Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008177.1 Hibiscus syriacus cultivar Beakdansim tig00110773_pilon, whole genome shotgun sequence
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: 1003138
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:261587 original size:2 final size:2
Alignment explanation
Indices: 261580--261614 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
261570 TCGGGCCGGG
261580 TA TA TA 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 TA TA TA T
261615 TTTTTTAATT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:261698 original size:12 final size:12
Alignment explanation
Indices: 261681--261714 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
261671 TTTTAATATT
*
261681 TATCGGGTCGGG
1 TATCGGGCCGGG
261693 TATCGGGCCGGG
1 TATCGGGCCGGG
261705 TATCGGGCCG
1 TATCGGGCCG
261715 AGTAATCTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.09, C:0.24, G:0.47, T:0.21
Consensus pattern (12 bp):
TATCGGGCCGGG
Found at i:263161 original size:20 final size:20
Alignment explanation
Indices: 263125--263192 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
263115 TTTATTTCAA
*
263125 GAAAATC-AATTTTGCAACTC
1 GAAAATCGAA-TTCGCAACTC
* *
263145 GAAAATCGAATTCGCAATTT
1 GAAAATCGAATTCGCAACTC
* ** *
263165 GAAACTTAAATTCGCAACAC
1 GAAAATCGAATTCGCAACTC
263185 GAAAATCG
1 GAAAATCG
263193 CAACTCGAAA
Statistics
Matches: 35, Mismatches: 12, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
20 33 0.94
21 2 0.06
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (20 bp):
GAAAATCGAATTCGCAACTC
Found at i:263240 original size:14 final size:14
Alignment explanation
Indices: 263223--263282 Score: 57
Period size: 14 Copynumber: 3.9 Consensus size: 14
263213 CAACTCGAAA
263223 TTCGAGTTGCGATT
1 TTCGAGTTGCGATT
*
263237 TTCGTGTTGCGAATTTCATT
1 TTCGAGTTGCG-A-----TT
263257 TTCGAGTTGCGATT
1 TTCGAGTTGCGATT
263271 TTCGAGTTGCGA
1 TTCGAGTTGCGA
263283 ATTTATGTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
14 24 0.63
15 1 0.03
19 1 0.03
20 12 0.32
ACGTcount: A:0.15, C:0.15, G:0.27, T:0.43
Consensus pattern (14 bp):
TTCGAGTTGCGATT
Found at i:263259 original size:20 final size:20
Alignment explanation
Indices: 263234--263273 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
263224 TCGAGTTGCG
*
263234 ATTTTCGTGTTGCGAATTTC
1 ATTTTCGAGTTGCGAATTTC
*
263254 ATTTTCGAGTTGCGATTTTC
1 ATTTTCGAGTTGCGAATTTC
263274 GAGTTGCGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.15, G:0.20, T:0.50
Consensus pattern (20 bp):
ATTTTCGAGTTGCGAATTTC
Found at i:263883 original size:40 final size:40
Alignment explanation
Indices: 263851--263982 Score: 147
Period size: 40 Copynumber: 3.3 Consensus size: 40
263841 ATTTAAATTT
* *
263851 GCGTTGTGAATTTGAAAATCGAGTTGCGAAATTGAAACTC
1 GCGTTGCGAATTTGAAAATCGAGTTACGAAATTGAAACTC
* * * * *
263891 ACTTTGCGAATTAGAAAATTGAGTTACGAAAATGAAACTC
1 GCGTTGCGAATTTGAAAATCGAGTTACGAAATTGAAACTC
* * ** *
263931 GTGTTGCGAATTTAAAAATCGAGTTACGAAAAAGAAATTC
1 GCGTTGCGAATTTGAAAATCGAGTTACGAAATTGAAACTC
*
263971 GAGTTGCGAATT
1 GCGTTGCGAATT
263983 CGACTTCTGT
Statistics
Matches: 76, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 76 1.00
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (40 bp):
GCGTTGCGAATTTGAAAATCGAGTTACGAAATTGAAACTC
Found at i:263885 original size:20 final size:20
Alignment explanation
Indices: 263862--263980 Score: 89
Period size: 20 Copynumber: 6.0 Consensus size: 20
263852 CGTTGTGAAT
263862 TTGAAAATCGAGTTGCGAAA
1 TTGAAAATCGAGTTGCGAAA
* *
263882 TTGAAACTC-ACTTTGCG-AA
1 TTGAAAATCGA-GTTGCGAAA
* *
263901 TTAGAAAATTGAGTTACGAAA
1 TT-GAAAATCGAGTTGCGAAA
* * * *
263922 ATGAAACTCGTGTTGCGAAT
1 TTGAAAATCGAGTTGCGAAA
* *
263942 TTAAAAATCGAGTTACGAAA
1 TTGAAAATCGAGTTGCGAAA
** *
263962 AAGAAATTCGAGTTGCGAA
1 TTGAAAATCGAGTTGCGAA
263981 TTCGACTTCT
Statistics
Matches: 72, Mismatches: 23, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
19 5 0.07
20 63 0.88
21 4 0.06
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (20 bp):
TTGAAAATCGAGTTGCGAAA
Found at i:265119 original size:28 final size:31
Alignment explanation
Indices: 265084--265155 Score: 107
Period size: 28 Copynumber: 2.5 Consensus size: 31
265074 AATAAACTAT
265084 TTATAATTAATATTAAA-ATAATT-ATAT-A
1 TTATAATTAATATTAAATATAATTAATATAA
265112 TTATAATTAATA-TAAATATAATTAATATAA
1 TTATAATTAATATTAAATATAATTAATATAA
*
265142 ATATAATTAATATT
1 TTATAATTAATATT
265156 TATATTATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
27 4 0.10
28 18 0.46
29 4 0.10
30 12 0.31
31 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
TTATAATTAATATTAAATATAATTAATATAA
Found at i:265134 original size:43 final size:43
Alignment explanation
Indices: 265085--265174 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 43
265075 ATAAACTATT
265085 TATAATTAATATTAAA-ATAATT-ATATATTATAATTAATAT-AAA
1 TATAATTAATA-TAAATATAATTAATAT-TTAT-ATTAATATAAAA
*
265128 TATAATTAATATAAATATAATTAATATTTATATTATTATAAAA
1 TATAATTAATATAAATATAATTAATATTTATATTAATATAAAA
265171 TATA
1 TATA
265175 GCCTATAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
42 11 0.26
43 28 0.65
44 4 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (43 bp):
TATAATTAATATAAATATAATTAATATTTATATTAATATAAAA
Found at i:265159 original size:28 final size:28
Alignment explanation
Indices: 265085--265174 Score: 78
Period size: 28 Copynumber: 3.1 Consensus size: 28
265075 ATAAACTATT
* *
265085 TATAATTAATA-TTA-AAATAATTATATAT
1 TATAATTAATATTTATAATTAA-TATA-AA
*
265113 TATAATTAATATAAATATAATTAATATAAA
1 TATAATTAATAT--TTATAATTAATATAAA
*
265143 TATAATTAATATTTAT-ATTATTATAAAA
1 TATAATTAATATTTATAATTAATAT-AAA
265171 TATA
1 TATA
265175 GCCTATAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
27 7 0.13
28 21 0.40
30 13 0.25
31 6 0.12
32 5 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTAATATTTATAATTAATATAAA
Found at i:265160 original size:15 final size:15
Alignment explanation
Indices: 265085--265154 Score: 101
Period size: 15 Copynumber: 4.8 Consensus size: 15
265075 ATAAACTATT
265085 TATAATTAATATTAAA
1 TATAATTAATA-TAAA
*
265101 -ATAATT-ATAT-AT
1 TATAATTAATATAAA
265113 TATAATTAATATAAA
1 TATAATTAATATAAA
265128 TATAATTAATATAAA
1 TATAATTAATATAAA
265143 TATAATTAATAT
1 TATAATTAATAT
265155 TTATATTATT
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
12 1 0.02
13 7 0.14
14 7 0.14
15 34 0.69
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TATAATTAATATAAA
Found at i:265165 original size:15 final size:15
Alignment explanation
Indices: 265085--265165 Score: 76
Period size: 15 Copynumber: 5.5 Consensus size: 15
265075 ATAAACTATT
*
265085 TATAATTAATATTAA
1 TATAATTAATATTTA
* *
265100 AATAATT-ATATAT-
1 TATAATTAATATTTA
**
265113 TATAATTAATATAAA
1 TATAATTAATATTTA
**
265128 TATAATTAATATAAA
1 TATAATTAATATTTA
265143 TATAATTAATATTTA
1 TATAATTAATATTTA
*
265158 TATTATTA
1 TATAATTA
265166 TAAAATATAG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
13 6 0.11
14 9 0.16
15 41 0.73
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATAATTAATATTTA
Found at i:265224 original size:58 final size:59
Alignment explanation
Indices: 265122--265281 Score: 147
Period size: 58 Copynumber: 2.8 Consensus size: 59
265112 TTATAATTAA
* *
265122 TATAAA-TATA-ATTAATATAAATAT-AATTAATAT-TTATATTATTATAAAATATAGCC
1 TATAAACTATATATTAATATTAATATAAATT-ATATGTTATATAATTATAAAATATAGCC
* * * * **
265178 TATAAAAT-TAATATTAATATTAATATAAACTATATGTTATA-AATTATATAGTATAGTT
1 TATAAACTAT-ATATTAATATTAATATAAATTATATGTTATATAATTATAAAATATAGCC
* *
265236 TATAAACTATATACT-ATATTAATATAAATTATA-GTTAAGATAATTA
1 TATAAACTATATATTAATATTAATATAAATTATATGTT-ATATAATTA
265282 ACATTAATAT
Statistics
Matches: 85, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
56 10 0.12
57 21 0.25
58 45 0.53
59 9 0.11
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (59 bp):
TATAAACTATATATTAATATTAATATAAATTATATGTTATATAATTATAAAATATAGCC
Found at i:265225 original size:21 final size:21
Alignment explanation
Indices: 265201--265268 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
265191 TTAATATTAA
*
265201 TATAAACTATATGTTATAAAT
1 TATATACTATATGTTATAAAT
* *
265222 TATATAGTATA-GTTTATAAAC
1 TATATACTATATG-TTATAAAT
265243 TATATACTATAT-TAATATAAAT
1 TATATACTATATGT--TATAAAT
265265 TATA
1 TATA
265269 GTTAAGATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
20 2 0.05
21 26 0.68
22 10 0.26
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (21 bp):
TATATACTATATGTTATAAAT
Found at i:265268 original size:15 final size:15
Alignment explanation
Indices: 265106--265300 Score: 70
Period size: 15 Copynumber: 12.8 Consensus size: 15
265096 TTAAAATAAT
*
265106 TATATATTATAATTAA
1 TATAAATTAT-ATTAA
265122 TATAAA-TATAATTAA
1 TATAAATTAT-ATTAA
265137 TATAAA-TATAATTAA
1 TATAAATTAT-ATTAA
*
265152 TAT---TTATATTAT
1 TATAAATTATATTAA
*
265164 TATAAAATATAGCCTATAA
1 TATAAATTATA---T-TAA
*
265183 AATTAATATTAATATTAA
1 TA-TAA-ATT-ATATTAA
*
265201 TATAAACTATATGT--
1 TATAAATTATAT-TAA
*
265215 TATAAATTATA-TAG
1 TATAAATTATATTAA
* *
265229 TAT-AGTT-TATAAA
1 TATAAATTATATTAA
* *
265242 CTATATACTATATTAA
1 -TATAAATTATATTAA
265258 TATAAATTATAGTTAA
1 TATAAATTATA-TTAA
* *
265274 GAT-AATTAACATTAA
1 TATAAATT-ATATTAA
*
265289 TATAAACTATAT
1 TATAAATTATAT
265301 AGTACATTAA
Statistics
Matches: 135, Mismatches: 23, Indels: 43
0.67 0.11 0.21
Matches are distributed among these distances:
12 10 0.07
13 7 0.05
14 16 0.12
15 58 0.43
16 24 0.18
17 3 0.02
18 5 0.04
19 4 0.03
20 3 0.02
21 2 0.01
22 3 0.02
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (15 bp):
TATAAATTATATTAA
Found at i:265323 original size:20 final size:21
Alignment explanation
Indices: 265282--265323 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
265272 AAGATAATTA
265282 ACATTAATATAAACTATATAGT
1 ACATTAATATAAAC-ATATAGT
