Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001466.1 Hibiscus syriacus cultivar Beakdansim tig00002841_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: 1236886
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:298119 original size:31 final size:33
Alignment explanation
Indices: 298066--298141 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 33
298056 ATATAAAATA
298066 ATTATTTTATA-AGAT--TTTGATAAGATTTAA-T
1 ATTATTTTATATA-ATAATTTGATAA-ATTTAATT
298097 ATT-TTTTA-ATAATAATTTGATAAATTTAATT
1 ATTATTTTATATAATAATTTGATAAATTTAATT
298128 ATTATTTTATATAA
1 ATTATTTTATATAA
298142 ATTTAATAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
29 3 0.08
30 12 0.31
31 15 0.38
32 5 0.13
33 4 0.10
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (33 bp):
ATTATTTTATATAATAATTTGATAAATTTAATT
Found at i:298144 original size:22 final size:22
Alignment explanation
Indices: 298116--298159 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
298106 TAATAATTTG
* *
298116 ATAAATTTAATTATTATTTTAT
1 ATAAATTTAATAACTATTTTAT
298138 ATAAATTTAATAACTATTTTAT
1 ATAAATTTAATAACTATTTTAT
298160 GACCACTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
ATAAATTTAATAACTATTTTAT
Found at i:298145 original size:31 final size:32
Alignment explanation
Indices: 298066--298150 Score: 90
Period size: 31 Copynumber: 2.8 Consensus size: 32
298056 ATATAAAATA
*
298066 ATTATTTTATA-AGATTTTGATAAGATTTAAT
1 ATTATTTTATATAGAATTTGATAAGATTTAAT
*
298097 ATT-TTTTA-ATAATAATTTGATAA-ATTTAATT
1 ATTATTTTATAT-AGAATTTGATAAGATTTAA-T
*
298128 ATTATTTTATATA-AATTTAATAA
1 ATTATTTTATATAGAATTTGATAA
298151 CTATTTTATG
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
29 1 0.02
30 11 0.24
31 26 0.57
32 6 0.13
33 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (32 bp):
ATTATTTTATATAGAATTTGATAAGATTTAAT
Found at i:317632 original size:109 final size:108
Alignment explanation
Indices: 317435--317654 Score: 431
Period size: 109 Copynumber: 2.0 Consensus size: 108
317425 AATTTTCTCC
317435 GTTCCGAGCAACATCAGAGAAATGGGAAGACTTAATTAAGATAGGCTCACCACCAAAGGCATGAT
1 GTTCCGAGCAACATCAGAGAAATGGGAAGACTTAATTAAGATAGGCTCACCACCAAAGGCATGAT
317500 CAGATGTGAAGGTAGTGTGGATAGTACGCGTAACCCAACCAAG
66 CAGATGTGAAGGTAGTGTGGATAGTACGCGTAACCCAACCAAG
317543 GTTCCGCAGCAACATCAGAGAAATGGGAAGACTTAATTAAGATAGGCTCACCACCAAAGGCATGA
1 GTTCCG-AGCAACATCAGAGAAATGGGAAGACTTAATTAAGATAGGCTCACCACCAAAGGCATGA
317608 TCAGATGTGAAGGTAGTGTGGATAGTACGCGTAACCCAACCAAG
65 TCAGATGTGAAGGTAGTGTGGATAGTACGCGTAACCCAACCAAG
317652 GTT
1 GTT
317655 GAGCTTAAAT
Statistics
Matches: 111, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
108 6 0.05
109 105 0.95
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.19
Consensus pattern (108 bp):
GTTCCGAGCAACATCAGAGAAATGGGAAGACTTAATTAAGATAGGCTCACCACCAAAGGCATGAT
CAGATGTGAAGGTAGTGTGGATAGTACGCGTAACCCAACCAAG
Found at i:318550 original size:16 final size:16
Alignment explanation
Indices: 318529--318564 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
318519 TGGTTAAAGA
* *
318529 AATAAAAGATTACATG
1 AATAAAAAATTACAGG
318545 AATAAAAAATTACAGG
1 AATAAAAAATTACAGG
318561 AATA
1 AATA
318565 TATATTTTAC
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:0.61, C:0.06, G:0.11, T:0.22
Consensus pattern (16 bp):
AATAAAAAATTACAGG
Found at i:318657 original size:17 final size:15
Alignment explanation
Indices: 318619--318649 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
318609 AAATTCTAAA
*
318619 TATTTAAATAAAAAT
1 TATTTATATAAAAAT
318634 TATTTATATAAAAAT
1 TATTTATATAAAAAT
318649 T
1 T
318650 CTATTTATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTATATAAAAAT
Found at i:322550 original size:22 final size:22
Alignment explanation
Indices: 322498--322550 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
322488 AAACTATAAA
322498 ATTAGAAA-AAAATACTAAATT
1 ATTAGAAATAAAATACTAAATT
* *
322519 TTATAAAAATAAATATAC-AAATT
1 AT-TAGAAATAAA-ATACTAAATT
322542 ATTAGAAAT
1 ATTAGAAAT
322551 CTATTACTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
21 1 0.04
22 11 0.44
23 9 0.36
24 4 0.16
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (22 bp):
ATTAGAAATAAAATACTAAATT
Found at i:323575 original size:16 final size:16
Alignment explanation
Indices: 323534--323578 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
323524 ACAGAGCCTC
*
323534 TGAATCATTAAGCATT
1 TGAATCATTCAGCATT
*
323550 TGAATCATTCAGTATT
1 TGAATCATTCAGCATT
323566 TGAATCATTCAGC
1 TGAATCATTCAGC
323579 GCTTAATCAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (16 bp):
TGAATCATTCAGCATT
Found at i:325517 original size:5 final size:5
Alignment explanation
Indices: 325507--325537 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
325497 CGACTTAATA
325507 TATAT TATAT TATAT TATAT TATAT TATAT T
1 TATAT TATAT TATAT TATAT TATAT TATAT T
325538 TTAACAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:327982 original size:29 final size:28
Alignment explanation
Indices: 327941--328035 Score: 79
Period size: 26 Copynumber: 3.4 Consensus size: 28
327931 TTTTCAAATT
*
327941 AACCAAATATATTTGAAAATTATTAACCG
1 AACCAAAT-TATTTGAAAATTATTAATCG
***
327970 AACCGAAATTATTTG---ACCGTTAATCG
1 AACC-AAATTATTTGAAAATTATTAATCG
* *
327996 AACCGAAATTAATTTAAAAATTATTAATCA
1 AACC-AAATT-ATTTGAAAATTATTAATCG
328026 AACCAAATTA
1 AACCAAATTA
328036 ACCGAATTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 11
0.72 0.12 0.15
Matches are distributed among these distances:
26 17 0.33
27 4 0.08
28 1 0.02
29 15 0.29
30 15 0.29
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31
Consensus pattern (28 bp):
AACCAAATTATTTGAAAATTATTAATCG
Found at i:328034 original size:94 final size:94
Alignment explanation
Indices: 327935--328132 Score: 263
Period size: 94 Copynumber: 2.1 Consensus size: 94
327925 TAATAATTTT
*
327935 CAAATTAACCAAATATATTT-GAAAATTATTAACCGAACCGAAATTATTTGACCGTTAATCGAAC
1 CAAATTAACCAAATATATTTCGAAAA-CATTAACCGAACCGAAATTATTTGACCGTTAATCGAAC
*
327999 CGAAATTAATTTAAAAATTATTAATCAAAC
65 CGAAATTAATTTAAAAATTATTAACCAAAC
* * * *** * *
328029 CAAATTAACCGAATTTTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCTTTAATCGAACC
1 CAAATTAACCAAATATATTTCGAAAACATTAACCGAACCGAAATTATTTGACCGTTAATCGAACC
* * *
328094 GAAATTTATTTGAAAATTATTAACCGAAC
66 GAAATTAATTTAAAAATTATTAACCAAAC
328123 CAAATTAACC
1 CAAATTAACC
328133 GTTAATCGAT
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
94 88 0.98
95 2 0.02
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.33
Consensus pattern (94 bp):
CAAATTAACCAAATATATTTCGAAAACATTAACCGAACCGAAATTATTTGACCGTTAATCGAACC
GAAATTAATTTAAAAATTATTAACCAAAC
Found at i:328133 original size:94 final size:94
Alignment explanation
Indices: 327962--328133 Score: 290
Period size: 94 Copynumber: 1.8 Consensus size: 94
327952 TTTGAAAATT
*
327962 ATTAACCGAACCGAAATTATTTGACCGTTAATCGAACCGAAATTAATTTAAAAATTATTAATCAA
1 ATTAACCGAACCGAAATTATTTGACCGTTAATCGAACCGAAATTAATTTAAAAATTATTAACCAA
328027 ACCAAATTAACCGAATTTTTTTCTTTAAC
66 ACCAAATTAACCGAATTTTTTTCTTTAAC
* * * * *
328056 ATTAATCGAACCGAAATTATTTGACCTTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGA
1 ATTAACCGAACCGAAATTATTTGACCGTTAATCGAACCGAAATTAATTTAAAAATTATTAACCAA
328121 ACCAAATTAACCG
66 ACCAAATTAACCG
328134 TTAATCGATT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
94 72 1.00
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (94 bp):
ATTAACCGAACCGAAATTATTTGACCGTTAATCGAACCGAAATTAATTTAAAAATTATTAACCAA
ACCAAATTAACCGAATTTTTTTCTTTAAC
Found at i:328133 original size:133 final size:131
Alignment explanation
Indices: 327996--328238 Score: 285
Period size: 133 Copynumber: 1.8 Consensus size: 131
327986 CCGTTAATCG
* * * ***
327996 AACCG-AAATTAATTTAAAAATTATT-AATCAAACCAAATTAACCGAATTTTTTTCTTTAA-CAT
1 AACCGTAAATCAA-TTAAAAATT-TTAAAT-AAACCAAATTAACCAAATTTATTT-GAAAATCAT
* * * *
328058 TAATCGAACCGAAATTATTTGACCTTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAAC
62 TAACCGAACCGAAATTATTTAACCGTTAATCGAACC-AAAATTATTTGAAAATTATTAACCGAAC
328123 CAAATT
126 CAAATT
* * * *
328129 AACCGTTAATCGATTAATAATTTTCAAATAAACCAAATTAACCAAATTTATTTGAAAATTATTAA
1 AACCGTAAATCAATTAAAAATTTT-AAATAAACCAAATTAACCAAATTTATTTGAAAATCATTAA
328194 CCGAACCGAAATTATTTAACCGTTAATCGAACCAAAATTATTTGA
65 CCGAACCGAAATTATTTAACCGTTAATCGAACCAAAATTATTTGA
328239 CCGTTAATCG
Statistics
Matches: 92, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
132 15 0.16
133 70 0.76
134 7 0.08
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.34
Consensus pattern (131 bp):
