Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold415
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: 1242643
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 2 of 8
Found at i:196920 original size:150 final size:150
Alignment explanation
Indices: 196640--196969 Score: 437
Period size: 150 Copynumber: 2.2 Consensus size: 150
196630 CCCTTTTAAT
* * * * * * *
196640 GTCCTTTAAGATCACCGAGCAGTTTTAAGTCGATGGTAGACCTTAGGGATATTTTAGCATTTTCC
1 GTCCCTTAAGATCACCGGGCACTTCTAAGTCAATAGTAGACCTTAGAGATATTTTAGCATTTTCC
* * ** * * *
196705 TCGAAACCTAGTCTTATAAAATTACCGAGTCTGCTTTTACGCCTAATGTATGAATCATGAGTGGG
66 TCGAAACCTAGTCTTATAAAACTACCAAGTCCACTTTTACGCCGAAGGTATGAATCAAGAGTGGG
196770 TTCGTTTTTATCTTTTTCAA
131 TTCGTTTTTATCTTTTTCAA
*
196790 GTCCCTTAGGATCACCGGGCACTTCTAAGTCAATAGTAGACCTTAGAGATATTTTAGCATTTTCC
1 GTCCCTTAAGATCACCGGGCACTTCTAAGTCAATAGTAGACCTTAGAGATATTTTAGCATTTTCC
* * *
196855 TCGAAACCTAGT-TCTATAATACTACTAAGTCCACTTTTACGCCGAAGGTATGAATTAAGAGTGG
66 TCGAAACCTAGTCT-TATAAAACTACCAAGTCCACTTTTACGCCGAAGGTATGAATCAAGAGTGG
*
196919 GTTTGTTTTTATCTTTTTCAA
130 GTTCGTTTTTATCTTTTTCAA
* * **
196940 ATCCCTTAAAATCATTGGGCACTTCTAAGT
1 GTCCCTTAAGATCACCGGGCACTTCTAAGT
196970 TGATGGTAGG
Statistics
Matches: 155, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
149 1 0.01
150 154 0.99
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.37
Consensus pattern (150 bp):
GTCCCTTAAGATCACCGGGCACTTCTAAGTCAATAGTAGACCTTAGAGATATTTTAGCATTTTCC
TCGAAACCTAGTCTTATAAAACTACCAAGTCCACTTTTACGCCGAAGGTATGAATCAAGAGTGGG
TTCGTTTTTATCTTTTTCAA
Found at i:201143 original size:15 final size:16
Alignment explanation
Indices: 201101--201133 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
201091 TAAATTTAAT
201101 TAAA-ATTATA-AAAA
1 TAAATATTATATAAAA
201115 TAAATATTATATAAAA
1 TAAATATTATATAAAA
201131 TAA
1 TAA
201134 TATCTAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 6 0.35
16 7 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAATATTATATAAAA
Found at i:204328 original size:12 final size:12
Alignment explanation
Indices: 204311--204335 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
204301 ATATAAATTT
204311 AATTCAATTTTA
1 AATTCAATTTTA
204323 AATTCAATTTTA
1 AATTCAATTTTA
204335 A
1 A
204336 TGTTCGAAAA
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:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (12 bp):
AATTCAATTTTA
Found at i:204959 original size:298 final size:293
Alignment explanation
Indices: 204429--205078 Score: 987
Period size: 298 Copynumber: 2.2 Consensus size: 293
204419 AAGGAAAATT
* * * *
204429 TTTTCTTATTCATTTTACAGATAAATGAAAGCTCCTATTGAAAGTAGTTACCGAACAATGAAAAT
1 TTTT-TTAGTCATTTTACAGATAAATGAAAGCTCGTATT-TAAGTAGTTACCGAAAAATGAAAAT
* * * *
204494 GCGTCTGTAAATCCAAAATAAGTCGTTATTGAAAAAAGTAATTTATAGTTGGCTAACATAAATTT
64 GCGTCTGTAAATCCAAAACAAATCATTATCGAAAAAAGTAATTTATAGTTGGCTAACATAAATTT
204559 AAATTCTATCAATTATAAAAATAATACATGTATAATATTAATTAATTTTAATAAAAATAAATTTG
129 AAATTCTATCAATTATAAAAATAATACATGTATAATATTAATTAATTTTAATAAAAATAAATTTG
*
204624 TATAATTTATAAATAAATTAAAAATAATTTATAAATAAAAAGTAATAATAGATGCACAATATTAA
194 TATAATTTATAAATAAATTAAAAATAATTTATAAATAAAAAGTAATAATACATGCACAATATTAA
*
204689 TTAATTTTAATAAAAATAATACATATATAATAAAAA
259 TTAAATTTAATAAAAATAATACATATATAAT-AAAA
* * * * *
204725 TTTTTTGGATCATTTTACAAATAAATGAAAACTCGTATTTAAGTCGTTATCGAAAAATGAAATGT
1 TTTTTTAG-TCATTTTACAGATAAATGAAAGCTCGTATTTAAGTAGTTACCGAAAAATGAAA---
* ** *
204790 GTGCGTCTGTAAATCTGAAACAAATCATTATCGAAAAAAGTAATTTATTGTTGGCTAACATAAAT
62 ATGCGTCTGTAAATCCAAAACAAATCATTATCGAAAAAAGTAATTTATAGTTGGCTAACATAAAT
** *
204855 TTAGGTTTTATCAATTATAAAAATAATACATGTATAATATTAATTAATTTTAATAAAAATAAATT
127 TTAAATTCTATCAATTATAAAAATAATACATGTATAATATTAATTAATTTTAATAAAAATAAATT
*
204920 TGTATAATTTATAAATAAATTAAAAATAATTTATAAATAAAAAGTAATAATACATGTACAATATT
192 TGTATAATTTATAAATAAATTAAAAATAATTTATAAATAAAAAGTAATAATACATGCACAATATT
* *
204985 AATTAAATTTAATAAAAATAATACATGTATAATAAAT
257 AATTAAATTTAATAAAAATAATACATATATAATAAAA
*
205022 TTTTTTAGTCATTTTACAGATAAAAGAAAGCTCGTATTTAAGTTA-TTACCGAAAAAT
1 TTTTTTAGTCATTTTACAGATAAATGAAAGCTCGTATTTAAG-TAGTTACCGAAAAAT
205079 AATATATGTA
Statistics
Matches: 318, Mismatches: 31, Indels: 10
0.89 0.09 0.03
Matches are distributed among these distances:
295 21 0.07
296 73 0.23
297 11 0.03
298 213 0.67
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (293 bp):
TTTTTTAGTCATTTTACAGATAAATGAAAGCTCGTATTTAAGTAGTTACCGAAAAATGAAAATGC
GTCTGTAAATCCAAAACAAATCATTATCGAAAAAAGTAATTTATAGTTGGCTAACATAAATTTAA
ATTCTATCAATTATAAAAATAATACATGTATAATATTAATTAATTTTAATAAAAATAAATTTGTA
TAATTTATAAATAAATTAAAAATAATTTATAAATAAAAAGTAATAATACATGCACAATATTAATT
AAATTTAATAAAAATAATACATATATAATAAAA
Found at i:205433 original size:22 final size:22
Alignment explanation
Indices: 205399--205449 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
205389 AATCAGGTGG
*
205399 TGATTTCCCAACATTGTGATGA
1 TGATTTCCCAACATTGTCATGA
* *
205421 TGATTTGCTAACATTGTCATGA
1 TGATTTCCCAACATTGTCATGA
*
205443 CGATTTC
1 TGATTTC
205450 TTAATATATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (22 bp):
TGATTTCCCAACATTGTCATGA
Found at i:207304 original size:13 final size:13
Alignment explanation
Indices: 207286--207310 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
207276 CATAAAGTGT
207286 TGTATCGATACAA
1 TGTATCGATACAA
207299 TGTATCGATACA
1 TGTATCGATACA
207311 TAAGTGTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:207321 original size:32 final size:33
Alignment explanation
Indices: 207266--207329 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 33
207256 TTCAATGATT
207266 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
207299 TGTATCGATACAT-AAGTGTTGTATCGATACA
1 TGTATCGATACATAAAGTGTTGTATCGATACA
207330 TAAGTTTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 18 0.58
33 13 0.42
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:207323 original size:19 final size:19
Alignment explanation
Indices: 207265--207348 Score: 108
Period size: 19 Copynumber: 4.7 Consensus size: 19
207255 TTTCAATGAT
207265 TTGTATCGATACATAAAGTG
1 TTGTATCGATACAT-AAGTG
207285 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
207299 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
*
207317 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
207336 TTGTATCGATACA
1 TTGTATCGATACA
207349 ATATAAGCTA
Statistics
Matches: 57, Mismatches: 1, Indels: 13
0.80 0.01 0.18
Matches are distributed among these distances:
13 11 0.19
15 2 0.04
17 2 0.04
19 30 0.53
20 12 0.21
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:207425 original size:52 final size:52
Alignment explanation
Indices: 207390--207518 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
207380 CACTGATCTT
*
207390 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACCATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
** *
207442 TGTATTTATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
207494 TGTATCGATACATGTAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
207519 TCATATTTCG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:212372 original size:25 final size:25
Alignment explanation
Indices: 212310--212391 Score: 104
Period size: 25 Copynumber: 3.5 Consensus size: 25
212300 ATTAATATTT
212310 AAAATATTTAAAATATATTTAAT--
1 AAAATATTTAAAATATATTTAATAA
212333 -AAATA--T-AAATATATTTAATAA
1 AAAATATTTAAAATATATTTAATAA
*
212354 AAAATATTAAAAATATATTTAATAA
1 AAAATATTTAAAATATATTTAATAA
*
212379 AATATATTTAAAA
1 AAAATATTTAAAA
212392 CCAAAAAAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
19 13 0.26
20 1 0.02
22 10 0.20
25 26 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
AAAATATTTAAAATATATTTAATAA
Found at i:212380 original size:14 final size:14
Alignment explanation
Indices: 212334--212389 Score: 73
Period size: 14 Copynumber: 4.1 Consensus size: 14
212324 ATATTTAATA
212334 AATATAAATATATTT
1 AATA-AAATATATTT
*
212349 AATAAAAAATA-TT
1 AATAAAATATATTT
212362 -A-AAAATATATTT
1 AATAAAATATATTT
212374 AATAAAATATATTT
1 AATAAAATATATTT
212388 AA
1 AA
212390 AACCAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
11 7 0.19
12 3 0.08
13 3 0.08
14 19 0.53
15 4 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AATAAAATATATTT
Found at i:212400 original size:44 final size:44
Alignment explanation
Indices: 212310--212400 Score: 103
Period size: 44 Copynumber: 2.1 Consensus size: 44
212300 ATTAATATTT
* * ***
212310 AAAATATTTAAAATATATTTAATAAATATAAATATATTTAATAA
1 AAAATATTAAAAATATATTTAATAAATATAAATAAAACCAATAA
**
212354 AAAATATTAAAAATATATTTAATAAAATATATTTAAAACCAA-AA
1 AAAATATTAAAAATATATTTAAT-AAATATAAATAAAACCAATAA
212398 AAA
1 AAA
212401 TCGACCAACA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
44 27 0.69
45 12 0.31
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (44 bp):
AAAATATTAAAAATATATTTAATAAATATAAATAAAACCAATAA
Found at i:214890 original size:12 final size:12
Alignment explanation
Indices: 214873--214901 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
214863 TCATACTATT
214873 TTTTATATCACA
1 TTTTATATCACA
214885 TTTTATATCACA
1 TTTTATATCACA
214897 TTTTA
1 TTTTA
214902 ATTATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.55
Consensus pattern (12 bp):
TTTTATATCACA
Found at i:218807 original size:51 final size:53
Alignment explanation
Indices: 218720--218819 Score: 132
Period size: 51 Copynumber: 1.9 Consensus size: 53
218710 CTTTCTTTTT
* *
218720 TTTATAAAACTCAAATTTATTGCAAATTACTACTCCCC-TTTTTGTTATCCCCC
1 TTTATAAAAC-CAAATCTATTGCAAAATACTACTCCCCTTTTTTGTTATCCCCC
* * *
218773 TTTATAAAA-CAAATCTATTTCAAAATATTTCTCCCCTTTTTTGTTAT
1 TTTATAAAACCAAATCTATTGCAAAATACTACTCCCCTTTTTTGTTAT
218820 AGCAAAAACG
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
51 22 0.54
52 10 0.24
53 9 0.22
ACGTcount: A:0.30, C:0.22, G:0.03, T:0.45
Consensus pattern (53 bp):
TTTATAAAACCAAATCTATTGCAAAATACTACTCCCCTTTTTTGTTATCCCCC
Found at i:222213 original size:6 final size:6
Alignment explanation
Indices: 222204--222242 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
222194 AAAATATAAA
*
222204 TATTTT TATTTT TATTTT TATAATTT TATTTT AATTTT T
1 TATTTT TATTTT TATTTT TAT--TTT TATTTT TATTTT T
222243 TAAAAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 23 0.79
8 6 0.21
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (6 bp):
TATTTT
Found at i:222261 original size:15 final size:14
Alignment explanation
Indices: 222237--222267 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
222227 TTTTATTTTA
222237 ATTTTTTAAAAAAT
1 ATTTTTTAAAAAAT
222251 ATTTGTTTAAAAAAT
1 ATTT-TTTAAAAAAT
222266 AT
1 AT
