AAAAAATTAT
* * *
25574698 ATAAATTTGT
1 AAAAAATTAT
25574708 AATAAAATTAT
1 AA-AAAATTAT
25574719 AAAAAA
1 AAAAAA
25574725 AGTAAAGGAA
Statistics
Matches: 75, Mismatches: 21, Indels: 16
0.67 0.19 0.14
Matches are distributed among these distances:
8 10 0.13
9 10 0.13
10 35 0.47
11 20 0.27
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.33
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:25575303 original size:94 final size:93
Alignment explanation
Indices: 25575139--25575313 Score: 230
Period size: 94 Copynumber: 1.8 Consensus size: 93
25575129 CTCCCTTGGC
* * * *
25575139 CTTTTTGATGAATTTTGGTAGTTCAAGTATTCAATTGAGTGTAAAAAAATAGGGTCTTAATTGCT
1 CTTTTTGATGAATTTTGGTAGTTCAAGTATCCAATTGAGTGAAAAAAAAAAGGGGCTTAATTG--
25575204 TCTTTTTTT-AAAAAGAAAAAGTTTGAGGT
64 TCTTTTTTTGAAAAAGAAAAAGTTTGAGGT
*
25575233 CTTTTTGATGCATTTTGGTAGTTCAAGTA-CCGAATTGAGTGAAAAAAAAAAGCAGGAGCTTAAT
1 CTTTTTGATGAATTTTGGTAGTTCAAGTATCC-AATTGAGTGAAAAAAAAAAG--GG-GCTTAAT
25575297 TG-CTTTTTTTGAAAAAG
62 TGTCTTTTTTTGAAAAAG
25575314 TTTGAGGATT
Statistics
Matches: 71, Mismatches: 5, Indels: 9
0.84 0.06 0.11
Matches are distributed among these distances:
93 1 0.01
94 54 0.76
95 6 0.08
96 2 0.03
97 8 0.11
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (93 bp):
CTTTTTGATGAATTTTGGTAGTTCAAGTATCCAATTGAGTGAAAAAAAAAAGGGGCTTAATTGTC
TTTTTTTGAAAAAGAAAAAGTTTGAGGT
Found at i:25576404 original size:10 final size:9
Alignment explanation
Indices: 25576379--25576422 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
25576369 AAAAAATTCA
*
25576379 TTTAAACTT
1 TTTAAATTT
25576388 TTTAAATTT
1 TTTAAATTT
*
25576397 TTTAAAATT
1 TTTAAATTT
*
25576406 TTTAAATATA
1 TTTAAAT-TT
25576416 TTTAAAT
1 TTTAAAT
25576423 ATATATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
9 22 0.73
10 8 0.27
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (9 bp):
TTTAAATTT
Found at i:25576422 original size:18 final size:17
Alignment explanation
Indices: 25576372--25576422 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
25576362 ATGAAAAAAA
25576372 AAATTCATTTAAACTTTTT
1 AAATT-ATTTAAA-TTTTT
*
25576391 AAATTTTTTAAAATTTTT
1 AAATTATTT-AAATTTTT
25576409 AAATATATTTAAAT
1 AAAT-TATTTAAAT
25576423 ATATATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 16 0.57
19 12 0.43
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (17 bp):
AAATTATTTAAATTTTT
Found at i:25576637 original size:29 final size:29
Alignment explanation
Indices: 25576604--25576661 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
25576594 TAGTGGGTGG
*
25576604 TTTTTTTTAACAGAAAAAGATAATTATTCC
1 TTTTTTTGAA-AGAAAAAGATAATTATTCC
* *
25576634 TTTTTTTGTAATAAAAAGATAATTATTC
1 TTTTTTTGAAAGAAAAAGATAATTATTC
25576662 GTAAGTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (29 bp):
TTTTTTTGAAAGAAAAAGATAATTATTCC
Found at i:25585156 original size:20 final size:20
Alignment explanation
Indices: 25585131--25585168 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
25585121 ACCCACTAAA
* *
25585131 CAATTTAATCTCAAAATTCC
1 CAATTTAACCACAAAATTCC
25585151 CAATTTAACCACAAAATT
1 CAATTTAACCACAAAATT
25585169 TTACTTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.32
Consensus pattern (20 bp):
CAATTTAACCACAAAATTCC
Found at i:25585835 original size:152 final size:152
Alignment explanation
Indices: 25585576--25586302 Score: 935
Period size: 152 Copynumber: 4.8 Consensus size: 152
25585566 ATTAAAATAT
* * *
25585576 AATCACTACTTTACTTTAAAAA-TCAAAATTTTTATTTCGAAATAATT-AAAAAAATTAAAATTT
1 AATCACTACTTTA-TTTAAAAATTC-AAACTTTTATTTCGAAATAATTAAAAAAAATCAAAACTT
* *
25585639 TGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTTATTTTTTTAAAATCT
64 TGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTTATTTTTTAAAAATAT
* *
25585704 AAACTTTCTT-TTTTTTTGATGAA
129 AAACTTTCTTCTTTTTTTAAAGAA
25585727 AATCACTACTTTATTTAAAAATTCAAACTTTTATTTCGAAATAATTTAAAAAAAATCAAAACTTT
1 AATCACTACTTTATTTAAAAATTCAAACTTTTATTTCGAAATAA-TTAAAAAAAATCAAAACTTT
* * *
25585792 ATTTAAAATTTTAAACTTTTTCTTTAAAATAATTAAAAAATAG------ATTTTTTAAAAATATA
65 GTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTTATTTTTTAAAAATATA
* *
25585851 AACTTTCTCTCTTTTGTTTTAACAA
130 AACTTTCT-TCTTTT-TTTAAAGAA
* *
25585876 AATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAATTAAAAAAAATCAAAACTTTG
1 AATCACTACTTTATTTAAAAATTCAAACTTTTATTTCGAAATAATTAAAAAAAATCAAAACTTTG
* * * *
25585941 TTTAAAAATTTAAAATTTTTATTTAAAATAACTAAAAAATAAATTTTTATTTTTAAAAAATAT-A
66 TTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTTATTTTTTAAAAATATAA
* *
25586005 ATTTTTTTCTTTTTTTAAAAGAA
131 ACTTTCTTCTTTTTTT-AAAGAA
* * * * *
25586028 AATCACTATTTTACTTAAAAATTCAAACTTTTATTTCAAAATAGTTAAAAAAAATCAAAACTTTC
1 AATCACTACTTTATTTAAAAATTCAAACTTTTATTTCGAAATAATTAAAAAAAATCAAAACTTTG
25586093 TTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTTA--TTTTAAAAATATAA
66 TTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTTATTTTTTAAAAATATAA
*
25586156 A-TTTTTTCTTTTTTTTAAAAGAA
131 ACTTTCTTC-TTTTTTT-AAAGAA
* * * ** * *
25586179 AATCACTA-TTTTTCTTAAAAATCCAAACCTTTATTTCGAAATTTTTAAAAAAAATAAAAATTTT
1 AATCACTACTTTAT-TTAAAAATTCAAACTTTTATTTCGAAATAATTAAAAAAAATCAAAACTTT
* * *
25586243 GTTTAAAAATTTAAACCTTTTCTTTAAAATAACTAAAAAAACATATTTTTA-TTTTTAAAA
65 GTTTAAAAATTTAAACTTTTTCTTTAAAATAACT-AAAAAATAGATTTTTATTTTTTAAAA
25586303 GTTTGAATTT
Statistics
Matches: 514, Mismatches: 44, Indels: 34
0.87 0.07 0.06
Matches are distributed among these distances:
146 22 0.04
147 1 0.00
148 61 0.12
149 48 0.09
150 48 0.09
151 119 0.23
152 187 0.36
153 14 0.03
154 14 0.03
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (152 bp):
AATCACTACTTTATTTAAAAATTCAAACTTTTATTTCGAAATAATTAAAAAAAATCAAAACTTTG
TTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTTATTTTTTAAAAATATAA
ACTTTCTTCTTTTTTTAAAGAA
Found at i:25585947 original size:52 final size:52
Alignment explanation
Indices: 25585725--25586131 Score: 224
Period size: 52 Copynumber: 8.0 Consensus size: 52
25585715 TTTTTTGATG
** *
25585725 AAAATCACTACTTTATTTAAAAATTCAAACTTTTATTTCGAAATAATTTAAAA
1 AAAATCAAAACTTTATTTAAAAATTCAAACTTTTATTTCAAAATAA-TTAAAA
* * *
25585778 AAAATCAAAACTTTATTTAAAATTTTAAACTTTT-TCTTTAAAATAATT--AA
1 AAAATCAAAACTTTATTTAAAAATTCAAACTTTTAT-TTCAAAATAATTAAAA
* * * *** ** * *
25585828 AAAAT--AGA-TTT-TTTAAAAATAT-AAAC-TTTCTCTC-TTTTGTTTTAAC
1 AAAATCAAAACTTTATTTAAAAAT-TCAAACTTTTATTTCAAAATAATTAAAA
** * * *
25585874 AAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAATTAAAA
1 AAAATCAAAACTTTATTTAAAAATTCAAACTTTTATTTCAAAATAATTAAAA
* * * *
25585926 AAAATCAAAACTTTGTTTAAAAATTTAAAATTTTTATTT-AAAATAACT--AA
1 AAAATCAAAACTTTATTTAAAAA-TTCAAACTTTTATTTCAAAATAATTAAAA
** * ** **
25585976 AAAAT-AAATTTTTATTTTTAAAAAAT-ATAA-TTTT-TTTC--TTTTTTTAAAA
1 AAAATCAAAACTTTA--TTTAAAAATTCA-AACTTTTATTTCAAAATAATTAAAA
** * * *
25586025 GAAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCAAAATAGTTAAAA
1 -AAAATCAAAACTTTATTTAAAAATTCAAACTTTTATTTCAAAATAATTAAAA
* * * *
25586078 AAAATCAAAACTTTCTTTAAAAATTTAAACTTTT-TCTTTAAAATAACTAAAA
1 AAAATCAAAACTTTATTTAAAAATTCAAACTTTTAT-TTCAAAATAATTAAAA
25586130 AA
1 AA
25586132 TAGATTTTTA
Statistics
Matches: 263, Mismatches: 64, Indels: 55
0.69 0.17 0.14
Matches are distributed among these distances:
44 3 0.01
45 4 0.02
46 19 0.07
47 6 0.02
48 6 0.02
49 27 0.10
50 39 0.15
51 25 0.10
52 76 0.29
53 58 0.22
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (52 bp):
AAAATCAAAACTTTATTTAAAAATTCAAACTTTTATTTCAAAATAATTAAAA
Found at i:25586099 original size:19 final size:20
Alignment explanation
Indices: 25586077--25586120 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
25586067 AATAGTTAAA
25586077 AAAAATCAAAAC-TTTCTTT
1 AAAAATCAAAACTTTTCTTT
**
25586096 AAAAATTTAAACTTTTTCTTT
1 AAAAATCAAAAC-TTTTCTTT
25586117 AAAA
1 AAAA
25586121 TAACTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
21 11 0.52
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAAATCAAAACTTTTCTTT
Found at i:25586803 original size:3 final size:3
Alignment explanation
Indices: 25586795--25586822 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
25586785 CATAAAACCC
25586795 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
25586823 TTGGGCCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:25595147 original size:20 final size:20
Alignment explanation
Indices: 25595124--25595162 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
25595114 CAATTAAACC
25595124 AAAAAT-AAAATAAAATAAT
1 AAAAATAAAAATAAAATAAT
*
25595143 AAAAATAAAAATAATATAAT
1 AAAAATAAAAATAAAATAAT
25595163 TTATATCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAAATAAAAATAAAATAAT
Found at i:25595354 original size:21 final size:19
Alignment explanation
Indices: 25595297--25595354 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 19
25595287 CATGAATTAC
*
25595297 AAAAAAAAACTAAAAATAT
1 AAAAAAAAAATAAAAATAT
*
25595316 AAAAAAATAAACATAAAATAAT
1 AAAAAAA-AAATA-AAAAT-AT
*
25595338 AATGAAAAAAATAAAAA
1 AA-AAAAAAAATAAAAA
25595355 AAGAATAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 7 0.23
20 3 0.10
21 9 0.29
22 8 0.26
23 4 0.13
ACGTcount: A:0.79, C:0.03, G:0.02, T:0.16
Consensus pattern (19 bp):
AAAAAAAAAATAAAAATAT
Found at i:25595490 original size:24 final size:26
Alignment explanation
Indices: 25595463--25595510 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
25595453 AAGGATTTAA
25595463 TTAAAACT-AAAAACA-AATAAAAGG
1 TTAAAACTAAAAAACAGAATAAAAGG
**
25595487 TTAAATTTAAAAAACAGAATAAAA
1 TTAAAACTAAAAAACAGAATAAAA
25595511 AATTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 7 0.35
