Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold309
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: 1359455
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.31
Warning! 63696 characters in sequence are not A, C, G, or T
File 1 of 5
Found at i:2568 original size:43 final size:43
Alignment explanation
Indices: 2489--2577 Score: 115
Period size: 43 Copynumber: 2.1 Consensus size: 43
2479 CCATGTTTCC
* * * *
2489 AGACCGTGTACAATTCGAAATAGGGTTACACGGCCATGTCGCT
1 AGACCGTGTACAATTCAAAATAGGCTCACACAGCCATGTCGCT
* * *
2532 AGACCGTGTGCAATTCAAAATAGGCTCATACAGCCATGTCTCT
1 AGACCGTGTACAATTCAAAATAGGCTCACACAGCCATGTCGCT
2575 AGA
1 AGA
2578 ACATGTAGCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (43 bp):
AGACCGTGTACAATTCAAAATAGGCTCACACAGCCATGTCGCT
Found at i:3494 original size:21 final size:21
Alignment explanation
Indices: 3470--3541 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
3460 CTATAGCATC
3470 TTTTAGCTATGGTCTTACTCA
1 TTTTAGCTATGGTCTTACTCA
** * *
3491 TTTTAATTCATGTTGCCATAACGTC-
1 TTTTAGCT-ATG--GTC-TTAC-TCA
3516 TTTTAGCTATGGTCTTACTCA
1 TTTTAGCTATGGTCTTACTCA
3537 TTTTA
1 TTTTA
3542 ATTCATGTTG
Statistics
Matches: 37, Mismatches: 8, Indels: 12
0.65 0.14 0.21
Matches are distributed among these distances:
20 2 0.05
21 14 0.38
22 5 0.14
24 5 0.14
25 9 0.24
26 2 0.05
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.49
Consensus pattern (21 bp):
TTTTAGCTATGGTCTTACTCA
Found at i:3617 original size:45 final size:45
Alignment explanation
Indices: 3468--3685 Score: 310
Period size: 45 Copynumber: 4.8 Consensus size: 45
3458 TGCTATAGCA
*
3468 TCTTTTAGCTATGGTCTTACTCATTTTAATTCATGTTGCCATAACG
1 TCTTTCAGCTATGGTCTTACTCATTTTAA-TCATGTTGCCATAACG
* *
3514 TCTTTTAGCTATGGTCTTACTCATTTTAATTCATGTTGCCATAACA
1 TCTTTCAGCTATGGTCTTACTCATTTTAA-TCATGTTGCCATAACG
* * * *
3560 TTTTTCAACTATGGTCTTACTCTTTTTAATCATGTTGCCATAGCG
1 TCTTTCAGCTATGGTCTTACTCATTTTAATCATGTTGCCATAACG
* * **
3605 TCTTCCAGCTATGGTCTTACTCATTTTAATCATATTGCCATAGTG
1 TCTTTCAGCTATGGTCTTACTCATTTTAATCATGTTGCCATAACG
*
3650 TCTTTCAGCTATGGTCTTACCCATTTTAATCATGTT
1 TCTTTCAGCTATGGTCTTACTCATTTTAATCATGTT
3686 TATGATAACA
Statistics
Matches: 156, Mismatches: 16, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
45 86 0.55
46 70 0.45
ACGTcount: A:0.22, C:0.21, G:0.12, T:0.45
Consensus pattern (45 bp):
TCTTTCAGCTATGGTCTTACTCATTTTAATCATGTTGCCATAACG
Found at i:10697 original size:21 final size:20
Alignment explanation
Indices: 10658--10697 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
10648 TCTTAGTGTC
* *
10658 GAAATTTTGAAAATTTAAAA
1 GAAAATTTGAAAATATAAAA
10678 GAAAATTTGAATAATATAAA
1 GAAAATTTGAA-AATATAAA
10698 TTGGATGGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (20 bp):
GAAAATTTGAAAATATAAAA
Found at i:13610 original size:132 final size:132
Alignment explanation
Indices: 13496--13773 Score: 430
Period size: 132 Copynumber: 2.1 Consensus size: 132
13486 GCTGCTGTCC
* * **
13496 AAGGAGATAGGACTAGTGGCTTAAATCTGCTTCCCTACTACCTGGGGAAGATAAGATTCGTCGTC
1 AAGGAGATAGGACTAGTGACTTAAATCTGCTTCCCTACTACCTGGGAAAGATAAGATTCACCGTC
* ** * *
13561 TTCGATCTGATCCGCTACTGCTTAGGGAGATAAGATCTGTTATTTTCAACCTACTCCACCACTGC
66 TTCAATCTGATCAACTACTGCTTAGGGAGATAAGATCTGTAATATTCAACCTACTCCACCACTGC
13626 TT
131 TT
*
13628 AGGGAGATAGGACTAGTGACTTAAATCTGCTTCCCTACTACCTGGGAAAGATAAGATTCACCGTC
1 AAGGAGATAGGACTAGTGACTTAAATCTGCTTCCCTACTACCTGGGAAAGATAAGATTCACCGTC
* *
13693 TTCAATCTGCTCAACTACTGCTTAGGGAGATAAGATCTGTAATATTCAACCTACTCCACTACTGC
66 TTCAATCTGATCAACTACTGCTTAGGGAGATAAGATCTGTAATATTCAACCTACTCCACCACTGC
13758 TT
131 TT
* *
13760 AGGGAGATAAGACT
1 AAGGAGATAGGACT
13774 TACAATCTTT
Statistics
Matches: 133, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
132 133 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (132 bp):
AAGGAGATAGGACTAGTGACTTAAATCTGCTTCCCTACTACCTGGGAAAGATAAGATTCACCGTC
TTCAATCTGATCAACTACTGCTTAGGGAGATAAGATCTGTAATATTCAACCTACTCCACCACTGC
TT
Found at i:13625 original size:44 final size:45
Alignment explanation
Indices: 13575--13796 Score: 149
Period size: 44 Copynumber: 5.0 Consensus size: 45
13565 ATCTGATCCG
* *
13575 CTACTGCTTAGGGAGATAAGATCT-GTTATTTTCAACCTACTCCA
1 CTACTGCTTAGGGAGATAAGATCTAGTAATCTTCAACCTACTCCA
* * * * * *
13619 CCACTGCTTAGGGAGATAGGA-CTAGTGA-CTTAAATCTGCTTCC-
1 CTACTGCTTAGGGAGATAAGATCTAGTAATCTTCAACCTAC-TCCA
* * *** * * *
13662 CTACTACCT-GGGAAAGATAAGAT-TCA-CCGTCTTCAATCTGCTCAA
1 CTACTGCTTAGGG--AGATAAGATCT-AGTAATCTTCAACCTACTCCA
*
13707 CTACTGCTTAGGGAGATAAGATCT-GTAATATTCAACCTACTCCA
1 CTACTGCTTAGGGAGATAAGATCTAGTAATCTTCAACCTACTCCA
* * *
13751 CTACTGCTTAGGGAGATAAGA-CTTA-CAATCTTTAACCTATTCCA
1 CTACTGCTTAGGGAGATAAGATC-TAGTAATCTTCAACCTACTCCA
13795 CT
1 CT
13797 GTTGTCCAAG
Statistics
Matches: 136, Mismatches: 29, Indels: 26
0.71 0.15 0.14
Matches are distributed among these distances:
42 3 0.02
43 16 0.12
44 95 0.70
45 19 0.14
46 3 0.02
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (45 bp):
CTACTGCTTAGGGAGATAAGATCTAGTAATCTTCAACCTACTCCA
Found at i:13726 original size:176 final size:176
Alignment explanation
Indices: 13575--13928 Score: 450
Period size: 176 Copynumber: 2.0 Consensus size: 176
13565 ATCTGATCCG
* * *
13575 CTACTGCTTAGGGAGATAAGATCTGT-TAT-TTTCAACCTACTCCACCACTG-CTTAGGGAGATA
1 CTACTGCTTAGGGAGATAAGA-CT-TAAATCTTT-AACCTACTCCACCACTGTC-CAAGGAGATA
* * *
13637 GGACTAGTGACTTAAATCTGCTTCCCTACTACCTGGGAAAGATAAGATTCA-CCGTCTTCAATCT
62 GGACTAATGACTTAAATCTGCTTCCCTACTACATGGGAAAGATAAGATT-AGACGTCTTCAATCT
*
13701 GCTCAACTACTGCTTAGGGAGATAAGA-TCTGTAATATTCAACCTACTCCA
126 GCTCAACTACTGCTTAGGAAGATAAGATTCTGTAATATTCAACCTACTCCA
* ***
13751 CTACTGCTTAGGGAGATAAGACTTACAATCTTTAACCTATTCCACTGTTGTCCAAGGAGATAGGA
1 CTACTGCTTAGGGAGATAAGACTTA-AATCTTTAACCTACTCCACCACTGTCCAAGGAGATAGGA
* * *
13816 CTAATGGCTTAAATCTGCTTCCCTACTACATGGGGAAGATAAGATTAGACGTCTTCGATCTGCTC
65 CTAATGACTTAAATCTGCTTCCCTACTACATGGGAAAGATAAGATTAGACGTCTTCAATCTGCTC
* * * *
13881 CACTACTTCTTAGGAAGATAAGA-TCTGTAATCTTCAACCTATTCCA
130 AACTACTGCTTAGGAAGATAAGATTCTGTAATATTCAACCTACTCCA
13927 CT
1 CT
13929 GCTGTCTAGG
Statistics
Matches: 155, Mismatches: 18, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
174 1 0.01
175 3 0.02
176 147 0.95
177 4 0.03
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (176 bp):
CTACTGCTTAGGGAGATAAGACTTAAATCTTTAACCTACTCCACCACTGTCCAAGGAGATAGGAC
TAATGACTTAAATCTGCTTCCCTACTACATGGGAAAGATAAGATTAGACGTCTTCAATCTGCTCA
ACTACTGCTTAGGAAGATAAGATTCTGTAATATTCAACCTACTCCA
Found at i:13856 original size:132 final size:131
Alignment explanation
Indices: 13746--14039 Score: 403
Period size: 132 Copynumber: 2.2 Consensus size: 131
13736 ATTCAACCTA
* *
13746 CTCCACTACTGCTTAGGGAGATAAGA-CT-TACAATCTTTAACCTATTCCACTGTTGTCCAAGGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGT--AATCTTCAACCTATTCCACTGCTGTCCAAGGA
* * *
13809 GATAGGACTAATGGCTTAAATCTGCTTCCCTACTACATGGGGAAGATAAGATTAGACGTCTTCGA
64 AATAGGACTAATGACTTAAATCTGCTTCCCTACTACATGGGGAAGATAAGATTAGA-ATCTTCGA
13874 TCTG
128 TCTG
* * * *
13878 CTCCACTACTTCTTAGGAAGATAAGATCTGTAATCTTCAACCTATTCCACTGCTGTCTAGGGAAA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTATTCCACTGCTGTCCAAGGAAA
* * * * * *
13943 TAGGACTAGTGACTTAAATTTGCTTCCCTACTACTTGGGGAAGATAAGATTCGCCATCTTCGATT
66 TAGGACTAATGACTTAAATCTGCTTCCCTACTACATGGGGAAGATAAGATTAG-AATCTTCGATC
14008 TG
130 TG
14010 CTCCACTACTGCTTAGGGAGATAAGATCTG
1 CTCCACTACTGCTTAGGGAGATAAGATCTG
14040 ATGCGATCCA
Statistics
Matches: 142, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
132 139 0.98
133 2 0.01
134 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (131 bp):
CTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTATTCCACTGCTGTCCAAGGAAA
TAGGACTAATGACTTAAATCTGCTTCCCTACTACATGGGGAAGATAAGATTAGAATCTTCGATCT
G
Found at i:13948 original size:308 final size:308
Alignment explanation
Indices: 13371--14039 Score: 1036
Period size: 308 Copynumber: 2.2 Consensus size: 308
13361 GCTTGGGAGA
* * * *
13371 ATAAGATTCACCGTCTTCGATCTGCTCCACTATTGCTTAAGAAGATAAGAT-TGTAATTTTCAAC
1 ATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATATTCAAC
* *
13435 CTACTCCACTACTGCTTAGGGAGATAAGGCTTACAATCTTCAACCTATTACGCTGCTGTCCAAGG
66 CTACTCCACTACTGCTTAGGGAGATAAGACTTACAATCTTCAACCTATTACACTGCTGTCCAAGG
* * * *
13500 AGATAGGACTAGTGGCTTAAATCTGCTTCCCTACTACCTGGGGAAGATAAGATTCGTCGTCTTCG
131 AGATAGGACTAATGGCTTAAATCTGCTTCCCTACTACATGGGGAAGATAAGATTAGACGTCTTCG
* * * *
13565 ATCTGATCCGCTACTGCTTAGGGAGATAAGATCTGTTATTTTCAACCTACTCCACCACTGCTTAG
196 ATCTGATCCACTACTGCTTAGGAAGATAAGATCTGTAATCTTCAACCTACTCCACCACTGCTTAG
*
13630 GGAGATAGGACTAGTGACTTAAATCTGCTTCCCTACTACCTGGGAAAG
261 GGAAATAGGACTAGTGACTTAAATCTGCTTCCCTACTACCTGGGAAAG
* *
13678 ATAAGATTCACCGTCTTCAATCTGCTCAACTACTGCTTAGGGAGATAAGATCTGTAATATTCAAC
1 ATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATATTCAAC
* * *
13743 CTACTCCACTACTGCTTAGGGAGATAAGACTTACAATCTTTAACCTATTCCACTGTTGTCCAAGG
66 CTACTCCACTACTGCTTAGGGAGATAAGACTTACAATCTTCAACCTATTACACTGCTGTCCAAGG
13808 AGATAGGACTAATGGCTTAAATCTGCTTCCCTACTACATGGGGAAGATAAGATTAGACGTCTTCG
131 AGATAGGACTAATGGCTTAAATCTGCTTCCCTACTACATGGGGAAGATAAGATTAGACGTCTTCG
* * * **
13873 ATCTGCTCCACTACTTCTTAGGAAGATAAGATCTGTAATCTTCAACCTATTCCACTGCTG-TCTA
196 ATCTGATCCACTACTGCTTAGGAAGATAAGATCTGTAATCTTCAACCTACTCCACCACTGCT-TA
* * *
13937 GGGAAATAGGACTAGTGACTTAAATTTGCTTCCCTACTACTTGGGGAAG
260 GGGAAATAGGACTAGTGACTTAAATCTGCTTCCCTACTACCTGGGAAAG
* * *
13986 ATAAGATTCGCCATCTTCGATTTGCTCCACTACTGCTTAGGGAGATAAGATCTG
1 ATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
14040 ATGCGATCCA
Statistics
Matches: 327, Mismatches: 33, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
307 47 0.14
308 280 0.86
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (308 bp):
ATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATATTCAAC
CTACTCCACTACTGCTTAGGGAGATAAGACTTACAATCTTCAACCTATTACACTGCTGTCCAAGG
AGATAGGACTAATGGCTTAAATCTGCTTCCCTACTACATGGGGAAGATAAGATTAGACGTCTTCG
ATCTGATCCACTACTGCTTAGGAAGATAAGATCTGTAATCTTCAACCTACTCCACCACTGCTTAG
GGAAATAGGACTAGTGACTTAAATCTGCTTCCCTACTACCTGGGAAAG
Found at i:27070 original size:132 final size:133
Alignment explanation
Indices: 26903--27908 Score: 500
Period size: 132 Copynumber: 7.5 Consensus size: 133
26893 ATTCAACCTA
* *
26903 CTCCACTACTGCTTAGGGAGATAAGA-CT-TACAATCTTTAACCTATTCCACTGTTGTCCAAGGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTA-AATCTTCAACCTATTCCACTGCTGTCCAAGGA
* * *
26966 GATAGGACTAATGGCTTAAATCTGCTTCCCTACTACATGGGGAAGATAAGATTAGACGTCTTCGA
65 AATAGGACTAATGACTTAAATCTGCTTCCCTACTACATGGGGAAGATAAGATTAGACATCTTCGA
27031 TCTG
130 TCTG
* * * *
27035 CTCCACTACTTCTTAGGAAGATAAGATCTGT-AATCTTCAACCTATTCCACTGCTGTCTAGGGAA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTAAATCTTCAACCTATTCCACTGCTGTCCAAGGAA
* * * * *
27099 ATAGGACTAGTGACTTAAATTTGCTTCCCTACTACTTGGGGAAGATAAGATTCGCCATCTTCGAT
66 ATAGGACTAATGACTTAAATCTGCTTCCCTACTACATGGGGAAGATAAGATTAGACATCTTCGAT
*
27164 TTG
131 CTG
* * * **
27167 CTCCACTACTGCTTAGGGAGATAAGATCTG---ATGC--GATCC-ACTCCACTG-TAACCCAGGG
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTAAAT-CTTCAACCTATTCCACTGCT-GTCCA---
* * * ** * * ** ****
27225 AGGCAAGGCTAGTATCTACTTCG-CTTGGGAGAATAAGATTCACCGT-CTTCGATCTGCTCCACT
61 AGG-AA--ATAGGA-CTA-AT-GACTT---A-AATCTGCTTC-CC-TACTAC-ATGGGGAAGA-T
* * * * * *
27288 ATTGCTTAAGGAGATAAGATT-G-TAATT
112 A-AGATT-A-GACAT---CTTCGAT-CTG
* * * * *
27315 TTCAACCTACTCCACTACTGCTTAGGGAGATAAG-GCT-TACAATCTTCAACCTATTACGCTGCT
1 CTCCA-CTAC--------TGCTTAGGGAGATAAGATCTGTA-AATCTTCAACCTATTCCACTGCT
* * * * * * *
27378 GTCCAAGGAGATAGGACTAGTGGCTTAAATCTGCTTCCCTACTACCTGGGGAAAATAAGATTCGT
56 GTCCAAGGAAATAGGACTAATGACTTAAATCTGCTTCCCTACTACATGGGGAAGATAAGATTAGA
* * *
27443 CGTCTTTGATTTG
121 CATCTTCGATCTG
* * * * *
27456 CTCCACTACTGCTTTGGGAGATAAGATCTGT-AATTTTCGACCTATTCCACTGCTGTCCAGGGAG
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTAAATCTTCAACCTATTCCACTGCTGTCCAAGGAA