222268 GATATATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (14 bp):
ATTTTTTAAAAAAT
Found at i:222568 original size:15 final size:15
Alignment explanation
Indices: 222549--222609 Score: 52
Period size: 15 Copynumber: 4.0 Consensus size: 15
222539 TATTTCTTTT
222549 TTTTTTAATTTTTTAA
1 TTTTTTAA-TTTTTAA
**
222565 TTTTTTAAACTTTAA
1 TTTTTTAATTTTTAA
*
222580 TTATTTT-ATTATTAA
1 TT-TTTTAATTTTTAA
**
222595 TTAATTAATTTTTAA
1 TTTTTTAATTTTTAA
222610 ATATATAAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
14 2 0.06
15 21 0.60
16 12 0.34
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTTAATTTTTAA
Found at i:222659 original size:36 final size:35
Alignment explanation
Indices: 222592--222702 Score: 115
Period size: 36 Copynumber: 3.2 Consensus size: 35
222582 ATTTTATTAT
* *
222592 TAATTAATTAATTTTTAA-AT--ATATAAATTTAAA
1 TAATTTATT-ATTTTTAATATAAATATAATTTTAAA
222625 TAATTT-TGTATTATTTAATATAAATATAATTTT-AA
1 TAATTTAT-TATT-TTTAATATAAATATAATTTTAAA
* *
222660 TAATTTATTATTTTTAATATAAAAATAATTTTTAAT
1 TAATTTATTATTTTTAATATAAATATAA-TTTTAAA
222696 TAATTTA
1 TAATTTA
222703 ACATAAATAT
Statistics
Matches: 66, Mismatches: 4, Indels: 13
0.80 0.05 0.16
Matches are distributed among these distances:
32 4 0.06
33 11 0.17
34 17 0.26
35 16 0.24
36 18 0.27
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (35 bp):
TAATTTATTATTTTTAATATAAATATAATTTTAAA
Found at i:222660 original size:17 final size:17
Alignment explanation
Indices: 222638--222691 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
222628 TTTTGTATTA
222638 TTTAATATAAATATAAT
1 TTTAATATAAATATAAT
** *
222655 TTTAATA-ATTTATTATT
1 TTTAATATAAATA-TAAT
*
222672 TTTAATATAAAAATAAT
1 TTTAATATAAATATAAT
222689 TTT
1 TTT
222692 TAATTAATTT
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
16 3 0.11
17 23 0.82
18 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTAATATAAATATAAT
Found at i:222663 original size:35 final size:34
Alignment explanation
Indices: 222592--222702 Score: 120
Period size: 35 Copynumber: 3.2 Consensus size: 34
222582 ATTTTATTAT
* * *
222592 TAATTAATTAATTTTTAA-ATATATA-AATTTAAA
1 TAATTTATT-ATTTTTAATATAAATATAATTTTAA
222625 TAATTT-TGTATTATTTAATATAAATATAATTTTAA
1 TAATTTAT-TATT-TTTAATATAAATATAATTTTAA
*
222660 TAATTTATTATTTTTAATATAAAAATAATTTTTAA
1 TAATTTATTATTTTTAATATAAATATAA-TTTTAA
222695 TTAATTTA
1 -TAATTTA
222703 ACATAAATAT
Statistics
Matches: 67, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
32 4 0.06
33 11 0.16
34 21 0.31
35 23 0.34
36 8 0.12
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (34 bp):
TAATTTATTATTTTTAATATAAATATAATTTTAA
Found at i:222686 original size:25 final size:26
Alignment explanation
Indices: 222658--222718 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
222648 ATATAATTTT
*
222658 AATAATTTATT-ATT-TTTAATATAAA
1 AATAATTT-TTAATTATTTAACATAAA
222683 AATAATTTTTAATTAATTTAACATAAA
1 AATAATTTTTAATT-ATTTAACATAAA
*
222710 TATAATTTT
1 AATAATTTT
222719 AAAAATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 2 0.06
25 11 0.35
27 18 0.58
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (26 bp):
AATAATTTTTAATTATTTAACATAAA
Found at i:223205 original size:25 final size:24
Alignment explanation
Indices: 223129--223212 Score: 71
Period size: 25 Copynumber: 3.3 Consensus size: 24
223119 TCTCCGATAT
*
223129 AATTAAAAATAATAATAGTAATTAA
1 AATTAAAAATAATAATA-AAATTAA
* **
223154 ATTTATTATTATAATAATAAAATTAA
1 AATTA--AAAATAATAATAAAATTAA
*
223180 AATTTAAAAATAATAATTACAA-TAA
1 AA-TTAAAAATAATAA-TAAAATTAA
223205 AATTAAAA
1 AATTAAAA
223213 TAAAAAATTA
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
24 6 0.13
25 17 0.36
26 11 0.23
27 13 0.28
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (24 bp):
AATTAAAAATAATAATAAAATTAA
Found at i:223221 original size:24 final size:25
Alignment explanation
Indices: 223177--223223 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
223167 ATAATAAAAT
*
223177 TAAAATTTAAAAATAATAATTACAA
1 TAAAATTTAAAAATAAAAATTACAA
223202 TAAAA-TT-AAAATAAAAAATTAC
1 TAAAATTTAAAAAT-AAAAATTAC
223224 TTTTAAGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 10 0.50
25 5 0.25
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (25 bp):
TAAAATTTAAAAATAAAAATTACAA
Found at i:223323 original size:36 final size:36
Alignment explanation
Indices: 223231--223337 Score: 114
Period size: 36 Copynumber: 3.0 Consensus size: 36
223221 TACTTTTAAG
* *
223231 AATATTAAATTAAAA-TATATATATAATAAATAATTAA
1 AATA-TAAATTAAAATTATATTTATATTAAATAA-TAA
*
223268 AAGT-T--ATTAAAGTTATATTTATATTAAATAATAA
1 AA-TATAAATTAAAATTATATTTATATTAAATAATAA
* *
223302 AATATAAATTAAAATTGTATTTACATTAAATAATAA
1 AATATAAATTAAAATTATATTTATATTAAATAATAA
223338 TTAGAAATAT
Statistics
Matches: 59, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
33 1 0.02
34 12 0.20
35 16 0.27
36 27 0.46
37 2 0.03
38 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (36 bp):
AATATAAATTAAAATTATATTTATATTAAATAATAA
Found at i:223353 original size:36 final size:34
Alignment explanation
Indices: 223259--223358 Score: 94
Period size: 36 Copynumber: 2.7 Consensus size: 34
223249 ATATATAATA
*
223259 AATAATTAAAAGTTATTAAAGTTATATTTATATTAAAT
1 AATAATTAAAA--TATTAAA-TT-TATTTACATTAAAT
* *
223297 AATAAAATATAAAT-TAAAATTGTATTTACATTAAAT
1 AAT-AATTA-AAATATTAAATT-TATTTACATTAAAT
223333 AATAATTAGAAATATTAAATTTATTT
1 AATAATTA-AAATATTAAATTTATTT
223359 TACTAATAAC
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
35 13 0.25
36 24 0.46
37 4 0.08
38 4 0.08
39 4 0.08
40 3 0.06
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (34 bp):
AATAATTAAAATATTAAATTTATTTACATTAAAT
Found at i:226033 original size:23 final size:24
Alignment explanation
Indices: 226007--226073 Score: 91
Period size: 23 Copynumber: 2.8 Consensus size: 24
225997 TTGATTGCTA
*
226007 TTTTGTTGGTGTTTGCTTGTTG-T
1 TTTTGTTGGTATTTGCTTGTTGTT
* *
226030 TTTTGCTGGTATTTGCTTGCTGTT
1 TTTTGTTGGTATTTGCTTGTTGTT
*
226054 TTTTGTTGGAATTTGCTTGT
1 TTTTGTTGGTATTTGCTTGT
226074 GCTATTGCTG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 19 0.51
24 18 0.49
ACGTcount: A:0.04, C:0.07, G:0.27, T:0.61
Consensus pattern (24 bp):
TTTTGTTGGTATTTGCTTGTTGTT
Found at i:226363 original size:20 final size:19
Alignment explanation
Indices: 226310--226363 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
226300 TGTTTCTTGC
*
226310 TTCGATTTTTCTCTTTTCT
1 TTCGATTTTTCTCTTTTAT
*
226329 TCTC-ATTTTTTTCTTGTTAT
1 T-TCGATTTTTCTCTT-TTAT
*
226349 TTCGATTTCTCTCTT
1 TTCGATTTTTCTCTT
226364 CTCTTCCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.07, C:0.20, G:0.06, T:0.67
Consensus pattern (19 bp):
TTCGATTTTTCTCTTTTAT
Found at i:227235 original size:10 final size:10
Alignment explanation
Indices: 227220--227252 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
227210 GCATGAAAGC
227220 AATGCAATGA
1 AATGCAATGA
*
227230 AATGCAATGC
1 AATGCAATGA
227240 AATGC-ATGA
1 AATGCAATGA
227249 AATG
1 AATG
227253 TTTTTGCCGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 7 0.33
10 14 0.67
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.21
Consensus pattern (10 bp):
AATGCAATGA
Found at i:227238 original size:15 final size:14
Alignment explanation
Indices: 227207--227243 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
227197 CAACAGCTTT
227207 AATGC-ATGAAAGC
1 AATGCAATGAAAGC
227220 AATGCAATGAAATGC
1 AATGCAATGAAA-GC
227235 AATGCAATG
1 AATGCAATG
227244 CATGAAATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 5 0.23
14 6 0.27
15 11 0.50
ACGTcount: A:0.46, C:0.14, G:0.22, T:0.19
Consensus pattern (14 bp):
AATGCAATGAAAGC
Found at i:227527 original size:7 final size:7
Alignment explanation
Indices: 227509--227551 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
227499 TACTATTTTG
227509 TTATTATA
1 TTATT-TA
227517 TTATTTA
1 TTATTTA
227524 TTATTTA
1 TTATTTA
*
227531 TTGTTTA
1 TTATTTA
227538 TTATTTA
1 TTATTTA
*
227545 TTTTTTA
1 TTATTTA
227552 ATTAATTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
7 27 0.84
8 5 0.16
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (7 bp):
TTATTTA
Found at i:227947 original size:32 final size:34
Alignment explanation
Indices: 227898--227984 Score: 99
Period size: 36 Copynumber: 2.6 Consensus size: 34
227888 CAACACTATC
227898 TTTC-AAGGCTAAGATAGAAAC-CTCCTTATC-T
1 TTTCAAAGGCTAAGATAGAAACTCTCCTTATCTT
** * *
227929 TTTCACGGGCTAAAATAGATACTTTCTCCTTATCTT
1 TTTCAAAGGCTAAGATAGAAAC--TCTCCTTATCTT
227965 TTTCAAAGGCTAAGATAGAA
1 TTTCAAAGGCTAAGATAGAA
227985 CCTTTCAATC
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
31 4 0.09
32 13 0.30
35 9 0.21
36 17 0.40
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (34 bp):
TTTCAAAGGCTAAGATAGAAACTCTCCTTATCTT
Found at i:227990 original size:36 final size:34
Alignment explanation
Indices: 227894--227990 Score: 96
Period size: 36 Copynumber: 2.9 Consensus size: 34
227884 CTTACAACAC
227894 TATC-TTTC-AAGGCTAAGATAGAAAC---CTCCT
1 TATCTTTTCAAAGGCTAAGATAG-AACTTTCTCCT
** *
227924 TATCTTTTCACGGGCTAAAATAGATACTTTCTCCT
1 TATCTTTTCAAAGGCTAAGATAGA-ACTTTCTCCT
227959 TATCTTTTTCAAAGGCTAAGATAGAACCTTTC
1 TATC-TTTTCAAAGGCTAAGATAGAA-CTTTC
227991 AATCACTTAG
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
30 4 0.08
31 5 0.09
32 12 0.23
35 10 0.19
36 22 0.42
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (34 bp):
TATCTTTTCAAAGGCTAAGATAGAACTTTCTCCT
Found at i:232117 original size:21 final size:21
Alignment explanation
Indices: 232070--232127 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
232060 AAAATTTATC
*
232070 CAAATGTATCGATACATTTAT
1 CAAATGTATCGATACATCTAT
**
232091 GGAATGTATCGATACATCCTA-
1 CAAATGTATCGATACAT-CTAT
232112 CAAATGTATCGATACA
1 CAAATGTATCGATACA
232128 GGGTCCCAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 29 0.94
22 2 0.06
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (21 bp):
CAAATGTATCGATACATCTAT
Found at i:232187 original size:19 final size:19
Alignment explanation
Indices: 232163--232230 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
232153 AATTCAACAA
232163 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
232182 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
232197 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
232214 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
232231 TTAGCTACTA
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:232202 original size:13 final size:13
Alignment explanation
Indices: 232184--232208 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
232174 ACATAAGTTT
232184 TGTATCGATACAA
1 TGTATCGATACAA
232197 TGTATCGATACA
1 TGTATCGATACA