26 7 0.35
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.21
Consensus pattern (26 bp):
TTAAAACTAAAAAACAGAATAAAAGG
Found at i:25595521 original size:25 final size:25
Alignment explanation
Indices: 25595471--25595523 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
25595461 AATTAAAACT
**
25595471 AAAAACAAATAAAAGGTTAAATTTA
1 AAAAACAAATAAAAAATTAAATTTA
25595496 AAAAACAGAATAAAAAATTAAA-TTA
1 AAAAACA-AATAAAAAATTAAATTTA
25595521 AAA
1 AAA
25595524 CAATATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.70, C:0.04, G:0.06, T:0.21
Consensus pattern (25 bp):
AAAAACAAATAAAAAATTAAATTTA
Found at i:25595651 original size:19 final size:19
Alignment explanation
Indices: 25595643--25595680 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 19
25595633 ATAAAATGAT
25595643 AAAATTAAAATGAAAAAAC
1 AAAATTAAAATGAAAAAAC
25595662 AAAATTAAAATGAATAAAA
1 AAAATTAAAATGAA-AAAA
25595681 ATGCGAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (19 bp):
AAAATTAAAATGAAAAAAC
Found at i:25595653 original size:14 final size:13
Alignment explanation
Indices: 25595628--25595666 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
25595618 TTGTAAAAAA
25595628 ATAAAATAAAATG
1 ATAAAATAAAATG
25595641 ATAAAATTAAAATG
1 ATAAAA-TAAAATG
* *
25595655 AAAAAACAAAAT
1 ATAAAATAAAAT
25595667 TAAAATGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.21
Consensus pattern (13 bp):
ATAAAATAAAATG
Found at i:25597611 original size:68 final size:68
Alignment explanation
Indices: 25597524--25597657 Score: 173
Period size: 68 Copynumber: 2.0 Consensus size: 68
25597514 CAAAATATTG
** *
25597524 TCGGTTTATTTGACTAGTGCA-AGGCACACCTATTGTCGAT-TTATCCGACCAACGCTGGGCACA
1 TCGGTTTATCCGACCAGTGCAGA-GCACACCTATTGTCGATATTA-CCGACCAACGCTGGGCACA
25597587 AAACA
64 AAACA
* * **
25597592 TCGGTTTATCCGACCAGTGCAGAGCACACCTATTGTTGGTATTACCGACCAGTGCTGGGCACAAA
1 TCGGTTTATCCGACCAGTGCAGAGCACACCTATTGTCGATATTACCGACCAACGCTGGGCACAAA
25597657 A
66 A
25597658 ACATTACTAC
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
68 53 0.93
69 4 0.07
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.25
Consensus pattern (68 bp):
TCGGTTTATCCGACCAGTGCAGAGCACACCTATTGTCGATATTACCGACCAACGCTGGGCACAAA
ACA
Found at i:25600566 original size:24 final size:25
Alignment explanation
Indices: 25600539--25600594 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
25600529 AATTGACCAA
*
25600539 AACTAATAATAAAAA-AATATTTAT
1 AACTAATAACAAAAACAATATTTAT
** *
25600563 AACTTTCTACCAAAAACAATATTTAT
1 AAC-TAATAACAAAAACAATATTTAT
25600589 AACTAA
1 AACTAA
25600595 AAAGCATAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
24 3 0.12
25 9 0.38
26 12 0.50
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.32
Consensus pattern (25 bp):
AACTAATAACAAAAACAATATTTAT
Found at i:25601016 original size:26 final size:28
Alignment explanation
Indices: 25600985--25601054 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
25600975 CCTGAGAATT
* *
25600985 ATTAATATTTATTTAT-TATAGT-TATA
1 ATTAATATTTATTTATATATAATAAATA
* * *
25601011 ATTAATGTTTAATTATATATAATAAAATT
1 ATTAATATTTATTTATATATAAT-AAATA
25601040 ATTAATATTTATTTA
1 ATTAATATTTATTTA
25601055 ACAGTTCTCC
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
26 14 0.41
27 5 0.15
29 15 0.44
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (28 bp):
ATTAATATTTATTTATATATAATAAATA
Found at i:25603392 original size:16 final size:16
Alignment explanation
Indices: 25603346--25603392 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
25603336 CAAAAATATT
25603346 TATATTGTTTTATTTTA
1 TATATT-TTTTATTTTA
* *
25603363 -ATATTTAATAATTTTA
1 TATATTT-TTTATTTTA
25603379 TATATTTTTTATTT
1 TATATTTTTTATTT
25603393 ATTGAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 1 0.04
16 17 0.71
17 6 0.25
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
TATATTTTTTATTTTA
Found at i:25617631 original size:30 final size:30
Alignment explanation
Indices: 25617535--25617743 Score: 244
Period size: 30 Copynumber: 7.0 Consensus size: 30
25617525 GGGAAAAAGG
25617535 GTAATTTTGGAAAAGTTTA-GGGTTAAAAT
1 GTAATTTTGGAAAAGTTTAGGGGTTAAAAT
* *
25617564 GTAATTTTAGAAAAATTTA-GGGTTAAAAT
1 GTAATTTTGGAAAAGTTTAGGGGTTAAAAT
* *
25617593 GGAATTTTGGAAAAGTTTAGGGGTCAAAAT
1 GTAATTTTGGAAAAGTTTAGGGGTTAAAAT
* * * * *
25617623 TTACTTTTGGAAGAGTTTAGTGGTCAAAAAT
1 GTAATTTTGGAAAAGTTTAGGGGT-TAAAAT
* *
25617654 GTAATTTTGGAAGAGTTT-GAGGGTCAAAAT
1 GTAATTTTGGAAAAGTTTAG-GGGTTAAAAT
* * *
25617684 GCAATTTTAGAGAAGTTTAGGGGTTAAAAT
1 GTAATTTTGGAAAAGTTTAGGGGTTAAAAT
*
25617714 GTAATTTTGGAGAAGTTTAGGGGTTAAAAT
1 GTAATTTTGGAAAAGTTTAGGGGTTAAAAT
25617744 ATGATTGTTA
Statistics
Matches: 153, Mismatches: 23, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
29 43 0.28
30 85 0.56
31 25 0.16
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.35
Consensus pattern (30 bp):
GTAATTTTGGAAAAGTTTAGGGGTTAAAAT
Found at i:25617690 original size:91 final size:88
Alignment explanation
Indices: 25617535--25617735 Score: 251
Period size: 91 Copynumber: 2.2 Consensus size: 88
25617525 GGGAAAAAGG
* * * *
25617535 GTAATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTAGAAAAATTTAGGGTTAAAATGGAATTT
1 GTAATTTTGGAAGAGTTTAGGGTAAAAATGTAATTTTAGAAAAATTTAGGGTCAAAATGCAATTT
*
25617600 TGGAAAAGTTTAGGGGTCAAAAT
66 TAGAAAAGTTTAGGGGTCAAAAT
* * * * *
25617623 TTACTTTTGGAAGAGTTTAGTGGTCAAAAATGTAATTTTGGAAGAGTTTGAGGGTCAAAATGCAA
1 GTAATTTTGGAAGAGTTTAG-GGT-AAAAATGTAATTTTAGAAAAATTT-AGGGTCAAAATGCAA
* *
25617688 TTTTAGAGAAGTTTAGGGGTTAAAAT
63 TTTTAGAAAAGTTTAGGGGTCAAAAT
25617714 GTAATTTTGG-AGAAGTTTAGGG
1 GTAATTTTGGAAG-AGTTTAGGG
25617736 GTTAAAATAT
Statistics
Matches: 95, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
88 17 0.18
89 3 0.03
90 24 0.25
91 51 0.54
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.35
Consensus pattern (88 bp):
GTAATTTTGGAAGAGTTTAGGGTAAAAATGTAATTTTAGAAAAATTTAGGGTCAAAATGCAATTT
TAGAAAAGTTTAGGGGTCAAAAT
Found at i:25617760 original size:60 final size:59
Alignment explanation
Indices: 25617535--25617766 Score: 254
Period size: 61 Copynumber: 3.9 Consensus size: 59
25617525 GGGAAAAAGG
* *
25617535 GTAATTTTGGAAAAGTTTA-GGGTTAAAATGTAATTTTAGAAAAATTTA-GGGTTAAAAT
1 GTAATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTAG-AAAGTTTAGGGGTTAAAAT
* * * * * *
25617593 GGAATTTTGGAAAAGTTTAGGGGTCAAAATTTACTTTTGGAAGAGTTTAGTGGTCAAAAAT
1 GTAATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTAGAA-AGTTTAGGGGT-TAAAAT
* *
25617654 GTAATTTTGGAAGAGTTT-GAGGGTCAAAATGCAATTTTAGAGAAGTTTAGGGGTTAAAAT
1 GTAATTTTGGAAAAGTTTAG-GGGTCAAAATGTAATTTTAGA-AAGTTTAGGGGTTAAAAT
* * * * *
25617714 GTAATTTTGGAGAAGTTTAGGGGTTAAAATATGATTGTTAGAAAGTTCAGGGG
1 GTAATTTTGGAAAAGTTTAGGGGTCAAAATGTAATT-TTAGAAAGTTTAGGGG
25617767 CCTCCTGAGT
Statistics
Matches: 143, Mismatches: 23, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
58 20 0.14
59 21 0.15
60 47 0.33
61 54 0.38
62 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.35
Consensus pattern (59 bp):
GTAATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTAGAAAGTTTAGGGGTTAAAAT
Found at i:25619045 original size:26 final size:28
Alignment explanation
Indices: 25619006--25619058 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 28
25618996 TATCAACTGC
*
25619006 TCTGTCTTTTATTGATTTT-GAATGTAT
1 TCTGTCTTGTATTGATTTTCGAATGTAT
25619033 TCTGT-TTGTATTGATTTTCGAATGTA
1 TCTGTCTTGTATTGATTTTCGAATGTA
25619059 GAAAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.19, C:0.08, G:0.17, T:0.57
Consensus pattern (28 bp):
TCTGTCTTGTATTGATTTTCGAATGTAT
Found at i:25621423 original size:30 final size:30
Alignment explanation
Indices: 25621378--25621666 Score: 251
Period size: 30 Copynumber: 9.8 Consensus size: 30
25621368 ATTTTAAGCA
*
25621378 TTTAGGGGGTAAAAATGTAATTTTGGGAAGT
1 TTTA-GGGGTAAAAATGTAATTTTGAGAAGT
* * *
25621409 TTTAGGGTTAAAAATGGAATTTTTAGAA-T
1 TTTAGGGGTAAAAATGTAATTTTGAGAAGT
*
25621438 TTGAGGGGTAAAAATGTAATTTTGAGAAGT
1 TTTAGGGGTAAAAATGTAATTTTGAGAAGT
25621468 TTT-GGGGTTAAAAATGTAATTTT-AGGAAGT
1 TTTAGGGG-TAAAAATGTAATTTTGA-GAAGT
* * *
25621498 TTTA-GGGTCAAAATGTAATTGTCGAAAAG-
1 TTTAGGGGTAAAAATGTAATT-TTGAGAAGT
*
25621527 TTTAGGGGTAAAAATGTAATTTTTGAAAAG-
1 TTTAGGGGTAAAAATGTAA-TTTTGAGAAGT
* * * *
25621557 TTTAAGGGCAAAAA--TATTTTTGAAAAG-
1 TTTAGGGGTAAAAATGTAATTTTGAGAAGT
*
25621584 -TTCGGAGGTAAAAATGTAATTTTAGAGAAGT
1 TTTAGG-GGTAAAAATGTAATTTT-GAGAAGT
* * *
25621615 TTT-GGGGTTAAAATATAATTTTTAGATAGT
1 TTTAGGGGTAAAAATGTAATTTTGAGA-AGT
* *
25621645 TTTA-GGGTCAAAATATAATTTT
1 TTTAGGGGTAAAAATGTAATTTT
25621667 TGGACAATTT
Statistics
Matches: 216, Mismatches: 26, Indels: 33
0.79 0.09 0.12
Matches are distributed among these distances:
26 3 0.01
27 17 0.08
28 2 0.01
29 55 0.25
30 128 0.59
31 9 0.04
32 2 0.01
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (30 bp):
TTTAGGGGTAAAAATGTAATTTTGAGAAGT
Found at i:25621446 original size:59 final size:58
Alignment explanation
Indices: 25621350--25621657 Score: 211
Period size: 59 Copynumber: 5.2 Consensus size: 58
25621340 AAAATGGTAA
* * * *
25621350 TTTT-GGGTTTAAAAT-GACATTTTAAGCATTTAGGGGGTAAAAATGTAATTTTGGGAAG
1 TTTTAGGGTTAAAAATGGA-ATTTTTAGAATTTA-GGGGTAAAAATGTAATTTTGAGAAG
25621408 TTTTAGGGTTAAAAATGGAATTTTTAGAATTTGAGGGGTAAAAATGTAATTTTGAGAAG
1 TTTTAGGGTTAAAAATGGAATTTTTAGAATTT-AGGGGTAAAAATGTAATTTTGAGAAG
* * * * *
25621467 TTTTGGGGTTAAAAATGTAA-TTTTAGGAAGTTTTA-GGGTCAAAATGTAATTGTCGAAAAG
1 TTTTAGGGTTAAAAATGGAATTTTTA-GAA--TTTAGGGGTAAAAATGTAATT-TTGAGAAG
* * * * * * *
25621527 -TTTAGGGGTAAAAATGTAATTTTTGAAAAGTTTAAGGGCAAAAA--TATTTTTGAAAAG