AACCGTAAATCAATTAAAAATTTTAAATAAACCAAATTAACCAAATTTATTTGAAAATCATTAAC
CGAACCGAAATTATTTAACCGTTAATCGAACCAAAATTATTTGAAAATTATTAACCGAACCAAAT
T
Found at i:328206 original size:39 final size:39
Alignment explanation
Indices: 328090--328207 Score: 118
Period size: 39 Copynumber: 3.0 Consensus size: 39
328080 CCTTTAATCG
328090 AACCGAAATTTATTTGAAAATTATTAACCGAACCAAATT
1 AACCGAAATTTATTTGAAAATTATTAACCGAACCAAATT
* ** ***
328129 AACCGTTAATCGA-TT-AATAATT-TTCAAATAAACCAAATT
1 AACCG-AAATTTATTTGAA-AATTATT-AACCGAACCAAATT
328168 AACC-AAATTTATTTGAAAATTATTAACCGAACCGAAATT
1 AACCGAAATTTATTTGAAAATTATTAACCGAACC-AAATT
328207 A
1 A
328208 TTTAACCGTT
Statistics
Matches: 60, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
37 4 0.07
38 16 0.27
39 36 0.60
40 4 0.07
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31
Consensus pattern (39 bp):
AACCGAAATTTATTTGAAAATTATTAACCGAACCAAATT
Found at i:328225 original size:159 final size:147
Alignment explanation
Indices: 328156--328428 Score: 354
Period size: 148 Copynumber: 1.9 Consensus size: 147
328146 TAATTTTCAA
* *
328156 ATAAACCA-AATT-AACC-AAATTTATTTGAAAATTATTAACCGAACCGAAATTATTTAACCGTT
1 ATAAA-CATAATTAAACCGAAA-TTATTTGAAAATTATTAAACGAA-CGAAATTATTTAACCATT
**
328218 AATCGAACCAAAATTATTTGACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAAGTGAACC
63 AATCGAACCAAAATTATTTGACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACC
*
328283 AAATTAACTGAATTTTTTTC
128 AAATTAACTAAATTTTTTTC
* * ***** *
328303 TTTAACATTAATTAAACCGAAATTATTTGAAAATTATTAAACGAATTTTTTTCTTTAACCATTAA
1 ATAAACA-TAATTAAACCGAAATTATTTGAAAATTATTAAACGAACGAAATTATTTAACCATTAA
* *
328368 TCGAACCAAAATTATTTGACCGTTAATCAAACCCAAATTTATTTGAAAATTATTAACCGAA
65 TCGAACCAAAATTATTTGACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAA
328429 TTAACTGAAT
Statistics
Matches: 108, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
146 2 0.02
147 3 0.03
148 74 0.69
149 26 0.24
150 3 0.03
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.36
Consensus pattern (147 bp):
ATAAACATAATTAAACCGAAATTATTTGAAAATTATTAAACGAACGAAATTATTTAACCATTAAT
CGAACCAAAATTATTTGACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAA
TTAACTAAATTTTTTTC
Found at i:328226 original size:26 final size:26
Alignment explanation
Indices: 328190--328263 Score: 112
Period size: 26 Copynumber: 2.8 Consensus size: 26
328180 TTGAAAATTA
*
328190 TTAACCGAACCGAAATTATTTAACCG
1 TTAATCGAACCGAAATTATTTAACCG
* *
328216 TTAATCGAACCAAAATTATTTGACCG
1 TTAATCGAACCGAAATTATTTAACCG
328242 TTAATCGAACCGAAATTTATTT
1 TTAATCGAACCGAAA-TTATTT
328264 GAAAATTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
26 37 0.86
27 6 0.14
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (26 bp):
TTAATCGAACCGAAATTATTTAACCG
Found at i:328260 original size:82 final size:79
Alignment explanation
Indices: 328057--328288 Score: 246
Period size: 82 Copynumber: 2.9 Consensus size: 79
328047 TTCTTTAACA
*
328057 TTAATCGAACCGAAATTATTTGACCTTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAA
1 TTAATCGAACCAAAATTATTTGACC-TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAA
328122 CC-AA--ATTAACCG
65 CCAAATTATTAACCG
** * * *
328134 TTAATCG-ATTAATAATT-TTCAAATAAACC-AAAT-TAACC-AAATTTATTTGAAAATTATTAA
1 TTAATCGAACCAA-AATTATT----T-GACCTTAATCGAACCGAAATTTATTTGAAAATTATTAA
328194 CCGAACCGAAATTATTTAACCG
60 CCGAACC-AAATTA-TTAACCG
**
328216 TTAATCGAACCAAAATTATTTGACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAAGTGAA
1 TTAATCGAACCAAAATTATTTGACC-TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAA
328281 CCAAATTA
65 CCAAATTA
328289 ACTGAATTTT
Statistics
Matches: 125, Mismatches: 13, Indels: 30
0.74 0.08 0.18
Matches are distributed among these distances:
76 4 0.03
77 40 0.32
78 7 0.06
79 6 0.05
80 4 0.03
81 14 0.11
82 45 0.36
83 5 0.04
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.33
Consensus pattern (79 bp):
TTAATCGAACCAAAATTATTTGACCTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAAC
CAAATTATTAACCG
Found at i:328743 original size:95 final size:93
Alignment explanation
Indices: 328629--328815 Score: 295
Period size: 95 Copynumber: 2.0 Consensus size: 93
328619 TTTTACCTTA
*
328629 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAATCAAATTAACCAATTTTTTTTC
1 ACCGTTAATCGAACCGAAATTTATTTAAAAATTATTAACCGAATCAAATTAACCAA--TTTTTTC
*
328694 TTTAACCATTAATCGAACTGAAA-TTATTTG
64 TTTAA-CATTAATCGAACCGAAATTTATTTG
** *
328724 ACCGTTAATCGAATTGAAATTTATTTAAAAATTATTAACCGAATCAATTTAACCAATTTTTTCTT
1 ACCGTTAATCGAACCGAAATTTATTTAAAAATTATTAACCGAATCAAATTAACCAATTTTTTCTT
328789 TAACATTAATCGAACCGAAATTTATTT
66 TAACATTAATCGAACCGAAATTTATTT
328816 TAAAATTATT
Statistics
Matches: 86, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
92 16 0.19
93 18 0.21
95 52 0.60
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (93 bp):
ACCGTTAATCGAACCGAAATTTATTTAAAAATTATTAACCGAATCAAATTAACCAATTTTTTCTT
TAACATTAATCGAACCGAAATTTATTTG
Found at i:328745 original size:170 final size:169
Alignment explanation
Indices: 328346--328831 Score: 715
Period size: 168 Copynumber: 2.9 Consensus size: 169
328336 TTATTAAACG
** * * *
328346 AATTTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATCAAACCCAAATTTATT
1 AATTTTTTTCTTTAACCATTAATCGAACTGAAATTATTTGACCGTTAATCGAATCGAAATTTATT
*
328411 TGAAAATTATTAACCGAATTAA-CTGAATAAAATAAATTATTTTTA-TTTATCCGTTAATCGAAC
66 TGAAAATTATTAACCGAATTAATC-GAATAAAATAAATTATTTTTACTTTAACCGTTAATCGAAC
328474 CGAAATTTATTTGAAAATTATTAACCGAACCAAATCAACC
130 CGAAATTTATTTGAAAATTATTAACCGAACCAAATCAACC
*
328514 AAGTTTTTTCTTTAACCATTAATCGAACTGAAATTATTTGACCGTTAATCGAATCGAAATTTATT
1 AATTTTTTTCTTTAACCATTAATCGAACTGAAATTATTTGACCGTTAATCGAATCGAAATTTATT
*
328579 TGAAAATTATTAACCGAATTAATCGAATAAAATAAATTATTTTTACCTTAACCGTTAATCGAACC
66 TGAAAATTATTAACCGAATTAATCGAATAAAATAAATTATTTTTACTTTAACCGTTAATCGAACC
* *
328644 GAAATTTATTTGAAAATTATTAACCGAATCAAATTAACC
131 GAAATTTATTTGAAAATTATTAACCGAACCAAATCAACC
*
328683 AATTTTTTTTCTTTAACCATTAATCGAACTGAAATTATTTGACCGTTAATCGAATTGAAATTTAT
1 AA-TTTTTTTCTTTAACCATTAATCGAACTGAAATTATTTGACCGTTAATCGAATCGAAATTTAT
* ** ** *
328748 TTAAAAATTATTAACCG----AATC-AATTTAACCAA-T-TTTTT-CTTTAA-CATTAATCGAAC
65 TTGAAAATTATTAACCGAATTAATCGAATAAAATAAATTATTTTTACTTTAACCGTTAATCGAAC
*
328804 CGAAATTTATTTTAAAATTATTAACCGA
130 CGAAATTTATTTGAAAATTATTAACCGA
328832 TTAACGGTTA
Statistics
Matches: 295, Mismatches: 20, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
161 38 0.13
162 5 0.02
163 5 0.02
164 1 0.00
165 7 0.02
166 4 0.01
168 102 0.35
169 57 0.19
170 76 0.26
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (169 bp):
AATTTTTTTCTTTAACCATTAATCGAACTGAAATTATTTGACCGTTAATCGAATCGAAATTTATT
TGAAAATTATTAACCGAATTAATCGAATAAAATAAATTATTTTTACTTTAACCGTTAATCGAACC
GAAATTTATTTGAAAATTATTAACCGAACCAAATCAACC
Found at i:330584 original size:2 final size:2
Alignment explanation
Indices: 330577--330607 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
330567 CATATCTCAA
330577 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 A
330608 GGTCAGATTA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:341800 original size:22 final size:23
Alignment explanation
Indices: 341766--341819 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
341756 TTCAATGATT
*
341766 TATTTAATCTTTTAAGA-AGAAATA
1 TATTTAA-ATTTTAA-ATAGAAATA
*
341790 T-TTTAAATTTTAAATATAAATA
1 TATTTAAATTTTAAATAGAAATA
341812 TATTTAAA
1 TATTTAAA
341820 AATAAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 1 0.04
22 13 0.50
23 11 0.42
24 1 0.04
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (23 bp):
TATTTAAATTTTAAATAGAAATA
Found at i:351962 original size:15 final size:15
Alignment explanation
Indices: 351942--351971 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
351932 GATTTGTATC
351942 ATCATAGTCTTGTGT
1 ATCATAGTCTTGTGT
351957 ATCATAGTCTTGTGT
1 ATCATAGTCTTGTGT
351972 TACTTGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (15 bp):
ATCATAGTCTTGTGT
Found at i:352645 original size:8 final size:8
Alignment explanation
Indices: 352634--352674 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
352624 TAAATACATG
352634 CATGCATA
1 CATGCATA
352642 CATG-ATA
1 CATGCATA
*
352649 CGTGCATA
1 CATGCATA
352657 CATGCATA
1 CATGCATA
*
352665 CATACATA
1 CATGCATA
352673 CA
1 CA
352675 GAGTTACAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
7 6 0.21
8 23 0.79
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (8 bp):
CATGCATA
Found at i:352656 original size:15 final size:16
