Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold100
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1174989
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 153044 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:4881 original size:199 final size:198
Alignment explanation
Indices: 4539--4937 Score: 789
Period size: 199 Copynumber: 2.0 Consensus size: 198
4529 TAAAAAGATG
4539 ATTATTTTTAACAATTTTTTTTGTCTGAATCTTAACTCTGTGTTTTTTCTTTTAAATCTGGCTCT
1 ATTATTTTTAACAATTTTTTTTGTCTGAATCTTAACTCTGTGTTTTTTCTTTTAAATCTGGCTCT
4604 TTTCTTTTTGCAGAAAGTAAAAGTGGATCAAGTGTGCTAAATGAAGTTTATACAAAACGCTATGA
66 TTTCTTTTTGCAGAAAGTAAAAGTGGATCAAGTGTGCTAAATGAAGTTTATACAAAACGCTATGA
4669 TTATGTTGTGAGCCCTCAGTTACCAGGCAATGAAAAAACTGTTCACCATCATCAATTAGAATATT
131 TTATGTTGTGAGCCCTCAGTTACCAGGCAATGAAAAAACTGTTCACCATCATCAATTAGAATATT
4734 CTA
196 CTA
4737 ATNTATTTTTAACAATTTTTTTTGTCTGAATCTTAACTCTGTGTTTTTTCTTTTAAATCTGGCTC
1 AT-TATTTTTAACAATTTTTTTTGTCTGAATCTTAACTCTGTGTTTTTTCTTTTAAATCTGGCTC
4802 TTTTCTTTTTGCAGAAAGTAAAAGTGGATCAAGTGTGCTAAATGAAGTTTATACAAAACGCTATG
65 TTTTCTTTTTGCAGAAAGTAAAAGTGGATCAAGTGTGCTAAATGAAGTTTATACAAAACGCTATG
4867 ATTATGTTGTGAGCCCTCAGTTACCAGGCAATGAAAAAACTGTTCACCATCATCAATTAGAATAT
130 ATTATGTTGTGAGCCCTCAGTTACCAGGCAATGAAAAAACTGTTCACCATCATCAATTAGAATAT
4932 TCTA
195 TCTA
4936 AT
1 AT
4938 ATCGACAACC
Statistics
Matches: 200, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
198 2 0.01
199 198 0.99
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (198 bp):
ATTATTTTTAACAATTTTTTTTGTCTGAATCTTAACTCTGTGTTTTTTCTTTTAAATCTGGCTCT
TTTCTTTTTGCAGAAAGTAAAAGTGGATCAAGTGTGCTAAATGAAGTTTATACAAAACGCTATGA
TTATGTTGTGAGCCCTCAGTTACCAGGCAATGAAAAAACTGTTCACCATCATCAATTAGAATATT
CTA
Found at i:5010 original size:2 final size:2
Alignment explanation
Indices: 5003--5036 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
4993 TTGAAAAAGG
*
5003 TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5037 NNNNNNNNNN
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:11965 original size:28 final size:28
Alignment explanation
Indices: 11925--12931 Score: 1086
Period size: 28 Copynumber: 38.0 Consensus size: 28
11915 NNNNNNATAA
*
11925 CATGACATCACAGTAGTCAGATTAATAA
1 CATGACATCACAGTAGTCAGATTAATAT
* * *
11953 AATTACATTACAGTAGTCAGA-T-A-A-
1 CATGACATCACAGTAGTCAGATTAATAT
11977 CATGACATCACAGTAGTCAGATTAATAT
1 CATGACATCACAGTAGTCAGATTAATAT
*
12005 AATGACATCACAGTAGTCAGATTAATAT
1 CATGACATCACAGTAGTCAGATTAATAT
*
12033 CATGACATTACAGTAGTCAGATTAATAT
1 CATGACATCACAGTAGTCAGATTAATAT
*
12061 CATGACATTACAGTAGTCAGA-T-A-A-
1 CATGACATCACAGTAGTCAGATTAATAT
12085 CATGACATCACAGTAGTCAGATTAATAT
1 CATGACATCACAGTAGTCAGATTAATAT
* *
12113 AATGACATCACA-AAGTCAGA-T-A-A-
1 CATGACATCACAGTAGTCAGATTAATAT
12136 CATGACATCACAGTAGTCAGATTAATAT
1 CATGACATCACAGTAGTCAGATTAATAT
* * *
12164 AATGACATCACAAATA-TCAGATAAATAT
1 CATGACATCAC-AGTAGTCAGATTAATAT
* *
12192 AATGACATCACAGTAGTCAGAATAATAT
1 CATGACATCACAGTAGTCAGATTAATAT
12220 CATGACATCACAGTAGTCAGATTAATAT
1 CATGACATCACAGTAGTCAGATTAATAT
12248 CATGACATCACAGTAGTCAGATTAATAT
1 CATGACATCACAGTAGTCAGATTAATAT
** *
12276 CATGACATCACAAAAGTC--A--AATAA
1 CATGACATCACAGTAGTCAGATTAATAT
*
12300 CATGACATCACAGTAGTCAGATTTATAT
1 CATGACATCACAGTAGTCAGATTAATAT
* *
12328 AATGACATCACA-AAGTCAGA-T-A-A-
1 CATGACATCACAGTAGTCAGATTAATAT
12351 CATGACATCACAGTAGTCAGATTAATAT
1 CATGACATCACAGTAGTCAGATTAATAT
* *
12379 CATGACATCATCA-AAGTC--A--AATAA
1 CATGACATCA-CAGTAGTCAGATTAATAT
12403 CATGACATCACAGTAGTCAGATTAATAT
1 CATGACATCACAGTAGTCAGATTAATAT
* *
12431 AATGACATCACA-AAGTCAGA-T-A-A-
1 CATGACATCACAGTAGTCAGATTAATAT
*
12454 CATGACATCACAGTAGTCAGAATAATAT
1 CATGACATCACAGTAGTCAGATTAATAT
12482 CATGACATCACAGTAGTCAGATTAATAT
1 CATGACATCACAGTAGTCAGATTAATAT
*
12510 TATGACATCACAGTAGTCAGA-T-A-A-
1 CATGACATCACAGTAGTCAGATTAATAT
* *
12534 CATGGCAGCACAGTAGTCAGATTAATAT
1 CATGACATCACAGTAGTCAGATTAATAT
*
12562 AATGACATCACAGTAGTCAGA-T-A-A-
1 CATGACATCACAGTAGTCAGATTAATAT
* *
12586 CATGGCAGCACAGTAGTCAGATTAATAT
1 CATGACATCACAGTAGTCAGATTAATAT
12614 CATGACATCACAGTAGTCAGATTAATAT
1 CATGACATCACAGTAGTCAGATTAATAT
* *
12642 AATGACATCACA-AAGTCAGA-T-A-A-
1 CATGACATCACAGTAGTCAGATTAATAT
*
12665 CATGACATCACAGTAGTCAGAATAATAT
1 CATGACATCACAGTAGTCAGATTAATAT
*
12693 CATGACATCACAGTAGTCAGATTAAAAT
1 CATGACATCACAGTAGTCAGATTAATAT
* *
12721 TATGGCATCACAGTAGTCAGA-T-A-A-
1 CATGACATCACAGTAGTCAGATTAATAT
* *
12745 CATGGCAGCACAGTAGTCAGATTAATAT
1 CATGACATCACAGTAGTCAGATTAATAT
* *
12773 AATGACATCACAGTAGTC--A--AATAA
1 CATGACATCACAGTAGTCAGATTAATAT
* * * *
12797 CATGGCAGCACAGTAGTCAGAGTAATTT
1 CATGACATCACAGTAGTCAGATTAATAT
* * *
12825 TATGACATCACAGTAGTCAGATTAACAA
1 CATGACATCACAGTAGTCAGATTAATAT
* * * *
12853 AATGACATCACAGAAGTCAGA-CAA-GT
1 CATGACATCACAGTAGTCAGATTAATAT
*
12879 --TGACATTACAGTAGTCAGATTAATAT
1 CATGACATCACAGTAGTCAGATTAATAT
** *
12905 CATGACATCACAAAAATCAGATTAATA
1 CATGACATCACAGTAGTCAGATTAATA
12932 GATGGAAACC
Statistics
Matches: 826, Mismatches: 93, Indels: 120
0.79 0.09 0.12
Matches are distributed among these distances:
23 46 0.06
24 199 0.24
25 20 0.02
26 25 0.03
27 47 0.06
28 484 0.59
29 5 0.01
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (28 bp):
CATGACATCACAGTAGTCAGATTAATAT
Found at i:11999 original size:52 final size:52
Alignment explanation
Indices: 11921--12916 Score: 1046
Period size: 52 Copynumber: 18.8 Consensus size: 52
11911 NNNNNNNNNN
** * *
11921 ATAACATGACATCACAGTAGTCAGATTAATAAAATTACATTACAGTAGTCAG
1 ATAACATGACATCACAGTAGTCAGATTAATATCATGACATCACAGTAGTCAG
*
11973 ATAACATGACATCACAGTAGTCAGATTAATATAATGACATCACAGTAGTCAG
1 ATAACATGACATCACAGTAGTCAGATTAATATCATGACATCACAGTAGTCAG
* *
12025 ATTAATATCATGACATTACAGTAGTCAGATTAATATCATGACATTACAGTAGTCAG
1 A-T-A-A-CATGACATCACAGTAGTCAGATTAATATCATGACATCACAGTAGTCAG
* *
12081 ATAACATGACATCACAGTAGTCAGATTAATATAATGACATCACA-AAGTCAG
1 ATAACATGACATCACAGTAGTCAGATTAATATCATGACATCACAGTAGTCAG
* *
12132 ATAACATGACATCACAGTAGTCAGATTAATATAATGACATCACAAATA-TCAG
1 ATAACATGACATCACAGTAGTCAGATTAATATCATGACATCAC-AGTAGTCAG
* *
12184 ATAAATATAATGACATCACAGTAGTCAGAATAATATCATGACATCACAGTAGTCAG
1 AT--A-A-CATGACATCACAGTAGTCAGATTAATATCATGACATCACAGTAGTCAG
** *
12240 ATTAATATCATGACATCACAGTAGTCAGATTAATATCATGACATCACAAAAGTCAA
1 A-T-A-A-CATGACATCACAGTAGTCAGATTAATATCATGACATCACAGTAGTCAG
* * *
12296 ATAACATGACATCACAGTAGTCAGATTTATATAATGACATCACA-AAGTCAG
1 ATAACATGACATCACAGTAGTCAGATTAATATCATGACATCACAGTAGTCAG
* *
12347 ATAACATGACATCACAGTAGTCAGATTAATATCATGACATCATCA-AAGTCAA
1 ATAACATGACATCACAGTAGTCAGATTAATATCATGACATCA-CAGTAGTCAG
* *
12399 ATAACATGACATCACAGTAGTCAGATTAATATAATGACATCACA-AAGTCAG
1 ATAACATGACATCACAGTAGTCAGATTAATATCATGACATCACAGTAGTCAG
*
12450 ATAACATGACATCACAGTAGTCAGAATAATATCATGACATCACAGTAGTCAG
1 ATAACATGACATCACAGTAGTCAGATTAATATCATGACATCACAGTAGTCAG
* * *
12502 ATTAATATTATGACATCACAGTAGTCAGA-T-A-A-CATGGCAGCACAGTAGTCAG
1 A-T-A-A-CATGACATCACAGTAGTCAGATTAATATCATGACATCACAGTAGTCAG
* * *
12554 ATTAATATAATGACATCACAGTAGTCAGA-T-A-A-CATGGCAGCACAGTAGTCAG
1 A-T-A-A-CATGACATCACAGTAGTCAGATTAATATCATGACATCACAGTAGTCAG
* *
12606 ATTAATATCATGACATCACAGTAGTCAGATTAATATAATGACATCACA-AAGTCAG
1 A-T-A-A-CATGACATCACAGTAGTCAGATTAATATCATGACATCACAGTAGTCAG
*
12661 ATAACATGACATCACAGTAGTCAGAATAATATCATGACATCACAGTAGTCAG
1 ATAACATGACATCACAGTAGTCAGATTAATATCATGACATCACAGTAGTCAG
* * * *
12713 ATTAAAATTATGGCATCACAGTAGTCAGA-T-A-A-CATGGCAGCACAGTAGTCAG
1 A-T--AA-CATGACATCACAGTAGTCAGATTAATATCATGACATCACAGTAGTCAG
* * * *
12765 ATTAATATAATGACATCACAGTAGTC--A--AATAACATGGCAGCACAGTAGTCAG
1 A-T-A-A-CATGACATCACAGTAGTCAGATTAATATCATGACATCACAGTAGTCAG
* * ** *
12817 AGTAATTTTATGACATCACAGTAGTCAGATTAACAAAATGACATCACAGAAGTCAG
1 A-TAA---CATGACATCACAGTAGTCAGATTAATATCATGACATCACAGTAGTCAG
* ** *
12873 ACAAGTTGACATTACAGTAGTCAGATTAATATCATGACATCACA
1 ATAACATGACATCACAGTAGTCAGATTAATATCATGACATCACA
12917 AAAATCAGAT
Statistics
Matches: 844, Mismatches: 63, Indels: 74
0.86 0.06 0.08
Matches are distributed among these distances:
50 3 0.00
51 187 0.22
52 406 0.48
53 10 0.01
54 10 0.01
55 22 0.03
56 205 0.24
57 1 0.00
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (52 bp):
ATAACATGACATCACAGTAGTCAGATTAATATCATGACATCACAGTAGTCAG
Found at i:12620 original size:211 final size:211
Alignment explanation
Indices: 11921--12931 Score: 1061
Period size: 211 Copynumber: 4.8 Consensus size: 211
11911 NNNNNNNNNN
* * ** **
11921 ATAACATGACATCACAGTAGTCAGATTAATAAAATTACATTACAGTAGTCAGA-T-A-A-CATGA
1 ATAAAATGACATCACAGTAGTCAGA-T--TAACATGGCAGCACAGTAGTCAGATTAATATCATGA
* *
11982 CATCACAGTAGTCAGATTAATATAATGACATCACAGTAGTCAGATTAATATCATGACATTACAGT
63 CATCACAGTAGTCAGATTAATATAATGACATCACAGAAGTCAGA-T-A-A-CATGACATCACAGT
*
12047 AGTCAGATTAATATCATGACATTACAGTAGTCAGA-T-A-A-CATGACATCACAGTAGTCAGATT
124 AGTCAGATTAATATCATGACATCACAGTAGTCAGATTAATATCATGACATCACAGTAGTCAGATT
*
12108 AATATAATGACATCACAAAGTCAG
189 -ATATAATGACAGCACAAAGTCAG
* * * * * * *
12132 ATAACATGACATCACAGTAGTCAGATTAATATAATGACATCACAAATA-TCAGATAAATATAATG
1 ATAAAATGACATCACAGTAGTCAGATT-A-A-CATGGCAGCAC-AGTAGTCAGATTAATATCATG
* * *
12196 ACATCACAGTAGTCAGAATAATATCATGACATCACAGTAGTCAGATTAATATCATGACATCACAG
62 ACATCACAGTAGTCAGATTAATATAATGACATCACAGAAGTCAGA-T-A-A-CATGACATCACAG
** *
12261 TAGTCAGATTAATATCATGACATCACAAAAGTC--A--AATAACATGACATCACAGTAGTCAGAT
123 TAGTCAGATTAATATCATGACATCACAGTAGTCAGATTAATATCATGACATCACAGTAGTCAGA-
*
12322 TTATATAATGACATCACAAAGTCAG
187 TTATATAATGACAGCACAAAGTCAG
* * * * *
12347 ATAACATGACATCACAGTAGTCAGATTAATAT--CATG-ACA-TCA-TCAAAGTCAAATAACATG
1 ATAAAATGACATCACAGTAGTCAGATTAACATGGCA-GCACAGT-AGTCAGA-T-TAATATCATG
12407 ACATCACAGTAGTCAGATTAATATAATGACATCACA-AAGTCAGATAACATGACATCACAGTAGT
62 ACATCACAGTAGTCAGATTAATATAATGACATCACAGAAGTCAGATAACATGACATCACAGTAGT
* *
12471 CAGAATAATATCATGACATCACAGTAGTCAGATTAATATTATGACATCACAGTAGTCAGA-TA-A
127 CAGATTAATATCATGACATCACAGTAGTCAGATTAATATCATGACATCACAGTAGTCAGATTATA
* * *
12534 -CATGGCAGCACAGTAGTCAG
192 TAATGACAGCACA-AAGTCAG
12554 ATTAATATAATGACATCACAGTAGTCAGA-TAACATGGCAGCACAGTAGTCAGATTAATATCATG
1 A-T-A-A-AATGACATCACAGTAGTCAGATTAACATGGCAGCACAGTAGTCAGATTAATATCATG
12618 ACATCACAGTAGTCAGATTAATATAATGACATCACA-AAGTCAGATAACATGACATCACAGTAGT
62 ACATCACAGTAGTCAGATTAATATAATGACATCACAGAAGTCAGATAACATGACATCACAGTAGT
* * * *
12682 CAGAATAATATCATGACATCACAGTAGTCAGATTAAAATTATGGCATCACAGTAGTCAGA-TA-A
127 CAGATTAATATCATGACATCACAGTAGTCAGATTAATATCATGACATCACAGTAGTCAGATTATA
* * *
12745 -CATGGCAGCACAGTAGTCAG
192 TAATGACAGCACA-AAGTCAG
* * * *
12765 ATTAATATAATGACATCACAGTAGTCA-AATAACATGGCAGCACAGTAGTCAGAGTAATTTTATG
1 A-T-A-A-AATGACATCACAGTAGTCAGATTAACATGGCAGCACAGTAGTCAGATTAATATCATG
* * * ** *
12829 ACATCACAGTAGTCAGATTAACAAAATGACATCACAGAAGTCAGACAAGTTGACATTACAGTAGT
62 ACATCACAGTAGTCAGATTAATATAATGACATCACAGAAGTCAGATAACATGACATCACAGTAGT
** *
12894 CAGATTAATATCATGACATCACAAAAATCAGATTAATA
127 CAGATTAATATCATGACATCACAGTAGTCAGATTAATA
12932 GATGGAAACC
Statistics
Matches: 719, Mismatches: 49, Indels: 63
0.87 0.06 0.08
Matches are distributed among these distances:
206 52 0.07
207 9 0.01
208 7 0.01
209 9 0.01
210 45 0.06
211 348 0.48
212 69 0.10
213 9 0.01
214 3 0.00
215 166 0.23
216 2 0.00
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (211 bp):
ATAAAATGACATCACAGTAGTCAGATTAACATGGCAGCACAGTAGTCAGATTAATATCATGACAT
CACAGTAGTCAGATTAATATAATGACATCACAGAAGTCAGATAACATGACATCACAGTAGTCAGA
TTAATATCATGACATCACAGTAGTCAGATTAATATCATGACATCACAGTAGTCAGATTATATAAT
GACAGCACAAAGTCAG
Found at i:17450 original size:2 final size:2
Alignment explanation
Indices: 17395--17432 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
17385 GAAAATGCAC
*
17395 AG AG AG AG AG AC AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
17433 CACAAAAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17773 original size:2 final size:2
Alignment explanation
