Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold229
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 751352
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 14889 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:904 original size:22 final size:20
Alignment explanation
Indices: 856--898 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
846 AAATGTAGTG
* *
856 TATTTTTAAAATAAAAAATA
1 TATTTTAAAAATAAAAAAAA
876 TATTTTAAAAATAAAAAAAA
1 TATTTTAAAAATAAAAAAAA
896 TAT
1 TAT
899 GATTTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TATTTTAAAAATAAAAAAAA
Found at i:18327 original size:31 final size:31
Alignment explanation
Indices: 18278--18340 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
18268 GTCACAAAAT
*
18278 AGTCACCGAGCTACTTGAACA-TTTTCATTTA
1 AGTCACCGAACTACTTGAA-AGTTTTCATTTA
* * *
18309 AGTCATCGAACTATTTGAAAGTTTTTATTTA
1 AGTCACCGAACTACTTGAAAGTTTTCATTTA
18340 A
1 A
18341 ATTATTGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.40
Consensus pattern (31 bp):
AGTCACCGAACTACTTGAAAGTTTTCATTTA
Found at i:30916 original size:24 final size:24
Alignment explanation
Indices: 30883--30933 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
30873 TACACAAATA
* * *
30883 TGAGACAAAAGTCTTGTTTTATTT
1 TGAGACAAAACTATTGTTGTATTT
*
30907 TGAGAGAAAACTATTGTTGTATTT
1 TGAGACAAAACTATTGTTGTATTT
30931 TGA
1 TGA
30934 TAAAAATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.43
Consensus pattern (24 bp):
TGAGACAAAACTATTGTTGTATTT
Found at i:34294 original size:11 final size:11
Alignment explanation
Indices: 34280--34328 Score: 89
Period size: 11 Copynumber: 4.5 Consensus size: 11
34270 TATTTTTTAA
34280 TTTTAAAATAC
1 TTTTAAAATAC
34291 TTTTAAAATAC
1 TTTTAAAATAC
34302 TTTTAAAATAC
1 TTTTAAAATAC
*
34313 TTTTAAAATAT
1 TTTTAAAATAC
34324 TTTTA
1 TTTTA
34329 TTTTTAAAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 37 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:38193 original size:26 final size:26
Alignment explanation
Indices: 38167--38215 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
38157 ATAAATTAAT
38167 TTAAATGAAAT-TTAATATTATGAAA
1 TTAAATGAAATGTTAATATTATGAAA
* * *
38192 TTAATTTAAGTGTTAATATTATGA
1 TTAAATGAAATGTTAATATTATGA
38216 TATATATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 8 0.40
26 12 0.60
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (26 bp):
TTAAATGAAATGTTAATATTATGAAA
Found at i:41293 original size:22 final size:23
Alignment explanation
Indices: 41263--41431 Score: 78
Period size: 24 Copynumber: 7.4 Consensus size: 23
41253 AAAATTTGGA
* *
41263 CAGCTTATATACAACAAA-TGGG
1 CAGCATATATACAACAAATTGAG
* * * *
41285 CAGCATATACATACCAAATTTAG
1 CAGCATATATACAACAAATTGAG
* * * * *
41308 CAGCATTTTTACACCAAAATTTAA
1 CAGCATATATACAAC-AAATTGAG
*
41332 CAGCATATATACAACAAA-TGGG
1 CAGCATATATACAACAAATTGAG
*
41354 CAGCATATACGTAC--CGAATTGAG
1 CAGCATATA--TACAACAAATTGAG
* * * * * *
41377 CAACATTTTTACACCAAAATTTAA
1 CAGCATATATACAAC-AAATTGAG
* *
41401 CCGCATATATACAACAAA-TGGG
1 CAGCATATATACAACAAATTGAG
41423 CAGCATATA
1 CAGCATATA
41432 CATAATACGT
Statistics
Matches: 105, Mismatches: 34, Indels: 16
0.68 0.22 0.10
Matches are distributed among these distances:
21 3 0.03
22 36 0.34
23 29 0.28
24 37 0.35
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (23 bp):
CAGCATATATACAACAAATTGAG
Found at i:41344 original size:24 final size:24
Alignment explanation
Indices: 41231--41349 Score: 73
Period size: 24 Copynumber: 5.0 Consensus size: 24
41221 ATCATAAACG
* * *
41231 AATTAAACAACATTTATACACCAA
1 AATTTAACAGCATATATACACCAA
* * *
41255 AATTTGGACAGCTTATATACAAC-A
1 AATTT-AACAGCATATATACACCAA
*** * *
41279 AA-TGGGCAGCATATACATACC-A
1 AATTTAACAGCATATATACACCAA
* * *
41301 AATTTAGCAGCATTTTTACACCAA
1 AATTTAACAGCATATATACACCAA
*
41325 AATTTAACAGCATATATACAACAA
1 AATTTAACAGCATATATACACCAA
41349 A
1 A
41350 TGGGCAGCAT
Statistics
Matches: 70, Mismatches: 22, Indels: 6
0.71 0.22 0.06
Matches are distributed among these distances:
22 15 0.21
23 14 0.20
24 29 0.41
25 12 0.17
ACGTcount: A:0.46, C:0.19, G:0.08, T:0.26
Consensus pattern (24 bp):
AATTTAACAGCATATATACACCAA
Found at i:41353 original size:69 final size:69
Alignment explanation
Indices: 41238--41435 Score: 315
Period size: 69 Copynumber: 2.9 Consensus size: 69
41228 ACGAATTAAA
* * *
41238 CAACATTTATACACCAAAATTTGGACAGCTTATATACAACAAATGGGCAGCATATACATACCAAA
1 CAACATTTTTACACCAAAATTT-AACAGCATATATACAACAAATGGGCAGCATATACATACCAAA
*
41303 TTTAG
65 TTGAG
* * *
41308 CAGCATTTTTACACCAAAATTTAACAGCATATATACAACAAATGGGCAGCATATACGTACCGAAT
1 CAACATTTTTACACCAAAATTTAACAGCATATATACAACAAATGGGCAGCATATACATACCAAAT
41373 TGAG
66 TGAG
*
41377 CAACATTTTTACACCAAAATTTAACCGCATATATACAACAAATGGGCAGCATATACATA
1 CAACATTTTTACACCAAAATTTAACAGCATATATACAACAAATGGGCAGCATATACATA
41436 ATACGTCATA
Statistics
Matches: 118, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
69 98 0.83
70 20 0.17
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (69 bp):
CAACATTTTTACACCAAAATTTAACAGCATATATACAACAAATGGGCAGCATATACATACCAAAT
TGAG
Found at i:42950 original size:15 final size:15
Alignment explanation
Indices: 42932--42964 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
42922 TGTTGGACAT
42932 AAGCCTATCTCACAA
1 AAGCCTATCTCACAA
42947 AAGCCTATCTCACAA
1 AAGCCTATCTCACAA
42962 AAG
1 AAG
42965 GATTCTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.42, C:0.30, G:0.09, T:0.18
Consensus pattern (15 bp):
AAGCCTATCTCACAA
Found at i:44221 original size:25 final size:25
Alignment explanation
Indices: 44187--44243 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
44177 GTGAAAATCT
44187 AATGCATATGATGCAATGCGATGCA
1 AATGCATATGATGCAATGCGATGCA
44212 AATGCATATGATGCAATGCGATGCA
1 AATGCATATGATGCAATGCGATGCA
44237 AATGCAT
1 AATGCAT
44244 GGAATGAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.25
Consensus pattern (25 bp):
AATGCATATGATGCAATGCGATGCA
Found at i:46824 original size:3 final size:3
Alignment explanation
Indices: 46806--46854 Score: 73
Period size: 3 Copynumber: 16.3 Consensus size: 3
46796 GTATATATAT
*
46806 ATA AGTA ATT ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
46851 ATA A
1 ATA A
46855 GACAAATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:48590 original size:44 final size:44
Alignment explanation
Indices: 48511--48616 Score: 108
Period size: 44 Copynumber: 2.4 Consensus size: 44
48501 CTAATTCGGC
* * *
48511 CTACTGCAACTTCAGAGG-TATATGATTCATCGTTTTAGTCCGCT
1 CTACTGCAACTTCAG-GGAGATAGGATTCATAGTTTTAGTCCGCT
**
48555 CTACTGCAACTTCAGGGAGATAGGATT-AGTAGTTTTAGTTTGCT
1 CTACTGCAACTTCAGGGAGATAGGATTCA-TAGTTTTAGTCCGCT
* * *
48599 CCACTGTAACTTCGGGGA
1 CTACTGCAACTTCAGGGA
48617 TCTTACTACA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
43 3 0.06
44 49 0.94
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.34
Consensus pattern (44 bp):
CTACTGCAACTTCAGGGAGATAGGATTCATAGTTTTAGTCCGCT
Found at i:49050 original size:44 final size:44
Alignment explanation
Indices: 48944--49051 Score: 130
Period size: 44 Copynumber: 2.5 Consensus size: 44
48934 TTTGACCCAT
* *
48944 TCCACTGCAACTTCAGGGAGATAGGACTCGTATCTTCAACTTGC
1 TCCACTGCAACTTCAGGGGGATAAGACTCGTATCTTCAACTTGC
* *
48988 TCCACAGCAACTTCAGGGGGATAAGACTTGTAAT-TTCAACTTGC
1 TCCACTGCAACTTCAGGGGGATAAGACTCGT-ATCTTCAACTTGC
* *
49032 -CCTGCTGCAATTTCAGGGGG
1 TCC-ACTGCAACTTCAGGGGG
49052 CAAGGTTTTG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
43 2 0.04
44 51 0.93
45 2 0.04
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (44 bp):
TCCACTGCAACTTCAGGGGGATAAGACTCGTATCTTCAACTTGC
Found at i:49310 original size:44 final size:44
Alignment explanation
Indices: 49218--49369 Score: 112
Period size: 44 Copynumber: 3.5 Consensus size: 44
49208 TTAATCCGTT
* * * * *
49218 CCACTGTAACTTCAGGGAGGTAGGATTAGTAACTTTAATCTGCT
1 CCACTGTAACTTCAGGGAGATAAGATTAGTAACTTCAACCTGCC
* *
49262 CCACTGTAACTTTAGGGAGATAAGACTT-GTATCTTCAACCTGCC
1 CCACTGTAACTTCAGGGAGATAAGA-TTAGTAACTTCAACCTGCC
** * * * *
49306 CCACTACAACTTCATGGG-GATAAGGTTTGCT-ATTTCAACCTGCT
1 CCACTGTAACTTCA-GGGAGATAAGATTAG-TAACTTCAACCTGCC
* * *
49350 CTACTGCAACTTCAGAGAGA
1 CCACTGTAACTTCAGGGAGA
49370 CAAAATTTGA
Statistics
Matches: 86, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
43 4 0.05
44 76 0.88
45 6 0.07
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (44 bp):
CCACTGTAACTTCAGGGAGATAAGATTAGTAACTTCAACCTGCC
Found at i:49425 original size:41 final size:41
Alignment explanation
Indices: 49345--49426 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
49335 CTATTTCAAC
*
49345 CTGCTCTACTGCAACTTCAGAGAGACAAAATTTGATATGAT
1 CTGCTCTACTGCAACTTCAGAGAGACAAAATCTGATATGAT
* * * *
49386 CTGCTCTACTGCAACTTTAGAGAGACGAGATCTGTTATGAT
1 CTGCTCTACTGCAACTTCAGAGAGACAAAATCTGATATGAT
49427 AGATTTAATC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (41 bp):