* * ** * * * * * * * * *
27520 ATAAGAATGGT-ATCTTCAACCT-ATTCCATTGCTGTC-TAGGG-AGATAAGATTCA-CCGTCTT
66 ATAGGACTAATGA-CTTAAATCTGCTTCC-CTACT-ACATGGGGAAGATAAGATT-AGACATCTT
27580 CGATCTG
127 CGATCTG
* * * * * *
27587 CTTCACTACTGCTTAGGGAGATAAGATCTGT-AATTTTCGACCTATTCCACTGTTGTCCAGGGAG
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTAAATCTTCAACCTATTCCACTGCTGTCCAAGGAA
* * * * * *
27651 ATAGGACTAGTGGCTTTAATCTGCTTCCCTACTACCTGGGGAAGATAAGATTCGCCATCTTCGAT
66 ATAGGACTAATGACTTAAATCTGCTTCCCTACTACATGGGGAAGATAAGATTAGACATCTTCGAT
*
27716 ATG
131 CTG
* * ** * * * *
27719 CTTCACTACTGCTTAGGGAGATAAGATCTGT-AATTTTTGACCTATTTCACTACTGTCCAGGGAG
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTAAATCTTCAACCTATTCCACTGCTGTCCAAGGAA
* * * * * * * *
27783 ATAGGACTAGTGGCTTAAATCTGCTTCCCTACTACCT-GGGAAGATAAGATTCGCCGTTTTTGAT
66 ATAGGACTAATGACTTAAATCTGCTTCCCTACTACATGGGGAAGATAAGATTAGACATCTTCGAT
27847 CTG
131 CTG
* * * *
27850 CTCCTCTACTGCTTAGGGAGATAAGATC--TACAATTTTCGACCTATTCCACAGCTGTCCA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTA-AATCTTCAACCTATTCCACTGCTGTCCA
27909 GGGAGATAAG
Statistics
Matches: 675, Mismatches: 137, Indels: 125
0.72 0.15 0.13
Matches are distributed among these distances:
127 1 0.00
128 10 0.01
129 4 0.01
130 3 0.00
131 186 0.28
132 329 0.49
133 5 0.01
134 6 0.01
135 3 0.00
136 4 0.01
137 1 0.00
139 1 0.00
140 13 0.02
141 10 0.01
142 5 0.01
143 4 0.01
144 3 0.00
145 3 0.00
146 5 0.01
147 5 0.01
148 10 0.01
149 13 0.02
150 1 0.00
152 1 0.00
153 4 0.01
154 3 0.00
155 4 0.01
156 2 0.00
157 17 0.03
158 4 0.01
159 2 0.00
160 3 0.00
161 9 0.01
162 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (133 bp):
CTCCACTACTGCTTAGGGAGATAAGATCTGTAAATCTTCAACCTATTCCACTGCTGTCCAAGGAA
ATAGGACTAATGACTTAAATCTGCTTCCCTACTACATGGGGAAGATAAGATTAGACATCTTCGAT
CTG
Found at i:27505 original size:44 final size:43
Alignment explanation
Indices: 27457--27653 Score: 143
Period size: 44 Copynumber: 4.5 Consensus size: 43
27447 TTTGATTTGC
* *
27457 TCCACTACTG-CTTTGGGAGATAAGATCTGTAATTTTCGACCTAT
1 TCCACTACTGTC-TAGGGAGATAAGAT-TGTAATCTTCGACCTAT
* * * *
27501 TCCACTGCTGTCCAGGGAGATAAGAATGGT-ATCTTCAACCTAT
1 TCCACTACTGTCTAGGGAGATAAG-ATTGTAATCTTCGACCTAT
* * * * * *
27544 TCCATTGCTGTCTAGGGAGATAAGATT-CACCGTCTTCGATCTGCT
1 TCCACTACTGTCTAGGGAGATAAGATTGTA--ATCTTCGACCT-AT
*
27589 T-CACTACTG-CTTAGGGAGATAAGATCTGTAATTTTCGACCTAT
1 TCCACTACTGTC-TAGGGAGATAAGAT-TGTAATCTTCGACCTAT
** *
27632 TCCACTGTTGTCCAGGGAGATA
1 TCCACTACTGTCTAGGGAGATA
27654 GGACTAGTGG
Statistics
Matches: 118, Mismatches: 24, Indels: 22
0.72 0.15 0.13
Matches are distributed among these distances:
42 2 0.02
43 36 0.31
44 72 0.61
45 7 0.06
46 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (43 bp):
TCCACTACTGTCTAGGGAGATAAGATTGTAATCTTCGACCTAT
Found at i:27555 original size:175 final size:175
Alignment explanation
Indices: 27251--27565 Score: 400
Period size: 175 Copynumber: 1.8 Consensus size: 175
27241 TACTTCGCTT
* *
27251 GGGAGAATAAGATTCACCGTCTTCGATCTGCTCCACTATTGCTTAAGGAGATAAGATTGTAATTT
1 GGGAAAATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAAGGAGATAAGATTGTAATTT
* ** *
27316 TCAACCTACTCCACTACTGCTTAGGGAGATAAGGCTTACAATCTTCAACCTATTACGCTGCTGTC
66 TCAACCTACTCCACTACTGCTCAGGGAGATAAGGAATACAATCTTCAACCTATTACACTGCTGTC
27381 CAAGGAGATAGGACTAGTGGCTTAAATCTGCTTCCCTACTACCTG
131 CAAGGAGATAGGACTAGTGGCTTAAATCTGCTTCCCTACTACCTG
** * * **
27426 GGGAAAATAAGATTCGTCGTCTTTGATTTGCTCCACTACTGCTTTGGGAGATAAGATCTGTAATT
1 GGGAAAATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAAGGAGATAAGAT-TGTAATT
* * * *** * *
27491 TTCGACCTATTCCACTGCTG-TCCAGGGAGATAA-GAATGGTATCTTCAACCTATTCCATTGCTG
65 TTCAACCTACTCCACTACTGCT-CAGGGAGATAAGGAATACAATCTTCAACCTATTACACTGCTG
* *
27554 TCTAGGGAGATA
129 TCCAAGGAGATA
27566 AGATTCACCG
Statistics
Matches: 116, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
175 82 0.71
176 34 0.29
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (175 bp):
GGGAAAATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAAGGAGATAAGATTGTAATTT
TCAACCTACTCCACTACTGCTCAGGGAGATAAGGAATACAATCTTCAACCTATTACACTGCTGTC
CAAGGAGATAGGACTAGTGGCTTAAATCTGCTTCCCTACTACCTG
Found at i:27609 original size:131 final size:132
Alignment explanation
Indices: 27324--27940 Score: 697
Period size: 131 Copynumber: 4.7 Consensus size: 132
27314 TTTCAACCTA
* * * * * *
27324 CTCCACTACTGCTTAGGGAGATAAG-GCT-TACAATCTTCAACCTATTACGCTGCTGTCCAAGGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGT--AATTTTCGACCTATTCCACTGCTGTCCAGGGA
* * * * * * * * *
27387 GATAGGACTAGTGGCTTAAATCTGCTTCCCTACTACCTGGGGAAAATAAGATTCGTCGTCTTTGA
64 GATAAGACTAGTAGCTTCAACCTGATTCCCTACTACCTAGGGAAGATAAGATTCGCCGTCTTCGA
*
27452 TTTG
129 TCTG
*
27456 CTCCACTACTGCTTTGGGAGATAAGATCTGTAATTTTCGACCTATTCCACTGCTGTCCAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCGACCTATTCCACTGCTGTCCAGGGAGA
* * * * * ** *
27521 TAAGAATGGTATCTTCAACCT-ATTCCATTGCTGTCTAGGG-AGATAAGATTCACCGTCTTCGAT
66 TAAGACTAGTAGCTTCAACCTGATTCC-CTACTACCTAGGGAAGATAAGATTCGCCGTCTTCGAT
27584 CTG
130 CTG
* *
27587 CTTCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCGACCTATTCCACTGTTGTCCAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCGACCTATTCCACTGCTGTCCAGGGAGA
* * * * * * * *
27652 TAGGACTAGTGGCTTTAATCTGCTTCCCTACTACCTGGGGAAGATAAGATTCGCCATCTTCGATA
66 TAAGACTAGTAGCTTCAACCTGATTCCCTACTACCTAGGGAAGATAAGATTCGCCGTCTTCGATC
27717 TG
131 TG
* * * *
27719 CTTCACTACTGCTTAGGGAGATAAGATCTGTAATTTTTGACCTATTTCACTACTGTCCAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCGACCTATTCCACTGCTGTCCAGGGAGA
* * * * * * *
27784 TAGGACTAGTGGCTTAAATCTGCTTCCCTACTACCT-GGGAAGATAAGATTCGCCGTTTTTGATC
66 TAAGACTAGTAGCTTCAACCTGATTCCCTACTACCTAGGGAAGATAAGATTCGCCGTCTTCGATC
27848 TG
131 TG
* ** *
27850 CTCCTCTACTGCTTAGGGAGATAAGATCTACAATTTTCGACCTATTCCACAGCTGTCCAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCGACCTATTCCACTGCTGTCCAGGGAGA
* *
27915 TAAGACTGGTATCTTCAACCT-ATTCC
66 TAAGACTAGTAGCTTCAACCTGATTCC
27941 ACTGCTGCCC
Statistics
Matches: 412, Mismatches: 68, Indels: 12
0.84 0.14 0.02
Matches are distributed among these distances:
130 4 0.01
131 207 0.50
132 198 0.48
133 2 0.00
134 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.32
Consensus pattern (132 bp):
CTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCGACCTATTCCACTGCTGTCCAGGGAGA
TAAGACTAGTAGCTTCAACCTGATTCCCTACTACCTAGGGAAGATAAGATTCGCCGTCTTCGATC
TG
Found at i:27613 original size:175 final size:173
Alignment explanation
Indices: 27247--27613 Score: 369
Period size: 175 Copynumber: 2.1 Consensus size: 173
27237 TATCTACTTC
*
27247 GCTTGGGAGAATAAGATTCACCGTCTTCGATCTGCTCCACTATTGCTTAAGGAGATAAGATTGTA
1 GCTTGGGAG-ATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAAGGAGATAAGATTGTA
* ** *
27312 ATTTTCAACCTACTCCACTACTGCTTAGGGAGATAAGGCTTACAATCTTCAACCTATTACGCTGC
65 ATTTTCAACCTACTCCACTACTGCTCAGGGAGATAAGGAATACAATCTTCAACCTATTACACTGC
* ** *
27377 TGTCCAAGGAGATAGGACTAGTGGCTTAAATCTGCTTCCCTACT
130 TGTCCAAGGAGATAAGACTACCGGCTTAAATCTGCTTCACTACT
* * * ** * * **
27421 ACCTGGGGAAAATAAGATTCGTCGTCTTTGATTTGCTCCACTACTGCTTTGGGAGATAAGATCTG
1 -GCTTGGG-AGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAAGGAGATAAGAT-TG
* * * *** * *
27486 TAATTTTCGACCTATTCCACTGCTG-TCCAGGGAGATAA-GAATGGTATCTTCAACCTATTCCAT
63 TAATTTTCAACCTACTCCACTACTGCT-CAGGGAGATAAGGAATACAATCTTCAACCTATTACAC
* * * * **
27549 TGCTGTCTAGGGAGATAAGATTCACCGTCTTCGATCTGCTTCACTACT
127 TGCTGTCCAAGGAGATAAGACT-ACCGGCTTAAATCTGCTTCACTACT
27597 GCTTAGGGAGATAAGAT
1 GCTT-GGGAGATAAGAT
27614 CTGTAATTTT
Statistics
Matches: 152, Mismatches: 35, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
175 95 0.62
176 57 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (173 bp):
GCTTGGGAGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAAGGAGATAAGATTGTAA
TTTTCAACCTACTCCACTACTGCTCAGGGAGATAAGGAATACAATCTTCAACCTATTACACTGCT
GTCCAAGGAGATAAGACTACCGGCTTAAATCTGCTTCACTACT
Found at i:27830 original size:263 final size:262
Alignment explanation
Indices: 27324--27921 Score: 779
Period size: 263 Copynumber: 2.3 Consensus size: 262
27314 TTTCAACCTA
* * * * * *
27324 CTCCACTACTGCTTAGGGAGATAAG-GCTTACAATCTTCAACCTATTACGCTGCTGTCCAAGGAG
1 CTCCACTACTGCTTAGGGAGATAAGATCTT--AATTTTCGACCTATTCCACTGCTGTCCAGGGAG
* * *
27388 ATAGGACTAGTGGCTTAAATCTGCTTCCCTACTACCTGGGGAAAATAAGATTCGTCGTCTTTGAT
64 ATAGGACTAGTGGCTTAAATCTGCTTCCCTACTACCTGGGGAAAATAAGATTCGCCATCTTCGAT
* * *
27453 TTGCTCCACTACTGCTTTGGGAGATAAGATCTGTAATTTTCGACCTATTCCACTGCTGTCCAGGG
129 ATGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCGACCTATTCCACTACTGTCCAGGG
* * * * * **
27518 AGATAAGAATGGTATCTTCAACCTATTCCATTGCTGTCTAGGGAGATAAGATTCACCGTCTTCGA
194 AGATAAGAATAGTAGCTTAAACCTATTCCACTACTACCTAGGGAGATAAGATTCACCGTCTTCGA
27583 TCTG
259 TCTG
* *
27587 CTTCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCGACCTATTCCACTGTTGTCCAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCT-TAATTTTCGACCTATTCCACTGCTGTCCAGGGAGA
* *
27652 TAGGACTAGTGGCTTTAATCTGCTTCCCTACTACCTGGGGAAGATAAGATTCGCCATCTTCGATA
65 TAGGACTAGTGGCTTAAATCTGCTTCCCTACTACCTGGGGAAAATAAGATTCGCCATCTTCGATA
* * *
27717 TGCTTCACTACTGCTTAGGGAGATAAGATCTGTAATTTTTGACCTATTTCACTACTGTCCAGGGA
130 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCGACCTATTCCACTACTGTCCAGGGA
* * * * * * * *
27782 GATAGGACTAGTGGCTTAAATCTGCTTCC-CTACTACCT-GGGAAGATAAGATTCGCCGTTTTTG
195 GATAAGAATAGTAGCTTAAACCT-ATTCCACTACTACCTAGGG-AGATAAGATTCACCGTCTTCG
27845 ATCTG
258 ATCTG
* * *
27850 CTCCTCTACTGCTTAGGGAGATAAGATCTACAATTTTCGACCTATTCCACAGCTGTCCAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCT-TAATTTTCGACCTATTCCACTGCTGTCCAGGGAGA
*
27915 TAAGACT
65 TAGGACT
27922 GGTATCTTCA
Statistics
Matches: 290, Mismatches: 41, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
262 3 0.01
263 280 0.97
264 6 0.02
265 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.31
Consensus pattern (262 bp):
CTCCACTACTGCTTAGGGAGATAAGATCTTAATTTTCGACCTATTCCACTGCTGTCCAGGGAGAT
AGGACTAGTGGCTTAAATCTGCTTCCCTACTACCTGGGGAAAATAAGATTCGCCATCTTCGATAT
GCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCGACCTATTCCACTACTGTCCAGGGAG
ATAAGAATAGTAGCTTAAACCTATTCCACTACTACCTAGGGAGATAAGATTCACCGTCTTCGATC
TG
Found at i:27912 original size:44 final size:43
Alignment explanation
Indices: 27864--27965 Score: 123
Period size: 43 Copynumber: 2.3 Consensus size: 43
27854 TCTACTGCTT
* * *
27864 AGGGAGATAAGATCTACAATTTTCGACCTATTCCACAGCTGTCC
1 AGGGAGATAAGA-CTACAATCTTCAACCTATTCCACAGCTGCCC
*** *
27908 AGGGAGATAAGACTGGTATCTTCAACCTATTCCACTGCTGCCC
1 AGGGAGATAAGACTACAATCTTCAACCTATTCCACAGCTGCCC
*
27951 AGGGAGATAGGACTA
1 AGGGAGATAAGACTA
27966 GTGGTTTAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
43 37 0.76
44 12 0.24
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.25
Consensus pattern (43 bp):
AGGGAGATAAGACTACAATCTTCAACCTATTCCACAGCTGCCC
Found at i:27990 original size:306 final size:307
Alignment explanation
Indices: 27601--28237 Score: 992
Period size: 306 Copynumber: 2.1 Consensus size: 307
27591 ACTACTGCTT
* * * *
27601 AGGGAGATAAGATCT-GTAATTTTCGACCTATTCCACTGTTGTCCAGGGAGATAGGACTAGTGGC
1 AGGGAGATAAGA-CTGGT-ATCTTCAACCTATTCCACTGCTGCCCAGGGAGATAGGACTAGTGGC
* *
27665 TTTAATCTGCTTCCCTACTACCTGGGGAAGATAAGATTCGCCATCTTCGATATGCTTCACTACTG
64 TTTAATCTGCTTACCTACTACCTGGGGAAGATAAGATTCGCCATCTTCGATATGCTTCACTACTA
*
27730 CTTAGGGAGATAAGATCTGTAATTTTTGACCTATTTCACTACTGTCCAGGGAGATAGGACTAGTG
129 CTTAGGGAGATAAGATCTGTAATTTTTGACCTATTCCACTACTGTCCAGGGAGATAGGACTAGTG
* * * * *
27795 GCTTAAATCTGCTTCCCTACTACCT-GGGAAGATAAGATTCGCCGTTTTTGATCTGCTCCTCTAC
194 GCTTAAATCAGCTTCCCTACTAACTGGGGAAGATAAAATTCGCCGTATTTGATCTGCTCCACTAC
*
27859 TGCTTAGGGAGATAAGATCTACAATTTTCGACCTATTCCACAGCTGTCC
259 TACTTAGGGAGATAAGATCTACAATTTTCGACCTATTCCACAGCTGTCC
27908 AGGGAGATAAGACTGGTATCTTCAACCTATTCCACTGCTGCCCAGGGAGATAGGACTAGTGG-TT