Indices: 17766--17796 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17756 CTACGTGCCT
17766 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
17797 TGTGAACATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19055 original size:2 final size:2
Alignment explanation
Indices: 19048--19087 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
19038 CGTAATTAAT
19048 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
19088 AGAGAGAGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:19092 original size:2 final size:2
Alignment explanation
Indices: 19087--19128 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
19077 GTGTGTGTGT
19087 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
19129 TTTTAGTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:22157 original size:12 final size:12
Alignment explanation
Indices: 22137--22179 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
22127 TACCCTTGTG
*
22137 TGTCTGTCTGTC
1 TGTCCGTCTGTC
22149 TGTCCGTCTGTC
1 TGTCCGTCTGTC
*
22161 TGTCTGTCTGTC
1 TGTCCGTCTGTC
*
22173 CGTCCGT
1 TGTCCGT
22180 AACAAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.00, C:0.30, G:0.26, T:0.44
Consensus pattern (12 bp):
TGTCCGTCTGTC
Found at i:22179 original size:4 final size:4
Alignment explanation
Indices: 22137--22172 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
22127 TACCCTTGTG
*
22137 TGTC TGTC TGTC TGTC CGTC TGTC TGTC TGTC TGTC
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC
22173 CGTCCGTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.00, C:0.28, G:0.25, T:0.47
Consensus pattern (4 bp):
TGTC
Found at i:26397 original size:2 final size:2
Alignment explanation
Indices: 26390--26434 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
26380 ATATGTAACG
26390 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
26432 GT G
1 GT G
26435 GACTTTACAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Found at i:27080 original size:140 final size:141
Alignment explanation
Indices: 26828--27103 Score: 509
Period size: 140 Copynumber: 2.0 Consensus size: 141
26818 ATATCACGAT
* *
26828 CCTAAAATGTTGCACAGACAACTGCATGACGAGGAACGGAAACAAATAAGAGAATTAAGCTAGTA
1 CCTAAAATGTTGCAAAGACAACTGCATGACGAGGAACGAAAACAAATAAGAGAATTAAGCTAGTA
* *
26893 ATCTAATTGTTATATTATCTTTTGTTTGTTTATATATCAAACTTTAGGTCCTCTACAAAAC-AGA
66 ATCTAATTGTTATATTATCTTTCGTTTGTTTATATATCAAACTTTAGGTCCTCTACAAAACAAAA
26957 CACTTATTATG
131 CACTTATTATG
26968 CCTAAAATGTTGCAAAGACAACTGCATGACGAGGAACGAAAACAAATAAGAGAATTAAGCTAGTA
1 CCTAAAATGTTGCAAAGACAACTGCATGACGAGGAACGAAAACAAATAAGAGAATTAAGCTAGTA
27033 ATCTAATTGTTATATTATCTTTCGTTTGTTTATATATCAAACTTTAGGTCCTCTACAAAACAAAA
66 ATCTAATTGTTATATTATCTTTCGTTTGTTTATATATCAAACTTTAGGTCCTCTACAAAACAAAA
27098 CACTTA
131 CACTTA
27104 AAACGTTAGG
Statistics
Matches: 131, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
140 123 0.94
141 8 0.06
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (141 bp):
CCTAAAATGTTGCAAAGACAACTGCATGACGAGGAACGAAAACAAATAAGAGAATTAAGCTAGTA
ATCTAATTGTTATATTATCTTTCGTTTGTTTATATATCAAACTTTAGGTCCTCTACAAAACAAAA
CACTTATTATG
Found at i:27118 original size:33 final size:32
Alignment explanation
Indices: 27071--27135 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
27061 TTTATATATC
*
27071 AAACTTTAGGTCCTCTACAAAACAAAACACTTA
1 AAACGTTAGGTCCTCTACAAAAC-AAACACTTA
*
27104 AAACGTTAGGTCCTCTACAAAACAGACACTTA
1 AAACGTTAGGTCCTCTACAAAACAAACACTTA
27136 TTATGCCTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 8 0.27
33 22 0.73
ACGTcount: A:0.43, C:0.25, G:0.09, T:0.23
Consensus pattern (32 bp):
AAACGTTAGGTCCTCTACAAAACAAACACTTA
Found at i:34778 original size:30 final size:30
Alignment explanation
Indices: 34742--34870 Score: 179
Period size: 30 Copynumber: 4.3 Consensus size: 30
34732 GTTTGAAAGT
* * *
34742 GATCTATTCAACTGCCGTTCAATAGACTGC
1 GATCTATTGAACCGCCGGTCAATAGACTGC
*
34772 GATCTATT-AGACCGCCGGTCAATAGACTGT
1 GATCTATTGA-ACCGCCGGTCAATAGACTGC
*
34802 GATCTATTGGACCGCCGGTCAATAGACTGC
1 GATCTATTGAACCGCCGGTCAATAGACTGC
* *
34832 GATCTATTGGACAGCCGGTCAATAGACTGC
1 GATCTATTGAACCGCCGGTCAATAGACTGC
34862 GATCTATTG
1 GATCTATTG
34871 GACGGGCAAC
Statistics
Matches: 91, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
29 1 0.01
30 90 0.99
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (30 bp):
GATCTATTGAACCGCCGGTCAATAGACTGC
Found at i:34782 original size:15 final size:15
Alignment explanation
Indices: 34764--34869 Score: 56
Period size: 15 Copynumber: 7.1 Consensus size: 15
34754 TGCCGTTCAA
34764 TAGACTGCGATCTAT
1 TAGACTGCGATCTAT
* * *
34779 TAGACCGCCGGTC-AA
1 TAGACTG-CGATCTAT
*
34794 TAGACTGTGATCTAT
1 TAGACTGCGATCTAT
* * * *
34809 TGGACCGCCGGTC-AA
1 TAGACTG-CGATCTAT
34824 TAGACTGCGATCTAT
1 TAGACTGCGATCTAT
* * * *
34839 TGGACAGCCGGTC-AA
1 TAGACTG-CGATCTAT
34854 TAGACTGCGATCTAT
1 TAGACTGCGATCTAT
34869 T
1 T
34870 GGACGGGCAA
Statistics
Matches: 61, Mismatches: 24, Indels: 12
0.63 0.25 0.12
Matches are distributed among these distances:
14 11 0.18
15 39 0.64
16 11 0.18
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (15 bp):
TAGACTGCGATCTAT
Found at i:34833 original size:60 final size:60
Alignment explanation
Indices: 34740--34873 Score: 205
Period size: 60 Copynumber: 2.2 Consensus size: 60
34730 AGGTTTGAAA
** * * *
34740 GTGATCTATTCAACTGCCGTTCAATAGACTGCGATCTATTAGACCGCCGGTCAATAGACT
1 GTGATCTATTGGACCGCCGGTCAATAGACTGCGATCTATTAGACAGCCGGTCAATAGACT
*
34800 GTGATCTATTGGACCGCCGGTCAATAGACTGCGATCTATTGGACAGCCGGTCAATAGACT
1 GTGATCTATTGGACCGCCGGTCAATAGACTGCGATCTATTAGACAGCCGGTCAATAGACT
*
34860 GCGATCTATTGGAC
1 GTGATCTATTGGAC
34874 GGGCAACGTA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 67 1.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (60 bp):
GTGATCTATTGGACCGCCGGTCAATAGACTGCGATCTATTAGACAGCCGGTCAATAGACT
Found at i:34871 original size:30 final size:30
Alignment explanation
Indices: 34755--34873 Score: 202
Period size: 30 Copynumber: 4.0 Consensus size: 30
34745 CTATTCAACT
* *
34755 GCCGTTCAATAGACTGCGATCTATTAGACC
1 GCCGGTCAATAGACTGCGATCTATTGGACC
*
34785 GCCGGTCAATAGACTGTGATCTATTGGACC
1 GCCGGTCAATAGACTGCGATCTATTGGACC
*
34815 GCCGGTCAATAGACTGCGATCTATTGGACA
1 GCCGGTCAATAGACTGCGATCTATTGGACC
34845 GCCGGTCAATAGACTGCGATCTATTGGAC
1 GCCGGTCAATAGACTGCGATCTATTGGAC
34874 GGGCAACGTA
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 84 1.00
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.25
Consensus pattern (30 bp):
GCCGGTCAATAGACTGCGATCTATTGGACC
Found at i:35586 original size:22 final size:22
Alignment explanation
Indices: 35558--35601 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
35548 CAATGCAGAG
35558 CAAATATTTATTAAGTGTCGAC
1 CAAATATTTATTAAGTGTCGAC
35580 CAAATATTTATTAAGTGTCGAC
1 CAAATATTTATTAAGTGTCGAC
35602 ATAGCCATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (22 bp):
CAAATATTTATTAAGTGTCGAC
Found at i:38734 original size:30 final size:30
Alignment explanation
Indices: 38711--38859 Score: 253
Period size: 30 Copynumber: 5.0 Consensus size: 30
38701 CTATTCAACT
* * *
38711 GCCGTTCAATAGACTGCGATCTATTAGACC
1 GCCGGTCAATAGACTGCGATCTATTGGACA
* *
38741 GCCGGTCAATAGACTGTGATCTATTGGACC
1 GCCGGTCAATAGACTGCGATCTATTGGACA
38771 GCCGGTCAATAGACTGCGATCTATTGGACA
1 GCCGGTCAATAGACTGCGATCTATTGGACA
38801 GCCGGTCAATAGACTGCGATCTATTGGACA
1 GCCGGTCAATAGACTGCGATCTATTGGACA
38831 GCCGGTCAATAGACTGCGATCTATTGGAC
1 GCCGGTCAATAGACTGCGATCTATTGGAC
38860 GGGCAACGTA
Statistics
Matches: 114, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 114 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.25
Consensus pattern (30 bp):
GCCGGTCAATAGACTGCGATCTATTGGACA
Found at i:39572 original size:22 final size:22
Alignment explanation
Indices: 39544--39587 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
39534 CAATGCAGAG
39544 CAAATATTTATTAAGTGTCGAC
1 CAAATATTTATTAAGTGTCGAC
39566 CAAATATTTATTAAGTGTCGAC
1 CAAATATTTATTAAGTGTCGAC
39588 ATAGCCATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (22 bp):
CAAATATTTATTAAGTGTCGAC
Found at i:43054 original size:4 final size:4
Alignment explanation
Indices: 43045--43146 Score: 186
Period size: 4 Copynumber: 25.5 Consensus size: 4
43035 TCCATTCTGA
43045 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
1 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
* *
43093 CTAT CTAT CTAT CTAT CTAT CCAT CTAT CCAT CTAT CTAT CTAT CTAT
1 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
43141 CTAT CT
1 CTAT CT
43147 CAGTCAAACT
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 94 1.00
ACGTcount: A:0.25, C:0.27, G:0.00, T:0.48
Consensus pattern (4 bp):
CTAT
Found at i:45904 original size:55 final size:55
Alignment explanation
Indices: 45820--45925 Score: 212
Period size: 55 Copynumber: 1.9 Consensus size: 55
45810 TCGCCATATA
45820 GCCATACAGTGTTAATGCATATTATGTTTACAAATCTTCTTCTCTACTCTCTATG
1 GCCATACAGTGTTAATGCATATTATGTTTACAAATCTTCTTCTCTACTCTCTATG
45875 GCCATACAGTGTTAATGCATATTATGTTTACAAATCTTCTTCTCTACTCTC
1 GCCATACAGTGTTAATGCATATTATGTTTACAAATCTTCTTCTCTACTCTC
45926 GCACATCTGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (55 bp):
GCCATACAGTGTTAATGCATATTATGTTTACAAATCTTCTTCTCTACTCTCTATG
Found at i:46228 original size:167 final size:168
Alignment explanation
Indices: 45877--46228 Score: 387
Period size: 167 Copynumber: 2.1 Consensus size: 168
45867 TCTCTATGGC
* * * * *
45877 CATACAGTGTTAATGCATATTATGTTTACAAATCTTCTTCTCTACTCTCGCACATCTGTAAAAAA
1 CATACAGTGTTAATGCATATTATGGTTACAAATCTTCCTATCTACTCCCACACATCTGTAAAAAA
* * * ** * * *
45942 ACTGACTTCATAATTATGTTAACCAAGAAGTCCTCTATTAAAATTGTAAATCTTATGTCCCCTGG
66 ACTGAATTCATAATTATGTAAACCAAGAAGCCCTCTAACAAAAGTATAAATCTTATATCCCCTGG
* *
46007 AGTATGGGTTTTGACTCTAGGGCGGGGCCAAAATGAAT
131 AGTAGGGGTTCTGACTCTAGGGCGGGGCCAAAATGAAT
* * *
46045 -GTATAGTGTAAATGCATA-TACTGGTTA-AAAT-TATCCTATCTACTCCCACACA-CATGTAAA
1 CATACAGTGTTAATGCATATTA-TGGTTACAAATCT-TCCTATCTACTCCCACACATC-TGTAAA
* * * *
46105 GAAAACTGAATTCATTATTTTGTAAACCAGGAAGCCCTCTAACAAAAGTATTAAT-TTCATATCC
63 -AAAACTGAATTCATAATTATGTAAACCAAGAAGCCCTCTAACAAAAGTATAAATCTT-ATATCC
*
46169 CCT-GAGGTAGGGGTTCTGACTCTAGGGCGGGGCCAAAAT-AGT
126 CCTGGA-GTAGGGGTTCTGACTCTAGGGCGGGGCCAAAATGAAT
46211 CATACAGTGTTAATGCAT
1 CATACAGTGTTAATGCAT
46229 TTAATATTTT
Statistics
Matches: 151, Mismatches: 26, Indels: 15
0.79 0.14 0.08
Matches are distributed among these distances:
165 2 0.01
166 33 0.22
167 116 0.77
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (168 bp):
CATACAGTGTTAATGCATATTATGGTTACAAATCTTCCTATCTACTCCCACACATCTGTAAAAAA
ACTGAATTCATAATTATGTAAACCAAGAAGCCCTCTAACAAAAGTATAAATCTTATATCCCCTGG
AGTAGGGGTTCTGACTCTAGGGCGGGGCCAAAATGAAT
Found at i:49225 original size:46 final size:46
Alignment explanation
Indices: 49155--49248 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
49145 TCAGGAAAGT
49155 ATTATTGATGGTCCGTGACATACTGAATATAACTGTTTGTCTCTCA
1 ATTATTGATGGTCCGTGACATACTGAATATAACTGTTTGTCTCTCA
* * * *
49201 ATTATTGATGGTCCGTGACCTACTGAGTATGACTGTTTGTCTTTCA
1 ATTATTGATGGTCCGTGACATACTGAATATAACTGTTTGTCTCTCA
49247 AT
1 AT
49249 AGATGACATG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.40
Consensus pattern (46 bp):
ATTATTGATGGTCCGTGACATACTGAATATAACTGTTTGTCTCTCA
Found at i:49813 original size:16 final size:16
Alignment explanation
Indices: 49792--49822 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49782 AATCGTTTTT
*
49792 CGCCAAATATCATACA
1 CGCCAAATATAATACA
49808 CGCCAAATATAATAC
1 CGCCAAATATAATAC
49823 GTTTTCAGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.29, G:0.06, T:0.19
Consensus pattern (16 bp):
CGCCAAATATAATACA
Found at i:51709 original size:2 final size:2
Alignment explanation
Indices: 51702--51750 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