CTGCTCTACTGCAACTTCAGAGAGACAAAATCTGATATGAT
Found at i:51131 original size:69 final size:69
Alignment explanation
Indices: 51049--51301 Score: 398
Period size: 69 Copynumber: 3.7 Consensus size: 69
51039 TTTGTACTAA
51049 CCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGTTGCTCAATTTGGTACGTATAT
1 CCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGTTGCTCAATTTGGTACGTATAT
**
51114 TATG
66 GCTG
*
51118 CCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATATTGCTCAATTTGGTACGTATAT
1 CCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGTTGCTCAATTTGGTACGTATAT
51183 GCTG
66 GCTG
* * * *
51187 CCCATTTGTTGTGTATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTAAATTTGGTATGTATAT
1 CCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGTTGCTCAATTTGGTACGTATAT
51252 GCTG
66 GCTG
* * * *
51256 CCCATTTGTTGTATATAAGTTGTCCAAATTTTGGTGTATAAATGTT
1 CCCATTTGTTGTATATATGCTGT-TAAATTTTGGTGTAAAAATGTT
51302 TTTTAATTTG
Statistics
Matches: 169, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
69 150 0.89
70 19 0.11
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.44
Consensus pattern (69 bp):
CCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGTTGCTCAATTTGGTACGTATAT
GCTG
Found at i:51253 original size:23 final size:23
Alignment explanation
Indices: 51162--51256 Score: 75
Period size: 23 Copynumber: 4.1 Consensus size: 23
51152 GTAAAAATAT
* *
51162 TGCTCAATTTGGTACGTATATGC
1 TGCTAAATTTGGTATGTATATGC
** * *
51185 TGC-CCATTTGTTGTGTATATGC
1 TGCTAAATTTGGTATGTATATGC
* * ** *
51207 TGTTAAATTTTGGTGTAAAAATGC
1 TGCTAAA-TTTGGTATGTATATGC
51231 TGCTAAATTTGGTATGTATATGC
1 TGCTAAATTTGGTATGTATATGC
51254 TGC
1 TGC
51257 CCATTTGTTG
Statistics
Matches: 54, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
22 17 0.31
23 19 0.35
24 18 0.33
ACGTcount: A:0.23, C:0.13, G:0.22, T:0.42
Consensus pattern (23 bp):
TGCTAAATTTGGTATGTATATGC
Found at i:51272 original size:22 final size:22
Alignment explanation
Indices: 51052--51295 Score: 57
Period size: 24 Copynumber: 10.5 Consensus size: 22
51042 GTACTAACCC
* *
51052 ATTTGTTGTATATATGCTGTTAA
1 ATTTGGTGTATATATGCTG-CAA
* * * *
51075 ATTTTGGTGTAAAAATGTTGCTCA
1 A-TTTGGTGTATATATGCTGC-AA
*
51099 ATTTGGTACGTATATTATGC--C-C
1 ATTTGGT--GTATA-TATGCTGCAA
* *
51121 ATTTGTTGTATATATGCTGTTAA
1 ATTTGGTGTATATATGCTG-CAA
*
51144 ATTTTGGTGTAAAAATATTGCT-C-A
1 A-TTTGGTGT--ATATA-TGCTGCAA
*** **
51168 ATTTGGTACGTATATGCTGCCC
1 ATTTGGTGTATATATGCTGCAA
* * *
51190 ATTTGTTGTGTATATGCTGTTAA
1 ATTTGGTGTATATATGCTG-CAA
* *
51213 ATTTTGGTGTAAAAATGCTGCTAA
1 A-TTTGGTGTATATATGCTGC-AA
* * **
51237 ATTTGGTATGTATATGCTGCCC
1 ATTTGGTGTATATATGCTGCAA
* * *
51259 ATTTGTTGTATATAAGTTGTCCAA
1 ATTTGGTGTATATATGCTG--CAA
51283 ATTTTGGTGTATA
1 A-TTTGGTGTATA
51296 AATGTTTTTT
Statistics
Matches: 154, Mismatches: 46, Indels: 40
0.64 0.19 0.17
Matches are distributed among these distances:
19 5 0.03
20 9 0.06
21 4 0.03
22 36 0.23
23 30 0.19
24 45 0.29
25 14 0.09
26 7 0.05
27 4 0.03
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.45
Consensus pattern (22 bp):
ATTTGGTGTATATATGCTGCAA
Found at i:51340 original size:138 final size:137
Alignment explanation
Indices: 51062--51341 Score: 355
Period size: 138 Copynumber: 2.0 Consensus size: 137
51052 ATTTGTTGTA
* * *
51062 TATATGCTGTTAAATTTTGGTGTAAAAATGTTGCTCAATTTGGTACGTATATTATGCCCATTTGT
1 TATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTAAATTTGGTACGTATATGATGCCCATTTGT
* * * * * *
51127 TGTATATATGCTGTTAAATTTTGGTGTAAAAATATTGCTCAATTTGGTACGTATATGCTGCCCAT
66 TGTATATAAGCTGTCAAATTTTGGTGTAAAAATATTGCTCAATTTGGTACATAAATGCTGCCAAA
*
51192 TTGTTGTG
131 TTG-TATG
* *
51200 TATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTAAATTTGGTATGTATATGCTGCCCATTTGT
1 TATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTAAATTTGGTACGTATATGATGCCCATTTGT
* * * ** * *
51265 TGTATATAAGTTGTCCAAATTTTGGTGTATAAATGTTTTTTAATTTGGTATATAAATGCTGTCCA
66 TGTATATAAGCTGT-CAAATTTTGGTGTAAAAATATTGCTCAATTTGGTACATAAATGCTG-CCA
51330 AATTG-ATG
129 AATTGTATG
51338 TATA
1 TATA
51342 AGAGCTGTCC
Statistics
Matches: 121, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
138 78 0.64
139 37 0.31
140 6 0.05
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44
Consensus pattern (137 bp):
TATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTAAATTTGGTACGTATATGATGCCCATTTGT
TGTATATAAGCTGTCAAATTTTGGTGTAAAAATATTGCTCAATTTGGTACATAAATGCTGCCAAA
TTGTATG
Found at i:55497 original size:18 final size:18
Alignment explanation
Indices: 55476--55513 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
55466 AGTTCAAAAC
55476 ATATGATTCTTAACGTGT
1 ATATGATTCTTAACGTGT
55494 ATATGATTCTTAACGTGT
1 ATATGATTCTTAACGTGT
55512 AT
1 AT
55514 GTATTCTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.45
Consensus pattern (18 bp):
ATATGATTCTTAACGTGT
Found at i:57824 original size:22 final size:21
Alignment explanation
Indices: 57785--57828 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
57775 AAATTTTTAA
57785 TAAATAAAAAATATTAAATAT
1 TAAATAAAAAATATTAAATAT
57806 TAAATTAAAATAATA-TAAATAT
1 TAAA-TAAAA-AATATTAAATAT
57828 T
1 T
57829 TTTAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.19
22 13 0.62
23 4 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAATAAAAAATATTAAATAT
Found at i:63805 original size:24 final size:26
Alignment explanation
Indices: 63777--63832 Score: 89
Period size: 25 Copynumber: 2.2 Consensus size: 26
63767 TTGATTAAAA
*
63777 ATAAAAAT-AAAAATATATATTTGAT
1 ATAAAAATAAAAAATATATATTTAAT
63802 -TAAAAATAAAAAATATATATTTAAT
1 ATAAAAATAAAAAATATATATTTAAT
63827 ATAAAA
1 ATAAAA
63833 TTCGAGCCGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 7 0.25
25 16 0.57
26 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (26 bp):
ATAAAAATAAAAAATATATATTTAAT
Found at i:63813 original size:25 final size:27
Alignment explanation
Indices: 63758--63832 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 27
63748 AAATATATAT
63758 AATATATATTTGATTAAAAATAAAAATAAA
1 AATATATATTTGATTAAAAAT---AATAAA
63788 AATATATATTTGATTAAAAAT-A-AAA
1 AATATATATTTGATTAAAAATAATAAA
*
63813 AATATATATTTAATATAAAA
1 AATATATATTTGAT-TAAAA
63833 TTCGAGCCGG
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
25 16 0.37
26 6 0.14
30 21 0.49
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (27 bp):
AATATATATTTGATTAAAAATAATAAA
Found at i:70684 original size:2 final size:2
Alignment explanation
Indices: 70679--70712 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
70669 TGTTTTTTTT
70679 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
70713 AATTAGTCGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:72921 original size:21 final size:21
Alignment explanation
Indices: 72897--72936 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
72887 GAAACACAGA
*
72897 GATTCAAATGAAAGGCAGCGT
1 GATTCAAATGAAAAGCAGCGT
72918 GATTCAAATGAAAAGCAGC
1 GATTCAAATGAAAAGCAGC
72937 AACAAAATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.17
Consensus pattern (21 bp):
GATTCAAATGAAAAGCAGCGT
Found at i:74501 original size:4 final size:4
Alignment explanation
Indices: 74487--74532 Score: 83
Period size: 4 Copynumber: 11.5 Consensus size: 4
74477 TGAAAATATA
*
74487 ATAC TTAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
74533 TTACAAATCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
ATAC
Found at i:81464 original size:22 final size:22
Alignment explanation
Indices: 81430--81471 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
81420 ATTTAAACAA
* *
81430 AAAAAAATTAAATATCAAATTG
1 AAAAAAATCAAATACCAAATTG
*
81452 AAAAAACTCAAATACCAAAT
1 AAAAAAATCAAATACCAAAT
81472 CTAATATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.02, T:0.21
Consensus pattern (22 bp):
AAAAAAATCAAATACCAAATTG
Found at i:81489 original size:31 final size:32
Alignment explanation
Indices: 81454--81519 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
81444 TCAAATTGAA
* *
81454 AAAACTCAAATACCAAATCT-AATATT-AAATC
1 AAAACTAAAATACCAAAT-TAAACATTAAAATC
*
81485 AAAACTAAAATACTAAATTAAACATTAAAATC
1 AAAACTAAAATACCAAATTAAACATTAAAATC
81517 AAA
1 AAA
81520 CTCTTAAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 1 0.03
31 21 0.70
32 8 0.27
ACGTcount: A:0.61, C:0.15, G:0.00, T:0.24
Consensus pattern (32 bp):
AAAACTAAAATACCAAATTAAACATTAAAATC
Found at i:84778 original size:15 final size:15
Alignment explanation
Indices: 84758--84790 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
84748 AAAACAATAT
84758 AAACAATGAATACTA
1 AAACAATGAATACTA
*
84773 AAACAATGAATGCTA
1 AAACAATGAATACTA
84788 AAA
1 AAA
84791 TAACTCTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.61, C:0.12, G:0.09, T:0.18
Consensus pattern (15 bp):
AAACAATGAATACTA
Found at i:87766 original size:3 final size:3
Alignment explanation
