Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 123 of 210
Found at i:41364095 original size:17 final size:17
Alignment explanation
Indices: 41364073--41364108 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
41364063 ATCATGCAAA
*
41364073 AACAATTTAAAGTAAAT
1 AACAATTTAAAATAAAT
41364090 AACAATTTAAAATAAAT
1 AACAATTTAAAATAAAT
41364107 AA
1 AA
41364109 TTTACAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.28
Consensus pattern (17 bp):
AACAATTTAAAATAAAT
Found at i:41365888 original size:44 final size:42
Alignment explanation
Indices: 41365837--41366107 Score: 162
Period size: 44 Copynumber: 6.3 Consensus size: 42
41365827 CTGCAACATC
*
41365837 AGGGAGATAGGATTGGTTTTTTTCTGCCTGCTCCACTACTGCTT
1 AGGGAGATAAGATTGG--TTTTTCTGCCTGCTCCACTACTGCTT
** ** **
41365881 AGGGAGATAAGATCTATGGTTTTAAT-CC-GCTCCACCGCAACTT
1 AGGGAGATAAGA--T-TGGTTTTTCTGCCTGCTCCACTACTGCTT
* *
41365924 CAGGGAGATAGGATTGGATTTTTCTGTCTGCTCCACTACTGCTT
1 -AGGGAGATAAGATTGG-TTTTTCTGCCTGCTCCACTACTGCTT
* * * *
41365968 AGGGAGATAAAACTT-G--ATGC-GATCTGCTCCACTACTGCTT
1 AGGGAGATAAGA-TTGGTTTTTCTG-CCTGCTCCACTACTGCTT
* ** * **
41366008 AAGGAGATAAGATCTGTGGTTTTAAT-CC-GCTCCACTGCAACTTT
1 AGGGAGATAAGA--T-TGGTTTTTCTGCCTGCTCCACTACTGC-TT
* *
41366052 AGGGAGATAGGATTGGTTTTTTTCTGTCTGCTCCACTACTGCTT
1 AGGGAGATAAGATTGG--TTTTTCTGCCTGCTCCACTACTGCTT
41366096 AGGGAGATAAGA
1 AGGGAGATAAGA
41366108 CTTGATGCGA
Statistics
Matches: 170, Mismatches: 37, Indels: 40
0.69 0.15 0.16
Matches are distributed among these distances:
39 1 0.01
40 30 0.18
41 8 0.05
42 8 0.05
43 39 0.23
44 64 0.38
45 16 0.09
46 1 0.01
47 3 0.02
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (42 bp):
AGGGAGATAAGATTGGTTTTTCTGCCTGCTCCACTACTGCTT
Found at i:41366144 original size:128 final size:128
Alignment explanation
Indices: 41365867--41366203 Score: 550
Period size: 128 Copynumber: 2.6 Consensus size: 128
41365857 TTTCTGCCTG
* *
41365867 CTCCACTACTGCTTAGGGAGATAAGATCTATGGTTTTAATCCGCTCCACCGCAACTTCAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGA
* * *
41365932 TAGGATTGG-ATTTTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAAACTTGATGCGATCTG
66 TAGGATTGGTTTTTTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAAACTTGATGCGACCTA
* *
41365994 CTCCACTACTGCTTAAGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGA
*
41366059 TAGGATTGGTTTTTTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGACCTA
66 TAGGATTGGTTTTTTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAAACTTGATGCGACCTA
* * * *
41366122 CTCTACTACTACTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTACAACTTCAAGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGA
*
41366187 TAGGATTAGTTTTTTTC
66 TAGGATTGGTTTTTTTC
41366204 AAATTGACTG
Statistics
Matches: 194, Mismatches: 15, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
127 70 0.36
128 124 0.64
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.33
Consensus pattern (128 bp):
CTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGA
TAGGATTGGTTTTTTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAAACTTGATGCGACCTA
Found at i:41366298 original size:50 final size:50
Alignment explanation
Indices: 41366210--41367611 Score: 793
Period size: 50 Copynumber: 28.1 Consensus size: 50
41366200 TTTCAAATTG
* * * * *
41366210 ACTGCAATGTCGGGGAA-CAAGATTCGCCGTCGTAGCTTCAATCTATTCC
1 ACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTCA
** * * * * *
41366259 ACTGCACCGTCAGGGAAGTAAGATTCACCGTTGCGGCTTCAATATTTTTA
1 ACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTCA
* * * ** * ** *
41366309 ATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTATCTTTAATCTGCTCC
1 ACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTCA
* * * * *
41366359 ACTGCATTGCCAGGGAAGTAAGATTCGCCGTTGCGGC-TCTAATCTTTTAA
1 ACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTC-AATCTTTTCA
* * * * * * ** *
41366409 ATTGCAATGTCAGAGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCT
1 ACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTCA
** * * * *
41366459 ACTGCACCGCCAGGGAGGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTA
1 ACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTCA
* * * * * * * *
41366509 ATTGTAATGTCGGGGAAGCAAGATTCGCTGTCGTAGCTTCAATCTGTTCC
1 ACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTCA
** * * * * *
41366559 ACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGCGGC-TCTAATATTTTAA
1 ACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTC-AATCTTTTCA
* * * * * * * ** *
41366609 ATTGCAATGTC-GGAGAAGCAAGATTTGCCGTCGTAGATTTATTCTGCTCT
1 ACTGCAATGTCAGG-GAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTCA
* * * * * *
41366659 ACTGCACTGCCAGGGAGGTAAGATTCACCGTTGTGGCTTCAAT-TTTTTA
1 ACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTCA
* * * * * ** *
41366708 ATTGCAATGTC-GTGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCC
1 ACTGCAATGTCAG-GGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTCA
* * * ** *
41366758 ACTGC-ATCGCCAGGGAAGTAAGATTCGTCGTTACGGCTTCAATCTTTTTA
1 ACTGCAAT-GTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTCA
* * * * * ** *
41366808 ATTGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTCC
1 ACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTCA
* * *
41366858 ACTGC-ATCGTCAGGGAAGTAAGATTCGTCGTTGCGGCTTCAATCTTTT-A
1 ACTGCAAT-GTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTCA
* * * * * ** *
41366907 ATTGTAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGCTCC
1 ACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTCA
** * * * *
41366957 ACTGC-ATCACCAGGGAAGTAAGATTCGCTGTTGCGGC-TCTAATCTTTTAA
1 ACTGCAAT-GTCAGGGAAGCAAGATTCGCCGTTGTGGCTTC-AATCTTTTCA
* * * * * * ** *
41367007 ATTGCAATGTCAGAGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCT
1 ACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTCA
** * * * * *
41367057 ACTGCACCG-CGAGGGAGGTAAGATTCACCGTTGTGGCTTTAATCTTTTTA
1 ACTGCAATGTC-AGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTCA
* * ** * * ** *
41367107 ATTGCAATGTCGGGGAAGCAAGATTCGCCGTCATAGCTTTAATCTACTCT
1 ACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTCA
** * * * * * * *
41367157 ACTGCACCGCCAGAGAGGTAAGATTTGCTGTTGTGGCTTCAAT-TTTTTA
1 ACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTCA
* * * * ** *
41367206 ATTGCAATGTCAGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTACTCC
1 ACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTCA
* * * * *
41367256 ACTGCATTGCCAGGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTA
1 ACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTCA
* * * * * * ** *
41367306 ATTGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCC
1 ACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTCA
* * * *
41367356 ACTGC-ATCGCCAGGGAAGTAAGATTTGCCGTTGCGGCTTCAATCTTTT-A
1 ACTGCAAT-GTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTCA
* * * * * *
41367405 ATTTGCAATGTCGGGGAAGCAAGATTCACCGTTGCGGCTTCAATATTTTAA
1 A-CTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTCA
* ** * * * * * *
41367456 ATTAAAATTTCAGGGAAGCAAGATTCGTCATTGTAGCTTCAATCTGTTCC
1 ACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTCA
* * * * * * *
41367506 ACCGC-ATCGCCAGAGAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTAA
1 ACTGCAAT-GTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTCA
* * * * * * *
41367556 ATTACAATGTCAGGGAAGCAAGATTCACCGTTATAGCTTCAATCTATTCC
1 ACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTCA
41367606 ACTGCA
1 ACTGCA
41367612 TCGCCAGAGA
Statistics
Matches: 954, Mismatches: 371, Indels: 55
0.69 0.27 0.04
Matches are distributed among these distances:
48 1 0.00
49 135 0.14
50 801 0.84
51 17 0.02
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (50 bp):
ACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTCA
Found at i:41366384 original size:100 final size:100
Alignment explanation
Indices: 41366212--41367436 Score: 1710
Period size: 100 Copynumber: 12.3 Consensus size: 100
41366202 TCAAATTGAC
* ** *
41366212 TGCAATGTCGGGGAA-CAAGATTCGCCGTCGTAGCTTCAATCTATTCCACTGCACCGTCAGGGAA
1 TGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTCCACTGCACCGCCAGGGAA
* *
41366276 GTAAGATTCACCGTTGCGGCTTCAATATTTTTAAT
66 GTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAAT
* * * **
41366311 TGCAATGTCGGGGAAGCAAGATTCACCGTTGTATCTTTAATCTGCTCCACTGCATTGCCAGGGAA
1 TGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTCCACTGCACCGCCAGGGAA
*
41366376 GTAAGATTCGCCGTTGCGGC-TCTAATCTTTTAAAT
66 GTAAGATTCGCCGTTGCGGCTTC-AATCTTTTTAAT
* * * * *
41366411 TGCAATGTCAGAGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCTACTGCACCGCCAGGGAG
1 TGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTCCACTGCACCGCCAGGGAA
*
41366476 GTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAAT
66 GTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAAT
* * * *
41366511 TGTAATGTCGGGGAAGCAAGATTCGCTGTCGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAA
1 TGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTCCACTGCACCGCCAGGGAA
* *
41366576 GTAAGATTCGCCGTTGCGGC-TCTAATATTTTAAAT
66 GTAAGATTCGCCGTTGCGGCTTC-AATCTTTTTAAT
* * * * * * *
41366611 TGCAATGTCGGAGAAGCAAGATTTGCCGTCGTAGATTTATTCTGCTCTACTGCACTGCCAGGGAG
1 TGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTCCACTGCACCGCCAGGGAA
* *
41366676 GTAAGATTCACCGTTGTGGCTTCAAT-TTTTTAAT
66 GTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAAT
* * *
41366710 TGCAATGTCGTGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCATCGCCAGGGAA
1 TGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTCCACTGCACCGCCAGGGAA
* *
41366775 GTAAGATTCGTCGTTACGGCTTCAATCTTTTTAAT
66 GTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAAT
* *
41366810 TGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTCCACTGCATCGTCAGGGAA
1 TGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTCCACTGCACCGCCAGGGAA
*
41366875 GTAAGATTCGTCGTTGCGGCTTCAATC-TTTTAAT
66 GTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAAT
* * * *
41366909 TGTAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGCTCCACTGCATCACCAGGGAA
1 TGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTCCACTGCACCGCCAGGGAA
* *
41366974 GTAAGATTCGCTGTTGCGGC-TCTAATCTTTTAAAT
66 GTAAGATTCGCCGTTGCGGCTTC-AATCTTTTTAAT
* * * * * *
41367009 TGCAATGTCAGAGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCTACTGCACCGCGAGGGAG
1 TGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTCCACTGCACCGCCAGGGAA
* * *
41367074 GTAAGATTCACCGTTGTGGCTTTAATCTTTTTAAT
66 GTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAAT
* * * * *
41367109 TGCAATGTCGGGGAAGCAAGATTCGCCGTCATAGCTTTAATCTACTCTACTGCACCGCCAGAGAG
1 TGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTCCACTGCACCGCCAGGGAA
* * *
41367174 GTAAGATTTGCTGTTGTGGCTTCAAT-TTTTTAAT
66 GTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAAT
* * **
41367208 TGCAATGTCAGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTACTCCACTGCATTGCCAGGGAA
1 TGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTCCACTGCACCGCCAGGGAA
41367273 GTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAAT
66 GTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAAT
* *
41367308 TGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCATCGCCAGGGAA
1 TGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTCCACTGCACCGCCAGGGAA
*
41367373 GTAAGATTTGCCGTTGCGGCTTCAATC-TTTTAATT
66 GTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAA-T
*
41367408 TGCAATGTCGGGGAAGCAAGATTCACCGT
1 TGCAATGTCGGGGAAGCAAGATTCGCCGT
41367437 TGCGGCTTCA
Statistics
Matches: 1001, Mismatches: 114, Indels: 21