Alignment explanation
Indices: 352636--352665 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
352626 AATACATGCA
352636 TGCATACATG-ATACG
1 TGCATACATGCATACG
352651 TGCATACATGCATAC
1 TGCATACATGCATAC
352666 ATACATACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (16 bp):
TGCATACATGCATACG
Found at i:354455 original size:10 final size:10
Alignment explanation
Indices: 354440--354468 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
354430 GTTACTGACA
354440 GTTGCTGGCG
1 GTTGCTGGCG
354450 GTTGCTGGCG
1 GTTGCTGGCG
354460 GTTGCTGGC
1 GTTGCTGGC
354469 AATAACTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.21, G:0.48, T:0.31
Consensus pattern (10 bp):
GTTGCTGGCG
Found at i:355420 original size:19 final size:21
Alignment explanation
Indices: 355385--355425 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
355375 GAGAGAGAGG
355385 GAAAAATATATAATAATAATA
1 GAAAAATATATAATAATAATA
*
355406 GAAAAAT-TA-AATAATTATA
1 GAAAAATATATAATAATAATA
355425 G
1 G
355426 TAATACAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 2 0.11
21 7 0.37
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.29
Consensus pattern (21 bp):
GAAAAATATATAATAATAATA
Found at i:356531 original size:31 final size:32
Alignment explanation
Indices: 356493--356570 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 32
356483 AGGTGCGTGA
* **
356493 GGCGCGAG-GGAACTCTGACCAAGGAAGTTGT
1 GGCGCGAGAGAAACTCTGACCAAGGAAGTTAC
*
356524 GGCGCGAGATGAAACTCTGACCAAGGGAGTTAC
1 GGCGCGAGA-GAAACTCTGACCAAGGAAGTTAC
356557 GGCGCGAGATGAAA
1 GGCGCGAGA-GAAA
356571 TGCTTGCTAG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 8 0.20
33 33 0.80
ACGTcount: A:0.29, C:0.19, G:0.37, T:0.14
Consensus pattern (32 bp):
GGCGCGAGAGAAACTCTGACCAAGGAAGTTAC
Found at i:356543 original size:33 final size:33
Alignment explanation
Indices: 356503--356570 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
356493 GGCGCGAGGG
**
356503 AACTCTGACCAAGGAAGTTGTGGCGCGAGATGA
1 AACTCTGACCAAGGAAGTTACGGCGCGAGATGA
*
356536 AACTCTGACCAAGGGAGTTACGGCGCGAGATGA
1 AACTCTGACCAAGGAAGTTACGGCGCGAGATGA
356569 AA
1 AA
356571 TGCTTGCTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.32, C:0.19, G:0.32, T:0.16
Consensus pattern (33 bp):
AACTCTGACCAAGGAAGTTACGGCGCGAGATGA
Found at i:356696 original size:22 final size:23
Alignment explanation
Indices: 356655--356702 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
356645 GAAAAAAATG
356655 TAAATATAGTATAATTTATAATA
1 TAAATATAGTATAATTTATAATA
356678 TAAATATA-TAT-ATTATATAATA
1 TAAATATAGTATAATT-TATAATA
356700 TAA
1 TAA
356703 GGATGAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 3 0.12
22 13 0.54
23 8 0.33
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TAAATATAGTATAATTTATAATA
Found at i:356937 original size:20 final size:20
Alignment explanation
Indices: 356914--356955 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
356904 GAATCATTCG
*
356914 TCGTGAAATTGAAATTGAAC
1 TCGTGAAATTGAAATCGAAC
*
356934 TCGTGAAGTTGAAATCGAAC
1 TCGTGAAATTGAAATCGAAC
356954 TC
1 TC
356956 AGAGTTCTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (20 bp):
TCGTGAAATTGAAATCGAAC
Found at i:357214 original size:105 final size:105
Alignment explanation
Indices: 357013--357646 Score: 1124
Period size: 105 Copynumber: 6.0 Consensus size: 105
357003 CGTTGTGAAG
* * *
357013 CTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTG
1 CTGAAATTGAGAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
357078 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
65 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
* *
357119 CTGAATTTGAGAAATGTTTGTTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
357184 CTGGAGTCCAATATCCTTCGTTGTGGAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
*
357224 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
357289 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
* *
357329 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
357394 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
* *
357434 CTGAAATTGATAAATGTTCGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
357499 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
* *
357539 CTGAAATTGATAAATGTTCGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
357604 CTGGAGTCCAATACCCTTCGTTGGGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
357644 CTG
1 CTG
357647 GGTAAAACCT
Statistics
Matches: 511, Mismatches: 17, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
105 499 0.98
106 12 0.02
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
Found at i:369247 original size:19 final size:21
Alignment explanation
Indices: 369213--369252 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
369203 GAGAGAGGGA
369213 AAAAATATATAATAATAATAG
1 AAAAATATATAATAATAATAG
*
369234 AAAAAT-TA-AATAATTATAG
1 AAAAATATATAATAATAATAG
369253 TAATACAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 2 0.11
21 6 0.33
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (21 bp):
AAAAATATATAATAATAATAG
Found at i:370363 original size:31 final size:32
Alignment explanation
Indices: 370325--370402 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 32
370315 AGGTGCGTGA
* **
370325 GGCGCGAG-GGAACTCTGACCAAGGAAGTTGT
1 GGCGCGAGAGAAACTCTGACCAAGGAAGTTAC
*
370356 GGCGCGAGATGAAACTCTGACCAAGGGAGTTAC
1 GGCGCGAGA-GAAACTCTGACCAAGGAAGTTAC
370389 GGCGCGAGATGAAA
1 GGCGCGAGA-GAAA
370403 TGCTTGCTAG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 8 0.20
33 33 0.80
ACGTcount: A:0.29, C:0.19, G:0.37, T:0.14
Consensus pattern (32 bp):
GGCGCGAGAGAAACTCTGACCAAGGAAGTTAC
Found at i:370375 original size:33 final size:33
Alignment explanation
Indices: 370335--370402 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
370325 GGCGCGAGGG
**
370335 AACTCTGACCAAGGAAGTTGTGGCGCGAGATGA
1 AACTCTGACCAAGGAAGTTACGGCGCGAGATGA
*
370368 AACTCTGACCAAGGGAGTTACGGCGCGAGATGA
1 AACTCTGACCAAGGAAGTTACGGCGCGAGATGA
370401 AA
1 AA
370403 TGCTTGCTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.32, C:0.19, G:0.32, T:0.16
Consensus pattern (33 bp):
AACTCTGACCAAGGAAGTTACGGCGCGAGATGA
Found at i:370530 original size:24 final size:23
Alignment explanation
Indices: 370487--370536 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 23
370477 GAAAAAAATG
370487 TAAATATAGTATAATTTATAATA
1 TAAATATAGTATAATTTATAATA
370510 TAAATATA-TATATATTATATAATA
1 TAAATATAGTATA-ATT-TATAATA
370534 TAA
1 TAA
370537 GGATGAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 4 0.16
23 11 0.44
24 10 0.40
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TAAATATAGTATAATTTATAATA
Found at i:372674 original size:19 final size:20
Alignment explanation
Indices: 372632--372675 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
372622 TCTTTTTTTC
* *
372632 TTTTTCTTTCGAATAGTCTT
1 TTTTTCGTTCGAATAGTCTG
*
372652 TTTTTCGTTCGAATTG-CTG
1 TTTTTCGTTCGAATAGTCTG
372671 TTTTT
1 TTTTT
372676 TTCCACATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.11, C:0.14, G:0.14, T:0.61
Consensus pattern (20 bp):
TTTTTCGTTCGAATAGTCTG
Found at i:380076 original size:25 final size:25
Alignment explanation
Indices: 380042--380092 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
380032 TAACTATTGT
380042 CATGTTCCATTGAAAATTCATGTTA
1 CATGTTCCATTGAAAATTCATGTTA
380067 CATGTTCCATTGAAAATTCATGTTA
1 CATGTTCCATTGAAAATTCATGTTA
380092 C
1 C
380093 CACTTTCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (25 bp):
CATGTTCCATTGAAAATTCATGTTA
Found at i:380314 original size:2 final size:2
Alignment explanation
Indices: 380307--380364 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
380297 ATATTTACGC
*
380307 AT AT AT AT AT GT 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 AT AT AT
380349 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
380365 GTATCAAATG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:384602 original size:15 final size:16
Alignment explanation
Indices: 384582--384614 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
384572 AGAATCTATC
*
384582 AAAATTTTATTT-TTT
1 AAAATTTGATTTATTT
384597 AAAATTTGATTTATTT
1 AAAATTTGATTTATTT
384613 AA
1 AA
384615 GTCCTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
AAAATTTGATTTATTT
Found at i:386854 original size:24 final size:24
Alignment explanation
Indices: 386834--386896 Score: 117
Period size: 24 Copynumber: 2.6 Consensus size: 24
386824 GTAGAGGCCA
386834 TGGACGAGGTGGAAGTCGAGGTCG