232209 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:232206 original size:32 final size:32
Alignment explanation
Indices: 232165--232227 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
232155 TTCAACAATT
*
232165 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
232197 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
232228 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:232294 original size:33 final size:33
Alignment explanation
Indices: 232252--232316 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
232242 CAAGGAAATG
***
232252 TATCGATACATTTTTCTGTGTATCGATACATTA
1 TATCGATACATGGATCTGTGTATCGATACATTA
*
232285 TATCGATACATGGATCTTTGTATCGATACATT
1 TATCGATACATGGATCTGTGTATCGATACATT
232317 TGGAAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (33 bp):
TATCGATACATGGATCTGTGTATCGATACATTA
Found at i:234885 original size:52 final size:50
Alignment explanation
Indices: 234826--234995 Score: 168
Period size: 52 Copynumber: 3.3 Consensus size: 50
234816 ATTTTCGAGT
*
234826 GGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTCCACAATCGG
1 GGATACTCCAACCCCGGTTTTATT-CTAAAACACAAATTTTTCC-CAATCGG
* * *
234878 GGATACTCCAACCCCGGTTTTATTTTCAAAACACCAA-TTTTCCTTTAATCGG
1 GGATACTCCAACCCCGGTTTTATTCT-AAAACACAAATTTTTCC--CAATCGG
* * * *
234930 GGATACTCCAACTCCGATTTTATTTCCAAAAAATACAAATTTTT--C-ATCGG
1 GGATACTCCAACCCCGGTTTTA-TT-C-TAAAACACAAATTTTTCCCAATCGG
234980 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
234996 TTACTTCCGA
Statistics
Matches: 100, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
50 20 0.20
51 7 0.07
52 59 0.59
53 2 0.02
54 8 0.08
55 4 0.04
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.31
Consensus pattern (50 bp):
GGATACTCCAACCCCGGTTTTATTCTAAAACACAAATTTTTCCCAATCGG
Found at i:235086 original size:79 final size:79
Alignment explanation
Indices: 234977--235180 Score: 223
Period size: 78 Copynumber: 2.6 Consensus size: 79
234967 AATTTTTCAT
* * *
234977 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAAT-A
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGATTTATTCCC-AAATCA
* * *
235041 TTGATTTCTCATAAT
65 TCGATTTCTCACAAC
* * * * ** *
235056 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCTAATCCC-GATTTTTTTTCTAATCAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGATTTATTCCCAAATCAT
235120 CGATTTCTCACAAC
66 CGATTTCTCACAAC
* * * * *
235134 CGGGGATACTCGAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
235181 TTATTATTTC
Statistics
Matches: 102, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
77 3 0.03
78 58 0.57
79 41 0.40
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGATTTATTCCCAAATCAT
CGATTTCTCACAAC
Found at i:247583 original size:12 final size:12
Alignment explanation
Indices: 247565--247599 Score: 61
Period size: 12 Copynumber: 2.8 Consensus size: 12
247555 CATTCTCTTA
247565 AAAAAAAAAGAGC
1 AAAAAAAAA-AGC
247578 AAAAAAAAAAGC
1 AAAAAAAAAAGC
247590 AAAAAAAAAA
1 AAAAAAAAAA
247600 AAACAAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 13 0.59
13 9 0.41
ACGTcount: A:0.86, C:0.06, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGC
Found at i:247599 original size:18 final size:18
Alignment explanation
Indices: 247578--247630 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
247568 AAAAAAGAGC
247578 AAAAAAAAAAGCAAAAAA
1 AAAAAAAAAAGCAAAAAA
*
247596 AAAAAAACAAAACAAAAAA
1 AAAAAAA-AAAGCAAAAAA
* *
247615 ACAAAACAAAG-AAAAA
1 AAAAAAAAAAGCAAAAA
247631 GAGAGAAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 5 0.17
18 10 0.33
19 15 0.50
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAGCAAAAAA
Found at i:247624 original size:13 final size:12
Alignment explanation
Indices: 247564--247620 Score: 60
Period size: 14 Copynumber: 4.3 Consensus size: 12
247554 ACATTCTCTT
247564 AAAAAAAAAAGAGC
1 AAAAAAAAAA-A-C
*
247578 AAAAAAAAAAGCAA
1 AAAAAAAAAA--AC
247592 AAAAAAAAAAAC
1 AAAAAAAAAAAC
247604 AAAACAAAAAAAC
1 AAAA-AAAAAAAC
247617 AAAA
1 AAAA
247621 CAAAGAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
12 5 0.13
13 12 0.32
14 20 0.53
15 1 0.03
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:247629 original size:14 final size:13
Alignment explanation
Indices: 247564--247629 Score: 64
Period size: 13 Copynumber: 4.9 Consensus size: 13
247554 ACATTCTCTT
247564 AAAA-AAAAAAGAGC
1 AAAACAAAAAA-A-C
*
247578 AAAA-AAAAAAGC
1 AAAACAAAAAAAC
*
247590 AAAAAAAAAAAAAC
1 -AAAACAAAAAAAC
247604 AAAACAAAAAAAC
1 AAAACAAAAAAAC
247617 AAAACAAAGAAAA
1 AAAACAAA-AAAA
247630 AGAGAGAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
12 1 0.02
13 24 0.52
14 21 0.46
ACGTcount: A:0.85, C:0.09, G:0.06, T:0.00
Consensus pattern (13 bp):
AAAACAAAAAAAC
Found at i:248692 original size:55 final size:54
Alignment explanation
Indices: 248610--249249 Score: 764
Period size: 55 Copynumber: 11.4 Consensus size: 54
248600 TCCTTCCGCT
* *
248610 TTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
*
248664 TTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
1 TTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
* *
248719 TTTCCAGTCTTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
1 TTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
* *
248774 TTTCCAGTCCTCAGAGAGTAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCAC
1 TTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCAC
* * *
248829 CTTCAGTCCTCAAAGAGCGGGACACATTTTCTTTTAAAGCCCACACAAGTTGGTGGCAC
1 TTTCAGTCCTCAAAGAGCAGGACAC-----CTTTCAAAGCCCACACAAGTTGGTGGCAC
* * ** *
248888 CTTCAGTCCTCAAAGAGCGGGATGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGACACC-TTTC----AAAGCCCACACAAGTTGGTGGCA-C
* *
248948 TTT-AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA-C
* *
249008 TTTCAGTCCCCAAAGAGCAGGACCCCTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-C
* * *
249063 TTTCAGTCCCCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCAT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
*
249117 TTTCCAGTCCTCAACGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACC
1 TTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-C
* *
249173 TTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCAC
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
* * *
249227 TTTTTACTCCTCAATGAGCAGGA
1 -TTTCAGTCCTCAAAGAGCAGGA
249250 TACACTTTAT
Statistics
Matches: 525, Mismatches: 35, Indels: 51
0.86 0.06 0.08
Matches are distributed among these distances:
54 29 0.06
55 346 0.66
56 7 0.01
58 2 0.00
59 89 0.17
60 30 0.06
61 17 0.03
64 4 0.01
65 1 0.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (54 bp):
TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
Found at i:250099 original size:19 final size:19
Alignment explanation
Indices: 250075--250142 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
250065 AATTCAACAA
250075 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
250094 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
250109 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
250126 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
250143 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:250114 original size:13 final size:13
Alignment explanation
Indices: 250096--250120 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
250086 ACATAAGTTT
250096 TGTATCGATACAA
1 TGTATCGATACAA
250109 TGTATCGATACA
1 TGTATCGATACA
250121 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:250118 original size:32 final size:32
Alignment explanation
Indices: 250077--250139 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
250067 TTCAACAATT
*
250077 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
250109 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
250140 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:250200 original size:13 final size:13
Alignment explanation
Indices: 250182--250207 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
250172 CATTTTTCTG
250182 TGTATCGATACAT
1 TGTATCGATACAT
250195 TGTATCGATACAT
1 TGTATCGATACAT
250208 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:250204 original size:33 final size:33
Alignment explanation
Indices: 250162--250228 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
250152 GCCAAGGAAA
***
250162 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
250195 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
250228 T
1 T
250229 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:252632 original size:51 final size:52
Alignment explanation
Indices: 252576--252907 Score: 209
Period size: 52 Copynumber: 6.3 Consensus size: 52
252566 AATTCTCCAC
* *
252576 AATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAATTTTCTAT
1 AATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAACACCAATTTTCTAT
* * *
252627 AATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAA-TTTCTTCAC
1 AATCGGGGATACTCCAACTCCGATTTTATTTTC-AAAAACACCAATTTTC-T-AT
* * ** * * * ***
252681 AATCGGGGATACTCCAAC-CCCA-TTAATCATCGAGGATACTCCAA-CCCCGT-T
1 AATCGGGGATACTCCAACTCCGATTTTATTTTC-A-AAAACACCAATTTTC-TAT
* * * * * * * *
252732 ATTTCTGAGTGGATACTCTAACCCCGATTTTA-TTGCTAAAACACTAATTTTTCCAC
1 A-ATC-G-G-GGATACTCCAACTCCGATTTTATTTTCAAAAACACCAA-TTTTCTAT
* * *
252788 AATCGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACACCAATTTTCCTCT
1 AATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAACACCAATTTT-CTAT
* *
252840 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAATACCAA-TTT-T-T
1 AATCGGGGATACTCCAACTCCGATTTTATTTTC-AAAAACACCAATTTTCTAT
*
252890 CATCGGGGATACTCCAAC
1 AATCGGGGATACTCCAAC
252908 CCCGTTACTT
Statistics
Matches: 213, Mismatches: 50, Indels: 37
0.71 0.17 0.12
Matches are distributed among these distances:
50 18 0.08
51 36 0.17
52 72 0.34
53 30 0.14
54 35 0.16
55 13 0.06
56 6 0.03
57 3 0.01
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (52 bp):
AATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAACACCAATTTTCTAT
Found at i:253837 original size:13 final size:13
Alignment explanation
Indices: 253818--253848 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
253808 TGTCAAATGC
253818 CAAAATTTATTTT
1 CAAAATTTATTTT
*
253831 TAAAATTTATTTT
1 CAAAATTTATTTT
253844 CAAAA
1 CAAAA
253849 ATTTCTCCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (13 bp):
CAAAATTTATTTT
Found at i:253851 original size:14 final size:13
Alignment explanation
Indices: 253819--253852 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
253809 GTCAAATGCC
*
253819 AAAATTTATTTTT
1 AAAATTTATTTTA
253832 AAAATTTATTTTCA
1 AAAATTTATTTT-A
253846 AAAATTT