0.88 0.10 0.02
Matches are distributed among these distances:
98 2 0.00
99 288 0.29
100 706 0.71
101 5 0.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (100 bp):
TGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTCCACTGCACCGCCAGGGAA
GTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAAT
Found at i:41366809 original size:299 final size:300
Alignment explanation
Indices: 41366212--41367436 Score: 1793
Period size: 299 Copynumber: 4.1 Consensus size: 300
41366202 TCAAATTGAC
* *
41366212 TGCAATGTCGGGGAA-CAAGATTCGCCGTCGTAGCTTCAATCTATTCCACTGCACCGTCAGGGAA
1 TGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTCAATCTACTCCACTGCACCGCCAGGGAA
* * *
41366276 GTAAGATTCACCGTTGCGGCTTCAATATTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTT
66 GTAAGATTCGCCGTTGCGGCTTCAATATTTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTC
*
41366341 GTATCTTTAATCTGCTCCACTGCATTGCCAGGGAAGTAAGATTCGCCGTTGCGGCTCTAATCTTT
131 GTAGCTTTAATCTGCTCCACTGCATTGCCAGGGAAGTAAGATTCGCCGTTGCGGCTCTAATCTTT
*
41366406 TAAATTGCAATGTCAGAGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCTACTGCACCGCCA
196 TAAATTGCAATGTCAGAGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCACCGCCA
* *
41366471 GGGAGGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAAT
261 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAAT
* * **
41366511 TGTAATGTCGGGGAAGCAAGATTCGCTGTCGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAA
1 TGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTCAATCTACTCCACTGCACCGCCAGGGAA
* * *
41366576 GTAAGATTCGCCGTTGCGGC-TCTAATATTTTAAATTGCAATGTCGGAGAAGCAAGATTTGCCGT
66 GTAAGATTCGCCGTTGCGGCTTC-AATATTTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGT
* * * * * * *
41366640 CGTAGATTTATTCTGCTCTACTGCACTGCCAGGGAGGTAAGATTCACCGTTGTGGCT-TCAAT-T
130 CGTAGCTTTAATCTGCTCCACTGCATTGCCAGGGAAGTAAGATTCGCCGTTGCGGCTCT-AATCT
* * *
41366703 TTTTAATTGCAATGTC-GTGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCATCG
194 TTTAAATTGCAATGTCAG-AGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCACCG
* *
41366767 CCAGGGAAGTAAGATTCGTCGTTACGGCTTCAATCTTTTTAAT
258 CCAGGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAAT
* * * *
41366810 TGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTCCACTGCATCGTCAGGGAA
1 TGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTCAATCTACTCCACTGCACCGCCAGGGAA
* * * *
41366875 GTAAGATTCGTCGTTGCGGCTTCAAT-CTTTTAATTGTAATGTCGGGGAAGCAAGATTCGCCGTT
66 GTAAGATTCGCCGTTGCGGCTTCAATATTTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTC
** *
41366939 GTAGCTTTAATCTGCTCCACTGCATCACCAGGGAAGTAAGATTCGCTGTTGCGGCTCTAATCTTT
131 GTAGCTTTAATCTGCTCCACTGCATTGCCAGGGAAGTAAGATTCGCCGTTGCGGCTCTAATCTTT
* *
41367004 TAAATTGCAATGTCAGAGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCTACTGCACCGCGA
196 TAAATTGCAATGTCAGAGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCACCGCCA
* * * *
41367069 GGGAGGTAAGATTCACCGTTGTGGCTTTAATCTTTTTAAT
261 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAAT
* * * * *
41367109 TGCAATGTCGGGGAAGCAAGATTCGCCGTCATAGCTTTAATCTACTCTACTGCACCGCCAGAGAG
1 TGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTCAATCTACTCCACTGCACCGCCAGGGAA
* * * *
41367174 GTAAGATTTGCTGTTGTGGCTTCAAT-TTTTTAATTGCAATGTCAGGGAAGCAAGATTCGCCGTC
66 GTAAGATTCGCCGTTGCGGCTTCAATATTTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTC
*
41367238 GTAGCTTTAATCTACTCCACTGCATTGCCAGGGAAGTAAGATTCGCCGTTGCGGCT-TCAATCTT
131 GTAGCTTTAATCTGCTCCACTGCATTGCCAGGGAAGTAAGATTCGCCGTTGCGGCTCT-AATCTT
* * * *
41367302 TTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCATCGCC
195 TTAAATTGCAATGTCAGAGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCACCGCC
*
41367367 AGGGAAGTAAGATTTGCCGTTGCGGCTTCAATC-TTTTAATT
260 AGGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAA-T
*
41367408 TGCAATGTCGGGGAAGCAAGATTCACCGT
1 TGCAATGTCGGGGAAGCAAGATTCGCCGT
41367437 TGCGGCTTCA
Statistics
Matches: 825, Mismatches: 91, Indels: 20
0.88 0.10 0.02
Matches are distributed among these distances:
298 89 0.11
299 580 0.70
300 156 0.19
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (300 bp):
TGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTCAATCTACTCCACTGCACCGCCAGGGAA
GTAAGATTCGCCGTTGCGGCTTCAATATTTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTC
GTAGCTTTAATCTGCTCCACTGCATTGCCAGGGAAGTAAGATTCGCCGTTGCGGCTCTAATCTTT
TAAATTGCAATGTCAGAGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCACCGCCA
GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAAT
Found at i:41366819 original size:199 final size:200
Alignment explanation
Indices: 41366212--41367436 Score: 1737
Period size: 199 Copynumber: 6.1 Consensus size: 200
41366202 TCAAATTGAC
* * ** *
41366212 TGCAATGTCGGGGAA-CAAGATTCGCCGTCGTAGCTTCAATCTATTCCACTGCACCGTCAGGGAA
1 TGCAATGTCGGAGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTCCACTGCACCGCCAGGGAA
* *
41366276 GTAAGATTCACCGTTGCGGCTTCAATATTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTT
66 GTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTC
* *
41366341 GTATCTTTAATCTGCTCCACTGCATTGCCAGGGAAGTAAGATTCGCCGTTGCGGCTCTAATCTTT
131 GTAGCTTTAATCTGCTCCACTGCATCGCCAGGGAAGTAAGATTCGCCGTTGCGGCTCTAATCTTT
41366406 TAAAT
196 TAAAT
* * * *
41366411 TGCAATGTCAGAGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCTACTGCACCGCCAGGGAG
1 TGCAATGTCGGAGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTCCACTGCACCGCCAGGGAA
* * * * *
41366476 GTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGTAATGTCGGGGAAGCAAGATTCGCTGTC
66 GTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTC
* * * *
41366541 GTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGCGGCTCTAATATTT
131 GTAGCTTTAATCTGCTCCACTGCATCGCCAGGGAAGTAAGATTCGCCGTTGCGGCTCTAATCTTT
41366606 TAAAT
196 TAAAT
* * * * * *
41366611 TGCAATGTCGGAGAAGCAAGATTTGCCGTCGTAGATTTATTCTGCTCTACTGCACTGCCAGGGAG
1 TGCAATGTCGGAGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTCCACTGCACCGCCAGGGAA
* *
41366676 GTAAGATTCACCGTTGTGGCTTCAAT-TTTTTAATTGCAATGTCGTGGAAGCAAGATTCACCGTC
66 GTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTC
* *
41366740 GTAGCTTTAATCTGCTCCACTGCATCGCCAGGGAAGTAAGATTCGTCGTTACGGCT-TCAATCTT
131 GTAGCTTTAATCTGCTCCACTGCATCGCCAGGGAAGTAAGATTCGCCGTTGCGGCTCT-AATCTT
*
41366804 TTTAAT
195 TTAAAT
* * *
41366810 TGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTCCACTGCATCGTCAGGGAA
1 TGCAATGTCGGAGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTCCACTGCACCGCCAGGGAA
** * * *
41366875 GTAAGATTCGTCGTTGCGGCTTCAATC-TTTTAATTGTAATGTCGGGGAAGCAAGATTCGCCGTT
66 GTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTC
* *
41366939 GTAGCTTTAATCTGCTCCACTGCATCACCAGGGAAGTAAGATTCGCTGTTGCGGCTCTAATCTTT
131 GTAGCTTTAATCTGCTCCACTGCATCGCCAGGGAAGTAAGATTCGCCGTTGCGGCTCTAATCTTT
41367004 TAAAT
196 TAAAT
* * * * *
41367009 TGCAATGTCAGAGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCTACTGCACCGCGAGGGAG
1 TGCAATGTCGGAGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTCCACTGCACCGCCAGGGAA
* * *
41367074 GTAAGATTCACCGTTGTGGCTTTAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTC
66 GTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTC
* * * * * * * * *
41367139 ATAGCTTTAATCTACTCTACTGCACCGCCAGAGAGGTAAGATTTGCTGTTGTGGCT-TCAAT-TT
131 GTAGCTTTAATCTGCTCCACTGCATCGCCAGGGAAGTAAGATTCGCCGTTGCGGCTCT-AATCTT
*
41367202 TTTAAT
195 TTAAAT
* **
41367208 TGCAATGTCAGG-GAAGCAAGATTCGCCGTCGTAGCTTTAATCTACTCCACTGCATTGCCAGGGA
1 TGCAATGTC-GGAGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTCCACTGCACCGCCAGGGA
*
41367272 AGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGT
65 AGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGT
*
41367337 CGTAGCTTTAATCTGCTCCACTGCATCGCCAGGGAAGTAAGATTTGCCGTTGCGGCT-TCAATCT
130 CGTAGCTTTAATCTGCTCCACTGCATCGCCAGGGAAGTAAGATTCGCCGTTGCGGCTCT-AATCT
*
41367401 TTTAATT
194 TTTAAAT
* *
41367408 TGCAATGTCGGGGAAGCAAGATTCACCGT
1 TGCAATGTCGGAGAAGCAAGATTCGCCGT
41367437 TGCGGCTTCA
Statistics
Matches: 909, Mismatches: 108, Indels: 17
0.88 0.10 0.02
Matches are distributed among these distances:
198 1 0.00
199 542 0.60
200 366 0.40
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (200 bp):
TGCAATGTCGGAGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTCCACTGCACCGCCAGGGAA
GTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTC
GTAGCTTTAATCTGCTCCACTGCATCGCCAGGGAAGTAAGATTCGCCGTTGCGGCTCTAATCTTT
TAAAT
Found at i:41367758 original size:43 final size:43
Alignment explanation
Indices: 41367677--41367841 Score: 206
Period size: 43 Copynumber: 3.8 Consensus size: 43
41367667 AGATCTATTT
* * * *
41367677 TCTTCGATCTACTTTGCC-ACCAGTATGGGAAGACAAGATTTACA
1 TCTTCGATCCAC-TT-CCTACCAATATAGGAAGACAAGATCTACA
* *
41367721 TCTTCGATCCACTTCCTACCAATATAGGAAGATAAGATCTGCA
1 TCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATCTACA
* * * *
41367764 TCTTCGATCTACTCCGCCACCAATATGGGAAGACAAGATCTACA
1 TCTTCGATCCACTTC-CTACCAATATAGGAAGACAAGATCTACA
41367808 TCTTCGATCCACTTCCTACCAATATAGGAAGACA
1 TCTTCGATCCACTTCCTACCAATATAGGAAGACA
41367842 TGACCTGCTA
Statistics
Matches: 103, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
42 2 0.02
43 53 0.51
44 48 0.47
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.27
Consensus pattern (43 bp):
TCTTCGATCCACTTCCTACCAATATAGGAAGACAAGATCTACA
Found at i:41367783 original size:87 final size:88
Alignment explanation
Indices: 41367677--41367864 Score: 297
Period size: 87 Copynumber: 2.1 Consensus size: 88
41367667 AGATCTATTT
** * *
41367677 TCTTCGATCTACTTTGCCACCAGTATGGGAAGACAAGATTTACATCTTCGATCCACTTCCTACCA
1 TCTTCGATCTACTCCGCCACCAATATGGGAAGACAAGATCTACATCTTCGATCCACTTCCTACCA
* *
41367742 ATATAGGAAGATAAGATCTGC-A
66 ATATAGGAAGACAAGACCTGCTA
41367764 TCTTCGATCTACTCCGCCACCAATATGGGAAGACAAGATCTACATCTTCGATCCACTTCCTACCA
1 TCTTCGATCTACTCCGCCACCAATATGGGAAGACAAGATCTACATCTTCGATCCACTTCCTACCA
*
41367829 ATATAGGAAGACATGACCTGCTA
66 ATATAGGAAGACAAGACCTGCTA
*
41367852 TCTCCGATCTACT
1 TCTTCGATCTACT
41367865 TCACGCCAAT
Statistics
Matches: 92, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
87 79 0.86
88 13 0.14
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (88 bp):
TCTTCGATCTACTCCGCCACCAATATGGGAAGACAAGATCTACATCTTCGATCCACTTCCTACCA
ATATAGGAAGACAAGACCTGCTA
Found at i:41367802 original size:44 final size:43
Alignment explanation
Indices: 41367677--41367982 Score: 261
Period size: 44 Copynumber: 7.0 Consensus size: 43
41367667 AGATCTATTT
* * * * *
41367677 TCTTCGATCTACTTTGCCACCAGTATGGGAAGACAAGATTTACA
1 TCTTCGATCTAC-TTCCCACCAATATAGGAAGACAAGATCTGCA
* * *
41367721 TCTTCGATCCACTTCCTACCAATATAGGAAGATAAGATCTGCA
1 TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGCA
* * *
41367764 TCTTCGATCTACTCCGCCACCAATATGGGAAGACAAGATCTACA
1 TCTTCGATCTACTTC-CCACCAATATAGGAAGACAAGATCTGCA
* * * *
41367808 TCTTCGATCCACTTCCTACCAATATAGGAAGACATGACCTGCTA
1 TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGC-A
* * * * * * **
41367852 TCTCCGATCTACTTCACGCCAATACATGAAGATAAGATCTGTTT
1 TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTG-CA
* * * * *
41367896 TCTTCGATCTATTTTGCCACCAGTATGGGAAGACAAGATCCGCA
1 TCTTCGATCTA-CTTCCCACCAATATAGGAAGACAAGATCTGCA
* * * * *
41367940 TTCTTCGATCTACTTCACGCCAATACATGAAGACAAGGTCTGC
1 -TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGC
41367983 TTTAATGACT
Statistics
Matches: 201, Mismatches: 56, Indels: 10
0.75 0.21 0.04
Matches are distributed among these distances:
43 59 0.29
44 111 0.55
45 31 0.15
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (43 bp):
TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGCA
Found at i:41367883 original size:87 final size:86