1 TGGACGAGGTGGAAGTCGAGGTCG
386858 TGGACGAGGTGGAAGTCGAGGTCG
1 TGGACGAGGTGGAAGTCGAGGTCG
386882 TGGACGAGGCTGGAA
1 TGGACGAGG-TGGAA
386897 TTACAACAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 33 0.87
25 5 0.13
ACGTcount: A:0.22, C:0.13, G:0.49, T:0.16
Consensus pattern (24 bp):
TGGACGAGGTGGAAGTCGAGGTCG
Found at i:390329 original size:29 final size:29
Alignment explanation
Indices: 390287--390368 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
390277 AAACTAAATT
390287 GATGTCATTGCTTACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
390316 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
390345 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
390369 GTTAGGTGAG
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 46 0.90
30 5 0.10
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:390842 original size:35 final size:34
Alignment explanation
Indices: 390721--390860 Score: 158
Period size: 36 Copynumber: 4.0 Consensus size: 34
390711 AAAAAATGAA
390721 CACTTGAATCGAAAGTGCGACG-TCTCCTTCCGTT
1 CACTTGAATCGAAAGTGCGACGCT-TCCTTCCGTT
* *
390755 CGACTTAAATCGAAAGTGTCGATGCTTCCTTCCGTT
1 C-ACTTGAATCGAAAGTG-CGACGCTTCCTTCCGTT
* * *
390791 CAGTTTGAATCGGAAGTGCCGATGCTTCCTTCCGTT
1 CA-CTTGAATCGAAAGTG-CGACGCTTCCTTCCGTT
*
390827 CACTTGAATC-AGAAGTGCGACGTTTCCTTCCGTT
1 CACTTGAATCGA-AAGTGCGACGCTTCCTTCCGTT
390861 ATTCTTGTTC
Statistics
Matches: 91, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
34 16 0.18
35 28 0.31
36 46 0.51
37 1 0.01
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.32
Consensus pattern (34 bp):
CACTTGAATCGAAAGTGCGACGCTTCCTTCCGTT
Found at i:390843 original size:71 final size:70
Alignment explanation
Indices: 390724--390860 Score: 172
Period size: 71 Copynumber: 1.9 Consensus size: 70
390714 AAATGAACAC
*
390724 TTGAATCGAAAGTGCGACGTCTCCTTCCGTTCGACTTAAATCGAAAGTGTCGATGCTTCCTTCCG
1 TTGAATCGAAAGTGCGACGTCTCCTTCCGTTCGACTTAAATCGAAAGTG-CGACGCTTCCTTCCG
390789 TTCAGT
65 TTCAGT
* * * *
390795 TTGAATCGGAAGTGCCGATG-CTTCCTTCCGTTC-ACTTGAATC-AGAAGTGCGACGTTTCCTTC
1 TTGAATCGAAAGTG-CGACGTC-TCCTTCCGTTCGACTTAAATCGA-AAGTGCGACGCTTCCTTC
390857 CGTT
63 CGTT
390861 ATTCTTGTTC
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
70 16 0.28
71 27 0.47
72 15 0.26
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.33
Consensus pattern (70 bp):
TTGAATCGAAAGTGCGACGTCTCCTTCCGTTCGACTTAAATCGAAAGTGCGACGCTTCCTTCCGT
TCAGT
Found at i:398818 original size:23 final size:23
Alignment explanation
Indices: 398788--398832 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
398778 TTCGTTTAAC
*
398788 TTTAACCAAATAAACGAATGAAT
1 TTTAACCAAACAAACGAATGAAT
398811 TTTAACCAAACAAACGAATGAA
1 TTTAACCAAACAAACGAATGAA
398833 CACGAATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.53, C:0.16, G:0.09, T:0.22
Consensus pattern (23 bp):
TTTAACCAAACAAACGAATGAAT
Found at i:399472 original size:19 final size:19
Alignment explanation
Indices: 399437--399473 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
399427 TTAAAAGATA
*
399437 AAATATTTAAAATTATAAT
1 AAATATTTAAAACTATAAT
*
399456 AAATATTTACAACTATAA
1 AAATATTTAAAACTATAA
399474 ACGTAAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATATTTAAAACTATAAT
Found at i:399766 original size:21 final size:21
Alignment explanation
Indices: 399719--399768 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
399709 CGTAAACATT
*
399719 ATAAA-TATCATATTAATATC
1 ATAAATTATCATATTAATATA
* *
399739 TTGAATTATCATATTAATATA
1 ATAAATTATCATATTAATATA
399760 ATAAATTAT
1 ATAAATTAT
399769 TATCTTAGTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (21 bp):
ATAAATTATCATATTAATATA
Found at i:405302 original size:31 final size:31
Alignment explanation
Indices: 405264--405331 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
405254 CTCAATGGTA
* * *
405264 AAATTAGTATCTTATCTAACATTTAGAGGTT
1 AAATTAGTATATTATCTAAAATTTAGAGGTC
*
405295 AAATTAGTATATTATCTAAAATTTAGATGTC
1 AAATTAGTATATTATCTAAAATTTAGAGGTC
405326 AAATTA
1 AAATTA
405332 AAATTTAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (31 bp):
AAATTAGTATATTATCTAAAATTTAGAGGTC
Found at i:406255 original size:42 final size:42
Alignment explanation
Indices: 406196--406278 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
406186 TCTTTTCTAG
406196 TTTGTTTATTGTTATTGTTGAACTCGGATAGATCGAGAGAAT
1 TTTGTTTATTGTTATTGTTGAACTCGGATAGATCGAGAGAAT
* *
406238 TTTGTTTATTGTTATTGTTGTACTCGGATAGATGGAGAGAA
1 TTTGTTTATTGTTATTGTTGAACTCGGATAGATCGAGAGAA
406279 CGGATGAAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.25, C:0.06, G:0.25, T:0.43
Consensus pattern (42 bp):
TTTGTTTATTGTTATTGTTGAACTCGGATAGATCGAGAGAAT
Found at i:414951 original size:28 final size:28
Alignment explanation
Indices: 414911--414967 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
414901 GAGAAGAAAG
414911 AACCCTAGGGCTAGGGTTTTATAGCTAT
1 AACCCTAGGGCTAGGGTTTTATAGCTAT
414939 AACCCTAGGGCTAGGGTTTTATAGCTAT
1 AACCCTAGGGCTAGGGTTTTATAGCTAT
414967 A
1 A
414968 GCTGGGGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.32
Consensus pattern (28 bp):
AACCCTAGGGCTAGGGTTTTATAGCTAT
Found at i:423113 original size:18 final size:18
Alignment explanation
Indices: 423087--423124 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
423077 CGCGATCGTG
423087 ATTTAAAATCCTGTAGTA
1 ATTTAAAATCCTGTAGTA
*
423105 ATTTGAAATCCTGTAGTA
1 ATTTAAAATCCTGTAGTA
423123 AT
1 AT
423125 GATCAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (18 bp):
ATTTAAAATCCTGTAGTA
Found at i:426140 original size:193 final size:189
Alignment explanation
Indices: 425767--426145 Score: 706
Period size: 193 Copynumber: 2.0 Consensus size: 189
425757 ATTTACAGTG
425767 TATTTAGGGTGGACTACACGTTTTTTTATTTTAGGGTAAACTAATGTTTGGTACCTAAACATCGT
1 TATTTAGGGTGGACTACACGTTTTTTTATTTTAGGGTAAACTAATGTTTGGTACCTAAACATCGT
425832 ATTGTTTCGTTTTTATTACCTATATTCTCATTTGTTTCAAAATCATATTTAAGTTTATTTTTGTT
66 ATTGTTTCGTTTTTATTACCTATATTCTCATTTGTTTCAAAATCATATTTAAGTTTATTTTTGTT
425897 TCATTTTAGTACACCATCGTTAAAAATTTAACGAAACTATTGCACGTGACATTTTTGGT
131 TCATTTTAGTACACCATCGTTAAAAATTTAACGAAACTATTGCACGTGACATTTTTGGT
425956 TATTTAGGGTGGACTACACGTTTTTTTATTTTAGGGTAAACTACATGTTTGGTACCTAAACTATC
1 TATTTAGGGTGGACTACACGTTTTTTTATTTTAGGGTAAACTA-ATGTTTGGTACCTAAAC-ATC
426021 GTATTGTTTCG-TTTTATTACCTATATTCTCATTTGTTTCAAAATCATATTTAAAGTTTATTTTT
64 GTATTGTTTCGTTTTTATTACCTATATTCTCATTTGTTTCAAAATCATATTT-AAGTTTA--TTT
426085 TTGTTTCATTTTAGTACACCATCGTTAAAAATTTAACGAAACTATTGCACGTGACATTTTT
126 TTGTTTCATTTTAGTACACCATCGTTAAAAATTTAACGAAACTATTGCACGTGACATTTTT
426146 ATTGGTAAAT
Statistics
Matches: 185, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
189 43 0.23
190 57 0.31
191 21 0.11
193 64 0.35
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.46
Consensus pattern (189 bp):
TATTTAGGGTGGACTACACGTTTTTTTATTTTAGGGTAAACTAATGTTTGGTACCTAAACATCGT
ATTGTTTCGTTTTTATTACCTATATTCTCATTTGTTTCAAAATCATATTTAAGTTTATTTTTGTT
TCATTTTAGTACACCATCGTTAAAAATTTAACGAAACTATTGCACGTGACATTTTTGGT
Found at i:427942 original size:2 final size:2
Alignment explanation
Indices: 427935--427964 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
427925 GAGAAATTAT
427935 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
427965 ATCCAAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:431624 original size:24 final size:25
Alignment explanation
Indices: 431597--431677 Score: 103
Period size: 25 Copynumber: 3.2 Consensus size: 25
431587 TCTTAATCTA
*
431597 TTTTTTTATTT-TTTAACAAAGCTG
1 TTTTTTTATTTAATTAACAAAGCTG
*
431621 TTTTTTAATTTAATTAACAAAGCTG
1 TTTTTTTATTTAATTAACAAAGCTG
*
431646 TTTTTTTAATTTAATTAAATAAAG-TG
1 TTTTTTT-ATTTAATT-AACAAAGCTG
431672 TTTTTT
1 TTTTTT
431678 GTCTCTTTGT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
24 10 0.20
25 18 0.36
26 16 0.32
27 6 0.12
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.57
Consensus pattern (25 bp):
TTTTTTTATTTAATTAACAAAGCTG
Found at i:431625 original size:25 final size:25
Alignment explanation
Indices: 431609--431677 Score: 104
Period size: 25 Copynumber: 2.7 Consensus size: 25
431599 TTTTTATTTT
431609 TTAACAAAGCTGTTTTTTAATTTAA
1 TTAACAAAGCTGTTTTTTAATTTAA
431634 TTAACAAAGCTGTTTTTTTAATTTAA
1 TTAACAAAGCTG-TTTTTTAATTTAA
*
431660 TTAAATAAAG-TGTTTTTT
1 TT-AACAAAGCTGTTTTTT
431678 GTCTCTTTGT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
25 18 0.44
26 17 0.41
27 6 0.15
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.51
Consensus pattern (25 bp):
TTAACAAAGCTGTTTTTTAATTTAA