Indices: 87758--87783 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
87748 GAGGAAATTA
87758 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
87784 AGGATATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:92278 original size:17 final size:17
Alignment explanation
Indices: 92248--92285 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
92238 ATTTGATTTG
92248 TTAT-TATCGCATAGAA
1 TTATATATCGCATAGAA
*
92264 TTATATATCGTATAGAA
1 TTATATATCGCATAGAA
92281 TTATA
1 TTATA
92286 CAAAGTCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (17 bp):
TTATATATCGCATAGAA
Found at i:103380 original size:16 final size:15
Alignment explanation
Indices: 103361--103391 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
103351 CTATAATATA
103361 ATATATATATATGTGC
1 ATATATAT-TATGTGC
103377 ATATATATTATGTGC
1 ATATATATTATGTGC
103392 TCTTATTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.45
Consensus pattern (15 bp):
ATATATATTATGTGC
Found at i:117406 original size:19 final size:19
Alignment explanation
Indices: 117382--117428 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
117372 AATCAGCAAT
117382 AATACATAAATGTCAAGTA
1 AATACATAAATGTCAAGTA
117401 AATACATAAATGTCAAGTA
1 AATACATAAATGTCAAGTA
*
117420 AATGCATAA
1 AATACATAA
117429 CATAGCAAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.26
Consensus pattern (19 bp):
AATACATAAATGTCAAGTA
Found at i:121108 original size:13 final size:13
Alignment explanation
Indices: 121090--121115 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
121080 TGACTTTGCA
121090 CGCTGAAATAGAC
1 CGCTGAAATAGAC
121103 CGCTGAAATAGAC
1 CGCTGAAATAGAC
121116 AATCCCAACC
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:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (13 bp):
CGCTGAAATAGAC
Found at i:124322 original size:790 final size:791
Alignment explanation
Indices: 122921--124504 Score: 3161
Period size: 790 Copynumber: 2.0 Consensus size: 791
122911 TAATTGATTT
122921 AAAATTAAATAGAATTTGTATCATTGGTTGAGTCAAGCAGAATATATGTTTTATATGTAATAAAT
1 AAAATTAAATAGAATTTGTATCATTGGTTGAGTCAAGCAGAATATATGTTTTATATGTAATAAAT
122986 TTAGTAGGAATTGATACCTCAAGTCATTCGAGCTCTCTGTAGAGTTAGGAGAAAAATTCTAAATT
66 TTAGTAGGAATTGATACCTCAAGTCATTCGAGCTCTCTGTAGAGTTAGGAGAAAAATTCTAAATT
123051 TGTCTTTTTTTAAAGGGAGGTTGACTACTTATATAGAAGTTTTTAAAGTGTTATTTGTTTAGAGT
131 TGTCTTTTTTTAAAGGGAGGTTGACTACTTATATAGAAGTTTTTAAAGTGTTATTTGTTTAGAGT
123116 TAATAGACCCTTCAATGAGTTGATATTGTGCCTGAATTTTGTCTACAAACTTTATGAAAAGCTCA
196 TAATAGACCCTTCAATGAGTTGATATTGTGCCTGAATTTTGTCTACAAACTTTATGAAAAGCTCA
123181 AGTGCATTGAAAAGATGCCCAAGAAGGTGATAGATTTACAAAGCAATAGTGTTCCATCATATCAA
261 AGTGCATTGAAAAGATGCCCAAGAAGGTGATAGATTTACAAAGCAATAGTGTTCCATCATATCAA
123246 ACCATGCATGGCACACGCCCACATACCAAGAGAACATGCACATTCGTGCTCGGTGGCTTAAACCC
326 ACCATGCATGGCACACGCCCACATACCAAGAGAACATGCACATTCGTGCTCGGTGGCTTAAACCC
123311 TTGACCTATAGCATATATGTCACAAGAGAGGATGCAAGTGTCTATATTTCTTTTTGGTAAATGAT
391 TTGACCTATAGCATATATGTCACAAGAGAGGATGCAAGTGTCTATATTTCTTTTTGGTAAATGAT
123376 TGTGCGCCACACACGATCCAATCTGATGAAATGTTCCTACTCAATGAATCTGTCGCTTATTTAGA
456 TGTGCGCCACACACGATCCAATCTGATGAAATGTTCCTACTCAATGAATCTGTCGCTTATTTAGA
123441 CAGCCATAGACACTTGGGCTCTTTACAAAGTTTAAAGTCAAAACCCTGACTTATTTTTTTGTTAA
521 CAGCCATAGACACTTGGGCTCTTTACAAAGTTTAAAGTCAAAACCCTGACTTATTTTTTTGTTAA
123506 AGGAAAGCCAATTCCTTTTAAACAAGTCTTCAAAGTGTTGTCTATTCATAACCAACAAACCCTCG
586 AGGAAAGCCAATTCCTTTTAAACAAGTCTTCAAAGTGTTGTCTATTCATAACCAACAAACCCTCG
123571 AATGGGTTGATATTGTCATTGGGTTTAGTTAGGGTTTTGAATTCTAACTTCACGGGGAACTGAGT
651 AATGGGTTGATATTGTCATTGGGTTTAGTTAGGGTTTTGAATTCTAACTTCACGGGGAACTGAGT
123636 ACCTTGATAGACTACCTAGCAATAGTACTGACTCGTTAAGGGTTCATCGACTCCATACGGATGAT
716 ACCTTGATAGACTACCTAGCAATAGTACTGACTCGTTAAGGGTTCATCGACTCCATACGGATGAT
123701 GCTTGAGGAGA
781 GCTTGAGGAGA
123712 AAAATTAAATAG-ATTTGTATCATTGGTTGAGTCAAGCAGAATATATGTTTTATATGTAATAAAT
1 AAAATTAAATAGAATTTGTATCATTGGTTGAGTCAAGCAGAATATATGTTTTATATGTAATAAAT
123776 TTAGTAGGAATTGATACCTCAAGTCATTCGAGCTCTCTGTAGAGTTAGGAGAAAAATTCTAAATT
66 TTAGTAGGAATTGATACCTCAAGTCATTCGAGCTCTCTGTAGAGTTAGGAGAAAAATTCTAAATT
123841 TGTCTTTTTTTAAAGGGAGGTTGACTACTTATATAGAAGTTTTTAAAGTGTTATTTGTTTAGAGT
131 TGTCTTTTTTTAAAGGGAGGTTGACTACTTATATAGAAGTTTTTAAAGTGTTATTTGTTTAGAGT
123906 TAATAGACCCTTCAATGAGTTGATATTGTGCCTGAATTTTGTCTACAAACTTTATGAAAAGCTCA
196 TAATAGACCCTTCAATGAGTTGATATTGTGCCTGAATTTTGTCTACAAACTTTATGAAAAGCTCA
123971 AGTGCATTGAAAAGATGCCCAAGAAGGTGATAGATTTACAAAGCAATAGTGTTCCATCATATCAA
261 AGTGCATTGAAAAGATGCCCAAGAAGGTGATAGATTTACAAAGCAATAGTGTTCCATCATATCAA
124036 ACCATGCATGGCACACGCCCACATACCAAGAGAACATGCACATTCGTGCTCGGTGGCTTAAACCC
326 ACCATGCATGGCACACGCCCACATACCAAGAGAACATGCACATTCGTGCTCGGTGGCTTAAACCC
124101 TTGACCTATAGCATATATGTCACAAGAGAGGATGCAAGTGTCTATATTTCTTTTTGGTAAATGAT
391 TTGACCTATAGCATATATGTCACAAGAGAGGATGCAAGTGTCTATATTTCTTTTTGGTAAATGAT
124166 TGTGCGCCACACACGATCCAATCTGATGAAATGTTCCTACTCAATGAATCTGTCGCTTATTTAGA
456 TGTGCGCCACACACGATCCAATCTGATGAAATGTTCCTACTCAATGAATCTGTCGCTTATTTAGA
124231 CAGCCATAGACACTTGGGCTCTTTACAAAGTTTAAAGTCAAAACCCTGACTTATTTTTTTGTTAA
521 CAGCCATAGACACTTGGGCTCTTTACAAAGTTTAAAGTCAAAACCCTGACTTATTTTTTTGTTAA
124296 AGGAAAGCCAATTCCTTTTAAACAAGTCTTCAAAGTGTTGTCTATTCATAACCAACAAACCCTCG
586 AGGAAAGCCAATTCCTTTTAAACAAGTCTTCAAAGTGTTGTCTATTCATAACCAACAAACCCTCG
124361 AATGGGTTGATATTGTCATTGGGTTTAGTTAGGGTTTTGAATTCTAACTTCACGGGGAACTGAGT
651 AATGGGTTGATATTGTCATTGGGTTTAGTTAGGGTTTTGAATTCTAACTTCACGGGGAACTGAGT
124426 ACCTTGATAGACTACCTAGCAATAGTACTGACTCGTTAAGGGTTCATCGACTCCATACGGATGAT
716 ACCTTGATAGACTACCTAGCAATAGTACTGACTCGTTAAGGGTTCATCGACTCCATACGGATGAT
124491 GCTTGAGGAGA
781 GCTTGAGGAGA
124502 AAA
1 AAA
124505 TAATCCAACT
Statistics
Matches: 793, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
790 781 0.98
791 12 0.02
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (791 bp):
AAAATTAAATAGAATTTGTATCATTGGTTGAGTCAAGCAGAATATATGTTTTATATGTAATAAAT
TTAGTAGGAATTGATACCTCAAGTCATTCGAGCTCTCTGTAGAGTTAGGAGAAAAATTCTAAATT
TGTCTTTTTTTAAAGGGAGGTTGACTACTTATATAGAAGTTTTTAAAGTGTTATTTGTTTAGAGT
TAATAGACCCTTCAATGAGTTGATATTGTGCCTGAATTTTGTCTACAAACTTTATGAAAAGCTCA
AGTGCATTGAAAAGATGCCCAAGAAGGTGATAGATTTACAAAGCAATAGTGTTCCATCATATCAA
ACCATGCATGGCACACGCCCACATACCAAGAGAACATGCACATTCGTGCTCGGTGGCTTAAACCC
TTGACCTATAGCATATATGTCACAAGAGAGGATGCAAGTGTCTATATTTCTTTTTGGTAAATGAT
TGTGCGCCACACACGATCCAATCTGATGAAATGTTCCTACTCAATGAATCTGTCGCTTATTTAGA
CAGCCATAGACACTTGGGCTCTTTACAAAGTTTAAAGTCAAAACCCTGACTTATTTTTTTGTTAA
AGGAAAGCCAATTCCTTTTAAACAAGTCTTCAAAGTGTTGTCTATTCATAACCAACAAACCCTCG
AATGGGTTGATATTGTCATTGGGTTTAGTTAGGGTTTTGAATTCTAACTTCACGGGGAACTGAGT
ACCTTGATAGACTACCTAGCAATAGTACTGACTCGTTAAGGGTTCATCGACTCCATACGGATGAT
GCTTGAGGAGA
Found at i:128467 original size:18 final size:19
Alignment explanation
Indices: 128428--128467 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
128418 TAAATGGTAG
128428 CAAAACAGTGAGAAAACAA
1 CAAAACAGTGAGAAAACAA
128447 CAAAACAGT-A-AAAATCAA
1 CAAAACAGTGAGAAAA-CAA
128465 CAA
1 CAA
128468 GAAAACAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 7 0.35
19 9 0.45
ACGTcount: A:0.65, C:0.17, G:0.10, T:0.07
Consensus pattern (19 bp):
CAAAACAGTGAGAAAACAA
Found at i:131663 original size:351 final size:350
Alignment explanation
Indices: 131016--131695 Score: 1191
Period size: 351 Copynumber: 1.9 Consensus size: 350
131006 TTTATATGGG
131016 TTTCATTTTTTCTATAATTTATTTTTGAGAAATATGTAAAATGTGGCTTCAAATTTGAAGTTTGG
1 TTTCATTTTTTCTATAATTTATTTTTGAGAAATATGTAAAATGTGGCTTCAAATTTGAAGTTTGG
*
131081 GGTAGAATGTATCTTTTTTTAGAGCTACAAAGTTACGCATTTTGGGTTTTTGGTAAGGTAAAAGG
66 GGTAGAATGTATCTTTTTATAGAGCTACAAAGTTACGCATTTTGGGTTTTTGGTAAGGTAAAAGG
131146 ATGGAAAGTTTTGATGGGTTCATTTCATATTAATTTGGGTCTTTGAGGAATTTCTTCATACATTT
131 ATGGAAAGTTTTGATGGGTTCATTTCATATTAATTTGGGTCTTTGAGGAATTTCTTCATACATTT
*
131211 ATCGAGCAACACTTTTTAACCACAGTTTGACCGCTTTAGTTCATCTCCTTGACTTCAATTTTGTG
196 ATCGAGCAACACTTTTTAACCACAGTTTGACCGCTTTAGTTCATCTCCTTGACTTCAAATTTGTG
* *
131276 AATTAAATATATTCTTAAAGCAGAATGTGTGTTATTATGTATGTTTTGAGTAAGTCCCTGATTCA
261 AATTAAATATATTCTTAAAGCACAATGTGAGTTATTATGTATGTTTTGAGTAAGTCCCTGATTCA
131341 TTTTGCCTGTATGTTTAAGGTTTCT
326 TTTTGCCTGTATGTTTAAGGTTTCT
* * *
131366 TTTCATTTTTTCTGTAATTTATTTTTGGGAAATATGTAAAATGTGGCTTCATATTTGAAGTTTGG
1 TTTCATTTTTTCTATAATTTATTTTTGAGAAATATGTAAAATGTGGCTTCAAATTTGAAGTTTGG
* *
131431 GGTGGAATGTATCTTTTTCATAGAGCTACAAAGTTAGGCATTTTGGGTTTTTGGTAAGGT-AAAG
66 GGTAGAATGTATCTTTTT-ATAGAGCTACAAAGTTACGCATTTTGGGTTTTTGGTAAGGTAAAAG
131495 AGATGGAAAGTTTTGATGGGTTCATTTCATATTAATTTGGGTCTTTGAGGAATTTCTTCATACAT
130 -GATGGAAAGTTTTGATGGGTTCATTTCATATTAATTTGGGTCTTTGAGGAATTTCTTCATACAT
* * * * * *
131560 TTATCGTGCAACATTTTTTTACCACAGTTTGACTGCTTTAGTTCATTTTCTTGACTTCAAATTTG
194 TTATCGAGCAACACTTTTTAACCACAGTTTGACCGCTTTAGTTCATCTCCTTGACTTCAAATTTG
*
131625 TGAATTAAATATGTTCTTAAAGCACAATGTGAGTTATTATGTATGTTTTGAGTAAGTCCCTGATT
259 TGAATTAAATATATTCTTAAAGCACAATGTGAGTTATTATGTATGTTTTGAGTAAGTCCCTGATT