Alignment explanation
Indices: 41367705--41367976 Score: 296
Period size: 87 Copynumber: 3.1 Consensus size: 86
41367695 ACCAGTATGG
* * *
41367705 GAAGACAAGATTTACATCTTCGATCCACTTCCTACCAATATAGGAAGATAAGATCTGCATCTTCG
1 GAAGACAAGATCTACATCTTCGATCCACTTCCTACCAATATAGGAAGACAAGACCTGCATCTTCG
* * * ***
41367770 ATCTACTCCGCCACCAATATGG
66 ATCTACTTC-ACGCCAATACAT
* *
41367792 GAAGACAAGATCTACATCTTCGATCCACTTCCTACCAATATAGGAAGACATGACCTGCTATCTCC
1 GAAGACAAGATCTACATCTTCGATCCACTTCCTACCAATATAGGAAGACAAGACCTGC-ATCTTC
41367857 GATCTACTTCACGCCAATACAT
65 GATCTACTTCACGCCAATACAT
* *** * * * *
41367879 GAAGATAAGATCTGTTTTCTTCGATCTATTTTGCC-ACCAGTATGGGAAGACAAGATCC-GCATT
1 GAAGACAAGATCT-ACATCTTCGATCCA-CTT-CCTACCAATATAGGAAGACAAGA-CCTGCA-T
41367942 CTTCGATCTACTTCACGCCAATACAT
61 CTTCGATCTACTTCACGCCAATACAT
41367968 GAAGACAAG
1 GAAGACAAG
41367977 GTCTGCTTTA
Statistics
Matches: 157, Mismatches: 22, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
87 73 0.46
88 25 0.16
89 55 0.35
90 4 0.03
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (86 bp):
GAAGACAAGATCTACATCTTCGATCCACTTCCTACCAATATAGGAAGACAAGACCTGCATCTTCG
ATCTACTTCACGCCAATACAT
Found at i:41369388 original size:8 final size:8
Alignment explanation
Indices: 41369375--41369455 Score: 74
Period size: 8 Copynumber: 9.8 Consensus size: 8
41369365 CCGGTAGAGG
41369375 TTTTTTGT
1 TTTTTTGT
41369383 TTTTTTGT
1 TTTTTTGT
*
41369391 CTCTTTTGT
1 -TTTTTTGT
41369400 TCTTTTT-T
1 T-TTTTTGT
41369408 TGTTTTTGT
1 T-TTTTTGT
*
41369417 GTTTTTGGT
1 -TTTTTTGT
*
41369426 TTTTATGT
1 TTTTTTGT
*
41369434 TTTTATGT
1 TTTTTTGT
*
41369442 TTTTGTGT
1 TTTTTTGT
41369450 TTTTTT
1 TTTTTT
41369456 ACCTCTACTG
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
8 42 0.69
9 18 0.30
10 1 0.02
ACGTcount: A:0.02, C:0.04, G:0.15, T:0.79
Consensus pattern (8 bp):
TTTTTTGT
Found at i:41369428 original size:23 final size:24
Alignment explanation
Indices: 41369375--41369455 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 24
41369365 CCGGTAGAGG
* *
41369375 TTTTTTGTTTTTTTGTCTCTTTTGTTCT
1 TTTTTTGTTTTTATG--T-TTTTG-TGT
*
41369403 TTTTTTGTTTTTGTGTTTTTG-GT
1 TTTTTTGTTTTTATGTTTTTGTGT
*
41369426 TTTTATGTTTTTATGTTTTTGTGT
1 TTTTTTGTTTTTATGTTTTTGTGT
41369450 TTTTTT
1 TTTTTT
41369456 ACCTCTACTG
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
23 20 0.43
24 7 0.15
25 5 0.11
26 1 0.02
28 14 0.30
ACGTcount: A:0.02, C:0.04, G:0.15, T:0.79
Consensus pattern (24 bp):
TTTTTTGTTTTTATGTTTTTGTGT
Found at i:41372910 original size:17 final size:17
Alignment explanation
Indices: 41372888--41372923 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
41372878 ATCATGCAAA
* *
41372888 AACAATTTTAAGTAAAT
1 AACAATTTAAAATAAAT
41372905 AACAATTTAAAATAAAT
1 AACAATTTAAAATAAAT
41372922 AA
1 AA
41372924 TTTACAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.31
Consensus pattern (17 bp):
AACAATTTAAAATAAAT
Found at i:41375161 original size:19 final size:19
Alignment explanation
Indices: 41375137--41375177 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
41375127 TATTTTAAAG
41375137 TTATTTAGGTAGATAAATC
1 TTATTTAGGTAGATAAATC
41375156 TTATTTAGGTAGATAAATC
1 TTATTTAGGTAGATAAATC
41375175 TTA
1 TTA
41375178 AAATAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.44
Consensus pattern (19 bp):
TTATTTAGGTAGATAAATC
Found at i:41375262 original size:41 final size:41
Alignment explanation
Indices: 41375215--41375296 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
41375205 ATATTTTATT
* *
41375215 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATTTTCC
1 TTATCTTTTAGTACTTTAGTAGAATAAGGGAATTATTTTCC
41375256 TTATCTTTTAGTACTTTAGTAGAATAAGGGAATTATTTTCC
1 TTATCTTTTAGTACTTTAGTAGAATAAGGGAATTATTTTCC
41375297 CAATTAGGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.48
Consensus pattern (41 bp):
TTATCTTTTAGTACTTTAGTAGAATAAGGGAATTATTTTCC
Found at i:41378147 original size:109 final size:107
Alignment explanation
Indices: 41377958--41378187 Score: 334
Period size: 109 Copynumber: 2.1 Consensus size: 107
41377948 TGGATTAAGA
* * * * * * *
41377958 TTTAAGAGGGTATTTGGCTATTTGGTTGGACGAGAAGTCGAAACCCAGCACATTAGGGCGCGTTT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACATTAGGGCACGTTT
41378023 TCTCGAATTTCCAAACGCAAAACACTGCCTTATTTTGAAATT
66 TCTCGAATTTCCAAACGCAAAACACTGCCTTATTTTGAAATT
41378065 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAACACATTAGGGCACGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAG--AAATCGAAACCCAACACATTAGGGCACGT
* * * * *
41378130 TTTTTTGAATTTCCAAACGCAAAATATTGTCTTATTTTGAAATT
64 TTTCTCGAATTTCCAAACGCAAAACACTGCCTTATTTTGAAATT
41378174 TTTAAAAGGATATT
1 TTTAAAAGGATATT
41378188 AGTATGCGTA
Statistics
Matches: 109, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
107 30 0.28
109 79 0.72
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (107 bp):
TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACATTAGGGCACGTTT
TCTCGAATTTCCAAACGCAAAACACTGCCTTATTTTGAAATT
Found at i:41379281 original size:11 final size:11
Alignment explanation
Indices: 41379265--41379307 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
41379255 TTCGGCGCAC
41379265 CTCCGCCGTAG
1 CTCCGCCGTAG
* *
41379276 CTCCGCCGCAC
1 CTCCGCCGTAG
*
41379287 CTCCGCCATAG
1 CTCCGCCGTAG
41379298 CTCCGCCGTA
1 CTCCGCCGTA
41379308 AGCGGCGGCC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.12, C:0.51, G:0.21, T:0.16
Consensus pattern (11 bp):
CTCCGCCGTAG
Found at i:41379288 original size:22 final size:22
Alignment explanation
Indices: 41379260--41379305 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
41379250 AAGGCTTCGG
*
41379260 CGCACCTCCGCCGTAGCTCCGC
1 CGCACCTCCGCCATAGCTCCGC
41379282 CGCACCTCCGCCATAGCTCCGC
1 CGCACCTCCGCCATAGCTCCGC
41379304 CG
1 CG
41379306 TAAGCGGCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.11, C:0.54, G:0.22, T:0.13
Consensus pattern (22 bp):
CGCACCTCCGCCATAGCTCCGC
Found at i:41383807 original size:74 final size:77
Alignment explanation
Indices: 41383710--41383942 Score: 251
Period size: 78 Copynumber: 3.0 Consensus size: 77
41383700 CAATTCTCCA
*
41383710 CATGGTATCAAATGTTTTTGGTTCTTTCCT-AG-GTGTTT-TTTTTCTGGTCAAATTCTTGCTTC
1 CATGGTATCAGATGTTTTTGGTTCTTTCCTAAGAGTGTTTCTTTTTCTGGTCAAATTCTTGCTTC
*
41383772 TCGTGTTTATTC
66 TCCTGTTTATTC
* * *
41383784 CATGATATCAGATGTTTTTGGTTCTTTCCTAAGAAGTGTTTCTTTTCCTGGTTGAAA-TCTTGCT
1 CATGGTATCAGATGTTTTTGGTTCTTTCCTAAG-AGTGTTTCTTTTTCTGG-TCAAATTCTTGCT
* * **
41383848 TATCTTGTCCATTC
64 TCTCCTGTTTATTC
* * * * *
41383862 CATGGTATCAGATATTTTTGGTCCCTTT-CTAAGAAGAGTTTCTTTTTCTTGGTCGAGTTCTTGC
1 CATGGTATCAGATGTTTTTGGT-TCTTTCCTAAG-AGTGTTTCTTTTTC-TGGTCAAATTCTTGC
41383926 TTCTCCTGTTCTATTC
63 TTCTCCTGTT-TATTC
41383942 C
1 C
41383943 CAAGTTCTTT
Statistics
Matches: 130, Mismatches: 20, Indels: 12
0.80 0.12 0.07
Matches are distributed among these distances:
74 28 0.22
75 2 0.02
77 6 0.05
78 65 0.50
79 24 0.18
80 5 0.04
ACGTcount: A:0.15, C:0.18, G:0.17, T:0.49
Consensus pattern (77 bp):
CATGGTATCAGATGTTTTTGGTTCTTTCCTAAGAGTGTTTCTTTTTCTGGTCAAATTCTTGCTTC
TCCTGTTTATTC
Found at i:41393707 original size:32 final size:32
Alignment explanation
Indices: 41393659--41393720 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
41393649 ATGATTTGAT
*
41393659 TTGTATTAAACCAGAAGTCA-AGATAAGGAACA
1 TTGTATTAAACAAGAAGTCACA-ATAAGGAACA
*
41393691 TTGTCTTAAACAAGAAGTCACAATAAGGAA
1 TTGTATTAAACAAGAAGTCACAATAAGGAA
41393721 ACACGGAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 26 0.96
33 1 0.04
ACGTcount: A:0.47, C:0.13, G:0.18, T:0.23
Consensus pattern (32 bp):
TTGTATTAAACAAGAAGTCACAATAAGGAACA
Found at i:41394639 original size:13 final size:13
Alignment explanation
Indices: 41394621--41394646 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41394611 CAAAATTTCT
41394621 TCAAAATTTAGCA
1 TCAAAATTTAGCA
41394634 TCAAAATTTAGCA
1 TCAAAATTTAGCA
41394647 AAAAAACTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TCAAAATTTAGCA
Found at i:41394881 original size:20 final size:21
Alignment explanation
Indices: 41394848--41394886 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
41394838 TTAATTTTAA
*
41394848 TTTTTGAATATTATTTAATAT
1 TTTTTGAATATTATGTAATAT
*
41394869 TTTTTTAAT-TTATGTAAT
1 TTTTTGAATATTATGTAAT
41394887 TTTAATTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (21 bp):
TTTTTGAATATTATGTAATAT
Found at i:41395852 original size:7 final size:7
Alignment explanation
Indices: 41395840--41395864 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41395830 AGTTGTTTCA
41395840 TATTTAG
1 TATTTAG
41395847 TATTTAG
1 TATTTAG
41395854 TATTTAG
1 TATTTAG
41395861 TATT
1 TATT
41395865 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:41396474 original size:18 final size:18
Alignment explanation
Indices: 41396451--41396493 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
41396441 TGCCAGGTGC
* *
41396451 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTACAT
41396469 GTATCCTAACCCTTACAT
1 GTATCCTAACCCTTACAT
*
41396487 GTTTCCT
1 GTATCCT
41396494 TTTCCCAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.30, G:0.09, T:0.40
Consensus pattern (18 bp):
GTATCCTAACCCTTACAT
Found at i:41400397 original size:127 final size:126
Alignment explanation
Indices: 41400002--41400396 Score: 591
Period size: 127 Copynumber: 3.1 Consensus size: 126
41399992 GGCCAAACAT
* ** * * *
41400002 GAACTACTGTAGAAAAAAAGTATCCACGTAGGTG-TTTTTTCAGT-AATTTTGCTAACAGTGCAT
1 GAACTACTGTAGAAAAAGAGCGTCCATGTAGGAGCTTTTTTCA-TCAATTTTGCTGACAGTGCAT
* * * *
41400065 CCTACTTGAAGCGTTTTTTTACACTATTTGTTTAGAAACATCTTCTCAAAATTATTTTTT-AG
65 CCTGCTTGAAGC-ATTTTTTACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAG
41400127 GAACTACTGTAGAAAAAGAGCGTCCATGTAGGAGCTTTTTTCATCAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCATGTAGGAGCTTTTTTCATCAATTTTGCTGACAGTGCATC
* * *
41400192 CTGCTTGAAGCATTTCTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTTCAA
66 CTGCTTGAAGCATTTTTTACACTATTTGTTCAGAAACGTCTTCTCAAAATTA-TTTTTTCAG
*
41400254 GAACTACTGTAGAAAAAGAGCGTCCATGTGGGAGCTTTTTTCATCAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCATGTAGGAGCTTTTTTCATCAATTTTGCTGACAGTGCATC
41400319 CTGCTTGAAGCATTTTTTACACTATTTGTTCA-AAACCGTCTTCTCAAAATTATTTTTTCAG
66 CTGCTTGAAGCATTTTTTACACTATTTGTTCAGAAA-CGTCTTCTCAAAATTATTTTTTCAG
*
41400380 GAACTACTATAGAAAAA
1 GAACTACTGTAGAAAAA
41400397 ACCAAAATCC
Statistics
Matches: 247, Mismatches: 18, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
125 66 0.27
126 70 0.28
127 111 0.45
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAGCGTCCATGTAGGAGCTTTTTTCATCAATTTTGCTGACAGTGCATC
CTGCTTGAAGCATTTTTTACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAG
Found at i:41400513 original size:34 final size:33
Alignment explanation
Indices: 41400467--41400566 Score: 119
Period size: 34 Copynumber: 3.0 Consensus size: 33
41400457 TTTTTTTAAA
*
41400467 ACTAAACTCAAATTTAATTAATTTTCTTAAAAAC
1 ACTAAACCCAAATTTAATTAATTTT-TTAAAAAC
* *
41400501 ACTAAACCCAAATTTAACTAATTTATTTAAAACC
1 ACTAAACCCAAATTTAATTAATTT-TTTAAAAAC
* * * *
41400535 CCTAAATCCTAATTTAATTAATTTTTAAAAAA
1 ACTAAACCCAAATTTAATTAATTTTTTAAAAA
41400567 GAACACTAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
33 6 0.11
34 49 0.88
35 1 0.02
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (33 bp):
ACTAAACCCAAATTTAATTAATTTTTTAAAAAC
Found at i:41407008 original size:18 final size:18
Alignment explanation
Indices: 41406967--41407010 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
41406957 TTCTTTCTTA
41406967 TTATTTTAAATTTTTTAT
1 TTATTTTAAATTTTTTAT
41406985 TATATTTT-AATTGTTTTAT
1 T-TATTTTAAATT-TTTTAT
41407004 TTATTTT
1 TTATTTT