1 TTTTAGGGTTAAAAATGGAATTTTT-AGAA-TTTAGGGGTAAAAATGTAATTTTGAGAAG
* * * * * * * *
25621584 --TTCGGAGGTAAAAATGTAATTTTAGAGAAGTTTTGGGGTTAAAATATAATTTTTAGATAG
1 TTTTAGG-GTTAAAAATGGAATTTT-TAGAA-TTTAGGGGTAAAAATGTAATTTTGAGA-AG
*
25621644 TTTTAGGGTCAAAA
1 TTTTAGGGTTAAAA
25621658 TATAATTTTT
Statistics
Matches: 203, Mismatches: 30, Indels: 31
0.77 0.11 0.12
Matches are distributed among these distances:
56 4 0.02
57 38 0.19
58 13 0.06
59 110 0.54
60 25 0.12
61 9 0.04
62 4 0.02
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (58 bp):
TTTTAGGGTTAAAAATGGAATTTTTAGAATTTAGGGGTAAAAATGTAATTTTGAGAAG
Found at i:25621570 original size:89 final size:89
Alignment explanation
Indices: 25621384--25621571 Score: 231
Period size: 89 Copynumber: 2.1 Consensus size: 89
25621374 AGCATTTAGG
* ** *
25621384 GGGT-AAAAATGTAATTTTGGGAAGTTTTAGGGTTAAAAATGGAATTTTTAGAATTTGAGGGGTA
1 GGGTCAAAAATGTAATTTTAGGAAGTTTTAGGGTTAAAAATGGAATTTCGAAAATTTGAGGGGTA
* **
25621448 AAAATGTAATTTTGAGAAGTTTTG
66 AAAATGTAATTTTGAAAAGTTTAA
* * *
25621472 GGGTTAAAAATGTAATTTTAGGAAGTTTTAGGG-TCAAAATGTAATTGTCGAAAAGTTT-AGGGG
1 GGGTCAAAAATGTAATTTTAGGAAGTTTTAGGGTTAAAAATGGAATT-TCGAAAA-TTTGAGGGG
25621535 TAAAAATGTAATTTTTGAAAAGTTTAA
64 TAAAAATGTAA-TTTTGAAAAGTTTAA
25621562 GGG-CAAAAAT
1 GGGTCAAAAAT
25621572 ATTTTTGAAA
Statistics
Matches: 86, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
88 15 0.17
89 53 0.62
90 18 0.21
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.35
Consensus pattern (89 bp):
GGGTCAAAAATGTAATTTTAGGAAGTTTTAGGGTTAAAAATGGAATTTCGAAAATTTGAGGGGTA
AAAATGTAATTTTGAAAAGTTTAA
Found at i:25621622 original size:87 final size:90
Alignment explanation
Indices: 25621507--25621668 Score: 215
Period size: 87 Copynumber: 1.8 Consensus size: 90
25621497 TTTTAGGGTC
* *
25621507 AAAATGTAATTGTCGAAAAGTTTAGGGGTAAAAATGTAATTTTT-GAAAAGTTTAAGGG-CAAAA
1 AAAATGTAATTGTAGAAAAGTTTAGGGGTAAAAATATAATTTTTAG-AAAGTTTAAGGGTCAAAA
25621570 -AT-ATTTTTGAAAAGTTCGGAGGTA
65 TATAATTTTTGAAAAGTTCGGAGGTA
* * * * * *
25621594 AAAATGTAATTTTAGAGAAGTTTTGGGGTTAAAATATAATTTTTAGATAGTTTTAGGGTCAAAAT
1 AAAATGTAATTGTAGAAAAGTTTAGGGGTAAAAATATAATTTTTAGAAAGTTTAAGGGTCAAAAT
25621659 ATAATTTTTG
66 ATAATTTTTG
25621669 GACAATTTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
87 48 0.76
88 6 0.10
89 2 0.03
90 7 0.11
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.37
Consensus pattern (90 bp):
AAAATGTAATTGTAGAAAAGTTTAGGGGTAAAAATATAATTTTTAGAAAGTTTAAGGGTCAAAAT
ATAATTTTTGAAAAGTTCGGAGGTA
Found at i:25624280 original size:201 final size:201
Alignment explanation
Indices: 25623889--25624918 Score: 1576
Period size: 201 Copynumber: 5.1 Consensus size: 201
25623879 TAACCTAGTC
* * * * *** * *
25623889 TTCTTCTCTGTGTCTCATCAGGAATATGACCTCAATTACTTGTTTAAATTCGCTTCTTTGGATCT
1 TTCTTCTCTGTATCTCATCAGGAAGATGACCGC-CTCGGTTGTTTTAATTCGCTTCTCTGGATCT
* * * *
25623954 CCTTAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTTATCAGAAAGCTAACCATTTTATTGCTT
65 CCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTT
* * * *
25624019 CGACCTGCTTCTCAGTGTCTCATCAAGAAGCTAGGTTTGAGGATTTGCTCGCGTTTGAGCGTTGA
130 CGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGCGTTTGAGCGTTGA
25624084 GTTGGTA
195 GTTGGTA
* *
25624091 TTCTTCTCTATATTTCATCAGGAAGATGACCGCCTCGGTTGTTTTAATTCGCTTCTCTGGATCTC
1 TTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGGTTGTTTTAATTCGCTTCTCTGGATCTC
* *
25624156 CTCAAGAAGACAAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTC
66 CTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTC
* * * * *
25624221 GTCCTACTTCTCAGTGTCTCATCAGGAAGCTGGGTTTGAAGATTTGCCCACGTTTGAGCGTTGAG
131 GACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGCGTTTGAGCGTTGAG
*
25624286 TTGGTT
196 TTGGTA
*
25624292 TTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTTGGTTGTTTTAATTCGCTTCTCTGGATCTC
1 TTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGGTTGTTTTAATTCGCTTCTCTGGATCTC
* *
25624357 CTCAGGAAGACAAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAATCATTTTATTGCTTC
66 CTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTC
* * * *
25624422 -ATCCTGCTTCTCAGTGTCTCATAAGGAAGCTAGGTTCGAAGATTTGCCCGCGTTTGAACGTTGA
131 GA-CCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGCGTTTGAGCGTTGA
25624486 GTTGGTA
195 GTTGGTA
25624493 TTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGGTTGTTTTAATTCGCTTCTCTGGATCTC
1 TTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGGTTGTTTTAATTCGCTTCTCTGGATCTC
* *
25624558 CTCAGGAAGACGAATTCGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCCTTTTATTGCTTC
66 CTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTC
* * *
25624623 GACCTGTTTCTCAGTGTCTCATCAGGAAGCTGGGTTCAAAGATTTGCTCGTGTTTGAGCGTTGAG
131 GACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGCGTTTGAGCGTTGAG
25624688 TTGGTA
196 TTGGTA
* * *
25624694 TTCTTCTTTGTATCTCATCAGGAAGATGACCGCCTCGGTTGTTTTAATTCGCTTCTTTGGATCTT
1 TTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGGTTGTTTTAATTCGCTTCTCTGGATCTC
* * *
25624759 CTCAAGAAGACGAATTTGGTCCACTTCTTTGTATCTCATCAGGAAGCTAACCCTTTTATTGCTTC
66 CTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTC
* * *
25624824 GACCTGCTTCTCAATGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTTGTGTTTGAGCGTTGAG
131 GACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGCGTTTGAGCGTTGAG
25624889 TTGGTA
196 TTGGTA
* * *
25624895 TTCTTCTTTATATTTCATCAGGAA
1 TTCTTCTCTGTATCTCATCAGGAA
25624919 AATTACTGCC
Statistics
Matches: 764, Mismatches: 62, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
201 735 0.96
202 29 0.04
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.37
Consensus pattern (201 bp):
TTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGGTTGTTTTAATTCGCTTCTCTGGATCTC
CTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTC
GACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGCGTTTGAGCGTTGAG
TTGGTA
Found at i:25629306 original size:13 final size:13
Alignment explanation
Indices: 25629288--25629314 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
25629278 AGAGAGATCA
25629288 CAATCTTGATTTT
1 CAATCTTGATTTT
25629301 CAATCTTGATTTT
1 CAATCTTGATTTT
25629314 C
1 C
25629315 TTCAAAGTCC
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:0.22, C:0.19, G:0.07, T:0.52
Consensus pattern (13 bp):
CAATCTTGATTTT
Found at i:25636426 original size:156 final size:157
Alignment explanation
Indices: 25636191--25636485 Score: 400
Period size: 156 Copynumber: 1.9 Consensus size: 157
25636181 TCGGAGTTTC
* * *
25636191 AAAATTGAAGGACGTTTCGAGAAATTTTGAAGAGAATATTCTATCGCGTGAATTATACGAAAATC
1 AAAATTGAAGGACGTTTCGAGAAATTTTGAAGAGAATATCCGATCGCATGAATTATACGAAAATC
* * * *
25636256 ACACCCAGCACGTTAGGGCATGGTGTT-TCGAGGTCTTCACACGAAAGGACATTGTCTCATTTTG
66 ACACCCAGCACGTTAGAGCACGAT-TTCTCGAGGTCTTCACACGAAAGGACATTGCCTCATTTTG
25636320 TTTTAAAATCCTTTTTATATAGATATAT
130 TTTTAAAATCCTTTTTATATAGATATAT
* * * *
25636348 AAAATTGAAGGATGTTTTG-GAAACTTTTGAAGAGGATATCCGATTTGCATGAA-T-TACGAAAA
1 AAAATTGAAGGACGTTTCGAGAAA-TTTTGAAGAGAATATCCGA-TCGCATGAATTATACGAAAA
* * * *
25636410 TCACACTCAGCACGTTAGAGCGCGATTTCTCGAGGTTTTCACACGAAAGGACATTGCCTCGTTTT
64 TCACACCCAGCACGTTAGAGCACGATTTCTCGAGGTCTTCACACGAAAGGACATTGCCTCATTTT
25636475 GTTTTAAAATC
129 GTTTTAAAATC
25636486 ACTCGTGAGG
Statistics
Matches: 120, Mismatches: 15, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
155 2 0.02
156 77 0.64
157 34 0.28
158 7 0.06
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (157 bp):
AAAATTGAAGGACGTTTCGAGAAATTTTGAAGAGAATATCCGATCGCATGAATTATACGAAAATC
ACACCCAGCACGTTAGAGCACGATTTCTCGAGGTCTTCACACGAAAGGACATTGCCTCATTTTGT
TTTAAAATCCTTTTTATATAGATATAT
Found at i:25637094 original size:29 final size:28
Alignment explanation
Indices: 25637054--25637182 Score: 109
Period size: 29 Copynumber: 4.4 Consensus size: 28
25637044 TTTTAGGTTT
* *
25637054 AAAATG-ACATTTGAGGCATTTAGGGGGTA
1 AAAATGTA-ATTTG-GGAATTTTGGGGGTA
*
25637083 AAAATGTAATTTTGGGAAGTTTTGGGGTTA
1 AAAATGTAA-TTTGGGAA-TTTTGGGGGTA
* *
25637113 AAAATGGAATTTTTGGAATTTTGGGGGTA
1 AAAATGTAA-TTTGGGAATTTTGGGGGTA
* * *
25637142 AAAATATAATTTTGGGAAGTTTT-AGGGTT
1 AAAATGTAA-TTTGGGAA-TTTTGGGGGTA
25637171 AAAATGTAATTT
1 AAAATGTAATTT
25637183 TTAAAAAGTT
Statistics
Matches: 84, Mismatches: 12, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
28 3 0.04
29 47 0.56
30 34 0.40
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.37
Consensus pattern (28 bp):
AAAATGTAATTTGGGAATTTTGGGGGTA
Found at i:25637117 original size:30 final size:29
Alignment explanation
Indices: 25637077--25637305 Score: 185
Period size: 30 Copynumber: 7.7 Consensus size: 29
25637067 AGGCATTTAG
25637077 GGGGTAAAAATGTAATTTTGGGAAGTTTT
1 GGGGTAAAAATGTAATTTTGGGAAGTTTT
* *
25637106 GGGGTTAAAAATGGAATTTTTGGAA-TTTT
1 GGGG-TAAAAATGTAATTTTGGGAAGTTTT
*
25637135 GGGGGTAAAAATATAATTTTGGGAAGTTTT
1 -GGGGTAAAAATGTAATTTTGGGAAGTTTT
* * *** *
25637165 AGGGTTAAAATGTAATTTTTAAAAAGTTTA
1 GGGGTAAAAATGTAA-TTTTGGGAAGTTTT
* ** *
25637195 GGGGAAAAAATGTAATTTTTGAAAAGTTTA
1 GGGGTAAAAATGTAA-TTTTGGGAAGTTTT
*** * *
25637225 ACTGCAAAAATGTAATTTTAGAGAAGTTTT
1 GGGGTAAAAATGTAATTTT-GGGAAGTTTT
*
25637255 GAGGT-AAAATGTAATATTT-GGATAGTTTT
1 GGGGTAAAAATGTAAT-TTTGGGA-AGTTTT
*
25637284 GGGGTTAAAATGTAATTCTTGG
1 GGGGTAAAAATGTAATT-TTGG
25637306 ACAGTTTAGG
Statistics
Matches: 162, Mismatches: 28, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
28 2 0.01
29 62 0.38
30 97 0.60
31 1 0.01
ACGTcount: A:0.36, C:0.01, G:0.25, T:0.38
Consensus pattern (29 bp):
GGGGTAAAAATGTAATTTTGGGAAGTTTT