131690 CATTTT
324 CATTTT
131696 TGCTTTCTGC
Statistics
Matches: 312, Mismatches: 16, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
350 83 0.27
351 229 0.73
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.44
Consensus pattern (350 bp):
TTTCATTTTTTCTATAATTTATTTTTGAGAAATATGTAAAATGTGGCTTCAAATTTGAAGTTTGG
GGTAGAATGTATCTTTTTATAGAGCTACAAAGTTACGCATTTTGGGTTTTTGGTAAGGTAAAAGG
ATGGAAAGTTTTGATGGGTTCATTTCATATTAATTTGGGTCTTTGAGGAATTTCTTCATACATTT
ATCGAGCAACACTTTTTAACCACAGTTTGACCGCTTTAGTTCATCTCCTTGACTTCAAATTTGTG
AATTAAATATATTCTTAAAGCACAATGTGAGTTATTATGTATGTTTTGAGTAAGTCCCTGATTCA
TTTTGCCTGTATGTTTAAGGTTTCT
Found at i:143619 original size:71 final size:71
Alignment explanation
Indices: 143503--143644 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
143493 ACCAATTTGA
143503 CAAAACATGTAAACATCGCAAACTAAATTTATTGTTATACCAATTAAAATTATGTACTGAATATA
1 CAAAACATGTAAACATCGCAAACTAAATTTATTGTTATACCAATTAAAATTATGTACTGAATATA
143568 TTAGTG
66 TTAGTG
143574 CAAAACATGTAAACATCGCAAACTAAATTTATTGTTATACCAATTAAAATTATGTACTGAATATA
1 CAAAACATGTAAACATCGCAAACTAAATTTATTGTTATACCAATTAAAATTATGTACTGAATATA
143639 TTAGTG
66 TTAGTG
143645 TCGCGGTTAA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.34
Consensus pattern (71 bp):
CAAAACATGTAAACATCGCAAACTAAATTTATTGTTATACCAATTAAAATTATGTACTGAATATA
TTAGTG
Found at i:144897 original size:38 final size:38
Alignment explanation
Indices: 144846--144921 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
144836 CGTTAGATTA
144846 ACTTGGATCTAAGGCATGTTTTCCTACTCGTTGTTGGG
1 ACTTGGATCTAAGGCATGTTTTCCTACTCGTTGTTGGG
144884 ACTTGGATCTAAGGCATGTTTTCCTACTCGTTGTTGGG
1 ACTTGGATCTAAGGCATGTTTTCCTACTCGTTGTTGGG
144922 TATTGATCCG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.16, C:0.18, G:0.26, T:0.39
Consensus pattern (38 bp):
ACTTGGATCTAAGGCATGTTTTCCTACTCGTTGTTGGG
Found at i:150931 original size:43 final size:43
Alignment explanation
Indices: 150866--150952 Score: 133
Period size: 43 Copynumber: 2.0 Consensus size: 43
150856 TCATCACCTA
*
150866 TTTGGTTTAAAGAATTTGTTTTTAAT-GTTCTTTTTTATAATTTT
1 TTTGGTTTAAAGAATTTATTTTTAATGGTTC-TTTTTAT-ATTTT
150910 TTTGG-TTAAAGAATTTATTTTTAATGGTTCTTTTTATATTTT
1 TTTGGTTTAAAGAATTTATTTTTAATGGTTCTTTTTATATTTT
150952 T
1 T
150953 AGAATTTATA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
42 6 0.15
43 26 0.63
44 9 0.22
ACGTcount: A:0.23, C:0.02, G:0.11, T:0.63
Consensus pattern (43 bp):
TTTGGTTTAAAGAATTTATTTTTAATGGTTCTTTTTATATTTT
Found at i:155858 original size:20 final size:20
Alignment explanation
Indices: 155835--156013 Score: 55
Period size: 20 Copynumber: 8.9 Consensus size: 20
155825 TAAAGTATTT
155835 AAAAATATATAAAAATTGTA
1 AAAAATATATAAAAATTGTA
* *
155855 AAAAA-A-ATAATTAAATTATT
1 AAAAATATATAA--AAATTGTA
* * * *
155875 AAAAA-AT-CAAATACTGTT
1 AAAAATATATAAAAATTGTA
* * * *
155893 AAAAAGATTTTAAATTTGTA
1 AAAAATATATAAAAATTGTA
* *
155913 AAAAATCTTATTAAAAATTATA
1 AAAAAT-ATA-TAAAAATTGTA
* * **
155935 AAACATTATTTAAATTTTGTA
1 AAA-AATATATAAAAATTGTA
* *
155956 AAAATTAT-TTAAAATTGT-
1 AAAAATATATAAAAATTGTA
* * *
155974 AAATATTTATTAAAAGTTGTA
1 AAAAATATA-TAAAAATTGTA
* *
155995 AAAATTATTTAAAAATTGT
1 AAAAATATATAAAAATTGT
156014 GAACCAATAG
Statistics
Matches: 111, Mismatches: 37, Indels: 22
0.65 0.22 0.13
Matches are distributed among these distances:
18 19 0.17
19 10 0.09
20 51 0.46
21 17 0.15
22 12 0.11
23 2 0.02
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (20 bp):
AAAAATATATAAAAATTGTA
Found at i:155984 original size:40 final size:39
Alignment explanation
Indices: 155901--156013 Score: 120
Period size: 40 Copynumber: 2.8 Consensus size: 39
155891 TTAAAAAGAT
* *
155901 TTTAAATTTGTAAAAAATCTTATTAAAAATTATAAAACATTA
1 TTTAAATTTGT-AAAAA--TTATTTAAAATTGTAAAACATTA
*
155943 TTTAAATTTTGTAAAAATTATTTAAAATTGTAAATA-TTTA
1 TTTAAA-TTTGTAAAAATTATTTAAAATTGTAAA-ACATTA
* *
155983 TTAAAAGTTGTAAAAATTATTTAAAAATTGT
1 TTTAAATTTGTAAAAATTATTT-AAAATTGT
156014 GAACCAATAG
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
39 15 0.24
40 31 0.49
41 1 0.02
42 11 0.17
43 5 0.08
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (39 bp):
TTTAAATTTGTAAAAATTATTTAAAATTGTAAAACATTA
Found at i:156233 original size:10 final size:10
Alignment explanation
Indices: 156218--156288 Score: 54
Period size: 10 Copynumber: 6.9 Consensus size: 10
156208 GATTATTTCC
156218 AATTTTTAAT
1 AATTTTTAAT
*
156228 AATTTTTAACA
1 AATTTTTAA-T
** *
156239 AAAATTAAAT
1 AATTTTTAAT
*
156249 AATGTTTAAT
1 AATTTTTAAT
*
156259 GATTTTTAAT
1 AATTTTTAAT
156269 AAATTTTTTAA-
1 -AA-TTTTTAAT
156280 AATTTTTAA
1 AATTTTTAA
156289 ATATTTTAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
9 7 0.15
10 26 0.55
11 7 0.15
12 7 0.15
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (10 bp):
AATTTTTAAT
Found at i:156294 original size:10 final size:10
Alignment explanation
Indices: 156268--156397 Score: 51
Period size: 9 Copynumber: 13.1 Consensus size: 10
156258 TGATTTTTAA
156268 TAAAT-TTTT
1 TAAATATTTT
156277 TAAA-ATTTT
1 TAAATATTTT
156286 TAAATATTTT
1 TAAATATTTT
*
156296 AAACAATATTTT
1 -TA-AATATTTT
*
156308 ATAAATTATTTA
1 -TAAA-TATTTT
*
156320 TAAAT-TTTC
1 TAAATATTTT
*** *
156329 TCCTTTTTTT
1 TAAATATTTT
*
156339 TAGA-ATTTT
1 TAAATATTTT
156348 TAAATATTTT
1 TAAATATTTT
*
156358 T-AATGTTTT
1 TAAATATTTT
*
156367 CT-AATA-ATT
1 -TAAATATTTT
156376 TAAATATTGTT
1 TAAATATT-TT
156387 TACAAT-TTTT
1 TA-AATATTTT
156397 T
1 T
156398 TGATTTGGTC
Statistics
Matches: 92, Mismatches: 17, Indels: 23
0.70 0.13 0.17
Matches are distributed among these distances:
8 1 0.01
9 37 0.40
10 23 0.25
11 13 0.14
12 18 0.20
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (10 bp):
TAAATATTTT
Found at i:175389 original size:27 final size:27
Alignment explanation
Indices: 175359--175413 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
175349 CCATATTATT
175359 TTTTATTTTTT-TATAATAAAAATTTTA
1 TTTTATTTTTTAT-TAATAAAAATTTTA
* *
175386 TTTTATTTTTTATTTATTAAAATTTTA
1 TTTTATTTTTTATTAATAAAAATTTTA
175413 T
1 T
175414 ATTCATGCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTTATTTTTTATTAATAAAAATTTTA
Found at i:192494 original size:32 final size:32
Alignment explanation
Indices: 192453--192514 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
192443 CACCACTATT
192453 ATTTTTAATCTTACTAAAGATAAATGCACTGC
1 ATTTTTAATCTTACTAAAGATAAATGCACTGC
*
192485 ATTTTTAATCTTACTGAAGATAAATGCACT
1 ATTTTTAATCTTACTAAAGATAAATGCACT
192515 ACACATCCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.39
Consensus pattern (32 bp):
ATTTTTAATCTTACTAAAGATAAATGCACTGC
Found at i:198304 original size:25 final size:25
Alignment explanation
Indices: 198270--198319 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
198260 TCAACTATTC
198270 GTTACTACAAATTTGAATCTTGATA
1 GTTACTACAAATTTGAATCTTGATA
198295 GTTACTACAAATTTGAATCTTGATA
1 GTTACTACAAATTTGAATCTTGATA
198320 TTTAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (25 bp):
GTTACTACAAATTTGAATCTTGATA
Found at i:199889 original size:31 final size:29
Alignment explanation
Indices: 199816--199891 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 29
199806 CTGAAATTTG
* *
199816 AAATTTAAAAAGTAGAGAGACTAAATTCCT
1 AAATTT-AAAAGTACAGAGACCAAATTCCT
** *
199846 AAAAATACAAGTACAGAGACCAAATTCCT
1 AAATTTAAAAGTACAGAGACCAAATTCCT
199875 AATATTTGAAAAGTACA
1 AA-ATTT-AAAAGTACA
199892 AATACTATAG
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 22 0.61
30 6 0.17
31 8 0.22
ACGTcount: A:0.51, C:0.13, G:0.12, T:0.24
Consensus pattern (29 bp):
AAATTTAAAAGTACAGAGACCAAATTCCT
Found at i:200228 original size:6 final size:6
Alignment explanation
Indices: 200216--200253 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
200206 AAATAATAAT
* *
200216 TTTATA ATTATA ATTATA TTTATA TTTATA TTTATA TT
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TT
200254 AAATCACTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
TTTATA
Found at i:201529 original size:24 final size:24
Alignment explanation
Indices: 201497--201546 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
201487 ATTAGAAAGA
*
201497 GAGAGAACTCTAGAAGGCAATGAT
1 GAGAGAACTCTAGAAGGCAACGAT
201521 GAGAGAACTCTAGAAGGCAACGAT
1 GAGAGAACTCTAGAAGGCAACGAT
201545 GA
1 GA
201547 TATTAGAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.42, C:0.14, G:0.30, T:0.14
Consensus pattern (24 bp):
GAGAGAACTCTAGAAGGCAACGAT
Found at i:201604 original size:31 final size:33
Alignment explanation
Indices: 201569--201633 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
201559 TTTGATGATA
*
201569 TTTTATAAATA-TTTAATTAGATA-ATTATTAT
1 TTTTATAAATATTTTAATGAGATATATTATTAT
* *
201600 TTTTATTAATATTTTAATGAGATATTTTATTAT
1 TTTTATAAATATTTTAATGAGATATATTATTAT
201633 T
1 T
201634 ATTTTATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 10 0.34