265304 ACATTAATATAAAC-TATAGT
1 ACATTAATATAAACATATAGT
265324 TTATAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.30
22 14 0.70
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.36
Consensus pattern (21 bp):
ACATTAATATAAACATATAGT
Found at i:265340 original size:21 final size:21
Alignment explanation
Indices: 265311--265363 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
265301 AGTACATTAA
* *
265311 TATAAACTATAGTTTATAAAT
1 TATAAACTATAGGTTATAAAG
*
265332 TATAGACTATAGGTTATAAAG
1 TATAAACTATAGGTTATAAAG
*
265353 TATAAATTATA
1 TATAAACTATA
265364 TAGTACACTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (21 bp):
TATAAACTATAGGTTATAAAG
Found at i:267795 original size:45 final size:44
Alignment explanation
Indices: 267732--267899 Score: 201
Period size: 45 Copynumber: 3.7 Consensus size: 44
267722 GTAAACATGA
* * * * *
267732 AAATAAGTTTAGGAGCTTATGGAATAAATGGCAAGTATATTAGT
1 AAATAAGCTTACGAGCTTATGAAATAAATGGTAAGTATATTGGT
* *
267776 AAAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGT
1 -AAATAAGCTTACGAGCTTATGAAATAAATGGTAAGTATATTGGT
* * *
267821 AAATAAGCTTACGAGCATATTAAATAAATGGTTTATGGTATATTGGT
1 AAATAAGCTTACGAGCTTATGAAATAAATGG--TA-AGTATATTGGT
*
267868 AAATAAGCTTACGAGCTTATAAAATAAATGGT
1 AAATAAGCTTACGAGCTTATGAAATAAATGGT
267900 TTATAGCATT
Statistics
Matches: 108, Mismatches: 12, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
44 27 0.25
45 40 0.37
46 2 0.02
47 39 0.36
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGAAATAAATGGTAAGTATATTGGT
Found at i:267880 original size:47 final size:47
Alignment explanation
Indices: 267732--267905 Score: 189
Period size: 47 Copynumber: 3.8 Consensus size: 47
267722 GTAAACATGA
* * ** * *
267732 AAATAAGTTTAGGAGCTTATGGAATAAATGG--CA-AGTATATTAGT
1 AAATAAGCTTACGAGCTTATAAAATAAATGGTTTATAGTATATTGGT
** *
267776 AAAATAAGCTTACGAGCTTATGGATTAAATGG--TA-AGTATATTGGT
1 -AAATAAGCTTACGAGCTTATAAAATAAATGGTTTATAGTATATTGGT
* * *
267821 AAATAAGCTTACGAGCATATTAAATAAATGGTTTATGGTATATTGGT
1 AAATAAGCTTACGAGCTTATAAAATAAATGGTTTATAGTATATTGGT
267868 AAATAAGCTTACGAGCTTATAAAATAAATGGTTTATAG
1 AAATAAGCTTACGAGCTTATAAAATAAATGGTTTATAG
267906 CATTTTGAAT
Statistics
Matches: 113, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
44 27 0.24
45 39 0.35
46 2 0.02
47 45 0.40
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.33
Consensus pattern (47 bp):
AAATAAGCTTACGAGCTTATAAAATAAATGGTTTATAGTATATTGGT
Found at i:268796 original size:314 final size:316
Alignment explanation
Indices: 268165--268796 Score: 1011
Period size: 320 Copynumber: 2.0 Consensus size: 316
268155 ACAAATTTGA
* * * * *
268165 AAATAAAATGGTAACTTTATAGTGGATAAATGTTAGGTTTTTATGAGTTTTAATTATATTTTGCT
1 AAATAAAATAGTAACTTTATAGTGGAGAAAAGTTAAGTTTTAATGAGTTTTAATTATATTTTGCT
*
268230 GAAATTACTGTAGCAGTGAATAATAATGAACAATACCTATGTTTAAAAATTTCCCAAAATGCTAT
66 GAAATTACTGTAGCAGTGAATAATAATGAACAATACCCATGTTTAAAAATTTCCCAAAATGCTAT
268295 AGGGGTAGCGATACCCTCATTGTTCACTGTTCACTGTTCACGGGACTATTCATAAAAAAACTCTT
131 AGGGGTAGCGATACCCTCATTGTTCACTGTTCA---TTCAC-GGACTATTCATAAAAAAACTCTT
* * *
268360 TTTAATTAAATTGGTTATAAATAAACATAATTCATATGATCTGATATTTTTATAATATCAGTTAC
192 TTGAATTAAATTAGTTATAAAGAAACATAATTCATATGATCTGATATTTTTATAATATCAGTTAC
*
268425 CATTTTAAGAAAATAAATTTTAAATCACTTTTGAATTGAGAAATGGTTTTAGAAATTCGG
257 CATTTTAAGAAAATAAATTTTAAATCACTTTTGAATTGAAAAATGGTTTTAGAAATTCGG
*
268485 AAATAAAATAGTAACTTTATAGTGGAGAAAAGTTAAGTTTTAATGAGTTTTAATTATATTTTGTT
1 AAATAAAATAGTAACTTTATAGTGGAGAAAAGTTAAGTTTTAATGAGTTTTAATTATATTTTGCT
* * * * *
268550 GAATTTACTGTAGCTGTGAATAGTAATGAACAGTACCCATGTTTAAAAATTTTCCAAAATGCTAT
66 GAAATTACTGTAGCAGTGAATAATAATGAACAATACCCATGTTTAAAAATTTCCCAAAATGCTAT
*
268615 AGGGGTA-CTGATACCCTCATTGTTCACTGTTCA-T-A-GTACTATTCATAAAAAAAACTCTTTT
131 AGGGGTAGC-GATACCCTCATTGTTCACTGTTCATTCACGGACTATTCAT-AAAAAAACTCTTTT
*
268676 GAATTAAATTAGTTATAAAGAAACATAATTCATATGATCTGATATTTTTATAATATCAGTTATCA
194 GAATTAAATTAGTTATAAAGAAACATAATTCATATGATCTGATATTTTTATAATATCAGTTACCA
*
268741 TTTTAAGAAAATAAATTTTAAATCGCTTTTGAATTGAAAAATGGTTTTAGAAATTC
259 TTTTAAGAAAATAAATTTTAAATCACTTTTGAATTGAAAAATGGTTTTAGAAATTC
268797 AAGTGACATC
Statistics
Matches: 291, Mismatches: 19, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
313 10 0.03
314 129 0.44
315 1 0.00
316 1 0.00
319 1 0.00
320 149 0.51
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (316 bp):
AAATAAAATAGTAACTTTATAGTGGAGAAAAGTTAAGTTTTAATGAGTTTTAATTATATTTTGCT
GAAATTACTGTAGCAGTGAATAATAATGAACAATACCCATGTTTAAAAATTTCCCAAAATGCTAT
AGGGGTAGCGATACCCTCATTGTTCACTGTTCATTCACGGACTATTCATAAAAAAACTCTTTTGA
ATTAAATTAGTTATAAAGAAACATAATTCATATGATCTGATATTTTTATAATATCAGTTACCATT
TTAAGAAAATAAATTTTAAATCACTTTTGAATTGAAAAATGGTTTTAGAAATTCGG
Found at i:270422 original size:31 final size:31
Alignment explanation
Indices: 270384--270451 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
270374 TATCGAACGG
270384 TTGCAATTGAGTCAAGAGAATAAAGAACCAA
1 TTGCAATTGAGTCAAGAGAATAAAGAACCAA
270415 TTGCAATTGAGTCAAGAGAATAAAGAACCAA
1 TTGCAATTGAGTCAAGAGAATAAAGAACCAA
270446 TTGCAA
1 TTGCAA
270452 GAGCTGCTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.47, C:0.13, G:0.19, T:0.21
Consensus pattern (31 bp):
TTGCAATTGAGTCAAGAGAATAAAGAACCAA
Found at i:271028 original size:33 final size:33
Alignment explanation
Indices: 270957--271051 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 33
270947 GCTAAAAATA
* * *
270957 AAAATAAAAAGAACAAAAAGAAGAAGAAGAAGAGG
1 AAAATAGAAAGAACAAAAA-AA-AAAAAGAAGAAG
270992 AAAATAGAAAGAACAAAAAAAAAAAAGAAGAAG
1 AAAATAGAAAGAACAAAAAAAAAAAAGAAGAAG
* *
271025 AAAATAGAAAAAAAAAAGAAAAAAAAA
1 AAAATAGAAAGAACAAA-AAAAAAAAA
271052 TGAGAGATGC
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
33 25 0.46
34 11 0.20
35 18 0.33
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.03
Consensus pattern (33 bp):
AAAATAGAAAGAACAAAAAAAAAAAAGAAGAAG
Found at i:271040 original size:24 final size:23
Alignment explanation
Indices: 271008--271052 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
270998 GAAAGAACAA
*
271008 AAAAAAAAAAGAAGAAGAAAATAG
1 AAAAAAAAAAGAA-AAAAAAATAG
271032 AAAAAAAAAAGAAAAAAAAAT
1 AAAAAAAAAAGAAAAAAAAAT
271053 GAGAGATGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.04
Consensus pattern (23 bp):
AAAAAAAAAAGAAAAAAAAATAG
Found at i:274327 original size:16 final size:16
Alignment explanation
Indices: 274306--274346 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
274296 TTATGAATTT
274306 GTGATTTATACAGATC
1 GTGATTTATACAGATC
274322 GTGATTTATACAGATC
1 GTGATTTATACAGATC
274338 GTGATTTAT
1 GTGATTTAT
274347 TTGTGATTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (16 bp):
GTGATTTATACAGATC
Found at i:275155 original size:25 final size:24
Alignment explanation
Indices: 275119--275202 Score: 57
Period size: 25 Copynumber: 3.5 Consensus size: 24
275109 TTGGTAAGTA
275119 TATTGATAAAATAAGCTTACAAGCT
1 TATTGAT-AAATAAGCTTACAAGCT
* * *
275144 TATTGAATAAAT--GGTT-CATGGT
1 TATTG-ATAAATAAGCTTACAAGCT
* *
275166 ATATTGGTAAATAAGCTTACGAGCT
1 -TATTGATAAATAAGCTTACAAGCT
*
275191 TATGGAATAAAT
1 TATTG-ATAAAT
275203 GGTTTATAGC
Statistics
Matches: 43, Mismatches: 10, Indels: 12
0.66 0.15 0.18
Matches are distributed among these distances:
22 9 0.21
23 8 0.19
24 7 0.16
25 17 0.40
26 2 0.05
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (24 bp):
TATTGATAAATAAGCTTACAAGCT
Found at i:275183 original size:47 final size:46
Alignment explanation
Indices: 275036--275206 Score: 231
Period size: 45 Copynumber: 3.7 Consensus size: 46
275026 GGTAAACATG
* *
275036 AAAATAAGCTTACGAGCTTATGGAATAAATGG-TAAATATATTAGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTTAAGTATATTGGT
* * *
275081 AAAATAAGCTTACGAGCTTATGGATTAATTGG-TAAGTATATTGAT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTTAAGTATATTGGT
* * *
275126 AAAATAAGCTTACAAGCTTATTGAATAAATGGTTCATGGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTT-A-AGTATATTGGT
275174 -AAATAAGCTTACGAGCTTATGGAATAAATGGTT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTT
275207 TATAGCATTT
Statistics
Matches: 110, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
45 68 0.62
46 1 0.01
47 32 0.29
48 9 0.08
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (46 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTTAAGTATATTGGT
Found at i:275826 original size:24 final size:24
Alignment explanation
Indices: 275785--275838 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
275775 ATATATAGTT
*
275785 TATATAGCATATAAATAGATTGTA
1 TATATAGCATATAAATAGATTATA
* *
275809 TATATA-CATATATTATAGGTTATA
1 TATATAGCATATA-AATAGATTATA
275833 TATATA
1 TATATA
275839 TAGTTTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (24 bp):
TATATAGCATATAAATAGATTATA
Found at i:275838 original size:13 final size:14
Alignment explanation
Indices: 275816--275852 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
275806 GTATATATAC
275816 ATATAT-TATAGGTT
1 ATATATATATA-GTT
275830 ATATATATATAGTT
1 ATATATATATAGTT
275844 -TATATATAT
1 ATATATATAT
275853 TATACATAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.41
14 9 0.41
15 4 0.18
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (14 bp):
ATATATATATAGTT
Found at i:275840 original size:15 final size:15
Alignment explanation
Indices: 275816--275852 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
275806 GTATATATAC
275816 ATATAT-TATAGGTT
1 ATATATATATAGGTT
*
275830 ATATATATATAGTTT
1 ATATATATATAGGTT
275845 ATATATAT
1 ATATATAT
275853 TATACATAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (15 bp):
ATATATATATAGGTT
Found at i:275856 original size:20 final size:19
Alignment explanation
Indices: 275807--275867 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 19
275797 AAATAGATTG
275807 TATATATACATA-TATTATA
1 TATATATACATAGT-TTATA
*
275826 GGTTATATATATATAGTTTATA