41407011 GTTAAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (18 bp):
TTATTTTAAATTTTTTAT
Found at i:41413083 original size:16 final size:18
Alignment explanation
Indices: 41413057--41413091 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
41413047 TAGGATTGGG
41413057 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
41413074 TTGA-AAAATTAATTTAA
1 TTGAGAAAATTAATTTAA
41413091 T
1 T
41413092 AAATAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:41414114 original size:51 final size:51
Alignment explanation
Indices: 41414036--41414223 Score: 177
Period size: 51 Copynumber: 3.7 Consensus size: 51
41414026 CATGAGAACT
* * *
41414036 CATGTGTAGTACTATATGTAGGCTACTATGAGTATAAGATAGTTATGGTCA
1 CATGTGTAGTACTATATGCAGGCTACTATGTGTATAGGATAGTTATGGTCA
* * **
41414087 CATGTGTAGTACTA-AGTGCAGGTTACTATGTATACCGGATAGCTT-TGGTCA
1 CATGTGTAGTACTATA-TGCAGGCTACTATGTGTATAGGATAG-TTATGGTCA
* * * ** * *
41414138 CGTGTATAGTACTATATGCAGGCTACTACGTGTACCGGA-CGGTATTGGTCA
1 CATGTGTAGTACTATATGCAGGCTACTATGTGTATAGGATAGTTA-TGGTCA
*
41414189 CATGTGTAGTACTA-AGTGTAGGCTACTATGTGTAT
1 CATGTGTAGTACTATA-TGCAGGCTACTATGTGTAT
41414224 CGAATAGCAT
Statistics
Matches: 112, Mismatches: 19, Indels: 12
0.78 0.13 0.08
Matches are distributed among these distances:
49 1 0.01
50 3 0.03
51 105 0.94
52 3 0.03
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.34
Consensus pattern (51 bp):
CATGTGTAGTACTATATGCAGGCTACTATGTGTATAGGATAGTTATGGTCA
Found at i:41423173 original size:56 final size:56
Alignment explanation
Indices: 41423087--41423192 Score: 185
Period size: 56 Copynumber: 1.9 Consensus size: 56
41423077 CGAAACTTAA
*
41423087 TCCTATATATCAGGAGTACATCAAAACAGAAAACAAGAGCAAAGAAATTTGAAATC
1 TCCTATATATCAGGAGTACATCAAAACAGAAAACAAAAGCAAAGAAATTTGAAATC
* *
41423143 TCCTATATATTAGGAGTACATCAAAACAGAAAACAAAAGTAAAGAAATTT
1 TCCTATATATCAGGAGTACATCAAAACAGAAAACAAAAGCAAAGAAATTT
41423193 CAAAATATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 47 1.00
ACGTcount: A:0.51, C:0.14, G:0.13, T:0.22
Consensus pattern (56 bp):
TCCTATATATCAGGAGTACATCAAAACAGAAAACAAAAGCAAAGAAATTTGAAATC
Found at i:41426256 original size:27 final size:27
Alignment explanation
Indices: 41426226--41426285 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
41426216 TTGGTGTTCA
*
41426226 CCAGTAGGTTTGGCGAAGCAAGGATCG
1 CCAGTAGGCTTGGCGAAGCAAGGATCG
* *
41426253 CCAGTAGGCTTGGCGAAGTAAGGATTG
1 CCAGTAGGCTTGGCGAAGCAAGGATCG
41426280 CCAGTA
1 CCAGTA
41426286 AGCCTGGTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.27, C:0.18, G:0.35, T:0.20
Consensus pattern (27 bp):
CCAGTAGGCTTGGCGAAGCAAGGATCG
Found at i:41426734 original size:16 final size:15
Alignment explanation
Indices: 41426703--41426742 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
41426693 AAACATCTTA
41426703 AATTAATTTT-AATT
1 AATTAATTTTCAATT
41426717 AATTAATTTCTCAATT
1 AATTAATTT-TCAATT
*
41426733 AAATAATTTT
1 AATTAATTTT
41426743 TCAACCCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 9 0.39
15 2 0.09
16 12 0.52
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (15 bp):
AATTAATTTTCAATT
Found at i:41426746 original size:16 final size:16
Alignment explanation
Indices: 41426700--41426746 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
41426690 AAGAAACATC
41426700 TTAAATTAA-TTTT-AA
1 TTAAA-TAATTTTTCAA
* *
41426715 TTAATTAATTTCTCAA
1 TTAAATAATTTTTCAA
41426731 TTAAATAATTTTTCAA
1 TTAAATAATTTTTCAA
41426747 CCCAATTCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 3 0.12
15 7 0.27
16 16 0.62
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAAATAATTTTTCAA
Found at i:41433071 original size:6 final size:6
Alignment explanation
Indices: 41433060--41433089 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
41433050 TGTTAAATAA
41433060 TATATT TATATT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT
41433090 AAATCACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:41443159 original size:16 final size:16
Alignment explanation
Indices: 41443122--41443157 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
41443112 GTGCATAGAT
41443122 GTAAATAACATGAAAA
1 GTAAATAACATGAAAA
*
41443138 GTAAATAACTTG-AAA
1 GTAAATAACATGAAAA
41443153 GTAAA
1 GTAAA
41443158 ATGAAATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.58, C:0.06, G:0.14, T:0.22
Consensus pattern (16 bp):
GTAAATAACATGAAAA
Found at i:41447012 original size:17 final size:18
Alignment explanation
Indices: 41446985--41447018 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
41446975 TTTCTCGACG
41446985 CTTTATCAAATTTTCTCT
1 CTTTATCAAATTTTCTCT
41447003 CTTT-TCAAATTTTCTC
1 CTTTATCAAATTTTCTC
41447019 AATGCCTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.56
Consensus pattern (18 bp):
CTTTATCAAATTTTCTCT
Found at i:41448780 original size:3 final size:3
Alignment explanation
Indices: 41448728--41448765 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
41448718 CTAGCTTTGC
41448728 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
41448766 ACTCCCATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:41453609 original size:24 final size:24
Alignment explanation
Indices: 41453570--41453623 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
41453560 ATGTCCCAAA
41453570 ATTACAGTAGACTGAACCTTGAAG
1 ATTACAGTAGACTGAACCTTGAAG
* * *
41453594 ATTACAGTGGATTGAACTTTGAAG
1 ATTACAGTAGACTGAACCTTGAAG
41453618 ATTACA
1 ATTACA
41453624 ATGGGGGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (24 bp):
ATTACAGTAGACTGAACCTTGAAG
Found at i:41453950 original size:44 final size:43
Alignment explanation
Indices: 41453895--41454091 Score: 139
Period size: 44 Copynumber: 4.5 Consensus size: 43
41453885 AGTAAAGATA
* * *
41453895 CAATCTTATCTCCCTGAGCAGCATTGGAGTAGGTTGAAGATTG
1 CAATCTTATCTCCCTAAGCAGCATTGGAGCAGATTGAAGATTG
* * *
41453938 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTG
1 CA-ATCTTATCTCCCTAAGCAGCATTGGAGCAGATTGAAGAT--TG
* * * * * ****
41453984 -AATCTTATCTTCCC-AAGGTAGTA-GGGAAGCAAATTTAAGCCAC
1 CAATCTTATC-TCCCTAA-GCAGCATTGG-AGCAGATTGAAGATTG
* * * *
41454027 CAACCTTATCTCCCTGAGCAGCATTGGAGTAGGTTGAAGATTG
1 CAATCTTATCTCCCTAAGCAGCATTGGAGCAGATTGAAGATTG
41454070 CAGATCTTATCTCCCTAAGCAG
1 CA-ATCTTATCTCCCTAAGCAG
41454092 TAGTAGAGCA
Statistics
Matches: 114, Mismatches: 30, Indels: 19
0.70 0.18 0.12
Matches are distributed among these distances:
43 20 0.18
44 73 0.64
45 19 0.17
46 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.27
Consensus pattern (43 bp):
CAATCTTATCTCCCTAAGCAGCATTGGAGCAGATTGAAGATTG
Found at i:41454136 original size:132 final size:133
Alignment explanation
Indices: 41453899--41454213 Score: 490
Period size: 132 Copynumber: 2.4 Consensus size: 133
41453889 AAGATACAAT
41453899 CTTATCTCCCTGAGCAGCATTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGTAGT
1 CTTATCTCCCTGAGCAGCATTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGTAGT
* * * *
41453964 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAAATTTAAGCCACCA
66 AGAGCAGATCAAAGACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAAATTTAAGCCACCA
41454029 -AC
131 GAC
41454031 CTTATCTCCCTGAGCAGCATTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGTAGT
1 CTTATCTCCCTGAGCAGCATTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGTAGT
* *
41454096 AGAGCAGATCAAAGACGGCGAATCTTATCTTCTCAAGGTAGTAGGGAAGCAGATTTAAGCCACCA
66 AGAGCAGATCAAAGACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAAATTTAAGCCACCA
*
41454161 GTC
131 GAC
* *** * * *
41454164 C-TATCTCCCTGAGCAGTAGCAGAGTAAGTCGAAGATTGTAGATCTTATCT
1 CTTATCTCCCTGAGCAGCATTGGAGTAGGTTGAAGATTGCAGATCTTATCT
41454214 TCCTGTACTG
Statistics
Matches: 168, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
132 166 0.99
133 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (133 bp):
CTTATCTCCCTGAGCAGCATTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGTAGT
AGAGCAGATCAAAGACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAAATTTAAGCCACCA
GAC
Found at i:41454278 original size:220 final size:220
Alignment explanation
Indices: 41454024--41454451 Score: 649
Period size: 220 Copynumber: 1.9 Consensus size: 220
41454014 AAATTTAAGC
* * *
41454024 CACCAACCTTATCTCCCTGAGCAGCATTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAG
1 CACCAACCTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCCTATCTCCCTAAG
* *
41454089 CAGTAGTAGAGCAGATCAAAGACGGCGAATCTTATCTTCTCAAGGTAGTAGGGAAGCAGATTTAA
66 CAGTAGTAGAGCAGATCAAAGACGGCGAATCTTATCTTCCCAAGGTAGTAGCGAAGCAGATTTAA
*
41454154 GCCACCAGTCCTATCTCCCTGAGCAGTAGCAGAGTAAGTCGAAGATTGTAGATCTTATCTTCCTG
131 GCCACCAGTCATATCTCCCTGAGCAGTAGCAGAGTAAGTCGAAGATTGTAGATCTTATCTTCCTG
*
41454219 TACTGGCAGTGAATTAGATCAAAAG
196 TACTGGCAATGAATTAGATCAAAAG
* * *
41454244 CACCAGCCTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATCCTGTCTCCCTAAG
1 CACCAACCTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCCTATCTCCCTAAG
* ** * *
41454309 CAGTAGTGGAGCAGATTGAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGCGTAGCAGATTTAA
66 CAGTAGTAGAGCAGATCAAAGACGGCGAATCTTATCTTCCCAAGGTAGTAGCGAAGCAGATTTAA
* * * ** * * *
41454374 GCTACTAGTCATATCTTCCTGAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTG
131 GCCACCAGTCATATCTCCCTGAGCAGTAGCAGAGTAAGTCGAAGATTGTAGATCTTATCTTCCTG
41454439 TACTGGCAATGAA
196 TACTGGCAATGAA
41454452 GCAGATCGAA
Statistics
Matches: 185, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
220 185 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.27
Consensus pattern (220 bp):
CACCAACCTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCCTATCTCCCTAAG
CAGTAGTAGAGCAGATCAAAGACGGCGAATCTTATCTTCCCAAGGTAGTAGCGAAGCAGATTTAA
GCCACCAGTCATATCTCCCTGAGCAGTAGCAGAGTAAGTCGAAGATTGTAGATCTTATCTTCCTG
TACTGGCAATGAATTAGATCAAAAG
Found at i:41454438 original size:44 final size:44
Alignment explanation
Indices: 41454251--41454437 Score: 144
Period size: 44 Copynumber: 4.2 Consensus size: 44
41454241 AAGCACCAGC
* * * *
41454251 CTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGAT
1 CTTATCTTCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAGAT
* * * **
41454295 CCTGTCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGT-GAAT
1 CTTATCTTCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAG-AT
* * * * * * **
41454339 CTTATCTTCCCAAGGTAGTAGCGTAGCAGATTTAAGCTACTAG-T
1 CTTATCTTCCTAA-GCAGTAGTGGAGCAGATTGAAGATTGTAGAT
* * * *
41454383 CATATCTTCCTGAGCAGTAGTGGAGTAGGTTGAAGATTGTAGAT
1 CTTATCTTCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAGAT
*
41454427 CTTGTCTTCCT
1 CTTATCTTCCT
41454438 GTACTGGCAA
Statistics
Matches: 106, Mismatches: 33, Indels: 8
0.72 0.22 0.05
Matches are distributed among these distances:
43 21 0.20
44 65 0.61
45 19 0.18
46 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (44 bp):
CTTATCTTCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAGAT
Found at i:41456251 original size:3 final size:3
Alignment explanation
Indices: 41456243--41456301 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
41456233 GTAGCTTTGC
41456243 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
41456291 ATT ATT ATT AT
1 ATT ATT ATT AT
41456302 ACACATATAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:41458689 original size:21 final size:21
Alignment explanation
Indices: 41458650--41458690 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
41458640 TACATGTAAT
* **
41458650 TATTTTTTTAATAGGAGCTAC
1 TATTTTTTAAATAAAAGCTAC
41458671 TATTTTTTAAATAAAAGCTA
1 TATTTTTTAAATAAAAGCTA
41458691 TTTTTTAATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (21 bp):
TATTTTTTAAATAAAAGCTAC
Found at i:41462953 original size:3 final size:3
Alignment explanation