1 AAAATTT
253853 CTCCCATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (13 bp):
AAAATTTATTTTA
Found at i:259023 original size:14 final size:16
Alignment explanation
Indices: 258992--259023 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
258982 GGTTGTGTTT
258992 AAGACCATTCACATAC
1 AAGACCATTCACATAC
259008 AAGA-CATTCA-ATAC
1 AAGACCATTCACATAC
259022 AA
1 AA
259024 AATGAAGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 6 0.38
16 4 0.25
ACGTcount: A:0.50, C:0.25, G:0.06, T:0.19
Consensus pattern (16 bp):
AAGACCATTCACATAC
Found at i:268010 original size:20 final size:20
Alignment explanation
Indices: 267983--268076 Score: 120
Period size: 20 Copynumber: 4.7 Consensus size: 20
267973 TTTACCCAGA
267983 TGTATCGATACATT-TTGCAT
1 TGTATCGATACATTGTT-CAT
* * *
268003 TATATCGACACATTGCTCAT
1 TGTATCGATACATTGTTCAT
268023 TGTATCGATACATTGTTCAT
1 TGTATCGATACATTGTTCAT
*
268043 TGTATCGATACATT-TTACAA
1 TGTATCGATACATTGTT-CAT
268063 TGTATCGATACATT
1 TGTATCGATACATT
268077 CAGGCATTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
19 2 0.03
20 62 0.95
21 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTGTTCAT
Found at i:268266 original size:17 final size:17
Alignment explanation
Indices: 268244--268283 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
268234 TGCAAAAAAG
268244 GCCAAATGTCATTTTCC
1 GCCAAATGTCATTTTCC
268261 GCCAAATGTCATTTTCC
1 GCCAAATGTCATTTTCC
*
268278 ACCAAA
1 GCCAAA
268284 GGACATGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.30, C:0.30, G:0.10, T:0.30
Consensus pattern (17 bp):
GCCAAATGTCATTTTCC
Found at i:277658 original size:20 final size:18
Alignment explanation
Indices: 277633--277698 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 18
277623 TGCATATATT
277633 GATACATTGAATAATGTATC
1 GATACATTGAAT--TGTATC
*
277653 GATACA-TCACATTGTATC
1 GATACATTGA-ATTGTATC
*
277671 GATACATTGATCTTTGTATC
1 GATACATTGA--ATTGTATC
277691 GATACATT
1 GATACATT
277699 TCCTTGGCAG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
18 12 0.30
19 4 0.10
20 24 0.60
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (18 bp):
GATACATTGAATTGTATC
Found at i:277670 original size:18 final size:19
Alignment explanation
Indices: 277647--277697 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
277637 CATTGAATAA
277647 TGTATCGATACATCA-CAT
1 TGTATCGATACATCATCAT
* *
277665 TGTATCGATACATTGATCTT
1 TGTATCGATACA-TCATCAT
277685 TGTATCGATACAT
1 TGTATCGATACAT
277698 TTCCTTGGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 12 0.41
19 3 0.10
20 14 0.48
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (19 bp):
TGTATCGATACATCATCAT
Found at i:278628 original size:49 final size:49
Alignment explanation
Indices: 278510--279334 Score: 842
Period size: 49 Copynumber: 16.9 Consensus size: 49
278500 ATGAAAAGAA
* * * * **
278510 TGCCAATGTGCTGATTCAAGGCCAACAACATTGGGTTTTAAAGATGAAGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATT-GGACTTAAAGAT---GAAGG
*
278563 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * *
278612 TGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGG
* *
278664 CGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * *
278713 TGCCAATGTGTTGATTCAAGGCCAACGACATTGGACTTAAAGATGACAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGG
* * *
278765 CGCCAATATGATGATTCAAGGCTAGCGATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * *
278814 TGCCAATGTGCTGATTCAAGGCGAGCGATATTGGACTTAAAAATGACAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGG
* * *
278866 CGCCAATATGTTGATTCAAAGCCAGCGATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * * * *
278915 TGCCAATGTGCTGATTCATGGCCAACGACATTAGACTTAAAGATAAAAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT---GAAGG
* * *
278967 CGCCAATATGCTAATTCAAGGCCAACGATATTGGACTT----A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * * *
279010 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAATGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
279059 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG--G-A--
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* ** * * * * *
279103 -GCTAAGGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATAAAAG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * *
279151 TGCCAATATACTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* *
279200 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAG--GCA--
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * *
279245 --CCAATATGCTGATTCAAGGCCAACGACATTGGTCTTAAAGA-CAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
*
279291 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA-AAGA
279335 AGACGCCACC
Statistics
Matches: 654, Mismatches: 88, Indels: 64
0.81 0.11 0.08
Matches are distributed among these distances:
43 109 0.17
44 1 0.00
46 2 0.00
47 2 0.00
48 36 0.06
49 299 0.46
52 177 0.27
53 28 0.04
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
Found at i:278687 original size:101 final size:101
Alignment explanation
Indices: 278510--279334 Score: 1015
Period size: 101 Copynumber: 8.4 Consensus size: 101
278500 ATGAAAAGAA
* ** *
278510 TGCCAATGTGCTGATTCAAGGCCAACAACATTGGGTTTTAAAGATGA-AGAAGGTGCCAATATGC
1 TGCCAATGTGCTGATTCAAGGCCAACGACATT-GGACTTAAAGATGATA-AAGGCGCCAATATGC
*
278574 TGATTCAAGGCCAGCGATATTGGTCTTAAAGATGAAGG
64 TGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* *
278612 TGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGATAAAGGCGCCAATATGCTG
1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGATAAAGGCGCCAATATGCTG
*
278677 ATTCAAGGCCAGCGATATTAGACTTAAAGATGAAGG
66 ATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * *
278713 TGCCAATGTGTTGATTCAAGGCCAACGACATTGGACTTAAAGATGACAAAGGCGCCAATATGATG
1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGATAAAGGCGCCAATATGCTG
*
278778 ATTCAAGGCTAGCGATATTGGACTTAAAGATGAAGG
66 ATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * * * *
278814 TGCCAATGTGCTGATTCAAGGCGAGCGATATTGGACTTAAAAATGACAAAGGCGCCAATATGTTG
1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGATAAAGGCGCCAATATGCTG
*
278879 ATTCAAAGCCAGCGATATTGGACTTAAAGATGAAGG
66 ATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * * *
278915 TGCCAATGTGCTGATTCATGGCCAACGACATTAGACTTAAAGATAAAAAAGGCGCCAATATGCTA
1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGATAAAGGCGCCAATATGCTG
*
278980 ATTCAAGGCCAACGATATTGGACTT----A--AAGG
66 ATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * *
279010 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT--A-ATGATAAAGGTGCCAATATGCTG
1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGATAAAGGCGCCAATATGCTG
279072 ATTCAAGGCCAGCGATATTGGACTTAAAG--G-A--
66 ATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * * *
279103 -GCTAAGGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGAT-A-AAA-GTGCCAATATACTG
1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGATAAAGGCGCCAATATGCTG
* * *
279164 ATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGG
66 ATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * *
279200 TGCCAATATGCTGATTCAAGGCCAACGATATTGGAC-------T--TAAAGGCACCAATATGCTG
1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGATAAAGGCGCCAATATGCTG
* * * *
279256 ATTCAAGGCCAACGACATTGGTCTTAAAGA-CAAGG
66 ATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* *
279291 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAGAAGA
1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTA-AAGA
279335 AGACGCCACC
Statistics
Matches: 639, Mismatches: 59, Indels: 53
0.85 0.08 0.07
Matches are distributed among these distances:
91 44 0.07
92 157 0.25
93 4 0.01
94 2 0.00
95 42 0.07
97 1 0.00
98 30 0.05
101 327 0.51
102 32 0.05
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (101 bp):
TGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGATAAAGGCGCCAATATGCTG
ATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
Found at i:279196 original size:141 final size:141
Alignment explanation
Indices: 279004--279334 Score: 522
Period size: 141 Copynumber: 2.3 Consensus size: 141
278994 ATATTGGACT
* *
279004 TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAATGATAAAGGTGCCAATATG
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATATG
* * *
279069 CTGATTCAAGGCCAGCGATATTGGACTTAAAGG-AGCTAAGGTGCTGATTCAAGGCCAACGACAT
66 CTGATTCAAGGCCAACGATATTGGACTTAAAGGCA-CCAAGATGCTGATTCAAGGCCAACGACAT
279133 TGGTCTTAAAGA
130 TGGTCTTAAAGA
* *
279145 TAAAAGTGCCAATATACTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATATG
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATATG
*
279210 CTGATTCAAGGCCAACGATATTGGACTTAAAGGCACCAATATGCTGATTCAAGGCCAACGACATT
66 CTGATTCAAGGCCAACGATATTGGACTTAAAGGCACCAAGATGCTGATTCAAGGCCAACGACATT
279275 GGTCTTAAAGA
131 GGTCTTAAAGA
* * * *
279286 -CAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAGAAGA
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTA-AAGA
279335 AGACGCCACC
Statistics
Matches: 174, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
140 38 0.22
141 135 0.78
142 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (141 bp):
TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATATG
CTGATTCAAGGCCAACGATATTGGACTTAAAGGCACCAAGATGCTGATTCAAGGCCAACGACATT
GGTCTTAAAGA
Found at i:279263 original size:21 final size:21
Alignment explanation
Indices: 279202--279264 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
279192 GATAAAGGTG
279202 CCAATATGCTGATTCAAGGCCA
1 CCAATATGCTGATTCAAGG-CA
* * *
279224 ACGATAT--TGGACTTAAAGGCA
1 CCAATATGCT-GA-TTCAAGGCA
279245 CCAATATGCTGATTCAAGGC
1 CCAATATGCTGATTCAAGGC
279265 CAACGACATT
Statistics
Matches: 31, Mismatches: 6, Indels: 9
0.67 0.13 0.20
Matches are distributed among these distances:
20 1 0.03
21 16 0.52
22 13 0.42
23 1 0.03
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (21 bp):
CCAATATGCTGATTCAAGGCA
Found at i:279376 original size:31 final size:32
Alignment explanation
Indices: 279340--279427 Score: 100
Period size: 31 Copynumber: 2.9 Consensus size: 32
279330 GAAGAAGACG
279340 CCACCAACTTGTGTGGGCTTTTGAAAGGGTT-
1 CCACCAACTTGTGTGGGCTTTTGAAAGGGTTA
*
279371 GCACCAACTTGTGT--GCTTTTG-AA-GGTTA
1 CCACCAACTTGTGTGGGCTTTTGAAAGGGTTA
*
279399 CCACTAAC-T-TGTGGGCTTTTGAAAAGGGT
1 CCACCAACTTGTGTGGGCTTTTG-AAAGGGT
279428 GCCACTGACT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
26 3 0.06
27 5 0.10
28 15 0.31
29 7 0.15
30 2 0.04
31 16 0.33
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (32 bp):
CCACCAACTTGTGTGGGCTTTTGAAAGGGTTA
Found at i:279408 original size:28 final size:28
Alignment explanation