Found at i:431657 original size:26 final size:26
Alignment explanation
Indices: 431597--431677 Score: 107
Period size: 26 Copynumber: 3.2 Consensus size: 26
431587 TCTTAATCTA
*
431597 TTTTTTT-ATTT-TTTAACAAAGCTG
1 TTTTTTTAATTTAATTAACAAAGCTG
431621 -TTTTTTAATTTAATTAACAAAGCTG
1 TTTTTTTAATTTAATTAACAAAGCTG
*
431646 TTTTTTTAATTTAATTAAATAAAG-TG
1 TTTTTTTAATTTAATT-AACAAAGCTG
431672 TTTTTT
1 TTTTTT
431678 GTCTCTTTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
23 6 0.12
24 4 0.08
25 12 0.24
26 23 0.45
27 6 0.12
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.57
Consensus pattern (26 bp):
TTTTTTTAATTTAATTAACAAAGCTG
Found at i:437815 original size:14 final size:14
Alignment explanation
Indices: 437796--437824 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
437786 AAATGATTCG
437796 ATAAATCTTATTTT
1 ATAAATCTTATTTT
437810 ATAAATCTTATTTT
1 ATAAATCTTATTTT
437824 A
1 A
437825 CCTTGACGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
ATAAATCTTATTTT
Found at i:438454 original size:12 final size:11
Alignment explanation
Indices: 438423--438462 Score: 53
Period size: 12 Copynumber: 3.4 Consensus size: 11
438413 TCATGATATT
438423 ATAAATATTTACA
1 ATAAA-ATTTA-A
438436 ATAAAATTTAA
1 ATAAAATTTAA
438447 ATATAAATTTAA
1 ATA-AAATTTAA
438459 ATAA
1 ATAA
438463 CTCGACTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 5 0.19
12 16 0.62
13 5 0.19
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (11 bp):
ATAAAATTTAA
Found at i:441864 original size:22 final size:22
Alignment explanation
Indices: 441839--441899 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
441829 TTAGAAAATA
* *
441839 AACTTATAAAATTTTAAAAGAT
1 AACTTATAAAATTTGAAAAGAG
*
441861 AACTTATAAAATTTGAAAGGAG
1 AACTTATAAAATTTGAAAAGAG
*
441883 AATTTATAAAATTTGAA
1 AACTTATAAAATTTGAA
441900 GGAAACAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.34
Consensus pattern (22 bp):
AACTTATAAAATTTGAAAAGAG
Found at i:443005 original size:21 final size:21
Alignment explanation
Indices: 442966--443005 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
442956 AAAAATAAAT
*
442966 TTAATAATTAAATTGATAACA
1 TTAATAATTAAATTCATAACA
442987 TTAATAATATAAA-TCATAA
1 TTAATAAT-TAAATTCATAA
443006 AAATACTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (21 bp):
TTAATAATTAAATTCATAACA
Found at i:443964 original size:2 final size:2
Alignment explanation
Indices: 443957--443984 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
443947 TAAGTTCGAT
443957 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
443985 CACTTTTGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:446720 original size:2 final size:2
Alignment explanation
Indices: 446713--446741 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
446703 GTACTTGTGT
446713 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
446742 GAAATGTGTT
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:447844 original size:15 final size:15
Alignment explanation
Indices: 447824--447853 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
447814 TATCACAATC
447824 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
447839 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
447854 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:462458 original size:32 final size:32
Alignment explanation
Indices: 462409--462569 Score: 155
Period size: 32 Copynumber: 5.1 Consensus size: 32
462399 ATTGTAAAGT
* * *
462409 TTTGAT-ATATTTAATGACCATATTGTAACAA
1 TTTGATAAAATTTAATGACAATTTTGTAACAA
* *
462440 TTTGATAAAATTTAATGACCATTTTGTAATAA
1 TTTGATAAAATTTAATGACAATTTTGTAACAA
* * ** * *
462472 ATTGATAAATTTTAATGATTATTTTGTAATAG
1 TTTGATAAAATTTAATGACAATTTTGTAACAA
* * *
462504 TTTGAT-AAATCTAATGACAATTTTATAACAG
1 TTTGATAAAATTTAATGACAATTTTGTAACAA
* * *
462535 TTTGACAAAATTTAATTACAATTTTGTAACTA
1 TTTGATAAAATTTAATGACAATTTTGTAACAA
462567 TTT
1 TTT
462570 AAAATTCAAT
Statistics
Matches: 107, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
31 30 0.28
32 77 0.72
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (32 bp):
TTTGATAAAATTTAATGACAATTTTGTAACAA
Found at i:463084 original size:2 final size:2
Alignment explanation
Indices: 463073--463101 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
463063 TCCGACACAA
463073 AT AT -T 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
463102 TAGGTAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:464755 original size:12 final size:12
Alignment explanation
Indices: 464740--464805 Score: 80
Period size: 12 Copynumber: 5.6 Consensus size: 12
464730 GATATTTAAA
464740 CGGGTATTGGGC
1 CGGGTATTGGGC
*
464752 CGGGTATTGGGT
1 CGGGTATTGGGC
*
464764 CGGGTATTGGGT
1 CGGGTATTGGGC
464776 C-GGTATTGGGC
1 CGGGTATTGGGC
* *
464787 CGGGAATCGGGC
1 CGGGTATTGGGC
*
464799 TGGGTAT
1 CGGGTAT
464806 ATATATATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
11 10 0.21
12 37 0.79
ACGTcount: A:0.11, C:0.14, G:0.48, T:0.27
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:464767 original size:24 final size:24
Alignment explanation
Indices: 464740--464805 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
464730 GATATTTAAA
*
464740 CGGGTATTGGGCCGGGTATTGGGT
1 CGGGTATTGGGCCGGGTATTGGGC
*
464764 CGGGTATTGGGTC-GGTATTGGGC
1 CGGGTATTGGGCCGGGTATTGGGC
* * *
464787 CGGGAATCGGGCTGGGTAT
1 CGGGTATTGGGCCGGGTAT
464806 ATATATATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 18 0.51
24 17 0.49
ACGTcount: A:0.11, C:0.14, G:0.48, T:0.27
Consensus pattern (24 bp):
CGGGTATTGGGCCGGGTATTGGGC
Found at i:464865 original size:24 final size:25
Alignment explanation
Indices: 464803--464865 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
464793 TCGGGCTGGG
464803 TATATA-TATATATATTTAAATTAAA
1 TATATATTATAT-TATTTAAATTAAA
*
464828 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
464852 T-T-TATTAATATTAT
1 TATATATT-ATATTAT
464866 ATATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 1 0.03
24 19 0.58
25 8 0.24
26 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:464920 original size:13 final size:14
Alignment explanation
Indices: 464904--464945 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
464894 AATATTTATC
464904 GGGTCGGGT-ATCG
1 GGGTCGGGTAATCG
464917 GGGT-GGGTAATCG
1 GGGTCGGGTAATCG
*
464930 GAG-CGGGTAATCG
1 GGGTCGGGTAATCG
464943 GGG
1 GGG
464946 AGGGATTACC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 4 0.16
13 21 0.84
ACGTcount: A:0.14, C:0.12, G:0.55, T:0.19
Consensus pattern (14 bp):
GGGTCGGGTAATCG
Found at i:468162 original size:14 final size:15
Alignment explanation
Indices: 468135--468163 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
468125 AGAGATTATC
468135 AATTTATGAGATATT
1 AATTTATGAGATATT
468150 AATTTAT-AGATATT
1 AATTTATGAGATATT
468164 GTACTGTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (15 bp):
AATTTATGAGATATT
Found at i:469133 original size:2 final size:2
Alignment explanation
Indices: 469126--469158 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
469116 TTTACATTGT
469126 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 T
469159 TTATTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:469177 original size:14 final size:14
Alignment explanation
Indices: 469160--469199 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
469150 TATATATATT
469160 TATTTTTTTATTAA
1 TATTTTTTTATTAA
* *
469174 TATTATTATATTAA
1 TATTTTTTTATTAA
469188 TA-TTTTTTATTA
1 TATTTTTTTATTA
469200 TTCTTTTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTTTTTTATTAA
Found at i:472305 original size:13 final size:13
Alignment explanation
Indices: 472260--472323 Score: 71
Period size: 12 Copynumber: 5.0 Consensus size: 13
472250 TTCAATCAAG
* *
472260 AACAAAAAGAGAA
1 AACAAAGAGAAAA
472273 AA-AAAGAGAAAA
1 AACAAAGAGAAAA
472285 AAGCAAAGAGAAAA
1 AA-CAAAGAGAAAA
472299 TAA-AAAGAGAAAA
1 -AACAAAGAGAAAA
472312 AACAAAG-GAAAA
1 AACAAAGAGAAAA
472324 TTGAAGAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
12 17 0.38
13 16 0.36
14 10 0.22
15 2 0.04
ACGTcount: A:0.77, C:0.05, G:0.17, T:0.02
Consensus pattern (13 bp):
AACAAAGAGAAAA
Found at i:472309 original size:27 final size:25
Alignment explanation
Indices: 472273--472324 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 25
472263 AAAAAGAGAA
472273 AAAAAGAGAAAAAAGCAAAGAGAAAAT
1 AAAAAGAGAAAAAA-CAAAG-GAAAAT
472300 AAAAAGAGAAAAAACAAAGGAAAAT
1 AAAAAGAGAAAAAACAAAGGAAAAT
472325 TGAAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