Indices: 41462947--41462998 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
41462937 TTACATAAAC
41462947 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41462995 ATA A
1 ATA A
41462999 AAAGGGGTGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:41464160 original size:17 final size:18
Alignment explanation
Indices: 41464127--41464160 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
41464117 GTGGGATCGC
41464127 TATGTATATGTTATCTAT
1 TATGTATATGTTATCTAT
*
41464145 TATGTA-ATGTTTTCTA
1 TATGTATATGTTATCTA
41464161 AACATATGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.26, C:0.06, G:0.12, T:0.56
Consensus pattern (18 bp):
TATGTATATGTTATCTAT
Found at i:41471409 original size:22 final size:22
Alignment explanation
Indices: 41471352--41471403 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
41471342 ATGTTATGTC
41471352 CTGATATGAAATATGATATACT
1 CTGATATGAAATATGATATACT
* **
41471374 CTGATAAGGGATATGATA-ACCT
1 CTGATATGAAATATGATATA-CT
41471396 CTGATATG
1 CTGATATG
41471404 TTATATAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (22 bp):
CTGATATGAAATATGATATACT
Found at i:41472204 original size:28 final size:28
Alignment explanation
Indices: 41472166--41472334 Score: 169
Period size: 28 Copynumber: 6.0 Consensus size: 28
41472156 GGTCGTGTGT
* ** *
41472166 CCCCTGTTTTTTAGATTTTGCAGTTTTC
1 CCCCTATTTTTTAGATTTTATAGTTTTG
*
41472194 CCCCTATTTTTTAGATTTTATTA-TTTTA
1 CCCCTATTTTTTAGATTTTA-TAGTTTTG
* *
41472222 CCCTTATTTTTTAAAATTTTATAGTTTTG
1 CCCCTATTTTTT-AGATTTTATAGTTTTG
* * *
41472251 CCCCTATTTTTTTAGATTTTACAATTTTT
1 CCCCTA-TTTTTTAGATTTTATAGTTTTG
* * * *
41472280 CCTCTATTTTTCAAATTTTATTGTTTTG
1 CCCCTATTTTTTAGATTTTATAGTTTTG
*
41472308 TCCCTATTTTTTAGATTTTATAGTTTT
1 CCCCTATTTTTTAGATTTTATAGTTTT
41472335 TCTCCTACTT
Statistics
Matches: 113, Mismatches: 24, Indels: 8
0.78 0.17 0.06
Matches are distributed among these distances:
28 73 0.65
29 34 0.30
30 6 0.05
ACGTcount: A:0.19, C:0.15, G:0.07, T:0.59
Consensus pattern (28 bp):
CCCCTATTTTTTAGATTTTATAGTTTTG
Found at i:41472233 original size:57 final size:56
Alignment explanation
Indices: 41472187--41472334 Score: 190
Period size: 57 Copynumber: 2.6 Consensus size: 56
41472177 TAGATTTTGC
* *
41472187 AGTTTTCCCCCTATTTTTTAGATTTTATTATTTTACCCT-TATTTTTTAAAATTTTAT
1 AGTTTTGCCCCTATTTTTTAGATTTTATAATTTT-CCCTCTA-TTTTTAAAATTTTAT
* * *
41472244 AGTTTTGCCCCTATTTTTTTAGATTTTACAATTTTTCCTCTATTTTTCAAATTTTAT
1 AGTTTTGCCCCTA-TTTTTTAGATTTTATAATTTTCCCTCTATTTTTAAAATTTTAT
* * *
41472301 TGTTTTGTCCCTATTTTTTAGATTTTATAGTTTT
1 AGTTTTGCCCCTATTTTTTAGATTTTATAATTTT
41472335 TCTCCTACTT
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
56 19 0.24
57 40 0.50
58 21 0.26
ACGTcount: A:0.20, C:0.14, G:0.06, T:0.60
Consensus pattern (56 bp):
AGTTTTGCCCCTATTTTTTAGATTTTATAATTTTCCCTCTATTTTTAAAATTTTAT
Found at i:41472346 original size:29 final size:27
Alignment explanation
Indices: 41472167--41472355 Score: 155
Period size: 28 Copynumber: 6.7 Consensus size: 27
41472157 GTCGTGTGTC
* ** *
41472167 CCCTGTTTTTTAGATTTTGCAGTTTTCC
1 CCCTATTTTTTAGATTTTATAGTTTT-T
*
41472195 CCCTATTTTTTAGATTTTATTA-TTTTA
1 CCCTATTTTTTAGATTTTA-TAGTTTTT
* *
41472222 CCCTTATTTTTTAAAATTTTATAGTTTTGC
1 CCC-TATTTTTT-AGATTTTATAGTTTT-T
* *
41472252 CCCTATTTTTTTAGATTTTACAATTTTT
1 CCCTA-TTTTTTAGATTTTATAGTTTTT
* * *
41472280 CCTCTATTTTTCAAATTTTATTGTTTTGT
1 CC-CTATTTTTTAGATTTTATAGTTTT-T
41472309 CCCTATTTTTTAGATTTTATAGTTTTT
1 CCCTATTTTTTAGATTTTATAGTTTTT
* * *
41472336 CTCCTACTTTTCAAATTTTA
1 C-CCTATTTTTTAGATTTTA
41472356 CAATTTTTTC
Statistics
Matches: 131, Mismatches: 21, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
27 5 0.04
28 85 0.65
29 32 0.24
30 9 0.07
ACGTcount: A:0.20, C:0.15, G:0.06, T:0.59
Consensus pattern (27 bp):
CCCTATTTTTTAGATTTTATAGTTTTT
Found at i:41472375 original size:56 final size:56
Alignment explanation
Indices: 41472259--41472375 Score: 128
Period size: 56 Copynumber: 2.1 Consensus size: 56
41472249 TGCCCCTATT
* *** ** *
41472259 TTTTTAGATTTTACAATTTTTCCTCTATTTTTCAAATTTTATTGTTTTGTCCCTAT
1 TTTTTAGATTTTACAATTTTTCCTCTACTTTTCAAATTTTACAATTTTGTCCAAAA
* * *
41472315 TTTTTAGATTTTATAGTTTTT-CTCCTACTTTTCAAATTTTACAATTTTTTCCAAAA
1 TTTTTAGATTTTACAATTTTTCCT-CTACTTTTCAAATTTTACAATTTTGTCCAAAA
41472371 TTTTT
1 TTTTT
41472376 TGTTTTGTTC
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
55 2 0.04
56 48 0.96
ACGTcount: A:0.22, C:0.14, G:0.04, T:0.60
Consensus pattern (56 bp):
TTTTTAGATTTTACAATTTTTCCTCTACTTTTCAAATTTTACAATTTTGTCCAAAA
Found at i:41479081 original size:27 final size:27
Alignment explanation
Indices: 41479051--41479103 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
41479041 TACAATTTTT
*
41479051 AATTA-TTATCCATGTGATTGATTAAAA
1 AATTATTTATCCAAGTG-TTGATTAAAA
41479078 AATTATTTATCCAAGTGTTGATTAAA
1 AATTATTTATCCAAGTGTTGATTAAA
41479104 CAAAAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.42
Consensus pattern (27 bp):
AATTATTTATCCAAGTGTTGATTAAAA
Found at i:41480171 original size:6 final size:6
Alignment explanation
Indices: 41480123--41480152 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
41480113 TGAGAAATGG
41480123 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
41480153 TTGCATTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:41486424 original size:27 final size:30
Alignment explanation
Indices: 41486359--41486429 Score: 92
Period size: 33 Copynumber: 2.3 Consensus size: 30
41486349 CAAAGAAAAT
41486359 AAAAGAAAAAGAATTAACTTGCTCTACTTCAAAG
1 AAAA-AAAAAGAATTAACTTGCTCTA---CAAAG
41486393 AAAAAAAAAGAATTAACTTGCTC-A-AAAG
1 AAAAAAAAAGAATTAACTTGCTCTACAAAG
41486421 AAAAAAAAA
1 AAAAAAAAA
41486430 TGCATGGACA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
28 13 0.35
32 1 0.03
33 19 0.51
34 4 0.11
ACGTcount: A:0.61, C:0.11, G:0.10, T:0.18
Consensus pattern (30 bp):
AAAAAAAAAGAATTAACTTGCTCTACAAAG
Found at i:41491766 original size:75 final size:75
Alignment explanation
Indices: 41491677--41491948 Score: 350
Period size: 75 Copynumber: 3.6 Consensus size: 75
41491667 TGTAATTATG
* * *
41491677 TATATCTGTCGGTTTATCTGACTAGTGCTGGGCGCAACCTTCGTCAGTTTATCTGACTAGTGCAT
1 TATATCTGTCGGTTTATCCGACTAGCGCTGGGCACAACCTTCGTCAGTTTATCTGACTAGTGCAT
41491742 GGCACACTAT
66 GGCACACTAT
* * * * *
41491752 TATATCTGTCGGTTTATCCAACTAGCGCTGGGTACAACCTTTGTCAGTTTATTTGACTAGTGCAG
1 TATATCTGTCGGTTTATCCGACTAGCGCTGGGCACAACCTTCGTCAGTTTATCTGACTAGTGCAT
*
41491817 GGCACACTGT
66 GGCACACTAT
* * * *
41491827 TTTATATGTCGGTTTATCCTACTAGCGTTGGGCACAACCTTCGTCAGTTTATCTGACTAGTGCAA
1 TATATCTGTCGGTTTATCCGACTAGCGCTGGGCACAACCTTCGTCAGTTTATCTGACTAGTGC-A
41491892 T-GCACACTAT
65 TGGCACACTAT
* * * **
41491902 TATATCTG-CTGATTTATCCGGCTAGCACTGGGTGCAACCTTCGTCAG
1 TATATCTGTC-GGTTTATCCGACTAGCGCTGGGCACAACCTTCGTCAG
41491949 ACACATCATT
Statistics
Matches: 168, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
74 1 0.01
75 166 0.99
76 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.35
Consensus pattern (75 bp):
TATATCTGTCGGTTTATCCGACTAGCGCTGGGCACAACCTTCGTCAGTTTATCTGACTAGTGCAT
GGCACACTAT
Found at i:41494304 original size:26 final size:24
Alignment explanation
Indices: 41494251--41494301 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
41494241 TTTTTCTGAC
41494251 AATTTGACATTTATTTTTTTAGTTA
1 AATTTGACATTTATTTTTTTA-TTA
*
41494276 AATTTGACCTTTAATTTTTTT-TTA
1 AATTTGACATTT-ATTTTTTTATTA
41494300 AA
1 AA
41494302 AATAAAGTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 5 0.21
25 11 0.46
26 8 0.33
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (24 bp):
AATTTGACATTTATTTTTTTATTA
Found at i:41500704 original size:24 final size:24
Alignment explanation
Indices: 41500677--41500722 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
41500667 TTATTAACAT
*
41500677 TGTTTGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTATA
*
41500701 TGTTCGTGAACATGTTCGATTA
1 TGTTCGTGAACATGTTCAATTA
41500723 AGTTAAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (24 bp):
TGTTCGTGAACATGTTCAATTATA
Found at i:41504267 original size:18 final size:19
Alignment explanation
Indices: 41504237--41504272 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
41504227 ATTTTTTTTA
*
41504237 AAAATTATAAAAATTAAAT
1 AAAATTATAAAAAATAAAT
41504256 AAAATT-TAAAAAATAAA
1 AAAATTATAAAAAATAAA
41504273 ATATTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAATTATAAAAAATAAAT
Found at i:41504269 original size:14 final size:15
Alignment explanation
Indices: 41504252--41504281 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
41504242 TATAAAAATT
41504252 AAATAAAAT-TTAAA
1 AAATAAAATATTAAA
41504266 AAATAAAATATTAAA
1 AAATAAAATATTAAA
41504281 A
1 A
41504282 TCATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAATAAAATATTAAA
Found at i:41504271 original size:25 final size:25
Alignment explanation
Indices: 41504233--41504294 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
41504223 AATAATTTTT
41504233 TTTAAAAATTATAAAA-ATTAAATAAAA
1 TTTAAAAA--ATAAAATATTAAA-AAAA
**
41504260 TTTAAAAAATAAAATATTAAAATCA
1 TTTAAAAAATAAAATATTAAAAAAA
41504285 TTTAAAAAAT
1 TTTAAAAAAT
41504295 TAATTCTAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 18 0.56
26 6 0.19
27 8 0.25
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (25 bp):
TTTAAAAAATAAAATATTAAAAAAA
Found at i:41504274 original size:19 final size:20
Alignment explanation
Indices: 41504235--41504275 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
41504225 TAATTTTTTT
*
41504235 TAAAAATTATAAAAATTAAA
1 TAAAAATTATAAAAATAAAA
*
41504255 TAAAATTTA-AAAAATAAAA
1 TAAAAATTATAAAAATAAAA
41504274 TA
1 TA
41504276 TTAAAATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAAAATTATAAAAATAAAA
Found at i:41505282 original size:25 final size:25
Alignment explanation
Indices: 41505249--41505298 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
41505239 TGTTATTCCT
41505249 TTCAAATTTTACTATTCTTTTTATC
1 TTCAAATTTTACTATTCTTTTTATC
*
41505274 TTCAAATTTTTCTATTCTTTTTATC
1 TTCAAATTTTACTATTCTTTTTATC
41505299 ATGTAAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.16, G:0.00, T:0.62
Consensus pattern (25 bp):
TTCAAATTTTACTATTCTTTTTATC
Found at i:41507621 original size:20 final size:19
Alignment explanation
Indices: 41507549--41507623 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 19
41507539 TGAACACAAT
* *
41507549 AAAAAAGGAGAAATCAAAGG
1 AAAAAAGAAGAAA-AAAAGG
*
41507569 AGTAAAAAGAAGAAAGAAAGG
1 A--AAAAAGAAGAAAAAAAGG
*
41507590 AAAAATAAAAGAAAAAAATGG
1 AAAAA-AGAAGAAAAAAA-GG
*
41507611 AAAGAAGAAGAAA
1 AAAAAAGAAGAAA
41507624 TAGTACAGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
19 4 0.09
20 18 0.40
21 12 0.27
22 11 0.24
ACGTcount: A:0.71, C:0.01, G:0.23, T:0.05
Consensus pattern (19 bp):
AAAAAAGAAGAAAAAAAGG
Found at i:41514834 original size:24 final size:24
Alignment explanation
Indices: 41514789--41514835 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
41514779 TATATATACC
41514789 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
41514813 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
41514836 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:41516750 original size:16 final size:16
Alignment explanation
Indices: 41516729--41516765 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
41516719 AAAAAATTAT
41516729 ATTTTTCATCCTTCCA
1 ATTTTTCATCCTTCCA
* *
41516745 ATTTTTCTTCTTTCCA
1 ATTTTTCATCCTTCCA
41516761 ATTTT
1 ATTTT
41516766 CTTTTTACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTTCATCCTTCCA
Found at i:41522189 original size:2 final size:2
Alignment explanation
Indices: 41522176--41522208 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