Indices: 279340--279421 Score: 94
Period size: 28 Copynumber: 2.8 Consensus size: 28
279330 GAAGAAGACG
279340 CCACCAACTTGTGTGGGCTTTTGAAAGGGTT
1 CCACCAACTTGTGT--GCTTTTG-AAGGGTT
*
279371 GCACCAACTTGTGTGCTTTTGAA-GGTT
1 CCACCAACTTGTGTGCTTTTGAAGGGTT
* *
279398 ACCACTAACTTGTGGGCTTTTGAA
1 -CCACCAACTTGTGTGCTTTTGAA
279422 AAGGGTGCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
27 4 0.09
28 22 0.48
29 7 0.15
31 13 0.28
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.34
Consensus pattern (28 bp):
CCACCAACTTGTGTGCTTTTGAAGGGTT
Found at i:279458 original size:27 final size:27
Alignment explanation
Indices: 279399--279476 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 27
279389 TTGAAGGTTA
*
279399 CCACTAACTTGTGGGCTTTTGAAAAGGGTG
1 CCACTGACTTGTGGGC--TT-AAAAGGGTG
279429 CCACTGACTTGTGGGCTTAAAAGGGTG
1 CCACTGACTTGTGGGCTTAAAAGGGTG
* *
279456 CCACTGAGTTGTGGACTTAAA
1 CCACTGACTTGTGGGCTTAAA
279477 GAGAAAAAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 28 0.62
28 2 0.04
30 15 0.33
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.28
Consensus pattern (27 bp):
CCACTGACTTGTGGGCTTAAAAGGGTG
Found at i:279460 original size:57 final size:57
Alignment explanation
Indices: 279351--279469 Score: 125
Period size: 57 Copynumber: 2.1 Consensus size: 57
279341 CACCAACTTG
* ** *
279351 TGTGGGCTTTTGAAAGGGTTGCACCAACTTGTGTGCTTTTGAAGGTTACCACTAACT
1 TGTGGGCTTTTGAAAGGGTTGCACCAACTTGTGGGCTTTAAAAGGGTACCACTAACT
** * * *
279408 TGTGGGCTTTTGAAAAGGG-TGCCACTGACTTGTGGGC-TTAAAAGGGTGCCACTGAGT
1 TGTGGGCTTTTG-AAAGGGTTG-CACCAACTTGTGGGCTTTAAAAGGGTACCACTAACT
279465 TGTGG
1 TGTGG
279470 ACTTAAAGAG
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
57 33 0.65
58 18 0.35
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.32
Consensus pattern (57 bp):
TGTGGGCTTTTGAAAGGGTTGCACCAACTTGTGGGCTTTAAAAGGGTACCACTAACT
Found at i:279590 original size:33 final size:33
Alignment explanation
Indices: 279520--279819 Score: 389
Period size: 33 Copynumber: 9.3 Consensus size: 33
279510 ACGGTTGCTG
* *
279520 CGGAGTCGTGGACTTAAAAAGAA-AAGGTGCCA
1 CGGAGTTGTGGACTTAAAAGGAACAAGGTGCCA
*
279552 CGGAGTTGTGGACTTAAAAGGAACAAGGTACCA
1 CGGAGTTGTGGACTTAAAAGGAACAAGGTGCCA
* * * *
279585 TGGAGTAGTGGACTTAAAAGGAAAAAGATGCCA
1 CGGAGTTGTGGACTTAAAAGGAACAAGGTGCCA
279618 CGGAGTTGTGGACTTAAAAGGAACAAGGTGCCA
1 CGGAGTTGTGGACTTAAAAGGAACAAGGTGCCA
*
279651 CGGAGTTGTGGACTTAAAAGGAACAAGGGGCCA
1 CGGAGTTGTGGACTTAAAAGGAACAAGGTGCCA
* *
279684 CGGAGTTGTGGACTTAAAAGGAAAAAGATGCCA
1 CGGAGTTGTGGACTTAAAAGGAACAAGGTGCCA
*
279717 CGGAGTTATGGACTTAAAAGGAACAAGGTGCCA
1 CGGAGTTGTGGACTTAAAAGGAACAAGGTGCCA
* *
279750 CGGAGTTGTGGGCTTAAAA-G-----GGTGTCA
1 CGGAGTTGTGGACTTAAAAGGAACAAGGTGCCA
* * * *
279777 CAGAGTTATAGACTTAAAAGGAAAAAGAGTGCCA
1 CGGAGTTGTGGACTTAAAAGGAACAAG-GTGCCA
279811 CGGAGTTGT
1 CGGAGTTGT
279820 ACTGATTCAA
Statistics
Matches: 231, Mismatches: 29, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
27 21 0.09
28 1 0.00
32 22 0.10
33 175 0.76
34 12 0.05
ACGTcount: A:0.36, C:0.13, G:0.32, T:0.19
Consensus pattern (33 bp):
CGGAGTTGTGGACTTAAAAGGAACAAGGTGCCA
Found at i:279782 original size:27 final size:27
Alignment explanation
Indices: 279743--279797 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
279733 AAAGGAACAA
* * * *
279743 GGTGCCACGGAGTTGTGGGCTTAAAAG
1 GGTGCCACAGAGTTATAGACTTAAAAG
*
279770 GGTGTCACAGAGTTATAGACTTAAAAG
1 GGTGCCACAGAGTTATAGACTTAAAAG
279797 G
1 G
279798 AAAAAGAGTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.29, C:0.13, G:0.35, T:0.24
Consensus pattern (27 bp):
GGTGCCACAGAGTTATAGACTTAAAAG
Found at i:279887 original size:43 final size:44
Alignment explanation
Indices: 279821--279940 Score: 161
Period size: 48 Copynumber: 2.7 Consensus size: 44
279811 CGGAGTTGTA
*
279821 CTGATTCAAGGCCAGCGATATTGGACTTA-AAGGTGCCAATGTG
1 CTGATTCAAGGCCAGCGATATTGGACTTACAAGGTGCCAATATG
* * *
279864 CTGATTCAAGGCCAACGACATTGGCCTTAAAGACAAGGTGCCAATATG
1 CTGATTCAAGGCCAGCGATATTGGACTT----ACAAGGTGCCAATATG
279912 CTGATTCAAGGCCAGCGATATTGGACTTA
1 CTGATTCAAGGCCAGCGATATTGGACTTA
279941 GAAGAAGACG
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
43 25 0.38
44 1 0.02
47 1 0.02
48 38 0.58
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (44 bp):
CTGATTCAAGGCCAGCGATATTGGACTTACAAGGTGCCAATATG
Found at i:279990 original size:31 final size:32
Alignment explanation
Indices: 279950--280052 Score: 116
Period size: 31 Copynumber: 3.4 Consensus size: 32
279940 AGAAGAAGAC
279950 GCCACCAACTTGTGTGGGCTTTTGAAAGGGTT
1 GCCACCAACTTGTGTGGGCTTTTGAAAGGGTT
279982 G-CACCAACTTGTGT--GCTTTTG-AA-GGTT
1 GCCACCAACTTGTGTGGGCTTTTGAAAGGGTT
*
280009 GCCACTAAC-T-TGTGGGCTTTTGAAAAGGG-T
1 GCCACCAACTTGTGTGGGCTTTTG-AAAGGGTT
280039 GCCA-CAGACTTGTG
1 GCCACCA-ACTTGTG
280053 GGTTTAAAAG
Statistics
Matches: 60, Mismatches: 2, Indels: 18
0.75 0.03 0.22
Matches are distributed among these distances:
26 3 0.05
27 6 0.10
28 15 0.25
29 8 0.13
30 9 0.15
31 16 0.27
32 3 0.05
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.31
Consensus pattern (32 bp):
GCCACCAACTTGTGTGGGCTTTTGAAAGGGTT
Found at i:280019 original size:28 final size:29
Alignment explanation
Indices: 279950--280032 Score: 107
Period size: 28 Copynumber: 2.8 Consensus size: 29
279940 AGAAGAAGAC
279950 GCCACCAACTTGTGTGGGCTTTTGAAAGGGTT
1 GCCACCAACTTGTGT--GCTTTTG-AAGGGTT
279982 G-CACCAACTTGTGTGCTTTTGAA-GGTT
1 GCCACCAACTTGTGTGCTTTTGAAGGGTT
* *
280009 GCCACTAACTTGTGGGCTTTTGAA
1 GCCACCAACTTGTGTGCTTTTGAA
280033 AAGGGTGCCA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
27 5 0.10
28 22 0.46
29 7 0.15
31 13 0.27
32 1 0.02
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (29 bp):
GCCACCAACTTGTGTGCTTTTGAAGGGTT
Found at i:280069 original size:27 final size:29
Alignment explanation
Indices: 279962--280073 Score: 103
Period size: 28 Copynumber: 3.9 Consensus size: 29
279952 CACCAACTTG
*
279962 TGTGGGCTTTTG-AAAGGGTTG-CACCAACT
1 TGTGGGC-TTTGAAAAGGG-TGCCACTAACT
* *
279991 TGTGTGCTTTTG--AAGGTTGCCACTAACT
1 TGTGGGC-TTTGAAAAGGGTGCCACTAACT
280019 TGTGGGCTTTTGAAAAGGGTGCCAC-AGACT
1 TGTGGGC-TTTGAAAAGGGTGCCACTA-ACT
280049 TGTGGG-TTT-AAAAGGGTGCCACTAA
1 TGTGGGCTTTGAAAAGGGTGCCACTAA
280074 GTTATGGACT
Statistics
Matches: 73, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
27 16 0.22
28 26 0.36
29 12 0.16
30 19 0.26
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.31
Consensus pattern (29 bp):
TGTGGGCTTTGAAAAGGGTGCCACTAACT
Found at i:280069 original size:57 final size:57
Alignment explanation
Indices: 279962--280073 Score: 140
Period size: 57 Copynumber: 2.0 Consensus size: 57
279952 CACCAACTTG
** *
279962 TGTGGGCTTTTGAAAGGGTTGCACCAACTTGTGTGCTTTTGAAGGTTGCCACTAACT
1 TGTGGGCTTTTGAAAGGGTTGCACCAACTTGTGTGCTTTAAAAGGGTGCCACTAACT
*
280019 TGTGGGCTTTTGAAAAGGG-TGC-CACAGACTTGTG-GGTTTAAAAGGGTGCCACTAA
1 TGTGGGCTTTTG-AAAGGGTTGCAC-CA-ACTTGTGTGCTTTAAAAGGGTGCCACTAA
280074 GTTATGGACT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
56 1 0.02
57 34 0.71
58 13 0.27
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.31
Consensus pattern (57 bp):
TGTGGGCTTTTGAAAGGGTTGCACCAACTTGTGTGCTTTAAAAGGGTGCCACTAACT
Found at i:280113 original size:61 final size:60
Alignment explanation
Indices: 280031--280627 Score: 393
Period size: 61 Copynumber: 9.6 Consensus size: 60
280021 TGGGCTTTTG
* * * ** ** *
280031 AAAAGGGTGCCACAGACTTGTGGGTTTAAAAGGGTGCCACTAAGTTATGGACTTAAAGAGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAA-AGA
* * * *
280092 AAAAGAGTACCACGGAGTTGTGGGCTTAAACA-GTTGCCACGGAGTCGTGGACTTAAAA-A
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAA-AGGGTGCCACGGAGTTGTGGACTTAAAAGA
* * *
280151 GAAAAG-GTGCCACAGAGTTGTGGACTTAAAAGGAACAAGGTGCCATGGAGTAGTGGACTTAAAA
1 -AAAAGAGTGCCACGGAGTTGTGGACTTAAAA-G-----GGTGCCACGGAGTTGTGGACTTAAAA
280215 GGA
59 -GA
280218 AAAAGA-TGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGACTTAAAAG
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAA-G-----GGTGCCACGGAGTTGTGGACTTAAAA-
280282 GA
59 GA
* * *
280284 ACAAGAG-GCCACAGAGTAGTGGACTTAAAAGGGTGCCACGGAGTTGT-GAGCTT-----A
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGA-CTTAAAAGA
* * * *
280338 AAATG-GTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGAAGTTGTGGGCTTAAAG
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAA-G-----G-GTGCCACGGAGTTGTGGACTTAAA-
*
280402 GGA
58 AGA
*
280405 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA-GA
* * * *
280466 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAGGGAAAAAGAGTGCCATGGAGTTGTGGGCTTAAAA
1 AAAAGAGTGCCACGGAGTTGTGGACTT-------AAAAGGGTGCCACGGAGTTGTGGACTTAAAA
280531 G-
59 GA
* *
280532 ----G-GTGCCACGGAGTTGTGGGCTTAAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAA
1 AAAAGAGTGCCACGGAGTTGTGGACTT-AAAAG-----G-GTGCCACGGAGTTGTGGACTTAAAA
280592 GGA
59 -GA
* * *
280595 AAAAGAGTACCACAGAGTTGTGGGCTTAAAAGG
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGG
280628 AAAAAGAGTG
Statistics
Matches: 445, Mismatches: 40, Indels: 101
0.76 0.07 0.17
Matches are distributed among these distances:
53 1 0.00
54 26 0.06
55 7 0.02
58 1 0.00
59 24 0.05
60 26 0.06
61 158 0.36
62 6 0.01
65 24 0.05
66 88 0.20
67 14 0.03
68 70 0.16
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.19
Consensus pattern (60 bp):
AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGA
Found at i:280120 original size:34 final size:33
Alignment explanation
Indices: 280058--280660 Score: 504
Period size: 34 Copynumber: 19.0 Consensus size: 33
280048 TTGTGGGTTT
* ** * *
280058 AAAAGGGTGCCACTAAGTTATGGACTTAAAGAGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAA-AGA
*
280092 AAAAGAGTACCACGGAGTTGTGGGCTT-----A
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGA
* * * *
280120 AACAG-TTGCCACGGAGTCGTGGACTTAAAA-A
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGA
* *
280151 GAAAAG-GTGCCACAGAGTTGTGGACTTAAAAGGA
1 -AAAAGAGTGCCACGGAGTTGTGGGCTTAAAA-GA
* * * *
280185 ACAAG-GTGCCATGGAGTAGTGGACTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAA-GA
*
280218 AAAAGA-TGCCACGGAGTTGTGGACTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAA-GA
* *
280251 ACAAG-GTGCCACGGAGTTGTGGACTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAA-GA
* * * *
280284 ACAAGAG-GCCACAGAGTAGTGGACTTAAAAG-
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGA
*
280315 ----G-GTGCCACGGAGTTGTGAGCTT-----A
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGA
* * *
280338 AAATG-GTGCCACAGAGTTGTGGACTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAA-GA
* *
280371 AAAAGAGTGCCACGAAGTTGTGGGCTTAAAGGGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAA-AGA