1 ---TATATATACATAGTTTATA
275848 TATATTATACATAGTTTATA
1 TATA-TATACATAGTTTATA
275868 CATACATGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 4 0.11
20 14 0.40
22 16 0.46
23 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (19 bp):
TATATATACATAGTTTATA
Found at i:275893 original size:59 final size:59
Alignment explanation
Indices: 275775--275895 Score: 149
Period size: 57 Copynumber: 2.1 Consensus size: 59
275765 TTACAGTTAC
* * *
275775 ATATATAGTTTATATAGCATATAAATAGATTGTATATATACATATATTATAGGTTATAT
1 ATATATAGTTTATATAGCATATAAATAGATTGTATACATACATATACTATAAGTTATAT
* * * *
275834 ATATATAGTTTATATA-TATTATACATAG-TT-TATACATACATGTACTATAAGTTACAT
1 ATATATAGTTTATATAGCA-TATAAATAGATTGTATACATACATATACTATAAGTTATAT
275891 ATATA
1 ATATA
275896 GTTTACATGT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
57 27 0.50
58 3 0.06
59 24 0.44
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (59 bp):
ATATATAGTTTATATAGCATATAAATAGATTGTATACATACATATACTATAAGTTATAT
Found at i:275897 original size:35 final size:36
Alignment explanation
Indices: 275858--275931 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
275848 TATATTATAC
*
275858 ATAGTTT-ATACATACATGTACTATAAGTTACATAT
1 ATAGTTTAATACATACATATACTATAAGTTACATAT
** *
275893 ATAGTTTACATGTATACATATACTATAGGTTACATAT
1 ATAGTTTA-ATACATACATATACTATAAGTTACATAT
275930 AT
1 AT
275932 TAACTATTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 7 0.21
37 26 0.79
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (36 bp):
ATAGTTTAATACATACATATACTATAAGTTACATAT
Found at i:276022 original size:2 final size:2
Alignment explanation
Indices: 276015--276052 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
276005 TTTCTATAAA
*
276015 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT AT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
276053 ATATATATAT
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:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:276086 original size:25 final size:25
Alignment explanation
Indices: 276052--276352 Score: 149
Period size: 25 Copynumber: 12.3 Consensus size: 25
276042 TCTCTATCTC
276052 TATATATATATTATATATATATATA
1 TATATATATATTATATATATATATA
276077 TATATATATA-TATATATATATATA
1 TATATATATATTATATATATATATA
* *
276101 TATA-ATATA-TATCTATAAAT-TA
1 TATATATATATTATATATATATATA
* *
276123 CT-TATAT-TAGTTAGATACATATATA
1 -TATATATATA-TTATATATATATATA
* *
276148 CTATAAATAAATTATA-AT-T-TATA
1 -TATATATATATTATATATATATATA
* *
276171 -A-ACTATATATTTTATATAGTTTATA
1 TATA-TATATATTATATATA-TATATA
* * *
276196 CATATATAGT-TTATATACATACATA
1 TATATATA-TATTATATATATATATA
276221 TATATATATATTATAT-TA-ATATA
1 TATATATATATTATATATATATATA
* *
276244 -A-AT-TATATTTTATAAACTATATA
1 TATATATATATTATATATA-TATATA
* * * *
276267 CTTTTTATAGT-TTATATAAACAGTATA
1 -TATATATA-TATTATATATATA-TATA
* *
276294 TAAATATATA-TAGTATATAAATATA
1 TATATATATATTA-TATATATATATA
*
276319 AACTATA-AT-TTATATATATAGTATA
1 TA-TATATATATTATATATATA-TATA
276344 TACTATATA
1 TA-TATATA
276353 AATAGTTTAT
Statistics
Matches: 210, Mismatches: 35, Indels: 61
0.69 0.11 0.20
Matches are distributed among these distances:
20 10 0.05
21 12 0.06
22 9 0.04
23 30 0.14
24 36 0.17
25 58 0.28
26 37 0.18
27 17 0.08
28 1 0.00
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (25 bp):
TATATATATATTATATATATATATA
Found at i:276365 original size:2 final size:2
Alignment explanation
Indices: 276052--276352 Score: 137
Period size: 2 Copynumber: 151.0 Consensus size: 2
276042 TCTCTATCTC
276052 TA TA TA TA TA T- 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 TA TA TA TA
* *
276093 TA TA TA TA TA TA -A TA TA TA TC TA TA AA T- TA CT- TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * * * * *
276132 GT- TA GA TA CA TA TA TA CTA TA AA TA AA T- TA TA -A TT TA TA AA
1 -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
276173 CTA TA TA T- TT TA TA TA GTT TA TA CA TA TA TA GTT TA TA TA CA
1 -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA
* *
276215 TA CA TA TA TA TA TA TA T- TA TA T- TA -A TA TA AA T- TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
276252 TT TA TA AA CTA TA TA CTT TT TA TA GTT TA TA TA AA CA GTA TA TA
1 TA TA TA TA -TA TA TA -TA TA TA TA -TA TA TA TA TA TA -TA TA TA
* * * *
276296 AA TA TA TA TA GTA TA TA AA TA TA AA CTA TA -A TT TA TA TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
276339 GTA TA TA CTA TA TA
1 -TA TA TA -TA TA TA
276353 AATAGTTTAT
Statistics
Matches: 223, Mismatches: 47, Indels: 58
0.68 0.14 0.18
Matches are distributed among these distances:
1 15 0.07
2 190 0.85
3 18 0.08
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:276433 original size:9 final size:9
Alignment explanation
Indices: 276404--276434 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
276394 ATATGTAAAC
276404 TATATAGTT
1 TATATAGTT
*
276413 TACATAGTT
1 TATATAGTT
276422 TATATAGTT
1 TATATAGTT
276431 TATA
1 TATA
276435 CGTATACTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (9 bp):
TATATAGTT
Found at i:276479 original size:11 final size:10
Alignment explanation
Indices: 276465--276516 Score: 52
Period size: 11 Copynumber: 5.1 Consensus size: 10
276455 TATATTGTAT
276465 ATATAGTTTA
1 ATATAGTTTA
*
276475 CATATAGTATA
1 -ATATAGTTTA
*
276486 ATTTAGTTT-
1 ATATAGTTTA
*
276495 ATATTGTTTA
1 ATATAGTTTA
276505 TATATAGTTTA
1 -ATATAGTTTA
276516 A
1 A
276517 ATACTACTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
9 7 0.21
10 8 0.24
11 18 0.55
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.52
Consensus pattern (10 bp):
ATATAGTTTA
Found at i:276646 original size:22 final size:22
Alignment explanation
Indices: 276597--276653 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
276587 CCGTAAATCA
* *
276597 TATATTATATATATATAAAAAC
1 TATATAATTTATATATAAAAAC
*
276619 TATATAGTTTATAT-TAATAAAC
1 TATATAATTTATATATAA-AAAC
276641 TATATAATTTATA
1 TATATAATTTATA
276654 CAATATTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 3 0.10
22 27 0.90
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.46
Consensus pattern (22 bp):
TATATAATTTATATATAAAAAC
Found at i:276723 original size:20 final size:20
Alignment explanation
Indices: 276690--276927 Score: 65
Period size: 20 Copynumber: 12.3 Consensus size: 20
276680 TAATATATAA
* *
276690 ATATAAATTGTATAGTTTAT
1 ATATAATTTATATAGTTTAT
*
276710 ATATAATTTATATA-TTAACT
1 ATATAATTTATATAGTTTA-T
*
276730 ATGTAA-TT-TATA--TTA-
1 ATATAATTTATATAGTTTAT
* *
276745 ATA-AA-TTATGTAGTTTCT
1 ATATAATTTATATAGTTTAT
* * **
276763 ATATAGTTCA-ATAGTTCCT
1 ATATAATTTATATAGTTTAT
*
276782 ATATAAATTATATAG--TAT
1 ATATAATTTATATAGTTTAT
* * *
276800 -TATAGTTTATACA-TGGTAT
1 ATATAATTTATATAGT-TTAT
* * *
276819 ATATAGTTTATACATAATATAT
1 ATATAATTTAT--ATAGTTTAT
276841 ATATAA--TATATAGTTTAT
1 ATATAATTTATATAGTTTAT
* * * * *
276859 ATATAGTATATAATAATATAA
1 ATATAATTTAT-ATAGTTTAT
**
276880 ATATAAACTATATAGTTTATAT
1 ATATAATTTATATAG-TT-TAT
** *
276902 ATATAATACATATACTTTAT
1 ATATAATTTATATAGTTTAT
276922 ATATAA
1 ATATAA
276928 ACCACATAGT
Statistics
Matches: 159, Mismatches: 39, Indels: 40
0.67 0.16 0.17
Matches are distributed among these distances:
14 4 0.03
15 5 0.03
17 14 0.09
18 20 0.13
19 23 0.14
20 52 0.33
21 17 0.11
22 23 0.14
23 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.46
Consensus pattern (20 bp):
ATATAATTTATATAGTTTAT
Found at i:276823 original size:2 final size:2
Alignment explanation
Indices: 276816--276970 Score: 81
Period size: 2 Copynumber: 77.0 Consensus size: 2
276806 TTATACATGG
* * *
276816 TA TA TA TA GTT TA TA CA TA -A TA TA TA TA TA -A TA TA TA GTT TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * *
276858 TA TA TA GTA TA TA -A TA -A TA TA AA TA TA AA CTA TA TA GTT TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA
* * * * * *
276899 TA TA TA TA -A TA CA TA TA CTT TA TA TA TA AA CCA CA TA GTT TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA -TA TA
276941 TA T- TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
276971 GTTGTTTCAT
Statistics
Matches: 117, Mismatches: 21, Indels: 30
0.70 0.12 0.18
Matches are distributed among these distances:
1 7 0.06
2 101 0.86
3 9 0.08
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:276850 original size:29 final size:28
Alignment explanation
Indices: 276817--276878 Score: 97
Period size: 29 Copynumber: 2.2 Consensus size: 28
276807 TATACATGGT
276817 ATATATAGTTTATACATAATATATATATA
1 ATATATAGTTTATACATAATATATA-ATA
* *
276846 ATATATAGTTTATATATAGTATATAATA
1 ATATATAGTTTATACATAATATATAATA
276874 ATATA
1 ATATA
276879 AATATAAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 8 0.26
29 23 0.74
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (28 bp):
ATATATAGTTTATACATAATATATAATA
Found at i:276970 original size:11 final size:11
Alignment explanation
Indices: 276835--276970 Score: 61
Period size: 11 Copynumber: 12.3 Consensus size: 11
276825 TTTATACATA
276835 ATATATATA-T
1 ATATATATATT
276845 A-ATATATAGTT
1 ATATATATA-TT
*
276856 -TATATATAGT
1 ATATATATATT
*
276866 ATATA-ATAAT
1 ATATATATATT
* *
276876 ATAAATATA-A
1 ATATATATATT
276886 ACTATATAGT-TT
1 A-TATATA-TATT
*
276898 ATATATATAAT
1 ATATATATATT
*
276909 ACATATACT-TT
1 ATATATA-TATT
* **
276920 ATATATAAACCAC
1 ATATATATA--TT
*
276933 ATAGTTTATATT
1 ATA-TATATATT
276945 ATATATATATAT
1 ATATATATAT-T
276957 ATATATATATT
1 ATATATATATT
276968 ATA
1 ATA
276971 GTTGTTTCAT
Statistics
Matches: 93, Mismatches: 18, Indels: 29
0.66 0.13 0.21
Matches are distributed among these distances:
9 7 0.08
10 12 0.13
11 50 0.54
12 17 0.18
13 3 0.03
14 4 0.04
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (11 bp):
ATATATATATT
Found at i:277690 original size:215 final size:214
Alignment explanation
Indices: 277068--277781 Score: 1218