51692 GCACATACAC
51702 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
51744 AG AG AG A
1 AG AG AG A
51751 TTTTAGTTCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:55963 original size:15 final size:16
Alignment explanation
Indices: 55943--55973 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
55933 AGCACACCTG
55943 GTTATTAT-TTTAAAA
1 GTTATTATGTTTAAAA
55958 GTTATTATGTTTAAAA
1 GTTATTATGTTTAAAA
55974 CTACTAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (16 bp):
GTTATTATGTTTAAAA
Found at i:57090 original size:1 final size:1
Alignment explanation
Indices: 57048--57072 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
57038 NNNNNNNNNN
57048 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
57073 GGAACACGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:60420 original size:32 final size:33
Alignment explanation
Indices: 60373--60447 Score: 125
Period size: 33 Copynumber: 2.3 Consensus size: 33
60363 ATTGACCCGG
*
60373 GTTGAAAATTGACCC-GGGGGTCATTTTTCAAC
1 GTTGAAAATTAACCCGGGGGGTCATTTTTCAAC
*
60405 GTTGAATATTAACCCGGGGGGTCATTTTTCAAC
1 GTTGAAAATTAACCCGGGGGGTCATTTTTCAAC
60438 GTTGAAAATT
1 GTTGAAAATT
60448 GATACCAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 13 0.33
33 26 0.67
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (33 bp):
GTTGAAAATTAACCCGGGGGGTCATTTTTCAAC
Found at i:63520 original size:17 final size:16
Alignment explanation
Indices: 63494--63527 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
63484 AAAGTAAACG
63494 TATAATAAGACTATAT
1 TATAATAAGACTATAT
63510 TATATATAAGACTATAT
1 TATA-ATAAGACTATAT
63527 T
1 T
63528 GTTCGTATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (16 bp):
TATAATAAGACTATAT
Found at i:63901 original size:56 final size:55
Alignment explanation
Indices: 63814--63925 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 55
63804 AATAAACGGA
63814 TCAGTGTTATCAAATTTTGACAGGGATTACTTTGTTAGAAAAAATTGTTTGATTT
1 TCAGTGTTATCAAATTTTGACAGGGATTACTTTGTTAGAAAAAATTGTTTGATTT
63869 TNCAGTGTTATCAAATTTTGACAGGGATTACTTTGTTAGAAAAAATTGTTTGATTT
1 T-CAGTGTTATCAAATTTTGACAGGGATTACTTTGTTAGAAAAAATTGTTTGATTT
63925 T
1 T
63926 TCTTGACGTT
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 1 0.02
56 55 0.98
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.44
Consensus pattern (55 bp):
TCAGTGTTATCAAATTTTGACAGGGATTACTTTGTTAGAAAAAATTGTTTGATTT
Found at i:73818 original size:2 final size:2
Alignment explanation
Indices: 73811--73874 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
73801 AATTTGGTAC
73811 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
73853 TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG
73875 NGATTAGGAG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:83072 original size:35 final size:35
Alignment explanation
Indices: 83033--83302 Score: 445
Period size: 35 Copynumber: 7.7 Consensus size: 35
83023 TTAAGGTACT
*
83033 AGTTTACTTAAAGCACTGGAGTTATTTTCAATACA
1 AGTTTACTTAAAGCACTTGAGTTATTTTCAATACA
83068 AGTTTACTTAAAGCACTTGAGTTATTTTCAATACA
1 AGTTTACTTAAAGCACTTGAGTTATTTTCAATACA
83103 AGTTTACTTAAAGCACTTGAGTTATTTTCAATACA
1 AGTTTACTTAAAGCACTTGAGTTATTTTCAATACA
*
83138 ACTTTACTTAAAGCACTTGAGTTATTTTCAATACA
1 AGTTTACTTAAAGCACTTGAGTTATTTTCAATACA
* *
83173 ACTTTACTTAAAGCACTGGAGTTATTTTCAATACA
1 AGTTTACTTAAAGCACTTGAGTTATTTTCAATACA
83208 AGTTTACTTAAAGCACTTGAGTTATTTTCAATACA
1 AGTTTACTTAAAGCACTTGAGTTATTTTCAATACA
*
83243 AGTTTACTTAAAGCA-TTGGAGTTATTTTCAATGCA
1 AGTTTACTTAAAGCACTT-GAGTTATTTTCAATACA
* * *
83278 TGTTTACTTACAGCA-TTGATTTATT
1 AGTTTACTTAAAGCACTTGAGTTATT
83303 AACTGTAAAA
Statistics
Matches: 225, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
34 9 0.04
35 216 0.96
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (35 bp):
AGTTTACTTAAAGCACTTGAGTTATTTTCAATACA
Found at i:83518 original size:40 final size:40
Alignment explanation
Indices: 83361--83511 Score: 248
Period size: 40 Copynumber: 3.7 Consensus size: 40
83351 GTATGATTTT
* *
83361 ACTTTACTTACAGCACTGTGTGATAAATATTTACAGACATTACA
1 ACTTAACTTACAGCACAGTGTGATAAATATTTACAG----TACA
83405 ACTTAACTTACAGCACAGTGTGATAAATATTTACAGTACA
1 ACTTAACTTACAGCACAGTGTGATAAATATTTACAGTACA
83445 ACTTAACTTACAGCACAGTGTGATAAATATTTACAGTACA
1 ACTTAACTTACAGCACAGTGTGATAAATATTTACAGTACA
83485 ACTTAACTTACAGCACAGTGTGATAAA
1 ACTTAACTTACAGCACAGTGTGATAAA
83512 ACTTTACTTA
Statistics
Matches: 105, Mismatches: 2, Indels: 4
0.95 0.02 0.04
Matches are distributed among these distances:
40 71 0.68
44 34 0.32
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (40 bp):
ACTTAACTTACAGCACAGTGTGATAAATATTTACAGTACA
Found at i:90403 original size:2 final size:2
Alignment explanation
Indices: 90396--90430 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
90386 TCGTAGGCTA
90396 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
90431 GTTTGTACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:92379 original size:2 final size:2
Alignment explanation
Indices: 92372--92396 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
92362 GCATGTAAGT
92372 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
92397 TTGTATTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:96552 original size:30 final size:30
Alignment explanation
Indices: 96516--96638 Score: 210
Period size: 30 Copynumber: 4.1 Consensus size: 30
96506 TACAAGAACT
96516 CAGGAACGGTAAGTCAATATCACTACAAGA
1 CAGGAACGGTAAGTCAATATCACTACAAGA
* *
96546 CAGGAACGGTAAGTCAATATCACGACAAGG
1 CAGGAACGGTAAGTCAATATCACTACAAGA
96576 CAGGAACGGTAAGTCAATATCACTACAAGA
1 CAGGAACGGTAAGTCAATATCACTACAAGA
* *
96606 CAGGAACGGTAAGTTAATATCACCACAAGA
1 CAGGAACGGTAAGTCAATATCACTACAAGA
96636 CAG
1 CAG
96639 AAATAAGGTG
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 87 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.15
Consensus pattern (30 bp):
CAGGAACGGTAAGTCAATATCACTACAAGA
Found at i:97398 original size:21 final size:21
Alignment explanation
Indices: 97372--97423 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
97362 AGTACACAGT
97372 CATGTACTTAGGGTGAATACA
1 CATGTACTTAGGGTGAATACA
* * *
97393 CATGTACGTAGGGTGAGTGCA
1 CATGTACTTAGGGTGAATACA
97414 CATGTACTTA
1 CATGTACTTA
97424 CTTTATACAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (21 bp):
CATGTACTTAGGGTGAATACA
Found at i:98692 original size:2 final size:2
Alignment explanation
Indices: 98679--98720 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
98669 TCTCGATCAG
* * *
98679 CT CT CT CC CT CT CT TT TT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
98721 GTTCTTTTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:104400 original size:46 final size:46
Alignment explanation
Indices: 104320--104850 Score: 488
Period size: 46 Copynumber: 11.6 Consensus size: 46
104310 TAATTCGGAA
* * * * *
104320 TTGTTAGCCATCATCCCACAGCAAATGTTTATTCTAGACCATGAAA
1 TTGTCAGCCATCATCCCACAGCAACTGTTTATTCTTGACCATGGAT
* * * * *
104366 TTGTCAGCCATCATCCCATACCAACTGATCATTCTGGACCATGGAT
1 TTGTCAGCCATCATCCCACAGCAACTGTTTATTCTTGACCATGGAT
** * *
104412 TTGTCAGCCA-CTATAACATAGCAACTGTTTATTCTTGACCATAGAT
1 TTGTCAGCCATC-ATCCCACAGCAACTGTTTATTCTTGACCATGGAT
** * * * *
104458 TTGTCAGCCA-CTAAACCACAACAGCTGTTTATTCTTGACCCTGAAT
1 TTGTCAGCCATC-ATCCCACAGCAACTGTTTATTCTTGACCATGGAT
* * * *** *
104504 TTGTCAGCCATCATCCCATATCAACTGTTCATTC-TG-GGTTGGAA
1 TTGTCAGCCATCATCCCACAGCAACTGTTTATTCTTGACCATGGAT
* * * *
104548 TTGTCAGCCA-CTATACCACAGCAACTGTTAATTATAGACCATGGAT
1 TTGTCAGCCATC-ATCCCACAGCAACTGTTTATTCTTGACCATGGAT
* * *
104594 TTGTCAGCCA-CTATACCAAAGCAACTGTTTATTCTTGACCGTGGAT
1 TTGTCAGCCATC-ATCCCACAGCAACTGTTTATTCTTGACCATGGAT
* *
104640 TTGTCAGCCA-CTATACCACAGCAACTGTTGATTCTTGACCATGGAT
1 TTGTCAGCCATC-ATCCCACAGCAACTGTTTATTCTTGACCATGGAT
* * * *
104686 TTGTCAGCCA-CTATACCACAGTAAATGTTTATTCTTGACCATGGAA
1 TTGTCAGCCATC-ATCCCACAGCAACTGTTTATTCTTGACCATGGAT
* *
104732 TTGTCAGCC-TCCACCCCACAGCAACTGTTTATT-ATGTACCATGGAT
1 TTGTCAGCCAT-CATCCCACAGCAACTGTTTATTCTTG-ACCATGGAT
* * *
104778 TTGTCAGCCATTATCCCACAGCAACTGTTTATTCTGGACCATGGAA
1 TTGTCAGCCATCATCCCACAGCAACTGTTTATTCTTGACCATGGAT
* * *
104824 TTGTCAGCCACCACCCCACAGGAACTG
1 TTGTCAGCCATCATCCCACAGCAACTG
104851 GTCATCATAG
Statistics
Matches: 403, Mismatches: 72, Indels: 20
0.81 0.15 0.04
Matches are distributed among these distances:
43 1 0.00
44 30 0.07
45 6 0.01
46 362 0.90
47 4 0.01
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (46 bp):
TTGTCAGCCATCATCCCACAGCAACTGTTTATTCTTGACCATGGAT
Found at i:104492 original size:92 final size:92
Alignment explanation
Indices: 104335--104834 Score: 558
Period size: 92 Copynumber: 5.5 Consensus size: 92
104325 AGCCATCATC
* * * * * * * *
104335 CCACAGCAAATGTTTATTCTAGACCATGAAATTGTCAGCCA-TCATCCCATACCAACTGATCATT
1 CCACAGCAACTGTTTATTCTTGACCATGGAATTGTCAGCCACT-ATACCACAGCAACTGTTTATT
104399 CTGGACCATGGATTTGTCAGCCACTATA
65 CTGGACCATGGATTTGTCAGCCACTATA
* * * * * * *
104427 ACATAGCAACTGTTTATTCTTGACCATAGATTTGTCAGCCACTAAACCACAACAGCTGTTTATTC
1 CCACAGCAACTGTTTATTCTTGACCATGGAATTGTCAGCCACTATACCACAGCAACTGTTTATTC
* * * *
104492 TTGACCCTGAATTTGTCAGCCA-TCATC
66 TGGACCATGGATTTGTCAGCCACT-ATA
* * * *** * *
104519 CCATATCAACTGTTCATTC-TG-GGTTGGAATTGTCAGCCACTATACCACAGCAACTGTTAATTA
1 CCACAGCAACTGTTTATTCTTGACCATGGAATTGTCAGCCACTATACCACAGCAACTGTTTATTC
*
104582 TAGACCATGGATTTGTCAGCCACTATA
66 TGGACCATGGATTTGTCAGCCACTATA
* * * *
104609 CCAAAGCAACTGTTTATTCTTGACCGTGGATTTGTCAGCCACTATACCACAGCAACTGTTGATTC
1 CCACAGCAACTGTTTATTCTTGACCATGGAATTGTCAGCCACTATACCACAGCAACTGTTTATTC
*
104674 TTGACCATGGATTTGTCAGCCACTATA
66 TGGACCATGGATTTGTCAGCCACTATA
* * * * ** *
104701 CCACAGTAAATGTTTATTCTTGACCATGGAATTGTCAGCCTCCACCCCACAGCAACTGTTTATTA
1 CCACAGCAACTGTTTATTCTTGACCATGGAATTGTCAGCCACTATACCACAGCAACTGTTTATTC
* * *
104766 TGTACCATGGATTTGTCAGCCATTATC
66 TGGACCATGGATTTGTCAGCCACTATA
*
104793 CCACAGCAACTGTTTATTCTGGACCATGGAATTGTCAGCCAC
1 CCACAGCAACTGTTTATTCTTGACCATGGAATTGTCAGCCAC
104835 CACCCCACAG
Statistics
Matches: 339, Mismatches: 64, Indels: 10
0.82 0.15 0.02
Matches are distributed among these distances:
90 69 0.20
91 6 0.02
92 263 0.78
93 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.31
Consensus pattern (92 bp):
CCACAGCAACTGTTTATTCTTGACCATGGAATTGTCAGCCACTATACCACAGCAACTGTTTATTC
TGGACCATGGATTTGTCAGCCACTATA
Found at i:104844 original size:138 final size:138
Alignment explanation
Indices: 104316--104834 Score: 596
Period size: 138 Copynumber: 3.8 Consensus size: 138
104306 GCTTTAATTC
* * * * * *
104316 GGAATTGTTAGCCATCATCCCACAGCAAATGTTTATTCTAGACCATGAAATTGTCAGCCATCATC
1 GGAATTGTCAGCCACCATACCACAGCAACTGTTTATTCTTGACCATGAATTTGTCAGCCATCATC
* * * * * *
104381 CCATACCAACTGATCATTCTGGACCATGGATTTGTCAGCCACTATAACATAGCAACTGTTTATTC
66 CCACAGCAACTGTTCATTCTGGACCATGGAATTGTCAGCCACTATACCACAGCAACTGTTTATTC
104446 TTGACCAT
131 TTGACCAT
* * * * * * *
104454 AGATTTGTCAGCCACTAAACCACAACAGCTGTTTATTCTTGACCCTGAATTTGTCAGCCATCATC
1 GGAATTGTCAGCCACCATACCACAGCAACTGTTTATTCTTGACCATGAATTTGTCAGCCATCATC
* * ** * *
104519 CCATATCAACTGTTCATTCTGG--GTTGGAATTGTCAGCCACTATACCACAGCAACTGTTAATTA
66 CCACAGCAACTGTTCATTCTGGACCATGGAATTGTCAGCCACTATACCACAGCAACTGTTTATTC
*
104582 TAGACCAT
131 TTGACCAT
* * * * *
104590 GGATTTGTCAGCCACTATACCAAAGCAACTGTTTATTCTTGACCGTGGATTTGTCAGCCA-CTAT
1 GGAATTGTCAGCCACCATACCACAGCAACTGTTTATTCTTGACCATGAATTTGTCAGCCATC-AT
* * * * * *
104654 ACCACAGCAACTGTTGATTCTTGACCATGGATTTGTCAGCCACTATACCACAGTAAATGTTTATT
65 CCCACAGCAACTGTTCATTCTGGACCATGGAATTGTCAGCCACTATACCACAGCAACTGTTTATT
104719 CTTGACCAT
130 CTTGACCAT
* ** * * *
104728 GGAATTGTCAGCCTCCACCCCACAGCAACTGTTTATT-ATGTACCATGGATTTGTCAGCCATTAT
1 GGAATTGTCAGCCACCATACCACAGCAACTGTTTATTCTTG-ACCATGAATTTGTCAGCCATCAT
*
104792 CCCACAGCAACTGTTTATTCTGGACCATGGAATTGTCAGCCAC
65 CCCACAGCAACTGTTCATTCTGGACCATGGAATTGTCAGCCAC