32 11 0.38
33 8 0.28
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (33 bp):
TTTTATAAATATTTTAATGAGATATATTATTAT
Found at i:201614 original size:11 final size:11
Alignment explanation
Indices: 201566--201641 Score: 59
Period size: 11 Copynumber: 6.9 Consensus size: 11
201556 TATTTTGATG
*
201566 ATATTTTATAA
1 ATATTTTATTA
*
201577 ATATTTAATTA
1 ATATTTTATTA
*
201588 GATA-ATTATT-
1 -ATATTTTATTA
201598 AT-TTTTATTA
1 ATATTTTATTA
*
201608 ATATTTTAATGA
1 ATATTTT-ATTA
201620 GATATTTTATTA
1 -ATATTTTATTA
*
201632 TTATTTTATT
1 ATATTTTATT
201642 TAGTATAAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
9 7 0.14
10 2 0.04
11 26 0.51
12 9 0.18
13 7 0.14
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (11 bp):
ATATTTTATTA
Found at i:201623 original size:32 final size:29
Alignment explanation
Indices: 201569--201636 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 29
201559 TTTGATGATA
* *
201569 TTTTATAAATATTTAATTAGATAATTATTAT
1 TTTTATTAATATTTAATGAGAT-ATT-TTAT
201600 TTTTATTAATATTTTAATGAGATATTTTAT
1 TTTTATTAATA-TTTAATGAGATATTTTAT
*
201630 TATTATT
1 TTTTATT
201637 TTATTTAGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 10 0.30
31 13 0.39
32 10 0.30
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (29 bp):
TTTTATTAATATTTAATGAGATATTTTAT
Found at i:203683 original size:33 final size:32
Alignment explanation
Indices: 203612--203687 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 32
203602 GTGTTTATAT
* * * *
203612 GTAAGACCATAGATGGGTTATGGCATTCTGAT
1 GTAAGACCATAGATGAGTTATGGCACTATGAC
203644 GATAAGACCATA-ACTGAGTTATGGCACTATGAAC
1 G-TAAGACCATAGA-TGAGTTATGGCACTATG-AC
203678 GTAAGACCAT
1 GTAAGACCAT
203688 GATTGGATCA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
32 2 0.05
33 33 0.89
34 2 0.05
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (32 bp):
GTAAGACCATAGATGAGTTATGGCACTATGAC
Found at i:211443 original size:3 final size:3
Alignment explanation
Indices: 211435--211494 Score: 102
Period size: 3 Copynumber: 19.7 Consensus size: 3
211425 CTATAATTTG
*
211435 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT TAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
211481 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
211495 AGAACCTTGA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
3 51 0.94
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:214716 original size:18 final size:18
Alignment explanation
Indices: 214679--214717 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
214669 ATCTAAATAT
*
214679 AATTAATTAATTAATTAA
1 AATTAATTAATTAATAAA
*
214697 AATTAATTAATTGATAAA
1 AATTAATTAATTAATAAA
214715 AAT
1 AAT
214718 AGTAGCAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
AATTAATTAATTAATAAA
Found at i:222416 original size:3 final size:3
Alignment explanation
Indices: 222410--222452 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
222400 CGTCGTCGTC
222410 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
222453 CTTAGGCTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:224031 original size:4 final size:4
Alignment explanation
Indices: 224022--224048 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
224012 ATTAGACCTA
224022 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
224049 GAATAGAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:226817 original size:18 final size:18
Alignment explanation
Indices: 226783--226817 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
226773 TTTAAAGTAT
**
226783 TTTTAAAATACTTTTTTA
1 TTTTAAAATACAATTTTA
226801 TTTTAAAATACAATTTT
1 TTTTAAAATACAATTTT
226818 GGTGTTTATT
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:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTAAAATACAATTTTA
Found at i:227842 original size:15 final size:16
Alignment explanation
Indices: 227817--227847 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
227807 TAAATTTTTA
227817 AAAATATTCAAAAAAT
1 AAAATATTCAAAAAAT
227833 AAAA-ATTCAAAAAAT
1 AAAATATTCAAAAAAT
227848 TAGCATAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATATTCAAAAAAT
Found at i:230075 original size:3 final size:3
Alignment explanation
Indices: 230059--230106 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
230049 AATTTATATG
*
230059 TTA TTA TT- TGA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
230106 T
1 T
230107 AAAAACTTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 1 0.02
3 41 0.98
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:232649 original size:34 final size:35
Alignment explanation
Indices: 232605--232671 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
232595 CAGTAAAATA
*
232605 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
232639 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
232672 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:232786 original size:20 final size:19
Alignment explanation
Indices: 232761--232808 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
232751 CATATATTGA
232761 TATATATATTAATAATTTT
1 TATATATATTAATAATTTT
*
232780 T-TATATATTAAATTATTTT
1 TATATATATT-AATAATTTT
*
232799 TACATATATT
1 TATATATATT
232809 GCAATGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 8 0.32
19 10 0.40
20 7 0.28
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATATATTAATAATTTT
Found at i:232793 original size:16 final size:19
Alignment explanation
Indices: 232763--232798 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
232753 TATATTGATA
232763 TATATATTAATAATT-TTT
1 TATATATTAATAATTATTT
232781 TATATATT-A-AATTATTT
1 TATATATTAATAATTATTT
232798 T
1 T
232799 TACATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.24
17 5 0.29
18 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TATATATTAATAATTATTT
Found at i:233314 original size:19 final size:19
Alignment explanation
Indices: 233291--233333 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
233281 TTAATGGTTA
* *
233291 AATTTATGTTTATATTTTT
1 AATTTAGGTTAATATTTTT
*
233310 TATTTAGGTTAATATTTTT
1 AATTTAGGTTAATATTTTT
233329 AATTT
1 AATTT
233334 GAATTTTGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (19 bp):
AATTTAGGTTAATATTTTT
Found at i:248336 original size:58 final size:58
Alignment explanation
Indices: 248201--248316 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
248191 ACATCATCAC
248201 TGCCACATAACAAAACGAAATTGGGCTTAGATGACAGGCCGTTATTTGGTCGTGCAAT
1 TGCCACATAACAAAACGAAATTGGGCTTAGATGACAGGCCGTTATTTGGTCGTGCAAT
248259 TGCCACATAACAAAACGAAATTGGGCTTAGATGACAGGCCGTTATTTGGTCGTGCAAT
1 TGCCACATAACAAAACGAAATTGGGCTTAGATGACAGGCCGTTATTTGGTCGTGCAAT
248317 GTCAGTAAAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (58 bp):
TGCCACATAACAAAACGAAATTGGGCTTAGATGACAGGCCGTTATTTGGTCGTGCAAT
Found at i:255828 original size:19 final size:18
Alignment explanation
Indices: 255795--255831 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
255785 TGTTCATATA
255795 ATAAAAATTAAAATTAAT
1 ATAAAAATTAAAATTAAT
*
255813 ATAAAAACTTAGAATTAAT
1 ATAAAAA-TTAAAATTAAT
255832 TATATATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (18 bp):
ATAAAAATTAAAATTAAT
Found at i:264365 original size:23 final size:23
Alignment explanation
Indices: 264334--264387 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
264324 CTCCTATATA
*
264334 TGCTCACTGAGTTCCTAATAATT
1 TGCTTACTGAGTTCCTAATAATT
* *
264357 TGCTTACTGATTTCGTAATAATT
1 TGCTTACTGAGTTCCTAATAATT
*
264380 TACTTACT
1 TGCTTACT
264388 CTGCTCGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.44
Consensus pattern (23 bp):
TGCTTACTGAGTTCCTAATAATT
Found at i:264521 original size:2 final size:2
Alignment explanation
Indices: 264514--264544 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
264504 TAAATCGAAA
264514 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
264545 AGATTTATTT
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:266360 original size:27 final size:29
Alignment explanation
Indices: 266326--266384 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
266316 AACTCTTTAT
*
266326 AAAAAAT-AATAATATTAATTTGA-ATTA
1 AAAAAATAAATAATATTAAATTGAGATTA
* *
266353 AAAAAATAAATTATTTTAAATTGAGATTA
1 AAAAAATAAATAATATTAAATTGAGATTA
266382 AAA
1 AAA
266385 TATCAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 7 0.26
28 13 0.48
29 7 0.26
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (29 bp):
AAAAAATAAATAATATTAAATTGAGATTA
Found at i:266374 original size:23 final size:25
Alignment explanation
Indices: 266327--266374 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
266317 ACTCTTTATA
*
266327 AAAAATAATAATATTAATTTGAATT
1 AAAAATAATAATATTAATTTAAATT
*
266352 AAAAA-AATAA-ATTATTTTAAATT
1 AAAAATAATAATATTAATTTAAATT
266375 GAGATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 11 0.52
24 5 0.24
25 5 0.24