Found at i:25637183 original size:29 final size:29
Alignment explanation
Indices: 25637023--25637305 Score: 143
Period size: 30 Copynumber: 9.5 Consensus size: 29
25637013 CCTTCAAGGC
* *
25637023 AAAATGGTAATTTTGGGAAAATTTTAGGTTT
1 AAAAT-GTAATTTTGGG-AAGTTTTAGGGTT
* *
25637054 AAAATG-ACA-TTTGAGGCA--TTTAGGGGGTA
1 AAAATGTA-ATTTTG-GGAAGTTTTA--GGGTT
*
25637083 AAAATGTAATTTTGGGAAGTTTTGGGGTT
1 AAAATGTAATTTTGGGAAGTTTTAGGGTT
* * * *
25637112 AAAAATGGAATTTTTGGAA-TTTTGGGGGTA
1 -AAAATGTAATTTTGGGAAGTTTT-AGGGTT
*
25637142 AAAATATAATTTTGGGAAGTTTTAGGGTT
1 AAAATGTAATTTTGGGAAGTTTTAGGGTT
*** **
25637171 AAAATGTAATTTTTAAAAAG-TTTAGGGGAA
1 AAAATGTAA-TTTTGGGAAGTTTTA-GGGTT
** * ** **
25637201 AAAATGTAATTTTTGAAAAGTTTAACTGCA
1 AAAATGTAA-TTTTGGGAAGTTTTAGGGTT
*
25637231 AAAATGTAATTTTAGAGAAGTTTT-GAGG-T
1 AAAATGTAATTTT-GGGAAGTTTTAG-GGTT
*
25637260 AAAATGTAATATTT-GGATAGTTTTGGGGTT
1 AAAATGTAAT-TTTGGGA-AGTTTTAGGGTT
25637290 AAAATGTAATTCTTGG
1 AAAATGTAATT-TTGG
25637306 ACAGTTTAGG
Statistics
Matches: 199, Mismatches: 31, Indels: 44
0.73 0.11 0.16
Matches are distributed among these distances:
27 4 0.02
28 2 0.01
29 81 0.41
30 100 0.50
31 12 0.06
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (29 bp):
AAAATGTAATTTTGGGAAGTTTTAGGGTT
Found at i:25637312 original size:59 final size:57
Alignment explanation
Indices: 25637023--25637312 Score: 201
Period size: 59 Copynumber: 4.9 Consensus size: 57
25637013 CCTTCAAGGC
* * ** * *
25637023 AAAATGGTAATTTTGGGAAAATTTTAGGTTTAAAATG-ACATTTGAGGCA-TTTAGGGGGT
1 AAAAT-GTAATTTTGGG-AAGTTTTAGGGTTAAAATGTA-ATTTTTGGAAGTTT-TGGGGT
* *
25637082 AAAAATGTAATTTTGGGAAGTTTTGGGGTTAAAAATGGAATTTTTGGAA-TTTTGGGGGT
1 -AAAATGTAATTTTGGGAAGTTTTAGGGTT-AAAATGTAATTTTTGGAAGTTTT-GGGGT
* ** * *
25637141 AAAAATATAATTTTGGGAAGTTTTAGGGTTAAAATGTAATTTTTAAAAAGTTTAGGGGAA
1 -AAAATGTAATTTTGGGAAGTTTTAGGGTTAAAATGTAATTTTT-GGAAGTTTTGGGG-T
** * ** ** * *
25637201 AAAATGTAATTTTTGAAAAGTTTAACTGCAAAAATGTAATTTTAGAGAAGTTTTGAGGT
1 AAAATGTAA-TTTTGGGAAGTTTTAGGGTTAAAATGTAATTTTTG-GAAGTTTTGGGGT
* *
25637260 AAAATGTAATATTT-GGATAGTTTTGGGGTTAAAATGTAATTCTTGGACAGTTT
1 AAAATGTAAT-TTTGGGA-AGTTTTAGGGTTAAAATGTAATTTTTGGA-AGTTT
25637313 AGGGACCTTC
Statistics
Matches: 181, Mismatches: 38, Indels: 23
0.75 0.16 0.10
Matches are distributed among these distances:
58 27 0.15
59 110 0.61
60 44 0.24
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (57 bp):
AAAATGTAATTTTGGGAAGTTTTAGGGTTAAAATGTAATTTTTGGAAGTTTTGGGGT
Found at i:25639138 original size:17 final size:18
Alignment explanation
Indices: 25639118--25639158 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
25639108 AATTTTATGC
25639118 AAATTTAAATTCAAAA-T
1 AAATTTAAATTCAAAACT
* *
25639135 AAATCT-AATTTAAAACT
1 AAATTTAAATTCAAAACT
25639152 AAATTTA
1 AAATTTA
25639159 TATCCCATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 3
0.76 0.12 0.12
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATTTAAATTCAAAACT
Found at i:25639876 original size:12 final size:12
Alignment explanation
Indices: 25639843--25639900 Score: 66
Period size: 12 Copynumber: 4.7 Consensus size: 12
25639833 ACCGAAGTAT
25639843 AAGAAGAAAAGAG
1 AAGAAGAAAA-AG
25639856 AA-AAG-AAAAG
1 AAGAAGAAAAAG
25639866 AAGAAGAAAAAG
1 AAGAAGAAAAAG
25639878 CAGAGAAGGAAAAAG
1 -A-AGAA-GAAAAAG
25639893 AAGAAGAA
1 AAGAAGAA
25639901 GTTGTCTCGA
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
10 4 0.10
11 6 0.15
12 11 0.28
13 7 0.17
14 5 0.12
15 7 0.17
ACGTcount: A:0.71, C:0.02, G:0.28, T:0.00
Consensus pattern (12 bp):
AAGAAGAAAAAG
Found at i:25642460 original size:25 final size:25
Alignment explanation
Indices: 25642426--25642476 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
25642416 TCTTTCAAGG
*
25642426 AGACCTTGATTTATACTAGAGTGTA
1 AGACCCTGATTTATACTAGAGTGTA
*
25642451 AGACCCTGATTTGTACTAGAGTGTA
1 AGACCCTGATTTATACTAGAGTGTA
25642476 A
1 A
25642477 ACTTCAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (25 bp):
AGACCCTGATTTATACTAGAGTGTA
Found at i:25644067 original size:36 final size:36
Alignment explanation
Indices: 25644018--25644112 Score: 118
Period size: 36 Copynumber: 2.6 Consensus size: 36
25644008 TTTGTTAGTA
*
25644018 GCATGTTTTACATGCGAATCAGAATATCAGAAAACG
1 GCATGTTTAACATGCGAATCAGAATATCAGAAAACG
* * * * *
25644054 GCATGCTTAACATGCAAATAAGAATATTAGAAAATG
1 GCATGTTTAACATGCGAATCAGAATATCAGAAAACG
* *
25644090 ACATGTTTAACATGCGAAACAGA
1 GCATGTTTAACATGCGAATCAGA
25644113 TGTCACATAA
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.24
Consensus pattern (36 bp):
GCATGTTTAACATGCGAATCAGAATATCAGAAAACG
Found at i:25646239 original size:14 final size:15
Alignment explanation
Indices: 25646207--25646253 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
25646197 TTTTAGAGTT
*
25646207 TAGGTTTTCACAA-C
1 TAGGTTTTCAGAATC
25646221 ATA-GTTTTCAGAATC
1 -TAGGTTTTCAGAATC
25646236 TAGTGTTTTCAGAATC
1 TAG-GTTTTCAGAATC
25646252 TA
1 TA
25646254 AAGTCTCACA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 11 0.39
15 3 0.11
16 14 0.50
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (15 bp):
TAGGTTTTCAGAATC
Found at i:25647026 original size:27 final size:28
Alignment explanation
Indices: 25646985--25647055 Score: 71
Period size: 26 Copynumber: 2.7 Consensus size: 28
25646975 ATGTCATGCA
* *
25646985 AAAATAATCCC-AAATATAACAT-CATTC
1 AAAAT-ATCCCAAAATATAAAATCCAGTC
25647012 AAAATATCCCAAAAT-TAAAATCCAGTC
1 AAAATATCCCAAAATATAAAATCCAGTC
*
25647039 AAAA-GTCCCAAAA-ATAA
1 AAAATATCCCAAAATATAA
25647056 TAGTCCAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
26 21 0.55
27 17 0.45
ACGTcount: A:0.55, C:0.21, G:0.03, T:0.21
Consensus pattern (28 bp):
AAAATATCCCAAAATATAAAATCCAGTC
Found at i:25647865 original size:23 final size:23
Alignment explanation
Indices: 25647815--25647861 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
25647805 GAGTAATAGG
* * *
25647815 AATCACATAAATCAGTATCACAG
1 AATCACACAAATCAGCATCACAA
25647838 AATCACACAAATCA-CATCACAA
1 AATCACACAAATCAGCATCACAA
25647860 AA
1 AA
25647862 ATCAGAGGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.53, C:0.26, G:0.04, T:0.17
Consensus pattern (23 bp):
AATCACACAAATCAGCATCACAA
Found at i:25648847 original size:21 final size:21
Alignment explanation
Indices: 25648797--25648872 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
25648787 ATAGTGCAGA
** *
25648797 CTTCTACCGATACCTATGATAG
1 CTTCTACCGATACAAAT-AAAG
* *
25648819 -TTCCACCGATACAAGTAAAG
1 CTTCTACCGATACAAATAAAG
* * *
25648839 CTTCTACCGAAACAAATCATG
1 CTTCTACCGATACAAATAAAG
25648860 CTTCTACCGATAC
1 CTTCTACCGATAC
25648873 TTAAAACTCC
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
20 3 0.07
21 39 0.93
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.26
Consensus pattern (21 bp):
CTTCTACCGATACAAATAAAG
Found at i:25649985 original size:193 final size:191
Alignment explanation
Indices: 25649704--25650066 Score: 528
Period size: 193 Copynumber: 1.9 Consensus size: 191
25649694 CTATACTATA
* * * * * *
25649704 AATTATTCCCTAACGATGCTGCTCACACAAGCTGTTGAGAGTATGTATAAAGCATAGTCCCAGCC
1 AATTATTCCCTAACGATACTACTCACACAAGCTGTTGAGAATATGCATAAAGCATAATCCCAACC
* * *
25649769 ATCGTAGGGTCTGAAATCCATTTAGGATCCATATCTCTTTCTCGAGTCACGATGGTGCTCATACG
66 ATCGTAGGGTCTGAAATCCATTTAGGATCCATATCTCTTTCCCGAGTCACGATGCTGCTCACACG
* * *
25649834 AGCTATCGAGGACTCGCAACATATGTGGTACCTCAGCCATTGATACGGTATCTGTGCATAT
131 AGCTATCGAGGACTCGCAACACATGCGGTACATCAGCCATTGATACGGTATCTGTGCATAT
* * * * * *
25649895 AATTGTTCCTTAACGATACTACTCACACGAGCTGTTGAGAATATGCACTTATGCATAAATCTCAA
1 AATTATTCCCTAACGATACTACTCACACAAGCTGTTGAGAATATGCA-TAAAGCAT-AATCCCAA
*
25649960 CCATCGTAGGGTCTGTAATCCATTTAGGATCCATATCTCTTTCCCGAGTCACGATGCTGCTCACA
64 CCATCGTAGGGTCTGAAATCCATTTAGGATCCATATCTCTTTCCCGAGTCACGATGCTGCTCACA
*
25650025 CGAGCTATCGAGGACTCGTAACACATGCGGTACATCAGCCAT
129 CGAGCTATCGAGGACTCGCAACACATGCGGTACATCAGCCAT
25650067 CACGTCGATT
Statistics
Matches: 150, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
191 40 0.27
192 6 0.04
193 104 0.69
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (191 bp):
AATTATTCCCTAACGATACTACTCACACAAGCTGTTGAGAATATGCATAAAGCATAATCCCAACC
ATCGTAGGGTCTGAAATCCATTTAGGATCCATATCTCTTTCCCGAGTCACGATGCTGCTCACACG
AGCTATCGAGGACTCGCAACACATGCGGTACATCAGCCATTGATACGGTATCTGTGCATAT
Found at i:25671099 original size:9 final size:9
Alignment explanation
Indices: 25671085--25671130 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
25671075 CAAAAATTTC
25671085 TTTCTTTTT
1 TTTCTTTTT
25671094 TTTCTTTTT
1 TTTCTTTTT
* *
25671103 CTTCCTTTT
1 TTTCTTTTT
*
25671112 TTTCATTTTG
1 TTTC-TTTTT
25671122 TTTCTTTTT
1 TTTCTTTTT
25671131 CAATTGACTG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
9 23 0.77
10 7 0.23
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.80
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:25671105 original size:19 final size:19
Alignment explanation
Indices: 25671081--25671130 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
25671071 TTATCAAAAA
*
25671081 TTTCTTTCTTTTTTTTCTT
1 TTTCTTTCTTTTTTTTCAT
*
25671100 TTTC-TTCCTTTTTTTCAT
1 TTTCTTTCTTTTTTTTCAT
*
25671118 TTTGTTTCTTTTT
1 TTTCTTTCTTTTT
25671131 CAATTGACTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTCTTTCTTTTTTTTCAT
Found at i:25671757 original size:16 final size:18
Alignment explanation
Indices: 25671715--25671754 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
25671705 AACAAAAGGG
25671715 ATGCAATGACAAAATAAA
1 ATGCAATGACAAAATAAA
*
25671733 ATGCAATGACAATA-AAA
1 ATGCAATGACAAAATAAA
25671750 ATGCA
1 ATGCA
25671755 TGAAAACTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.57, C:0.12, G:0.12, T:0.17