Period size: 215 Copynumber: 3.3 Consensus size: 214
277058 AATCCCATTT
*
277068 TGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTTAATTTAGTCCTTAAAATT
1 TGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAAATT
* *
277133 ATATTTGCAACTGAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTT
66 ATATTTGCATCTGAAATTGACCCATACTTATTACTTATTTATATTTTTTAATTGGCCCATAACTT
277198 TTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTAAACCTCACAATTTAAAATTATTTCG
131 TTTAAAT-GGTATAATTTAGTAC-TTTTTGTATTAATTTAAACCTCACAATTTAAAATTATTTCG
277263 ATTTGATCCCTCATCAATGTG
194 ATTTGATCCCTCATCAATGTG
* *
277284 TGTTATTTAATTTATTTAAATTTTAATTTGTGATTTCATATTTGTTCAATTTAGTCCTTAAAATT
1 TGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAAATT
277349 ATATTTGCATCTGAAA---ACCCATACTTATTACTTATTTATATTTTTTAATTGGCCCATAACTT
66 ATATTTGCATCTGAAATTGACCCATACTTATTACTTATTTATATTTTTTAATTGGCCCATAACTT
277411 TTTAAATGGTATAATTTAGTACTTTTCTGTATTAATTTAAACCTCACAATTTAAAATTATTTCGA
131 TTTAAATGGTATAATTTAGTACTTTT-TGTATTAATTTAAACCTCACAATTTAAAATTATTTCGA
*
277476 TTTTATCCCTCATCAATGTG
195 TTTGATCCCTCATCAATGTG
*
277496 TGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTATTCAATTTAGTCCTTAAAATT
1 TGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAAATT
*
277561 ATATTTGCATCTGAAATTGACCCATACTTATTACTTATTTATATTTTTTAATTGACCCATAACTT
66 ATATTTGCATCTGAAATTGACCCATACTTATTACTTATTTATATTTTTTAATTGGCCCATAACTT
277626 TTTAAATGGTATAATTTAGTACTTTATTGTATTAATTTAAACCTCACAATTTAAAATTATTTCGA
131 TTTAAATGGTATAATTTAGTACTTT-TTGTATTAATTTAAACCTCACAATTTAAAATTATTTCGA
***
277691 TTTGATCCCTCATCAATACA
195 TTTGATCCCTCATCAATGTG
* * * * *
277711 TGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATAATTGTTTAATTTAATTCTTAAATTT
1 TGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAAATT
*
277776 GTATTT
66 ATATTT
277782 TTCATAAAAT
Statistics
Matches: 472, Mismatches: 21, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
211 4 0.01
212 150 0.32
213 52 0.11
215 188 0.40
216 78 0.17
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (214 bp):
TGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAAATT
ATATTTGCATCTGAAATTGACCCATACTTATTACTTATTTATATTTTTTAATTGGCCCATAACTT
TTTAAATGGTATAATTTAGTACTTTTTGTATTAATTTAAACCTCACAATTTAAAATTATTTCGAT
TTGATCCCTCATCAATGTG
Found at i:279754 original size:64 final size:65
Alignment explanation
Indices: 279658--279783 Score: 209
Period size: 64 Copynumber: 2.0 Consensus size: 65
279648 AAGAAATTTC
*
279658 AAGTTTTAATCATTGCTTTAAGTATAATTATTTACTAAGATAATTGTAAGGTTGGTATAAGTGTT
1 AAGTTTTAATCATTGCTTTAAGTATAATTATTTACTAAGATAATTGTAAGGTTGGTACAAGTGTT
* * *
279723 AAGTTTTGATCATTTC-TTGAGTATAATTATTTACTAAGATAATTGTAAGGTTGGTACAAGT
1 AAGTTTTAATCATTGCTTTAAGTATAATTATTTACTAAGATAATTGTAAGGTTGGTACAAGT
279784 CTTATTTGAG
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
64 43 0.75
65 14 0.25
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (65 bp):
AAGTTTTAATCATTGCTTTAAGTATAATTATTTACTAAGATAATTGTAAGGTTGGTACAAGTGTT
Found at i:285972 original size:50 final size:50
Alignment explanation
Indices: 285897--285999 Score: 206
Period size: 50 Copynumber: 2.1 Consensus size: 50
285887 TTGAAGTAGG
285897 ATTTGAGTCGTATCTCTTGTCTCAACAATGTTAATGATAAGGTTATGCTT
1 ATTTGAGTCGTATCTCTTGTCTCAACAATGTTAATGATAAGGTTATGCTT
285947 ATTTGAGTCGTATCTCTTGTCTCAACAATGTTAATGATAAGGTTATGCTT
1 ATTTGAGTCGTATCTCTTGTCTCAACAATGTTAATGATAAGGTTATGCTT
285997 ATT
1 ATT
286000 ATTGGGGATC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (50 bp):
ATTTGAGTCGTATCTCTTGTCTCAACAATGTTAATGATAAGGTTATGCTT
Found at i:286531 original size:27 final size:27
Alignment explanation
Indices: 286493--286557 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
286483 TTAAACGAGC
286493 CGAGTCGAACTCAAGTATTGCTAAGCT
1 CGAGTCGAACTCAAGTATTGCTAAGCT
*
286520 CGAGTCGAACTCGAGTATTGCTAAGCT
1 CGAGTCGAACTCAAGTATTGCTAAGCT
*
286547 CGACTCGAACT
1 CGAGTCGAACT
286558 TAAAAACTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (27 bp):
CGAGTCGAACTCAAGTATTGCTAAGCT
Found at i:288592 original size:29 final size:29
Alignment explanation
Indices: 288510--288581 Score: 135
Period size: 29 Copynumber: 2.5 Consensus size: 29
288500 CCCAAAACAT
*
288510 AGGTCGCCATGCCCTCCGGGCGACCAAGG
1 AGGTCGCCATGCACTCCGGGCGACCAAGG
288539 AGGTCGCCATGCACTCCGGGCGACCAAGG
1 AGGTCGCCATGCACTCCGGGCGACCAAGG
288568 AGGTCGCCATGCAC
1 AGGTCGCCATGCAC
288582 GCCCCGCGAC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.19, C:0.36, G:0.33, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCGGGCGACCAAGG
Found at i:288640 original size:22 final size:22
Alignment explanation
Indices: 288608--288656 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
288598 TTTGGCCCTA
*
288608 CTCCCCGCTGCATGCTCACCTG
1 CTCCCCACTGCATGCTCACCTG
*
288630 CTCCCCACTGCATGCTCGCCTG
1 CTCCCCACTGCATGCTCACCTG
288652 CTCCC
1 CTCCC
288657 GCTACTCCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.08, C:0.53, G:0.16, T:0.22
Consensus pattern (22 bp):
CTCCCCACTGCATGCTCACCTG
Found at i:288985 original size:11 final size:11
Alignment explanation
Indices: 288969--288995 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
288959 TTATTAGTTT
288969 GTTAGTTTAGG
1 GTTAGTTTAGG
288980 GTTAGTTTAGG
1 GTTAGTTTAGG
288991 GTTAG
1 GTTAG
288996 GGTAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.37, T:0.44
Consensus pattern (11 bp):
GTTAGTTTAGG
Found at i:289200 original size:30 final size:30
Alignment explanation
Indices: 289132--289236 Score: 140
Period size: 30 Copynumber: 3.4 Consensus size: 30
289122 TTTAGTTAAT
* *
289132 TAGTTTTTTAGTAGTGAA-TTATAATTAAAAAA
1 TAGTTTATTAGT--TGAAGTTAT-ATTAAAGAA
* *
289164 TCGTTTATTAGTTTAAGTTATATTAAAGAA
1 TAGTTTATTAGTTGAAGTTATATTAAAGAA
289194 TAGTTTATTAGTTGAAGTTATATTAAAGAA
1 TAGTTTATTAGTTGAAGTTATATTAAAGAA
289224 TAGTTTATTAGTT
1 TAGTTTATTAGTT
289237 ATTTAAAGAA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
30 52 0.79
31 4 0.06
32 10 0.15
ACGTcount: A:0.38, C:0.01, G:0.14, T:0.47
Consensus pattern (30 bp):
TAGTTTATTAGTTGAAGTTATATTAAAGAA
Found at i:289227 original size:22 final size:22
Alignment explanation
Indices: 289202--289246 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
289192 AATAGTTTAT
289202 TAGTTGA-AGTTATATTAAAGAA
1 TAGTTGATAGTTAT-TTAAAGAA
*
289224 TAGTTTATTAGTTATTTAAAGAA
1 TAGTTGA-TAGTTATTTAAAGAA
289247 AATTCACGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 6 0.30
23 8 0.40
24 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (22 bp):
TAGTTGATAGTTATTTAAAGAA
Found at i:289232 original size:15 final size:16
Alignment explanation
Indices: 289179--289233 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
289169 TATTAGTTTA
289179 AGTTATATTAAAGAAT
1 AGTTATATTAAAGAAT
**
289195 AGTT-TATTAGTTG-A-
1 AGTTATATTA-AAGAAT
289209 AGTTATATTAAAGAAT
1 AGTTATATTAAAGAAT
289225 AGTT-TATTA
1 AGTTATATTA
289234 GTTATTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
14 5 0.16
15 17 0.55
16 9 0.29
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.44
Consensus pattern (16 bp):
AGTTATATTAAAGAAT
Found at i:289304 original size:16 final size:16
Alignment explanation
Indices: 289279--289314 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
289269 TAAAAAGTTT
*
289279 AGTTTGTTACTTTATA
1 AGTTTGTTACATTATA
*
289295 AGTTTTTTACATTATA
1 AGTTTGTTACATTATA
289311 AGTT
1 AGTT
289315 ATTATATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.11, T:0.56
Consensus pattern (16 bp):
AGTTTGTTACATTATA
Found at i:289355 original size:4 final size:4
Alignment explanation
Indices: 289346--289372 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
289336 GGGTTGTAAA
289346 TTAG TTAG TTAG TTAG TTAG TTAG TTA
1 TTAG TTAG TTAG TTAG TTAG TTAG TTA
289373 ACATTAGATT
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:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TTAG
Found at i:291617 original size:22 final size:22
Alignment explanation
Indices: 291592--291645 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
291582 AAATATATTT
291592 TATTATTAACTTAATTTAAAAA
1 TATTATTAACTTAATTTAAAAA
** *
291614 TATT-TTATTTTTTATTTAAAAA
1 TATTATTA-ACTTAATTTAAAAA
291636 TATATATTAA
1 TAT-TATTAA
291646 ATAATATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
21 3 0.12
22 18 0.72
23 1 0.04
24 3 0.12
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
TATTATTAACTTAATTTAAAAA
Found at i:291703 original size:42 final size:41
Alignment explanation
Indices: 291639--291744 Score: 133
Period size: 42 Copynumber: 2.5 Consensus size: 41
291629 TTAAAAATAT
*
291639 ATATTAAATAATATT-TTAAATCATTAGTATCAAATAATTAA
1 ATATT-AATAATATTAATAAATCATTAGTATCAAATAATTAA
* *
291680 ATATTAATAATAATTAGTAAATCATTAGTATCAAATCATTAA
1 ATATTAATAAT-ATTAATAAATCATTAGTATCAAATAATTAA
*
291722 ATATTTAAAAATCATTAATAAAT
1 ATA-TTAATAAT-ATTAATAAAT
291745 TCGACTATGT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
40 6 0.11
41 8 0.14
42 27 0.47
43 16 0.28
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.40
Consensus pattern (41 bp):
ATATTAATAATATTAATAAATCATTAGTATCAAATAATTAA
Found at i:291844 original size:14 final size:13
Alignment explanation
Indices: 291825--292108 Score: 76
Period size: 14 Copynumber: 22.0 Consensus size: 13
291815 TAGTAATAAT
291825 TATTAAATCATTA
1 TATTAAATCATTA
291838 GTATTAAATCATTA
1 -TATTAAATCATTA
*
291852 TTATAAAATCA-T-
1 -TATTAAATCATTA
*
291864 TACTAAATCATTA
1 TATTAAATCATTA
291877 CTATTAAATCA-T-
1 -TATTAAATCATTA
291889 TATT--ATCA-T-
1 TATTAAATCATTA
*
291898 TATTATAATGATTA
1 TATTA-AATCATTA
*
291912 TTACTAAATCATTA
1 -TATTAAATCATTA
*
291926 T-TGT-AATGATTA
1 TAT-TAAATCATTA
* *
291938 TTATCAAATTATTAAA
1 -TATTAAATCATT--A
291954 TATTTAAATCA-T-
1 TA-TTAAATCATTA
*
291966 TATTAAATAATTA
1 TATTAAATCATTA
291979 T-TATAATGATCA-T-
1 TAT-TAA--ATCATTA
291992 TATTAAATCATTA
1 TATTAAATCATTA
292005 T-TATAATGATCA-T-