41522166 CTTGATGCCA
*
41522176 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41522209 AATAGGATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:41527917 original size:275 final size:276
Alignment explanation
Indices: 41527413--41527966 Score: 1101
Period size: 275 Copynumber: 2.0 Consensus size: 276
41527403 TAAAATTTAA
41527413 ATTTTAATGATAGTTGTTGACACTATTTTTTGATAAAAACGGGGTCGACTTGGACTTTGAAAACG
1 ATTTTAATGATAGTTGTTGACACTATTTTTTGATAAAAACGGGGTCGACTTGGACTTTGAAAACG
41527478 AAAACGAAAACGAAAACATGAGTCGCCACCAATCTTTTTTTTTTGATGAGGTGTGATCGGGTCAC
66 AAAACGAAAACGAAAACATGAGTCGCCACCAATCTTTTTTTTTTGATGAGGTGTGATCGGGTCAC
41527543 CTCGAAAAACGGTTTTTTTAATAAATAGTTTAGATTGATTAAAACAATGTCTTTGGTCTGCGAAA
131 CTCGAAAAACGGTTTTTTTAATAAATAGTTTAGATTGATTAAAACAATGTCTTTGGTCTGCGAAA
41527608 TTCAGGAAAATGGGTTCGGGAGTCGATTACGTACGAGGAAGGATTAGCAACCTCGTAAACCCAAA
196 TTCAGGAAAATGGGTTCGGGAGTCGATTACGTACGAGGAAGGATTAGCAACCTCGTAAACCCAAA
41527673 AATTGGTACCTAGTTG
261 AATTGGTACCTAGTTG
41527689 ATTTTAATGATA-TTGTTGACACTATTTTTTGATAAAAACGGGGTCGACTTGGACTTTGAAAACG
1 ATTTTAATGATAGTTGTTGACACTATTTTTTGATAAAAACGGGGTCGACTTGGACTTTGAAAACG
41527753 AAAACGAAAACGAAAACATGAGTCGCCACCAATCTTTTTTTTTTGATGAGGTGTGATCGGGTCAC
66 AAAACGAAAACGAAAACATGAGTCGCCACCAATCTTTTTTTTTTGATGAGGTGTGATCGGGTCAC
41527818 CTCGAAAAACGGTTTTTTTAATAAATAGTTTAGATTGATTAAAACAATGTCTTTGGTCTGCGAAA
131 CTCGAAAAACGGTTTTTTTAATAAATAGTTTAGATTGATTAAAACAATGTCTTTGGTCTGCGAAA
41527883 TTCAGGAAAATGGGTTCGGGAGTCGATTACGTACGAGGAAGGATTAGCAACCTCGTAAACCCAAA
196 TTCAGGAAAATGGGTTCGGGAGTCGATTACGTACGAGGAAGGATTAGCAACCTCGTAAACCCAAA
41527948 AATTGGTACCTAGTTG
261 AATTGGTACCTAGTTG
41527964 ATT
1 ATT
41527967 AATTAGTGTC
Statistics
Matches: 278, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
275 266 0.96
276 12 0.04
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (276 bp):
ATTTTAATGATAGTTGTTGACACTATTTTTTGATAAAAACGGGGTCGACTTGGACTTTGAAAACG
AAAACGAAAACGAAAACATGAGTCGCCACCAATCTTTTTTTTTTGATGAGGTGTGATCGGGTCAC
CTCGAAAAACGGTTTTTTTAATAAATAGTTTAGATTGATTAAAACAATGTCTTTGGTCTGCGAAA
TTCAGGAAAATGGGTTCGGGAGTCGATTACGTACGAGGAAGGATTAGCAACCTCGTAAACCCAAA
AATTGGTACCTAGTTG
Found at i:41528239 original size:106 final size:106
Alignment explanation
Indices: 41528048--41528267 Score: 370
Period size: 106 Copynumber: 2.1 Consensus size: 106
41528038 ATGACATGAA
* * * *
41528048 TTGAAA-TTTAAGAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCTAGCACGTTAGGG
1 TTGAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACAAGAAATCGAAACCCAGCACGTTAAGG
* *
41528112 CACGTTTTCTCGATTTTCCAAACTCAAAATATTGCCTTACT
66 CACGTTTCCTCGATTTTCCAAACGCAAAATATTGCCTTACT
41528153 TTGAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACAAGAAATCGAAACCCAGCACGTTAAGG
1 TTGAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACAAGAAATCGAAACCCAGCACGTTAAGG
*
41528218 CACGTTTCCTCGATTTTCCAAACGCAAAATATTGCCTTATT
66 CACGTTTCCTCGATTTTCCAAACGCAAAATATTGCCTTACT
41528259 TTGAAATTT
1 TTGAAATTT
41528268 GTTACGAATT
Statistics
Matches: 107, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
105 6 0.06
106 101 0.94
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (106 bp):
TTGAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACAAGAAATCGAAACCCAGCACGTTAAGG
CACGTTTCCTCGATTTTCCAAACGCAAAATATTGCCTTACT
Found at i:41528531 original size:30 final size:30
Alignment explanation
Indices: 41528476--41528536 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
41528466 TCGATCATGC
*
41528476 ATAAACAAAAATAATAATGGAAACAACAAT
1 ATAAACAAAAATAATAATGGAAACAAAAAT
* *
41528506 ATAAACAACAGTAATAAT-GATAACAAAAAT
1 ATAAACAAAAATAATAATGGA-AACAAAAAT
41528536 A
1 A
41528537 ATAATAGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.66, C:0.10, G:0.07, T:0.18
Consensus pattern (30 bp):
ATAAACAAAAATAATAATGGAAACAAAAAT
Found at i:41528665 original size:19 final size:19
Alignment explanation
Indices: 41528641--41528684 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
41528631 CAATTTAAAG
41528641 TAATAAATAAAAAAGATAA
1 TAATAAATAAAAAAGATAA
* *
41528660 TAATAAATGAATAAGATAA
1 TAATAAATAAAAAAGATAA
41528679 -AATAAA
1 TAATAAA
41528685 AGCTAATGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (19 bp):
TAATAAATAAAAAAGATAA
Found at i:41528760 original size:14 final size:15
Alignment explanation
Indices: 41528741--41528769 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41528731 AGATAAATAA
41528741 AATATTAAA-AAAAC
1 AATATTAAATAAAAC
41528755 AATATTAAATAAAAC
1 AATATTAAATAAAAC
41528770 TTTCCTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (15 bp):
AATATTAAATAAAAC
Found at i:41532859 original size:2 final size:2
Alignment explanation
Indices: 41532852--41532877 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41532842 ATAGTCAAAC
41532852 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
41532878 CGAATTAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41546588 original size:2 final size:2
Alignment explanation
Indices: 41546581--41546606 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41546571 ATGTTGGAGT
41546581 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
41546607 AATTTAGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41549011 original size:102 final size:102
Alignment explanation
Indices: 41548829--41549032 Score: 365
Period size: 102 Copynumber: 2.0 Consensus size: 102
41548819 GCTTGATATT
*
41548829 GTAACGAGTCAAAGTCTAAGTGTAGGTCCCAGTCGGCGGCCTTGATGCAGTCAAGGGTTCGAATA
1 GTAACGAGTCAAAGTCTAAGTGGAGGTCCCAGTCGGCGGCCTTGATGCAGTCAAGGGTTCGAATA
*
41548894 TAATCGGGGGACAATTGACGGTCGTTATGCGATCACG
66 TAATCAGGGGACAATTGACGGTCGTTATGCGATCACG
41548931 GTAACGAGTCAAAGTCTAAGTGGAGG-CCCTAGTCGGCGGCCTTGATGCAGTCAAGGGTTCGAAT
1 GTAACGAGTCAAAGTCTAAGTGGAGGTCCC-AGTCGGCGGCCTTGATGCAGTCAAGGGTTCGAAT
*
41548995 ATAATCAGGGGTCAATTGACGGTCGTTATGCGATCACG
65 ATAATCAGGGGACAATTGACGGTCGTTATGCGATCACG
41549033 AGTTCAAGCT
Statistics
Matches: 98, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
101 3 0.03
102 95 0.97
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (102 bp):
GTAACGAGTCAAAGTCTAAGTGGAGGTCCCAGTCGGCGGCCTTGATGCAGTCAAGGGTTCGAATA
TAATCAGGGGACAATTGACGGTCGTTATGCGATCACG
Found at i:41550238 original size:13 final size:13
Alignment explanation
Indices: 41550220--41550247 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
41550210 AATTTAAATT
41550220 TAATTATATTAAA
1 TAATTATATTAAA
41550233 TAATTATATTAAA
1 TAATTATATTAAA
41550246 TA
1 TA
41550248 TTCTATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAATTATATTAAA
Found at i:41551664 original size:20 final size:20
Alignment explanation
Indices: 41551639--41551684 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
41551629 TAGTAAAGCT
*
41551639 TAACAACCTATTTAAATAAG
1 TAACAACCTATTTAAATAAA
*
41551659 TAACAACCTATTTGAATAAA
1 TAACAACCTATTTAAATAAA
41551679 TAACAA
1 TAACAA
41551685 AATATTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.52, C:0.15, G:0.04, T:0.28
Consensus pattern (20 bp):
TAACAACCTATTTAAATAAA
Found at i:41551690 original size:20 final size:20
Alignment explanation
Indices: 41551647--41551690 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
41551637 CTTAACAACC
* **
41551647 TATTTAAATAAGTAACAACC
1 TATTTAAATAAATAACAAAA
*
41551667 TATTTGAATAAATAACAAAA
1 TATTTAAATAAATAACAAAA
41551687 TATT
1 TATT
41551691 AACAGATTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.34
Consensus pattern (20 bp):
TATTTAAATAAATAACAAAA
Found at i:41555358 original size:7 final size:7
Alignment explanation
Indices: 41555346--41555376 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
41555336 ATGTGCATCC
41555346 CTGATAT
1 CTGATAT
41555353 CTGATAT
1 CTGATAT
*
41555360 TTGATAT
1 CTGATAT
41555367 CTGATAT
1 CTGATAT
41555374 CTG
1 CTG
41555377 TTTTTGCATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (7 bp):
CTGATAT
Found at i:41555675 original size:22 final size:22
Alignment explanation
Indices: 41555650--41555714 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
41555640 CATATGATTT
41555650 TGATATGTTCTGCATCTGTATC
1 TGATATGTTCTGCATCTGTATC
* * * *
41555672 TGATTTGTTTTACATCTGCATC
1 TGATATGTTCTGCATCTGTATC
*
41555694 TGATATG-TCTGCACCT-TATC
1 TGATATGTTCTGCATCTGTATC
41555714 T
1 T
41555715 AAACTATTAC
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 4 0.12
21 6 0.18
22 24 0.71
ACGTcount: A:0.18, C:0.20, G:0.15, T:0.46
Consensus pattern (22 bp):
TGATATGTTCTGCATCTGTATC
Found at i:41556351 original size:7 final size:7
Alignment explanation
Indices: 41556339--41556372 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
41556329 ATGTTATTTT
41556339 TATTTAA
1 TATTTAA
41556346 TATTTAA
1 TATTTAA
41556353 TATTTAA
1 TATTTAA
*
41556360 CAATTTAA
1 -TATTTAA
41556368 TATTT
1 TATTT
41556373 TTTCTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (7 bp):
TATTTAA
Found at i:41568101 original size:21 final size:22
Alignment explanation
Indices: 41568077--41568122 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
41568067 CGGAATAACG
*
41568077 AAATTATAATT-TAAATATAA-A
1 AAATTAAAATTCTAAA-ATAAGA
41568098 AAATTAAAATTCTAAAATAAGA
1 AAATTAAAATTCTAAAATAAGA
41568120 AAA
1 AAA
41568123 AAGACACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (22 bp):
AAATTAAAATTCTAAAATAAGA
Found at i:41569891 original size:21 final size:21
Alignment explanation
Indices: 41569861--41569900 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
41569851 AACCTTGCAG
*
41569861 GTGAATTCTATCACAAGAAGT
1 GTGAACTCTATCACAAGAAGT
41569882 GTGAACTCTATCACAAGAA
1 GTGAACTCTATCACAAGAA
41569901 AATTAGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.25
Consensus pattern (21 bp):
GTGAACTCTATCACAAGAAGT
Found at i:41570175 original size:22 final size:22
Alignment explanation
Indices: 41570148--41570203 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
41570138 TTACACCACA
41570148 TTGTGGATGAAAC-CACTCATTG
1 TTGTGGAT-AAACACACTCATTG
*
41570170 TTGTGGATAAACACACTTATTG
1 TTGTGGATAAACACACTCATTG
**
41570192 TTGCAGATAAAC
1 TTGTGGATAAAC
41570204 TGCTCATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (22 bp):
TTGTGGATAAACACACTCATTG
Found at i:41572876 original size:25 final size:25
Alignment explanation
Indices: 41572837--41572933 Score: 99
Period size: 25 Copynumber: 3.8 Consensus size: 25
41572827 AGGTTTAAGC
* *
41572837 GAGCCAATAAT-GGGAAGCTCCGGA
1 GAGCCATTAATCGGGAAGCTCCGAA
*
41572861 GAGCCATTAATCGGGAAGCTCATGAAA
1 GAGCCATTAATCGGGAAGCTC-CG-AA
* *
41572888 GAGCCTTTAATCGTGAAGCTCCGAA
1 GAGCCATTAATCGGGAAGCTCCGAA
*
41572913 GAGCCA-TATATCGGGATGCTC
1 GAGCCATTA-ATCGGGAAGCTC
41572934 ATAAGAGCTA
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
24 12 0.20
25 26 0.43
26 2 0.03
27 20 0.33
ACGTcount: A:0.31, C:0.22, G:0.28, T:0.20
Consensus pattern (25 bp):
GAGCCATTAATCGGGAAGCTCCGAA
Found at i:41574033 original size:503 final size:503
Alignment explanation
Indices: 41573086--41574087 Score: 1988
Period size: 503 Copynumber: 2.0 Consensus size: 503
41573076 GTGTGTCCGC
41573086 AACACATGCAAGACCACAACCAATTCGGGAACCCTGTATCCATCGAATTTTATTTATTCAAATGG
1 AACACATGCAAGACCACAACCAATTCGGGAACCCTGTATCCATCGAATTTTATTTATTCAAATGG
41573151 GACTTAATATTTGTCGGGCATTATCGGATATGTAATCAATTTCATATATATGACATTTACACAAT
66 GACTTAATATTTGTCGGGCATTATCGGATATGTAATCAATTTCATATATATGACATTTACACAAT
41573216 TCACATATACAACATTCAATTCAAACATATAAATATACTAAATTGCAGAAATACCAAAATTTAGG
131 TCACATATACAACATTCAATTCAAACATATAAATATACTAAATTGCAGAAATACCAAAATTTAGG
41573281 GGCATTTTGGAAATTTTCTATTTTCCTCGATTTTCCACCCCGATCTTGATTAAATTAATAATTTC
196 GGCATTTTGGAAATTTTCTATTTTCCTCGATTTTCCACCCCGATCTTGATTAAATTAATAATTTC
41573346 ATTTAATATATTAATTTAGACGATAAAAAAATTTACTCCATGCAATTTGGTTATTTTTAAGTTTT