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
AAAAATAATAATATTAATTTAAATT
Found at i:272923 original size:21 final size:21
Alignment explanation
Indices: 272869--272925 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 21
272859 TAGGTGCAAA
*
272869 ATTAATATAATT-TTATATTT
1 ATTAATATAATTGTTAAATTT
* *
272889 TTTTATAATTAATTGTTAAATTT
1 ATTAAT-A-TAATTGTTAAATTT
272912 ATTAATATAATTGT
1 ATTAATATAATTGT
272926 ATTTATTATG
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
20 4 0.14
21 8 0.28
22 6 0.21
23 11 0.38
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (21 bp):
ATTAATATAATTGTTAAATTT
Found at i:278039 original size:26 final size:26
Alignment explanation
Indices: 277984--278040 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
277974 TATACGATAA
* * * *
277984 AAGTAAATTTAATTTATTTTTATTTC
1 AAGTAAATATAATTAATTTATATGTC
278010 AAGTAAATATAATTAATTGTATATGT-
1 AAGTAAATATAATTAATT-TATATGTC
278036 AAGTA
1 AAGTA
278041 GGCAAAAGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (26 bp):
AAGTAAATATAATTAATTTATATGTC
Found at i:284694 original size:27 final size:28
Alignment explanation
Indices: 284638--284699 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
284628 AATTCTAAAC
* * * *
284638 TTTGGGTTCGATGTTCAAGGTTTAATG-
1 TTTGGGTTCAATATTCAAGGTTCAAAGT
*
284665 TTTGGGTTCAATATTCAATGTTCAAAGT
1 TTTGGGTTCAATATTCAAGGTTCAAAGT
284693 TTTGGGT
1 TTTGGGT
284700 ATGGGGTTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.21, C:0.08, G:0.26, T:0.45
Consensus pattern (28 bp):
TTTGGGTTCAATATTCAAGGTTCAAAGT
Found at i:287714 original size:6 final size:6
Alignment explanation
Indices: 287703--287729 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
287693 TTGTAAGGAT
287703 GGGAAG GGGAAG GGGAAG GGGAAG GGG
1 GGGAAG GGGAAG GGGAAG GGGAAG GGG
287730 TTGTTCGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.70, T:0.00
Consensus pattern (6 bp):
GGGAAG
Found at i:287773 original size:110 final size:110
Alignment explanation
Indices: 287650--287870 Score: 392
Period size: 110 Copynumber: 2.0 Consensus size: 110
287640 TAAGAACTTT
* *
287650 TAGTGGCTTTTTTTTTTTTTTTTTTGGGGGGGGG-GG-AGGGCATTTGTAAGGATGGGAAGGGGA
1 TAGTGGC-TTTTTTTTTTTTTTTTGGGGGGGGGGAGGCAGGGC-TTTGTAAGGAGGGGAAGGGGA
287713 AGGGGAAGGGGAAGGGGTTGTTCGAGATTTGAACCCTACACCTGATG
64 AGGGGAAGGGGAAGGGGTTGTTCGAGATTTGAACCCTACACCTGATG
287760 TAGTGGCTTTTTTTTTTTTTTTTGGGGGGGGGGAGGCAGGGCTTTGTAAGGAGGGGAAGGGGAAG
1 TAGTGGCTTTTTTTTTTTTTTTTGGGGGGGGGGAGGCAGGGCTTTGTAAGGAGGGGAAGGGGAAG
287825 GGGAAGGGGAAGGGGTTGTTCGAGATTTGAACCCTACACCTGATG
66 GGGAAGGGGAAGGGGTTGTTCGAGATTTGAACCCTACACCTGATG
287870 T
1 T
287871 CAATCGGGAC
Statistics
Matches: 107, Mismatches: 2, Indels: 4
0.95 0.02 0.04
Matches are distributed among these distances:
109 25 0.23
110 77 0.72
111 5 0.05
ACGTcount: A:0.19, C:0.09, G:0.42, T:0.31
Consensus pattern (110 bp):
TAGTGGCTTTTTTTTTTTTTTTTGGGGGGGGGGAGGCAGGGCTTTGTAAGGAGGGGAAGGGGAAG
GGGAAGGGGAAGGGGTTGTTCGAGATTTGAACCCTACACCTGATG
Found at i:287822 original size:6 final size:6
Alignment explanation
Indices: 287811--287839 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
287801 CTTTGTAAGG
287811 AGGGGA AGGGGA AGGGGA AGGGGA AGGGG
1 AGGGGA AGGGGA AGGGGA AGGGGA AGGGG
287840 TTGTTCGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (6 bp):
AGGGGA
Found at i:288821 original size:11 final size:11
Alignment explanation
Indices: 288805--288854 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
288795 TTGCTTCTTC
288805 TTCTTCTTTCT
1 TTCTTCTTTCT
288816 TTCTTCTTTCT
1 TTCTTCTTTCT
*
288827 TTCTTCTCTCT
1 TTCTTCTTTCT
* *
288838 CTC-TCTCTC-
1 TTCTTCTTTCT
288847 TTCTTCTT
1 TTCTTCTT
288855 CCCCCACCCC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
9 2 0.06
10 9 0.26
11 23 0.68
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (11 bp):
TTCTTCTTTCT
Found at i:288917 original size:1 final size:1
Alignment explanation
Indices: 288874--288899 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
288864 CACCCCCCCC
288874 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
288900 CATTTTTGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:294691 original size:43 final size:43
Alignment explanation
Indices: 294630--294800 Score: 342
Period size: 43 Copynumber: 4.0 Consensus size: 43
294620 TCATTACAAT
294630 GGTTTGAAAAAGAAAGAATTGAAGATATTTTTATTAGTTCAAC
1 GGTTTGAAAAAGAAAGAATTGAAGATATTTTTATTAGTTCAAC
294673 GGTTTGAAAAAGAAAGAATTGAAGATATTTTTATTAGTTCAAC
1 GGTTTGAAAAAGAAAGAATTGAAGATATTTTTATTAGTTCAAC
294716 GGTTTGAAAAAGAAAGAATTGAAGATATTTTTATTAGTTCAAC
1 GGTTTGAAAAAGAAAGAATTGAAGATATTTTTATTAGTTCAAC
294759 GGTTTGAAAAAGAAAGAATTGAAGATATTTTTATTAGTTCAA
1 GGTTTGAAAAAGAAAGAATTGAAGATATTTTTATTAGTTCAA
294801 AAATATCATG
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 128 1.00
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (43 bp):
GGTTTGAAAAAGAAAGAATTGAAGATATTTTTATTAGTTCAAC
Found at i:302245 original size:2 final size:2
Alignment explanation
Indices: 302238--302277 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
302228 AACTCAAGCT
302238 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
302278 AATTAATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:305617 original size:9 final size:9
Alignment explanation
Indices: 305603--305635 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
305593 TGTGAAAGAT
305603 AATATTAAA
1 AATATTAAA
305612 AATATTAAA
1 AATATTAAA
305621 AATATTAAA
1 AATATTAAA
305630 AATATT
1 AATATT
305636 CAGATCAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
AATATTAAA
Found at i:308855 original size:44 final size:45
Alignment explanation
Indices: 308795--308886 Score: 116
Period size: 44 Copynumber: 2.0 Consensus size: 45
308785 TATTACAACA
* *
308795 TCTATTCCATTTAACCAAAC-ATAAGAATT-TTATTACAGCTCTAT
1 TCTATTCCATTCAACCAAACAAT-AGAATTATGATTACAGCTCTAT
* *
308839 TCTATTTCATTCAACCAAACAATTGAATTACTGATTACAGCTCTAT
1 TCTATTCCATTCAACCAAACAATAGAATTA-TGATTACAGCTCTAT
308885 TC
1 TC
308887 AATTAGAACC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
44 23 0.56
45 2 0.05
46 16 0.39
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.38
Consensus pattern (45 bp):
TCTATTCCATTCAACCAAACAATAGAATTATGATTACAGCTCTAT
Found at i:318928 original size:11 final size:11
Alignment explanation
Indices: 318912--318945 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
318902 TGGGTTCTTT
318912 TACAAAAATAA
1 TACAAAAATAA
318923 TACAAAAA-AA
1 TACAAAAATAA
*
318933 TACTAAAATAA
1 TACAAAAATAA
318944 TA
1 TA
318946 TAATTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.21
Consensus pattern (11 bp):
TACAAAAATAA
Found at i:319214 original size:155 final size:155
Alignment explanation
Indices: 319047--319399 Score: 688
Period size: 155 Copynumber: 2.3 Consensus size: 155
319037 ATTTTGACCC
*
319047 TTTGTTCGTATTTTTTCCCAAATTTTATTACTTTTAATAAAAATATATTATTTTTATATTTTATT
1 TTTGTTCATATTTTTTCCCAAATTTTATTACTTTTAATAAAAATATATTATTTTTATATTTTATT
319112 ATTTTACATTATTTTAATACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAAATAAATT
66 ATTTTACATTATTTTAATACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAAATAAATT
319177 TTTAAAAAAACTCTTATTTCAGCCA
131 TTTAAAAAAACTCTTATTTCAGCCA
319202 TTTGTTCATATTTTTTCCCAAATTTTATTACTTTTAATAAAAATATATTATTTTTATATTTTATT
1 TTTGTTCATATTTTTTCCCAAATTTTATTACTTTTAATAAAAATATATTATTTTTATATTTTATT
319267 ATTTTACATTATTTTAATACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAAATAAATT
66 ATTTTACATTATTTTAATACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAAATAAATT
319332 TTTAAAAAAACTCTTATTTCAGCCA
131 TTTAAAAAAACTCTTATTTCAGCCA
*
319357 TTTGTTCATATTTTTTCCCAAATTTTATTACTTTCAATAAAAA
1 TTTGTTCATATTTTTTCCCAAATTTTATTACTTTTAATAAAAA
319400 AAGCCTAAAT
Statistics
Matches: 196, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
155 196 1.00
ACGTcount: A:0.33, C:0.09, G:0.05, T:0.53
Consensus pattern (155 bp):
TTTGTTCATATTTTTTCCCAAATTTTATTACTTTTAATAAAAATATATTATTTTTATATTTTATT
ATTTTACATTATTTTAATACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAAATAAATT
TTTAAAAAAACTCTTATTTCAGCCA
Found at i:321181 original size:3 final size:3
Alignment explanation
Indices: 321173--321197 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
321163 ACATGCATAT
321173 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
321198 AGAAACCACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:327915 original size:108 final size:108
Alignment explanation
Indices: 327726--327942 Score: 416
Period size: 108 Copynumber: 2.0 Consensus size: 108
327716 TTTTGGATAA
*
327726 AAAAAATTATATTTACATATTTCAATATTAGAAGCCGGCTATGTAAGTTGGTTTGGTTAAAAAAA
1 AAAAAATTATATATACATATTTCAATATTAGAAGCCGGCTATGTAAGTTGGTTTGGTTAAAAAAA
327791 TTCATAATCGATAACTATGCACTACAAGACCACTTTAACCATC
66 TTCATAATCGATAACTATGCACTACAAGACCACTTTAACCATC
*
327834 AAAAAATTATATATACATATTTTAATATTAGAAGCCGGCTATGTAAGTTGGTTTGGTTAAAAAAA