280405 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAG-
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGA
*
280437 ----G-GTGCCACGGAGTTGTGGACTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAA-GA
*
280466 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAGGGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAA-AGA
*
280500 AAAAGAGTGCCATGGAGTTGTGGGCTTAAAAG-
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGA
280532 ----G-GTGCCACGGAGTTGTGGGCTTAAAAAGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTT-AAAAGA
280561 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAA-GA
* *
280595 AAAAGAGTACCACAGAGTTGTGGGCTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAA-GA
* * *
280629 AAAAGAGTGCCACGAAGTTGGGGGCATAAAAG
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAG
280661 GGTGCCACGA
Statistics
Matches: 477, Mismatches: 52, Indels: 81
0.78 0.09 0.13
Matches are distributed among these distances:
26 1 0.00
27 96 0.20
28 13 0.03
31 1 0.00
32 27 0.06
33 129 0.27
34 210 0.44
ACGTcount: A:0.35, C:0.13, G:0.33, T:0.19
Consensus pattern (33 bp):
AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGA
Found at i:280463 original size:95 final size:95
Alignment explanation
Indices: 280031--280627 Score: 654
Period size: 95 Copynumber: 6.3 Consensus size: 95
280021 TGGGCTTTTG
* * * * ** *
280031 AAAAGGGTGCCACAGACTTGTGGGTTTAAAAGGGTGCCACTAAGTTATGGACTT-AAAGAGAAAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG-GAAAA
*
280095 AGAGTACCACGGAGTTGTGGGCTT------A
65 AGAGTGCCACGGAGTTGTGGGCTTAAAGGGA
* * * * *
280120 AACAG-TTGCCACGGAGTCGTGGACTTAAAAAGAAAAGGTGCCACAGAGTTGTGGACTTAAAAGG
1 AAAAGAGTGCCACGGAGTTGTGGGCTT-AAAAG----GGTGCCACGGAGTTGTGGACTTAAAAGG
* * * * *
280184 AACAAG-GTGCCATGGAGTAGTGGACTTAAAAGGA
61 AAAAAGAGTGCCACGGAGTTGTGGGCTTAAAGGGA
*
280218 AAAAGA-TGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGACTTAAAAG
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAA-G-----GGTGCCACGGAGTTGTGGACTTAAAAG
* * * *
280282 GAACAAGAG-GCCACAGAGTAGTGGACTT-------
60 GAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAGGGA
* * * *
280310 AAAAGGGTGCCACGGAGTTGTGAGCTTAAAATGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
*
280375 GAGTGCCACGAAGTTGTGGGCTTAAAGGGA
66 GAGTGCCACGGAGTTGTGGGCTTAAAGGGA
280405 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
280470 GAGTGCCACGGAGTTGTGGGCTTAAAGGGA
66 GAGTGCCACGGAGTTGTGGGCTTAAAGGGA
* * *
280500 AAAAGAGTGCCATGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGGCTTAAAAAGAAAAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
*
280565 GAGTGCCACGGAGTTGTGGGCTTAAAAGGA
66 GAGTGCCACGGAGTTGTGGGCTTAAAGGGA
* *
280595 AAAAGAGTACCACAGAGTTGTGGGCTTAAAAGG
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGG
280628 AAAAAGAGTG
Statistics
Matches: 440, Mismatches: 43, Indels: 44
0.83 0.08 0.08
Matches are distributed among these distances:
87 34 0.08
88 30 0.07
89 9 0.02
92 22 0.05
93 47 0.11
94 4 0.01
95 211 0.48
97 4 0.01
98 25 0.06
99 53 0.12
100 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.19
Consensus pattern (95 bp):
AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
GAGTGCCACGGAGTTGTGGGCTTAAAGGGA
Found at i:280700 original size:33 final size:33
Alignment explanation
Indices: 280663--280856 Score: 253
Period size: 33 Copynumber: 6.0 Consensus size: 33
280653 CATAAAAGGG
280663 TGCCAC-GAAGTCGTGGACTTTGAAGAAAAAAGA
1 TGCCACTG-AGTCGTGGACTTTGAAGAAAAAAGA
280696 TGCCACTGAGTCGTGGAC-TTGAAAGAAAAAAGA
1 TGCCACTGAGTCGTGGACTTTG-AAGAAAAAAGA
*
280729 TGCCACTAAGTCGTGGACTTTGAAGAAAAAAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
* *
280762 TGCCACTAAGTCGTGGACTTTG--G-AAAGAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
*
280792 TGCTACTG-GTTCGTGGACTTTGAAG--AAAAGA
1 TGCCACTGAG-TCGTGGACTTTGAAGAAAAAAGA
280823 TGCCACTGAGTCGTGGACTTTGAA-AAAAAGAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAA-AGA
280856 T
1 T
280857 TTGAAGAGTT
Statistics
Matches: 145, Mismatches: 6, Indels: 20
0.85 0.04 0.12
Matches are distributed among these distances:
29 1 0.01
30 24 0.17
31 27 0.19
32 8 0.06
33 81 0.56
34 4 0.03
ACGTcount: A:0.36, C:0.15, G:0.27, T:0.22
Consensus pattern (33 bp):
TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
Found at i:280835 original size:94 final size:97
Alignment explanation
Indices: 280663--280856 Score: 265
Period size: 94 Copynumber: 2.0 Consensus size: 97
280653 CATAAAAGGG
280663 TGCCACGAAGTCGTGGACTTTGAAGAAAAAAGATGCCACTGAGTCGTGGACTTGAAAGAAAAAAG
1 TGCCACGAAGTCGTGGACTTTG-AGAAAAAAGATGCCACTGAGTCGTGGACTTGAAAG-AAAAAG
280728 ATGCCACTAAGTCGTGGACTTTGAAGAAAAA-AGA
64 ATGCCACTAAGTCGTGGACTTTGAA-AAAAAGAGA
* * *
280762 TGCCACTAAGTCGTGGACTTTG-G-AAAGAGATGCTACTG-GTTCGTGGACTTTG-AAG-AAAAG
1 TGCCACGAAGTCGTGGACTTTGAGAAAAAAGATGCCACTGAG-TCGTGGAC-TTGAAAGAAAAAG
*
280822 ATGCCACTGAGTCGTGGACTTTGAAAAAAAGAGA
64 ATGCCACTAAGTCGTGGACTTTGAAAAAAAGAGA
280856 T
1 T
280857 TTGAAGAGTT
Statistics
Matches: 88, Mismatches: 4, Indels: 11
0.85 0.04 0.11
Matches are distributed among these distances:
93 5 0.06
94 33 0.38
95 1 0.01
96 24 0.27
97 4 0.05
99 21 0.24
ACGTcount: A:0.36, C:0.15, G:0.27, T:0.22
Consensus pattern (97 bp):
TGCCACGAAGTCGTGGACTTTGAGAAAAAAGATGCCACTGAGTCGTGGACTTGAAAGAAAAAGAT
GCCACTAAGTCGTGGACTTTGAAAAAAAGAGA
Found at i:282231 original size:12 final size:12
Alignment explanation
Indices: 282134--282232 Score: 53
Period size: 12 Copynumber: 8.0 Consensus size: 12
282124 ACCTTTGCAC
*
282134 TTTTTTGTGTGCT
1 TTTTTTGTGT-TT
282147 TTTTTTGT-TTT
1 TTTTTTGTGTTT
*
282158 GTTTTTGTGTTT
1 TTTTTTGTGTTT
** **
282170 ACTTTTGACTTT
1 TTTTTTGTGTTT
282182 TTCATTTT-T-TTT
1 TT--TTTTGTGTTT
282194 TGTTTTT-TGTTT
1 T-TTTTTGTGTTT
282206 TTTTTTACGTTGTTT
1 TTTTTT--G-TGTTT
282221 TTTTTTGTGTTT
1 TTTTTTGTGTTT
282233 GTACTTTTGA
Statistics
Matches: 68, Mismatches: 9, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
11 18 0.26
12 25 0.37
13 10 0.15
14 4 0.06
15 11 0.16
ACGTcount: A:0.04, C:0.05, G:0.14, T:0.77
Consensus pattern (12 bp):
TTTTTTGTGTTT
Found at i:297178 original size:10 final size:9
Alignment explanation
Indices: 297163--297243 Score: 69
Period size: 9 Copynumber: 9.0 Consensus size: 9
297153 CATTCTTTTT
297163 CAAAAAAAA
1 CAAAAAAAA
297172 CCAAAAAACAA
1 -CAAAAAA-AA
*
297183 CGAAAAAAA
1 CAAAAAAAA
297192 CAAAAAAAA
1 CAAAAAAAA
297201 -ACAAAAAAA
1 CA-AAAAAAA
297210 C--AAAAAA
1 CAAAAAAAA
*
297217 CAAAACAAA
1 CAAAAAAAA
* *
297226 GAAAAAAGA
1 CAAAAAAAA
*
297235 GAAAAAAAA
1 CAAAAAAAA
297244 AAGAATTTGC
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
7 7 0.12
8 1 0.02
9 36 0.61
10 13 0.22
11 2 0.03
ACGTcount: A:0.83, C:0.12, G:0.05, T:0.00
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:297189 original size:1 final size:1
Alignment explanation
Indices: 297185--297245 Score: 50
Period size: 1 Copynumber: 61.0 Consensus size: 1
297175 AAAAACAACG
* * * * * * * *
297185 AAAAAAACAAAAAAAAACAAAAAAACAAAAAACAAAACAAAGAAAAAAGAGAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
297246 GAATTTGCTT
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.87, C:0.08, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:297189 original size:12 final size:10
Alignment explanation
Indices: 297163--297243 Score: 76
Period size: 10 Copynumber: 8.0 Consensus size: 10
297153 CATTCTTTTT
*
297163 CAAAAAAAAC
1 CAAAAAAAAA
*
297173 CAAAAAACAA
1 CAAAAAAAAA
*
297183 C-GAAAAAAA
1 CAAAAAAAAA
297192 CAAAAAAAAA
1 CAAAAAAAAA
297202 CAAAAAAACAA
1 CAAAAAAA-AA
*
297213 -AAAACAAAA
1 CAAAAAAAAA
297222 CAAAGAAAAAA
1 CAAA-AAAAAA
*
297233 GAGAAAAAAAA
1 CA-AAAAAAAA
297244 AAGAATTTGC
Statistics
Matches: 58, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
9 9 0.16
10 33 0.57
11 14 0.24
12 2 0.03
ACGTcount: A:0.83, C:0.12, G:0.05, T:0.00
Consensus pattern (10 bp):
CAAAAAAAAA
Found at i:297190 original size:19 final size:18
Alignment explanation
Indices: 297165--297219 Score: 83
Period size: 18 Copynumber: 2.9 Consensus size: 18
297155 TTCTTTTTCA
297165 AAAAAAACCAAAAAACAAC
1 AAAAAAA-CAAAAAACAAC
*
297184 GAAAAAAACAAAAAAAAAC
1 -AAAAAAACAAAAAACAAC
297203 AAAAAAACAAAAAACAA
1 AAAAAAACAAAAAACAA
297220 AACAAAGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
18 16 0.48
19 10 0.30
20 7 0.21
ACGTcount: A:0.84, C:0.15, G:0.02, T:0.00
Consensus pattern (18 bp):
AAAAAAACAAAAAACAAC
Found at i:297196 original size:18 final size:18
Alignment explanation
Indices: 297165--297230 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 18
297155 TTCTTTTTCA
*
297165 AAAAAAACCAAAAAACAAC
1 AAAAAAA-CAAAAAAAAAC
297184 GAAAAAAACAAAAAAAAAC
1 -AAAAAAACAAAAAAAAAC
297203 AAAAAAACAAAAAACAAAAC
1 AAAAAAAC-AAAAA-AAAAC
297223 AAAGAAAA
1 AAA-AAAA
297231 AAGAGAAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
18 8 0.19
19 15 0.36
20 15 0.36
21 4 0.10
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00
Consensus pattern (18 bp):
AAAAAAACAAAAAAAAAC
Found at i:297200 original size:30 final size:30
Alignment explanation
Indices: 297164--297245 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 30
297154 ATTCTTTTTC
* *
297164 AAAAAAAACCAAAAAACAACGAAA-AAAACA
1 AAAAAAAACAAAAAAACAA-AAAACAAAACA
297194 AAAAAAAACAAAAAAACAAAAAACAAAACA
1 AAAAAAAACAAAAAAACAAAAAACAAAACA
* *
297224 AAGAAAAAAGAGAAAAA-AAAAA
1 AA-AAAAAACAAAAAAACAAAAA
297246 GAATTTGCTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
29 3 0.07
30 31 0.67
31 12 0.26
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (30 bp):
AAAAAAAACAAAAAAACAAAAAACAAAACA
Found at i:299434 original size:79 final size:78
Alignment explanation
Indices: 299301--299499 Score: 202
Period size: 79 Copynumber: 2.5 Consensus size: 78
299291 AATAACGGGG
* * ** * *
299301 TTGGAGTATCCCCTTGAAAATAACAGGGTTAGAGTATCCCCGTTTGTGAAAAATCGATGA-TTAG
1 TTGGAGTATCCCCTAG-AAATAACAGGGTTGGAGTATCCCCAATTATGAAAAATCAAT-ATTTAG
299365 AAAATAAAATCAGGA
64 AAAATAAAATCAGGA
** * * *
299380 TTGGAGTATCCCCTCAGAAATAATGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCCCT-AGAAATAACAGGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTAGA
* * *
299445 AAATAAAGTCGGGG
65 AAATAAAATCAGGA
* **
299459 TTGGAGTATCCCCTTGGAGGTAACAGGGTTGGAGTATCCCC
1 TTGGAGTATCCCC-TAGAAATAACAGGGTTGGAGTATCCCC
299500 GATGAAATAA
Statistics
Matches: 98, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
78 1 0.01
79 95 0.97
80 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (78 bp):
TTGGAGTATCCCCTAGAAATAACAGGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTAGAA
AATAAAATCAGGA
Found at i:299507 original size:107 final size:108