1 AGGGAGATAAGACTGGTATCTTCAACCTATTCCACTGCTGCCCAGGGAGATAGGACTAGTGGCTT
* ** *
27972 TAAATCTGCTTACCTACTACTTGGGGAAGATAAGATTCGCTGTCTTCGATCTGCTTCACTACTAC
66 T-AATCTGCTTACCTACTACCTGGGGAAGATAAGATTCGCCATCTTCGATATGCTTCACTACTAC
** *
28037 TTAGGGAGATAAGATCTGTAATTTTTGACCTATTCCACTGTTGTCTAGGGAGATAGGACTAGTGG
130 TTAGGGAGATAAGATCTGTAATTTTTGACCTATTCCACTACTGTCCAGGGAGATAGGACTAGTGG
* *
28102 CTTAAATCAGCTTCCCTACTAACTGGGGAAGATAAAATTTGTCGTATTTGATCTGCTCCACTACT
195 CTTAAATCAGCTTCCCTACTAACTGGGGAAGATAAAATTCGCCGTATTTGATCTGCTCCACTACT
* * *
28167 ACTTAGGGAGATAAGATCTGCAATTTTTGACCTATTCCACTGCTGTCC
260 ACTTAGGGAGATAAGATCTACAATTTTCGACCTATTCCACAGCTGTCC
*
28215 AGGGAGATAGGACTGGTATCTTC
1 AGGGAGATAAGACTGGTATCTTC
28238 GATCTGCTTC
Statistics
Matches: 301, Mismatches: 26, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
305 3 0.01
306 183 0.61
307 115 0.38
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (307 bp):
AGGGAGATAAGACTGGTATCTTCAACCTATTCCACTGCTGCCCAGGGAGATAGGACTAGTGGCTT
TAATCTGCTTACCTACTACCTGGGGAAGATAAGATTCGCCATCTTCGATATGCTTCACTACTACT
TAGGGAGATAAGATCTGTAATTTTTGACCTATTCCACTACTGTCCAGGGAGATAGGACTAGTGGC
TTAAATCAGCTTCCCTACTAACTGGGGAAGATAAAATTCGCCGTATTTGATCTGCTCCACTACTA
CTTAGGGAGATAAGATCTACAATTTTCGACCTATTCCACAGCTGTCC
Found at i:28003 original size:131 final size:130
Alignment explanation
Indices: 27454--28007 Score: 517
Period size: 131 Copynumber: 4.2 Consensus size: 130
27444 GTCTTTGATT
* * *
27454 TGCTCCACTACTGCTTTGGGAGATAAGATCTGTAATTTTCGACCTATTCCACTGCTGTCCAGGGA
1 TGCTTCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCGACCTATTCCACAGCTGTCCAGGGA
* * * * * *
27519 GATAAGAATGGTATCTTCAACCTATTCCATTGCTGTCTAGGGAGATAAGATTCA-CCGTCTTCGA
66 GATAAGACTAGTATCTTCAACCTATTCCACTGCTGCCTAGGGAGATAAGATT-AGCGGT-TTAGA
27583 TC
129 TC
* *
27585 TGCTTCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCGACCTATTCCACTGTTGTCCAGGGA
1 TGCTTCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCGACCTATTCCACAGCTGTCCAGGGA
* ** * * * * * * * ** *
27650 GATAGGACTAGTGGCTTTAATCTGCTTCC-CTACTACCTGGGGAAGATAAGATTCGCCATCTTCG
66 GATAAGACTAGTATCTTCAACCT-ATTCCACTGCTGCCTAGGG-AGATAAGATTAGCGGT-TTAG
*
27714 ATA
128 ATC
* *
27717 TGCTTCACTACTGCTTAGGGAGATAAGATCTGTAATTTTTGACCTATTTCACTA-CTGTCCAGGG
1 TGCTTCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCGACCTATTCCAC-AGCTGTCCAGGG
* ** * * * * * * * *
27781 AGATAGGACTAGTGGCTTAAATCTGCTTCC-CTACTACCT-GGGAAGATAAGATTCGCCGTTTTT
65 AGATAAGACTAGTATCTTCAACCT-ATTCCACTGCTGCCTAGGG-AGATAAGATTAG-CGGTTTA
27844 GATC
127 GATC
* * **
27848 TGCTCCTCTACTGCTTAGGGAGATAAGATCTACAATTTTCGACCTATTCCACAGCTGTCCAGGGA
1 TGCTTCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCGACCTATTCCACAGCTGTCCAGGGA
* * * * * *
27913 GATAAGACTGGTATCTTCAACCTATTCCACTGCTGCCCAGGGAGATAGGACTAGTGGTTTAAATC
66 GATAAGACTAGTATCTTCAACCTATTCCACTGCTGCCTAGGGAGATAAGATTAGCGGTTTAGATC
* *
27978 TGCTT-ACCTACTACTTGGGGAAGATAAGAT
1 TGCTTCA-CTACTGCTTAGGG-AGATAAGAT
28008 TCGCTGTCTT
Statistics
Matches: 358, Mismatches: 55, Indels: 20
0.83 0.13 0.05
Matches are distributed among these distances:
130 27 0.08
131 205 0.57
132 126 0.35
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.31
Consensus pattern (130 bp):
TGCTTCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCGACCTATTCCACAGCTGTCCAGGGA
GATAAGACTAGTATCTTCAACCTATTCCACTGCTGCCTAGGGAGATAAGATTAGCGGTTTAGATC
Found at i:28042 original size:175 final size:174
Alignment explanation
Indices: 27758--28096 Score: 498
Period size: 175 Copynumber: 1.9 Consensus size: 174
27748 GTAATTTTTG
* * *
27758 ACCTATTTCACTACTGTCCAGGGAGATAGGACTAGTGGCTTAAATCTGCTTCCCTACTACCTGGG
1 ACCTATTCCACTACTGCCCAGGGAGATAGGACTAGTGGCTTAAATCTGCTTACCTACTACCTGGG
* * * *
27823 AAGATAAGATTCGCCGTTTTTGATCTGCTCCTCTACTGCTTAGGGAGATAAGATCTACAATTTTC
66 AAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTACAATTTTC
27888 GACCTATTCCACAGCTGTCCAGGGAGATAAGACTGGTATCTTCA
131 GACCTATTCCACAGCTGTCCAGGGAGATAAGACTGGTATCTTCA
* * *
27932 ACCTATTCCACTGCTGCCCAGGGAGATAGGACTAGTGGTTTAAATCTGCTTACCTACTACTTGGG
1 ACCTATTCCACTACTGCCCAGGGAGATAGGACTAGTGGCTTAAATCTGCTTACCTACTACCT-GG
* * **
27997 GAAGATAAGATTCGCTGTCTTCGATCTGCTTCACTACTACTTAGGGAGATAAGATCTGTAATTTT
65 GAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTACAATTTT
* * * * *
28062 TGACCTATTCCACTGTTGTCTAGGGAGATAGGACT
130 CGACCTATTCCACAGCTGTCCAGGGAGATAAGACT
28097 AGTGGCTTAA
Statistics
Matches: 145, Mismatches: 19, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
174 56 0.39
175 89 0.61
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (174 bp):
ACCTATTCCACTACTGCCCAGGGAGATAGGACTAGTGGCTTAAATCTGCTTACCTACTACCTGGG
AAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTACAATTTTC
GACCTATTCCACAGCTGTCCAGGGAGATAAGACTGGTATCTTCA
Found at i:28095 original size:132 final size:132
Alignment explanation
Indices: 27932--28228 Score: 454
Period size: 132 Copynumber: 2.2 Consensus size: 132
27922 GGTATCTTCA
* * *
27932 ACCTATTCCACTGCTGCCCAGGGAGATAGGACTAGTGGTTTAAATCTGCTTACCTACT-ACTTGG
1 ACCTATTCCACTGCTGTCCAGGGAGATAGGACTAGTGGCTTAAATCAGCTTACCTACTAAC-TGG
* * * *
27996 GGAAGATAAGATTCG-CTGTCTTCGATCTGCTTCACTACTACTTAGGGAGATAAGATCTGTAATT
65 GGAAGATAAAATTCGTC-GTATTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGCAATT
28060 TTTG
129 TTTG
* * *
28064 ACCTATTCCACTGTTGTCTAGGGAGATAGGACTAGTGGCTTAAATCAGCTTCCCTACTAACTGGG
1 ACCTATTCCACTGCTGTCCAGGGAGATAGGACTAGTGGCTTAAATCAGCTTACCTACTAACTGGG
* *
28129 GAAGATAAAATTTGTCGTATTTGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGCAATTTT
66 GAAGATAAAATTCGTCGTATTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGCAATTTT
28194 TG
131 TG
28196 ACCTATTCCACTGCTGTCCAGGGAGATAGGACT
1 ACCTATTCCACTGCTGTCCAGGGAGATAGGACT
28229 GGTATCTTCG
Statistics
Matches: 149, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
132 146 0.98
133 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32
Consensus pattern (132 bp):
ACCTATTCCACTGCTGTCCAGGGAGATAGGACTAGTGGCTTAAATCAGCTTACCTACTAACTGGG
GAAGATAAAATTCGTCGTATTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGCAATTTT
TG
Found at i:28326 original size:88 final size:89
Alignment explanation
Indices: 28233--28407 Score: 235
Period size: 88 Copynumber: 2.0 Consensus size: 89
28223 AGGACTGGTA
28233 TCTTCGATCTGCTTCACCGTCAGTACAGGAAGGCAAGATCTG-TTATTTTCAACCTGCTCCGCTG
1 TCTTCGATCTGCTTCACCGTCAGTACAGGAAGGCAAGATCTGATTATTTTCAACCTGCTCCGCTG
28297 AAACCAAGGGAGGCAAGGCTGGCG
66 AAACCAAGGGAGGCAAGGCTGGCG
* * ** * * * *
28321 TCTTCGATCTGCTTCGCTGTCAGTGTAGGAAGGCAAGATCTGCTATTTTTTTTAACCTGTTCCGT
1 TCTTCGATCTGCTTCACCGTCAGTACAGGAAGGCAAGATCTG--ATTATTTTCAACCTGCTCCGC
* *
28386 TGTAACCCAGGGAGGCAAGGCT
64 TGAAACCAAGGGAGGCAAGGCT
28408 TTGTAATTTC
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
88 38 0.51
91 36 0.49
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.29
Consensus pattern (89 bp):
TCTTCGATCTGCTTCACCGTCAGTACAGGAAGGCAAGATCTGATTATTTTCAACCTGCTCCGCTG
AAACCAAGGGAGGCAAGGCTGGCG
Found at i:29653 original size:15 final size:15
Alignment explanation
Indices: 29633--29666 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
29623 GGCCTCTCCA
29633 TTTTCTTTTCT-TTTT
1 TTTTCTTTT-TATTTT
29648 TTTTCTTTTTATTTT
1 TTTTCTTTTTATTTT
29663 TTTT
1 TTTT
29667 TTTGGATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 1 0.06
15 17 0.94
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTCTTTTTATTTT
Found at i:29716 original size:48 final size:47
Alignment explanation
Indices: 29663--29803 Score: 165
Period size: 48 Copynumber: 2.9 Consensus size: 47
29653 TTTTTATTTT
* *
29663 TTTTTTTGGATTTAAAGCGCCCTTTGCGGGTTTTCACTTTGGTCTCTC
1 TTTTTTTGGAATCAAAGCGCCCTTTGCGGGTTTTCAC-TTGGTCTCTC
* * * * * *
29711 TTTTTTAGGAATCAAAGTGCCCTTTGTGGGTTTTCCCCTTGGTCTTTT
1 TTTTTTTGGAATCAAAGCGCCCTTTGCGGGTTTT-CACTTGGTCTCTC
*
29759 TTTTTTTAGGAATCAAAGCGCCATTTGCGGGTTTTCAACTTGGTC
1 TTTTTTT-GGAATCAAAGCGCCCTTTGCGGGTTTTC-ACTTGGTC
29804 CCTTTTCCTT
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
48 44 0.57
49 33 0.43
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.45
Consensus pattern (47 bp):
TTTTTTTGGAATCAAAGCGCCCTTTGCGGGTTTTCACTTGGTCTCTC
Found at i:30659 original size:22 final size:22
Alignment explanation
Indices: 30631--30672 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
30621 TTAACCTCTC
*
30631 CTTTTTTCTTTTC-TTTTCATCT
1 CTTTTTT-TTATCATTTTCATCT
30653 CTTTTTTTTATCATTTTCAT
1 CTTTTTTTTATCATTTTCAT
30673 TTTTTCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.10, C:0.19, G:0.00, T:0.71
Consensus pattern (22 bp):
CTTTTTTTTATCATTTTCATCT
Found at i:30690 original size:14 final size:15
Alignment explanation
Indices: 30657--30692 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
30647 TCATCTCTTT
30657 TTTTTATCATTTTCA
1 TTTTTATCATTTTCA
*
30672 TTTTT-TCATTTTGA
1 TTTTTATCATTTTCA
30686 TTTTTAT
1 TTTTTAT
30693 TTTTATCTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.17, C:0.08, G:0.03, T:0.72
Consensus pattern (15 bp):
TTTTTATCATTTTCA
Found at i:30715 original size:26 final size:26
Alignment explanation
Indices: 30686--30749 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 26
30676 TTCATTTTGA
*
30686 TTTTTATTTTTATCTAGATTTTTCCTT
1 TTTTTATTTTT-TCTAGATTTTTCATT
* *
30713 TTTTTATTTTTTCTTGATTTTTGA-T
1 TTTTTATTTTTTCTAGATTTTTCATT
*
30738 TTTTGATTTTTT
1 TTTTTATTTTTT
30750 TTTGAATTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 12 0.36
26 10 0.30
27 11 0.33
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.75
Consensus pattern (26 bp):
TTTTTATTTTTTCTAGATTTTTCATT
Found at i:35065 original size:27 final size:25
Alignment explanation
Indices: 35028--35097 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 25
35018 AAGTAATATG
*
35028 TAAAACAACTTAAAATAAAATGACATA
1 TAAAGCAACTTAAAATAAAA-GAC-TA
* * *
35055 TAAAGTAACTTAAAATAATAGTCTA
1 TAAAGCAACTTAAAATAAAAGACTA
*
35080 TAAAGCAAGTTAAAATAA
1 TAAAGCAACTTAAAATAA
35098 TCATATACAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
25 18 0.49
26 2 0.05
27 17 0.46
ACGTcount: A:0.59, C:0.09, G:0.07, T:0.26
Consensus pattern (25 bp):
TAAAGCAACTTAAAATAAAAGACTA
Found at i:36664 original size:45 final size:46
Alignment explanation
Indices: 36567--36683 Score: 155
Period size: 45 Copynumber: 2.6 Consensus size: 46
36557 TGCCATAGCA
* *
36567 TCTTTCAACTATGGTCTTACTTATTTTAATTCATGTTGCCACAACG
1 TCTTTCAACTATGGTCTTACTTGTTTTAATTCATGTTCCCACAACG
* * *
36613 TCTTTCAACTATAGTCTTACTTGTTTTAA-TCATGTTCCCATAATG
1 TCTTTCAACTATGGTCTTACTTGTTTTAATTCATGTTCCCACAACG
* * *
36658 TTTTTCAGCTATGGTCTTACTCGTTT
1 TCTTTCAACTATGGTCTTACTTGTTT
36684 ACTCATATTG
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
45 35 0.56
46 27 0.44
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.47
Consensus pattern (46 bp):
TCTTTCAACTATGGTCTTACTTGTTTTAATTCATGTTCCCACAACG
Found at i:45305 original size:25 final size:25
Alignment explanation
Indices: 45253--45308 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
45243 AAGCCAAACC
* *
45253 AAGCTTTTGTGGTGAGTTATTTGTA
1 AAGCCTTTGTGGTGAGTTATTAGTA
45278 AAGCCTTTGTGGTGAGTTATCTAG-A
1 AAGCCTTTGTGGTGAGTTAT-TAGTA
45303 AAGCCT
1 AAGCCT
45309 GTAAGGCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 26 0.93
26 2 0.07
ACGTcount: A:0.23, C:0.11, G:0.27, T:0.39
Consensus pattern (25 bp):
AAGCCTTTGTGGTGAGTTATTAGTA
Found at i:45975 original size:180 final size:180
Alignment explanation
Indices: 45674--46034 Score: 697
Period size: 180 Copynumber: 2.0 Consensus size: 180
45664 AATATCGCGC
45674 TTATTTCCTGTACTATTATTAATTAATTTGAAACCATTTTTTTCATTATTTATTGTATATTATTT
1 TTATTTCCTGTACTATTATTAATTAATTTGAAACCATTTTTTTCATTATTTATTGTATATTATTT
45739 TTAAATACACACTTGTGTTCGAAATTTGTGGTATGGACATGCATATGCGTGTGATAAGATTTCTA
66 TTAAATACACACTTGTGTTCGAAATTTGTGGTATGGACATGCATATGCGTGTGATAAGATTTCTA
45804 GTATACTAGATGCACATGGGTGAGGAAAAACTATATT-AAAATATATTTA