1 AAAAAATTATATATACATATTTCAATATTAGAAGCCGGCTATGTAAGTTGGTTTGGTTAAAAAAA
327899 TTCATAATCGATAACTATGCACTACAAGACCACTTTAACCATC
66 TTCATAATCGATAACTATGCACTACAAGACCACTTTAACCATC
327942 A
1 A
327943 TAACCGACTC
Statistics
Matches: 107, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
108 107 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (108 bp):
AAAAAATTATATATACATATTTCAATATTAGAAGCCGGCTATGTAAGTTGGTTTGGTTAAAAAAA
TTCATAATCGATAACTATGCACTACAAGACCACTTTAACCATC
Found at i:329057 original size:27 final size:27
Alignment explanation
Indices: 329025--329080 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
329015 AGAATAAGCA
329025 TCTCTAGCATATTAAAGAAAATGTCAT
1 TCTCTAGCATATTAAAGAAAATGTCAT
329052 TCTCTAGCATATTAAAGAAAATGTCAT
1 TCTCTAGCATATTAAAGAAAATGTCAT
329079 TC
1 TC
329081 ATACCTGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (27 bp):
TCTCTAGCATATTAAAGAAAATGTCAT
Found at i:334804 original size:86 final size:85
Alignment explanation
Indices: 334698--334873 Score: 246
Period size: 86 Copynumber: 2.1 Consensus size: 85
334688 CTGTTATAGA
* *
334698 AAAGTGGTTAAAAACATATAAGAGCTGTATGAATTATTGTTTTTATGTAAAT-TTTTATTTTACA
1 AAAGTGGTTAAAAACATATAAAAGCTGCATGAATTATTGTTTTTATG-AAATATTTTATTTTACA
*
334762 TTCTTCTACACGATTAACTAT
65 TTCTTCCACACGATTAACTAT
* * * * *
334783 AAAGTGGTTAAAAAACGTATAAAAGGTGCATGAATTATTGTTTTTATGCATTATTTTATTTTGCA
1 AAAGTGGTT-AAAAACATATAAAAGCTGCATGAATTATTGTTTTTATGAAATATTTTATTTTACA
*
334848 TTCTTCCACACGATTAATTAT
65 TTCTTCCACACGATTAACTAT
334869 AAAGT
1 AAAGT
334874 TCATAAGTTT
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
85 11 0.14
86 69 0.86
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (85 bp):
AAAGTGGTTAAAAACATATAAAAGCTGCATGAATTATTGTTTTTATGAAATATTTTATTTTACAT
TCTTCCACACGATTAACTAT
Found at i:335845 original size:21 final size:19
Alignment explanation
Indices: 335819--335873 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
335809 TCAAATTTAG
*
335819 AATTTTAATATTATTTATTTT
1 AATTTTAAT-TTATTTA-ATT
335840 AATTTTAATTTTAATTTAATT
1 AATTTTAA-TTT-ATTTAATT
*
335861 AATTTCAATTTAT
1 AATTTTAATTTAT
335874 CAGTTTACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 2 0.07
20 3 0.10
21 19 0.63
22 6 0.20
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
AATTTTAATTTATTTAATT
Found at i:335864 original size:15 final size:14
Alignment explanation
Indices: 335819--335873 Score: 60
Period size: 15 Copynumber: 3.9 Consensus size: 14
335809 TCAAATTTAG
335819 AATTTTAATATTATT
1 AATTTTAAT-TTATT
*
335834 TATTTTAA-TT-TT
1 AATTTTAATTTATT
335846 AATTTTAATTTAATT
1 AATTTTAATTT-ATT
*
335861 AATTTCAATTTAT
1 AATTTTAATTTAT
335874 CAGTTTACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 9 0.26
13 4 0.12
14 2 0.06
15 19 0.56
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (14 bp):
AATTTTAATTTATT
Found at i:336646 original size:167 final size:167
Alignment explanation
Indices: 336370--336707 Score: 491
Period size: 167 Copynumber: 2.0 Consensus size: 167
336360 ATTGGGTTTG
* * *
336370 GGTAAAACTAGACCTGTCTATAGGGCGGATCACTCGACTCGAAAGCCTACCCAAAAAGTAGGAGG
1 GGTAAAACTAGACCTGTCCATAGGGCGGATCACCCGACCCGAAAGCCTACCCAAAAAGTAGGAGG
* ** *
336435 GTTTGGATAAAATATAGGCCTGAAAAATGAGCTTTGGGCAAAAAATAAGGCCCGTTTGAAAAACG
66 GTTTAGATAAAATATAGGCCCAAAAAATGAGCTTGGGGCAAAAAATAAGGCCCGTTTGAAAAACG
*
336500 GGTCAAGTAT-TGGGTAAGACTTTTTTGGTCTTGAGTA
131 GGTCAAGCATCT-GGTAAGACTTTTTTGGTCTTGAGTA
* * * ** *
336537 GGTAAAACTAGACCTGTCCATGGGGCAGG-TCACCCGACCCGAAAGCTTGCCTGAAAAGTGGGAG
1 GGTAAAACTAGACCTGTCCATAGGGC-GGATCACCCGACCCGAAAGCCTACCCAAAAAGTAGGAG
*
336601 GGTTTAGATAAAATATAGGCCCAAAAAATGAGCTTGGGGCAAAAAATAAGGCTCGTTTGAAAAAC
65 GGTTTAGATAAAATATAGGCCCAAAAAATGAGCTTGGGGCAAAAAATAAGGCCCGTTTGAAAAAC
* *
336666 GGGTCAAGCATCTTGTAAGACTTTTTTGGTCTTGAGTG
130 GGGTCAAGCATCTGGTAAGACTTTTTTGGTCTTGAGTA
336704 GGTA
1 GGTA
336708 TGACTAGGGG
Statistics
Matches: 152, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
167 149 0.98
168 3 0.02
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (167 bp):
GGTAAAACTAGACCTGTCCATAGGGCGGATCACCCGACCCGAAAGCCTACCCAAAAAGTAGGAGG
GTTTAGATAAAATATAGGCCCAAAAAATGAGCTTGGGGCAAAAAATAAGGCCCGTTTGAAAAACG
GGTCAAGCATCTGGTAAGACTTTTTTGGTCTTGAGTA
Found at i:336930 original size:13 final size:13
Alignment explanation
Indices: 336912--336941 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
336902 AGCCCAAACT
*
336912 CAATTATCCAACC
1 CAATTACCCAACC
336925 CAATTACCCAACC
1 CAATTACCCAACC
336938 CAAT
1 CAAT
336942 AAAACTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:337123 original size:9 final size:9
Alignment explanation
Indices: 337084--337140 Score: 62
Period size: 9 Copynumber: 6.2 Consensus size: 9
337074 TAAAAAAAAT
*
337084 TTCGGGCAA
1 TTCGGGTAA
*
337093 TTCGGGTATTT
1 TTCGGGTA--A
337104 TTC-GGTAA
1 TTCGGGTAA
*
337112 TTCGGTTAA
1 TTCGGGTAA
337121 TTCGGGTAA
1 TTCGGGTAA
337130 TTCGGGTAA
1 TTCGGGTAA
337139 TT
1 TT
337141 TTTAACCAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
8 3 0.08
9 30 0.75
10 4 0.10
11 3 0.08
ACGTcount: A:0.19, C:0.12, G:0.28, T:0.40
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:337526 original size:20 final size:21
Alignment explanation
Indices: 337501--337545 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
337491 CTGTTGAATT
*
337501 TTTTTTACTGTTTTCTTAC-A
1 TTTTTTACTGTTTTATTACTA
*
337521 TTTTTTATTGTTTTATTACTA
1 TTTTTTACTGTTTTATTACTA
337542 TTTT
1 TTTT
337546 CTTGTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.16, C:0.09, G:0.04, T:0.71
Consensus pattern (21 bp):
TTTTTTACTGTTTTATTACTA
Found at i:337550 original size:19 final size:20
Alignment explanation
Indices: 337503--337551 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
337493 GTTGAATTTT
* * *
337503 TTTTACTGTTTTCTTACATT
1 TTTTATTGTTTTATTACATA
337523 TTTTATTGTTTTATTAC-TA
1 TTTTATTGTTTTATTACATA
*
337542 TTTTCTTGTT
1 TTTTATTGTT
337552 ATTTTTTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.14, C:0.10, G:0.06, T:0.69
Consensus pattern (20 bp):
TTTTATTGTTTTATTACATA
Found at i:340494 original size:16 final size:16
Alignment explanation
Indices: 340453--340487 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
340443 ACGAGATTGT
*
340453 AACCTCTTCAACTAAC
1 AACCACTTCAACTAAC
340469 AACCACTTCAACTAAC
1 AACCACTTCAACTAAC
340485 AAC
1 AAC
340488 TAGTTCACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (16 bp):
AACCACTTCAACTAAC
Found at i:341475 original size:61 final size:61
Alignment explanation
Indices: 341371--341485 Score: 151
Period size: 61 Copynumber: 1.9 Consensus size: 61
341361 AAGTCTACCT
* * * *
341371 AACTCTAGTGACCTAAATCTCATTACAAATATTGAATTAAATAACTAACTCAACGTAATTC
1 AACTCTAATGACCCAAATCTCATTACAAATATCGAAATAAATAACTAACTCAACGTAATTC
* * *
341432 AACTCTAATTACCCAAATCTCATTACAAGTA-CGAAATAGAATAATTAACTCAAC
1 AACTCTAATGACCCAAATCTCATTACAAATATCGAAATA-AATAACTAACTCAAC
341486 TCTAATTGAC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
60 5 0.11
61 41 0.89
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.29
Consensus pattern (61 bp):
AACTCTAATGACCCAAATCTCATTACAAATATCGAAATAAATAACTAACTCAACGTAATTC
Found at i:343059 original size:2 final size:2
Alignment explanation
Indices: 343052--343080 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
343042 AGATGGATCC
343052 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
343081 TAATGCCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:350023 original size:7 final size:7
Alignment explanation
Indices: 350013--350049 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
350003 ATAAATAAAA
350013 AAATATT
1 AAATATT
*
350020 AAAT-TA
1 AAATATT
350026 AAATATT
1 AAATATT
350033 AAATATT
1 AAATATT
350040 AAATATT
1 AAATATT
350047 AAA
1 AAA
350050 ATAAAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AAATATT
Found at i:350030 original size:13 final size:13
Alignment explanation
Indices: 350012--350057 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
350002 AATAAATAAA
350012 AAAATATTAAATT
1 AAAATATTAAATT
350025 AAAATATTAAATAT
1 AAAATATTAAAT-T
* *
350039 TAAATATTAAAAT
1 AAAATATTAAATT
350052 AAAATA
1 AAAATA
350058 AAATAAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 18 0.62
14 11 0.38
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AAAATATTAAATT
Found at i:351703 original size:5 final size:5
Alignment explanation
Indices: 351693--351723 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
351683 GTCATTTTCA
351693 ATAAT ATAAT ATAAT ATAAT ATTAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT A-TAAT ATAAT
351724 GATTCCTTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATAAT
Found at i:352183 original size:18 final size:18
Alignment explanation
Indices: 352147--352191 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
352137 AGCTTTTAAG
*