Consensus pattern (18 bp):
ATGCAATGACAAAATAAA
Found at i:25674006 original size:20 final size:21
Alignment explanation
Indices: 25673981--25674019 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
25673971 GCAAGGAATT
25673981 TGAAAC-AACAAAAGTAAAAG
1 TGAAACAAACAAAAGTAAAAG
*
25674001 TGAAACAAATAAAAGTAAA
1 TGAAACAAACAAAAGTAAA
25674020 TAAACAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.67, C:0.08, G:0.13, T:0.13
Consensus pattern (21 bp):
TGAAACAAACAAAAGTAAAAG
Found at i:25677362 original size:21 final size:21
Alignment explanation
Indices: 25677338--25677387 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
25677328 CCTATGATAG
* *
25677338 TTTTACCGATACAAGTAA-AGC
1 TTTTACCGAAACAAATAACA-C
*
25677359 TTTTACTGAAACAAATAACAC
1 TTTTACCGAAACAAATAACAC
25677380 TTTTACCG
1 TTTTACCG
25677388 GTGCTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (21 bp):
TTTTACCGAAACAAATAACAC
Found at i:25678551 original size:194 final size:194
Alignment explanation
Indices: 25678145--25678590 Score: 499
Period size: 194 Copynumber: 2.3 Consensus size: 194
25678135 ACCAGTACTT
* * * * *
25678145 GATGCTGCTAACACGAGCTTTCGAGGACTCGCAACCTATGTGGTACCCCAGCCATCGATATGGTG
1 GATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATCGATATGGTG
* * * * *
25678210 CCTCTCTGTACTATAAACTGTTCTCTAACGATGCTGCTCACACGAGATGTCGAGAGTATGCGTAA
66 -CTCTCTGCACTATAAACTGTTCCCTAACAATGCTGCTCACACGAGATGTCGAGAATATGCCTAA
* * * *
25678275 AGCATAGTCCCAGCCATCGTAGGGCCTATAATCCATTTAGGATCCATATCTCTTTCCTGGGCCAC
130 AGCATAATCCCAACCATCGTAGGGCCTATAATCCATTTAGGATCCATATCTCTTTCCTCGACCAC
* * *
25678340 AATGCTACTCACACGAGCTGTCGAGGACTCGCAACATATGCGATACCTCAG-CATCGATATGGTG
1 GATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATCGATATGGTG
* ** * * *
25678404 -TCTGTGCA-TAT-AACTGTTCCCTAACAATTTTGCTCGCACGAGCTGTCGAGAATATGCACTTA
66 CTCTCTGCACTATAAACTGTTCCCTAACAATGCTGCTCACACGAGATGTCGAGAATATGC-CTAA
* * * * * * *
25678466 TGCATAAATCTCAATCATCGTAGGGCCTGTAATCCATTCTTGGAT-TATTTTCTCATTT-CTCGA
130 AGCAT-AATCCCAACCATCGTAGGGCCTATAATCCATT-TAGGATCCA-TATCTC-TTTCCTCGA
25678529 CTCAC
191 C-CAC
* *
25678534 GATGATGCTCACACGAGCTGTTGAGGACTCGCAACATATGCGGTACCTCAGCCATCG
1 GATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATCG
25678591 CGTCGGTTTC
Statistics
Matches: 209, Mismatches: 35, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
190 39 0.19
191 9 0.04
192 34 0.16
193 14 0.07
194 65 0.31
195 48 0.23
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.28
Consensus pattern (194 bp):
GATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATCGATATGGTG
CTCTCTGCACTATAAACTGTTCCCTAACAATGCTGCTCACACGAGATGTCGAGAATATGCCTAAA
GCATAATCCCAACCATCGTAGGGCCTATAATCCATTTAGGATCCATATCTCTTTCCTCGACCAC
Found at i:25680277 original size:20 final size:21
Alignment explanation
Indices: 25680252--25680291 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
25680242 CACTTATACT
25680252 AACTTT-T-AATTCAATAATTA
1 AACTTTGTCAATTCAA-AATTA
25680272 AACTTTGTCAATTCAAAATT
1 AACTTTGTCAATTCAAAATT
25680292 CCATATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 5 0.28
22 7 0.39
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (21 bp):
AACTTTGTCAATTCAAAATTA
Found at i:25688727 original size:12 final size:12
Alignment explanation
Indices: 25688710--25688748 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
25688700 TTAAAGAATC
25688710 ATAGGCTAATTT
1 ATAGGCTAATTT
*
25688722 ATAGGCTAATTA
1 ATAGGCTAATTT
* *
25688734 ATAGGTTTATTT
1 ATAGGCTAATTT
25688746 ATA
1 ATA
25688749 TTATATTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (12 bp):
ATAGGCTAATTT
Found at i:25702611 original size:17 final size:18
Alignment explanation
Indices: 25702574--25702613 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
25702564 GGACTGTAGC
25702574 AATAATAATATAAAATAT
1 AATAATAATATAAAATAT
* *
25702592 AATAAT-ATATAGAATTT
1 AATAATAATATAAAATAT
25702609 AATAA
1 AATAA
25702614 ACATCAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
AATAATAATATAAAATAT
Found at i:25705715 original size:21 final size:21
Alignment explanation
Indices: 25705682--25705723 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
25705672 TTCCTGATTG
25705682 GTTTATTGACTTT-TATTATTT
1 GTTTATTGACTTTCT-TTATTT
**
25705703 GTTTATTTTCTTTCTTTATTT
1 GTTTATTGACTTTCTTTATTT
25705724 ATTTTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.71
Consensus pattern (21 bp):
GTTTATTGACTTTCTTTATTT
Found at i:25711823 original size:46 final size:44
Alignment explanation
Indices: 25711741--25711830 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 44
25711731 AAATCTATTC
*
25711741 CATTCAACCAAATACAAGAATACTATTACAGTTCTATTCCATTA
1 CATTCAACCAAATACAAGAATACTATTACAGCTCTATTCCATTA
25711785 CATTCAACC-AA-ACAATTGAATTACTAATTACAGCTCTATTCCATTA
1 CATTCAACCAAATACAA--GAA-TACT-ATTACAGCTCTATTCCATTA
25711831 TAACTTTATT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
42 4 0.10
43 2 0.05
44 12 0.29
45 4 0.10
46 19 0.46
ACGTcount: A:0.40, C:0.23, G:0.04, T:0.32
Consensus pattern (44 bp):
CATTCAACCAAATACAAGAATACTATTACAGCTCTATTCCATTA
Found at i:25711840 original size:16 final size:16
Alignment explanation
Indices: 25711811--25711857 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
25711801 TGAATTACTA
*
25711811 ATTACAGCTCTATTCC
1 ATTACAACTCTATTCC
* *
25711827 ATTATAACTTTATTCC
1 ATTACAACTCTATTCC
25711843 ATTACAACTCTATTC
1 ATTACAACTCTATTC
25711858 GTCAAAACGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.30, C:0.26, G:0.02, T:0.43
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:25713051 original size:31 final size:31
Alignment explanation
Indices: 25713014--25713146 Score: 100
Period size: 31 Copynumber: 4.4 Consensus size: 31
25713004 TAAAAAAAGA
25713014 TTAGGTACCAAATTAGGAAAAATAGTCAAGT
1 TTAGGTACCAAATTAGGAAAAATAGTCAAGT
* *
25713045 TCAGGTACCAAATT-GGATAAAA-A--AAAGT
1 TTAGGTACCAAATTAGGA-AAAATAGTCAAGT
* * *
25713073 TTAAGTACCAACTTA-AAAAAAGT-GTCAAGT
1 TTAGGTACCAAATTAGGAAAAA-TAGTCAAGT
* * *
25713103 TTAGATACTAAATTAGGAAAAAATA-TCAATT
1 TTAGGTACCAAATTAGG-AAAAATAGTCAAGT
**
25713134 TTATATACCAAAT
1 TTAGGTACCAAAT
25713147 GTTATATTAA
Statistics
Matches: 78, Mismatches: 15, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
27 4 0.05
28 16 0.21
30 19 0.24
31 34 0.44
32 5 0.06
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.28
Consensus pattern (31 bp):
TTAGGTACCAAATTAGGAAAAATAGTCAAGT
Found at i:25713100 original size:58 final size:59
Alignment explanation
Indices: 25713005--25713125 Score: 140
Period size: 58 Copynumber: 2.1 Consensus size: 59
25712995 AGTTAATATT
* * *
25713005 AAAAAAAGATTAGGTACCAAATTAGGAAAAATAGTCAAGTTCAGGTACCAAATT-GGATA
1 AAAAAAAGATTAAGTACCAAATTAGAAAAAATAGTCAAGTTCAGATACCAAATTAGGA-A
* * * *
25713064 AAAAAAAGTTTAAGTACCAACTTA-AAAAAAGT-GTCAAGTTTAGATACTAAATTAGGAA
1 AAAAAAAGATTAAGTACCAAATTAGAAAAAA-TAGTCAAGTTCAGATACCAAATTAGGAA
25713122 AAAA
1 AAAA
25713126 TATCAATTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
58 28 0.53
59 25 0.47
ACGTcount: A:0.52, C:0.09, G:0.16, T:0.23
Consensus pattern (59 bp):
AAAAAAAGATTAAGTACCAAATTAGAAAAAATAGTCAAGTTCAGATACCAAATTAGGAA
Found at i:25713444 original size:8 final size:8
Alignment explanation
Indices: 25713423--25713460 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
25713413 TCAGCTTGAG
25713423 GAAACAAAA
1 GAAA-AAAA
*
25713432 TAAAAAAA
1 GAAAAAAA
25713440 GAAAAAAA
1 GAAAAAAA
25713448 G-AAAAAA
1 GAAAAAAA
25713455 GAAAAA
1 GAAAAA
25713461 TAAAAAGAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
7 7 0.27
8 16 0.62
9 3 0.12
ACGTcount: A:0.84, C:0.03, G:0.11, T:0.03
Consensus pattern (8 bp):
GAAAAAAA
Found at i:25723602 original size:36 final size:36
Alignment explanation
Indices: 25723555--25723626 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
25723545 CACAGGGAGT
25723555 CTGTTTTAGAACATACAATGGATTGACTTTGATTGA
1 CTGTTTTAGAACATACAATGGATTGACTTTGATTGA
25723591 CTGTTTTAGAACATACAATGGATTGACTTTGATTGA
1 CTGTTTTAGAACATACAATGGATTGACTTTGATTGA
25723627 AAATACCCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (36 bp):
CTGTTTTAGAACATACAATGGATTGACTTTGATTGA
Found at i:25729839 original size:18 final size:19
Alignment explanation
Indices: 25729787--25729827 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
25729777 ATTTTTAAAG
*
25729787 ATTCTAATTAGGAGATATT
1 ATTCTAATTAAGAGATATT
25729806 ATTCTAATTAAGAGATATT
1 ATTCTAATTAAGAGATATT
25729825 ATT
1 ATT
25729828 TCCTTAATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (19 bp):
ATTCTAATTAAGAGATATT
Found at i:25732442 original size:20 final size:21
Alignment explanation
Indices: 25732404--25732442 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
25732394 TTTAGGTTTC
*
25732404 TTGATTATATTTTTATTTTAG
1 TTGATTATATTTTCATTTTAG
*
25732425 TTGATT-TATTTTCCTTTT
1 TTGATTATATTTTCATTTT
25732443 GTAATAGGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.18, C:0.05, G:0.08, T:0.69
Consensus pattern (21 bp):
TTGATTATATTTTCATTTTAG
Found at i:25738754 original size:60 final size:60
Alignment explanation
Indices: 25738672--25738804 Score: 221
Period size: 60 Copynumber: 2.2 Consensus size: 60
25738662 GCACTGAGTT
* * *
25738672 GATGTCGCGACATTGAACTAGATTGCTCTAATGACTCCAATGCCGCAACACTGAAGGTTG
1 GATGTCGCAACATTGAAATAGATTGCTCTAATGACTCCAATGCCGCAACACTGAAGGTTA
* *
25738732 GATGTCGCAACATTGAAATAGATTGCTCTAATGACTCCAATGTCGCGACACTGAAGGTTA
1 GATGTCGCAACATTGAAATAGATTGCTCTAATGACTCCAATGCCGCAACACTGAAGGTTA
25738792 GATGTCGCAACAT
1 GATGTCGCAACAT