131 GTATACTAGATGCACATGGGTGAGGAAAAACTATATTAAAAATATATTTA
*
45853 TTATTTCTTGTACTATTATTAATTAATTTGAAACCATTTTTTTTCATTATTTATTGTATATTATT
1 TTATTTCCTGTACTATTATTAATTAATTTGAAACCA-TTTTTTTCATTATTTATTGTATATTATT
45918 TTTAAATACACACTTGTGTTCGAAATTTGTGGTATGGACATGCATATGCGTGTGATAAGATTTCT
65 TTTAAATACACACTTGTGTTCGAAATTTGTGGTATGGACATGCATATGCGTGTGATAAGATTTCT
45983 AGTATACTAGATGCACATGGGTGAGGAAAAACTATATTAAAAATATATTTA
130 AGTATACTAGATGCACATGGGTGAGGAAAAACTATATTAAAAATATATTTA
46034 T
1 T
46035 AAAATTTTAT
Statistics
Matches: 179, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
179 35 0.20
180 131 0.73
181 13 0.07
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.43
Consensus pattern (180 bp):
TTATTTCCTGTACTATTATTAATTAATTTGAAACCATTTTTTTCATTATTTATTGTATATTATTT
TTAAATACACACTTGTGTTCGAAATTTGTGGTATGGACATGCATATGCGTGTGATAAGATTTCTA
GTATACTAGATGCACATGGGTGAGGAAAAACTATATTAAAAATATATTTA
Found at i:46478 original size:16 final size:16
Alignment explanation
Indices: 46457--46495 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
46447 AGGGCTAGAA
46457 TATGCCCAAGAAAGAG
1 TATGCCCAAGAAAGAG
* *
46473 TATGCCTAAGGAAGAG
1 TATGCCCAAGAAAGAG
*
46489 TACGCCC
1 TATGCCC
46496 GAGAGTTTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.23, G:0.26, T:0.15
Consensus pattern (16 bp):
TATGCCCAAGAAAGAG
Found at i:47756 original size:11 final size:12
Alignment explanation
Indices: 47735--47780 Score: 51
Period size: 11 Copynumber: 3.8 Consensus size: 12
47725 TATATACATA
47735 TATTATATATTT
1 TATTATATATTT
47747 TATTAT-TATTT
1 TATTATATATTT
*
47758 TATTTTCATAGTTT
1 TATTAT-ATA-TTT
47772 TA-TATATAT
1 TATTATATAT
47781 GTATATATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
11 11 0.38
12 9 0.31
13 4 0.14
14 5 0.17
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (12 bp):
TATTATATATTT
Found at i:53307 original size:15 final size:16
Alignment explanation
Indices: 53262--53308 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 16
53252 TGAAAAGATG
*
53262 AAAATGAAAAATGAAAA
1 AAAATGAAAAATG-GAA
53279 AAAATGAAAAATGGAA
1 AAAATGAAAAATGGAA
53295 AAAAT-AAAAATGGA
1 AAAATGAAAAATGGA
53309 GAGGCTAAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 9 0.31
16 7 0.24
17 13 0.45
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (16 bp):
AAAATGAAAAATGGAA
Found at i:54717 original size:88 final size:88
Alignment explanation
Indices: 54563--54890 Score: 505
Period size: 88 Copynumber: 3.7 Consensus size: 88
54553 CGGAGCAGAC
* * * * *
54563 TGAAAATGGCAGATCTTGCCTTCCTGTACTGAGAGCGAAGCAGATCGAAGATATCAGCTTTGTCT
1 TGAAAATGACAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGATACCAGCCTTATCT
54628 CCCTGGGCAGTAGTGGAGTAGGT
66 CCCTGGGCAGTAGTGGAGTAGGT
*
54651 TGAAAATGACAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGATCGAAGATACCAGCCTTATCT
1 TGAAAATGACAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGATACCAGCCTTATCT
54716 CCCTGGGCAGTAGTGGAGTAGGT
66 CCCTGGGCAGTAGTGGAGTAGGT
* * * *
54739 GGAAAATAACAGATCTTGCCTTCCTGTACTGACAGCGAGGCAGATCGAAGATACCAGCCTTGTCT
1 TGAAAATGACAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGATACCAGCCTTATCT
*
54804 CCCTGGGCAGTAGTGGACTAGGT
66 CCCTGGGCAGTAGTGGAGTAGGT
* * * *
54827 TGAAAAT-AGCAGATCTTGCCTTCCTGTACTGGCAGCGAAGCAGATCAAAGACACCAGTCTTATC
1 TGAAAATGA-CAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGATACCAGCCTTATC
54891 GCCTTGACAT
Statistics
Matches: 220, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
87 1 0.00
88 219 1.00
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.24
Consensus pattern (88 bp):
TGAAAATGACAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGATACCAGCCTTATCT
CCCTGGGCAGTAGTGGAGTAGGT
Found at i:55387 original size:267 final size:266
Alignment explanation
Indices: 54912--55739 Score: 1343
Period size: 267 Copynumber: 3.1 Consensus size: 266
54902 GCAATGGAAT
* *
54912 AGATTGAAGCCACAACGGCGGATCTTATTTTCCTAGCGTCGCAGTGGAGCAGATTGAAGCCACGA
1 AGATTGAAGCCACAACGGCGGATCTTATTTTCCTGGCGTCGCAGTGGAGTAGATTGAAGCCACGA
* * *
54977 CAGCGGGTCTTATCTCCCTGGTGTTAAGGCTTGGATTAGCTGAAGTGGAATGGATTGAAGCTGTG
66 TAGCGGATCTTATCTCCCTGGTGTTAAGGCTTGGATTAGCTGAAGTGGAGTGGATTGAAGCTGTG
* *
55042 GGCAGCGAATCCTATCTCTTTAGCATTACAGTGGAAAAGATTGAAGTCGCAACGGTGGATCTTAC
131 GGCAGCGAATCCTATCTCTTTAGCATTACAGTGGAAAAGATTGAAGCCACAACGGTGGATCTTAC
*
55107 TTCCCTGGCGGTGTAGTGGAACAGATTAAAGCTACGACGGCAGATTTGGTTTCCCCGACATTGCA
196 TT-CCTGGCGGTGTAGTGGAACAGATTAAAGCTACGACGGCAGATCTGGTTTCCCCGACATTGCA
55172 ATTAAAA
260 ATTAAAA
* *
55179 AGATTGAAGCCACAACGGCAGATCTTATTTTCCTGGCGTCGCAGTGGAGTAGATTGAAGCCGCGA
1 AGATTGAAGCCACAACGGCGGATCTTATTTTCCTGGCGTCGCAGTGGAGTAGATTGAAGCCACGA
* * *
55244 TGGCGGATCTTATCTCCCAGGTGTTAAGGCTTGGATTAGATGAAGTGGAGTGGATTGAAGCTGTG
66 TAGCGGATCTTATCTCCCTGGTGTTAAGGCTTGGATTAGCTGAAGTGGAGTGGATTGAAGCTGTG
55309 GGCAGCGAATCCTATCTCTTTAGCATTACAGTGGAAAAGATTGAAGCCACAACGGTGGATCTTAC
131 GGCAGCGAATCCTATCTCTTTAGCATTACAGTGGAAAAGATTGAAGCCACAACGGTGGATCTTAC
*
55374 TTCCGTGGCGGTGTAGTGGAACAGATTAAAGCTACGACGGCAGATCTGGTTTCCCCAACATTGCA
196 TTCC-TGGCGGTGTAGTGGAACAGATTAAAGCTACGACGGCAGATCTGGTTTCCCCGACATTGCA
55439 ATTAAAA
260 ATTAAAA
* * *
55446 AGATTGAAGCCACAACGGCGGATCTTATTTTCCTGGAGTCGCAGCGGAATAGATTGAAGCCACGA
1 AGATTGAAGCCACAACGGCGGATCTTATTTTCCTGGCGTCGCAGTGGAGTAGATTGAAGCCACGA
* ** * *
55511 TTGCAAATCTTATCTCCCTGGCGTTAAGGCTTTGATTAGCTGAAGTGGAGTGGATTGAAGCTGTG
66 TAGCGGATCTTATCTCCCTGGTGTTAAGGCTTGGATTAGCTGAAGTGGAGTGGATTGAAGCTGTG
* *
55576 GGCAGCGAATCCTATCTCTTTAGCATTACAGTGGAAAAGATTGAAGCCACAACAGAGGATCTTAC
131 GGCAGCGAATCCTATCTCTTTAGCATTACAGTGGAAAAGATTGAAGCCACAACGGTGGATCTTAC
* * * *
55641 TTTCCTGGTGGTGTAGTGGAACAGATTGAAG-TCACGACGGCGGATCTGGTTTCCCTGACATTGC
196 -TTCCTGGCGGTGTAGTGGAACAGATTAAAGCT-ACGACGGCAGATCTGGTTTCCCCGACATTGC
* *
55705 GATTTAAA
259 AATTAAAA
55713 AGATTGAAGCCACAACGGCGGATCTTA
1 AGATTGAAGCCACAACGGCGGATCTTA
55740 CTTCCCTAGC
Statistics
Matches: 523, Mismatches: 35, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
266 3 0.01
267 516 0.99
268 4 0.01
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (266 bp):
AGATTGAAGCCACAACGGCGGATCTTATTTTCCTGGCGTCGCAGTGGAGTAGATTGAAGCCACGA
TAGCGGATCTTATCTCCCTGGTGTTAAGGCTTGGATTAGCTGAAGTGGAGTGGATTGAAGCTGTG
GGCAGCGAATCCTATCTCTTTAGCATTACAGTGGAAAAGATTGAAGCCACAACGGTGGATCTTAC
TTCCTGGCGGTGTAGTGGAACAGATTAAAGCTACGACGGCAGATCTGGTTTCCCCGACATTGCAA
TTAAAA
Found at i:55728 original size:100 final size:100
Alignment explanation
Indices: 55610--55849 Score: 322
Period size: 100 Copynumber: 2.4 Consensus size: 100
55600 ATTACAGTGG
* * * * ** *
55610 AAAAGATTGAAGCCACAACAGAGGATCTTACTTTCCTGGTGGTGTAGTGGAACAGATTGAAG-T-
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTAGCAGTGTAATGGAACAGATTGAAGCTG
* * * *
55673 CACGACGGCGGATCTGGTTTCCCTGACATTGCGATTT
66 CA--ACGGCGGATCTGGTTCCCCCGACATTGCAATTA
55710 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTAGCAGTGTAATGGAACAGATTGAAGCTG
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTAGCAGTGTAATGGAACAGATTGAAGCTG
* *
55775 CAACGGTGGATCTGGTTCCCCCGTCATTGCAATTA
66 CAACGGCGGATCTGGTTCCCCCGACATTGCAATTA
*
55810 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGC
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTAGC
55850 GGTGCAGTGG
Statistics
Matches: 124, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
100 121 0.98
101 1 0.01
102 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.25
Consensus pattern (100 bp):
AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTAGCAGTGTAATGGAACAGATTGAAGCTG
CAACGGCGGATCTGGTTCCCCCGACATTGCAATTA
Found at i:55745 original size:50 final size:50
Alignment explanation
Indices: 55663--55844 Score: 161
Period size: 50 Copynumber: 3.6 Consensus size: 50
55653 GTAGTGGAAC
* * *** * *
55663 AGATTGAAGTCACGACGGCGGATCTGGTTTCCCTGACATTGCGATTTAAA
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTGACATTGCAATTAAAA
* * ** *
55713 AGATTGAAGCCACAACGGCGGATCTTACTTCCCT-AGCAGTGTAATGGAAC
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTGA-CATTGCAATTAAAA
** * ** * *
55763 AGATTGAAGCTGCAACGGTGGATC-TGGTTCCCCCGTCATTGCAATTAAAA
1 AGATTGAAGCCACAACGGCGGATCTTACTT-CCCTGACATTGCAATTAAAA
55813 AGATTGAAGCCACAACGGCGGATCTTACTTCC
1 AGATTGAAGCCACAACGGCGGATCTTACTTCC
55845 TTAGCGGTGC
Statistics
Matches: 100, Mismatches: 28, Indels: 8
0.74 0.21 0.06
Matches are distributed among these distances:
49 4 0.04
50 93 0.93
51 3 0.03
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (50 bp):
AGATTGAAGCCACAACGGCGGATCTTACTTCCCTGACATTGCAATTAAAA
Found at i:56539 original size:6 final size:6
Alignment explanation
Indices: 56530--56555 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
56520 TTTTTTCTCC
56530 TTTTAT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TT
56556 GTTCTTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:56805 original size:17 final size:17
Alignment explanation
Indices: 56783--56817 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
56773 TATGGGTTAT
56783 TTATGCTTTTAATCCTC
1 TTATGCTTTTAATCCTC
56800 TTATGCTTTTAATCCTC
1 TTATGCTTTTAATCCTC
56817 T
1 T
56818 CATGTTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.23, G:0.06, T:0.54
Consensus pattern (17 bp):
TTATGCTTTTAATCCTC
Found at i:64977 original size:12 final size:12
Alignment explanation
Indices: 64962--64993 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
64952 AAAATTTACC
64962 TTTATTTTTAAT
1 TTTATTTTTAAT
64974 TTTATTTTTAAT
1 TTTATTTTTAAT
*
64986 TATATTTT
1 TTTATTTT
64994 ATTTTTAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTATTTTTAAT
Found at i:70594 original size:16 final size:16
Alignment explanation
Indices: 70557--70606 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
70547 AGTCTATTCA
*
70557 TGTTGTGTTATATTAT-
1 TGTTGTGTT-TATTTTC
*
70573 TATTGTGTTTATTTTC
1 TGTTGTGTTTATTTTC
*
70589 TGTTGTGATTATTTTC
1 TGTTGTGTTTATTTTC
70605 TG
1 TG
70607 CAAGGCATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 5 0.17
16 24 0.83
ACGTcount: A:0.14, C:0.04, G:0.18, T:0.64
Consensus pattern (16 bp):
TGTTGTGTTTATTTTC
Found at i:77029 original size:22 final size:22
Alignment explanation
Indices: 76979--77031 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
76969 CTGTATTATG
* *
76979 TATAAT-TTTGATTAAATTGAA
1 TATAATATGTGATTAAATTCAA
*
77000 TGTAATATGTGATTAAA-TCAA
1 TATAATATGTGATTAAATTCAA
77021 TATATATATGT
1 TATA-ATATGT
77032 TAGTATGCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.45
Consensus pattern (22 bp):
TATAATATGTGATTAAATTCAA
Found at i:81636 original size:26 final size:26
Alignment explanation
Indices: 81558--81626 Score: 120
Period size: 26 Copynumber: 2.7 Consensus size: 26
81548 CGTTCCGACC
81558 CACAGCTCGTGTGAGCAGACCCATTT
1 CACAGCTCGTGTGAGCAGACCCATTT
*
81584 CACAGCTCGTGTGAGCAGGCCCATTT
1 CACAGCTCGTGTGAGCAGACCCATTT
*
81610 CACATCTCGTGTGAGCA
1 CACAGCTCGTGTGAGCA
81627 TACTCTTTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.22, C:0.30, G:0.25, T:0.23
Consensus pattern (26 bp):
CACAGCTCGTGTGAGCAGACCCATTT
Found at i:94591 original size:25 final size:25
Alignment explanation
Indices: 94557--94629 Score: 103
Period size: 25 Copynumber: 2.9 Consensus size: 25
94547 ATAGGCTTCC
*
94557 CAGATGACTCGCC-CTAAAGTCTTTA
1 CAGATGACTCGCCAC-AAAGGCTTTA
*
94582 CAGATGACTCACCACAAAGGCTTTA
1 CAGATGACTCGCCACAAAGGCTTTA
*
94607 CAGATGACTCGCCACAAGGGCTT
1 CAGATGACTCGCCACAAAGGCTT
94630 CCCAAATGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
25 42 0.98
26 1 0.02
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (25 bp):
CAGATGACTCGCCACAAAGGCTTTA
Found at i:94638 original size:25 final size:25
Alignment explanation
Indices: 94549--94630 Score: 94
Period size: 25 Copynumber: 3.3 Consensus size: 25
94539 TTCACCTTAT
*
94549 AGGCTTCCCAGATGACTCGCC-CTAA
1 AGGCTTCACAGATGACTCGCCAC-AA
* * *
94574 AGTCTTTACAGATGACTCACCACAA
1 AGGCTTCACAGATGACTCGCCACAA