261 ATTTAATATATTAATTTAGACGATAAAAAAATTTACTCCATGCAATTTGGTTATTTTTAAGTTTT
41573411 TACAAAATTTCCCCTAAAGTTTTACTTTTATTCAATTTAGTCCCTAAACCCAAAACATGCAAATT
326 TACAAAATTTCCCCTAAAGTTTTACTTTTATTCAATTTAGTCCCTAAACCCAAAACATGCAAATT
41573476 AACCATTTTTAATGCAAACCCATGCTAGCTGAATATTCATGGCATTCAATACAGCCCATTTTTGC
391 AACCATTTTTAATGCAAACCCATGCTAGCTGAATATTCATGGCATTCAATACAGCCCATTTTTGC
41573541 AATAATTTCACAACAAACCCTTGTATTTTTACTAACTTAACAACCCGA
456 AATAATTTCACAACAAACCCTTGTATTTTTACTAACTTAACAACCCGA
41573589 AACACATGCAAGACCACAACCAATTCGGGAACCCTGTATCCATCGAATTTTATTTATTCAAATGG
1 AACACATGCAAGACCACAACCAATTCGGGAACCCTGTATCCATCGAATTTTATTTATTCAAATGG
41573654 GACTTAATATTTGTCGGGCATTATCGGATATGTAATCAATTTCATATATATGACATTTACACAAT
66 GACTTAATATTTGTCGGGCATTATCGGATATGTAATCAATTTCATATATATGACATTTACACAAT
41573719 TCACATATACAACATTCAATTCAAACATATAAATATACTAAATTGCAGAAATACCAAAATTTAGG
131 TCACATATACAACATTCAATTCAAACATATAAATATACTAAATTGCAGAAATACCAAAATTTAGG
41573784 GGCATTTTGGAAATTTTCTATTTTCCTCGATTTTCCA-CCCGATCTTGATCTAAATTAATAATTT
196 GGCATTTTGGAAATTTTCTATTTTCCTCGATTTTCCACCCCGATCTTGAT-TAAATTAATAATTT
41573848 CATTTAATATATTAATTTAGACGATAAAAAAATTTACTCCATGCAATTTGGTTATTTTTAAGTTT
260 CATTTAATATATTAATTTAGACGATAAAAAAATTTACTCCATGCAATTTGGTTATTTTTAAGTTT
41573913 TTACAAAATTTCCCCTAAAGTTTTACTTTTATTCAATTTAGTCCCTAAACCCAAAACATGCAAAT
325 TTACAAAATTTCCCCTAAAGTTTTACTTTTATTCAATTTAGTCCCTAAACCCAAAACATGCAAAT
41573978 TAACCATTTTTAATGCAAACCCATGCTAGCTGAATATTCATGGCATTCAATACAGCCCATTTTTG
390 TAACCATTTTTAATGCAAACCCATGCTAGCTGAATATTCATGGCATTCAATACAGCCCATTTTTG
41574043 CAATAATTTCACAACAAACCCTTGTATTTTTACTAACTTAACAAC
455 CAATAATTTCACAACAAACCCTTGTATTTTTACTAACTTAACAAC
41574088 TTAATCCTTA
Statistics
Matches: 498, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
502 12 0.02
503 486 0.98
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (503 bp):
AACACATGCAAGACCACAACCAATTCGGGAACCCTGTATCCATCGAATTTTATTTATTCAAATGG
GACTTAATATTTGTCGGGCATTATCGGATATGTAATCAATTTCATATATATGACATTTACACAAT
TCACATATACAACATTCAATTCAAACATATAAATATACTAAATTGCAGAAATACCAAAATTTAGG
GGCATTTTGGAAATTTTCTATTTTCCTCGATTTTCCACCCCGATCTTGATTAAATTAATAATTTC
ATTTAATATATTAATTTAGACGATAAAAAAATTTACTCCATGCAATTTGGTTATTTTTAAGTTTT
TACAAAATTTCCCCTAAAGTTTTACTTTTATTCAATTTAGTCCCTAAACCCAAAACATGCAAATT
AACCATTTTTAATGCAAACCCATGCTAGCTGAATATTCATGGCATTCAATACAGCCCATTTTTGC
AATAATTTCACAACAAACCCTTGTATTTTTACTAACTTAACAACCCGA
Found at i:41574480 original size:18 final size:20
Alignment explanation
Indices: 41574459--41574497 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
41574449 TTTTTTTGTT
41574459 TTATTATAT-AT-TAATATA
1 TTATTATATAATATAATATA
41574477 TTATTATATAATATAATATA
1 TTATTATATAATATAATATA
41574497 T
1 T
41574498 ATATACTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
19 2 0.11
20 8 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTATTATATAATATAATATA
Found at i:41574502 original size:18 final size:16
Alignment explanation
Indices: 41574460--41574502 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
41574450 TTTTTTGTTT
41574460 TATTATATAT-TAATA
1 TATTATATATATAATA
41574475 TATTAT-TATATAATA
1 TATTATATATATAATA
*
41574490 TAATATATATATA
1 TATTATATATATA
41574503 CTTAACACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 3 0.12
15 16 0.64
16 6 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TATTATATATATAATA
Found at i:41576449 original size:17 final size:19
Alignment explanation
Indices: 41576413--41576449 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
41576403 TTTGATTTAT
41576413 TTAATTTTACTTTATCAAAA
1 TTAATTTTA-TTTATCAAAA
41576433 TTAATTTT-TTT-TCAAAA
1 TTAATTTTATTTATCAAAA
41576450 ATCACTTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.35
18 3 0.18
20 8 0.47
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (19 bp):
TTAATTTTATTTATCAAAA
Found at i:41578083 original size:40 final size:40
Alignment explanation
Indices: 41578034--41578155 Score: 244
Period size: 40 Copynumber: 3.0 Consensus size: 40
41578024 TACAGAGTTA
41578034 TTATTTAGGTATGTGAAGGTTTGATTCAGAAATTTTATTG
1 TTATTTAGGTATGTGAAGGTTTGATTCAGAAATTTTATTG
41578074 TTATTTAGGTATGTGAAGGTTTGATTCAGAAATTTTATTG
1 TTATTTAGGTATGTGAAGGTTTGATTCAGAAATTTTATTG
41578114 TTATTTAGGTATGTGAAGGTTTGATTCAGAAATTTTATTG
1 TTATTTAGGTATGTGAAGGTTTGATTCAGAAATTTTATTG
41578154 TT
1 TT
41578156 TGATTAGTAA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.27, C:0.02, G:0.22, T:0.48
Consensus pattern (40 bp):
TTATTTAGGTATGTGAAGGTTTGATTCAGAAATTTTATTG
Found at i:41578158 original size:21 final size:21
Alignment explanation
Indices: 41578052--41578168 Score: 64
Period size: 21 Copynumber: 5.8 Consensus size: 21
41578042 GTATGTGAAG
41578052 GTTTGATTCAGAAATTTTATT
1 GTTTGATTCAGAAATTTTATT
* ** * * **
41578073 G-TT-ATTTAGGTATGTGAAG
1 GTTTGATTCAGAAATTTTATT
41578092 GTTTGATTCAGAAATTTTATT
1 GTTTGATTCAGAAATTTTATT
* ** * * **
41578113 G-TT-ATTTAGGTATGTGAAG
1 GTTTGATTCAGAAATTTTATT
41578132 GTTTGATTCAGAAATTTTATT
1 GTTTGATTCAGAAATTTTATT
41578153 GTTTGATT-AGTAAATT
1 GTTTGATTCAG-AAATT
41578169 AATTAAAAAG
Statistics
Matches: 63, Mismatches: 28, Indels: 10
0.62 0.28 0.10
Matches are distributed among these distances:
19 20 0.32
20 10 0.16
21 33 0.52
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.49
Consensus pattern (21 bp):
GTTTGATTCAGAAATTTTATT
Found at i:41585603 original size:41 final size:41
Alignment explanation
Indices: 41585541--41585685 Score: 254
Period size: 41 Copynumber: 3.5 Consensus size: 41
41585531 GACTACACGT
41585541 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
41585582 CTAGCAGGCTAAGTGCTGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
41585623 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
41585664 CTAGCAGGCTAAGCGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
41585686 ATCTATTAAA
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 99 1.00
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.23
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:41595050 original size:25 final size:24
Alignment explanation
Indices: 41595000--41595057 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 24
41594990 GCCTCTCCGC
*
41595000 AGCTTCCCGATATTGGGTCGCTTG
1 AGCTTCCCGATATTGGCTCGCTTG
*
41595024 AGCCTTCCCGATATTGGCTTG-TATG
1 AG-CTTCCCGATATTGGCTCGCT-TG
41595049 AGCTTCCCG
1 AGCTTCCCG
41595058 TTAATAGCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 10 0.33
25 20 0.67
ACGTcount: A:0.14, C:0.28, G:0.26, T:0.33
Consensus pattern (24 bp):
AGCTTCCCGATATTGGCTCGCTTG
Found at i:41595137 original size:24 final size:25
Alignment explanation
Indices: 41595071--41595145 Score: 82
Period size: 25 Copynumber: 3.0 Consensus size: 25
41595061 ATAGCTATTT
* *
41595071 AGAGCTTCTCGTTACATGGCTCACA
1 AGAGCTTCCCGTTATATGGCTCACA
* *
41595096 TGAGCTTTCCGTTATATGGCTCGA-A
1 AGAGCTTCCCGTTATATGGCTC-ACA
41595121 AGAGCTTCCCGTT-TATGTGCTCACA
1 AGAGCTTCCCGTTATATG-GCTCACA
41595146 TAAGCATTCC
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
24 5 0.12
25 35 0.85
26 1 0.02
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.32
Consensus pattern (25 bp):
AGAGCTTCCCGTTATATGGCTCACA
Found at i:41596986 original size:24 final size:23
Alignment explanation
Indices: 41596953--41597068 Score: 79
Period size: 24 Copynumber: 4.8 Consensus size: 23
41596943 GGCTCTTTGT
41596953 GAGCTTCCCGTTAATGGCTCTCC
1 GAGCTTCCCGTTAATGGCTCTCC
* * * *
41596976 GCAGCTTCCCGATATTGGCTCGCTT
1 G-AGCTTCCCGTTAATGGCTCTC-C
* * * * **
41597001 GAACCTTCCCGATATTAGCTCGTAT
1 G-AGCTTCCCGTTAATGGCTC-TCC
41597026 GAGCTTCCCGTTAATGGCTCTCC
1 GAGCTTCCCGTTAATGGCTCTCC
*
41597049 GGAGCTTCCCATTACATGGC
1 -GAGCTTCCCGTTA-ATGGC
41597069 ACACATGAGC
Statistics
Matches: 72, Mismatches: 16, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
23 2 0.03
24 45 0.62
25 25 0.35
ACGTcount: A:0.16, C:0.32, G:0.22, T:0.30
Consensus pattern (23 bp):
GAGCTTCCCGTTAATGGCTCTCC
Found at i:41597078 original size:25 final size:24
Alignment explanation
Indices: 41597024--41597080 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
41597014 ATTAGCTCGT
* * *
41597024 ATGAGCTTCCCGTTAATGGCTCTC
1 ATGAGCTTCCCATTAATGGCACAC
**
41597048 CGGAGCTTCCCATTACATGGCACAC
1 ATGAGCTTCCCATTA-ATGGCACAC
41597073 ATGAGCTT
1 ATGAGCTT
41597081 TTCGTTATAT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.28
Consensus pattern (24 bp):
ATGAGCTTCCCATTAATGGCACAC
Found at i:41597994 original size:16 final size:16
Alignment explanation
Indices: 41597973--41598003 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41597963 GAGTATTATC
41597973 TCTATTTTGAAAATTT
1 TCTATTTTGAAAATTT
*
41597989 TCTATTTTTAAAATT
1 TCTATTTTGAAAATT
41598004 GAGTAAAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.58
Consensus pattern (16 bp):
TCTATTTTGAAAATTT
Found at i:41605766 original size:20 final size:19
Alignment explanation
Indices: 41605741--41605806 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
41605731 CTTGTTTACA
41605741 TTGATTTGATTCTCAATCTT
1 TTGATTTGATTCTCAATC-T
** * *
41605761 TTGATTTCTTTC-CATTACA
1 TTGATTTGATTCTCAAT-CT
41605780 TTGATTTGATTCTCAATCCT
1 TTGATTTGATTCTCAAT-CT
41605800 TTGATTT
1 TTGATTT
41605807 CTTTCCATTA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
19 13 0.37
20 22 0.63
ACGTcount: A:0.20, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTGATTTGATTCTCAATCT
Found at i:41605785 original size:19 final size:19
Alignment explanation
Indices: 41605761--41605817 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
41605751 TCTCAATCTT
41605761 TTGATTTCTTTCCATTACA
1 TTGATTTCTTTCCATTACA
** * * *
41605780 TTGATTTGATTCTCAATCCT
1 TTGATTTCTTTC-CATTACA
41605800 TTGATTTCTTTCCATTAC
1 TTGATTTCTTTCCATTAC
41605818 TGTTTTGCTT
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.19, C:0.21, G:0.07, T:0.53
Consensus pattern (19 bp):
TTGATTTCTTTCCATTACA
Found at i:41605790 original size:39 final size:39
Alignment explanation
Indices: 41605736--41605817 Score: 155
Period size: 39 Copynumber: 2.1 Consensus size: 39
41605726 AAAATCTTGT
*
41605736 TTACATTGATTTGATTCTCAATCTTTTGATTTCTTTCCA
1 TTACATTGATTTGATTCTCAATCCTTTGATTTCTTTCCA
41605775 TTACATTGATTTGATTCTCAATCCTTTGATTTCTTTCCA
1 TTACATTGATTTGATTCTCAATCCTTTGATTTCTTTCCA
41605814 TTAC
1 TTAC
41605818 TGTTTTGCTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.21, C:0.20, G:0.07, T:0.52
Consensus pattern (39 bp):
TTACATTGATTTGATTCTCAATCCTTTGATTTCTTTCCA
Found at i:41609566 original size:13 final size:13
Alignment explanation
Indices: 41609548--41609577 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
41609538 TTCTTCCTCC
41609548 CCCCAAACCCAAA
1 CCCCAAACCCAAA
*
41609561 CCCCAACCCCAAA
1 CCCCAAACCCAAA
41609574 CCCC
1 CCCC
41609578 TCCTTTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.63, G:0.00, T:0.00
Consensus pattern (13 bp):
CCCCAAACCCAAA
Found at i:41616313 original size:43 final size:43
Alignment explanation
Indices: 41616252--41616433 Score: 242
Period size: 43 Copynumber: 4.3 Consensus size: 43
41616242 TTTATGATAA
*
41616252 AAACGCCGCTAAAGAACATGATCTTTAGTGGCGCTTTACCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
*
41616295 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTA-CCATC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCA-C
* * * *
41616338 AAACGCCACTAAAGAACATAATCTTTAGCGGCGCGTTACCCAA
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
* * * * *
41616381 AAACGCCGCTAAAGATCAAGACCTTTAGCGACGCTTT-CTCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
41616423 AAACGCCGCTA
1 AAACGCCGCTA
41616434 TAAATCACAA
Statistics
Matches: 121, Mismatches: 16, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
42 17 0.14
43 101 0.83
44 3 0.02