25738805 CAGAGACAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 68 1.00
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.26
Consensus pattern (60 bp):
GATGTCGCAACATTGAAATAGATTGCTCTAATGACTCCAATGCCGCAACACTGAAGGTTA
Found at i:25741686 original size:34 final size:34
Alignment explanation
Indices: 25741616--25741692 Score: 91
Period size: 34 Copynumber: 2.3 Consensus size: 34
25741606 ACACATATAC
* * ** *
25741616 AATGTCTTATTATCAAAAACATATATTAGCTTAG
1 AATGTCATATTATCAAAAACATATATCAAATCAG
* *
25741650 AATGTCATATTTTCAAAAGCATATATCAAATCAG
1 AATGTCATATTATCAAAAACATATATCAAATCAG
25741684 AATGTCATA
1 AATGTCATA
25741693 ATAAATCAGA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (34 bp):
AATGTCATATTATCAAAAACATATATCAAATCAG
Found at i:25744001 original size:24 final size:24
Alignment explanation
Indices: 25743968--25744088 Score: 208
Period size: 24 Copynumber: 5.0 Consensus size: 24
25743958 AACTTGAGTT
*
25743968 TCAGGAAACAAAAGAATTGCCACC
1 TCAGGTAACAAAAGAATTGCCACC
25743992 TCAGGTAACAAAAGAATTGCCACC
1 TCAGGTAACAAAAGAATTGCCACC
25744016 TCAGGTAACAAAAGAATTGCCGA-C
1 TCAGGTAACAAAAGAATTGCC-ACC
25744040 TCAGGTAACAAAAGAATTGCCACC
1 TCAGGTAACAAAAGAATTGCCACC
*
25744064 TCAGGTAACAAAAGAATTGTCACC
1 TCAGGTAACAAAAGAATTGCCACC
25744088 T
1 T
25744089 AAGGAAAGTG
Statistics
Matches: 93, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
23 1 0.01
24 91 0.98
25 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.17
Consensus pattern (24 bp):
TCAGGTAACAAAAGAATTGCCACC
Found at i:25745798 original size:23 final size:23
Alignment explanation
Indices: 25745766--25745812 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
25745756 TTTGTTTAAG
25745766 TTAAACGAACATATTCGTGAACA
1 TTAAACGAACATATTCGTGAACA
* *
25745789 TTAAATGAACATGTTCGTGAACA
1 TTAAACGAACATATTCGTGAACA
25745812 T
1 T
25745813 ATAATTGAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (23 bp):
TTAAACGAACATATTCGTGAACA
Found at i:25750580 original size:17 final size:17
Alignment explanation
Indices: 25750558--25750594 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
25750548 ATTAAGAGTG
*
25750558 TAAATTGATTTTAAATT
1 TAAATTGACTTTAAATT
*
25750575 TAAATTTACTTTAAATT
1 TAAATTGACTTTAAATT
25750592 TAA
1 TAA
25750595 TCAAATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (17 bp):
TAAATTGACTTTAAATT
Found at i:25752558 original size:27 final size:28
Alignment explanation
Indices: 25752514--25752798 Score: 116
Period size: 29 Copynumber: 9.8 Consensus size: 28
25752504 CCTTAAGCTG
* *
25752514 TCCAAAAATTATACTTTGAACCCCAAAC-
1 TCCAAAAATTACATTTTG-ACCCCAAACT
*
25752542 T-CAAAAATTACATTTTGACCTCAAAACT
1 TCCAAAAATTACATTTTGACC-CCAAACT
* *
25752570 TCCCAACATTACATTTTTG-CCCCGAAACT
1 TCCAAAAATTACA-TTTTGACCCC-AAACT
* *
25752599 TCCAAAAATTACATTTTTACCCTCGAACTT
1 TCCAAAAATTACATTTTGACCC-CAAAC-T
* **
25752629 TCC-AAAATT-CTATTTTTGACCCCGATTT
1 TCCAAAAATTAC-A-TTTTGACCCCAAACT
** * *
25752657 TATTAAAAATTACATTTTTACCCCCGAACTT
1 T-CCAAAAATTACATTTTGA-CCCCAAAC-T
* ***
25752688 TCC-AAAATTATATTTTTGACCCCATTTT
1 TCCAAAAATTACA-TTTTGACCCCAAACT
* * *
25752716 TAACAAAAATTACATTTTTACCCTCGAACT
1 T-CCAAAAATTACATTTTGACCC-CAAACT
* * * * **
25752746 TTCTAAAATTCCATTTTTAACCCCAATTT
1 TCCAAAAATTACA-TTTTGACCCCAAACT
*
25752775 TACCAAAAAGTACCATTTT-ACCCC
1 T-CCAAAAATTA-CATTTTGACCCC
25752799 CGAATATTTA
Statistics
Matches: 191, Mismatches: 44, Indels: 43
0.69 0.16 0.15
Matches are distributed among these distances:
26 3 0.02
27 19 0.10
28 12 0.06
29 87 0.46
30 65 0.34
31 5 0.03
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (28 bp):
TCCAAAAATTACATTTTGACCCCAAACT
Found at i:25752673 original size:59 final size:58
Alignment explanation
Indices: 25752601--25752802 Score: 271
Period size: 59 Copynumber: 3.4 Consensus size: 58
25752591 CCGAAACTTC
* *
25752601 CAAAAATTACATTTTTACCCTCGAACTTTCCAAAATTCTATTTTTGACCCCGATTTTAT
1 CAAAAATTACATTTTTACCCCCGAACTTTCCAAAATTCTATTTTTGACCCC-ATTTTAA
* *
25752660 TAAAAATTACATTTTTACCCCCGAACTTTCCAAAATTATATTTTTGACCCCATTTTTAA
1 CAAAAATTACATTTTTACCCCCGAACTTTCCAAAATTCTATTTTTGACCCCA-TTTTAA
* * * * *
25752719 CAAAAATTACATTTTTACCCTCGAACTTTCTAAAATTCCATTTTTAACCCCAATTTTAC
1 CAAAAATTACATTTTTACCCCCGAACTTTCCAAAATTCTATTTTTGACCCC-ATTTTAA
*
25752778 CAAAAAGTACCA-TTTTACCCCCGAA
1 CAAAAATTA-CATTTTTACCCCCGAA
25752803 TATTTAAAAT
Statistics
Matches: 127, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
58 1 0.01
59 123 0.97
60 3 0.02
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.38
Consensus pattern (58 bp):
CAAAAATTACATTTTTACCCCCGAACTTTCCAAAATTCTATTTTTGACCCCATTTTAA
Found at i:25752764 original size:29 final size:28
Alignment explanation
Indices: 25752542--25752769 Score: 172
Period size: 29 Copynumber: 7.8 Consensus size: 28
25752532 AACCCCAAAC
* **
25752542 TCAAAAATTACATTTTGACCTCAAAACTT
1 TCAAAAATTACATTTTTACC-CCGAACTT
* * * *
25752571 CCCAACATTACATTTTTGCCCCGAAACTT
1 TCAAAAATTACATTTTTACCCCG-AACTT
*
25752600 CCAAAAATTACATTTTTACCCTCGAACTT
1 TCAAAAATTACATTTTTACCC-CGAACTT
* **
25752629 TCCAAAATT-CTATTTTTGACCCCGATTTT
1 TCAAAAATTAC-ATTTTT-ACCCCGAACTT
*
25752658 ATTAAAAATTACATTTTTACCCCCGAACTT
1 -TCAAAAATTACATTTTTA-CCCCGAACTT
* * **
25752688 TCCAAAATTATATTTTTGACCCC-ATTTT
1 TCAAAAATTACATTTTT-ACCCCGAACTT
25752716 TAACAAAAATTACATTTTTACCCTCGAACTT
1 T--CAAAAATTACATTTTTACCC-CGAACTT
* *
25752747 TCTAAAATTCCATTTTTAACCCC
1 TCAAAAATTACATTTTT-ACCCC
25752770 AATTTTACCA
Statistics
Matches: 157, Mismatches: 29, Indels: 26
0.74 0.14 0.12
Matches are distributed among these distances:
28 6 0.04
29 99 0.63
30 47 0.30
31 5 0.03
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.38
Consensus pattern (28 bp):
TCAAAAATTACATTTTTACCCCGAACTT
Found at i:25752843 original size:118 final size:118
Alignment explanation
Indices: 25752601--25752861 Score: 291
Period size: 118 Copynumber: 2.2 Consensus size: 118
25752591 CCGAAACTTC
* * * **
25752601 CAAAAATTACATTTTTACCCTCGAACTTTCCAAAATTCTATTTTTGACCCCGATTTTATTAAAAA
1 CAAAAATTACATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCAATTTTACCAAAAA
* * ** *
25752666 TTACATTTTTACCCCCGAACTTTCCAAAATTATATTTTTGACCCCATTTTTAA
66 GTACATTTTTACCCCCGAACTTTCCAAAATTACATTTTACACCCAATTTTTAA
*
25752719 CAAAAATTACATTTTTACCCTCGAACTTTCTAAAATTCCATTTTTAACCCCAATTTTACCAAAAA
1 CAAAAATTACATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCAATTTTACCAAAAA
* **
25752784 GTACCA-TTTTACCCCCGAA-TATT-TAAAATGT-CATTTTACATCCCAAATTTTTCT
66 GTA-CATTTTTACCCCCGAACT-TTCCAAAAT-TACATTTTACA-CCC-AATTTTTAA
*
25752838 C-AAAATTACCA-TTTTGCCCTCGAA
1 CAAAAATTA-CATTTTTACCCTCGAA
25752862 AGTCCAAAAT
Statistics
Matches: 122, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
117 12 0.10
118 99 0.81
119 11 0.09
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.38
Consensus pattern (118 bp):
CAAAAATTACATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCAATTTTACCAAAAA
GTACATTTTTACCCCCGAACTTTCCAAAATTACATTTTACACCCAATTTTTAA
Found at i:25765198 original size:205 final size:204
Alignment explanation
Indices: 25764847--25765511 Score: 946
Period size: 205 Copynumber: 3.3 Consensus size: 204
25764837 GGTTATACAC
* * * *
25764847 AAACAGCGAGGCGGTCATCTTCCTGATGAAACACAGAGAAGAATACC-AA-C---TCAACGCTCA
1 AAACAGCGAGGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCAACGCTCA
*
25764907 ATGCAAGCAAATCTTCAAACCCAGCTTCCTGATGAGACACTAAGAAGCAGGTTGAAGCAATAAAA
66 ATGCAAGCAAATCTTCGAACCCAGCTTCCTGATGAGACACTAAGAAGCAGGTTGAAGCAATAAAA
* * *
25764972 TGGTTAGCTTCCTGATGAGACACAAAGAAGTGGACCAAATTCGTCTTCTTGAGGAGATCCAAAGA
131 TGGTTAGCTTCCTGATGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGA
*
25765037 AGCAAATTA
196 AGCGAATTA
25765046 AAACAAGCGAGGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCAACGCTC
1 AAAC-AGCGAGGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCAACGCTC
* * * *
25765111 AATGCAAGTAAATCTTTGAACCCAGCTTCCTGATGAGACACTGAGAAGTAGGTTGAAGCAATAAA
65 AATGCAAGCAAATCTTCGAACCCAGCTTCCTGATGAGACACTAAGAAGCAGGTTGAAGCAATAAA
* *
25765176 ATGGTTAGCTTCCTAATGAGACACAGAGAAGTGGACCAAATTTGTCTTCCTGAGGAGATCCAGAG
130 ATGGTTAGCTTCCTGATGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAG
*
25765241 AAGCGATTTA
195 AAGCGAATTA
* *
25765251 AAACAAGAGAGGCGGTCATCTTCCTTATGAGACACTGAGAAGAAGACCAAATCAAACCAACGCTC
1 AAAC-AGCGAGGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCAACGCTC
* * * * * *
25765316 AATGCAAGCAAATCTTCGAACCCAGCTTCCTAAGGAGACACTAAGAAGCAAGTCGAAGTAATGAA
65 AATGCAAGCAAATCTTCGAACCCAGCTTCCTGATGAGACACTAAGAAGCAGGTTGAAGCAATAAA
* * *
25765381 ATGGTTAGCTTCCTGATGAGACATAGAGAAGTGGACTAAATTCGTCTTCCTGAGGAGATCTAGAG
130 ATGGTTAGCTTCCTGATGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAG
25765446 AAGCGAATTA
195 AAGCGAATTA
** ** * *
25765456 AAACAGATAATTACGGTCATCTTCCTGATAAGACA-TAGAGAAGAAGACCATATCAA
1 AAACAG-CGA-GGCGGTCATCTTCCTGATGAGACACT-GAGAAGAAGACCAAATCAA
25765512 TGAAATCAGA
Statistics
Matches: 416, Mismatches: 41, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
199 4 0.01
200 40 0.10
201 2 0.00
202 1 0.00
204 2 0.00
205 329 0.79
206 38 0.09
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (204 bp):
AAACAGCGAGGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCAACGCTCA
ATGCAAGCAAATCTTCGAACCCAGCTTCCTGATGAGACACTAAGAAGCAGGTTGAAGCAATAAAA
TGGTTAGCTTCCTGATGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGA
AGCGAATTA
Found at i:25765901 original size:17 final size:17
Alignment explanation
Indices: 25765861--25765899 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
25765851 AGTTTAAATT
*
25765861 TTTAAATTTAATTTAAA
1 TTTAAATTTAATTCAAA
25765878 TTTAAATTTAA-TCAAA