*
94599 AGGCTTTACAGATGACTCGCCACAA
1 AGGCTTCACAGATGACTCGCCACAA
*
94624 GGGCTTC
1 AGGCTTC
94631 CCAAATGATT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
25 47 0.98
26 1 0.02
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (25 bp):
AGGCTTCACAGATGACTCGCCACAA
Found at i:94646 original size:25 final size:25
Alignment explanation
Indices: 94549--94646 Score: 72
Period size: 25 Copynumber: 3.9 Consensus size: 25
94539 TTCACCTTAT
* * *
94549 AGGCTTCCCAGATGACTCGCC-CTAA
1 AGGCTTCACAAATGACTCACCAC-AA
* * *
94574 AGTCTTTACAGATGACTCACCACAA
1 AGGCTTCACAAATGACTCACCACAA
* * *
94599 AGGCTTTACAGATGACTCGCCACAA
1 AGGCTTCACAAATGACTCACCACAA
* * *
94624 GGGCTTCCCAAATGATTCACCAC
1 AGGCTTCACAAATGACTCACCAC
94647 TAGATGTCTT
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
25 59 0.98
26 1 0.02
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (25 bp):
AGGCTTCACAAATGACTCACCACAA
Found at i:94692 original size:25 final size:25
Alignment explanation
Indices: 94658--94719 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
94648 AGATGTCTTG
* *
94658 CCATAAAGGCTTTATATATGACTCA
1 CCATAAAGGCTTTACAGATGACTCA
*
94683 CCATAAAGGCTTTACAGATGACTCT
1 CCATAAAGGCTTTACAGATGACTCA
*
94708 CCACAAAGGCTT
1 CCATAAAGGCTT
94720 CCTAGATGTC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (25 bp):
CCATAAAGGCTTTACAGATGACTCA
Found at i:94736 original size:25 final size:25
Alignment explanation
Indices: 94645--94739 Score: 70
Period size: 25 Copynumber: 3.8 Consensus size: 25
94635 ATGATTCACC
* *
94645 ACTAGATGTCTTGCCATAAAGGCTTT
1 ACTAGATGACTTGCCACAAAGGC-TT
* ** *
94671 A-TATATGACTCACCATAAAGGCTTT
1 ACTAGATGACTTGCCACAAAGGC-TT
94696 AC-AGATGACTCT-CCACAAAGGCTT
1 ACTAGATGACT-TGCCACAAAGGCTT
* *
94720 CCTAGATGTCTTGCCACAAA
1 ACTAGATGACTTGCCACAAA
94740 ATCTTCCCAA
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
24 4 0.07
25 51 0.91
26 1 0.02
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (25 bp):
ACTAGATGACTTGCCACAAAGGCTT
Found at i:95789 original size:20 final size:23
Alignment explanation
Indices: 95764--95806 Score: 65
Period size: 20 Copynumber: 2.0 Consensus size: 23
95754 AATTTTAAAC
95764 AATTTTT-ATTTT-GAAA-AATA
1 AATTTTTCATTTTAGAAATAATA
95784 AATTTTTCATTTTAGAAATAATA
1 AATTTTTCATTTTAGAAATAATA
95807 TTAATCTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.35
21 5 0.25
22 4 0.20
23 4 0.20
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (23 bp):
AATTTTTCATTTTAGAAATAATA
Found at i:95829 original size:33 final size:33
Alignment explanation
Indices: 95786--95904 Score: 95
Period size: 33 Copynumber: 3.6 Consensus size: 33
95776 GAAAAATAAA
* * *
95786 TTTTTCATTTTAGAAATAATATTAATCTAATAC
1 TTTTTAATTTTAAAAATAATATTAATATAATAC
*
95819 TTTTTAATTTTAAAAAATGAATTTTTAA-ATAAT--
1 TTTTTAATTTT-AAAAAT-AA-TATTAATATAATAC
* * *
95852 TTTTTCATTTTTTAGAAATAATA--CATATAATAC
1 TTTTT-A-ATTTTAAAAATAATATTAATATAATAC
95885 TTTTTAATTTTAAAAATAAT
1 TTTTTAATTTTAAAAATAAT
95905 GTTTTAAAAC
Statistics
Matches: 68, Mismatches: 10, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
30 1 0.01
31 17 0.25
32 2 0.03
33 22 0.32
34 11 0.16
35 10 0.15
36 5 0.07
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (33 bp):
TTTTTAATTTTAAAAATAATATTAATATAATAC
Found at i:95859 original size:66 final size:64
Alignment explanation
Indices: 95779--95912 Score: 182
Period size: 66 Copynumber: 2.0 Consensus size: 64
95769 TTATTTTGAA
*
95779 AAATAAATTTTTCA-TTTTAGAAATAATATTAATCTAATACTTTTTAATTTTAAAAAATGAAT-T
1 AAATAAATTTTTCATTTTTAGAAATAATA--AATATAATACTTTTTAATTTT-AAAAAT-AATGT
95842 TTT
62 TTT
* *
95845 AAATAATTTTTTCATTTTTTAGAAATAATACATATAATACTTTTTAATTTTAAAAATAATGTTTT
1 AAATAAATTTTTCA-TTTTTAGAAATAATAAATATAATACTTTTTAATTTTAAAAATAATGTTTT
95910 AAA
1 AAA
95913 ACTTGTAAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
64 3 0.05
65 13 0.21
66 32 0.52
68 14 0.23
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (64 bp):
AAATAAATTTTTCATTTTTAGAAATAATAAATATAATACTTTTTAATTTTAAAAATAATGTTTT
Found at i:96535 original size:20 final size:19
Alignment explanation
Indices: 96510--96561 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 19
96500 AATAATGAAT
96510 CTGTTCACCAAGAGATAAAA
1 CTGTTCA-CAAGAGATAAAA
*
96530 CTGTTCA-AA-AGATACAA
1 CTGTTCACAAGAGATAAAA
*
96547 CTGCTCATCAAGAGA
1 CTGTTCA-CAAGAGA
96562 CGGGACTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 13 0.48
18 2 0.07
19 2 0.07
20 10 0.37
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.21
Consensus pattern (19 bp):
CTGTTCACAAGAGATAAAA
Found at i:96982 original size:15 final size:15
Alignment explanation
Indices: 96960--96997 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
96950 AAATACTAAT
*
96960 AATAATAACAATAA-
1 AATAATAAAAATAAC
96974 AAGTAATAAAAATAAC
1 AA-TAATAAAAATAAC
96990 AATAATAA
1 AATAATAA
96998 TACTAAAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 17 0.81
16 2 0.10
ACGTcount: A:0.71, C:0.05, G:0.03, T:0.21
Consensus pattern (15 bp):
AATAATAAAAATAAC
Found at i:105940 original size:20 final size:20
Alignment explanation
Indices: 105912--105960 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
105902 GAATGTTATA
*
105912 AATTGGCATTAAAAATGATT
1 AATTTGCATTAAAAATGATT
*
105932 AATTTGCATTAAAAATGGTT
1 AATTTGCATTAAAAATGATT
105952 AATTTGCAT
1 AATTTGCAT
105961 GTTTTGTGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (20 bp):
AATTTGCATTAAAAATGATT
Found at i:107562 original size:3 final size:3
Alignment explanation
Indices: 107554--107624 Score: 56
Period size: 3 Copynumber: 23.3 Consensus size: 3
107544 TTTAGTAATT
* * *
107554 TTA TTA TTA TTT TTA TTA TTA CTA TTA TTTA TTA TTG TT- TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA T-TA TTA
* *
107600 TTG TTA CTTA TCA -TA TTA TTA TTA T
1 TTA TTA -TTA TTA TTA TTA TTA TTA T
107625 ATAATAGCTT
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
2 2 0.04
3 45 0.83
4 7 0.13
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:107581 original size:18 final size:17
Alignment explanation
Indices: 107558--107624 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 17
107548 GTAATTTTAT
107558 TATTATTTTTATTATTA
1 TATTATTTTTATTATTA
*
107575 CTATTATTTATTATTGTTTA
1 -TATTATTT-TTATT-ATTA
* *
107595 TATTATTGTTACTTATCA
1 TATTATTTTTA-TTATTA
*
107613 TATTATTATTAT
1 TATTATTTTTAT
107625 ATAATAGCTT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
17 1 0.02
18 23 0.56
19 14 0.34
20 3 0.07
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.64
Consensus pattern (17 bp):
TATTATTTTTATTATTA
Found at i:107610 original size:25 final size:25
Alignment explanation
Indices: 107557--107624 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 25
107547 AGTAATTTTA
*
107557 TTATTATTTTTATTATTACTATTAT
1 TTATTATTTTTATTATTACTATTAC
* *
107582 TTATTATTGTTTA-TATTATTGTTAC
1 TTATTATT-TTTATTATTACTATTAC
*
107607 TTATCATATTATTATTAT
1 TTAT--TATTTTTATTAT
107625 ATAATAGCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
25 21 0.60
26 7 0.20
27 7 0.20
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.65
Consensus pattern (25 bp):
TTATTATTTTTATTATTACTATTAC
Found at i:107774 original size:2 final size:2
Alignment explanation
Indices: 107767--107821 Score: 53
Period size: 2 Copynumber: 29.0 Consensus size: 2
107757 ATACTTATTC
* * * *
107767 AT AT AT AT AT AT AT TT AT AT AT -T A- AA AT AT GT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
107807 AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT
107822 TTTATCTTAC
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
1 3 0.07
2 40 0.93
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (2 bp):
AT
Found at i:107864 original size:15 final size:15
Alignment explanation
Indices: 107846--107877 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
107836 TTTATATAAT
107846 CCACATATATATTTC
1 CCACATATATATTTC
107861 CCACATATATATTTC
1 CCACATATATATTTC
107876 CC
1 CC
107878 TTAAATGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (15 bp):
CCACATATATATTTC
Found at i:108312 original size:109 final size:109
Alignment explanation
Indices: 108147--108446 Score: 439
Period size: 109 Copynumber: 2.8 Consensus size: 109
108137 ATATTCAGCA
* * *
108147 TTTGGAAATACGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATAA
1 TTTGGAAATTCGAGGAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATAG
* *
108212 CTAAGTATCCTTTTAAAATTTTCAAAATAAGGCAATGTTTTACG
66 CCAAATATCCTTTTAAAATTTTCAAAATAAGGCAATGTTTTACG
* *
108256 TTTGGTAATTCGAGGAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCTAATAG
1 TTTGGAAATTCGAGGAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATAG
** *
108321 CCAAATATCCTTCCAAAAATTTCAAAATAAGGCAATGTTTTACG
66 CCAAATATCCTTTTAAAATTTTCAAAATAAGGCAATGTTTTACG
* * *
108365 TTTGGAAATTTGAGG-AACGTGCCCCAATGTGCT-GGTTTCGA--TTTCTCGTTTAACCAAATAG
1 TTTGGAAATTCGAGGAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATAG
*
108426 CCAAATATCCTCTT-AAATTTT
66 CCAAATATCCTTTTAAAATTTT
108447 AATCCATGTC
Statistics
Matches: 172, Mismatches: 19, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
104 6 0.03
105 29 0.17
107 8 0.05
108 17 0.10
109 112 0.65
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (109 bp):
TTTGGAAATTCGAGGAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATAG
CCAAATATCCTTTTAAAATTTTCAAAATAAGGCAATGTTTTACG
Found at i:109950 original size:25 final size:25
Alignment explanation
Indices: 109914--109973 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
109904 TTGTACATGC
*
109914 ATGCTCATACGAGCTATGAATCGGT
1 ATGCTCATACGAGCTATAAATCGGT
*
109939 ATGCTC-TCACGAGCTGTAAATCGGT
1 ATGCTCAT-ACGAGCTATAAATCGGT
*
109964 AAGCTCATAC
1 ATGCTCATAC
109974 AAGTTGAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 1 0.03
25 28 0.93
26 1 0.03
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (25 bp):
ATGCTCATACGAGCTATAAATCGGT
Found at i:110031 original size:49 final size:49
Alignment explanation
Indices: 109916--110057 Score: 187
Period size: 49 Copynumber: 2.9 Consensus size: 49
109906 GTACATGCAT
* * *
109916 GCTCATACGAGCT-ATGAATCGGTATGCTCTCACGAGCTGTAAATCGGTAA
1 GCTCATACGAGCTGA-GAATCAGTATGCTCTCACGAGCTG-CAATCAGTAA
* * * *
109966 GCTCATACAAGTTGAGAATTAGTATGCTCTCACAAGCTGCAATCAGTAA
1 GCTCATACGAGCTGAGAATCAGTATGCTCTCACGAGCTGCAATCAGTAA
*
110015 GCTCATACGAGCTGAGAATCAGTAAGCTCTCACGAGCTGCAAT
1 GCTCATACGAGCTGAGAATCAGTATGCTCTCACGAGCTGCAAT
110058 TGGTAATCCC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
49 46 0.58
50 32 0.41
51 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.25
Consensus pattern (49 bp):
GCTCATACGAGCTGAGAATCAGTATGCTCTCACGAGCTGCAATCAGTAA
Found at i:110039 original size:25 final size:25
Alignment explanation
Indices: 109922--110053 Score: 112
Period size: 25 Copynumber: 5.3 Consensus size: 25
109912 GCATGCTCAT
* *
109922 ACGAGCT-ATGAATCGGTATGCTCTC
1 ACGAGCTGA-GAATCAGTAAGCTCTC
*
109947 ACGAGCTGTA-AATCGGTAAGCTCAT-
1 ACGAGCTG-AGAATCAGTAAGCTC-TC
* * * *
109972 ACAAGTTGAGAATTAGTATGCTCTC
1 ACGAGCTGAGAATCAGTAAGCTCTC
* *
109997 ACAAGCTG-CAATCAGTAAGCTCAT-
1 ACGAGCTGAGAATCAGTAAGCTC-TC
110021 ACGAGCTGAGAATCAGTAAGCTCTC
1 ACGAGCTGAGAATCAGTAAGCTCTC
110046 ACGAGCTG
1 ACGAGCTG
110054 CAATTGGTAA
Statistics
Matches: 87, Mismatches: 12, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
24 21 0.24
25 64 0.74
26 1 0.01
27 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (25 bp):
ACGAGCTGAGAATCAGTAAGCTCTC
Found at i:113853 original size:61 final size:61
Alignment explanation
Indices: 113738--113853 Score: 144
Period size: 61 Copynumber: 1.9 Consensus size: 61
113728 ATGTGAGTAA
* * * * ** * *
113738 TAGTGGTGGAATGTGTTATATGTGGAACCATTTGTGGTTGTTCTTTGTTTCATGTAAGCCT
1 TAGTGGTGAAATATGTCATATGTGGAACCATTTGTGGTTATTCCCTATTACATGTAAGCCT
113799 TAGTGGTGAAATATGTCATATGTGGAAGCC-TTTGTGGTTATTCCCTATTACATGT