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
Found at i:41616447 original size:42 final size:42
Alignment explanation
Indices: 41616381--41616521 Score: 171
Period size: 42 Copynumber: 3.3 Consensus size: 42
41616371 CGTTACCCAA
* *
41616381 AAACGCCGCTAAAGATCAAGACCTTTAGCGACGCTTT-CTCAC
1 AAACGCCGCTAAA-ATCAAGACCTTTAGCGACGCTTTGATTAC
*
41616423 AAACGCCGCTATAAATCACA-ACCTTTAACGACGCTTTGATTAC
1 AAACGCCGCTA-AAATCA-AGACCTTTAGCGACGCTTTGATTAC
*
41616466 AAACGCCAC-AAAAGCTCAAGACCTTTAAGCGACGCTTTGATTAC
1 AAACGCCGCTAAAA--TCAAGACCTTT-AGCGACGCTTTGATTAC
41616510 AAACGCCGCTAA
1 AAACGCCGCTAA
41616522 CTTTTTAAAA
Statistics
Matches: 85, Mismatches: 6, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
41 3 0.04
42 33 0.39
43 23 0.27
44 24 0.28
45 2 0.02
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.21
Consensus pattern (42 bp):
AAACGCCGCTAAAATCAAGACCTTTAGCGACGCTTTGATTAC
Found at i:41617348 original size:32 final size:32
Alignment explanation
Indices: 41617302--41617371 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
41617292 TCCACAAGAT
41617302 TAAATGGATTTGAACAATTTCAGATGATCCACA
1 TAAA-GGATTTGAACAATTTCAGATGATCCACA
41617335 TAAAGGATTTGAACAATTTCAGATGATCCACA
1 TAAAGGATTTGAACAATTTCAGATGATCCACA
41617367 TAAAG
1 TAAAG
41617372 CTTTCATGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 33 0.89
33 4 0.11
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (32 bp):
TAAAGGATTTGAACAATTTCAGATGATCCACA
Found at i:41619548 original size:57 final size:58
Alignment explanation
Indices: 41619466--41619579 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 58
41619456 TGCTATGCTA
*
41619466 TGCTAAAAGGGGGATTTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATATAAAT
1 TGCTAAAAGGGGGATTTTTTTTAAAGTAAAATTATTTTGTGACGTTTTTTATATAAAT
41619524 TGCTAAAAGGGGG-TTTTTTTTAAAGTAAAATTATTTTGTGACGTTTTTTATATAAA
1 TGCTAAAAGGGGGATTTTTTTTAAAGTAAAATTATTTTGTGACGTTTTTTATATAAA
41619580 CGCCGCTATT
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
57 42 0.76
58 13 0.24
ACGTcount: A:0.32, C:0.04, G:0.18, T:0.46
Consensus pattern (58 bp):
TGCTAAAAGGGGGATTTTTTTTAAAGTAAAATTATTTTGTGACGTTTTTTATATAAAT
Found at i:41619691 original size:204 final size:204
Alignment explanation
Indices: 41619333--41619705 Score: 694
Period size: 204 Copynumber: 1.8 Consensus size: 204
41619323 AGGGCGCAAA
*
41619333 TTTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATATAAACGCCGCTATTGCTTACCTTTAG
1 TTTTTTTTAAAGTAAAATTATTTTGTGACGTTTTTTATATAAACGCCGCTATTGCTTACCTTTAG
* *
41619398 CGGCGTTTTTCATAAAAGCGCCGCAAAAAAAATTATTTTGAACAAAACTATGTCGTTTTGCTATG
66 CGGCGTTTTTCATAAAAGCACCGCAAAAAAAATTATTTTGAACAAAACTATGCCGTTTTGCTATG
*
41619463 CTATGCTAAAAGGGGGATTTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATATAAATTGCT
131 CTATGCTAAAAGGGGGACTTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATATAAATTGCT
41619528 AAAAGGGGG
196 AAAAGGGGG
41619537 TTTTTTTTAAAGTAAAATTATTTTGTGACGTTTTTTATATAAACGCCGCTATTGCTTACCTTTAG
1 TTTTTTTTAAAGTAAAATTATTTTGTGACGTTTTTTATATAAACGCCGCTATTGCTTACCTTTAG
41619602 CGGCGTTTTTCATAAAAGCACCGCAAAAAAAATTCATTTTGAACAAAACTATGCCGTTTTGCTAT
66 CGGCGTTTTTCATAAAAGCACCGCAAAAAAAATT-ATTTTGAACAAAACTATGCCGTTTTGCTAT
41619667 GCTATGCTAAAAGGGGG-CTTTTTTTAAAGTAAAATTATT
130 GCTATGCTAAAAGGGGGACTTTTTTTAAAGTAAAATTATT
41619706 ATCTCTTAAA
Statistics
Matches: 164, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
204 118 0.72
205 46 0.28
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.40
Consensus pattern (204 bp):
TTTTTTTTAAAGTAAAATTATTTTGTGACGTTTTTTATATAAACGCCGCTATTGCTTACCTTTAG
CGGCGTTTTTCATAAAAGCACCGCAAAAAAAATTATTTTGAACAAAACTATGCCGTTTTGCTATG
CTATGCTAAAAGGGGGACTTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATATAAATTGCT
AAAAGGGGG
Found at i:41619912 original size:49 final size:50
Alignment explanation
Indices: 41619859--41619999 Score: 153
Period size: 49 Copynumber: 2.9 Consensus size: 50
41619849 ATTTAATATG
* *
41619859 TAAATTAA-AAAACACTCAGTAATGTACCCAAAAAACTTAAAAATTATTT
1 TAAATTAATAAAACACTAAATAATGTACCCAAAAAACTTAAAAATTATTT
** ***
41619908 TAAA-TAATAGTATTTTAAATAATGTACCCAAAAAACTTAAAAATTATTT
1 TAAATTAATAAAACACTAAATAATGTACCCAAAAAACTTAAAAATTATTT
** ***
41619957 TAAA-TAATAGTATTTTAAATAATGTACCCAAAAAACTTAAAAA
1 TAAATTAATAAAACACTAAATAATGTACCCAAAAAACTTAAAAA
41620000 AAAAATTTTG
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
48 3 0.04
49 81 0.96
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.32
Consensus pattern (50 bp):
TAAATTAATAAAACACTAAATAATGTACCCAAAAAACTTAAAAATTATTT
Found at i:41620075 original size:41 final size:41
Alignment explanation
Indices: 41620009--41620125 Score: 139
Period size: 41 Copynumber: 2.9 Consensus size: 41
41619999 AAAAAATTTT
* * *
41620009 GCGGCACTTTTTCAAAAACGTCGCTAAAGCCCTGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * *
41620050 GTGGCGCTT-TTTAAAAAGTGCCGCTAAAGACCC-GAGCATTA
1 GCGGCGCTTCTTCAAAAA-CGCCGCTAAAG-CCCTGAGCATTA
*
41620091 GCGGCGCTTCTTCAAAAACGCCGCTAACGCCCTGA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCTGA
41620126 AAACTCAAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
40 10 0.16
41 43 0.68
42 10 0.16
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.22
Consensus pattern (41 bp):
GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
Found at i:41620292 original size:40 final size:40
Alignment explanation
Indices: 41620157--41620293 Score: 152
Period size: 40 Copynumber: 3.5 Consensus size: 40
41620147 TGTGCTTCAG
* * ** * *
41620157 TTTTTTGCGGCGCTTTTTGGAAAACGCCGCTAATGC-TCA
1 TTTTTAGCGGCGTTTTTTCTAAAACGCCGCTAATACTTGA
* * *
41620196 TTTTTAGCGGCG-TTTTCCTAAAAACGCTGCTAATACTGGA
1 TTTTTAGCGGCGTTTTTTCT-AAAACGCCGCTAATACTTGA
* *
41620236 TCTTTAGCGGCGTTTTTTCTAAAGCGCCGCTAATACTTGA
1 TTTTTAGCGGCGTTTTTTCTAAAACGCCGCTAATACTTGA
41620276 TTTTTAGCGGCGTTTTTT
1 TTTTTAGCGGCGTTTTTT
41620294 ATCCAAACGC
Statistics
Matches: 81, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
38 4 0.05
39 25 0.31
40 46 0.57
41 6 0.07
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.39
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTTCTAAAACGCCGCTAATACTTGA
Found at i:41626018 original size:29 final size:29
Alignment explanation
Indices: 41625985--41626043 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
41625975 TGAATCTTTA
*
41625985 TACGAGTGTGGATGTTAATTTTTATGAAG
1 TACGAGCGTGGATGTTAATTTTTATGAAG
41626014 TACGAGCGTGGATGTTAATTTTTATGAAG
1 TACGAGCGTGGATGTTAATTTTTATGAAG
41626043 T
1 T
41626044 TTTGAGCTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.27, C:0.05, G:0.27, T:0.41
Consensus pattern (29 bp):
TACGAGCGTGGATGTTAATTTTTATGAAG
Found at i:41628564 original size:10 final size:10
Alignment explanation
Indices: 41628522--41628564 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
41628512 TTGAATAGAG
41628522 TATGTATATA
1 TATGTATATA
*
41628532 TATATATATA
1 TATGTATATA
* *
41628542 TATGTAAAAA
1 TATGTATATA
*
41628552 TATGTATGTA
1 TATGTATATA
41628562 TAT
1 TAT
41628565 AAAATATAGA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (10 bp):
TATGTATATA
Found at i:41628626 original size:14 final size:14
Alignment explanation
Indices: 41628607--41628633 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41628597 GTATAAATAC
41628607 TAATAATAATACAG
1 TAATAATAATACAG
41628621 TAATAATAATACA
1 TAATAATAATACA
41628634 ATTTAACAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (14 bp):
TAATAATAATACAG
Found at i:41630027 original size:20 final size:20
Alignment explanation
Indices: 41629996--41630046 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
41629986 ATGAAATCTT
41629996 TAGAAA-TTTGGTA-AACCCA
1 TAGAAATTTTGGTATAA-CCA
*
41630015 TAGAAATTTTGGTATAACCT
1 TAGAAATTTTGGTATAACCA
*
41630035 TAGAAGTTTTGG
1 TAGAAATTTTGG
41630047 CAAGACTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 6 0.21
20 20 0.71
21 2 0.07
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (20 bp):
TAGAAATTTTGGTATAACCA
Found at i:41639310 original size:43 final size:43
Alignment explanation
Indices: 41639225--41639371 Score: 154
Period size: 43 Copynumber: 3.4 Consensus size: 43
41639215 CGAGACTACA
* * * *
41639225 TGTAAGACCATATCTGTGATA-TGGCATCGCTATGAGACTTCG
1 TGTAAGACCATATCTGGGACATTGGCATCGATATGAGATTTCG
* * *
41639267 TGTAAGACCATGTCTGGGACATTGGCATGGATATGTGATTTCG
1 TGTAAGACCATATCTGGGACATTGGCATCGATATGAGATTTCG
** * * * *
41639310 TGTAAGACCATGGCTAGG-CTATTGGCATCGATACGAGATTACA
1 TGTAAGACCATATCTGGGAC-ATTGGCATCGATATGAGATTTCG
41639353 TGTAAGACCATATCTGGGA
1 TGTAAGACCATATCTGGGA
41639372 TATGACATTG
Statistics
Matches: 85, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
42 19 0.22
43 66 0.78
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (43 bp):
TGTAAGACCATATCTGGGACATTGGCATCGATATGAGATTTCG
Found at i:41644796 original size:18 final size:17
Alignment explanation
Indices: 41644769--41644811 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
41644759 TAAGTGATAA
*
41644769 TGGGCTCACACGCCTGTG
1 TGGGCCCACACGCC-GTG
*
41644787 TGGGCCCACACGTCGTG
1 TGGGCCCACACGCCGTG
41644804 T-GGCCCAC
1 TGGGCCCAC
41644812 TCAGCCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 7 0.30
17 4 0.17
18 12 0.52
ACGTcount: A:0.12, C:0.37, G:0.33, T:0.19
Consensus pattern (17 bp):
TGGGCCCACACGCCGTG
Found at i:41651035 original size:9 final size:10
Alignment explanation
Indices: 41651020--41651047 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
41651010 AACTTTTTCG
41651020 TATTTTTTAT
1 TATTTTTTAT
41651030 TATTTTTTAT
1 TATTTTTTAT
41651040 TATTTTTT
1 TATTTTTT
41651048 CCTTAAATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (10 bp):
TATTTTTTAT
Found at i:41652750 original size:20 final size:21
Alignment explanation
Indices: 41652707--41652755 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
41652697 AATAGAAATC
*
41652707 AATAGAATTGTTATTTTGGAA
1 AATAGAATTGTTATTTTAGAA
41652728 AATAGAA-T-TTATATTTAGAA
1 AATAGAATTGTTAT-TTTAGAA
41652748 AATA-AATT
1 AATAGAATT
41652756 CTCACTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 6 0.24
20 12 0.48
21 7 0.28
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (21 bp):
AATAGAATTGTTATTTTAGAA
Found at i:41671065 original size:42 final size:42
Alignment explanation
Indices: 41671013--41671107 Score: 163
Period size: 42 Copynumber: 2.3 Consensus size: 42
41671003 TGAACAGCAG
*
41671013 TAAGTGTGCGAAACTAAAATGACGATGTTGAATAATGGGCAC
1 TAAGTGTGCGAAACTAAAATGACGATGTTGAATAACGGGCAC
* *
41671055 TAAGTGTGCGAAATTAAAATGATGATGTTGAATAACGGGCAC
1 TAAGTGTGCGAAACTAAAATGACGATGTTGAATAACGGGCAC
41671097 TAAGTGTGCGA
1 TAAGTGTGCGA
41671108 TACTGAGAGC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.37, C:0.11, G:0.27, T:0.25
Consensus pattern (42 bp):
TAAGTGTGCGAAACTAAAATGACGATGTTGAATAACGGGCAC
Found at i:41673740 original size:9 final size:9
Alignment explanation
Indices: 41673707--41673732 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
41673697 AATTTAGCCT
41673707 TTTTTTTTA
1 TTTTTTTTA
41673716 TTTTTTTTA
1 TTTTTTTTA
41673725 TTTTTTTT
1 TTTTTTTT
41673733 GTTATTTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:41673783 original size:3 final size:3
Alignment explanation
Indices: 41673775--41673848 Score: 85
Period size: 3 Copynumber: 24.3 Consensus size: 3
41673765 GAATTTGATT
* **
41673775 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TCG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* **
41673823 TCA TTA GCA TTA TTA TTA TTTA TTA T
1 TTA TTA TTA TTA TTA TTA -TTA TTA T
41673849 ATACCTATAT
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
3 57 0.95
4 3 0.05
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (3 bp):
TTA
Done.