1 TAT-TAA--ATCATTA
292018 TATTAAATCATTA
1 TATTAAATCATTA
*
292031 CTA-T-AATGATTA
1 -TATTAAATCATTA
*
292043 TTACTAAATCATTA
1 -TATTAAATCATTA
*
292057 CTA-T-AATGATTA
1 -TATTAAATCATTA
*
292069 TTATCAAATCATTA
1 -TATTAAATCATTA
*
292083 CTA-T-AATGATTA
1 -TATTAAATCATTA
*
292095 TTATCAAATCATTA
1 -TATTAAATCATTA
292109 CTGAATCATC
Statistics
Matches: 203, Mismatches: 30, Indels: 74
0.66 0.10 0.24
Matches are distributed among these distances:
9 9 0.04
11 27 0.13
12 45 0.22
13 25 0.12
14 76 0.37
15 14 0.07
16 7 0.03
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (13 bp):
TATTAAATCATTA
Found at i:291922 original size:26 final size:25
Alignment explanation
Indices: 291810--292108 Score: 245
Period size: 26 Copynumber: 11.7 Consensus size: 25
291800 TTATTCTATA
* *
291810 ATTATTAGT-AATAATTATTA-AATC
1 ATTATTA-TAAATCATTATTATAATG
* *
291834 ATTAGTATTAAATCATTATTATAA-A
1 ATTATTA-TAAATCATTATTATAATG
* *
291859 ATCATTACTAAATCATTACTATTAA--
1 ATTATTA-TAAATCATTATTA-TAATG
* *
291884 ATCATTAT-TATCATTATTATAATG
1 ATTATTATAAATCATTATTATAATG
*
291908 ATTATTACTAAATCATTATTGTAATG
1 ATTATTA-TAAATCATTATTATAATG
* *
291934 ATTATTATCAAATTATTAAATATTTAA--
1 ATTATTAT-AAATCATT--AT-TATAATG
* *
291961 ATCATTATTAAATAATTATTATAATG
1 ATTATTA-TAAATCATTATTATAATG
*
291987 ATCATTATTAAATCATTATTATAATG
1 ATTATTA-TAAATCATTATTATAATG
* *
292013 ATCATTATTAAATCATTACTATAATG
1 ATTATTA-TAAATCATTATTATAATG
*
292039 ATTATTACTAAATCATTACTATAATG
1 ATTATTA-TAAATCATTATTATAATG
*
292065 ATTATTATCAAATCATTACTATAATG
1 ATTATTAT-AAATCATTATTATAATG
292091 ATTATTATCAAATCATTA
1 ATTATTAT-AAATCATTA
292109 CTGAATCATC
Statistics
Matches: 238, Mismatches: 22, Indels: 28
0.83 0.08 0.10
Matches are distributed among these distances:
22 3 0.01
23 9 0.04
24 18 0.08
25 39 0.16
26 149 0.63
27 13 0.05
28 3 0.01
29 4 0.02
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.45
Consensus pattern (25 bp):
ATTATTATAAATCATTATTATAATG
Found at i:292025 original size:105 final size:102
Alignment explanation
Indices: 291857--292045 Score: 272
Period size: 105 Copynumber: 1.8 Consensus size: 102
291847 CATTATTATA
* *
291857 AAATCATTACTAAATCATTACTATTAAATCATTATTATCATTATTATAATGATTATTACTAAATC
1 AAATCATTACTAAATAATTACTATTAAATCATTATTATCATTATTATAATGATCATTACTAAATC
* *
291922 ATTATTGTAATGATTATTATCAAATTATTAAATATTT
66 ATTACTATAATGATTATTATCAAATTATTAAATATTT
* * *
291959 AAATCATTATTAAATAATTATTA-TAATGATCATTATTAAATCATTATTATAATGATCATTATTA
1 AAATCATTACTAAATAATTACTATTAA--ATCATTATT--ATCATTATTATAATGATCATTACTA
292023 AATCATTACTATAATGATTATTA
62 AATCATTACTATAATGATTATTA
292046 CTAAATCATT
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
101 3 0.04
102 20 0.26
103 9 0.12
105 44 0.58
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (102 bp):
AAATCATTACTAAATAATTACTATTAAATCATTATTATCATTATTATAATGATCATTACTAAATC
ATTACTATAATGATTATTATCAAATTATTAAATATTT
Found at i:292037 original size:52 final size:52
Alignment explanation
Indices: 291834--292108 Score: 294
Period size: 52 Copynumber: 5.3 Consensus size: 52
291824 TTATTAAATC
* * *
291834 ATTAGTATTAAATCATTATTATAA-AATCATTACTAAATCATTACTATTAA--
1 ATTATTATTAAATCATTATTATAATGATCATTATTAAATCATTACTA-TAATG
* * * * *
291884 ATCATTATT--ATCATTATTATAATGATTATTACTAAATCATTATTGTAATG
1 ATTATTATTAAATCATTATTATAATGATCATTATTAAATCATTACTATAATG
* * * * *
291934 ATTATTATCAAATTATTAAATATTTAA--ATCATTATTAAATAATTATTATAATG
1 ATTATTATTAAATCATT--AT-TATAATGATCATTATTAAATCATTACTATAATG
*
291987 ATCATTATTAAATCATTATTATAATGATCATTATTAAATCATTACTATAATG
1 ATTATTATTAAATCATTATTATAATGATCATTATTAAATCATTACTATAATG
* * * *
292039 ATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTACTATAATG
1 ATTATTATTAAATCATTATTATAATGATCATTATTAAATCATTACTATAATG
*
292091 ATTATTATCAAATCATTA
1 ATTATTATTAAATCATTA
292109 CTGAATCATC
Statistics
Matches: 188, Mismatches: 27, Indels: 18
0.81 0.12 0.08
Matches are distributed among these distances:
48 16 0.09
49 18 0.10
50 18 0.10
51 2 0.01
52 92 0.49
53 36 0.19
54 2 0.01
55 4 0.02
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (52 bp):
ATTATTATTAAATCATTATTATAATGATCATTATTAAATCATTACTATAATG
Found at i:292047 original size:131 final size:127
Alignment explanation
Indices: 291839--292082 Score: 364
Period size: 131 Copynumber: 1.9 Consensus size: 127
291829 AAATCATTAG
* *
291839 TATTAAATCATTATTATAAAATCATTACTAAATCATTACTATTAAATCATTATTATCATTATTAT
1 TATTAAATAATTATTATAAAATCATTACTAAATCATTACTATTAAATCATTATTATCATTACTAT
* * *
291904 AATGATTATTACTAAATCATTATTGTAATGATTATTATCAAATTATTAAATATTTAAATCAT
66 AATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTAAATATTTAAATCAT
* * *
291966 TATTAAATAATTATTATAATGATCATTATTAAATCATTATTA-TAATGATCATTATTAAATCATT
1 TATTAAATAATTATTATAA-AATCATTACTAAATCATTACTATTAA--ATCATTATT--ATCATT
292030 ACTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTA
61 ACTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTA
292083 CTATAATGAT
Statistics
Matches: 104, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
127 21 0.20
128 19 0.18
129 9 0.09
131 55 0.53
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (127 bp):
TATTAAATAATTATTATAAAATCATTACTAAATCATTACTATTAAATCATTATTATCATTACTAT
AATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTAAATATTTAAATCAT
Found at i:292401 original size:12 final size:12
Alignment explanation
Indices: 292384--292442 Score: 70
Period size: 12 Copynumber: 5.1 Consensus size: 12
292374 ATTCATTAAA
292384 TATTAAATTCAT
1 TATTAAATTCAT
*
292396 TATTAAATTTAT
1 TATTAAATTCAT
*
292408 TATGAAA-TCAT
1 TATTAAATTCAT
292419 TATTTAAATT-AT
1 TA-TTAAATTCAT
292431 TATTAAA-TCAT
1 TATTAAATTCAT
292442 T
1 T
292443 TTTATGGTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
10 1 0.03
11 13 0.32
12 25 0.62
13 1 0.03
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (12 bp):
TATTAAATTCAT
Found at i:292419 original size:23 final size:23
Alignment explanation
Indices: 292392--292446 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
292382 AATATTAAAT
292392 TCATTA-TTAAATTTATTATGAAA
1 TCATTATTTAAA-TTATTATGAAA
*
292415 TCATTATTTAAATTATTATTAAA
1 TCATTATTTAAATTATTATGAAA
292438 TCATT-TTTA
1 TCATTATTTA
292447 TGGTTAATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 4 0.13
23 21 0.70
24 5 0.17
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (23 bp):
TCATTATTTAAATTATTATGAAA
Found at i:292772 original size:22 final size:22
Alignment explanation
Indices: 292598--292674 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
292588 TATTATAAAA
292598 TCATTAAATATTAATAATAATT
1 TCATTAAATATTAATAATAATT
* *
292620 TCATTATTACTAATCATTACT-ATCAA-A
1 TC---ATTA--AAT-ATTAATAAT-AATT
292647 TCATTAAATATTAATAATAATT
1 TCATTAAATATTAATAATAATT
292669 TCATTA
1 TCATTA
292675 TTACTAATCA
Statistics
Matches: 42, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
21 7 0.17
22 13 0.31
24 4 0.10
25 4 0.10
27 7 0.17
28 7 0.17
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.44
Consensus pattern (22 bp):
TCATTAAATATTAATAATAATT
Found at i:292796 original size:14 final size:14
Alignment explanation
Indices: 292777--292803 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
292767 TCATTATTAC
292777 TAATCATTACTATA
1 TAATCATTACTATA
292791 TAATCATTACTAT
1 TAATCATTACTAT
292804 CAAATAATTA
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:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (14 bp):
TAATCATTACTATA
Found at i:292811 original size:49 final size:49
Alignment explanation
Indices: 292586--292799 Score: 385
Period size: 49 Copynumber: 4.4 Consensus size: 49
292576 TTAAATCATT
* *
292586 ATTATTATAAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
292635 ATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
292684 ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
292733 ATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
292782 ATTACTAT-ATAATCATTA
1 ATTACTATCA-AATCATTA
292800 CTATCAAATA
Statistics
Matches: 160, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
48 1 0.01
49 159 0.99
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (49 bp):
ATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
Found at i:292841 original size:21 final size:21
Alignment explanation
Indices: 292745--292841 Score: 51
Period size: 21 Copynumber: 4.6 Consensus size: 21
292735 TACTATCAAA
*
292745 TCATTAAATATTAATAATAATT
1 TCATT-AATATTACTAATAATT
*
292767 TCA-T--TATTACTAATCATT
1 TCATTAATATTACTAATAATT
* *
292785 ACTATATAATCATTACT-ATCAA-A
1 TC-AT-TAAT-ATTACTAAT-AATT
* *
292808 TAATTAAAAATTACTAATAATT
1 TCATT-AATATTACTAATAATT
292830 TCATTAATATTA
1 TCATTAATATTA
292842 GTTATGTAAC
Statistics
Matches: 54, Mismatches: 11, Indels: 21
0.63 0.13 0.24
Matches are distributed among these distances:
18 13 0.24
19 1 0.02
21 17 0.31
22 13 0.24
23 3 0.06
24 7 0.13
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.43
Consensus pattern (21 bp):
TCATTAATATTACTAATAATT
Found at i:294364 original size:30 final size:30
Alignment explanation
Indices: 294330--294402 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
294320 CCCGAAGGAC
294330 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
294360 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
294390 CTGTCCATAGGTC
1 CTATCCAGAGGTC
294403 CCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:294426 original size:31 final size:31
Alignment explanation
Indices: 294388--294515 Score: 152
Period size: 31 Copynumber: 4.1 Consensus size: 31
294378 GATCCTCGGT
* * *
294388 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
**
294419 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
*
294450 TACTGTCCATATGTAT-CGAA-AGACATAGGTAA
1 AACTGTCCATATGT-TCCGAAGA-ACATAGGT-A
*
294482 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
294513 AAC
1 AAC
294516 CCTCGACTCT