1 TAGTGGTGAAATATGTCATATGTGGAA-CCATTTGTGGTTATTCCCTATTACATGT
113854 GAACCTTTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
61 44 0.96
62 2 0.04
ACGTcount: A:0.21, C:0.11, G:0.26, T:0.42
Consensus pattern (61 bp):
TAGTGGTGAAATATGTCATATGTGGAACCATTTGTGGTTATTCCCTATTACATGTAAGCCT
Found at i:113871 original size:61 final size:61
Alignment explanation
Indices: 113755--113871 Score: 132
Period size: 61 Copynumber: 1.9 Consensus size: 61
113745 GGAATGTGTT
* ** * * *
113755 ATATGTGGAACCATTTGTGGTTGTTCTTTGTTTCATGTAAGCCTTAGTGGTGAAATATGTC
1 ATATGTGGAACCATTTGTGGTTATTCCCTATTACATGTAAGCCTTAGTGGAGAAATATGTC
113816 ATATGTGGAAGCC-TTTGTGGTTATTCCCTATTACATGTGAA-CCTTTA-TGGAGAAAT
1 ATATGTGGAA-CCATTTGTGGTTATTCCCTATTACATGT-AAGCC-TTAGTGGAGAAAT
113872 CATTAAGGAG
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
61 40 0.85
62 7 0.15
ACGTcount: A:0.24, C:0.13, G:0.23, T:0.40
Consensus pattern (61 bp):
ATATGTGGAACCATTTGTGGTTATTCCCTATTACATGTAAGCCTTAGTGGAGAAATATGTC
Found at i:113963 original size:30 final size:30
Alignment explanation
Indices: 113922--113997 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
113912 TATCTAGACC
* * *
113922 CCTTTGGGGCTATCTAATGATGTGTGGATG
1 CCTTTGTGGCTATCTAATGATGTATGGATA
* *
113952 CTTTTGTGGCTATCTAATGGTGTATGGATA
1 CCTTTGTGGCTATCTAATGATGTATGGATA
*
113982 CCTCTGTGGCTATCTA
1 CCTTTGTGGCTATCTA
113998 TGTAAAGTAG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.17, C:0.16, G:0.28, T:0.39
Consensus pattern (30 bp):
CCTTTGTGGCTATCTAATGATGTATGGATA
Found at i:117697 original size:60 final size:61
Alignment explanation
Indices: 117605--117753 Score: 205
Period size: 61 Copynumber: 2.5 Consensus size: 61
117595 TGGCTAAATC
* * *
117605 TGTTATATAT-G-AGCCATTGTGGTTGTTCTCTGTTTCATGTGAGCC-TAGTAGCAGAATG
1 TGTTATATATGGAAGCCTTTGTGGTTGTTCTCTGTTTCATGCGAGCCTTAGTAGCAGAATA
* * *
117663 TGTTATATATGGAAGCCTTTGTGGTTGTTTTCTGTTTCATGCGAGCCTTAGTGGCGGAATA
1 TGTTATATATGGAAGCCTTTGTGGTTGTTCTCTGTTTCATGCGAGCCTTAGTAGCAGAATA
* *
117724 TGTTATATGTGGAAGCCTTTGTGGCTGTTC
1 TGTTATATATGGAAGCCTTTGTGGTTGTTC
117754 CCTATTACAT
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
58 10 0.13
59 1 0.01
60 31 0.39
61 37 0.47
ACGTcount: A:0.18, C:0.13, G:0.28, T:0.41
Consensus pattern (61 bp):
TGTTATATATGGAAGCCTTTGTGGTTGTTCTCTGTTTCATGCGAGCCTTAGTAGCAGAATA
Found at i:118690 original size:26 final size:26
Alignment explanation
Indices: 118631--118690 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
118621 TTTTCTTTTC
** *
118631 TTTTTCTTTTCATTTTTAGTTTAGGT
1 TTTTTCTTTTCATTTTTAGAGTAGAT
*
118657 TTTCTCTTTT-ATTTTTAGAGTAGAT
1 TTTTTCTTTTCATTTTTAGAGTAGAT
118682 TTTATTCTT
1 TTT-TTCTT
118691 GTAGTTTTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
25 15 0.54
26 13 0.46
ACGTcount: A:0.15, C:0.08, G:0.10, T:0.67
Consensus pattern (26 bp):
TTTTTCTTTTCATTTTTAGAGTAGAT
Found at i:120356 original size:19 final size:19
Alignment explanation
Indices: 120332--120369 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
120322 TTATCATACT
120332 TTTATTTTTAAGAATTTAA
1 TTTATTTTTAAGAATTTAA
120351 TTTATTTTTAAGAATTTAA
1 TTTATTTTTAAGAATTTAA
120370 CTCCTCTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTATTTTTAAGAATTTAA
Found at i:126894 original size:20 final size:20
Alignment explanation
Indices: 126839--126894 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
126829 AGGAAAATTT
126839 TATTTTT-A-TTAATTTAGA
1 TATTTTTAATTTAATTTAGA
* *
126857 TATTTTTTATTTTTATTTCA-A
1 TA-TTTTTAATTTAATTT-AGA
126878 TATTTTTAATTTAATTT
1 TATTTTTAATTTAATTT
126895 TTACATCTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
18 2 0.07
19 5 0.17
20 13 0.43
21 9 0.30
22 1 0.03
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (20 bp):
TATTTTTAATTTAATTTAGA
Found at i:134797 original size:12 final size:12
Alignment explanation
Indices: 134780--134809 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
134770 AGGGTTGCAT
134780 ACACGGCTTGGC
1 ACACGGCTTGGC
134792 ACACGGCTTGGC
1 ACACGGCTTGGC
*
134804 AGACGG
1 ACACGG
134810 GCGTGAGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.20, C:0.30, G:0.37, T:0.13
Consensus pattern (12 bp):
ACACGGCTTGGC
Found at i:136931 original size:14 final size:15
Alignment explanation
Indices: 136912--136940 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
136902 AATTTAACCC
136912 AAAATTAT-ATTTTT
1 AAAATTATAATTTTT
136926 AAAATTATAATTTTT
1 AAAATTATAATTTTT
136941 CCCCTATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AAAATTATAATTTTT
Found at i:149879 original size:12 final size:11
Alignment explanation
Indices: 149859--149897 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
149849 AATATTAAAT
149859 TTTATTTAATA
1 TTTATTTAATA
149870 TTTATCTTAATA
1 TTTAT-TTAATA
* *
149882 TTAATATAATA
1 TTTATTTAATA
149893 TTTAT
1 TTTAT
149898 CTTGATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTATTTAATA
Found at i:153791 original size:26 final size:26
Alignment explanation
Indices: 153755--153806 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
153745 ATTGCCAGAA
*
153755 GGTTTTGATC-TTCAAATAAAATAGTT
1 GGTTTTGATCTTTC-AAGAAAATAGTT
153781 GGTTTTGATCTTTCAAGAAAATAGTT
1 GGTTTTGATCTTTCAAGAAAATAGTT
153807 TTTCTCTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 21 0.88
27 3 0.12
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (26 bp):
GGTTTTGATCTTTCAAGAAAATAGTT
Found at i:160951 original size:51 final size:50
Alignment explanation
Indices: 160875--160993 Score: 143
Period size: 50 Copynumber: 2.4 Consensus size: 50
160865 CGGTGGCCTG
*
160875 CACATAGTACCAC-CTTTGTTGCCAAAGCTACCTTCATCACAAAGTGGCATT
1 CACATAGTACCACAC-TTGTTGCCAAAACTACC-TCATCACAAAGTGGCATT
* * * * *
160926 CACATAATACCACACTTG-TGACCAAAACTATCTCCTCTCAAAGTGGCCTT
1 CACATAGTACCACACTTGTTG-CCAAAACTACCTCATCACAAAGTGGCATT
160976 CACATAGTACCACACTTG
1 CACATAGTACCACACTTG
160994 AGCCACTAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
50 34 0.58
51 24 0.41
52 1 0.02
ACGTcount: A:0.31, C:0.31, G:0.12, T:0.26
Consensus pattern (50 bp):
CACATAGTACCACACTTGTTGCCAAAACTACCTCATCACAAAGTGGCATT
Found at i:165818 original size:50 final size:50
Alignment explanation
Indices: 165707--165832 Score: 168
Period size: 50 Copynumber: 2.5 Consensus size: 50
165697 GGATATCCGA
*
165707 TGGCCTGCACATAGTACCAC-CTTTGTTGCCAAAGCTACCTTCTTCACAAAG
1 TGGCCTTCACATAGTACCACAC-TTGTTGCCAAAGCTA-CTTCTTCACAAAG
* *
165758 TGGCCTTCACATGGTACCACACTTG-TGACCAAAGCTA-TGTCTTCTCAAAG
1 TGGCCTTCACATAGTACCACACTTGTTG-CCAAAGCTACT-TCTTCACAAAG
165808 TGGCCTTCACATAGTACCACACTTG
1 TGGCCTTCACATAGTACCACACTTG
165833 AGCCACTAGT
Statistics
Matches: 68, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
49 1 0.01
50 36 0.53
51 30 0.44
52 1 0.01
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (50 bp):
TGGCCTTCACATAGTACCACACTTGTTGCCAAAGCTACTTCTTCACAAAG
Found at i:170956 original size:41 final size:41
Alignment explanation
Indices: 170673--170955 Score: 422
Period size: 41 Copynumber: 6.9 Consensus size: 41
170663 TGAGTTTTGG
* *
170673 GGGCATTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* * * * *
170714 GAGCCTTTAGCTGCATTTTTGAGAAAGCGCCGCTAATGCTT
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
*
170755 GGGCCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* *
170796 GGGCCTTTAGTGGCGTTTTTAAAAAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* *
170837 GGGCCTTTAGCGGTGTTTTTGAAAAAGCACCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* * *
170878 GGGCCTTTAGCGGCGTTTTTGAAAAAGAGCCACTAATACTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
*
170919 GAGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
170956 AATAATAAAA
Statistics
Matches: 216, Mismatches: 26, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 216 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
Found at i:171952 original size:14 final size:15
Alignment explanation
Indices: 171917--171955 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
171907 TATTTTAAGG
*
171917 TTTAGGGAATATGGA
1 TTTAGGGATTATGGA
171932 TTTAGGGATTATGGA
1 TTTAGGGATTATGGA
171947 -TTAGGGATT
1 TTTAGGGATT
171956 TAAAGTTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 9 0.39
15 14 0.61
ACGTcount: A:0.28, C:0.00, G:0.33, T:0.38
Consensus pattern (15 bp):
TTTAGGGATTATGGA
Found at i:171969 original size:22 final size:22
Alignment explanation
Indices: 171910--171970 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
171900 GAGTTCATAT
* *
171910 TTTAAGGTTTAGGGAATATGGA
1 TTTAAGGTTTAGGGATTAGGGA
* * *
171932 TTTAGGGATTATGGATTAGGGA
1 TTTAAGGTTTAGGGATTAGGGA
*
171954 TTTAAAGTTTAGGGATT
1 TTTAAGGTTTAGGGATT
171971 CAGGAGTCGG
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.30, C:0.00, G:0.31, T:0.39
Consensus pattern (22 bp):
TTTAAGGTTTAGGGATTAGGGA
Found at i:176473 original size:43 final size:43
Alignment explanation
Indices: 176202--176473 Score: 345
Period size: 43 Copynumber: 6.3 Consensus size: 43
176192 GAACCGTACT
* * *
176202 TTTAGCGGCGTTTGT-GATAAAAGCGCCGCTAAATATCATGTTC
1 TTTAGCGGCGTTTTTGGGT-AAAGCGCCGCTAAAGATCATGTTC
* *
176245 TTTAAG-GGCGTTTTTTGGTAAAGTGCCGCTAAAGATCATGTTC
1 TTT-AGCGGCGTTTTTGGGTAAAGCGCCGCTAAAGATCATGTTC
* * *
176288 TTTAGCGGCGTTTGTGTGTAAAGCGCCGCTAAAGATCATGTTA
1 TTTAGCGGCGTTTTTGGGTAAAGCGCCGCTAAAGATCATGTTC
*
176331 TTTAGCGGCGATTTTT--GTAAAGCGCCGCTAAAGGTCATGTTC
1 TTTAGCGGCG-TTTTTGGGTAAAGCGCCGCTAAAGATCATGTTC
* * *
176373 TTTAGCGGTGTTTGTGGGTAAAGCGCCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTTTGGGTAAAGCGCCGCTAAAGATCATGTTC
* * * *
176416 TTTAGCGGCATTTTTGGGTAAAGCGCCACTAAAGAACATGATC
1 TTTAGCGGCGTTTTTGGGTAAAGCGCCGCTAAAGATCATGTTC
176459 TTTAGCGGCGTTTTT
1 TTTAGCGGCGTTTTT
176474 TCACATAAAT
Statistics
Matches: 201, Mismatches: 22, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
41 4 0.02
42 35 0.17
43 154 0.77
44 8 0.04
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (43 bp):
TTTAGCGGCGTTTTTGGGTAAAGCGCCGCTAAAGATCATGTTC
Found at i:176474 original size:128 final size:129
Alignment explanation
Indices: 176202--176473 Score: 370
Period size: 128 Copynumber: 2.1 Consensus size: 129
176192 GAACCGTACT
* * * *
176202 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAATATCATGTTCTTTAAGGGCGTTTTTTGGTAAA
1 TTTAGCGGCGTTTTTGATAAAAGCGCCGCTAAAGATCATGTTCTTTAAGGGCGTTTGTGGGTAAA
* * * * * *
176267 GTGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGTGTAAAGCGCCGCTAAAGATCATGTTA
66 GCGCCGCTAAAGATCATGTTCTTTAGCGGCATTTGTGGGTAAAGCGCCACTAAAGAACATGATA
* *
176331 TTTAGCGGCGATTTTTG-T-AAAGCGCCGCTAAAGGTCATGTTCTTT-AGCGGTGTTTGTGGGTA
1 TTTAGCGGCG-TTTTTGATAAAAGCGCCGCTAAAGATCATGTTCTTTAAG-GGCGTTTGTGGGTA
* *
176393 AAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCATTTTTGGGTAAAGCGCCACTAAAGAACATGAT
64 AAGCGCCGCTAAAGATCATGTTCTTTAGCGGCATTTGTGGGTAAAGCGCCACTAAAGAACATGAT
*
176458 C
129 A
176459 TTTAGCGGCGTTTTT
1 TTTAGCGGCGTTTTT
176474 TCACATAAAT
Statistics
Matches: 126, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
127 7 0.06
128 103 0.82
129 11 0.09
130 5 0.04
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (129 bp):
TTTAGCGGCGTTTTTGATAAAAGCGCCGCTAAAGATCATGTTCTTTAAGGGCGTTTGTGGGTAAA
GCGCCGCTAAAGATCATGTTCTTTAGCGGCATTTGTGGGTAAAGCGCCACTAAAGAACATGATA
Found at i:181476 original size:21 final size:20
Alignment explanation
Indices: 181450--181488 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
181440 TTATATTTTC
181450 AATTGCCATTTATTTTATTCT
1 AATTGCCA-TTATTTTATTCT
*
181471 AATTGCTATTATTTTATT
1 AATTGCCATTATTTTATT
181489 TTGTTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.26, C:0.10, G:0.05, T:0.59
Consensus pattern (20 bp):
AATTGCCATTATTTTATTCT
Found at i:186516 original size:3 final size:3
Alignment explanation
Indices: 186508--186555 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
186498 NNNNNNNNNT