Alignment explanation
Indices: 299375--299579 Score: 252
Period size: 107 Copynumber: 1.9 Consensus size: 108
299365 AAAATAAAAT
* * *
299375 CAGGATTGGAGTATCCCCTCAGAAATAATGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CAGGATTGGAGTATCCCCTCAGAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATAT
* * *
299440 TTT-GGAAATAAAGTCGGGGTTGGAGTATCCCCTTGGAGGTAA
66 TTTCGAAAATAAAATCGGAGTTGGAGTATCCCCTTGGAGGTAA
* * * * * *** *
299482 CAGGGTTGGAGTATCCCC-GATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTG
1 CAGGATTGGAGTATCCCCTCA-GAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATA
299546 TTTTCGAAAATAAAATCGGAGTTGGAGTATCCCC
65 TTTTCGAAAATAAAATCGGAGTTGGAGTATCCCC
299580 GATTAAAGGA
Statistics
Matches: 81, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
106 1 0.01
107 54 0.67
108 26 0.32
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.27
Consensus pattern (108 bp):
CAGGATTGGAGTATCCCCTCAGAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATAT
TTTCGAAAATAAAATCGGAGTTGGAGTATCCCCTTGGAGGTAA
Found at i:299510 original size:28 final size:28
Alignment explanation
Indices: 299456--299530 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
299446 AATAAAGTCG
* **
299456 GGGTTGGAGTATCCCC-TTGGAGGTAAC
1 GGGTTGGAGTATCCCCGATGGAAATAAC
299483 AGGGTTGGAGTATCCCCGAT-GAAATAAC
1 -GGGTTGGAGTATCCCCGATGGAAATAAC
*
299511 GAGGTTGGAGTATCCTCGAT
1 G-GGTTGGAGTATCCCCGAT
299531 TGTGAAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 1 0.02
28 39 0.95
29 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.25
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCGATGGAAATAAC
Found at i:299583 original size:52 final size:51
Alignment explanation
Indices: 299514--299908 Score: 269
Period size: 52 Copynumber: 7.6 Consensus size: 51
299504 AAATAACGAG
* *
299514 GTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTCGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTT-GAAAATAAAATCGGA
* * *
299566 GTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAA-CCGA
1 GTTGGAGTATCCCCGATT-ATGAAAAATTGGTGTTTTGAAAATAAAATCGGA
* * * * *
299617 GGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTT-AGAAATAAAACCGGG
1 -GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGA-AAATAAAATCGGA
* * *** * ** * *
299669 GTTGGAGTATCCTCGATTATGAGAAATCAATATTTTGGGAATAAAGTCGGG
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGAAAATAAAATCGGA
* *** * * ***** *
299720 GTTGGAGTATCCCC--TTGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAAC-GA
1 GTTGGAGTATCCCCGATT--ATG-AA--AAATTGGTGTTTTGAAAAT-AAA-ATCGGA
* * *
299775 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGGA
1 -GTTGGAGTATCCCCGATTATGAAAAATTGGTG-TTTTGAAAATAAAATCGGA
* * * *
299828 GTTGGAGTATCCCCGATTAAAGGAAATTTGGTGTTTTGAAAATAAAATCGGG
1 GTTGGAGTATCCCCGATT-ATGAAAAATTGGTGTTTTGAAAATAAAATCGGA
*
299880 GTTGGAGTATCCCCGATTATGAACAATTG
1 GTTGGAGTATCCCCGATTATGAAAAATTG
299909 AGAAACTTAA
Statistics
Matches: 259, Mismatches: 66, Indels: 37
0.72 0.18 0.10
Matches are distributed among these distances:
49 2 0.01
50 1 0.00
51 87 0.34
52 102 0.39
53 35 0.14
54 9 0.03
55 6 0.02
56 15 0.06
58 2 0.01
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGAAAATAAAATCGGA
Found at i:299756 original size:28 final size:28
Alignment explanation
Indices: 299716--299792 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 28
299706 GGAATAAAGT
* **
299716 CGGGGTTGGAGTATCCCC-TTGGAGGTAA
1 CGGGGTTGGAGTATCCCCGAT-GAAATAA
299744 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
299772 CGAGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
299793 TGTGAAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 42 0.98
29 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.35, T:0.25
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:299869 original size:262 final size:262
Alignment explanation
Indices: 299404--299897 Score: 907
Period size: 262 Copynumber: 1.9 Consensus size: 262
299394 CAGAAATAAT
299404 GGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTATC
1 GGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTATC
299469 CCCTTGGAGGTAACAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGT
66 CCCTTGGAGGTAACAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGT
299534 GAAAAATTGGTGTTTTCGAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTG
131 GAAAAATTGGTGTTTTCGAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTG
299599 TTTTGAAAATAAAACCGAGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAA
196 TTTTGAAAATAAAACCGAGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAA
299664 CC
261 CC
* * *
299666 GGGGTTGGAGTATCCTCGATTATGAGAAATCAATATTTTGGGAATAAAGTCGGGGTTGGAGTATC
1 GGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTATC
*
299731 CCCTTGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGT
66 CCCTTGGAGGTAACAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGT
* * *
299796 GAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAATTTGGTG
131 GAAAAATTGGTGTTTTCGAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTG
* *
299861 TTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATT
196 TTTTGAAAATAAAACCGAGGTTGGAGTATCCCCGATT
299898 ATGAACAATT
Statistics
Matches: 223, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
262 223 1.00
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.29
Consensus pattern (262 bp):
GGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTATC
CCCTTGGAGGTAACAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGT
GAAAAATTGGTGTTTTCGAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTG
TTTTGAAAATAAAACCGAGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAA
CC
Found at i:302302 original size:21 final size:21
Alignment explanation
Indices: 302278--302319 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
302268 GTATCAATAC
*
302278 AATGTATCGATACATTTCCTT
1 AATGTATCAATACATTTCCTT
302299 AATGTATCAATACATTTCCTT
1 AATGTATCAATACATTTCCTT
302320 GGCAGTAGCT
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:0.31, C:0.19, G:0.07, T:0.43
Consensus pattern (21 bp):
AATGTATCAATACATTTCCTT
Found at i:302368 original size:19 final size:20
Alignment explanation
Indices: 302344--302392 Score: 84
Period size: 19 Copynumber: 2.5 Consensus size: 20
302334 AGCGATACAT
302344 TGTATCGATACCAA-ACTTA
1 TGTATCGATACCAACACTTA
302363 TGTATCGATA-CAACACTTA
1 TGTATCGATACCAACACTTA
302382 TGTATCGATAC
1 TGTATCGATAC
302393 ATTTACGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 3 0.11
19 25 0.89
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (20 bp):
TGTATCGATACCAACACTTA
Found at i:302933 original size:55 final size:54
Alignment explanation
Indices: 302829--303019 Score: 190
Period size: 62 Copynumber: 3.4 Consensus size: 54
302819 TCTCCTTTCG
* *
302829 CCCTTTAGT-CTCAAAGAGCATGACGCCTTTAAAGCCCACACAAGTTGGTGGCA
1 CCCTTCAGTCCTCAAAGAGCAGGACGCCTTTAAAGCCCACACAAGTTGGTGGCA
302882 CCCTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCCTTCAGTCCTCAAAGAGCAGGACGCCTTT-AAAGCCCACACAAGTTGGTGGCA
*** * * *
302937 TTTTTTTAGTCCTCAAAGAGCATGATGCTTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 -CCCTTCAGTCCTCAAAGAGCA-G--G---ACGCC-TTTAAAGCCCACACAAGTTGGTGGCA
302999 --CTTCCTAGTCCTCAAAGAGCA
1 CCCTT-C-AGTCCTCAAAGAGCA
303020 TGACACTCTC
Statistics
Matches: 116, Mismatches: 10, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
53 8 0.07
54 20 0.17
55 23 0.20
56 17 0.15
57 1 0.01
59 3 0.03
61 15 0.13
62 26 0.22
63 3 0.03
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (54 bp):
CCCTTCAGTCCTCAAAGAGCAGGACGCCTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:303152 original size:210 final size:209
Alignment explanation
Indices: 302723--303652 Score: 1324
Period size: 210 Copynumber: 4.4 Consensus size: 209
302713 GGTGTCTACA
* *
302723 GTGGCA-TTTTTCAGTCCTCAAAGAGCATGATGCTTTCTTCTTTTAAAGCCCACACAAGTTGGTG
1 GTGGCATTTTTTTAGTCCTCAAAGAGCAGGATGCTTTC-TCTTTTAAAGCCCACACAAGTTGGTG
* * * *
302787 GCACTTCCTAGTCCTTAAAGAGCAAGACGCTCTCTCCTTTCGCCCTTTAGT-CTCAAAGAGCATG
65 GCACTTCCTAGTCCTCAAAGAGCAGGACACTCTCTCCTTTCGCCCTTTAGTCCTCAAAGAGCAGG
302851 ACGCCTTTAAAGCCCACACAAGTTGGTGGCACCCTTCAGTCCTCAAAGAGCAGGACGCCTTTCAA
130 ACGCCTTTAAAGCCCACACAAGTTGGTGGCACCCTTCAGTCCTCAAAGAGCAGGACGCCTTTCAA
302916 AGCCCACACAAGTTG
195 AGCCCACACAAGTTG
*
302931 GTGGCATTTTTTTAGTCCTCAAAGAGCATGATGCTTTCTCCTTTTAAAGCCCACACAAGTTGGTG
1 GTGGCATTTTTTTAGTCCTCAAAGAGCAGGATGCTTTCT-CTTTTAAAGCCCACACAAGTTGGTG
* * * *
302996 GCACTTCCTAGTCCTCAAAGAGCATGACACTCTCTCTTTTCGCCCTTTAGTCCTCAAAGGGTAGG
65 GCACTTCCTAGTCCTCAAAGAGCAGGACACTCTCTCCTTTCGCCCTTTAGTCCTCAAAGAGCAGG
*
303061 ATGCCTTTAAAGCCCACACAAGTTGGTGGCACCCTTCAGTCCTCAAAGAGCAGGACGCCTTTCAA
130 ACGCCTTTAAAGCCCACACAAGTTGGTGGCACCCTTCAGTCCTCAAAGAGCAGGACGCCTTTCAA
*
303126 AGTCCACACAAGTTG
195 AGCCCACACAAGTTG
* *
303141 GTGGCATTTTTTTAGTCCTCAAAGTGCAGGATGCTTTCTCCTTCTAAAGCCCACACAAGTTGGTG
1 GTGGCATTTTTTTAGTCCTCAAAGAGCAGGATGCTTTCT-CTTTTAAAGCCCACACAAGTTGGTG
* * *
303206 GCACTTCCTAGTCCTCAAAGAGCAGGACACTCTCTCTTTTCGCCCTTTAGTCCTCAAAGGGTAGG
65 GCACTTCCTAGTCCTCAAAGAGCAGGACACTCTCTCCTTTCGCCCTTTAGTCCTCAAAGAGCAGG
* * * * *
303271 ACACCTTTAAAGCCCACACAAGTTAGTGACACCCTTCAGTCCTCAAAGAGCAAGATGCCTTTCAA
130 ACGCCTTTAAAGCCCACACAAGTTGGTGGCACCCTTCAGTCCTCAAAGAGCAGGACGCCTTTCAA
*
303336 AGCTCACACAAGTTG
195 AGCCCACACAAGTTG
* **
303351 GTGGCATTTTCTTTAGTCCTCAAAGAGTAGGATG-----TCTTTCGAAGCCCACACAAGTTGGTG
1 GTGGCATTTT-TTTAGTCCTCAAAGAGCAGGATGCTTTCTCTTTTAAAGCCCACACAAGTTGGTG
303411 GCACTTCCTAGTCCTCAAAGAGCAGGACACTCTCTCCTTTCGCCCTTTAGTCCTCAAAGAGCAGG
65 GCACTTCCTAGTCCTCAAAGAGCAGGACACTCTCTCCTTTCGCCCTTTAGTCCTCAAAGAGCAGG
* * * *
303476 ATGCCTTTTAAAGCCTACACAAGTTGGTGGCA--CTTCCGGTCCTCAAAGAGCAGGATGCTTTCT
130 ACGCC-TTTAAAGCCCACACAAGTTGGTGGCACCCTT-CAGTCCTCAAAGAGCAGGA--C--GC-
303539 CTTTGCAAAGCCCACACAAGTTG
188 CTTT-CAAAGCCCACACAAGTTG
** * *
303562 GTGGCA-CCTTCTAGTCCTCAAAGAGCAGGATGCCTTT-TCTTTTCAAAGCCCACACGAGTTGGT
1 GTGGCATTTTTTTAGTCCTCAAAGAGCAGGATG-CTTTCTCTTTT-AAAGCCCACACAAGTTGGT
**
303625 GGCACTTTTTAGTCCTCAAAGAGCAGGA
64 GGCACTTCCTAGTCCTCAAAGAGCAGGA
303653 TGCCTTTTCT
Statistics
Matches: 655, Mismatches: 49, Indels: 29
0.89 0.07 0.04
Matches are distributed among these distances:
204 3 0.00
205 104 0.16
206 24 0.04
208 7 0.01
209 124 0.19
210 301 0.46
211 44 0.07
214 5 0.01
215 43 0.07
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (209 bp):
GTGGCATTTTTTTAGTCCTCAAAGAGCAGGATGCTTTCTCTTTTAAAGCCCACACAAGTTGGTGG
CACTTCCTAGTCCTCAAAGAGCAGGACACTCTCTCCTTTCGCCCTTTAGTCCTCAAAGAGCAGGA
CGCCTTTAAAGCCCACACAAGTTGGTGGCACCCTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAA