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.01
31 54 0.66
32 26 0.32
33 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGAAGAACATAGGTA
Found at i:295913 original size:21 final size:21
Alignment explanation
Indices: 295889--295933 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
295879 TTTTGTTCGT
* *
295889 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
295910 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
295931 TTG
1 TTG
295934 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:299761 original size:29 final size:28
Alignment explanation
Indices: 299684--299789 Score: 133
Period size: 29 Copynumber: 3.7 Consensus size: 28
299674 TTGGACGCCG
** *
299684 GGCGTGCATGGCGACCTATAAGGTCGCT
1 GGCGTGCATGGCGACCTACCATGTCGCT
299712 GTGCGTGCATGGCGACCTACCATGTCGCCT
1 G-GCGTGCATGGCGACCTACCATGTCG-CT
299742 GGCGTGCATGGCGACCTACCATGTCGCT
1 GGCGTGCATGGCGACCTACCATGTCGCT
*
299770 GG-GATGCCCTGGCGACCTAC
1 GGCG-TG-CATGGCGACCTAC
299790 GACAACACTG
Statistics
Matches: 70, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
27 1 0.01
28 7 0.10
29 59 0.84
30 3 0.04
ACGTcount: A:0.15, C:0.31, G:0.33, T:0.21
Consensus pattern (28 bp):
GGCGTGCATGGCGACCTACCATGTCGCT
Found at i:303144 original size:31 final size:31
Alignment explanation
Indices: 303108--303167 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
303098 GTACAAGAAG
303108 ATAGTTTGAATTTCTTTAGAAGACATACCAA
1 ATAGTTTGAATTTCTTTAGAAGACATACCAA
* *
303139 ATAGTTTGAATTTCTTTCGAAGGCATACC
1 ATAGTTTGAATTTCTTTAGAAGACATACC
303168 GGATTTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (31 bp):
ATAGTTTGAATTTCTTTAGAAGACATACCAA
Found at i:308385 original size:112 final size:112
Alignment explanation
Indices: 308058--308539 Score: 708
Period size: 112 Copynumber: 4.3 Consensus size: 112
308048 AACTTTCAAC
* ** * * *
308058 AAAGTATCGATACATGTACAAAAAGTATCTATACTTTCAACATATTAGGTAGCTCTTTACCGGTT
1 AAAGTATCGATACATTTTTATAAAGTATCGATACTTTCAACATATCAGGTAGCTCTTTACCGGTT
*
308123 TTGTCATAATGAAACT-GATTTTGTCATATTTTTACCTGTTATATTAT
66 TTGTCATAATGAAACTAG-TTTTGTCATATTTTTACCTGTTATATTGT
* * *
308170 AAAGTATCGATACATTTTTATAAAAAGTATCGATACTTTCAATATATTAGGTAG-----TACCAG
1 AAAGTATCGATACATTTTTAT--AAAGTATCGATACTTTCAACATATCAGGTAGCTCTTTACCGG
*
308230 TTTTGTCATAATGAAACTACTTTTGTCATATTTTTACCTGTTATATTGT
64 TTTTGTCATAATGAAACTAGTTTTGTCATATTTTTACCTGTTATATTGT
** *
308279 AAAGTATAAATACATTTTTATAAAGTGTCGATACTTTCAACATATCAGGTAGCTCTTTACCGGTT
1 AAAGTATCGATACATTTTTATAAAGTATCGATACTTTCAACATATCAGGTAGCTCTTTACCGGTT
*
308344 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
66 TTGTCATAATGAAACTAGTTTTGTCATATTTTTACCTGTTATATTGT
* *
308391 AAAATATCGATACATTTTTTTAAAGTATCGATACTTT-AGACATATCAGGTAGCTCTTTACCGGT
1 AAAGTATCGATACATTTTTATAAAGTATCGATACTTTCA-ACATATCAGGTAGCTCTTTACCGGT
308455 TTTGTCATAATGAAACTAGTTTTGTCATATTTTTACCTGTTATATTGT
65 TTTGTCATAATGAAACTAGTTTTGTCATATTTTTACCTGTTATATTGT
* *
308503 AAAGTATCGATACATTTATATAAAGTATTGATACTTT
1 AAAGTATCGATACATTTTTATAAAGTATCGATACTTT
308540 ATAGGCGCTA
Statistics
Matches: 334, Mismatches: 27, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
107 28 0.08
109 70 0.21
111 1 0.00
112 206 0.62
114 29 0.09
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.43
Consensus pattern (112 bp):
AAAGTATCGATACATTTTTATAAAGTATCGATACTTTCAACATATCAGGTAGCTCTTTACCGGTT
TTGTCATAATGAAACTAGTTTTGTCATATTTTTACCTGTTATATTGT
Found at i:308542 original size:20 final size:21
Alignment explanation
Indices: 308502--308542 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
308492 TGTTATATTG
308502 TAAAGTATCGATACATTTATA
1 TAAAGTATCGATACATTTATA
*
308523 TAAAGTATTGATAC-TTTATA
1 TAAAGTATCGATACATTTATA
308543 GGCGCTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (21 bp):
TAAAGTATCGATACATTTATA
Found at i:308742 original size:74 final size:73
Alignment explanation
Indices: 308620--308868 Score: 392
Period size: 74 Copynumber: 3.4 Consensus size: 73
308610 TCAACATATC
* * *
308620 CGGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCAT
1 CGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTT
308685 CAAAAAAA
66 CAAAAAAA
* * *
308693 TCGGTAGGTATTTTAATGTAATAGGTAGC-ACTATTTTTTTTTACGGTTTACATTATTATCAACC
1 -CGGTAGGTATTTTAATGTAATAGGTAGCGCCTA-TTTTTTTTACCGTTTACATTATTAACAACC
308757 TTCAAAAAAA
64 TTCAAAAAAA
308767 CTGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCT
1 C-GGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCT
*
308832 TAAAAAAAA
65 TCAAAAAAA
308841 CCGGTAGGTATTTTAATGTAATAGGTAG
1 -CGGTAGGTATTTTAATGTAATAGGTAG
308869 TTTAAATTTT
Statistics
Matches: 162, Mismatches: 9, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
73 4 0.02
74 154 0.95
75 4 0.02
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.39
Consensus pattern (73 bp):
CGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTT
CAAAAAAA
Found at i:309134 original size:25 final size:25
Alignment explanation
Indices: 309105--309157 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
309095 ATCGGTTATG
309105 TTATCCTTAGTAACATTTTAGGAGT
1 TTATCCTTAGTAACATTTTAGGAGT
309130 TTATCCTTAGTAACATTTTAGGAGT
1 TTATCCTTAGTAACATTTTAGGAGT
309155 TTA
1 TTA
309158 CTTAATATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.45
Consensus pattern (25 bp):
TTATCCTTAGTAACATTTTAGGAGT
Found at i:309217 original size:23 final size:23
Alignment explanation
Indices: 309191--309241 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
309181 TAAGTAATTA
** *
309191 ACCTATTTTATTATATAAGCGGT
1 ACCTATTACATTATATAAGCGCT
309214 ACCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
309237 ACCTA
1 ACCTA
309242 ATATGTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:311334 original size:199 final size:202
Alignment explanation
Indices: 311031--311397 Score: 605
Period size: 201 Copynumber: 1.8 Consensus size: 202
311021 GTCGGGTTGA
*
311031 GTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCCAAAAATATATATAATTTTACCCTATATAT
1 GTTCGGGTTTAGGGTGAAAAATACCCGACCCAACCCAAAAATATATATAATTTTACCCTATATAT
311096 TTAGGAATAATTACAATAATACCCCTATATATATAA-TTTTTTCCAATTAAGTCACTATTTTTAT
66 TTAGGAATAATTACAATAATACCCCTATATATATAATTTTTTTCCAATTAAGTCACTATTTTTAT
*
311160 TGAATAAAAATAATTCTTTTATTATTTCGGGTTGGGTCGGGTCGGGTCGGTTTTTTTAAGTGTGA
131 TGAATAAAAATAATTCTTTTATTATTTCGGGTCGGGTCGGGTCGGGTCGGTTTTTTTAAGTGTGA
311225 TATTCAG
196 TATTCAG
* *
311232 GTTCGGGTTTA-GGTGAAAAATACCTGACCCAACCCAAAAA-ATATATAATTTTACCTTATATAT
1 GTTCGGGTTTAGGGTGAAAAATACCCGACCCAACCCAAAAATATATATAATTTTACCCTATATAT
* * * * *
311295 TTATGAATAATTACAATAATACCCCTCTATATATAATTTTTTTTTCAATTAAGTCATTGTTTTTA
66 TTAGGAATAATTACAATAATACCCCTATATATATAA-TTTTTTTCCAATTAAGTCACTATTTTTA
* *
311360 TTGAATAAAAATATTTTTTTTATTATTTCGGGTCGGGT
130 TTGAATAAAAATAATTCTTTTATTATTTCGGGTCGGGT
311398 TTCTAATTCA
Statistics
Matches: 153, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
199 56 0.37
200 27 0.18
201 70 0.46
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (202 bp):
GTTCGGGTTTAGGGTGAAAAATACCCGACCCAACCCAAAAATATATATAATTTTACCCTATATAT
TTAGGAATAATTACAATAATACCCCTATATATATAATTTTTTTCCAATTAAGTCACTATTTTTAT
TGAATAAAAATAATTCTTTTATTATTTCGGGTCGGGTCGGGTCGGGTCGGTTTTTTTAAGTGTGA
TATTCAG
Found at i:311846 original size:17 final size:18
Alignment explanation
Indices: 311820--311866 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
311810 CATGGAATTT
* *
311820 GATTCCAATTCC-TGACA
1 GATTTCAATTCCTTCACA
*
311837 GATTTTAATTCCTTCACA
1 GATTTCAATTCCTTCACA
311855 GATTTCAATTCC
1 GATTTCAATTCC
311867 CTCGTAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.38
Consensus pattern (18 bp):
GATTTCAATTCCTTCACA
Found at i:311987 original size:16 final size:16
Alignment explanation
Indices: 311961--312024 Score: 60
Period size: 16 Copynumber: 3.8 Consensus size: 16
311951 AGGTGTAATA
311961 TATAA-TTATTTAAAT
1 TATAATTTATTTAAAT
*
311976 TATAATTTATTT-ATT
1 TATAATTTATTTAAAT
311991 TATATACTTTTATATTTAAAT
1 TATA-A---TT-TATTTAAAT
312012 TATAATTTATTTA
1 TATAATTTATTTA
312025 TTTATATACT
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
15 11 0.28
16 13 0.32
17 2 0.05
19 2 0.05
20 6 0.15
21 6 0.15
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
TATAATTTATTTAAAT
Found at i:311991 original size:20 final size:20
Alignment explanation
Indices: 311966--312028 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
311956 TAATATATAA
311966 TTATTTAAATTATAATTTAT
1 TTATTTAAATTATAATTTAT
*
311986 TTATTT--A-TATACTTT-T
1 TTATTTAAATTATAATTTAT
*
312002 ATATTTAAATTATAATTTAT
1 TTATTTAAATTATAATTTAT
312022 TTATTTA
1 TTATTTA
312029 TATACTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 6 0.17
17 7 0.20
18 2 0.06
19 7 0.20
20 13 0.37
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTAAATTATAATTTAT
Found at i:312007 original size:36 final size:37
Alignment explanation
Indices: 311967--312047 Score: 155
Period size: 36 Copynumber: 2.2 Consensus size: 37
311957 AATATATAAT
311967 TATTTAAATTATAATTTATTTATTTATATAC-TTTTA
1 TATTTAAATTATAATTTATTTATTTATATACTTTTTA
312003 TATTTAAATTATAATTTATTTATTTATATACTTTTTA
1 TATTTAAATTATAATTTATTTATTTATATACTTTTTA
312040 TATTTAAA
1 TATTTAAA
312048 CTATCTTTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 31 0.70
37 13 0.30
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (37 bp):
TATTTAAATTATAATTTATTTATTTATATACTTTTTA
Found at i:312396 original size:17 final size:17
Alignment explanation
Indices: 312319--312403 Score: 57
Period size: 17 Copynumber: 4.8 Consensus size: 17
312309 AATTAATAAC
* *
312319 AAAATTAAATAAAAATT
1 AAAATAAAATAAAATTT
*
312336 AAGAA-AAAATCAACATTTT
1 AA-AATAAAAT-AA-AATTT
312355 AAAATAAAATAATAA-TT
1 AAAATAAAATAA-AATTT
**
312372 ATTCATAAAATAAAATTT
1 A-AAATAAAATAAAATTT
*
312390 AAAATAATATAAAA
1 AAAATAAAATAAAA
312404 ATTTCTAACA
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
17 21 0.40
18 21 0.40
19 10 0.19