186508 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
186556 AAGTCATCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:186888 original size:24 final size:24
Alignment explanation
Indices: 186856--186902 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
186846 AAAACAAAAG
186856 CTAAGGTGAGTAATTACTAAATAA
1 CTAAGGTGAGTAATTACTAAATAA
186880 CTAAGGTGAGTAATTACTAAATA
1 CTAAGGTGAGTAATTACTAAATA
186903 TTTATCCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.30
Consensus pattern (24 bp):
CTAAGGTGAGTAATTACTAAATAA
Found at i:189043 original size:92 final size:92
Alignment explanation
Indices: 188931--189111 Score: 308
Period size: 92 Copynumber: 2.0 Consensus size: 92
188921 TATGATACAT
*
188931 TAGGTCAAATTATTAATAATACCGAAAGAAATTTATTACCTTACATAACCTAGGAATAATGTGAT
1 TAGGTCAAATTAGTAATAATACCGAAAGAAATTTATTACCTTACATAACCTAGGAATAATGTGAT
*
188996 TAAATTGTTTTAGTATATAAATATCAC
66 TAAATTGTTTCAGTATATAAATATCAC
* * *
189023 TAGGTCAAATTAGTAATAATATCGAAAGAAATTTATTACCTTGCATAACCTAGGATTAATGTGAT
1 TAGGTCAAATTAGTAATAATACCGAAAGAAATTTATTACCTTACATAACCTAGGAATAATGTGAT
*
189088 TAAATTGTTTCAGTATATATATAT
66 TAAATTGTTTCAGTATATAAATAT
189112 ATATATATAT
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
92 83 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (92 bp):
TAGGTCAAATTAGTAATAATACCGAAAGAAATTTATTACCTTACATAACCTAGGAATAATGTGAT
TAAATTGTTTCAGTATATAAATATCAC
Found at i:191952 original size:21 final size:21
Alignment explanation
Indices: 191926--191972 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
191916 TGCAATTGAG
191926 GCACACGCCCGTATGCAAGAA
1 GCACACGCCCGTATGCAAGAA
* * *
191947 GCACACGCCTGTGTGGAAGAA
1 GCACACGCCCGTATGCAAGAA
191968 GCACA
1 GCACA
191973 TAACCATATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.30, G:0.28, T:0.11
Consensus pattern (21 bp):
GCACACGCCCGTATGCAAGAA
Found at i:192151 original size:21 final size:21
Alignment explanation
Indices: 192097--192153 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
192087 GTGGAAAACT
* *
192097 CACACGCCCGTGTGGCTAAGG
1 CACATGCCCGTGTGGCCAAGG
* * * *
192118 GACATGACAGTGTGTCCAAGG
1 CACATGCCCGTGTGGCCAAGG
192139 CACATGCCCGTGTGG
1 CACATGCCCGTGTGG
192154 AAATTTACAA
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.28, G:0.33, T:0.18
Consensus pattern (21 bp):
CACATGCCCGTGTGGCCAAGG
Found at i:199702 original size:55 final size:59
Alignment explanation
Indices: 199620--199767 Score: 150
Period size: 62 Copynumber: 2.5 Consensus size: 59
199610 CTAAAATTCA
*
199620 AAAATCTAATTTAAAA-TCTAA-AGTTGAAAATCC-T-AA-AT-TCTAAG-AAATCTAAATC
1 AAAATTTAATTTAAAACT-TAATA-TTGAAAATCCTTAAATATATCTAAGAAAATC-AAATC
199675 AAAATTTAATTTAAAACTTAATATTGAAAA-CCTTAAAATATAAGATCTAAGAAAATCAAATC
1 AAAATTTAATTTAAAACTTAATATTGAAAATCCTT-AAATAT---ATCTAAGAAAATCAAATC
* *
199737 AAAATTTAATTTAAAACCTAATATTTAAAAT
1 AAAATTTAATTTAAAACTTAATATTGAAAAT
199768 GCAATACATA
Statistics
Matches: 78, Mismatches: 3, Indels: 16
0.80 0.03 0.16
Matches are distributed among these distances:
54 2 0.03
55 26 0.33
56 2 0.03
57 2 0.03
58 2 0.03
62 39 0.50
63 5 0.06
ACGTcount: A:0.53, C:0.10, G:0.04, T:0.32
Consensus pattern (59 bp):
AAAATTTAATTTAAAACTTAATATTGAAAATCCTTAAATATATCTAAGAAAATCAAATC
Found at i:202148 original size:21 final size:23
Alignment explanation
Indices: 202102--202150 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
202092 TAAGTTTTGT
202102 AAGAAAAAGTAAAAAAGACAATGA
1 AAGAAAAAG-AAAAAAGACAATGA
202126 AAGAAAAA-AAAAATAGA-AA-GA
1 AAGAAAAAGAAAAA-AGACAATGA
202147 AAGA
1 AAGA
202151 GGATAGGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 6 0.25
22 7 0.29
23 3 0.12
24 8 0.33
ACGTcount: A:0.76, C:0.02, G:0.16, T:0.06
Consensus pattern (23 bp):
AAGAAAAAGAAAAAAGACAATGA
Found at i:203577 original size:5 final size:5
Alignment explanation
Indices: 203560--203609 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
203550 GTCCATGCCC
* *
203560 AAAAT AAATT AAAAT -AAAT AAAAT ATAATT AATAA- AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT AA-AAT AAAAT AAAAT AAAAT
203610 GGGTTACCTC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 6 0.16
5 26 0.70
6 5 0.14
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (5 bp):
AAAAT
Found at i:203587 original size:21 final size:22
Alignment explanation
Indices: 203563--203609 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
203553 CATGCCCAAA
*
203563 ATAAATTAA-AATAAATAAAAT
1 ATAAATTAATAAAAAATAAAAT
203584 AT-AATTAATAAAAAATAAAAT
1 ATAAATTAATAAAAAATAAAAT
203605 A-AAAT
1 ATAAAT
203610 GGGTTACCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (22 bp):
ATAAATTAATAAAAAATAAAAT
Found at i:204601 original size:16 final size:16
Alignment explanation
Indices: 204576--204620 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
204566 ATTTAGTTAA
*
204576 TTTCTCTTGAGTATAT
1 TTTCTCTTGAATATAT
*
204592 TTTCTTTTGAATATAT
1 TTTCTCTTGAATATAT
204608 TTT-TCTTGAATAT
1 TTTCTCTTGAATAT
204621 GATCATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 9 0.35
16 17 0.65
ACGTcount: A:0.22, C:0.09, G:0.09, T:0.60
Consensus pattern (16 bp):
TTTCTCTTGAATATAT
Found at i:204618 original size:15 final size:15
Alignment explanation
Indices: 204575--204620 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
204565 AATTTAGTTA
* *
204575 ATTTCTCTTGAGTAT
1 ATTTTTCTTGAATAT
*
204590 ATTTTCTTTTGAATAT
1 ATTTT-TCTTGAATAT
204606 ATTTTTCTTGAATAT
1 ATTTTTCTTGAATAT
204621 GATCATTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.59
Consensus pattern (15 bp):
ATTTTTCTTGAATAT
Found at i:208561 original size:13 final size:13
Alignment explanation
Indices: 208543--208657 Score: 124
Period size: 13 Copynumber: 9.5 Consensus size: 13
208533 TTAATTTTTT
208543 CTAAATATTATCA
1 CTAAATATTATCA
208556 CTAAATAATT-T--
1 CTAAAT-ATTATCA
208567 -TAAATATTATCA
1 CTAAATATTATCA
208579 CTAAATATTATCA
1 CTAAATATTATCA
*
208592 CTAAATA--AT-T
1 CTAAATATTATCA
*
208602 CTAAATGTTATCA
1 CTAAATATTATCA
208615 CTAAATATTATCA
1 CTAAATATTATCA
*
208628 CTAAATA--AT-T
1 CTAAATATTATCA
208638 CTAAATATTATCA
1 CTAAATATTATCA
208651 CTAAATA
1 CTAAATA
208658 ATTCAAAATT
Statistics
Matches: 85, Mismatches: 6, Indels: 22
0.75 0.05 0.19
Matches are distributed among these distances:
9 3 0.04
10 19 0.22
11 4 0.05
12 4 0.05
13 52 0.61
14 3 0.04
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.39
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:208566 original size:36 final size:36
Alignment explanation
Indices: 208543--208657 Score: 173
Period size: 36 Copynumber: 3.2 Consensus size: 36
208533 TTAATTTTTT
208543 CTAAATATTATCACTAAATAATTT-TAAATATTATCA
1 CTAAATATTATCACTAAATAATTTAT-AATATTATCA
*
208579 CTAAATATTATCACTAAATAATTCTA-AATGTTATCA
1 CTAAATATTATCACTAAATAATT-TATAATATTATCA
208615 CTAAATATTATCACTAAATAATTCTA-AATATTATCA
1 CTAAATATTATCACTAAATAATT-TATAATATTATCA
208651 CTAAATA
1 CTAAATA
208658 ATTCAAAATT
Statistics
Matches: 75, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
36 74 0.99
37 1 0.01
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.39
Consensus pattern (36 bp):
CTAAATATTATCACTAAATAATTTATAATATTATCA
Found at i:208661 original size:23 final size:23
Alignment explanation
Indices: 208541--208666 Score: 123
Period size: 23 Copynumber: 5.3 Consensus size: 23
208531 AGTTAATTTT
208541 TTCTAAATATTATCACTAAATAA
1 TTCTAAATATTATCACTAAATAA
*
208564 TTTTAAATATTATCACTAAATATTA
1 TTCTAAATATTATCACTAAATA--A
* * *
208589 TCACTAAATA--AT-TCTAAATGTTA
1 T-TCTAAATATTATCACTAAA--TAA
*
208612 TCACTAAATATTATCACTAAATAA
1 T-TCTAAATATTATCACTAAATAA
208636 TTCTAAATATTATCACTAAATAA
1 TTCTAAATATTATCACTAAATAA
*
208659 TTCAAAAT
1 TTCTAAAT
208667 TTAAAAATCA
Statistics
Matches: 86, Mismatches: 9, Indels: 16
0.77 0.08 0.14
Matches are distributed among these distances:
23 65 0.76
24 5 0.06
25 5 0.06
26 11 0.13
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.40
Consensus pattern (23 bp):
TTCTAAATATTATCACTAAATAA
Found at i:210179 original size:10 final size:11
Alignment explanation
Indices: 210150--210181 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
210140 AACTAGAATT
210150 TAAAATAAA-A
1 TAAAATAAATA
210160 TAAAATAAATA
1 TAAAATAAATA
210171 -AAAATAAATA
1 TAAAATAAATA
210181 T
1 T
210182 GGGTTGCCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 19 0.95
11 1 0.05
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
TAAAATAAATA
Found at i:216523 original size:13 final size:13
Alignment explanation
Indices: 216499--216532 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
216489 CAAAAAGGTT
*
216499 GAAAGTAAAAAAAG
1 GAAAG-AAAAAAAA
216513 GAAAGAAAAAAAA
1 GAAAGAAAAAAAA
216526 GAAAGAA
1 GAAAGAA
216533 TTTATTAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (13 bp):
GAAAGAAAAAAAA
Found at i:216661 original size:23 final size:23
Alignment explanation
Indices: 216631--216681 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
216621 TAGATTTTTC
**
216631 CTAAATATTATCTTTAAATAATT
1 CTAAATATTATCACTAAATAATT
216654 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
216677 -TAAAT
1 CTAAAT
216682 TTTAAAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:220942 original size:9 final size:8
Alignment explanation
Indices: 220919--220943 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
220909 TAATTAATTT
220919 TTTAAAAA
1 TTTAAAAA
220927 TTTAAAAA
1 TTTAAAAA
220935 TTTAAAAA
1 TTTAAAAA
220943 T
1 T
220944 ATATATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TTTAAAAA
Found at i:232675 original size:17 final size:17
Alignment explanation
Indices: 232653--232686 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
232643 GATGATCGAG
*
232653 TTAATAAATATTATTTA
1 TTAATAAATAATATTTA
232670 TTAATAAATAATATTTA
1 TTAATAAATAATATTTA
232687 CAAGGTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATAAATAATATTTA
Found at i:237912 original size:100 final size:101
Alignment explanation
Indices: 237738--237953 Score: 308
Period size: 100 Copynumber: 2.1 Consensus size: 101
237728 CAATTATTCA
* * *
237738 AACGTAAGATCATGGTTGGATCATGGCAGTGTTTATATGTAAGACCATAGCTAGGTTATGACATT
1 AACGTAAGACCATGGTTGGACCATGGAAGTGTTTATATGTAAGACCATAGCTAGGTTATGACATT
* * * *
237803 ATGATGATAATACCATAA-TTGGTTATGGCACTATG
66 ATGATGATAAGACCATAACTAGGTTATGACACTACG
* * *
237838 GACGTAAGACCATGGTTGGACCATGGAAGTGTTTATATGTAAGACCATAGCTGGGTTATGGCATT
1 AACGTAAGACCATGGTTGGACCATGGAAGTGTTTATATGTAAGACCATAGCTAGGTTATGACATT
* *
237903 CTGATGATAAGACCATAACTAGGTTATTACACTACG
66 ATGATGATAAGACCATAACTAGGTTATGACACTACG
*
237939 AATGTAAGACCATGG
1 AACGTAAGACCATGG
237954 CAGCGCCATG
Statistics
Matches: 101, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
100 75 0.74
101 26 0.26
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (101 bp):
AACGTAAGACCATGGTTGGACCATGGAAGTGTTTATATGTAAGACCATAGCTAGGTTATGACATT
ATGATGATAAGACCATAACTAGGTTATGACACTACG
Found at i:244636 original size:17 final size:17
Alignment explanation
Indices: 244610--244642 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
244600 TTTTACTTCC
244610 AAAAAATAAAATAAATT
1 AAAAAATAAAATAAATT
*
244627 AAAAATTAAAATAAAT
1 AAAAAATAAAATAAAT
244643 AACTAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAAATAAAATAAATT
Found at i:245271 original size:33 final size:32
Alignment explanation
Indices: 245198--245275 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 32
245188 CAGTGTTTAT
* *
245198 ATGTAAGACCATAGCTGGGCTATGACATTCTG
1 ATGTAAGACCATAACTGGGCTATGACATACTG
* *
245230 ATGATAAGACCATAACTGGGTTATGGCACTAC-G
1 ATG-TAAGACCATAACTGGGCTATGACA-TACTG
245263 AATGTAAGACCAT
1 -ATGTAAGACCAT
245276 GGCAGGGCCA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
32 3 0.08
33 31 0.79
34 5 0.13
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (32 bp):
ATGTAAGACCATAACTGGGCTATGACATACTG
Found at i:245289 original size:101 final size:101