104835 CACCCCACAG
Statistics
Matches: 320, Mismatches: 56, Indels: 10
0.83 0.15 0.03
Matches are distributed among these distances:
135 1 0.00
136 114 0.36
137 2 0.01
138 203 0.63
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.31
Consensus pattern (138 bp):
GGAATTGTCAGCCACCATACCACAGCAACTGTTTATTCTTGACCATGAATTTGTCAGCCATCATC
CCACAGCAACTGTTCATTCTGGACCATGGAATTGTCAGCCACTATACCACAGCAACTGTTTATTC
TTGACCAT
Found at i:108556 original size:21 final size:21
Alignment explanation
Indices: 108526--108565 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
108516 CTGTCCCTTT
* *
108526 ACATTTATTCTTGGAATAGCC
1 ACATTCATTCTTGAAATAGCC
108547 ACATTCATTCTTGAAATAG
1 ACATTCATTCTTGAAATAG
108566 TCGTCAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (21 bp):
ACATTCATTCTTGAAATAGCC
Found at i:115935 original size:15 final size:15
Alignment explanation
Indices: 115915--115945 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
115905 AAAGAAGACG
115915 CTTATACAAATAAAA
1 CTTATACAAATAAAA
115930 CTTATACAAATAAAA
1 CTTATACAAATAAAA
115945 C
1 C
115946 AATGCTAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (15 bp):
CTTATACAAATAAAA
Found at i:117323 original size:9 final size:9
Alignment explanation
Indices: 117309--117342 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
117299 TTAAATTTGA
117309 GGTGGGGGT
1 GGTGGGGGT
*
117318 GGTGGGATGT
1 GGTGGG-GGT
117328 GGTGGGGGT
1 GGTGGGGGT
117337 GGTGGG
1 GGTGGG
117343 ATGTGGTGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.03, C:0.00, G:0.74, T:0.24
Consensus pattern (9 bp):
GGTGGGGGT
Found at i:117331 original size:10 final size:10
Alignment explanation
Indices: 117316--117350 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
117306 TGAGGTGGGG
117316 GTGGTGGGAT
1 GTGGTGGGAT
*
117326 GTGGTGGG-G
1 GTGGTGGGAT
117335 GTGGTGGGAT
1 GTGGTGGGAT
117345 GTGGTG
1 GTGGTG
117351 TCGAACCCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.06, C:0.00, G:0.66, T:0.29
Consensus pattern (10 bp):
GTGGTGGGAT
Found at i:117333 original size:19 final size:19
Alignment explanation
Indices: 117309--117350 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
117299 TTAAATTTGA
117309 GGTGGGGGTGGTGGGATGT
1 GGTGGGGGTGGTGGGATGT
117328 GGTGGGGGTGGTGGGATGT
1 GGTGGGGGTGGTGGGATGT
117347 GGTG
1 GGTG
117351 TCGAACCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.05, C:0.00, G:0.69, T:0.26
Consensus pattern (19 bp):
GGTGGGGGTGGTGGGATGT
Found at i:123564 original size:11 final size:11
Alignment explanation
Indices: 123548--124085 Score: 541
Period size: 11 Copynumber: 53.6 Consensus size: 11
123538 CAAGAAGGAG
123548 AGTAATACAGC
1 AGTAATACAGC
123559 AGTAATACAGC
1 AGTAATACAGC
123570 AGTAATA-AG-
1 AGTAATACAGC
* *
123579 A-TAACACAAC
1 AGTAATACAGC
123589 AGTAATACAGC
1 AGTAATACAGC
*
123600 AGTAATACAAC
1 AGTAATACAGC
123611 AGTAATACAGC
1 AGTAATACAGC
123622 AGTAATA-A-C
1 AGTAATACAGC
123631 -GTAATACAGC
1 AGTAATACAGC
*
123641 AGTAATACAAC
1 AGTAATACAGC
*
123652 AGTAATACTGC
1 AGTAATACAGC
*
123663 AGTAATACAAC
1 AGTAATACAGC
123674 AGTAATACAGC
1 AGTAATACAGC
*
123685 AGTAATACAAC
1 AGTAATACAGC
*
123696 AGTAATACTGC
1 AGTAATACAGC
123707 AGTAATACAGC
1 AGTAATACAGC
123718 AGTAATA-A-C
1 AGTAATACAGC
123727 A-TAATACAGC
1 AGTAATACAGC
123737 AGTAATA-A-C
1 AGTAATACAGC
* *
123746 -GTAATATAAC
1 AGTAATACAGC
*
123756 -GTAATACAAC
1 AGTAATACAGC
123766 AGTAATACAGC
1 AGTAATACAGC
123777 AGTAATA-A-C
1 AGTAATACAGC
**
123786 -GTAATACAAT
1 AGTAATACAGC
123796 AGTAATA-A--
1 AGTAATACAGC
*
123804 AATAATACAGC
1 AGTAATACAGC
*
123815 AGTAATTCAGC
1 AGTAATACAGC
123826 AGTAATA-A-C
1 AGTAATACAGC
123835 A-TAATACAGC
1 AGTAATACAGC
123845 AGTAATACAGC
1 AGTAATACAGC
*
123856 AGTAAT-TA-C
1 AGTAATACAGC
123865 -GTAATACAGC
1 AGTAATACAGC
123875 AGTAATACAGC
1 AGTAATACAGC
123886 AGTAAT-CA-C
1 AGTAATACAGC
123895 -GTAATACAGC
1 AGTAATACAGC
123905 AGTAATACAGC
1 AGTAATACAGC
123916 AGTAATA-A-C
1 AGTAATACAGC
123925 -GTAATACAGC
1 AGTAATACAGC
123935 AGTAATA-A-C
1 AGTAATACAGC
123944 -GTAATACAGC
1 AGTAATACAGC
*
123954 AATAATA-A-C
1 AGTAATACAGC
123963 -GTAATACAGC
1 AGTAATACAGC
123973 AGTAATA-A-C
1 AGTAATACAGC
123982 -GTAATACAGC
1 AGTAATACAGC
123992 AGTAATA-A-C
1 AGTAATACAGC
*
124001 -GTAATGCAGC
1 AGTAATACAGC
124011 AGTAATA-A-C
1 AGTAATACAGC
*
124020 -GTAATACAAC
1 AGTAATACAGC
124030 AGTAATA-A-C
1 AGTAATACAGC
124039 -GTAATACAGC
1 AGTAATACAGC
124049 AGTAATACAGC
1 AGTAATACAGC
124060 AGTAATA-A-C
1 AGTAATACAGC
124069 -GTAATACAGC
1 AGTAATACAGC
124079 AGTAATA
1 AGTAATA
124086 ATGTAATACA
Statistics
Matches: 447, Mismatches: 29, Indels: 102
0.77 0.05 0.18
Matches are distributed among these distances:
8 94 0.21
9 36 0.08
10 45 0.10
11 272 0.61
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.21
Consensus pattern (11 bp):
AGTAATACAGC
Found at i:123739 original size:30 final size:30
Alignment explanation
Indices: 123561--124085 Score: 443
Period size: 30 Copynumber: 17.5 Consensus size: 30
123551 AATACAGCAG
*
123561 TAATACAGCAGTAATA-AG-A-TAACACAACA
1 TAATACAGCAGTAATACAGCAGT-A-ATAACA
*
123590 GTAATACAGCAGTAATACAACAGTAATACAGCA
1 -TAATACAGCAGTAATACAGCAGTAATA-A-CA
123623 GTAATA-A-C-GTAATACAGCAGTAATACAACA
1 -TAATACAGCAGTAATACAGCAGTAAT--AACA
* *
123653 GTAATACTGCAGTAATACAACAGTAATACAGCA
1 -TAATACAGCAGTAATACAGCAGTAATA-A-CA
* *
123686 GTAATACAACAGTAATACTGCAGTAATACAGCA
1 -TAATACAGCAGTAATACAGCAGTAATA-A-CA
*
123719 GTAATA-A-CA-TAATACAGCAGTAATAACG
1 -TAATACAGCAGTAATACAGCAGTAATAACA
* * *
123747 TAATATAAC-GTAATACAACAGTAATACAGCA
1 TAATACAGCAGTAATACAGCAGTAATA-A-CA
** *
123778 GTAATA-A-C-GTAATACAATAGTAATAAAA
1 -TAATACAGCAGTAATACAGCAGTAATAACA
*
123806 TAATACAGCAGTAATTCAGCAGTAATAACA
1 TAATACAGCAGTAATACAGCAGTAATAACA
* *
123836 TAATACAGCAGTAATACAGCAGTAATTACG
1 TAATACAGCAGTAATACAGCAGTAATAACA
* *
123866 TAATACAGCAGTAATACAGCAGTAATCACG
1 TAATACAGCAGTAATACAGCAGTAATAACA
*
123896 TAATACAGCAGTAATACAGCAGTAATAACG
1 TAATACAGCAGTAATACAGCAGTAATAACA
123926 TAATACAGCAGTAATA-A-C-GTAATACAGCAA
1 TAATACAGCAGTAATACAGCAGTAATA-A-C-A
*
123956 TAATA-A-C-GTAATACAGCAGTAATAACG
1 TAATACAGCAGTAATACAGCAGTAATAACA
*
123983 TAATACAGCAGTAATA-A-C-GTAATGCAGCA
1 TAATACAGCAGTAATACAGCAGTAAT--AACA
* *
124012 GTAATA-A-C-GTAATACAACAGTAATAACG
1 -TAATACAGCAGTAATACAGCAGTAATAACA
*
124040 TAATACAGCAGTAATACAGCAGTAATAACG
1 TAATACAGCAGTAATACAGCAGTAATAACA
124070 TAATACAGCAGTAATA
1 TAATACAGCAGTAATA
124086 ATGTAATACA
Statistics
Matches: 425, Mismatches: 31, Indels: 78
0.80 0.06 0.15
Matches are distributed among these distances:
27 43 0.10
28 16 0.04
29 31 0.07
30 251 0.59
31 10 0.02
32 13 0.03
33 61 0.14
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.21
Consensus pattern (30 bp):
TAATACAGCAGTAATACAGCAGTAATAACA
Found at i:124084 original size:19 final size:19
Alignment explanation
Indices: 123590--124106 Score: 491
Period size: 19 Copynumber: 27.0 Consensus size: 19
123580 TAACACAACA
123590 GTAATACAGCAGTAATACAAC
1 GTAATACAGCAGTAAT--AAC
123611 AGTAATACAGCAGTAATAAC
1 -GTAATACAGCAGTAATAAC
123631 GTAATACAGCAGTAATACAAC
1 GTAATACAGCAGTAAT--AAC
*
123652 AGTAATACTGCAGTAATACAAC
1 -GTAATACAGCAGTAAT--AAC
123674 AGTAATACAGCAGTAAT-AC
1 -GTAATACAGCAGTAATAAC
* * * *
123693 ---A-ACAGTAATACT-GC
1 GTAATACAGCAGTAATAAC
123707 AGTAATACAGCAGTAATAAC
1 -GTAATACAGCAGTAATAAC
*
123727 ATAATACAGCAGTAATAAC
1 GTAATACAGCAGTAATAAC
* *
123746 GTAATATAAC-GTAATACAAC
1 GTAATACAGCAGTAAT--AAC
123766 AGTAATACAGCAGTAATAAC
1 -GTAATACAGCAGTAATAAC
** *
123786 GTAATACAATAGTAATAAA
1 GTAATACAGCAGTAATAAC
* *
123805 ATAATACAGCAGTAATTCAGC
1 GTAATACAGCAGTAA-T-AAC
123826 AGTAATA-A-CA-TAATACAGC
1 -GTAATACAGCAGTAATA-A-C
*
123845 AGTAATACAGCAGTAATTAC
1 -GTAATACAGCAGTAATAAC
123865 GTAATACAGCAGTAATACAGC
1 GTAATACAGCAGTAATA-A-C
123886 AGTAAT-CA-C-GTAATACAGC
1 -GTAATACAGCAGTAATA-A-C
123905 AGTAATACAGCAGTAATAAC
1 -GTAATACAGCAGTAATAAC
123925 GTAATACAGCAGTAATAAC
1 GTAATACAGCAGTAATAAC
*
123944 GTAATACAGCAATAATAAC
1 GTAATACAGCAGTAATAAC
123963 GTAATACAGCAGTAATAAC
1 GTAATACAGCAGTAATAAC
123982 GTAATACAGCAGTAATAAC
1 GTAATACAGCAGTAATAAC
*
124001 GTAATGCAGCAGTAATAAC
1 GTAATACAGCAGTAATAAC
*
124020 GTAATACAACAGTAATAAC
1 GTAATACAGCAGTAATAAC
124039 GTAATACAGC-------A-
1 GTAATACAGCAGTAATAAC
124050 GTAATACAGCAGTAATAAC
1 GTAATACAGCAGTAATAAC
*
124069 GTAATACAGCAGTAATAAT
1 GTAATACAGCAGTAATAAC
*
124088 GTAATACAGCAGTTATAAC
1 GTAATACAGCAGTAATAAC
124107 AGGTCTGATC
Statistics
Matches: 423, Mismatches: 37, Indels: 73
0.79 0.07 0.14
Matches are distributed among these distances:
11 10 0.02
12 1 0.00
14 9 0.02
15 1 0.00
17 1 0.00
18 8 0.02
19 275 0.65
20 20 0.05
21 21 0.05
22 77 0.18
ACGTcount: A:0.48, C:0.16, G:0.15, T:0.22
Consensus pattern (19 bp):
GTAATACAGCAGTAATAAC
Found at i:124645 original size:16 final size:16
Alignment explanation
Indices: 124624--126170 Score: 1218
Period size: 16 Copynumber: 95.1 Consensus size: 16
124614 GGAATGGTTG
124624 GAATAGTCTCGGTATT
1 GAATAGTCTCGGTATT
* *
124640 GAATAGTCTTGGTAAT
1 GAATAGTCTCGGTATT
* *
124656 GAAAAGTCTCGATATGGT
1 GAATAGTCTCGGTAT--T
* * *
124674 CGAAAAAATCTAGGTATT
1 -G-AATAGTCTCGGTATT
* *
124692 AAATAGTCTCGTTATT
1 GAATAGTCTCGGTATT
**
124708 GAATAGTCTAAGTATT
1 GAATAGTCTCGGTATT
124724 GAATAGTCTCGGTATT
1 GAATAGTCTCGGTATT
* *
124740 AAATAGTCTCGTTATT
1 GAATAGTCTCGGTATT
*
124756 GAATAGTC-CAGATATT
1 GAATAGTCTC-GGTATT
*
124772 AAATAGTCTCGGTATT
1 GAATAGTCTCGGTATT
* * **
124788 AAAAAGTCTCCTTATT
1 GAATAGTCTCGGTATT
*
124804 GAATAGTCTAGGTATT
1 GAATAGTCTCGGTATT
* *
124820 GAATAATCTTGGTATT
1 GAATAGTCTCGGTATT
* *
124836 -ACATAGTCTTGTTATT
1 GA-ATAGTCTCGGTATT
**
124852 GAATAGTCTATGTATT
1 GAATAGTCTCGGTATT
* *
124868 GAATAATCTCGTTATT
1 GAATAGTCTCGGTATT
* *
124884 AAATAGTCTAGGTATT
1 GAATAGTCTCGGTATT
*
124900 GTATAGTCTCGGTATT
1 GAATAGTCTCGGTATT
* *
124916 AAATAGTCTCGTTATT
1 GAATAGTCTCGGTATT
*
124932 GAATAGTCTAGGTATT
1 GAATAGTCTCGGTATT
* * *
124948 AAATAGTTTCGTTATT
1 GAATAGTCTCGGTATT
* *
124964 AAATAGTCTCGCTATT
1 GAATAGTCTCGGTATT
**
124980 GAATAGTCAAGGTATT
1 GAATAGTCTCGGTATT
*
124996 GAATAGTCTCGTTATT
1 GAATAGTCTCGGTATT
* *
125012 AAATAGTCTCGTTATT
1 GAATAGTCTCGGTATT
*
125028 GAATAGTC-CAGGTTTT
1 GAATAGTCTC-GGTATT
* *
125044 AAATAGTATCGGTATT
1 GAATAGTCTCGGTATT
* *
125060 -ATATAGTCTCGTTACT
1 GA-ATAGTCTCGGTATT
125076 GAATAGTC-CAGGTATT
1 GAATAGTCTC-GGTATT
*
125092 GAATAGTCTGGGTATT
1 GAATAGTCTCGGTATT
* *
125108 AAATAGTCTCGTTATT
1 GAATAGTCTCGGTATT
*
125124 GAATAGTCTGGGTATT
1 GAATAGTCTCGGTATT
* *
125140 AAATAGTCTCGTTATT
1 GAATAGTCTCGGTATT
*
125156 GAATAGTC-CAGATATT
1 GAATAGTCTC-GGTATT
125172 GAATAGTCTCGGTATT
1 GAATAGTCTCGGTATT
* * **
125188 AAAAAGTCTCCTTATT
1 GAATAGTCTCGGTATT
* *
125204 GAATAGTCTAGGTTTT
1 GAATAGTCTCGGTATT
* *
125220 GAATAATCTTGGTATT
1 GAATAGTCTCGGTATT
* * *
125236 AAATAGTCTTGTTATT
1 GAATAGTCTCGGTATT
* *
125252 TAATAGTCTAGGTATT
1 GAATAGTCTCGGTATT
* * *
125268 GAAAATTCTCGTTATT
1 GAATAGTCTCGGTATT
* * *
125284 AAATAGTATAGGTATT
1 GAATAGTCTCGGTATT
*
125300 GTATAGTCTCGGTATT
1 GAATAGTCTCGGTATT
* *
125316 AAATAGTCTCGTTATT
1 GAATAGTCTCGGTATT
*
125332 GAATAGTCTAGGTATT
1 GAATAGTCTCGGTATT
*
125348 GTATAGTCTCGGTATT
1 GAATAGTCTCGGTATT
* *
125364 AAATAGTCTAGGTATT
1 GAATAGTCTCGGTATT
* *
125380 GAATAATCTTGGTATT
1 GAATAGTCTCGGTATT
* * *
125396 AAATAGTCTTGTTATT
1 GAATAGTCTCGGTATT
*
125412 GAATAGTCTAGGTATT
1 GAATAGTCTCGGTATT
* * *
125428 GAATAATCTCGTTATC
1 GAATAGTCTCGGTATT
* *
125444 AAATAGTCTAGGTATT
1 GAATAGTCTCGGTATT
*
125460 GTATAGTCTCGGTATT
1 GAATAGTCTCGGTATT
* * *
125476 AAATAGTTTCGTTATT
1 GAATAGTCTCGGTATT
* *
125492 AAATAGTCTCGCTATT
1 GAATAGTCTCGGTATT
*
125508 GAATAGTCTCTGTATGATT
1 GAATAGTCTC-G-GT-ATT
*
125527 GGAATAGTCTAGG---T
1 -GAATAGTCTCGGTATT
*
125541 --ATAGTCACGGTATT
1 GAATAGTCTCGGTATT
* *
125555 AAATAGTCTCGTTATT