ACGTcount: A:0.66, C:0.04, G:0.01, T:0.29
Consensus pattern (17 bp):
AAAATAAAATAAAATTT
Found at i:317891 original size:13 final size:13
Alignment explanation
Indices: 317875--317899 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
317865 AATTCATGAC
317875 TAAAAATAAAAAG
1 TAAAAATAAAAAG
317888 TAAAAATAAAAA
1 TAAAAATAAAAA
317900 ATGAGTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
TAAAAATAAAAAG
Found at i:317979 original size:5 final size:5
Alignment explanation
Indices: 317966--318058 Score: 66
Period size: 5 Copynumber: 18.4 Consensus size: 5
317956 TTACTAAAAG
* * *
317966 AAATG AAATA AAATA AAATA AAATAA AAATCC TAA-A AAATA AAA-A AATATA
1 AAATA AAATA AAATA AAATA AAAT-A AAAT-A AAATA AAATA AAATA AA-ATA
* * * *
318017 AAATA AGAT- AAATA AAACA AAATA AAGTA AAGTAA AAATA AA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAAT-A AAATA AA
318059 CCACAAATAA
Statistics
Matches: 70, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
4 8 0.11
5 48 0.69
6 14 0.20
ACGTcount: A:0.74, C:0.03, G:0.04, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:318047 original size:19 final size:20
Alignment explanation
Indices: 318016--318053 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
318006 AAAAAAATAT
318016 AAAATAAGATAAA-TAAAAC
1 AAAATAAGATAAAGTAAAAC
318035 AAAATAA-AGTAAAGTAAAA
1 AAAATAAGA-TAAAGTAAAA
318054 ATAAACCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 1 0.06
19 11 0.65
20 5 0.29
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.16
Consensus pattern (20 bp):
AAAATAAGATAAAGTAAAAC
Found at i:318153 original size:21 final size:22
Alignment explanation
Indices: 318123--318164 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
318113 AAAATAGAAA
318123 AATAAAAC-AAAGT-AAAAAAT
1 AATAAAACAAAAGTCAAAAAAT
318143 AATAGAAACAAAAGTCAAAAAA
1 AATA-AAACAAAAGTCAAAAAA
318165 ACATATTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 4 0.21
22 5 0.26
23 6 0.32
ACGTcount: A:0.74, C:0.07, G:0.07, T:0.12
Consensus pattern (22 bp):
AATAAAACAAAAGTCAAAAAAT
Found at i:318351 original size:21 final size:21
Alignment explanation
Indices: 318309--318356 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
318299 AAAAACCCAA
*
318309 AAATAATAAAATAAAAAGAAT
1 AAATAATAAAATAAAAAAAAT
318330 AAATAA-AAAATATATAAAAATAT
1 AAATAATAAAATA-A-AAAAA-AT
318353 AAAT
1 AAAT
318357 GACTGAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 6 0.26
21 7 0.30
22 4 0.17
23 6 0.26
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (21 bp):
AAATAATAAAATAAAAAAAAT
Found at i:319418 original size:26 final size:26
Alignment explanation
Indices: 319382--319450 Score: 138
Period size: 26 Copynumber: 2.7 Consensus size: 26
319372 GAAGGACCAC
319382 TATGTCCCGAAGGACCATATATCACA
1 TATGTCCCGAAGGACCATATATCACA
319408 TATGTCCCGAAGGACCATATATCACA
1 TATGTCCCGAAGGACCATATATCACA
319434 TATGTCCCGAAGGACCA
1 TATGTCCCGAAGGACCA
319451 CTATGTCCCG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (26 bp):
TATGTCCCGAAGGACCATATATCACA
Found at i:319805 original size:2 final size:2
Alignment explanation
Indices: 319798--319831 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
319788 ACTCATAATC
*
319798 AT AT AT AT AT AT AT AT AT AT CAT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT A
319832 ATAACTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:323142 original size:83 final size:83
Alignment explanation
Indices: 322998--323308 Score: 419
Period size: 83 Copynumber: 3.7 Consensus size: 83
322988 TCGAGCTAAA
* * * *
322998 TGTAATC-AAACTCGAAGGTTTTTATTAACAGATAACCCTTCTTGCCTTGAGTTAT-CTTGTAAA
1 TGTAATCGAAA-TCGAAGG--TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC-TGTAAA
**
323061 TTTGATATGTTATTGAGCTGAG
62 TTTGATATGTCCTTGAGCTGAG
*
323083 TGTAATCGAAATCGAAGGTTTGTTGACAAATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTG
1 TGTAATCGAAATCGAAGGTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTG
323148 ATATGTCCTTGAGCTGAG
66 ATATGTCCTTGAGCTGAG
* * * * *
323166 TGTAATCGAACTCGAAGGTCTGTTGACAGATAACCTTTCTCGCCTTAAGCTATGTTGTAAATTTG
1 TGTAATCGAAATCGAAGGTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTG
*
323231 ATATGTCCTTGAGATGAG
66 ATATGTCCTTGAGCTGAG
* * * *
323249 TGTAATCGAACTCGAAGTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATACTGTAA
1 TGTAATCGAAATCGAAGGTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAA
323309 TAGGCTAGGA
Statistics
Matches: 203, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
83 185 0.91
84 1 0.00
85 14 0.07
86 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (83 bp):
TGTAATCGAAATCGAAGGTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTG
ATATGTCCTTGAGCTGAG
Found at i:326133 original size:27 final size:27
Alignment explanation
Indices: 326074--326149 Score: 99
Period size: 22 Copynumber: 3.0 Consensus size: 27
326064 AATATTAAGA
326074 GGTACCGATACCCCTATGAATGGGTA-
1 GGTACCGATACCCCTATGAATGGGTAT
*
326100 --T--CAATACCCCTATGAATGGGTAT
1 GGTACCGATACCCCTATGAATGGGTAT
*
326123 GGTACCGATACCCCTATGAAGGGGTAT
1 GGTACCGATACCCCTATGAATGGGTAT
326150 TAATGCCCCT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
22 20 0.48
24 1 0.02
25 1 0.02
27 20 0.48
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (27 bp):
GGTACCGATACCCCTATGAATGGGTAT
Found at i:326165 original size:22 final size:22
Alignment explanation
Indices: 326081--326166 Score: 91
Period size: 22 Copynumber: 3.7 Consensus size: 22
326071 AGAGGTACCG
* *
326081 ATACCCCTATGAATGGGTATCA
1 ATACCCCTATGAAGGGGTATTA
*
326103 ATACCCCTATGAATGGGTATGGTA
1 ATACCCCTATGAAGGGGTAT--TA
326127 CCGATACCCCTATGAAGGGGTATTA
1 ---ATACCCCTATGAAGGGGTATTA
*
326152 ATGCCCCTATGAAGG
1 ATACCCCTATGAAGG
326167 ATCAAACATC
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
22 34 0.61
24 1 0.02
25 2 0.04
27 19 0.34
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (22 bp):
ATACCCCTATGAAGGGGTATTA
Found at i:326209 original size:19 final size:19
Alignment explanation
Indices: 326185--326221 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
326175 TCGAATGCAA
326185 AAAGGGTATCAATACCATG
1 AAAGGGTATCAATACCATG
*
326204 AAAGGGTATCGATACCAT
1 AAAGGGTATCAATACCAT
326222 AGTGTAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.22
Consensus pattern (19 bp):
AAAGGGTATCAATACCATG
Found at i:335174 original size:25 final size:25
Alignment explanation
Indices: 335146--335290 Score: 66
Period size: 25 Copynumber: 5.6 Consensus size: 25
335136 AAAACCCTAA
335146 AAATAAAAAAAATATAAAATAAGAT
1 AAATAAAAAAAATATAAAATAAGAT
* * * *
335171 AAATAAAACAGA-ATAAATTAAAGTAA
1 AAATAAAAAAAATATAAAAT-AAG-AT
* *
335197 AAATAAACCACAAATA-AAGAAGAAGA-
1 AAATAAA--AAAAATATAA-AATAAGAT
*
335223 AAATAATAAAAACAAAT-AAATAA-AT
1 AAATAA-AAAAA-ATATAAAATAAGAT
* * *
335248 AAATAAACTAAAAACATAAAAATAAAAC
1 AAATAAA--AAAAATAT-AAAATAAGAT
335276 AAAGTAAAAAAAATA
1 AAA-TAAAAAAAATA
335291 AATAATAGAA
Statistics
Matches: 91, Mismatches: 13, Indels: 30
0.68 0.10 0.22
Matches are distributed among these distances:
24 8 0.09
25 29 0.32
26 21 0.23
27 14 0.15
28 13 0.14
29 6 0.07
ACGTcount: A:0.74, C:0.06, G:0.05, T:0.16
Consensus pattern (25 bp):
AAATAAAAAAAATATAAAATAAGAT
Found at i:335241 original size:13 final size:13
Alignment explanation
Indices: 335223--335305 Score: 62
Period size: 13 Copynumber: 6.2 Consensus size: 13
335213 AAGAAGAAGA
335223 AAATAATAAAAAC
1 AAATAATAAAAAC
* *
335236 AAATAA-ATAAAT
1 AAATAATAAAAAC
335248 AAATAAACTAAAAAC
1 AAAT-AA-TAAAAAC
*
335263 ATAAAAAT-AAAAC
1 A-AATAATAAAAAC
* *
335276 AAAGTAAAAAAAAT
1 AAA-TAATAAAAAC
*
335290 AAATAATAGAAAC
1 AAATAATAAAAAC
335303 AAA
1 AAA
335306 AGTCGAAAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
12 10 0.19
13 26 0.49
14 8 0.15
15 7 0.13
16 2 0.04
ACGTcount: A:0.76, C:0.06, G:0.02, T:0.16
Consensus pattern (13 bp):
AAATAATAAAAAC
Found at i:335476 original size:28 final size:29
Alignment explanation
Indices: 335420--335489 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 29
335410 AAAAGGAAGA
335420 AAAAAATAATAAAACAGAAGCAAAAAAAT
1 AAAAAATAATAAAACAGAAGCAAAAAAAT
* * * *
335449 CAAAAATAATAAAATA-AAGCGAATAAAT
1 AAAAAATAATAAAACAGAAGCAAAAAAAT
335477 AAAAAAT-ATAAAA
1 AAAAAATAATAAAA
335490 ATGATATAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
27 6 0.17
28 16 0.44
29 14 0.39
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.14
Consensus pattern (29 bp):
AAAAAATAATAAAACAGAAGCAAAAAAAT
Found at i:336974 original size:24 final size:24
Alignment explanation
Indices: 336948--337000 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 24
336938 TTTACTTATT
* *
336948 TATTATTATAT-AT-TTTCAAATA
1 TATTATTATTTAATATTTAAAATA
336970 -ATTATTATTTAATATTTAAAATA
1 TATTATTATTTAATATTTAAAATA
336993 TATTATTA
1 TATTATTA
337001 AAATAGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 9 0.35
22 2 0.08
23 8 0.31
24 7 0.27
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
TATTATTATTTAATATTTAAAATA
Found at i:337023 original size:28 final size:30
Alignment explanation
Indices: 336992--337048 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
336982 TATTTAAAAT
*
336992 ATATT-ATTAAAAT-AGAAATATAATATTC
1 ATATTAATTAAAATAAAAAATATAATATTC
*
337020 ATATTAATTAAAATAAAAAATTTAATATT
1 ATATTAATTAAAATAAAAAATATAATATT
337049 TATCAACAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.20
29 8 0.32
30 12 0.48
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (30 bp):
ATATTAATTAAAATAAAAAATATAATATTC
Found at i:337347 original size:17 final size:19
Alignment explanation
Indices: 337327--337363 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
337317 ATTAAATATA
337327 TAACTA-CA-ATAAATTTT
1 TAACTATCATATAAATTTT
*
337344 TAACTATCATATTAATTTT
1 TAACTATCATATAAATTTT
337363 T
1 T
337364 TATTGAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 2 0.12