27 14 0.56
ACGTcount: A:0.75, C:0.04, G:0.17, T:0.04
Consensus pattern (25 bp):
AAAAAGAGAAAAAACAAAGGAAAAT
Found at i:473553 original size:32 final size:32
Alignment explanation
Indices: 473445--473539 Score: 145
Period size: 32 Copynumber: 2.9 Consensus size: 32
473435 TGAGGGCATC
*
473445 TTTGAAGATTCAACATCAAATGCTGGGGCATTT
1 TTTG-AGATTCAACATCAAATGTTGGGGCATTT
* *
473478 TTTGAGATTTAACATCAAATGTAGGGGCATTT
1 TTTGAGATTCAACATCAAATGTTGGGGCATTT
*
473510 TTTGAGATTCAACATCAAATATTGGGGCAT
1 TTTGAGATTCAACATCAAATGTTGGGGCAT
473540 ATTTGGGAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
32 52 0.93
33 4 0.07
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.35
Consensus pattern (32 bp):
TTTGAGATTCAACATCAAATGTTGGGGCATTT
Found at i:473891 original size:21 final size:21
Alignment explanation
Indices: 473865--473906 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
473855 AACTTCACAA
473865 CGAAGGATATTGGACTCAAAG
1 CGAAGGATATTGGACTCAAAG
*
473886 CGAAGGATATTGTACTCAAAG
1 CGAAGGATATTGGACTCAAAG
473907 TGACACAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.21
Consensus pattern (21 bp):
CGAAGGATATTGGACTCAAAG
Found at i:474786 original size:37 final size:37
Alignment explanation
Indices: 474729--474841 Score: 165
Period size: 37 Copynumber: 3.1 Consensus size: 37
474719 TTTCCAAGTT
*
474729 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
1 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATC
* *
474766 TTGTCTCTCTTAAGATAGTTTCCCTTGAAAC-AAATT
1 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATC
* *
474802 TTGTCTCTATTGAGATAGTTTCCCTTGAAAATAAAATC
1 TTGTCTCTCTTGAGATAGTTTCCCTTG-AAACAAAATC
474840 TT
1 TT
474842 TGAATATCTT
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
36 29 0.43
37 32 0.48
38 6 0.09
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.40
Consensus pattern (37 bp):
TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATC
Found at i:474818 original size:36 final size:37
Alignment explanation
Indices: 474727--474831 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 37
474717 AATTTCCAAG
*
474727 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAA
1 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAA
* *
474764 TCTTGTCTCTCTTAAGATAGTTTCCCTTGAAAC-AAA
1 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAA
*
474800 TTTTGTCTCTATTGAGATAGTTTCCCTTGAAA
1 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAA
474832 ATAAAATCTT
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
36 32 0.52
37 30 0.48
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (37 bp):
TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAA
Found at i:474927 original size:15 final size:15
Alignment explanation
Indices: 474877--474927 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
474867 TTCGTCTCCC
474877 TTGAGACAGTTTCTT
1 TTGAGACAGTTTCTT
474892 TT-AGAACTAAGTTT-TT
1 TTGAG-AC--AGTTTCTT
474908 CTTGAGACAGTTTCTT
1 -TTGAGACAGTTTCTT
474924 TTGA
1 TTGA
474928 AACAAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
14 2 0.07
15 13 0.43
16 4 0.13
17 9 0.30
18 2 0.07
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.47
Consensus pattern (15 bp):
TTGAGACAGTTTCTT
Found at i:474954 original size:36 final size:35
Alignment explanation
Indices: 474856--474967 Score: 108
Period size: 36 Copynumber: 3.2 Consensus size: 35
474846 TATCTTTTCC
*
474856 TTGAAACAAATTTCGTCTCC-CTTGAGACAGTTTCTT
1 TTGAAACAAATTT-TTC-CCTCTTGAGACAGTTTCTT
* *
474892 TT-AGAACTAAGTTTT---TCTTGAGACAGTTTCTT
1 TTGA-AACAAATTTTTCCCTCTTGAGACAGTTTCTT
*
474924 TTGAAACAAATTTTATCCCTCTTGAGACAGTTTCTC
1 TTGAAACAAATTTT-TCCCTCTTGAGACAGTTTCTT
*
474960 TTAAAACA
1 TTGAAACA
474968 CAAAAAAACC
Statistics
Matches: 62, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
32 26 0.42
33 2 0.03
35 2 0.03
36 32 0.52
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (35 bp):
TTGAAACAAATTTTTCCCTCTTGAGACAGTTTCTT
Found at i:475174 original size:83 final size:83
Alignment explanation
Indices: 475035--475373 Score: 459
Period size: 83 Copynumber: 4.1 Consensus size: 83
475025 GAAACATCAA
* * * * * *
475035 ACCTTCGAGTTCGACTACGCTCAGCTTCAAGACACATTATTTTCAGCATAACTCAAGGCTAGAAG
1 ACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAACATAACTCAAGGCTAGAAG
475100 GGTTATCTGCCAACAAAG
66 GGTTATCTGCCAACAAAG
* *
475118 ACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTACAACATAACTCAAGGCTAGAAG
1 ACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAACATAACTCAAGGCTAGAAG
*
475183 GGTTATCTGCCAACAAAA
66 GGTTATCTGCCAACAAAG
*
475201 ACCTTCGAGTTCGACTATACTCAGCTCCAAGGCACATCATTTACAACATAACTCAAGGCTAGAAG
1 ACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAACATAACTCAAGGCTAGAAG
* *
475266 GGTTATCTGTCAACAATG
66 GGTTATCTGCCAACAAAG
* * * * * * * *
475284 ACCTCCGAGTTCGACTCCACTCAGCTCAAATGCACCATCATTTGCAGCATAGCTCAAGGCAAGAA
1 ACCTTCGAGTTCGACTACACTCAGCTCCAAGGCA-CATCATTTACAACATAACTCAAGGCTAGAA
*
475349 GGGCTATCTG-C--CAAAG
65 GGGTTATCTGCCAACAAAG
475365 ACCTTCGAG
1 ACCTTCGAG
475374 CTTGATTCCA
Statistics
Matches: 230, Mismatches: 25, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
81 12 0.05
83 183 0.80
84 35 0.15
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (83 bp):
ACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAACATAACTCAAGGCTAGAAG
GGTTATCTGCCAACAAAG
Found at i:475737 original size:9 final size:8
Alignment explanation
Indices: 475721--475771 Score: 56
Period size: 9 Copynumber: 6.6 Consensus size: 8
475711 CTACAAAAAC
475721 ATTTTATT
1 ATTTTATT
475729 ATATTTATT
1 AT-TTTATT
475738 A--TTATT
1 ATTTTATT
475744 ATTATTATT
1 ATT-TTATT
475753 ATTTTATT
1 ATTTTATT
475761 -TTTT-TT
1 ATTTTATT
475767 ATTTT
1 ATTTT
475772 TGTATGCCCC
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
6 8 0.21
7 8 0.21
8 7 0.18
9 15 0.39
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
ATTTTATT
Found at i:475739 original size:3 final size:3
Alignment explanation
Indices: 475724--475760 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
475714 CAAAAACATT
475724 TTA TTA -TA TTTA TTA TTA TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
475761 TTTTTTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.13
3 25 0.81
4 2 0.06
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:475870 original size:33 final size:33
Alignment explanation
Indices: 475823--475904 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
475813 GAACATAAAT
*
475823 CAACGTATTTGAGTCCTATTGAAACACTAAAAC
1 CAACATATTTGAGTCCTATTGAAACACTAAAAC
*
475856 CAACATATTTGAGTCTTATTGAAACACTAAAAC
1 CAACATATTTGAGTCCTATTGAAACACTAAAAC
* * *
475889 TAAAACATTTGAGTCC
1 CAACATATTTGAGTCC
475905 AAGTAAGACT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (33 bp):
CAACATATTTGAGTCCTATTGAAACACTAAAAC
Found at i:476903 original size:20 final size:20
Alignment explanation
Indices: 476878--476929 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
476868 GGTAACTTGA
476878 TTGCAATCAAATAAAAAGTT
1 TTGCAATCAAATAAAAAGTT
476898 TTGCAATCAAATAAAAAGTT
1 TTGCAATCAAATAAAAAGTT
*
476918 TTGCGATCAAAT
1 TTGCAATCAAAT
476930 TGATAATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.31
Consensus pattern (20 bp):
TTGCAATCAAATAAAAAGTT
Found at i:487426 original size:2 final size:2
Alignment explanation
Indices: 487419--487445 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
487409 CGAGTACCTC
487419 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 A
487446 AGAATATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:488140 original size:60 final size:60
Alignment explanation
Indices: 488001--488147 Score: 154
Period size: 60 Copynumber: 2.5 Consensus size: 60
487991 TTTGGGGACT
* ** * * * * *
488001 AATTTAGAATGGTGATTGTAGTTTGGGGATGAAATTGAAATGTTTAAAAATTTAAGGATT
1 AATTTAGAATGATGATCATAGTTTGAGGATAAAATTAAAATGTTTAAAAATTCAAGGATC
** *
488061 AATTTAGAAT-AAAAGTCATAGTTTGAGGATAAAATTAAAAT-TTTCAAAAGTTCAAGGATC
1 AATTTAGAATGATGA-TCATAGTTTGAGGATAAAATTAAAATGTTT-AAAAATTCAAGGATC
*
488121 AATTTAAAATGATGATCATAGTTTGAG
1 AATTTAGAATGATGATCATAGTTTGAG
488148 AATATATGAT
Statistics
Matches: 70, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
59 4 0.06
60 64 0.91
61 2 0.03
ACGTcount: A:0.41, C:0.03, G:0.20, T:0.35
Consensus pattern (60 bp):
AATTTAGAATGATGATCATAGTTTGAGGATAAAATTAAAATGTTTAAAAATTCAAGGATC
Found at i:488289 original size:22 final size:22
Alignment explanation
Indices: 488263--488305 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