1 GAATAGTCTCGGTATT
*
125571 GAATAGTCTGGGTATT
1 GAATAGTCTCGGTATT
* *
125587 AAATAGTCTCGTTATT
1 GAATAGTCTCGGTATT
125603 GAATAGTC-CAGGTATT
1 GAATAGTCTC-GGTATT
*
125619 GAATAGTCTCAGTATT
1 GAATAGTCTCGGTATT
* *
125635 AAATAGTCTCGTTATT
1 GAATAGTCTCGGTATT
*
125651 GAATAGTCTCTGTATGATT
1 GAATAGTCTC-G-GT-ATT
*
125670 GGAATAGTCTAGGTATT
1 -GAATAGTCTCGGTATT
* *
125687 GTATTGTCTCGGTATT
1 GAATAGTCTCGGTATT
*
125703 GAATAGTCTTGGTATGGTTT
1 GAATAGTCTCGGTA----TT
*
125723 GAATAGTC-CAGGTATG
1 GAATAGTCTC-GGTATT
* *
125739 GTATAGTCTTGGTATT
1 GAATAGTCTCGGTATT
*
125755 GAATAGTCTCGTTATT
1 GAATAGTCTCGGTATT
*
125771 GAATAGTCTCTGTATGGTT
1 GAATAGTCTCGGTA---TT
125790 GGAATAGTC-CAGGTATT
1 -GAATAGTCTC-GGTATT
*
125807 GTATAGTCTCGGTATT
1 GAATAGTCTCGGTATT
* * * *
125823 AAATAGTCTTGGAAAT
1 GAATAGTCTCGGTATT
*
125839 GAATAGTCTCGATATGGT
1 GAATAGTCTCGGTAT--T
*
125857 CGAAATAATCTCGGTATT
1 -G-AATAGTCTCGGTATT
* *
125875 AAATAGTCTCGTTATT
1 GAATAGTCTCGGTATT
*
125891 GAATATTC-CAGGTATT
1 GAATAGTCTC-GGTATT
125907 GAATAGTCTCGGTATT
1 GAATAGTCTCGGTATT
* *
125923 AAATAGTCTCGTTATT
1 GAATAGTCTCGGTATT
* ***
125939 GAAAAGTCTTAATATGGT
1 GAATAGTCTCGGTAT--T
* * *
125957 CGGAA-AATTTTGGTATT
1 --GAATAGTCTCGGTATT
* * *
125974 AAATAGTCTTGTTATT
1 GAATAGTCTCGGTATT
*
125990 GAATAGTCTAGGTATT
1 GAATAGTCTCGGTATT
*
126006 GAATAGTATCGGTATT
1 GAATAGTCTCGGTATT
* *
126022 AAATAGTCTCGTTATT
1 GAATAGTCTCGGTATT
*
126038 GAATAGTCTAGGTATT
1 GAATAGTCTCGGTATT
*
126054 GAATAGTATCGGTATT
1 GAATAGTCTCGGTATT
* *
126070 AAATAGTCTCGTTATT
1 GAATAGTCTCGGTATT
*
126086 GAATAGTCTAGGTATT
1 GAATAGTCTCGGTATT
126102 GAATAGTCTCGGTATT
1 GAATAGTCTCGGTATT
126118 GAATAGTCTCGGTATTGTT
1 GAATAGTCTCGGTA---TT
*
126137 GGAATAGTCTGGGTATT
1 -GAATAGTCTCGGTATT
* *
126154 GAATAGTTTCTGTATT
1 GAATAGTCTCGGTATT
126170 G
1 G
126171 TTGGAATAGT
Statistics
Matches: 1205, Mismatches: 268, Indels: 116
0.76 0.17 0.07
Matches are distributed among these distances:
11 8 0.01
14 2 0.00
15 10 0.01
16 1055 0.88
17 18 0.01
18 8 0.01
19 22 0.02
20 82 0.07
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (16 bp):
GAATAGTCTCGGTATT
Found at i:125745 original size:36 final size:36
Alignment explanation
Indices: 125697--125821 Score: 136
Period size: 36 Copynumber: 3.6 Consensus size: 36
125687 GTATTGTCTC
*
125697 GGTATTGAATAGTCTTGGTATGGTTTGAATAGTCCA
1 GGTATTGTATAGTCTTGGTATGGTTTGAATAGTCCA
*
125733 GGTATGGTATAGTCTTGGTA----TTGAATAGTCTC-
1 GGTATTGTATAGTCTTGGTATGGTTTGAATAGTC-CA
* * *
125765 GTTATTGAATAGTCTCT-GTATGGTTGGAATAGTCCA
1 GGTATTGTATAGTCT-TGGTATGGTTTGAATAGTCCA
*
125801 GGTATTGTATAGTCTCGGTAT
1 GGTATTGTATAGTCTTGGTAT
125822 TAAATAGTCT
Statistics
Matches: 72, Mismatches: 9, Indels: 16
0.74 0.09 0.16
Matches are distributed among these distances:
32 25 0.35
33 2 0.03
35 1 0.01
36 44 0.61
ACGTcount: A:0.23, C:0.10, G:0.27, T:0.40
Consensus pattern (36 bp):
GGTATTGTATAGTCTTGGTATGGTTTGAATAGTCCA
Found at i:127506 original size:2 final size:2
Alignment explanation
Indices: 127499--127566 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
127489 TTTTACTTTA
127499 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
127541 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
127567 GTGTGTACCT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:127780 original size:2 final size:2
Alignment explanation
Indices: 127773--127823 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
127763 AAAGCACAAT
*
127773 AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
127815 AG AG AG AG A
1 AG AG AG AG A
127824 CTTACGGGTG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:128624 original size:25 final size:25
Alignment explanation
Indices: 128590--128640 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
128580 CCTATCGGAA
128590 AGGTGATTTACCCTAATGTAGCGGT
1 AGGTGATTTACCCTAATGTAGCGGT
128615 AGGTGATTTACCCTAATGTAGCGGT
1 AGGTGATTTACCCTAATGTAGCGGT
128640 A
1 A
128641 ACATTGACGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.31
Consensus pattern (25 bp):
AGGTGATTTACCCTAATGTAGCGGT
Found at i:130084 original size:21 final size:20
Alignment explanation
Indices: 130060--130098 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
130050 TCCACAAGTC
130060 TGTTTGTTGTTTTGTTTTTTT
1 TGTTTGTTGTTTT-TTTTTTT
*
130081 TGTTTTTTGTTTTTTTTT
1 TGTTTGTTGTTTTTTTTT
130099 GACAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (20 bp):
TGTTTGTTGTTTTTTTTTTT
Found at i:130099 original size:17 final size:17
Alignment explanation
Indices: 130062--130097 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
130052 CACAAGTCTG
130062 TTTGTTGTTTTGTTTTT
1 TTTGTTGTTTTGTTTTT
130079 TTTGTT-TTTTGTTTTT
1 TTTGTTGTTTTGTTTTT
130095 TTT
1 TTT
130098 TGACAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (17 bp):
TTTGTTGTTTTGTTTTT
Found at i:130292 original size:40 final size:40
Alignment explanation
Indices: 130248--130333 Score: 172
Period size: 40 Copynumber: 2.1 Consensus size: 40
130238 ACATGTACAT
130248 GTACATGTAGGTTCTCAGCTATATAGAGATATTCTGTAGC
1 GTACATGTAGGTTCTCAGCTATATAGAGATATTCTGTAGC
130288 GTACATGTAGGTTCTCAGCTATATAGAGATATTCTGTAGC
1 GTACATGTAGGTTCTCAGCTATATAGAGATATTCTGTAGC
130328 GTACAT
1 GTACAT
130334 CGCTATATAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (40 bp):
GTACATGTAGGTTCTCAGCTATATAGAGATATTCTGTAGC
Found at i:130339 original size:30 final size:30
Alignment explanation
Indices: 130305--130454 Score: 264
Period size: 30 Copynumber: 5.0 Consensus size: 30
130295 TAGGTTCTCA
130305 GCTATATAGAGATATTCTGTAGCGTACATC
1 GCTATATAGAGATATTCTGTAGCGTACATC
*
130335 GCTATATAGATATATTCTGTAGCGTACATC
1 GCTATATAGAGATATTCTGTAGCGTACATC
*
130365 GCTATATAGAGATATTCTGTAGCGTACATA
1 GCTATATAGAGATATTCTGTAGCGTACATC
* *
130395 GCTATATAGAGATATTCTGTAGCGAACATA
1 GCTATATAGAGATATTCTGTAGCGTACATC
130425 GCTATATAGAGATATTCTGTAGCGTACATC
1 GCTATATAGAGATATTCTGTAGCGTACATC
130455 CGCAATATCT
Statistics
Matches: 114, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 114 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.33
Consensus pattern (30 bp):
GCTATATAGAGATATTCTGTAGCGTACATC
Found at i:135160 original size:2 final size:2
Alignment explanation
Indices: 135155--135213 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
135145 GACAAGTGTA
*
135155 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
135197 TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC T
135214 TCTAAAGCTA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:137969 original size:40 final size:34
Alignment explanation
Indices: 137877--137944 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
137867 CCTCGTTGTA
137877 ATGAATTCTGTAGATATGAACAATATTTGACCTT
1 ATGAATTCTGTAGATATGAACAATATTTGACCTT
*
137911 ATGAATCCTGTAGATATGAACAATATTTGACCTT
1 ATGAATTCTGTAGATATGAACAATATTTGACCTT
137945 GATATAGTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (34 bp):
ATGAATTCTGTAGATATGAACAATATTTGACCTT
Found at i:137987 original size:35 final size:34
Alignment explanation
Indices: 137936--138047 Score: 140
Period size: 35 Copynumber: 3.2 Consensus size: 34
137926 ATGAACAATA
*
137936 TTTGACCTTGATATAGTGAATTCTGTAGATATGAT
1 TTTGACCTTG-TATAGTGAATTCTGTTGATATGAT
137971 TTTGACCTTGTCATAGTCG-ATTCTGTTGATATGAT
1 TTTGACCTTGT-ATAGT-GAATTCTGTTGATATGAT
*
138006 TTTGA-CTTATTATAGAT-AATTCTGTTGATATGAT
1 TTTGACCTT-GTATAG-TGAATTCTGTTGATATGAT
138040 TTTGACCT
1 TTTGACCT
138048 ATAGATAAAT
Statistics
Matches: 69, Mismatches: 2, Indels: 12
0.83 0.02 0.14
Matches are distributed among these distances:
34 29 0.42
35 39 0.57
36 1 0.01
ACGTcount: A:0.25, C:0.11, G:0.18, T:0.46
Consensus pattern (34 bp):
TTTGACCTTGTATAGTGAATTCTGTTGATATGAT
Found at i:138033 original size:34 final size:34
Alignment explanation
Indices: 137948--138045 Score: 126
Period size: 34 Copynumber: 2.9 Consensus size: 34
137938 TGACCTTGAT
* * *
137948 ATAGTGAATTCTGTAGATATGATTTTGACCTTGTC
1 ATAGTCAATTCTGTTGATATGATTTTGA-CTTATC
* *
137983 ATAGTCGATTCTGTTGATATGATTTTGACTTATT
1 ATAGTCAATTCTGTTGATATGATTTTGACTTATC
138017 ATAGAT-AATTCTGTTGATATGATTTTGAC
1 ATAG-TCAATTCTGTTGATATGATTTTGAC
138046 CTATAGATAA
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
34 30 0.54
35 26 0.46
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.46
Consensus pattern (34 bp):
ATAGTCAATTCTGTTGATATGATTTTGACTTATC
Found at i:145810 original size:2 final size:2
Alignment explanation
Indices: 145803--145885 Score: 159
Period size: 2 Copynumber: 42.0 Consensus size: 2
145793 AATTCACCGC
145803 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -T CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
145844 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
145886 TCGTGACTTT
Statistics
Matches: 80, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 79 0.99
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:148817 original size:1 final size:1
Alignment explanation
Indices: 148811--148854 Score: 88
Period size: 1 Copynumber: 44.0 Consensus size: 1
148801 TATTTCTTTC
148811 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
148855 ACAGTTTTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:149345 original size:17 final size:19
Alignment explanation
Indices: 149303--149345 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
149293 ACATGAATGA
*
149303 TTTTTGTTCGTTCGTTTCT
1 TTTTTGTTCGTTCGTTACT
*
149322 TTATTGTT-GTT-GTTACT
1 TTTTTGTTCGTTCGTTACT
149339 TTTTTGT
1 TTTTTGT
149346 GGAAGTTGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 11 0.52
18 3 0.14
19 7 0.33
ACGTcount: A:0.05, C:0.09, G:0.16, T:0.70
Consensus pattern (19 bp):
TTTTTGTTCGTTCGTTACT
Found at i:150137 original size:2 final size:2
Alignment explanation
Indices: 150132--150203 Score: 126
Period size: 2 Copynumber: 36.0 Consensus size: 2
150122 TATTAGATTT
150132 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* *
150174 GA GA GA GA GA GA GA GA GA AA AA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
150204 CCTACATTTT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:150452 original size:24 final size:24
Alignment explanation
Indices: 150423--150499 Score: 136
Period size: 24 Copynumber: 3.2 Consensus size: 24
150413 AACGGGTACT
*
150423 AGGGTGAGGTATGAACGTACCCTG
1 AGGGTGAGGTATGAACGTACCCTC
*
150447 GGGGTGAGGTATGAACGTACCCTC
1 AGGGTGAGGTATGAACGTACCCTC
150471 AGGGTGAGGTATGAACGTACCCTC
1 AGGGTGAGGTATGAACGTACCCTC
150495 AGGGT
1 AGGGT
150500 CTGCAGTGCT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.23, C:0.18, G:0.38, T:0.21
Consensus pattern (24 bp):
AGGGTGAGGTATGAACGTACCCTC
Found at i:154544 original size:12 final size:12
Alignment explanation
Indices: 154527--154555 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
154517 GGCATTGTTG
154527 TTACAGTAACAA
1 TTACAGTAACAA
154539 TTACAGTAACAA
1 TTACAGTAACAA
154551 TTACA
1 TTACA
154556 TTAGATATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.48, C:0.17, G:0.07, T:0.28
Consensus pattern (12 bp):
TTACAGTAACAA
Found at i:155535 original size:45 final size:45
Alignment explanation
Indices: 155471--157406 Score: 3180
Period size: 45 Copynumber: 43.0 Consensus size: 45
155461 AAAAATAGTC
* * *
155471 TATAAGGTCAGTGCACGATCTACTACAGTGTATGGGTTACGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
* *
155516 TATAATGTCAATGCACGATCTACTACAGTGTATGGTTTGCGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
* * *
155561 TATAATATCACTTCACGATCTTCTACAGTGTATGGTTTACGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
*
155606 TATAATGTCACTGCACGATCTTCTACAGTGTATGGTTTACGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
*
155651 TATAATTTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
* * * *
155696 TATAATATCACTTCACGATCTTCTACAGTGTTTGGTTTACGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