1 TTTAAATTTAATTCAAA
25765894 TTTAAA
1 TTTAAA
25765900 ATAATATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTAAATTTAATTCAAA
Found at i:25767856 original size:28 final size:27
Alignment explanation
Indices: 25767805--25767872 Score: 84
Period size: 27 Copynumber: 2.4 Consensus size: 27
25767795 AAATTGTCTA
*
25767805 AAAATTACACTTTGACCCTCAAACTTCTT
1 AAAATTACA--TTGACCCTCAAACTTCCT
25767834 AGAAATTACATTGA-CCTCAAAACTTCCT
1 A-AAATTACATTGACCCTC-AAACTTCCT
25767862 AAAATTACATT
1 AAAATTACATT
25767873 TTTGCCCCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
27 14 0.39
28 13 0.36
29 1 0.03
30 8 0.22
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (27 bp):
AAAATTACATTGACCCTCAAACTTCCT
Found at i:25767916 original size:29 final size:28
Alignment explanation
Indices: 25767851--25767906 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 28
25767841 ACATTGACCT
*
25767851 CAAAACTTCCTAAAATTACATTTTTGCCC
1 CAAAACTTCC-AAAATTACATTTATGCCC
25767880 CAAAACTTCCAAAAATTACATTTATGC
1 CAAAACTTCC-AAAATTACATTTATGC
25767907 TCTCGAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.25, G:0.04, T:0.32
Consensus pattern (28 bp):
CAAAACTTCCAAAATTACATTTATGCCC
Found at i:25767927 original size:58 final size:57
Alignment explanation
Indices: 25767836--25768083 Score: 234
Period size: 58 Copynumber: 4.3 Consensus size: 57
25767826 AACTTCTTAG
* * * ** **
25767836 AAATTACA-TTGACCTCAAAAC-TTCCTAAAATTACATTTTTGCCCCAAAACTT-CCAA
1 AAATTACATTTTACCTC-GAACTTTCC-AAAATTACATTTTTGACCCTGATTTTACCAA
* *
25767892 AAATTACATTTATGCTCTCGAACTTTCCAAAATTACGTTTTTGACCCTGATTTTACCAA
1 AAATTACATTT-TAC-CTCGAACTTTCCAAAATTACATTTTTGACCCTGATTTTACCAA
* * * * *
25767951 AAATTACCATTTTACCCTCAAACTTTCAAAAACTCCATTTTTGACCTTGATTTTACCAA
1 AAATTA-CATTTTA-CCTCGAACTTTCCAAAATTACATTTTTGACCCTGATTTTACCAA
* *
25768010 AAATTATATTTTTACCTCGAACTTTCCAAAATTCCATTTTTGA-CCTCGATTTTACCAA
1 AAATTACA-TTTTACCTCGAACTTTCCAAAATTACATTTTTGACCCT-GATTTTACCAA
*
25768068 AAAGTACCATTTTACC
1 AAATTA-CATTTTACC
25768084 CCCGGATATT
Statistics
Matches: 159, Mismatches: 23, Indels: 18
0.80 0.12 0.09
Matches are distributed among these distances:
56 8 0.05
57 4 0.03
58 74 0.47
59 67 0.42
60 6 0.04
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (57 bp):
AAATTACATTTTACCTCGAACTTTCCAAAATTACATTTTTGACCCTGATTTTACCAA
Found at i:25767950 original size:29 final size:30
Alignment explanation
Indices: 25767891--25768069 Score: 110
Period size: 29 Copynumber: 6.1 Consensus size: 30
25767881 AAAACTTCCA
* * *
25767891 AAAATTACATTTATG-CTCTCGAACTTT-CC
1 AAAATTACATTTTTGACCCTCG-ATTTTACC
*
25767920 AAAATTACGTTTTTGACCCT-GATTTTACC
1 AAAATTACATTTTTGACCCTCGATTTTACC
* * *
25767949 AAAAATTACCA-TTTT-ACCCTCAAACTTT-CA
1 -AAAATTA-CATTTTTGACCCTC-GATTTTACC
* * *
25767979 AAAACTCCATTTTTGA-CCTTGATTTTACC
1 AAAATTACATTTTTGACCCTCGATTTTACC
* *
25768008 AAAAATTATATTTTT-A-CCTCGAACTTT-CC
1 -AAAATTACATTTTTGACCCTCG-ATTTTACC
*
25768037 AAAATTCCATTTTTGA-CCTCGATTTTACC
1 AAAATTACATTTTTGACCCTCGATTTTACC
25768066 AAAA
1 AAAA
25768070 AGTACCATTT
Statistics
Matches: 115, Mismatches: 22, Indels: 26
0.71 0.13 0.16
Matches are distributed among these distances:
28 26 0.23
29 53 0.46
30 31 0.27
31 5 0.04
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.39
Consensus pattern (30 bp):
AAAATTACATTTTTGACCCTCGATTTTACC
Found at i:25767975 original size:59 final size:58
Alignment explanation
Indices: 25767888--25768084 Score: 245
Period size: 59 Copynumber: 3.3 Consensus size: 58
25767878 CCCAAAACTT
* * * *
25767888 CCAAAAATTACATTTATGCTCTCGAACTTTCCAAAATTACGTTTTTGACCCTGATTTTA
1 CCAAAAATTACATTT-TACCCTCGAACTTTCCAAAATTCCATTTTTGACCCTGATTTTA
* * * *
25767947 CCAAAAATTACCATTTTACCCTCAAACTTTCAAAAACTCCATTTTTGACCTTGATTTTA
1 CCAAAAATTA-CATTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCCTGATTTTA
*
25768006 CCAAAAATTATATTTTTA-CCTCGAACTTTCCAAAATTCCATTTTTGA-CCTCGATTTTA
1 CCAAAAATTACA-TTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCCT-GATTTTA
*
25768064 CCAAAAAGTACCATTTTACCC
1 CCAAAAATTA-CATTTTACCC
25768085 CCGGATATTT
Statistics
Matches: 118, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
57 2 0.02
58 48 0.41
59 63 0.53
60 5 0.04
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (58 bp):
CCAAAAATTACATTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCCTGATTTTA
Found at i:25771718 original size:17 final size:17
Alignment explanation
Indices: 25771698--25771742 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
25771688 AATTTGAATT
*
25771698 TTTTTAAAAAAATAGAA
1 TTTTTAAAAAAATAAAA
**
25771715 TTTTGGAAAAAATAAAA
1 TTTTTAAAAAAATAAAA
25771732 TTTTTCAAAAA
1 TTTTT-AAAAA
25771743 TTATAAAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (17 bp):
TTTTTAAAAAAATAAAA
Found at i:25771752 original size:9 final size:9
Alignment explanation
Indices: 25771738--25771783 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
25771728 AAAATTTTTC
25771738 AAAAATTAT
1 AAAAATTAT
*
25771747 AAAAATAAT
1 AAAAATTAT
25771756 ATAAAATTATT
1 A-AAAATTA-T
25771767 AAAAA-T-T
1 AAAAATTAT
25771774 AAAAATTAT
1 AAAAATTAT
25771783 A
1 A
25771784 TGGAATACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
7 6 0.19
8 1 0.03
9 12 0.39
10 10 0.32
11 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:25772531 original size:41 final size:40
Alignment explanation
Indices: 25772404--25772542 Score: 129
Period size: 41 Copynumber: 3.4 Consensus size: 40
25772394 TAGTGGCGCT
* * *
25772404 AAGCGCCGCTAAA-AGTCAGGGCATTAGCAGCGCTTATACAA
1 AAGCGCCGCTAAAGA-TCAGAGCATTAGCGGCGC-TATAAAA
* * *
25772445 AAGCACCGCTAAAGCTC-GAGGCATTAGCGACGCATATAAAA
1 AAGCGCCGCTAAAGATCAGA-GCATTAGCGGCGC-TATAAAA
* * *
25772486 AAGCGCCGCTAAAGATCAGAGCATTAGCGGCGCTGGTAGAG
1 AAGCGCCGCTAAAGATCAGAGCATTAGCGGCGCT-ATAAAA
*
25772527 AAGCGCAGCTAAAGAT
1 AAGCGCCGCTAAAGAT
25772543 GGATTTTAAC
Statistics
Matches: 80, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
40 2 0.03
41 76 0.95
42 2 0.03
ACGTcount: A:0.35, C:0.23, G:0.27, T:0.15
Consensus pattern (40 bp):
AAGCGCCGCTAAAGATCAGAGCATTAGCGGCGCTATAAAA
Found at i:25775058 original size:32 final size:32
Alignment explanation
Indices: 25775017--25775082 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
25775007 AAGGCCTGCA
*
25775017 AATCCTGTGTATCCTAGTTGGGTGTTTTGATT
1 AATCCTGTGTATCCTAGCTGGGTGTTTTGATT
25775049 AATCCTGTGTATCCTAGCTGGGTGTTTTGATT
1 AATCCTGTGTATCCTAGCTGGGTGTTTTGATT
25775081 AA
1 AA
25775083 CTTCTTTGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.18, C:0.14, G:0.24, T:0.44
Consensus pattern (32 bp):
AATCCTGTGTATCCTAGCTGGGTGTTTTGATT
Found at i:25776098 original size:43 final size:43
Alignment explanation
Indices: 25776045--25776137 Score: 116
Period size: 43 Copynumber: 2.2 Consensus size: 43
25776035 ATTTGTTAAT
* *
25776045 TTTAGTGGCGTTTGTGAAAAAAGCGCTGCTAAAAA-CTATGTTC
1 TTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAAATC-ATGTTC
* * * *
25776088 TTTAGCGGCGTTTGTTAGAAAAGTGCCGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAAATCATGTTC
25776131 TTTAGCG
1 TTTAGCG
25776138 ACATTTTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 42 0.98
44 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAAATCATGTTC
Found at i:25779857 original size:19 final size:18
Alignment explanation
Indices: 25779833--25779883 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
25779823 CATCCAAACA
25779833 CCAGAAAATATTAACTTTT
1 CCAGAAAATATTAA-TTTT
*
25779852 CCAGAAAAGTAATTCATTTT
1 CCAGAAAA-T-ATTAATTTT
*
25779872 CCAGAAACTATT
1 CCAGAAAATATT
25779884 TTCAGTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 3 0.11
19 9 0.32
20 12 0.43
21 4 0.14
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (18 bp):
CCAGAAAATATTAATTTT
Found at i:25784382 original size:20 final size:19
Alignment explanation
Indices: 25784342--25784395 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
25784332 TTTTAAATTC
25784342 TAATTTTT-TTATTTATAAA
1 TAATTTTTATTATTT-TAAA
*
25784361 TAGTTTTCTATTATTTTAAA
1 TAATTTT-TATTATTTTAAA
25784381 TAATTTTTA-TATTTT
1 TAATTTTTATTATTTT
25784396 CCATCTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 6 0.19
19 8 0.26
20 11 0.35
21 6 0.19
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (19 bp):
TAATTTTTATTATTTTAAA
Found at i:25786049 original size:61 final size:62
Alignment explanation
Indices: 25785968--25786098 Score: 192
Period size: 61 Copynumber: 2.1 Consensus size: 62
25785958 ACATTTGATA
* * *
25785968 ACTCACGATGACACAGAGTCACCGGACCTTTAATCCATAATAGAATTCA-TTCTCATTTAGT
1 ACTCACGATGACACAAAGTCACCGGACCTTTAATCCATAATAGAATTCATTTCTCATTCAAT
* * * *
25786029 ACTCACGATGACACAAAGTCATCGGGCCTTTAATCCTTAATAGGATTCATTTCTCATTCAAT
1 ACTCACGATGACACAAAGTCACCGGACCTTTAATCCATAATAGAATTCATTTCTCATTCAAT
25786091 ACTCACGA
1 ACTCACGA
25786099 CGACTCTAAG
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
61 44 0.71
62 18 0.29
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (62 bp):
ACTCACGATGACACAAAGTCACCGGACCTTTAATCCATAATAGAATTCATTTCTCATTCAAT
Found at i:25792190 original size:15 final size:15
Alignment explanation
Indices: 25792148--25792192 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
25792138 TCTTTCTTAA
*
25792148 CTCTCGGAACCTGTT
1 CTCTCGGAACCTTTT
*
25792163 CTCTCGGTACCTTTT
1 CTCTCGGAACCTTTT
25792178 CTCTCGGAACCTTTT
1 CTCTCGGAACCTTTT
25792193 GTGATTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.11, C:0.33, G:0.16, T:0.40
Consensus pattern (15 bp):
CTCTCGGAACCTTTT
Found at i:25794185 original size:61 final size:61
Alignment explanation
Indices: 25794077--25794226 Score: 192