Alignment explanation
Indices: 245061--245320 Score: 335
Period size: 101 Copynumber: 2.6 Consensus size: 101
245051 CAATTATTCA
* * * *
245061 AACGTCAGACCATGGTTGGACCATGACAGTGTTTATATGTAAGACCATAGTTAGGCTATGGCATT
1 AACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGTTGGGCTATGACATT
* *
245126 ATGATGATAAAACCATAACTTGGTTATGGCACTATG
66 ATGATGATAAAACCATAACTGGGTTATGGCACTACG
* * *
245162 GACGTAAGACCATGGTTGGACTATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGACATT
1 AACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGTTGGGCTATGACATT
* *
245227 CTGATGATAAGACCATAACTGGGTTATGGCACTACG
66 ATGATGATAAAACCATAACTGGGTTATGGCACTACG
* ** * * * * *
245263 AATGTAAGACCATGGCAGGGCCATGGCAATG--CATATGTAATACCATAGTTGGACTATG
1 AACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGTTGGGCTATG
245321 GCACAAAGGA
Statistics
Matches: 137, Mismatches: 22, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
99 23 0.17
101 114 0.83
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.28
Consensus pattern (101 bp):
AACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGTTGGGCTATGACATT
ATGATGATAAAACCATAACTGGGTTATGGCACTACG
Found at i:251437 original size:20 final size:20
Alignment explanation
Indices: 251412--251453 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
251402 TATAATTTTT
251412 ATTTTAGAAAATAGAAAAAC
1 ATTTTAGAAAATAGAAAAAC
251432 ATTTTAGAAAATAGAAAAAC
1 ATTTTAGAAAATAGAAAAAC
251452 AT
1 AT
251454 GTATTGGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.60, C:0.05, G:0.10, T:0.26
Consensus pattern (20 bp):
ATTTTAGAAAATAGAAAAAC
Found at i:254232 original size:294 final size:295
Alignment explanation
Indices: 253703--254293 Score: 1175
Period size: 294 Copynumber: 2.0 Consensus size: 295
253693 GGGCCACTCG
253703 TATCACAAACATATGAATGATTGTTATTCTCTGAATCATGCCTGAATCAATTAGTTATTCATGCC
1 TATCACAAACATATGAATGATTGTTATTCTCTGAATCATGCCTGAATCAATTAGTTATTCATGCC
253768 AACCAAACATGCCATTCGTGTTTGGTGACTTAAAGTGAATGATGTGAGAGAAGTTGATAAGGATA
66 AACCAAACATGCCATTCGTGTTTGGTGACTTAAAGTGAATGATGTGAGAGAAGTTGATAAGGATA
253833 AAATATAAAATAGTATGTGAGGGAAAACAAAAAAGAGCGGTGATTTTTTATTAAAAGATCTTTTA
131 AAATATAAAATAGTATGTGAGGGAAAACAAAAAAGAGCGGTGATTTTTTATTAAAAGATCTTTTA
253898 AAAATTATTAGAACTATTAAAATTTTAGAAAAATATAAAAAATAAAAATTGTAGGAAAGTATATA
196 AAAATTATTAGAACTATTAAAATTTTAGAAAAATATAAAAAATAAAAATTGTAGGAAAGTATATA
253963 AATTATTTAAAAATTTTATTAAAA-TATAAAAAAT
261 AATTATTTAAAAATTTTATTAAAATTATAAAAAAT
253997 TATCACAAACATATGAATGATTGTTATTCTCTGAATCATGCCTGAATCAATTAGTTATTCATGCC
1 TATCACAAACATATGAATGATTGTTATTCTCTGAATCATGCCTGAATCAATTAGTTATTCATGCC
254062 AACCAAACATGCCATTCGTGTTTGGTGACTTAAAGTGAATGATGTGAGAGAAGTTGATAAGGATA
66 AACCAAACATGCCATTCGTGTTTGGTGACTTAAAGTGAATGATGTGAGAGAAGTTGATAAGGATA
254127 AAATATAAAATAGTATGTGAGGGAAAACAAAAAAGAGCGGTGATTTTTTATTAAAAGATCTTTTA
131 AAATATAAAATAGTATGTGAGGGAAAACAAAAAAGAGCGGTGATTTTTTATTAAAAGATCTTTTA
254192 AAAATTATTAGAACTATTAAAATTTTAGAAAAATATAAAAAATAAAAATTGTAGGAAAGTATATA
196 AAAATTATTAGAACTATTAAAATTTTAGAAAAATATAAAAAATAAAAATTGTAGGAAAGTATATA
254257 AATTATTTAAAAATTTTATTAAAATTATAAAAAAT
261 AATTATTTAAAAATTTTATTAAAATTATAAAAAAT
254292 TA
1 TA
254294 AAAATTAGTA
Statistics
Matches: 296, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
294 284 0.96
295 12 0.04
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.33
Consensus pattern (295 bp):
TATCACAAACATATGAATGATTGTTATTCTCTGAATCATGCCTGAATCAATTAGTTATTCATGCC
AACCAAACATGCCATTCGTGTTTGGTGACTTAAAGTGAATGATGTGAGAGAAGTTGATAAGGATA
AAATATAAAATAGTATGTGAGGGAAAACAAAAAAGAGCGGTGATTTTTTATTAAAAGATCTTTTA
AAAATTATTAGAACTATTAAAATTTTAGAAAAATATAAAAAATAAAAATTGTAGGAAAGTATATA
AATTATTTAAAAATTTTATTAAAATTATAAAAAAT
Found at i:255975 original size:11 final size:11
Alignment explanation
Indices: 255959--255998 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
255949 TTCAAAAATT
255959 CTCTTAAGTTC
1 CTCTTAAGTTC
255970 CTCTTAAGTTC
1 CTCTTAAGTTC
*
255981 CTCTTAAGTTT
1 CTCTTAAGTTC
255992 CTCTTAA
1 CTCTTAA
255999 CTCCCTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.20, C:0.25, G:0.07, T:0.47
Consensus pattern (11 bp):
CTCTTAAGTTC
Found at i:256221 original size:11 final size:11
Alignment explanation
Indices: 256189--256231 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
256179 TTAACTCCCT
256189 TTTTTTAAATAA
1 TTTTTTAAAT-A
**
256201 TTTTAAAAATA
1 TTTTTTAAATA
*
256212 TTTTTTAAATT
1 TTTTTTAAATA
256223 TTTTTTAAA
1 TTTTTTAAA
256232 CCGTAAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 18 0.69
12 8 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTTTAAATA
Found at i:256757 original size:30 final size:29
Alignment explanation
Indices: 256723--256848 Score: 119
Period size: 30 Copynumber: 4.2 Consensus size: 29
256713 AAAAACAAAA
* *
256723 AAAATTACATTTTAACCCCTCAACTTTTTT
1 AAAATTACATTTTGACCCCT-AACTTTCTT
* *
256753 AAAATTACATTTTCACCCCTACACTTTCCT
1 AAAATTACATTTTGACCCCTA-ACTTTCTT
* *
256783 AAAATTACATTTTGGCCCATCAAC-TTCTT
1 AAAATTACATTTTGACCCCT-AACTTTCTT
* * * *
256812 GAAATTATATTTTGACCCCTAAATTTTCTC
1 AAAATTACATTTTGACCCCT-AACTTTCTT
256842 AAAATTA
1 AAAATTA
256849 TGCTTGGCCC
Statistics
Matches: 78, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
29 23 0.29
30 54 0.69
31 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.40
Consensus pattern (29 bp):
AAAATTACATTTTGACCCCTAACTTTCTT
Found at i:256846 original size:59 final size:60
Alignment explanation
Indices: 256723--256848 Score: 148
Period size: 59 Copynumber: 2.1 Consensus size: 60
256713 AAAAACAAAA
* * *
256723 AAAATTACATTTTAACCCCTCAACTTTTTTAAAATTACATTTTCACCCCTACACTTTCCT
1 AAAATTACATTTTAACCCATCAACTTTCTTAAAATTACATTTTCACCCCTAAACTTTCCT
** * * * *
256783 AAAATTACATTTTGGCCCATCAAC-TTCTTGAAATTATATTTTGACCCCTAAA-TTTTCT
1 AAAATTACATTTTAACCCATCAACTTTCTTAAAATTACATTTTCACCCCTAAACTTTCCT
256841 CAAAATTA
1 -AAAATTA
256849 TGCTTGGCCC
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
58 5 0.09
59 30 0.54
60 21 0.38
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.40
Consensus pattern (60 bp):
AAAATTACATTTTAACCCATCAACTTTCTTAAAATTACATTTTCACCCCTAAACTTTCCT
Found at i:257645 original size:30 final size:29
Alignment explanation
Indices: 257604--257718 Score: 115
Period size: 30 Copynumber: 3.9 Consensus size: 29
257594 AAAAAATAAA
*
257604 AAATTATATTTTGACCCCCTAAACTTTTTG
1 AAATTACATTTTGA-CCCCTAAACTTTTTG
* * * *
257634 AAATTGCATTTTCACCCCTAAACTTTCCTA
1 AAATTACATTTTGACCCCTAAACTTT-TTG
* * * *
257664 AAATTACATTTTGGCCCATCAACTTCTTG
1 AAATTACATTTTGACCCCTAAACTTTTTG
*
257693 AAATTATATTTTGACCCCTAAA-TTTT
1 AAATTACATTTTGACCCCTAAACTTTT
257719 CTCAAAATTA
Statistics
Matches: 66, Mismatches: 18, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
28 3 0.05
29 31 0.47
30 32 0.48
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.41
Consensus pattern (29 bp):
AAATTACATTTTGACCCCTAAACTTTTTG
Found at i:258258 original size:4 final size:4
Alignment explanation
Indices: 258245--258324 Score: 71
Period size: 4 Copynumber: 20.5 Consensus size: 4
258235 ACGGAGAAGG
* *
258245 AAGA AA-A AAGA AAG- AAGA AAGA AAGA AAGA AA-A AAGA AGGA AGACA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA A-AGA
*
258291 AAGA AAGA AA-A AAGA GAA-A AAAA AAGGA AAGA AA
1 AAGA AAGA AAGA AAGA -AAGA AAGA AA-GA AAGA AA
258325 AAAAATAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
3 14 0.22
4 42 0.67
5 7 0.11
ACGTcount: A:0.76, C:0.01, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:258265 original size:11 final size:11
Alignment explanation
Indices: 258245--258324 Score: 65
Period size: 11 Copynumber: 7.2 Consensus size: 11
258235 ACGGAGAAGG
*
258245 AAGAAAAAAGA
1 AAGAAGAAAGA
258256 AAGAAGAAAGA
1 AAGAAGAAAGA
258267 AAGAAAGAAA-A
1 AAG-AAGAAAGA
*
258278 AAGAAGGAAGA
1 AAGAAGAAAGA
*
258289 CA-AAGAAAGA
1 AAGAAGAAAGA
* *
258299 AAAAAGAGAAAA
1 AAGAAGA-AAGA
*
258311 AAAAAGGAAAGA
1 AAGAA-GAAAGA
258323 AA
1 AA
258325 AAAAATAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
10 13 0.23
11 23 0.40
12 19 0.33
13 2 0.04
ACGTcount: A:0.76, C:0.01, G:0.23, T:0.00
Consensus pattern (11 bp):
AAGAAGAAAGA
Found at i:258321 original size:17 final size:17
Alignment explanation
Indices: 258272--258329 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
258262 AAAGAAAGAA
*
258272 AGAAAAAAGAAGG-AAG
1 AGAAAAAAAAAGGAAAG
*
258288 ACAAAGAAAGAAA--AAAG
1 AGAAA-AAA-AAAGGAAAG
258305 AGAAAAAAAAAGGAAAG
1 AGAAAAAAAAAGGAAAG
258322 A-AAAAAAA
1 AGAAAAAAA
258330 TAAAAAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
15 3 0.09
16 14 0.41
17 15 0.44
18 2 0.06
ACGTcount: A:0.78, C:0.02, G:0.21, T:0.00
Consensus pattern (17 bp):
AGAAAAAAAAAGGAAAG
Found at i:258325 original size:15 final size:14
Alignment explanation
Indices: 258248--258329 Score: 65
Period size: 15 Copynumber: 5.4 Consensus size: 14
258238 GAGAAGGAAG
258248 AAAAAAGAAAGAAGA
1 AAAAAAGAAAGAA-A
*
258263 AAGAAAGAAAGAAA
1 AAAAAAGAAAGAAA
* *
258277 AAAGAAGGAAGACAAA
1 AAA-AAAGAA-AGAAA
*
258293 GAAAGAAAAAAGAGAAA
1 -AAA-AAAGAA-AGAAA
258310 AAAAAAGGAAAGAAA
1 AAAAAA-GAAAGAAA
258325 AAAAA
1 AAAAA
258330 TAAAAAAATA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
14 3 0.05
15 30 0.55
16 9 0.16
17 13 0.24
ACGTcount: A:0.78, C:0.01, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAGAAA
Found at i:258335 original size:33 final size:33
Alignment explanation
Indices: 258262--258336 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
258252 AAGAAAGAAG
* * *
258262 AAAGAAAGAA-AGAAAAAAGAAGGAAGACAAAG
1 AAAGAAAAAAGAGAAAAAAAAAGGAAGACAAAA
258294 AAAGAAAAAAGAGAAAAAAAAAGGAAAGA-AAAA
1 AAAGAAAAAAGAGAAAAAAAAAGG-AAGACAAAA
*
258327 AAATAAAAAA
1 AAAGAAAAAA
258337 ATAAATTAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 9 0.24
33 24 0.65
34 4 0.11
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.01
Consensus pattern (33 bp):
AAAGAAAAAAGAGAAAAAAAAAGGAAGACAAAA
Found at i:258673 original size:21 final size:19
Alignment explanation
Indices: 258647--258690 Score: 70
Period size: 21 Copynumber: 2.2 Consensus size: 19
258637 AACATCCAGC
258647 AAAAAAAAAAGGAAAGAGAAG
1 AAAAAAAAAAGGAAA-A-AAG
258668 AAAAAAAAAAGGAAAAAAG
1 AAAAAAAAAAGGAAAAAAG
258687 AAAA
1 AAAA
258691 GGGCCCACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 7 0.30
20 1 0.04
21 15 0.65
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAGGAAAAAAG
Found at i:259240 original size:16 final size:16
Alignment explanation
Indices: 259221--259325 Score: 84
Period size: 16 Copynumber: 6.2 Consensus size: 16
259211 GTTTTCAAAA
259221 AAAATTCTCGTGTTTT
1 AAAATTCTCGTGTTTT
* * *
259237 AAAATTCTCATGCTTC
1 AAAATTCTCGTGTTTT
* *
259253 AAAATTGTTGTGTTTT
1 AAAATTCTCGTGTTTT
* *
259269 CAAAAATTTTTGTGTTTTT
1 --AAAATTCTCGTG-TTTT
* *
259288 AATAATTTTCGTGTCTCT
1 AA-AATTCTCGTGT-TTT
259306 AAAATTCTCGTGTTTT
1 AAAATTCTCGTGTTTT
259322 AAAA
1 AAAA
259326 ATATTTTCGT
Statistics
Matches: 71, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
16 30 0.42
17 13 0.18
18 24 0.34
19 4 0.06
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (16 bp):
AAAATTCTCGTGTTTT
Found at i:259240 original size:18 final size:17
Alignment explanation
Indices: 259220--259327 Score: 78
Period size: 18 Copynumber: 6.4 Consensus size: 17
259210 TGTTTTCAAA
259220 AAAAATTCTCGTGTTTT
1 AAAAATTCTCGTGTTTT
* *
259237 -AAAATTCTCATG-CTT
1 AAAAATTCTCGTGTTTT
* * *
259252 CAAAATTGTTGTGTTTT
1 AAAAATTCTCGTGTTTT
* *
259269 CAAAAATTTTTGTGTTTTT
1 -AAAAATTCTCGTG-TTTT
* * *
259288 AATAATTTTCGTGTCTCT
1 AAAAATTCTCGTGT-TTT
259306 -AAAATTCTCGTGTTTT
1 AAAAATTCTCGTGTTTT
259322 AAAAAT
1 AAAAAT
259328 ATTTTCGTGT
Statistics
Matches: 71, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
15 2 0.03
16 22 0.31
17 19 0.27
18 24 0.34
19 4 0.06
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (17 bp):
AAAAATTCTCGTGTTTT
Done.