* *
155741 TATAATGTCACTGCACGATCTACTACAGAGTATGGTTTACCCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
*
155786 TATAAGGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
* * *
155831 TATAAGGTCACTGCACGATCTACTACAGTGGATGGTTTATGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
155876 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
* *
155921 TATAATATCACTGCACGATCTACTACAGTGTATGGTTCATC-CATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTA-CGCATT
* *
155966 TATAATGTCATTGAACGATCTACTACAGTGTATGGTTTACGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
* *
156011 TATAATGTCACTGCACGATCTACTACAGAGTATGGTTTACCCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
*
156056 TATAAGGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
156101 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTATC-CATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTA-CGCATT
* *
156146 TATAATGTCACTGCACGATCTACTACAGAGTATGGTTTACCCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
156191 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
156236 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
*
156281 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACCCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
156326 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
* * *
156371 TATAATATCACTTCACGATCTTCTACAGTGTATGGTTTACGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
*
156416 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACCCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
*
156461 TATAAGGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
*
156506 TATAATGTCACTGCACGATCTACTACAGTGGATGGTTTACGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
156551 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTATC-CATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTA-CGCATT
* *
156596 TATAATGTCACTGCACGATCTACTACAGTGGATGGTTTATGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
* *
156641 TATAAGGTCACTGCACGATCTACTACAGTGTATGGTTCATC-CATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTA-CGCATT
* *
156686 TATAATGTCATTGAACGATCTACTACAGTGTATGGTTTACGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
156731 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTAC-CAATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGC-ATT
* * *
156776 TATAATGTCACTGCACGATCTACTACAGAGTATGGTTTTCCCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
*
156821 TATAAGGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
* * *
156866 TATAAGGTCACTGCACGATCTACTACAGTGGATGGTTTATGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
* *
156911 TATAAGGTCACTGCACGATCTACTAAAGTGTATGGTTTACGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
* *
156956 TATAATGTCATTGAACGATCTACTACAGTGTATGGTTTACGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
*
157001 TATAATGTCACTGCACGATTTACTACAGTGTATGGTTTACGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
157046 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
*
157091 TATAATGTCACTGTACGATCTACTACAGTGTATGGTTTACGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
* *
157136 TATAATGTCACTGCACGATCTACTACAATGTATGGTTGACGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
* *
157181 TATAATGTCACTGCACGATCTACAACAGTGTATGGTTTACACATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
* * * *
157226 TATAATGTCACTGCACGATCCACTATAGTGTATAGTTTATGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
* *
157271 TATAATGTCACTGCACGATCTAATACAGTGTATGGTTGACGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
*
157316 TATAATGTCACTGCACGATCTAATACAGTGTATGGTTTACGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
* *
157361 TATAATGTCACTGCACGATCTAATACAGTGTATGGTTTATGCATT
1 TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
157406 T
1 T
157407 GCAAAATAAC
Statistics
Matches: 1766, Mismatches: 115, Indels: 20
0.93 0.06 0.01
Matches are distributed among these distances:
44 4 0.00
45 1758 1.00
46 4 0.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (45 bp):
TATAATGTCACTGCACGATCTACTACAGTGTATGGTTTACGCATT
Found at i:162316 original size:19 final size:18
Alignment explanation
Indices: 162294--162331 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
162284 TTTTTATTCG
162294 TTTGTTTGTTGTTGTTTTT
1 TTTGTTTGTTGTT-TTTTT
*
162313 TTTGTTTTTTGTTTTTTT
1 TTTGTTTGTTGTTTTTTT
162331 T
1 T
162332 AAATTTGTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (18 bp):
TTTGTTTGTTGTTTTTTT
Found at i:164168 original size:2 final size:2
Alignment explanation
Indices: 164161--164214 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
164151 CATGGCATGG
164161 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
164203 GA GA GA GA GA GA
1 GA GA GA GA GA GA
164215 AATAAGGGAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:165750 original size:20 final size:20
Alignment explanation
Indices: 165725--165770 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
165715 AAATATCCAT
165725 TAGGAAAATCGT-TTTTCCTG
1 TAGGAAAAT-GTATTTTCCTG
*
165745 TAGGAAAATTTATTTTCCTG
1 TAGGAAAATGTATTTTCCTG
165765 TAGGAA
1 TAGGAA
165771 TTTAATTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (20 bp):
TAGGAAAATGTATTTTCCTG
Found at i:165774 original size:18 final size:19
Alignment explanation
Indices: 165737--165779 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
165727 GGAAAATCGT
165737 TTTTCCTGTAGGAAAATTTA
1 TTTTCCTGTAGG-AAATTTA
165757 TTTTCCTGTAGG-AATTTA
1 TTTTCCTGTAGGAAATTTA
*
165775 ATTTC
1 TTTTC
165780 TAAAGGTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.45
20 12 0.55
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.49
Consensus pattern (19 bp):
TTTTCCTGTAGGAAATTTA
Found at i:180678 original size:21 final size:21
Alignment explanation
Indices: 180617--181001 Score: 371
Period size: 21 Copynumber: 18.2 Consensus size: 21
180607 CATTTTAAAT
180617 AGATCTTTTCTCGTAATAACG
1 AGATCTTTTCTCGTAATAACG
* **
180638 AGATAATTAACTCGTAATAACG
1 AGAT-CTTTTCTCGTAATAACG
* *
180660 AGATTTTTTCTCTTAATAACG
1 AGATCTTTTCTCGTAATAACG
* * *
180681 AGATTTTTTCTCGCAATTACG
1 AGATCTTTTCTCGTAATAACG
*
180702 AGATCTTTTCTCGTAATTACG
1 AGATCTTTTCTCGTAATAACG
180723 AGATCTTTTCTCGTAATAACG
1 AGATCTTTTCTCGTAATAACG
* **
180744 AGATAATTAACTCGTAATAACG
1 AGAT-CTTTTCTCGTAATAACG
*
180766 AGATCTTTTCTCGTAATTACG
1 AGATCTTTTCTCGTAATAACG
180787 AGATCTTTTCTCGTAATAACG
1 AGATCTTTTCTCGTAATAACG
* **
180808 AGATAATTAACTCGTAATAACG
1 AGAT-CTTTTCTCGTAATAACG
*
180830 AGATCTTTTCTCGTAATTACG
1 AGATCTTTTCTCGTAATAACG
**
180851 AGATCTTTTCTCGTAATAATA
1 AGATCTTTTCTCGTAATAACG
* ** *
180872 AGATAATTAACTCGTTATAACG
1 AGAT-CTTTTCTCGTAATAACG
* ** *
180894 AGATAATTAACTCGT--T-ATG
1 AGAT-CTTTTCTCGTAATAACG
*
180913 AGATCTTTTCTCGTAATTACG
1 AGATCTTTTCTCGTAATAACG
*
180934 AGATCGTTTCTCGTAATAACG
1 AGATCTTTTCTCGTAATAACG
* ** *
180955 AGATGATTAACTCGTAATTACG
1 AGAT-CTTTTCTCGTAATAACG
* * *
180977 AAATCTTATCTCGTAATTACG
1 AGATCTTTTCTCGTAATAACG
180998 AGAT
1 AGAT
181002 AAAAATATTT
Statistics
Matches: 303, Mismatches: 53, Indels: 16
0.81 0.14 0.04
Matches are distributed among these distances:
18 7 0.02
19 6 0.02
20 2 0.01
21 193 0.64
22 95 0.31
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.37
Consensus pattern (21 bp):
AGATCTTTTCTCGTAATAACG
Found at i:180703 original size:64 final size:64
Alignment explanation
Indices: 180626--181003 Score: 442
Period size: 64 Copynumber: 5.9 Consensus size: 64
180616 TAGATCTTTT
* * * * **
180626 CTCGTAATAACGAGATAATTAACTCGTAATAACGAGATTTTTTCTCTTAATAACGAGAT-TTTTT
1 CTCGTAATAACGAGAT-ATTAACTCGTAATTACGAGATCTTTTCTCGTAATAACGAGATAATTAA
* * * **
180690 CTCGCAATTACGAGATCTTTTCTCGTAATTACGAGATCTTTTCTCGTAATAACGAGATAATTAA
1 CTCGTAATAACGAGATATTAACTCGTAATTACGAGATCTTTTCTCGTAATAACGAGATAATTAA
* **
180754 CTCGTAATAACGAGATCTTTTCTCGTAATTACGAGATCTTTTCTCGTAATAACGAGATAATTAA
1 CTCGTAATAACGAGATATTAACTCGTAATTACGAGATCTTTTCTCGTAATAACGAGATAATTAA
* ** **
180818 CTCGTAATAACGAGATCTTTTCTCGTAATTACGAGATCTTTTCTCGTAATAATAAGATAATTAA
1 CTCGTAATAACGAGATATTAACTCGTAATTACGAGATCTTTTCTCGTAATAACGAGATAATTAA
* * * ** *
180882 CTCGTTATAACGAGATAATTAACTCG---TTATGAGATCTTTTCTCGTAATTACGAGATCGTT-T
1 CTCGTAATAACGAGAT-ATTAACTCGTAATTACGAGATCTTTTCTCGTAATAACGAGATAATTAA
* * *
180943 CTCGTAATAACGAGATGATTAACTCGTAATTACGAAATCTTATCTCGTAATTACGAGATAA
1 CTCGTAATAACGAGAT-ATTAACTCGTAATTACGAGATCTTTTCTCGTAATAACGAGATAA
181004 AAATATTTTT
Statistics
Matches: 276, Mismatches: 33, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
61 24 0.09
62 28 0.10
63 36 0.13
64 182 0.66
65 6 0.02
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (64 bp):
CTCGTAATAACGAGATATTAACTCGTAATTACGAGATCTTTTCTCGTAATAACGAGATAATTAA
Found at i:180762 original size:85 final size:85
Alignment explanation
Indices: 180617--181002 Score: 404
Period size: 85 Copynumber: 4.6 Consensus size: 85
180607 CATTTTAAAT
* *
180617 AGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAGATTTTTTCTCTTAATAACGA
1 AGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAGATATTTTCTCGTAATAACGA
*
180682 GATTTTTTCTCGCAATTACG
66 GATCTTTTCTCGCAATTACG
* * ** **
180702 AGATCTTTTCTCGTAATTACGAGAT-CTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACG
1 AGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAGAT-ATTTTCTCGTAATAACG
*
180766 AGATCTTTTCTCGTAATTACG
65 AGATCTTTTCTCGCAATTACG
* *
180787 AGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAGATCTTTTCTCGTAATTACGA
1 AGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAGATATTTTCTCGTAATAACGA
* * **
180852 GATCTTTTCTCGTAATAATA
66 GATCTTTTCTCGCAATTACG
* ** * * * *
180872 AGATAATTAACTCGTTATAACGAGATAATTAACTCGT--T-ATGAGATCTTTTCTCGTAATTACG
1 AGAT-CTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAGATATTTTCTCGTAATAACG
* * *
180934 AGATCGTTTCTCGTAATAACG
65 AGATCTTTTCTCGCAATTACG
* ** * * * * *
180955 AGATGATTAACTCGTAATTACGAAAT-CTTATCTCGTAATTACGAGATA
1 AGAT-CTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAGATA
181003 AAAATATTTT
Statistics
Matches: 258, Mismatches: 37, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
82 8 0.03
83 63 0.24
84 20 0.08
85 121 0.47
86 46 0.18
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (85 bp):
AGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAGATATTTTCTCGTAATAACGA
GATCTTTTCTCGCAATTACG
Found at i:180971 original size:43 final size:42
Alignment explanation
Indices: 180617--181001 Score: 371
Period size: 43 Copynumber: 9.1 Consensus size: 42
180607 CATTTTAAAT
* **
180617 AGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACG
1 AGATCTTTTCTCGTAATAACGAGAT-CTTTTCTCGTAATAACG
* * * * *
180660 AGATTTTTTCTCTTAATAACGAGATTTTTTCTCGCAATTACG
1 AGATCTTTTCTCGTAATAACGAGATCTTTTCTCGTAATAACG
*
180702 AGATCTTTTCTCGTAATTACGAGATCTTTTCTCGTAATAACG
1 AGATCTTTTCTCGTAATAACGAGATCTTTTCTCGTAATAACG
* ** *
180744 AGATAATTAACTCGTAATAACGAGATCTTTTCTCGTAATTACG
1 AGAT-CTTTTCTCGTAATAACGAGATCTTTTCTCGTAATAACG
* **
180787 AGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACG
1 AGATCTTTTCTCGTAATAACGAGAT-CTTTTCTCGTAATAACG
* **
180830 AGATCTTTTCTCGTAATTACGAGATCTTTTCTCGTAATAATA
1 AGATCTTTTCTCGTAATAACGAGATCTTTTCTCGTAATAACG
* ** * * ** *
180872 AGATAATTAACTCGTTATAACGAGATAATTAACTCGT--T-ATG
1 AGAT-CTTTTCTCGTAATAACGAGAT-CTTTTCTCGTAATAACG
* *
180913 AGATCTTTTCTCGTAATTACGAGATCGTTTCTCGTAATAACG
1 AGATCTTTTCTCGTAATAACGAGATCTTTTCTCGTAATAACG
* ** * * * *
180955 AGATGATTAACTCGTAATTACGAAATCTTATCTCGTAATTACG
1 AGAT-CTTTTCTCGTAATAACGAGATCTTTTCTCGTAATAACG
180998 AGAT
1 AGAT
181002 AAAAATATTT
Statistics
Matches: 277, Mismatches: 57, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
39 6 0.02
40 16 0.06
41 7 0.03
42 93 0.34
43 148 0.53