488253 AAGTTGTAAA
*
488263 GTTTTATAATATATGGTTTAGG
1 GTTTTAGAATATATGGTTTAGG
* *
488285 GTTTTAGACTTTATGGTTTAG
1 GTTTTAGAATATATGGTTTAG
488306 AATTTAGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.02, G:0.23, T:0.51
Consensus pattern (22 bp):
GTTTTAGAATATATGGTTTAGG
Found at i:488971 original size:28 final size:28
Alignment explanation
Indices: 488931--488995 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
488921 TCTGGTGCTT
488931 ATGAGTATTAAGTGTTACTAATTAACTC
1 ATGAGTATTAAGTGTTACTAATTAACTC
*
488959 ATGAGTATTAAGTGTTACTAATTAGCTC
1 ATGAGTATTAAGTGTTACTAATTAACTC
488987 ATGAGTATT
1 ATGAGTATT
488996 TTAAATTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (28 bp):
ATGAGTATTAAGTGTTACTAATTAACTC
Found at i:505174 original size:28 final size:26
Alignment explanation
Indices: 505141--505194 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
505131 TATAAAAGGT
505141 TATTTTTATT-TTAAAAAATAAAAATA
1 TATTTTT-TTATTAAAAAATAAAAATA
*
505167 TATTTTTTTATTAGAAAATAAAAATA
1 TATTTTTTTATTAAAAAATAAAAATA
505193 TA
1 TA
505195 AAAAGAAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
TATTTTTTTATTAAAAAATAAAAATA
Found at i:505356 original size:3 final size:3
Alignment explanation
Indices: 505348--505385 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
505338 CTTTTCTTAA
505348 AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
505386 CTTATAGAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:505391 original size:17 final size:17
Alignment explanation
Indices: 505348--505385 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
505338 CTTTTCTTAA
505348 AATAATAATAATAATAAT
1 AATAAT-ATAATAATAAT
505366 AATAATATAATAATAAT
1 AATAATATAATAATAAT
505383 AAT
1 AAT
505386 CTTATAGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AATAATATAATAATAAT
Found at i:510200 original size:24 final size:24
Alignment explanation
Indices: 510168--510239 Score: 103
Period size: 24 Copynumber: 3.0 Consensus size: 24
510158 ATCTAATTTT
*
510168 ATCCC-CTAAACTTTTATAAATAT-
1 ATCCCACTAAAATTTTATAAAT-TC
*
510191 GTCCCACTAAAATTTTATAAATTC
1 ATCCCACTAAAATTTTATAAATTC
510215 ATCCCACTAAAATTTTATAAATTC
1 ATCCCACTAAAATTTTATAAATTC
510239 A
1 A
510240 CCTGCCAAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.11
24 39 0.89
ACGTcount: A:0.40, C:0.21, G:0.01, T:0.38
Consensus pattern (24 bp):
ATCCCACTAAAATTTTATAAATTC
Found at i:511091 original size:12 final size:12
Alignment explanation
Indices: 511076--511126 Score: 66
Period size: 13 Copynumber: 4.0 Consensus size: 12
511066 ATTTTAATTG
511076 TATTTTTTAAAA
1 TATTTTTTAAAA
511088 TATTTTTTTAACAA
1 TA-TTTTTTAA-AA
*
511102 TACTTTTTAAAA
1 TATTTTTTAAAA
511114 TTATTTTTTAAAA
1 -TATTTTTTAAAA
511127 ATAATATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 4 0.12
13 26 0.76
14 4 0.12
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (12 bp):
TATTTTTTAAAA
Found at i:511123 original size:26 final size:26
Alignment explanation
Indices: 511079--511129 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
511069 TTAATTGTAT
*
511079 TTTTTAAAATATTTTTTTAACAATAC
1 TTTTTAAAATATTTTTTTAAAAATAC
511105 TTTTTAAAAT-TATTTTTTAAAAATA
1 TTTTTAAAATAT-TTTTTTAAAAATA
511130 ATATTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTTTAAAATATTTTTTTAAAAATAC
Found at i:518519 original size:17 final size:19
Alignment explanation
Indices: 518497--518532 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
518487 GCAGTCTAAA
518497 TTTGGAA-C-ATTTAAAAT
1 TTTGGAACCAATTTAAAAT
518514 TTTGGAACCAATTTAAAAT
1 TTTGGAACCAATTTAAAAT
518533 GAAGTTATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 1 0.06
19 9 0.53
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (19 bp):
TTTGGAACCAATTTAAAAT
Found at i:520867 original size:6 final size:6
Alignment explanation
Indices: 520856--521054 Score: 389
Period size: 6 Copynumber: 33.2 Consensus size: 6
520846 AACAATGCAT
520856 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
*
520904 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACACAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
520952 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
521000 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
521048 ACATAC A
1 ACATAC A
521055 TTCAATTTTA
Statistics
Matches: 191, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 191 1.00
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (6 bp):
ACATAC
Found at i:525025 original size:31 final size:31
Alignment explanation
Indices: 524990--525067 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
524980 TAAATATTAT
* * *
524990 GTGTCTAAAGTGCTGACATGACACATGTCAC
1 GTGTCTAAAGTGATGACATAAAACATGTCAC
*
525021 GTGTCTAAAGTGATGACATAAAACATGTTAC
1 GTGTCTAAAGTGATGACATAAAACATGTCAC
* *
525052 ATGTCTAAAATGATGA
1 GTGTCTAAAGTGATGA
525068 TGTGGTACAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (31 bp):
GTGTCTAAAGTGATGACATAAAACATGTCAC
Found at i:535044 original size:16 final size:17
Alignment explanation
Indices: 535013--535045 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
535003 AATAACATTA
535013 TAAAAAAAAGACAAAAT
1 TAAAAAAAAGACAAAAT
*
535030 TAAACAAAA-ACAAAAT
1 TAAAAAAAAGACAAAAT
535046 CTGAAATACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.76, C:0.09, G:0.03, T:0.12
Consensus pattern (17 bp):
TAAAAAAAAGACAAAAT
Found at i:538596 original size:58 final size:59
Alignment explanation
Indices: 538446--538607 Score: 211
Period size: 58 Copynumber: 2.8 Consensus size: 59
538436 CTCTTTCGAT
*
538446 CGACTTCTTCTGATGAATATCGAACTAGTTTTCAAACACCAAGATGCCTCCCTTCCGGC
1 CGACTTCTTCTGATGAACATCGAACTAGTTTTCAAACACCAAGATGCCTCCCTTCCGGC
* ** * ** * *
538505 CGCCACCTTCTGATGAACATCGAACTAGTTTTCAAACCCCAAGATG-CTCTGTTTCGGT
1 CGACTTCTTCTGATGAACATCGAACTAGTTTTCAAACACCAAGATGCCTCCCTTCCGGC
*
538563 TGACTTCTTCTGATGAACATCGAACTAGTTTTCAAA-AGCCAAGAT
1 CGACTTCTTCTGATGAACATCGAACTAGTTTTCAAACA-CCAAGAT
538608 ACCCTGTACA
Statistics
Matches: 88, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
58 47 0.53
59 41 0.47
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (59 bp):
CGACTTCTTCTGATGAACATCGAACTAGTTTTCAAACACCAAGATGCCTCCCTTCCGGC
Found at i:543736 original size:34 final size:35
Alignment explanation
Indices: 543693--543763 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
543683 AAGTTTTGAA
543693 ATTACTCCCCCTTAC-TTTAACACTTCTTCAATTT
1 ATTACTCCCCCTTACTTTTAACACTTCTTCAATTT
543727 ATTACTCCCCCTTACTTTTAACACTTCTTCAATTT
1 ATTACTCCCCCTTACTTTTAACACTTCTTCAATTT
543762 AT
1 AT
543764 CATGTAAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 15 0.42
35 21 0.58
ACGTcount: A:0.24, C:0.31, G:0.00, T:0.45
Consensus pattern (35 bp):
ATTACTCCCCCTTACTTTTAACACTTCTTCAATTT
Found at i:546109 original size:21 final size:21
Alignment explanation
Indices: 546055--546117 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
546045 ATTCCCCTGT
546055 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTT-CCC-TCAA
* *
546078 AGGGGGAATCGGTTCCCTCAG
1 GGGGGGAATCGGTTCCCTCAA
* *
546099 GGGGGGGATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
546118 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 19 0.54
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.25, G:0.38, T:0.21
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Found at i:549968 original size:22 final size:21
Alignment explanation
Indices: 549926--549965 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
549916 GAGTTTGTTT
*
549926 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
549947 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
549966 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:553383 original size:22 final size:21
Alignment explanation
Indices: 553358--553402 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
553348 AAAAGTATAC
553358 ATTAAAAATTATAAAATAATAA
1 ATTAAAAATTATAAAA-AATAA
** *
553380 ATTATTAATTATTAAAAATAA
1 ATTAAAAATTATAAAAAATAA
553401 AT
1 AT
553403 ATTGAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATTAAAAATTATAAAAAATAA
Found at i:556308 original size:15 final size:15
Alignment explanation
Indices: 556290--556322 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
556280 CGAGGGTTCT
556290 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
556305 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
556320 GTA
1 GTA
556323 ATGGTCCTAC
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:0.15, C:0.24, G:0.33, T:0.27