Period size: 61 Copynumber: 2.4 Consensus size: 61
25794067 ACCCGTTATT
* * * * *
25794077 GAATTCAATTCACATTTGATAACTCACGATGACACAGAGTCACCGGACCTTTAATCCATAATA
1 GAATTC-ATTCTCATTTAAT-ACTCACGATGACACAAAATCACCGGACCTTTAATCCATAACA
* *
25794140 GAATTCATTCTCATTTAATACTCACGATGACACAAAATCATCGGACCTTTAATCCTTAACA
1 GAATTCATTCTCATTTAATACTCACGATGACACAAAATCACCGGACCTTTAATCCATAACA
* *
25794201 GGATTCATTTCTCATTCAATACTCAC
1 GAATTCA-TTCTCATTTAATACTCAC
25794227 AACGAGTCTA
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
61 43 0.56
62 28 0.36
63 6 0.08
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.31
Consensus pattern (61 bp):
GAATTCATTCTCATTTAATACTCACGATGACACAAAATCACCGGACCTTTAATCCATAACA
Found at i:25794243 original size:62 final size:61
Alignment explanation
Indices: 25794098--25794251 Score: 173
Period size: 61 Copynumber: 2.5 Consensus size: 61
25794088 ACATTTGATA
* * * * * *
25794098 ACTCACGATGACACAGAGTCACCGGACCTTTAATCCATAATAGAATTCATTCTCATTTAAT
1 ACTCACAACGACACAAAGTCATCGGACCTTTAATCCATAACAGAATTCATTCTCATTCAAT
* * * * *
25794159 ACTCACGATGACACAAAATCATCGGACCTTTAATCCTTAACAGGATTCATTTCTCATTCAAT
1 ACTCACAACGACACAAAGTCATCGGACCTTTAATCCATAACAGAATTCA-TTCTCATTCAAT
** *
25794221 ACTCACAACGAGTCTAAGTCATCGGACCTTT
1 ACTCACAACGACACAAAGTCATCGGACCTTT
25794252 TAGCATTTAC
Statistics
Matches: 79, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
61 43 0.54
62 36 0.46
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (61 bp):
ACTCACAACGACACAAAGTCATCGGACCTTTAATCCATAACAGAATTCATTCTCATTCAAT
Found at i:25802173 original size:52 final size:52
Alignment explanation
Indices: 25802079--25802265 Score: 250
Period size: 52 Copynumber: 3.6 Consensus size: 52
25802069 ATTTCATTTA
* ** *
25802079 ATACTCATGATGACACATAGTCATCGGACCGC-TTGTTCCGTAAAGGAATCAT
1 ATACTCATGATGACACATAGTCATCGGACCTCATAATT-CGTAAAGGATTCAT
* * *
25802131 ACACTTATGATGACACATAGTCATCGAACCTCATAATTCGTAAAGGATTCAT
1 ATACTCATGATGACACATAGTCATCGGACCTCATAATTCGTAAAGGATTCAT
* * *
25802183 ATACTCATGATGACACATAGTCATCGGATCTCATAATCCATAAAGGATTCAT
1 ATACTCATGATGACACATAGTCATCGGACCTCATAATTCGTAAAGGATTCAT
* *
25802235 ATACTCACGATGACACATAGTCATCAGACCT
1 ATACTCATGATGACACATAGTCATCGGACCT
25802266 TAGTCATTTA
Statistics
Matches: 118, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
52 115 0.97
53 3 0.03
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (52 bp):
ATACTCATGATGACACATAGTCATCGGACCTCATAATTCGTAAAGGATTCAT
Found at i:25805323 original size:21 final size:21
Alignment explanation
Indices: 25805293--25805345 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 21
25805283 TCCAGACTCT
25805293 TACCGATACAAGTGACAATTC
1 TACCGATACAAGTGACAATTC
* **
25805314 TACTGATAC-A-TGACTCTTC
1 TACCGATACAAGTGACAATTC
25805333 TACCGATACAAGT
1 TACCGATACAAGT
25805346 ATGTAAACTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 15 0.58
20 2 0.08
21 9 0.35
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (21 bp):
TACCGATACAAGTGACAATTC
Found at i:25805790 original size:12 final size:12
Alignment explanation
Indices: 25805766--25805797 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
25805756 AAAGCACCTG
25805766 CAAAGACAAAAGA
1 CAAAGA-AAAAGA
25805779 CAAAGAAAAAGA
1 CAAAGAAAAAGA
25805791 CAAAGAA
1 CAAAGAA
25805798 GAAAAAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.72, C:0.12, G:0.16, T:0.00
Consensus pattern (12 bp):
CAAAGAAAAAGA
Found at i:25805801 original size:15 final size:14
Alignment explanation
Indices: 25805781--25805823 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
25805771 ACAAAAGACA
25805781 AAGAAAAAGACAAAG
1 AAGAAAAA-ACAAAG
*
25805796 AAGAAAAAACTAAG
1 AAGAAAAAACAAAG
*
25805810 AACAAAAGAACAAA
1 AAGAAAA-AACAAA
25805824 ATATGTAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.74, C:0.09, G:0.14, T:0.02
Consensus pattern (14 bp):
AAGAAAAAACAAAG
Found at i:25812487 original size:49 final size:49
Alignment explanation
Indices: 25812342--25812490 Score: 129
Period size: 49 Copynumber: 3.0 Consensus size: 49
25812332 ACCATGGAAA
* * * * ** *
25812342 CATGAAGATATGAAGGGAAAGGTTGAGGCCACAAC-AGCAAACTAGGTAC
1 CATGAAGATGTGAAAGGAAAGATTGAGGCCGCAACGA-CAAACCCGATAC
* * * * * * *
25812391 CTTAGAAGATGTGATAGGAAGGATTGAGGTCGCGACGGCAAATCCGATAC
1 CAT-GAAGATGTGAAAGGAAAGATTGAGGCCGCAACGACAAACCCGATAC
* *
25812441 CATGAAGATGTGAAAGGAAAGATTGAGGCCGTAACGACGAACCCGATAC
1 CATGAAGATGTGAAAGGAAAGATTGAGGCCGCAACGACAAACCCGATAC
25812490 C
1 C
25812491 TTAGAAACAT
Statistics
Matches: 75, Mismatches: 23, Indels: 4
0.74 0.23 0.04
Matches are distributed among these distances:
49 41 0.55
50 34 0.45
ACGTcount: A:0.37, C:0.17, G:0.30, T:0.16
Consensus pattern (49 bp):
CATGAAGATGTGAAAGGAAAGATTGAGGCCGCAACGACAAACCCGATAC
Found at i:25812743 original size:43 final size:43
Alignment explanation
Indices: 25812681--25812935 Score: 295
Period size: 43 Copynumber: 6.0 Consensus size: 43
25812671 TGCAGTCATC
* * *
25812681 CCAATCTTTTACCCCTAGTCAAGATGGGTAGATTGAAGACCTT
1 CCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGACCTT
* * * * * *
25812724 CCAATATTTCACCTCTAGTCTAGAGGGGTAGATTGAAGACCTT
1 CCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGACCTT
* *
25812767 CCAATCTTTTACCCCTAAGTCAAGAGGGGCAAATTTAAGA--TT
1 CCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAGACCTT
* *
25812809 CTAATCTTTTACCCCTAATCAAGAGAGGCAGATTGAAGA--TT
1 CCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGACCTT
* *
25812850 CCAATCTTTTACCCCAAACCAAGAGGGGCAGATTGAAG-CCATT
1 CCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGACC-TT
* * *
25812893 CCAATCTTTTACTCCTAATCAAGAGGGGTATATTGAAGACCTT
1 CCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGACCTT
25812936 TCTTTTACCA
Statistics
Matches: 181, Mismatches: 26, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
41 54 0.30
42 19 0.10
43 89 0.49
44 19 0.10
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (43 bp):
CCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGACCTT
Found at i:25815808 original size:12 final size:12
Alignment explanation
Indices: 25815791--25815823 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
25815781 TTTGCTACCC
25815791 GAAATTCTTAAA
1 GAAATTCTTAAA
25815803 GAAATTCTTAAA
1 GAAATTCTTAAA
25815815 GAAATTCTT
1 GAAATTCTT
25815824 TTTCTTCTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (12 bp):
GAAATTCTTAAA
Found at i:25817889 original size:23 final size:22
Alignment explanation
Indices: 25817835--25817889 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 22
25817825 AGTGTTGAGC
25817835 AACAGTAAGCACACACAGTGCG
1 AACAGTAAGCACACACAGTGCG
25817857 AATCAGTAAGCACACACAGTGCTG
1 AA-CAGTAAGCACACACAGTGC-G
*
25817881 AACAATAAG
1 AACAGTAAG
25817890 TGCGCTAGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 2 0.07
23 25 0.83
24 3 0.10
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.13
Consensus pattern (22 bp):
AACAGTAAGCACACACAGTGCG
Found at i:25821551 original size:26 final size:26
Alignment explanation
Indices: 25821517--25821861 Score: 291
Period size: 26 Copynumber: 13.3 Consensus size: 26
25821507 GTACATAGTA
*
25821517 CCTGCTAAA-AATTTACCGGCTCAAAG
1 CCTGCTAAATAA-TCACCGGCTCAAAG
*
25821543 CCTACTAAATAATCACCGGCTCAAAG
1 CCTGCTAAATAATCACCGGCTCAAAG
* * * *
25821569 CCTTCTATATAATCACCGGCTTAAAA
1 CCTGCTAAATAATCACCGGCTCAAAG
*
25821595 CCTGCTAAGTAATCACCGGCTCAAAG
1 CCTGCTAAATAATCACCGGCTCAAAG
* * * * *
25821621 CTTGCTAAAGAACCACCAGCTCGAAG
1 CCTGCTAAATAATCACCGGCTCAAAG
* * *
25821647 TCTACTAAATAATCACGGGCTCAAAG
1 CCTGCTAAATAATCACCGGCTCAAAG
* * * *
25821673 CCTACAAAACAATCACCGACTCAAAG
1 CCTGCTAAATAATCACCGGCTCAAAG
* * *
25821699 CCTGTTAAATAATCTCTGGCTCAAAG
1 CCTGCTAAATAATCACCGGCTCAAAG
* *
25821725 CCTGCTAAGTAATCACCAAG-TCAAAG
1 CCTGCTAAATAATCACC-GGCTCAAAG
* * * *
25821751 CTTGCTAAATAAACATCAGCTCAAAG
1 CCTGCTAAATAATCACCGGCTCAAAG
* * * *
25821777 TCTGTTAAATAACCACCAGCTCAAAG
1 CCTGCTAAATAATCACCGGCTCAAAG
* *
25821803 CCTCCTAAGTAATCA-CGGACTCAAAG
1 CCTGCTAAATAATCACCGG-CTCAAAG
* * * **
25821829 CTTGCTAAGTAATCACCGGTTCATGG
1 CCTGCTAAATAATCACCGGCTCAAAG
25821855 CCTGCTA
1 CCTGCTA
25821862 TTTAAGTACA
Statistics
Matches: 251, Mismatches: 63, Indels: 10
0.77 0.19 0.03
Matches are distributed among these distances:
25 4 0.02
26 241 0.96
27 6 0.02
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.22
Consensus pattern (26 bp):
CCTGCTAAATAATCACCGGCTCAAAG
Found at i:25824143 original size:90 final size:89
Alignment explanation
Indices: 25823981--25824223 Score: 295
Period size: 90 Copynumber: 2.8 Consensus size: 89
25823971 TACTAAAAAT
* * *
25823981 TCCTC-AA-TTTTTTAAAAGAAAGCGATTAAGTCCC-TACTTTTATTTTGTACTCAATTGGATAT
1 TCCTCAAACTTTTTT-AAAGAAAGCAATTAAG-CCCTTAC-TTTATTTTGCACTCAATTGGATAC
* *
25824043 TTGAATTTTCAAAATGTATTAAAAAG-
63 TTGAACTTTCAAAATGTATCAAAAAGA
*
25824069 GCTCTCAAACTTTTTTCAAAGAAAGCAATTAAGCCCTTACTTTATTTTGCACTCAATTGGATACT
1 TC-CTCAAACTTTTTT-AAAGAAAGCAATTAAGCCCTTACTTTATTTTGCACTCAATTGGATACT
25824134 TGAACTTTCAAAATGTATCAAAAAGA
64 TGAACTTTCAAAATGTATCAAAAAGA
* * * *
25824160 TCCTCAAAC-TTTTT-AA-AAAGCAATTAACCCCTGA-TTTTTTTTGCACTCAATTGGGTACTTG
1 TCCTCAAACTTTTTTAAAGAAAGCAATTAAGCCCTTACTTTATTTTGCACTCAATTGGATACTTG
25824221 AAC
66 AAC
25824224 ATCCCCTAAT
Statistics
Matches: 138, Mismatches: 12, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
85 28 0.20
86 16 0.12
87 2 0.01
88 1 0.01
89 8 0.06
90 58 0.42
91 25 0.18
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.37
Consensus pattern (89 bp):
TCCTCAAACTTTTTTAAAGAAAGCAATTAAGCCCTTACTTTATTTTGCACTCAATTGGATACTTG
AACTTTCAAAATGTATCAAAAAGA
Done.