44 7 0.03
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.37
Consensus pattern (42 bp):
AGATCTTTTCTCGTAATAACGAGATCTTTTCTCGTAATAACG
Found at i:186472 original size:11 final size:11
Alignment explanation
Indices: 186422--186478 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
186412 AGCGGGCATT
186422 TCAACGTTGAA
1 TCAACGTTGAA
* **
186433 ACAACGTTGTT
1 TCAACGTTGAA
* *
186444 TCAACGTCAGGCA
1 TCAACGT--TGAA
186457 TCAACGTTGAA
1 TCAACGTTGAA
186468 TCAACGTTGAA
1 TCAACGTTGAA
186479 ATAAGGTTGC
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
11 27 0.77
13 8 0.23
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (11 bp):
TCAACGTTGAA
Found at i:189323 original size:2 final size:2
Alignment explanation
Indices: 189316--189357 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
189306 ATCGATGAAT
189316 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
189358 CAGACAGACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:189362 original size:4 final size:4
Alignment explanation
Indices: 189355--189385 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
189345 AGAGAGAGAG
*
189355 AGAC AGAC AGAC AGAT AGAC AGAC AGAC AGA
1 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGA
189386 TAGAGAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.19, G:0.26, T:0.03
Consensus pattern (4 bp):
AGAC
Found at i:189374 original size:16 final size:16
Alignment explanation
Indices: 189355--189389 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
189345 AGAGAGAGAG
189355 AGACAGACAGACAGAT
1 AGACAGACAGACAGAT
189371 AGACAGACAGACAGAT
1 AGACAGACAGACAGAT
189387 AGA
1 AGA
189390 GAAATGAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.17, G:0.26, T:0.06
Consensus pattern (16 bp):
AGACAGACAGACAGAT
Found at i:197129 original size:53 final size:53
Alignment explanation
Indices: 197024--197129 Score: 133
Period size: 53 Copynumber: 2.0 Consensus size: 53
197014 TACTGAAATG
* * * *
197024 TTGCCGCTAGCTGCAACAACTTCTGGTAACATTGTGGCAATACTGCTGGAGTT
1 TTGCCGCTAGCTGCAACAACTTCTGGCAACATTCTGGCAATACTACTAGAGTT
* * *
197077 TTGCCGCTAG-TGGCAATAACTTCTGGCAGCATTCTGGCAATACTATTAGAGTT
1 TTGCCGCTAGCT-GCAACAACTTCTGGCAACATTCTGGCAATACTACTAGAGTT
197130 ATTTCTGTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
52 1 0.02
53 44 0.98
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (53 bp):
TTGCCGCTAGCTGCAACAACTTCTGGCAACATTCTGGCAATACTACTAGAGTT
Found at i:197315 original size:20 final size:16
Alignment explanation
Indices: 197263--197353 Score: 112
Period size: 16 Copynumber: 5.5 Consensus size: 16
197253 AACAACAGGT
197263 GCCTAAACAT-TTGGG
1 GCCTAAACATCTTGGG
197278 GCCTAAACATCTTGGG
1 GCCTAAACATCTTGGG
197294 GCCTAAACATCTAACCTGGG
1 GCCTAAACATCT----TGGG
* *
197314 GCCTAACCGTCTTGGG
1 GCCTAAACATCTTGGG
*
197330 GCCTAAACATGTTGGG
1 GCCTAAACATCTTGGG
197346 GCCTAAAC
1 GCCTAAAC
197354 GTCTGCAATT
Statistics
Matches: 66, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
15 10 0.15
16 42 0.64
20 14 0.21
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.23
Consensus pattern (16 bp):
GCCTAAACATCTTGGG
Found at i:197998 original size:2 final size:2
Alignment explanation
Indices: 197944--197982 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
197934 CAATACAGGT
197944 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
197983 CTGTATACAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:198539 original size:21 final size:21
Alignment explanation
Indices: 198513--198583 Score: 106
Period size: 21 Copynumber: 3.4 Consensus size: 21
198503 CATAGCATTG
*
198513 CATAGCATTGAAATCTCATAT
1 CATAGCATTGAAATCTCATAC
* *
198534 CATAGCATTGAAATTTCATAG
1 CATAGCATTGAAATCTCATAC
*
198555 CATAGCATTGGAATCTCATAC
1 CATAGCATTGAAATCTCATAC
198576 CATAGCAT
1 CATAGCAT
198584 ACAATCTCAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.31
Consensus pattern (21 bp):
CATAGCATTGAAATCTCATAC
Found at i:198797 original size:10 final size:10
Alignment explanation
Indices: 198779--198812 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
198769 GTTCAAATCT
198779 CATAGCATAC
1 CATAGCATAC
* *
198789 CATACCATAG
1 CATAGCATAC
198799 CATAGCATAC
1 CATAGCATAC
198809 CATA
1 CATA
198813 TCATTAAGCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.41, C:0.29, G:0.09, T:0.21
Consensus pattern (10 bp):
CATAGCATAC
Found at i:198799 original size:15 final size:15
Alignment explanation
Indices: 198779--198812 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
198769 GTTCAAATCT
198779 CATAGCATACCATAC
1 CATAGCATACCATAC
*
198794 CATAGCATAGCATAC
1 CATAGCATACCATAC
198809 CATA
1 CATA
198813 TCATTAAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.29, G:0.09, T:0.21
Consensus pattern (15 bp):
CATAGCATACCATAC
Found at i:198862 original size:21 final size:21
Alignment explanation
Indices: 198836--198915 Score: 117
Period size: 21 Copynumber: 3.8 Consensus size: 21
198826 AATTTCAATT
198836 TCTCATAGCATAGCATACAAA
1 TCTCATAGCATAGCATACAAA
198857 TCTCATAGCATAGCATACAAA
1 TCTCATAGCATAGCATACAAA
*
198878 TCTCATAGCATATCATTA-AAA
1 TCTCATAGCATAGCA-TACAAA
* *
198899 TCGCATACCATAGCATA
1 TCTCATAGCATAGCATA
198916 GCATACATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
20 2 0.04
21 50 0.93
22 2 0.04
ACGTcount: A:0.41, C:0.24, G:0.09, T:0.26
Consensus pattern (21 bp):
TCTCATAGCATAGCATACAAA
Found at i:202676 original size:21 final size:21
Alignment explanation
Indices: 202647--202706 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 21
202637 CGTTTCAATT
*
202647 TCTCCTAGCATAGCATAC-AAA
1 TCTCATAGCAT-GCATACGAAA
202668 TCTCATAGCACTGCAT-CGAAA
1 TCTCATAGCA-TGCATACGAAA
202689 TCTCATAGCATGGCATAC
1 TCTCATAGCAT-GCATAC
202707 CATAGCATTG
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
20 2 0.06
21 30 0.88
22 2 0.06
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.25
Consensus pattern (21 bp):
TCTCATAGCATGCATACGAAA
Found at i:202785 original size:17 final size:17
Alignment explanation
Indices: 202763--202796 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
202753 AGTTCGAACA
*
202763 CGGATATAGCAAATTTT
1 CGGATAAAGCAAATTTT
*
202780 CGGATAAAGGAAATTTT
1 CGGATAAAGCAAATTTT
202797 TGGAATCCCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (17 bp):
CGGATAAAGCAAATTTT
Found at i:203668 original size:2 final size:2
Alignment explanation
Indices: 203661--203707 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
203651 CCCCTACCAC
203661 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
203703 GA GA G
1 GA GA G
203708 CGGTCCCTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:204781 original size:9 final size:9
Alignment explanation
Indices: 204767--204792 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
204757 AAGAATAAAA
204767 GCCATTTAT
1 GCCATTTAT
204776 GCCATTTAT
1 GCCATTTAT
204785 GCCATTTA
1 GCCATTTA
204793 CATTGAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (9 bp):
GCCATTTAT
Found at i:218077 original size:7 final size:7
Alignment explanation
Indices: 218065--218131 Score: 82
Period size: 7 Copynumber: 9.6 Consensus size: 7
218055 GAGAAGGATC
218065 ATTCGAG
1 ATTCGAG
218072 ATTCGAG
1 ATTCGAG
*
218079 ATTCGAA
1 ATTCGAG
*
218086 ATACGAG
1 ATTCGAG
218093 ATTCGA-
1 ATTCGAG
*
218099 ACTACGAG
1 A-TTCGAG
218107 ATTCGAG
1 ATTCGAG
*
218114 ATTCGAA
1 ATTCGAG
218121 ATTCGAG
1 ATTCGAG
218128 ATTC
1 ATTC
218132 AATATCTAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
6 1 0.02
7 48 0.96
8 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.27
Consensus pattern (7 bp):
ATTCGAG
Found at i:219528 original size:200 final size:200
Alignment explanation
Indices: 219185--219584 Score: 800
Period size: 200 Copynumber: 2.0 Consensus size: 200
219175 AAAAAAAACA
219185 AGAAGCGATTATTGTGAGATGTCTTAGCCAATTATCGCAGTGATATAGTTTATGCAGTCCTGATA
1 AGAAGCGATTATTGTGAGATGTCTTAGCCAATTATCGCAGTGATATAGTTTATGCAGTCCTGATA
219250 CGAATTTAACGACATGTACAACTGGCAGTTGGTGCTTAAATTATCGATACCGCGTAATCAGACAT
66 CGAATTTAACGACATGTACAACTGGCAGTTGGTGCTTAAATTATCGATACCGCGTAATCAGACAT
219315 AGTAAAGGCTCATTTAAAATAAAACACAATTTCATAAATTATTTAAATATATGTACAAAATGATT
131 AGTAAAGGCTCATTTAAAATAAAACACAATTTCATAAATTATTTAAATATATGTACAAAATGATT
219380 AGCAG
196 AGCAG
219385 AGAAGCGATTATTGTGAGATGTCTTAGCCAATTATCGCAGTGATATAGTTTATGCAGTCCTGATA
1 AGAAGCGATTATTGTGAGATGTCTTAGCCAATTATCGCAGTGATATAGTTTATGCAGTCCTGATA
219450 CGAATTTAACGACATGTACAACTGGCAGTTGGTGCTTAAATTATCGATACCGCGTAATCAGACAT
66 CGAATTTAACGACATGTACAACTGGCAGTTGGTGCTTAAATTATCGATACCGCGTAATCAGACAT
219515 AGTAAAGGCTCATTTAAAATAAAACACAATTTCATAAATTATTTAAATATATGTACAAAATGATT
131 AGTAAAGGCTCATTTAAAATAAAACACAATTTCATAAATTATTTAAATATATGTACAAAATGATT
219580 AGCAG
196 AGCAG
219585 CTATAATGCT
Statistics
Matches: 200, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
200 200 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31
Consensus pattern (200 bp):
AGAAGCGATTATTGTGAGATGTCTTAGCCAATTATCGCAGTGATATAGTTTATGCAGTCCTGATA
CGAATTTAACGACATGTACAACTGGCAGTTGGTGCTTAAATTATCGATACCGCGTAATCAGACAT
AGTAAAGGCTCATTTAAAATAAAACACAATTTCATAAATTATTTAAATATATGTACAAAATGATT
AGCAG
Found at i:224859 original size:1 final size:1
Alignment explanation
Indices: 224855--224921 Score: 125
Period size: 1 Copynumber: 67.0 Consensus size: 1
224845 CCCCTGCCAN
*
224855 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
224920 TT
1 TT
224922 GGGGGGGGGG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.00, C:0.00, G:0.01, T:0.99
Consensus pattern (1 bp):
T
Found at i:226584 original size:4 final size:4
Alignment explanation
Indices: 226577--226667 Score: 83
Period size: 4 Copynumber: 22.8 Consensus size: 4
226567 ATACTGAGAG
* *
226577 AGAC AGAC AGAC AGAC AGAC AGAC GGAC GGAC AGAC AGAC AGAC AGAC
1 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC
* * * * * * * * *
226625 GGAC GGAC GGAC GGAC GGAC AAAC GGAC TGAC AGAC GGAC AGA
1 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGA
226668 AACAGAGAAT
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 76 1.00
ACGTcount: A:0.41, C:0.24, G:0.34, T:0.01
Consensus pattern (4 bp):
AGAC
Found at i:226592 original size:12 final size:12
Alignment explanation
Indices: 226578--226667 Score: 108
Period size: 12 Copynumber: 7.5 Consensus size: 12
226568 TACTGAGAGA
*
226578 GACAGACAGACA
1 GACAGACAGACG
226590 GACAGACAGACG
1 GACAGACAGACG
* *
226602 GACGGACAGACA
1 GACAGACAGACG
226614 GACAGACAGACG
1 GACAGACAGACG
* *
226626 GACGGACGGACG
1 GACAGACAGACG
* *
226638 GACGGACAAACG
1 GACAGACAGACG
*
226650 GACTGACAGACG
1 GACAGACAGACG
226662 GACAGA
1 GACAGA
226668 AACAGAGAAT
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 66 1.00
ACGTcount: A:0.40, C:0.24, G:0.34, T:0.01
Consensus pattern (12 bp):
GACAGACAGACG
Found at i:235529 original size:166 final size:165
Alignment explanation
Indices: 235265--235590 Score: 625
Period size: 166 Copynumber: 2.0 Consensus size: 165
235255 AATTCTTTAA
*
235265 CTCCTCATTTTAATATCTAATATATATAGGGTAAGACAACATATATAAGCATGATCTACTGTACT
1 CTCCTCATTTTAATATCTAATATATATAGGATAAGACAACATATATAAGCATGATCTACTGTACT
235330 AAGAGTTAAAAGTTTTTGTACGTCTAGATAATTTTGAATACAATGAAATTAAACTGCAACAAAAC
66 AAGAGTTAAAAGTTTTTGTACGTCTAGATAATTTTGAATACAATGAAATTAAACTGCAACAAAAC
235395 AATTTCACATTGAAAATCAACAAAATATTCTTTTC
131 AATTTCACATTGAAAATCAACAAAATATTCTTTTC
*
235430 CTCCTCATTTTAATATCTAAATATATATAGGATTAGACAACATATATAAGCATGATCTACTGTAC
1 CTCCTCATTTTAATATCT-AATATATATAGGATAAGACAACATATATAAGCATGATCTACTGTAC
235495 TAAGAGTTAAAAGTTTTTGTACGTCTAGATAATTTTGAATACAATGAAATTAAACTGCAACAAAA
65 TAAGAGTTAAAAGTTTTTGTACGTCTAGATAATTTTGAATACAATGAAATTAAACTGCAACAAAA
235560 CAATTTCACATTGAAAATCAACAAAATATTC
130 CAATTTCACATTGAAAATCAACAAAATATTC
235591 CTTCCAATAA
Statistics