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:559916 original size:75 final size:75
Alignment explanation
Indices: 559793--559943 Score: 239
Period size: 75 Copynumber: 2.0 Consensus size: 75
559783 TCTGTGCACG
**
559793 CAACTTTGAAAAGCAAATAAAGCTCCACCTAGGCCCTTGTACGTGAACATCCAGCATGGTGACCA
1 CAACTTTGAAAAGCAAATAAAGCTCCACCTAGGCCCCGGTACGTGAACATCCAGCATGGTGACCA
559858 TCATCCTCAT
66 TCATCCTCAT
* * * * *
559868 CAACTTTGAAAAGCAAATAGAGCTCCACCTAGGCCCCGGTATGTGAACATCCGGTATGGTGACCC
1 CAACTTTGAAAAGCAAATAAAGCTCCACCTAGGCCCCGGTACGTGAACATCCAGCATGGTGACCA
559933 TCATCCTCAT
66 TCATCCTCAT
559943 C
1 C
559944 TTAATGCCAT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.23
Consensus pattern (75 bp):
CAACTTTGAAAAGCAAATAAAGCTCCACCTAGGCCCCGGTACGTGAACATCCAGCATGGTGACCA
TCATCCTCAT
Found at i:568672 original size:4 final size:4
Alignment explanation
Indices: 568663--568713 Score: 59
Period size: 4 Copynumber: 12.8 Consensus size: 4
568653 CAAAATTACG
* * *
568663 TACA TACA TACA TATA TACA TACA TACA GACA TACA TA-G TGACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA T-ACA TACA
568711 TAC
1 TAC
568714 CTTGTGAAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 1 0.03
4 37 0.95
5 1 0.03
ACGTcount: A:0.47, C:0.22, G:0.06, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:569188 original size:8 final size:8
Alignment explanation
Indices: 569175--569204 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
569165 AGACTCGTCA
569175 ATGTATAC
1 ATGTATAC
569183 ATGTATAC
1 ATGTATAC
*
569191 ATGTATAA
1 ATGTATAC
569199 ATGTAT
1 ATGTAT
569205 GCTTAAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (8 bp):
ATGTATAC
Found at i:569213 original size:12 final size:12
Alignment explanation
Indices: 569196--569220 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
569186 TATACATGTA
569196 TAAATGTATGCT
1 TAAATGTATGCT
569208 TAAATGTATGCT
1 TAAATGTATGCT
569220 T
1 T
569221 GATTGGCGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TAAATGTATGCT
Found at i:583101 original size:13 final size:13
Alignment explanation
Indices: 583083--583107 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
583073 CATTCAGAAA
583083 GATAAGGAAACAG
1 GATAAGGAAACAG
583096 GATAAGGAAACA
1 GATAAGGAAACA
583108 TTAAACCCTT
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:0.56, C:0.08, G:0.28, T:0.08
Consensus pattern (13 bp):
GATAAGGAAACAG
Found at i:585758 original size:20 final size:21
Alignment explanation
Indices: 585733--585784 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
585723 TTTTCCCAAT
*
585733 TCGCAATGCGAATAAG-TAAA
1 TCGCAATGCGAATAAGAAAAA
* **
585753 TCGCAACGCGAATTGGAAAAA
1 TCGCAATGCGAATAAGAAAAA
585774 TCGCAATGCGA
1 TCGCAATGCGA
585785 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATAAGAAAAA
Found at i:585798 original size:20 final size:20
Alignment explanation
Indices: 585773--585866 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
585763 AATTGGAAAA
585773 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
585793 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
585813 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
585834 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
585854 TTCGCAACGCGAT
1 ATCGCAATGCGAT
585867 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.73
21 13 0.21
22 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:586446 original size:19 final size:19
Alignment explanation
Indices: 586422--586463 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
586412 ACGAGAGAAT
* *
586422 CGCAACTCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
*
586441 CGCAACGCGAAACAAAAAT
1 CGCAACGCGAAACAAAAAA
586460 CGCA
1 CGCA
586464 TTGCGATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.52, C:0.26, G:0.14, T:0.07
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:586481 original size:19 final size:19
Alignment explanation
Indices: 586459--586642 Score: 181
Period size: 19 Copynumber: 10.1 Consensus size: 19
586449 GAAACAAAAA
*
586459 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
586478 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
586497 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
586516 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
586535 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
586549 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
586568 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
586582 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
586601 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
586621 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
586641 TC
1 TC
586643 AACCAAAAGA
Statistics
Matches: 137, Mismatches: 16, Indels: 24
0.77 0.09 0.14
Matches are distributed among these distances:
14 19 0.14
16 4 0.03
17 5 0.04
19 77 0.56
20 31 0.23
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:586517 original size:38 final size:38
Alignment explanation
Indices: 586459--586642 Score: 181
Period size: 33 Copynumber: 5.1 Consensus size: 38
586449 GAAACAAAAA
*
586459 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
586497 TCGCGTTGCGATTTTTATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* * **
586535 TCGCGTTGCGA--TTC---TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* **
586568 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
586601 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
586641 TC
1 TC
586643 AACCAAAAGA
Statistics
Matches: 128, Mismatches: 11, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
33 48 0.38
34 10 0.08
36 4 0.03
38 47 0.37
39 1 0.01
40 18 0.14
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:588690 original size:42 final size:42
Alignment explanation
Indices: 588614--588702 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
588604 GACTCGCCTG
* * *
588614 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
588656 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
588698 TCATC
1 TCATC
588703 GTTGAAGATG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:590170 original size:18 final size:18
Alignment explanation
Indices: 590144--590188 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
590134 GTCGATCAGA
*
590144 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
590162 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
590180 TGATGGCTC
1 TGATGGCTC
590189 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:591535 original size:20 final size:20
Alignment explanation
Indices: 591512--591556 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
591502 AATGAAAATT
591512 GCAACACGAAAATGACTATC
1 GCAACACGAAAATGACTATC
* **
591532 GCAACGCGAATTTGACTATC
1 GCAACACGAAAATGACTATC
591552 GCAAC
1 GCAAC
591557 GAGAGAATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
GCAACACGAAAATGACTATC
Found at i:591847 original size:22 final size:22
Alignment explanation
Indices: 591820--591863 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
591810 GATGGAGATA
591820 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
591842 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
591864 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:592077 original size:20 final size:20
Alignment explanation
Indices: 592051--592164 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
592041 GATTATGTAT
592051 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
592071 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
592091 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
592111 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
592132 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
592152 TATCGCATTGCGA
1 TATCGCGTTGCGA
592165 TTTTCCCAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 3 0.04
20 63 0.79
21 12 0.15
22 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:592168 original size:41 final size:41
Alignment explanation
Indices: 592031--592166 Score: 159
Period size: 41 Copynumber: 3.3 Consensus size: 41
592021 TGCTTTGAAA
*
592031 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * * *
592072 ATCGCGTTGCGA--AAGTCAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* * * * *
592112 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
592153 ATCGCATTGCGATT
1 ATCGCATTGCGATT
592167 TTCCCAATTT
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
39 3 0.04
40 31 0.40
41 42 0.54
42 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Done.