352147 AAATACTTTTGGGACAAA
1 AAATACTTTTGAGACAAA
* *
352165 AAATGCTTTTGAGA-GAA
1 AAATACTTTTGAGACAAA
352182 AAATACTTTT
1 AAATACTTTT
352192 CAAACGCCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (18 bp):
AAATACTTTTGAGACAAA
Found at i:360913 original size:18 final size:18
Alignment explanation
Indices: 360875--360914 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
360865 GACTCGGAAA
* *
360875 AGGATACATATAAGGGTT
1 AGGATACATATAAAGGCT
*
360893 AGGATGCATATAAAGGCT
1 AGGATACATATAAAGGCT
360911 AGGA
1 AGGA
360915 AACGCAACTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.30, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAAGGCT
Found at i:361766 original size:19 final size:19
Alignment explanation
Indices: 361732--361779 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
361722 AGAAAAATTG
*
361732 TTATTGTTTTTTTCACCT-TT
1 TTATTG-TTATTTCA-CTATT
361752 TTATTGTTATTTCACTATT
1 TTATTGTTATTTCACTATT
*
361771 ATATTGTTA
1 TTATTGTTA
361780 CTATTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 17 0.68
20 6 0.24
ACGTcount: A:0.19, C:0.10, G:0.06, T:0.65
Consensus pattern (19 bp):
TTATTGTTATTTCACTATT
Found at i:361799 original size:14 final size:14
Alignment explanation
Indices: 361765--361800 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
361755 TTGTTATTTC
*
361765 ACTATTATATTGTT
1 ACTATTTTATTGTT
361779 ACTATTTTATTGTT
1 ACTATTTTATTGTT
*
361793 ATTATTTT
1 ACTATTTT
361801 GATATTGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.64
Consensus pattern (14 bp):
ACTATTTTATTGTT
Found at i:363918 original size:2 final size:2
Alignment explanation
Indices: 363911--363947 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
363901 ACTTTATTGA
363911 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
363948 AGCTACATCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:370443 original size:40 final size:40
Alignment explanation
Indices: 370399--370531 Score: 176
Period size: 40 Copynumber: 3.3 Consensus size: 40
370389 GCTCCTACGA
* *
370399 GGACGCGGTTTGCTGACACATCAGCAAAGCGCGCTGACGT
1 GGACGCGATTTGCTGACACATCAACAAAGCGCGCTGACGT
*
370439 GGACGCGATTTACTGACACATCAACAAAGCGCGCTGACGT
1 GGACGCGATTTGCTGACACATCAACAAAGCGCGCTGACGT
* ** * *
370479 GGACGCGATTTGCTGACACGTCCCCTGACATCGCGCTGACGT
1 GGACGCGATTTGCTGACACATCAAC--AAAGCGCGCTGACGT
370521 GGACGCGATTT
1 GGACGCGATTT
370532 CGGGGAAAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 58 0.71
42 24 0.29
ACGTcount: A:0.23, C:0.29, G:0.29, T:0.20
Consensus pattern (40 bp):
GGACGCGATTTGCTGACACATCAACAAAGCGCGCTGACGT
Found at i:373207 original size:18 final size:19
Alignment explanation
Indices: 373167--373208 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
373157 TTTTTTTACT
* *
373167 TTTTTTATTAACTTTTGTC
1 TTTTTTATTAACTTTTATA
*
373186 TTTTTT-TTAAGTTTTATA
1 TTTTTTATTAACTTTTATA
373204 TTTTT
1 TTTTT
373209 CTTATTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.74
Consensus pattern (19 bp):
TTTTTTATTAACTTTTATA
Found at i:373231 original size:23 final size:22
Alignment explanation
Indices: 373205--373247 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
373195 AGTTTTATAT
373205 TTTTC-TTATTTTATTTTATTTTA
1 TTTTCTTTA-TTTA-TTTATTTTA
*
373228 TTTTGTTTATTTATTTATTT
1 TTTTCTTTATTTATTTATTT
373248 AGGCGCGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 7 0.39
23 8 0.44
24 3 0.17
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.79
Consensus pattern (22 bp):
TTTTCTTTATTTATTTATTTTA
Found at i:373974 original size:17 final size:17
Alignment explanation
Indices: 373952--373985 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
373942 AAAAATGATT
373952 TTTTAATATAT-TTAAAA
1 TTTTAA-ATATGTTAAAA
373969 TTTTAAATATGTTAAAA
1 TTTTAAATATGTTAAAA
373986 GAAAATGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TTTTAAATATGTTAAAA
Found at i:375329 original size:21 final size:20
Alignment explanation
Indices: 375283--375333 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
375273 CCTGATCAGT
* *
375283 ATACGACACATAAGTGCTTG
1 ATACGACACAGAAGTGCCTG
* *
375303 AAACGACACACGAGGTGCCTG
1 ATACGACACA-GAAGTGCCTG
375324 ATACGACACA
1 ATACGACACA
375334 NNNNNNNNNN
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.16
Consensus pattern (20 bp):
ATACGACACAGAAGTGCCTG
Found at i:376234 original size:39 final size:39
Alignment explanation
Indices: 376180--376258 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
376170 AACTTAAATC
*
376180 ATGAGTATTTCACTCTAGGGTTCCAAAAACATCGAATTT
1 ATGAGTATTTCACTCTAGGGTTCCAAAAACATCAAATTT
376219 ATGAGTATTTCACTCTAGGGTTCCAAAAACATCAAATTT
1 ATGAGTATTTCACTCTAGGGTTCCAAAAACATCAAATTT
376258 A
1 A
376259 AACTTCAAGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (39 bp):
ATGAGTATTTCACTCTAGGGTTCCAAAAACATCAAATTT
Found at i:376567 original size:5 final size:5
Alignment explanation
Indices: 376559--376630 Score: 58
Period size: 5 Copynumber: 14.2 Consensus size: 5
376549 TATTTAATTT
* * * * *
376559 ATATA ATATA ATACA ATATA ATACA ATACA ATATA TTATATT ATATT ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA --ATATA ATATA ATATA
376611 ATA-A A-ATA ATATA TATATA A
1 ATATA ATATA ATATA -ATATA A
376631 AACATAAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
3 1 0.02
4 4 0.07
5 42 0.75
6 5 0.09
7 4 0.07
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:377259 original size:103 final size:103
Alignment explanation
Indices: 377075--377277 Score: 397
Period size: 103 Copynumber: 2.0 Consensus size: 103
377065 TGATATTTTT
377075 GTTTTCTCAGCCTTTCAATTTTAGTCTTCAATATATAATTTTATGTTTAAATTATATAGATAATT
1 GTTTTCTCAGCCTTTCAATTTTAGTCTTCAATATATAATTTTATGTTTAAATTATATAGATAATT
*
377140 GATTTATCATATTTTTATAAAAAAATTACCATACAGGA
66 GATTTATCATAATTTTATAAAAAAATTACCATACAGGA
377178 GTTTTCTCAGCCTTTCAATTTTAGTCTTCAATATATAATTTTATGTTTAAATTATATAGATAATT
1 GTTTTCTCAGCCTTTCAATTTTAGTCTTCAATATATAATTTTATGTTTAAATTATATAGATAATT
377243 GATTTATCATAATTTTATAAAAAAATTACCATACA
66 GATTTATCATAATTTTATAAAAAAATTACCATACA
377278 TGATGGTTAT
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 99 1.00
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (103 bp):
GTTTTCTCAGCCTTTCAATTTTAGTCTTCAATATATAATTTTATGTTTAAATTATATAGATAATT
GATTTATCATAATTTTATAAAAAAATTACCATACAGGA
Found at i:377384 original size:22 final size:22
Alignment explanation
Indices: 377354--377415 Score: 81
Period size: 21 Copynumber: 2.8 Consensus size: 22
377344 AATTTTAAAA
* *
377354 TTAATAATTTATGAAAATTATAT
1 TTAA-AATTTATAAAAAATATAT
377377 TTAAAATTT-TAAAAAATATAT
1 TTAAAATTTATAAAAAATATAT
377398 TTAAAATATTATAAAAAA
1 TTAAAAT-TTATAAAAAA
377416 AACAATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 17 0.49
22 7 0.20
23 11 0.31
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
TTAAAATTTATAAAAAATATAT
Found at i:377474 original size:25 final size:24
Alignment explanation
Indices: 377445--377514 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 24
377435 CATATCTTTA
*
377445 AAAATAATATATTTTAAATAATTTG
1 AAAATAATA-ATTTAAAATAATTTG
* *
377470 AAAATCATAGTTTAAAATAATTT-
1 AAAATAATAATTTAAAATAATTTG
* *
377493 ACAAATCATAA-TTAAAAAAATT
1 A-AAATAATAATTTAAAATAATT
377515 ATAAAACAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
23 11 0.28
24 20 0.51
25 8 0.21
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (24 bp):
AAAATAATAATTTAAAATAATTTG
Found at i:377510 original size:24 final size:23
Alignment explanation
Indices: 377460--377540 Score: 78
Period size: 24 Copynumber: 3.4 Consensus size: 23
377450 AATATATTTT
* *
377460 AAATAATTTGAAAATCATAGTTTA
1 AAATAATTT-AAAATCATAATTAA
377484 AAATAATTTACAAATCATAATTAA
1 AAATAATTTA-AAATCATAATTAA
377508 AAA-AATTATAAAA-CA-AATTAA
1 AAATAATT-TAAAATCATAATTAA
377529 AATATACATTTA
1 AA-ATA-ATTTA
377541 TAATATTATT
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
21 8 0.16
22 3 0.06
23 11 0.22
24 28 0.56
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.33
Consensus pattern (23 bp):
AAATAATTTAAAATCATAATTAA
Found at i:378251 original size:14 final size:14
Alignment explanation
Indices: 378234--378260 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
378224 GGGTTTATGA
378234 GTTTTGGTTATAGG
1 GTTTTGGTTATAGG
378248 GTTTTGGTTATAG
1 GTTTTGGTTATAG
378261 ACAAATGATG
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:0.15, C:0.00, G:0.33, T:0.52
Consensus pattern (14 bp):
GTTTTGGTTATAGG
Found at i:378374 original size:24 final size:25
Alignment explanation
Indices: 378347--378394 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
378337 AGAGGAAAGT
378347 TTAAAGAACATAAAA-GAAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAAA
** *
378371 TTAAATTACTTAAAACGAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAA
378395 TATGGGGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (25 bp):
TTAAAGAACATAAAACGAAAAAAAA
Done.