Matches: 158, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
165 18 0.11
166 140 0.89
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.33
Consensus pattern (165 bp):
CTCCTCATTTTAATATCTAATATATATAGGATAAGACAACATATATAAGCATGATCTACTGTACT
AAGAGTTAAAAGTTTTTGTACGTCTAGATAATTTTGAATACAATGAAATTAAACTGCAACAAAAC
AATTTCACATTGAAAATCAACAAAATATTCTTTTC
Found at i:235979 original size:19 final size:19
Alignment explanation
Indices: 235951--235992 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
235941 AAAAGTGTAA
*
235951 AAATAAACAGCA-CCAAAC
1 AAATAAACAGCATCAAAAC
235969 AAATAAAACAGCATCAAAAC
1 AAAT-AAACAGCATCAAAAC
235989 AAAT
1 AAAT
235993 GACAAAGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.19
19 8 0.38
20 9 0.43
ACGTcount: A:0.64, C:0.21, G:0.05, T:0.10
Consensus pattern (19 bp):
AAATAAACAGCATCAAAAC
Found at i:240913 original size:29 final size:31
Alignment explanation
Indices: 240881--240941 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
240871 ATTAATGAAG
240881 CAATTATCAATTG-T-TTATTTTTCATTGGT
1 CAATTATCAATTGATATTATTTTTCATTGGT
**
240910 CAATTATTTATTGATAATTATTTTTCATTGGT
1 CAATTATCAATTGAT-ATTATTTTTCATTGGT
240942 AACTACAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 11 0.41
30 1 0.04
32 15 0.56
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (31 bp):
CAATTATCAATTGATATTATTTTTCATTGGT
Found at i:241308 original size:66 final size:66
Alignment explanation
Indices: 241173--241362 Score: 201
Period size: 62 Copynumber: 2.9 Consensus size: 66
241163 ATGTAATATT
* ** * *
241173 AACAATAAATAAAAGAACCTACACCTCAGCTACTGACTGC--A-A-ACAAAGAACAGATAATATG
1 AACACTAAATAAAAGAGTCTACACCTCAGCTACTGACTGCAAACAGACAAAGAACAGCTAATATA
241234 A
66 A
* *
241235 AACACTAAATAAAAGAGTCTACACCTCACCTACTGACTGCAAACAGACAAAGAACAGCTACTATA
1 AACACTAAATAAAAGAGTCTACACCTCAGCTACTGACTGCAAACAGACAAAGAACAGCTAATATA
241300 A
66 A
* * * * *
241301 AATACTAATTAAAAGAGAGAGTTTACATCTCAGCTAATGACTGCAAACAGACAAA-AACAGCT
1 AACACTAA--ATAA-A-AGAGTCTACACCTCAGCTACTGACTGCAAACAGACAAAGAACAGCT
241363 CTAAACAACC
Statistics
Matches: 107, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
62 36 0.34
64 1 0.01
65 1 0.01
66 24 0.22
68 3 0.03
69 8 0.07
70 34 0.32
ACGTcount: A:0.48, C:0.22, G:0.12, T:0.18
Consensus pattern (66 bp):
AACACTAAATAAAAGAGTCTACACCTCAGCTACTGACTGCAAACAGACAAAGAACAGCTAATATA
A
Found at i:242123 original size:26 final size:27
Alignment explanation
Indices: 242083--242140 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 27
242073 AATACATAAT
* *
242083 CATTTTTTTATTCTGTCAATCAGTCTA
1 CATTTGTTTATTCTGTCAATCAGTCAA
242110 CATTTGTTT-TTCTGTCAATCAGTCAA
1 CATTTGTTTATTCTGTCAATCAGTCAA
242136 CATTT
1 CATTT
242141 AACTAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 21 0.72
27 8 0.28
ACGTcount: A:0.22, C:0.19, G:0.09, T:0.50
Consensus pattern (27 bp):
CATTTGTTTATTCTGTCAATCAGTCAA
Found at i:254364 original size:2 final size:2
Alignment explanation
Indices: 254357--254409 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
254347 AAACCCACAT
254357 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
254399 TC TC TC TC TC T
1 TC TC TC TC TC T
254410 TACGGATAGC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:255770 original size:18 final size:18
Alignment explanation
Indices: 255736--255770 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
255726 TTTTCATGGT
*
255736 ATTTTCATCAATAAATTG
1 ATTTTCATAAATAAATTG
*
255754 ATTTTCATAAATTAATT
1 ATTTTCATAAATAAATT
255771 ATAATGTCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.49
Consensus pattern (18 bp):
ATTTTCATAAATAAATTG
Found at i:256296 original size:13 final size:13
Alignment explanation
Indices: 256278--256303 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
256268 ATGATCATGA
256278 AGTCAGTTTTTCT
1 AGTCAGTTTTTCT
256291 AGTCAGTTTTTCT
1 AGTCAGTTTTTCT
256304 TCCGGCCTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (13 bp):
AGTCAGTTTTTCT
Found at i:264362 original size:14 final size:14
Alignment explanation
Indices: 264343--264369 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
264333 TTTAAAAATG
264343 ACATAATCACATTC
1 ACATAATCACATTC
264357 ACATAATCACATT
1 ACATAATCACATT
264370 ATGAGTAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.30
Consensus pattern (14 bp):
ACATAATCACATTC
Found at i:266494 original size:3 final size:3
Alignment explanation
Indices: 266486--266532 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
266476 TGCACTGCTG
266486 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
266533 TATTCCCAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:279756 original size:36 final size:36
Alignment explanation
Indices: 279716--279794 Score: 140
Period size: 36 Copynumber: 2.2 Consensus size: 36
279706 GATCATTAAA
279716 TGTTGATCATTTTTTAGGATTTTCAATTTTTTTCTG
1 TGTTGATCATTTTTTAGGATTTTCAATTTTTTTCTG
*
279752 TGTTGATCATTTTTTAGGGTTTTCAATTTTTTTCTG
1 TGTTGATCATTTTTTAGGATTTTCAATTTTTTTCTG
*
279788 TATTGAT
1 TGTTGAT
279795 TTCAGGTTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.16, C:0.08, G:0.15, T:0.61
Consensus pattern (36 bp):
TGTTGATCATTTTTTAGGATTTTCAATTTTTTTCTG
Found at i:279780 original size:17 final size:17
Alignment explanation
Indices: 279724--279783 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
279714 AATGTTGATC
*
279724 ATTTTTTAGGATTTTCA
1 ATTTTTTAGGGTTTTCA
* * *
279741 ATTTTTTTCTGTGTTGATC-
1 A-TTTTTT-AGGGTT-TTCA
279760 ATTTTTTAGGGTTTTCA
1 ATTTTTTAGGGTTTTCA
279777 ATTTTTT
1 ATTTTTT
279784 TCTGTATTGA
Statistics
Matches: 32, Mismatches: 7, Indels: 8
0.68 0.15 0.17
Matches are distributed among these distances:
16 2 0.06
17 12 0.38
18 12 0.38
19 4 0.12
20 2 0.06
ACGTcount: A:0.17, C:0.07, G:0.13, T:0.63
Consensus pattern (17 bp):
ATTTTTTAGGGTTTTCA
Found at i:280746 original size:2 final size:2
Alignment explanation
Indices: 280739--280774 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
280729 ATTATCTTTT
280739 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
280775 AGTAAACAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:283553 original size:13 final size:13
Alignment explanation
Indices: 283537--283562 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
283527 AAAATAACCT
283537 TCTATAATACATA
1 TCTATAATACATA
283550 TCTATAATACATA
1 TCTATAATACATA
283563 GTGCTATCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
TCTATAATACATA
Found at i:287804 original size:18 final size:18
Alignment explanation
Indices: 287756--287805 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
287746 TCTCTGTTTC
*
287756 CTCTTCTTCTTTAT-TTT
1 CTCTTCTTCCTTATCTTT
* *
287773 C-C-TCCTCCTCATCTTT
1 CTCTTCTTCCTTATCTTT
287789 CTCTTCTTCCTTATCTT
1 CTCTTCTTCCTTATCTT
287806 CACCATTTCC
Statistics
Matches: 25, Mismatches: 5, Indels: 5
0.71 0.14 0.14
Matches are distributed among these distances:
15 7 0.28
16 5 0.20
17 2 0.08
18 11 0.44
ACGTcount: A:0.06, C:0.36, G:0.00, T:0.58
Consensus pattern (18 bp):
CTCTTCTTCCTTATCTTT
Found at i:289219 original size:24 final size:24
Alignment explanation
Indices: 289174--289219 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
289164 TTCCTCAGGC
* *
289174 ACATTTTCGGGATCTTCATCTTGG
1 ACATTTCCGGCATCTTCATCTTGG
289198 ACATTTCCGGCATCATTC-TCTT
1 ACATTTCCGGCATC-TTCATCTT
289220 CCGTTTTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.17, C:0.26, G:0.15, T:0.41
Consensus pattern (24 bp):
ACATTTCCGGCATCTTCATCTTGG
Found at i:292526 original size:2 final size:2
Alignment explanation
Indices: 292519--292553 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
292509 NNNNNNNNNN
292519 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
292554 ATAAGTTCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:293037 original size:68 final size:67
Alignment explanation
Indices: 292927--293062 Score: 209
Period size: 68 Copynumber: 2.0 Consensus size: 67
292917 CATGAATCTC
* * * *
292927 ATAGTACCCTAAAGTCAGTGGATACGTTTTAAAAAGGAAAATACACTGTATCTGGGCTAGGGATA
1 ATAGTACCCTAAAGTCAATGGATACGTTTTAAAAAAGAAAATACACTGTATCTGGCCTAGGGAGA
292992 GT
66 GT
* *
292994 ANTAGTACCCTAGAGTCAATGGATACGTTTTAAAAAAGAAAATACACTGTATCTGTCCTAGGGAG
1 A-TAGTACCCTAAAGTCAATGGATACGTTTTAAAAAAGAAAATACACTGTATCTGGCCTAGGGAG
293059 AGT
65 AGT
293062 A
1 A
293063 GATCTGTTCA
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
67 1 0.02
68 61 0.98
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.26
Consensus pattern (67 bp):
ATAGTACCCTAAAGTCAATGGATACGTTTTAAAAAAGAAAATACACTGTATCTGGCCTAGGGAGA
GT
Found at i:293486 original size:38 final size:38
Alignment explanation
Indices: 293358--294097 Score: 1049
Period size: 38 Copynumber: 19.6 Consensus size: 38
293348 GTTCATAGGN
* *
293358 TCAGTGGATA--TTCATTGGTATCTAAATATAGCCTTGCG
1 TCAGTGGATATGTTCATAGGTATCT--ATATAGCTTTGCG
*
293396 TCAGTGGATATGTTCATAGGT-TCTAAATATAGCCTTGCG
1 TCAGTGGATATGTTCATAGGTATCT--ATATAGCTTTGCG
* *
293435 TCAGGGGATATGTTTATAGGTATCTATATAG-TCTTGCG
1 TCAGTGGATATGTTCATAGGTATCTATATAGCT-TTGCG
* * * * *
293473 CCAGTGGACATGTTCATAGATATCTATTTAGTTTTGCG
1 TCAGTGGATATGTTCATAGGTATCTATATAGCTTTGCG
*
293511 TCAGTGGATATGTTCATAGGTATCTATATATAGCATTGCG
1 TCAGTGGATATGTTCATAGGTATC--TATATAGCTTTGCG
293551 TCAGTGGATATGTTCATAGGTATCTAAATATAGCTTTGCG
1 TCAGTGGATATGTTCATAGGTATCT--ATATAGCTTTGCG
* *
293591 TCAGTGGATATGTTCATAGGTATCTATATAGCCTCGCG
1 TCAGTGGATATGTTCATAGGTATCTATATAGCTTTGCG
*
293629 TCAGT-G----G-----NGGTATCTATATAGCTTTGCG
1 TCAGTGGATATGTTCATAGGTATCTATATAGCTTTGCG
293657 TCAGTGGATATGTTCATAGGTATCTATATAGCTTTGCG
1 TCAGTGGATATGTTCATAGGTATCTATATAGCTTTGCG
*
293695 TCAGTGGATATGTTCATAGGTATCTATATAGCCTTGCG
1 TCAGTGGATATGTTCATAGGTATCTATATAGCTTTGCG
**
293733 TCAGTGGATATGTTCCCAGGTATCTATATAGCTTTGCG
1 TCAGTGGATATGTTCATAGGTATCTATATAGCTTTGCG
*
293771 TCAGTGGATATGTTCATAGGTATCTATATAGCCTTGCG
1 TCAGTGGATATGTTCATAGGTATCTATATAGCTTTGCG
**
293809 TCAGTGGATATGTTCCCAGGTATCTATATAGCTTTGCG
1 TCAGTGGATATGTTCATAGGTATCTATATAGCTTTGCG
*
293847 TCAGTGGATATGATCATAGGTATCTATATAGCTTTGCG
1 TCAGTGGATATGTTCATAGGTATCTATATAGCTTTGCG
*
293885 TCAGTGGATATGTTCATAGGTATCTATATAACTTTGCG
1 TCAGTGGATATGTTCATAGGTATCTATATAGCTTTGCG
293923 TCAGTGGATATGTTCATAGGTATCTATATAGCTTTGCG
1 TCAGTGGATATGTTCATAGGTATCTATATAGCTTTGCG
* *
293961 TCAGTGGATATGTTCATAGGTATCTATATAGCCTCGCG
1 TCAGTGGATATGTTCATAGGTATCTATATAGCTTTGCG
* *
293999 TCAGTGGATATGTTCATAGCTATCTATATAGCCTTGCG
1 TCAGTGGATATGTTCATAGGTATCTATATAGCTTTGCG
*
294037 TCAGTGGATATGTTCATAGGTATCTATATAGCTTTACG
1 TCAGTGGATATGTTCATAGGTATCTATATAGCTTTGCG
*
294075 TCAGTGGATATGTTCAAAGGTAT
1 TCAGTGGATATGTTCATAGGTAT
294098 AATATACCTT
Statistics
Matches: 636, Mismatches: 47, Indels: 38
0.88 0.07 0.05
Matches are distributed among these distances:
28 23 0.04
29 1 0.00
33 2 0.00
37 1 0.00
38 488 0.77
39 38 0.06
40 83 0.13
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.37
Consensus pattern (38 bp):
TCAGTGGATATGTTCATAGGTATCTATATAGCTTTGCG
Found at i:293649 original size:28 final size:27
Alignment explanation
Indices: 293609--293663 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
293599 TATGTTCATA
293609 GGTATCTATATAGCCTCGCGTCAGTGG
1 GGTATCTATATAGCCTCGCGTCAGTGG
* *
293636 NGGTATCTATATAGCTTTGCGTCAGTGG
1 -GGTATCTATATAGCCTCGCGTCAGTGG
293664 ATATGTTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.18, C:0.18, G:0.29, T:0.33
Consensus pattern (27 bp):
GGTATCTATATAGCCTCGCGTCAGTGG
Found at i:295203 original size:20 final size:21
Alignment explanation
Indices: 295163--295203 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
295153 AACGATAGAC
295163 TTCCAAATAGTTGTAAAAATT
1 TTCCAAATAGTTGTAAAAATT
* *
295184 TTCCATATAG-TGTAAGAATT
1 TTCCAAATAGTTGTAAAAATT
295204 GGCTGTTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TTCCAAATAGTTGTAAAAATT
Done.