19 9 0.53
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.49
Consensus pattern (19 bp):
TAACTATCATATAAATTTT
Found at i:338270 original size:19 final size:18
Alignment explanation
Indices: 338248--338292 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
338238 TCACCCTTAA
338248 TTTATAATATATATATTGT
1 TTTATAATATATATATT-T
338267 TTTA-AATTATATATATTT
1 TTTATAA-TATATATATTT
*
338285 TTTTTAAT
1 TTTATAAT
338293 TTTTATATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTATAATATATATATTT
Found at i:338293 original size:19 final size:19
Alignment explanation
Indices: 338255--338293 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
338245 TAATTTATAA
338255 TATATATATTGTTTTAAAT
1 TATATATATTGTTTTAAAT
* *
338274 TATATATATTTTTTTTAAT
1 TATATATATTGTTTTAAAT
338293 T
1 T
338294 TTTATATCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (19 bp):
TATATATATTGTTTTAAAT
Found at i:338299 original size:20 final size:21
Alignment explanation
Indices: 338254--338300 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
338244 TTAATTTATA
338254 ATATATATATTGTTTTAAATT
1 ATATATATATTGTTTTAAATT
* *
338275 ATATATAT-TTTTTTTAATTT
1 ATATATATATTGTTTTAAATT
*
338295 TTATAT
1 ATATAT
338301 CTATAAGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
ATATATATATTGTTTTAAATT
Found at i:347466 original size:18 final size:18
Alignment explanation
Indices: 347443--347485 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
347433 AGTGAAACCA
347443 ATCATTCAAGTATCACAT
1 ATCATTCAAGTATCACAT
347461 ATCATTCAAGTATCACAT
1 ATCATTCAAGTATCACAT
347479 ATCATTC
1 ATCATTC
347486 TATCATAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.35
Consensus pattern (18 bp):
ATCATTCAAGTATCACAT
Found at i:350898 original size:22 final size:22
Alignment explanation
Indices: 350873--350931 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
350863 ATCATGGCCT
*
350873 AATATTGATACTATGT-TCATAC
1 AATATTGATACTATATAT-ATAC
* *
350895 AATATTGATATTATATATTTAC
1 AATATTGATACTATATATATAC
*
350917 AATATCGATACTATA
1 AATATTGATACTATA
350932 GGCTAAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 30 0.97
23 1 0.03
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.42
Consensus pattern (22 bp):
AATATTGATACTATATATATAC
Found at i:351868 original size:16 final size:16
Alignment explanation
Indices: 351844--351881 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
351834 TAGAAATTTC
*
351844 ATTTAGATTTTCTAAG
1 ATTTGGATTTTCTAAG
351860 ATTTGGATTTTCTAAG
1 ATTTGGATTTTCTAAG
351876 ATTTGG
1 ATTTGG
351882 TGCATGAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.26, C:0.05, G:0.18, T:0.50
Consensus pattern (16 bp):
ATTTGGATTTTCTAAG
Found at i:354391 original size:2 final size:2
Alignment explanation
Indices: 354384--354419 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
354374 TGATCTCAAC
354384 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
354420 TGCTTTAAAT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:354802 original size:43 final size:42
Alignment explanation
Indices: 354707--354807 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 42
354697 CGGGAAGTTC
* *
354707 ATTTATGTTCGTTTATTT-ATTAAATGAACGAACATGAACAAG
1 ATTT-TGTTCGTTCATTTAATTAAATGAACGAACACGAACAAG
*
354749 ATTTTG--CGTTCGTTTAATTAAATGAACGAACACGAACAA-
1 ATTTTGTTCGTTCATTTAATTAAATGAACGAACACGAACAAG
354788 ATGGTTTGTTCGTTCATTTA
1 AT--TTTGTTCGTTCATTTA
354808 CGTTCGTGAA
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
39 9 0.18
40 22 0.44
41 6 0.12
42 4 0.08
43 9 0.18
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.39
Consensus pattern (42 bp):
ATTTTGTTCGTTCATTTAATTAAATGAACGAACACGAACAAG
Found at i:354855 original size:14 final size:14
Alignment explanation
Indices: 354836--354882 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
354826 TATATGTTTG
354836 TTTATGTTCGTTCA
1 TTTATGTTCGTTCA
354850 TTTA---T-GTTCA
1 TTTATGTTCGTTCA
*
354860 TTTATGTCCGTTCA
1 TTTATGTTCGTTCA
354874 TTTATGTTC
1 TTTATGTTC
354883 ATTTATGTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
10 9 0.33
11 1 0.04
14 17 0.63
ACGTcount: A:0.15, C:0.15, G:0.13, T:0.57
Consensus pattern (14 bp):
TTTATGTTCGTTCA
Found at i:354858 original size:10 final size:10
Alignment explanation
Indices: 354845--354892 Score: 60
Period size: 10 Copynumber: 4.4 Consensus size: 10
354835 GTTTATGTTC
354845 GTTCATTTAT
1 GTTCATTTAT
354855 GTTCATTTATGT
1 GTTCATTTA--T
354867 CCGTTCATTTAT
1 --GTTCATTTAT
354879 GTTCATTTAT
1 GTTCATTTAT
354889 GTTC
1 GTTC
354893 GAACAGAGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 23 0.68
12 2 0.06
14 9 0.26
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.56
Consensus pattern (10 bp):
GTTCATTTAT
Found at i:354863 original size:24 final size:24
Alignment explanation
Indices: 354818--354893 Score: 107
Period size: 24 Copynumber: 3.1 Consensus size: 24
354808 CGTTCGTGAA
**
354818 CGTTCGATTATATGTTTGTTTATGTT
1 CGTTC-ATT-TATGTTCATTTATGTT
*
354844 CGTTCATTTATGTTCATTTATGTC
1 CGTTCATTTATGTTCATTTATGTT
354868 CGTTCATTTATGTTCATTTATGTT
1 CGTTCATTTATGTTCATTTATGTT
354892 CG
1 CG
354894 AACAGAGGGC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 38 0.83
25 3 0.07
26 5 0.11
ACGTcount: A:0.16, C:0.13, G:0.16, T:0.55
Consensus pattern (24 bp):
CGTTCATTTATGTTCATTTATGTT
Found at i:355177 original size:22 final size:23
Alignment explanation
Indices: 355149--355218 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 23
355139 TTTATTTTTT
*
355149 TTGTGTTTGTGT-TGTTCGTTTA
1 TTGTGTTCGTGTATGTTCGTTTA
* *
355171 TTGTGTTCGTTTATGTTCGTTTG
1 TTGTGTTCGTGTATGTTCGTTTA
* * *
355194 TGTGTGTCCGTTTACGTTCGTTTA
1 T-TGTGTTCGTGTATGTTCGTTTA
355218 T
1 T
355219 GTTCGTTTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
22 10 0.25
23 10 0.25
24 20 0.50
ACGTcount: A:0.06, C:0.10, G:0.26, T:0.59
Consensus pattern (23 bp):
TTGTGTTCGTGTATGTTCGTTTA
Found at i:355189 original size:10 final size:10
Alignment explanation
Indices: 355174--355228 Score: 56
Period size: 10 Copynumber: 5.1 Consensus size: 10
355164 TCGTTTATTG
355174 TGTTCGTTTA
1 TGTTCGTTTA
*
355184 TGTTCGTTTGTG
1 TGTTCG-TT-TA
355196 TGTGTCCGTTTA
1 TGT-T-CGTTTA
*
355208 CGTTCGTTTA
1 TGTTCGTTTA
355218 TGTTCGTTTA
1 TGTTCGTTTA
355228 T
1 T
355229 CATTTAAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 22 0.59
11 3 0.08
12 7 0.19
13 3 0.08
14 2 0.05
ACGTcount: A:0.07, C:0.13, G:0.24, T:0.56
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:355205 original size:24 final size:23
Alignment explanation
Indices: 355161--355218 Score: 80
Period size: 24 Copynumber: 2.5 Consensus size: 23
355151 GTGTTTGTGT
*
355161 TGTTCGTTTATTGTGTTCGTTTA
1 TGTTCGTTTATTGTGTCCGTTTA
*
355184 TGTTCGTTTGTGTGTGTCCGTTTA
1 TGTTCGTTTAT-TGTGTCCGTTTA
*
355208 CGTTCGTTTAT
1 TGTTCGTTTAT
355219 GTTCGTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 10 0.33
24 20 0.67
ACGTcount: A:0.07, C:0.12, G:0.24, T:0.57
Consensus pattern (23 bp):
TGTTCGTTTATTGTGTCCGTTTA
Found at i:356150 original size:40 final size:40
Alignment explanation
Indices: 356106--356187 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
356096 ACCGTAGTGC
*
356106 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGATCGTGCCCACCATATACACCGAAGTGTAT
*
356146 TACACATAAGATCGTGCCCACTATATACACCGAAGTGTAT
1 TACACATAAGATCGTGCCCACCATATACACCGAAGTGTAT
356186 TA
1 TA
356188 TAAACCTGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAAGATCGTGCCCACCATATACACCGAAGTGTAT
Found at i:356931 original size:29 final size:30
Alignment explanation
Indices: 356883--356947 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
356873 ACAATCCATC
* **
356883 AATTTTCCAAAAATGCCAAAGTGATCCCCA
1 AATTTTCCAAAAATGACAAAACGATCCCCA
* *
356913 ACTTTT-CAAAAATTACAAAACGATCCCCA
1 AATTTTCCAAAAATGACAAAACGATCCCCA
356942 AATTTT
1 AATTTT
356948 TCTAAGGCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.28
Consensus pattern (30 bp):
AATTTTCCAAAAATGACAAAACGATCCCCA
Found at i:365553 original size:24 final size:25
Alignment explanation
Indices: 365521--365570 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
365511 TAATTGCATT
*
365521 ATCTGCTTCTTT-CCCCATCCTCTC
1 ATCTGCTTCTTTACCCCACCCTCTC
365545 ATCTGCTTCTTTACCCCCACCCTCTC
1 ATCTGCTTCTTTA-CCCCACCCTCTC
365571 CCACACACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.52
26 11 0.48
ACGTcount: A:0.10, C:0.48, G:0.04, T:0.38
Consensus pattern (25 bp):
ATCTGCTTCTTTACCCCACCCTCTC
Found at i:368489 original size:20 final size:20
Alignment explanation
Indices: 368464--368502 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
368454 AAAATCAAAT
368464 AAATATTAT-TTATTATTATA
1 AAATA-TATGTTATTATTATA
*
368484 AAATATATGTTTTTATTAT
1 AAATATATGTTATTATTAT
368503 CGTTGTCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
AAATATATGTTATTATTATA
Found at i:374581 original size:22 final size:22
Alignment explanation
Indices: 374553--374620 Score: 136
Period size: 22 Copynumber: 3.1 Consensus size: 22
374543 TCCTGGTTAC
374553 TTAATTAAACTCTCTACACCTT
1 TTAATTAAACTCTCTACACCTT
374575 TTAATTAAACTCTCTACACCTT
1 TTAATTAAACTCTCTACACCTT
374597 TTAATTAAACTCTCTACACCTT
1 TTAATTAAACTCTCTACACCTT
374619 TT
1 TT
374621 CACACCTTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.31, C:0.26, G:0.00, T:0.43
Consensus pattern (22 bp):
TTAATTAAACTCTCTACACCTT
Found at i:379092 original size:9 final size:9
Alignment explanation
Indices: 379080--379113 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
379070 GAATTCGGTT
379080 AATTAACCG
1 AATTAACCG
379089 AATTAACCG
1 AATTAACCG
379098 AATTAACCG
1 AATTAACCG
379107 AAATTAA
1 -AATTAA
379114 ATTTTAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.75
10 6 0.25
ACGTcount: A:0.50, C:0.18, G:0.09, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Done.