GCCCACACAAGTTG
Found at i:303178 original size:55 final size:55
Alignment explanation
Indices: 303038--303232 Score: 207
Period size: 54 Copynumber: 3.4 Consensus size: 55
303028 TCTCTTTTCG
* *
303038 CCCTTTAGTCCTCAAAGGGTAGGATGCCTTT-AAAGCCCACACAAGTTGGTGGCA
1 CCCTTTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
303092 CCCTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGTCCACACAAGTTGGTGGCA
1 CCCTTTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
*** *
303147 TTTTTTTAGTCCTCAAAGTGCAGGATGCTTTCTCCTTCTAAAGCCCACACAAGTTGGTGGCA
1 -CCCTTTAGTCCTCAAAGAGCAGGATGC---CT--TTC-AAAGCCCACACAAGTTGGTGGCA
303209 --CTTCCTAGTCCTCAAAGAGCAGGA
1 CCCTT--TAGTCCTCAAAGAGCAGGA
303233 CACTCTCTCT
Statistics
Matches: 117, Mismatches: 14, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
54 27 0.23
55 22 0.19
56 21 0.18
59 4 0.03
61 21 0.18
62 22 0.19
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (55 bp):
CCCTTTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:303390 original size:57 final size:55
Alignment explanation
Indices: 303250--303437 Score: 200
Period size: 57 Copynumber: 3.4 Consensus size: 55
303240 TCTTTTCGCC
* * ** * * **
303250 CTTTAGTCCTCAAAGGGTAGGACACCTTT-AAAGCCCACACAAGTTAGTGACACC
1 CTTTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCATT
* * *
303304 CTTCAGTCCTCAAAGAGCAAGATGCCTTTCAAAGCTCACACAAGTTGGTGGCATTTT
1 CTTTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA--TT
* * *
303361 CTTTAGTCCTCAAAGAGTAGGATGTCTTTCGAAGCCCACACAAGTTGGTGGCACTT
1 CTTTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA-TT
*
303417 C-CTAGTCCTCAAAGAGCAGGA
1 CTTTAGTCCTCAAAGAGCAGGA
303438 CACTCTCTCC
Statistics
Matches: 111, Mismatches: 20, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
54 23 0.21
55 38 0.34
56 3 0.03
57 47 0.42
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.25
Consensus pattern (55 bp):
CTTTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCATT
Found at i:303479 original size:151 final size:150
Alignment explanation
Indices: 303302--303591 Score: 399
Period size: 151 Copynumber: 1.9 Consensus size: 150
303292 GTTAGTGACA
* *
303302 CCCTTCAGTCCTCAAAGAGCAAGATGCCTTTCAAAG-CTCACACAAGTTGGTGGCATTTTCTTTA
1 CCCTTCAGTCCTCAAAGAGCAAGATGCCTTTCAAAGCCT-ACACAAGTTGGTGGCA-CTTC--CA
* *
303366 GTCCTCAAAGAGTAGGATG-TCTTT-CGAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCA
62 GTCCTCAAAGAGCAGGATGTTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTT-CTAGTCCTCA
303428 AAGAGCAGGACACTCTCTCCTTTCG
126 AAGAGCAGGACACTCTCTCCTTTCG
* * * *
303453 CCCTTTAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCTACACAAGTTGGTGGCACTTCCGGTCC
1 CCCTTCAGTCCTCAAAGAGCAAGATGCCTTTCAAAGCCTACACAAGTTGGTGGCACTTCCAGTCC
303518 TCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAA
66 TCAAAGAGCAGGATG---T-TCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAA
303583 AGAGCAGGA
127 AGAGCAGGA
303592 TGCCTTTTCT
Statistics
Matches: 123, Mismatches: 8, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
148 18 0.15
150 3 0.02
151 49 0.40
152 2 0.02
153 5 0.04
154 43 0.35
155 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (150 bp):
CCCTTCAGTCCTCAAAGAGCAAGATGCCTTTCAAAGCCTACACAAGTTGGTGGCACTTCCAGTCC
TCAAAGAGCAGGATGTTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAG
CAGGACACTCTCTCCTTTCG
Found at i:303603 original size:61 final size:61
Alignment explanation
Indices: 303454--303726 Score: 375
Period size: 61 Copynumber: 4.6 Consensus size: 61
303444 CTCCTTTCGC
*
303454 CCTT-TAGTCCTCAAAGAGCAGGATG-C----CTTTT-AAAGCCTACACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
** *
303508 -CTTCCGGTCCTCAAAGAGCAGGATG-CTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGATGCCTTT-TCTTTTCAAAGCCCACACAAGTTGGTGGCA
*
303568 CCTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
303629 CTTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
** *
303690 TTTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCTTTT
1 CCTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCTTTT
303727 TCTCCTTTGT
Statistics
Matches: 199, Mismatches: 11, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
53 3 0.02
54 20 0.10
59 4 0.02
60 22 0.11
61 146 0.73
62 4 0.02
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.30
Consensus pattern (61 bp):
CCTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:303828 original size:42 final size:42
Alignment explanation
Indices: 303775--303854 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
303765 CTTATTTTCC
* *
303775 CTTTTGTCCTCAAAGAGCATGACGTACTTT-GTTTTCCTCTTT
1 CTTTTGTCCTCAAAGAGCAAGACGCA-TTTCGTTTTCCTCTTT
303817 CTTTTGTCCTCAAAGAGCAAGACGCATTTCGTTTTCCT
1 CTTTTGTCCTCAAAGAGCAAGACGCATTTCGTTTTCCT
303855 TTTTTCCTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 3 0.09
42 32 0.91
ACGTcount: A:0.19, C:0.25, G:0.15, T:0.41
Consensus pattern (42 bp):
CTTTTGTCCTCAAAGAGCAAGACGCATTTCGTTTTCCTCTTT
Found at i:304663 original size:20 final size:19
Alignment explanation
Indices: 304634--304708 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 19
304624 TTTACCCAGA
304634 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTTT-CAT
* *
304654 TGTATTGATACATTGCTCAT
1 TGTATCGATACATT-TTCAT
*
304674 TGTATCGATACATTTTACAA
1 TGTATCGATACATTTT-CAT
304694 TGTATCGATACATTT
1 TGTATCGATACATTT
304709 AGGCATTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (19 bp):
TGTATCGATACATTTTCAT
Found at i:312103 original size:25 final size:24
Alignment explanation
Indices: 312066--312120 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
312056 GAATTTATTT
*
312066 ATTTTTATTTTTTAAATTTTTAGA
1 ATTTTTATATTTTAAATTTTTAGA
** *
312090 ATTTTTATGATTTTTTATTTTTTGA
1 ATTTTTAT-ATTTTAAATTTTTAGA
312115 ATTTTT
1 ATTTTT
312121 CTTAATTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (24 bp):
ATTTTTATATTTTAAATTTTTAGA
Found at i:312139 original size:34 final size:32
Alignment explanation
Indices: 312052--312140 Score: 90
Period size: 34 Copynumber: 2.7 Consensus size: 32
312042 TTTTAGACTA
*
312052 TTTT-GAATTTATTTATTTTTATTTTTTAAAT
1 TTTTAGAATTTTTTTATTTTTATTTTTTAAAT
* *
312083 TTTTAGAATTTTTATGATTTTTTATTTTTTGAAT
1 TTTTAGAATTTTT-TTA-TTTTTATTTTTTAAAT
**
312117 TTTTCTTAATTATTTTTATTTTTA
1 TTTT-AGAATT-TTTTTATTTTTA
312141 ATTATTTTCT
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
31 4 0.09
32 7 0.15
33 2 0.04
34 25 0.53
35 6 0.13
36 3 0.06
ACGTcount: A:0.24, C:0.01, G:0.04, T:0.71
Consensus pattern (32 bp):
TTTTAGAATTTTTTTATTTTTATTTTTTAAAT
Found at i:312828 original size:18 final size:18
Alignment explanation
Indices: 312805--312841 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
312795 GGCAAAAGTA
*
312805 TTTTAGCACAGGTACTTT
1 TTTTAGCACAAGTACTTT
*
312823 TTTTAGCATAAGTACTTT
1 TTTTAGCACAAGTACTTT
312841 T
1 T
312842 AGCATAGGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (18 bp):
TTTTAGCACAAGTACTTT
Found at i:312836 original size:32 final size:32
Alignment explanation
Indices: 312790--312855 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
312780 GCAAATATAC
*
312790 TTTTTGGCAAAAGTA-TTTTAGCACAGGTACTT
1 TTTTTAGCAAAAGTACTTTTAGCACAGGTA-TT
* *
312822 TTTTTAGCATAAGTACTTTTAGCATAGGTATT
1 TTTTTAGCAAAAGTACTTTTAGCACAGGTATT
312854 TT
1 TT
312856 GGTAGAAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.45
Consensus pattern (32 bp):
TTTTTAGCAAAAGTACTTTTAGCACAGGTATT
Found at i:312884 original size:14 final size:15
Alignment explanation
Indices: 312823--312886 Score: 60
Period size: 15 Copynumber: 4.4 Consensus size: 15
312813 CAGGTACTTT
312823 TTTTAGCATAAGTAC
1 TTTTAGCATAAGTAC
*
312838 TTTTAGCATAGGTA-
1 TTTTAGCATAAGTAC
* * * *
312852 TTTTGGTAGAAGTAT
1 TTTTAGCATAAGTAC
*
312867 TTTTAGCATTAGTA-
1 TTTTAGCATAAGTAC
312881 TTTTAG
1 TTTTAG
312887 AATAGATACT
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
14 16 0.41
15 23 0.59
ACGTcount: A:0.28, C:0.06, G:0.19, T:0.47
Consensus pattern (15 bp):
TTTTAGCATAAGTAC
Found at i:315509 original size:67 final size:67
Alignment explanation
Indices: 315330--315526 Score: 168
Period size: 67 Copynumber: 2.9 Consensus size: 67
315320 GTCTTGTGCT
* * * * ** * * ** **
315330 CACTTCCGTAACTTTCCCTAATATAAGTACTCTTAATGAAGAAGTTGACCATTGTGATCCCATGC
1 CACTTCTGTCACTCTCCCTAATATAAGTACTCTTAATGAAAAAGTCAACCATTATGGTTTCATAA
315395 GC
66 GC
* * *
315397 CACTTCTGTCATTCT-CCTATATATAAGT--TCTTCCAA-GTAATAAGTCAACTATTATGGTTTC
1 CACTTCTGTCACTCTCCCTA-ATATAAGTACTCTT--AATG-AAAAAGTCAACCATTATGGTTTC
315458 ATAAGC
62 ATAAGC
* * *
315464 CATTTCTGTCACTCTCCCTAATATAAGTACTCTTAATGAAAAAGTCAACCATAAAGGTTTCAT
1 CACTTCTGTCACTCTCCCTAATATAAGTACTCTTAATGAAAAAGTCAACCATTATGGTTTCAT
315527 GCATCATTTT
Statistics
Matches: 102, Mismatches: 20, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
65 4 0.04
66 5 0.05
67 84 0.82
68 5 0.05
69 4 0.04
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.35
Consensus pattern (67 bp):
CACTTCTGTCACTCTCCCTAATATAAGTACTCTTAATGAAAAAGTCAACCATTATGGTTTCATAA
GC
Found at i:315688 original size:134 final size:134
Alignment explanation
Indices: 315340--315690 Score: 334
Period size: 134 Copynumber: 2.6 Consensus size: 134
315330 CACTTCCGTA
* * * * *
315340 ACTTTCCCTAATATAAGTACTCTTAATGAAGAAGTTGACCATTGTGATCCCATGCGCCACTTCTG
1 ACTTCCCCTAATATAAGTACTCTTAATGAAAAAGTCGACCATTGTGGTCTCATGCGCCACTTCTG
* * * *
315405 TCA--TTCTCCTATATATAAGTTCTTCCAAGTAATAAGTCAACTATTATGGTTTCATAAGCCATT
66 TCACTTTCT-C-ATATATAAATTCTTCCAAGTAAGAAGTCAACTATCATGGTTCCATAAGCCATT
*
315468 TCTGTC
129 TCTATC
* *** * ** * *
315474 AC-TCTCCCTAATATAAGTACTCTTAATGAAAAAGTCAACCATAAAGGTTTCATGCATCATTTTT
1 ACTTC-CCCTAATATAAGTACTCTTAATGAAAAAGTCGACCATTGTGGTCTCATGCGCCACTTCT
* * * * * * * *
315538 ATTACTCTCTCGTATATAAATTCTTTCAA-TAGAGAAGTCGACTATCATGGTTCCCTATGCCATT
65 GTCACTTTCTCATATATAAATTCTTCCAAGTA-AGAAGTCAACTATCATGGTTCCATAAGCCATT
315602 T-TCATC
129 TCT-ATC
* * * * *
315608 ACTTCCCCCAATATAAGTATTCTTAATAAAAAAGTCGACCGTTGTGGTCTCATGTGCCACTTCTG
1 ACTTCCCCTAATATAAGTACTCTTAATGAAAAAGTCGACCATTGTGGTCTCATGCGCCACTTCTG
315673 TCACTTTCTCATATATAA
66 TCACTTTCTCATATATAA
315691 GTTCATCTAA
Statistics
Matches: 166, Mismatches: 45, Indels: 12
0.74 0.20 0.05
Matches are distributed among these distances:
133 4 0.02
134 156 0.94
135 3 0.02
136 3 0.02
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.36
Consensus pattern (134 bp):
ACTTCCCCTAATATAAGTACTCTTAATGAAAAAGTCGACCATTGTGGTCTCATGCGCCACTTCTG
TCACTTTCTCATATATAAATTCTTCCAAGTAAGAAGTCAACTATCATGGTTCCATAAGCCATTTC
TATC
Found at i:316866 original size:15 final size:15
Alignment explanation
Indices: 316845--317113 Score: 98
Period size: 15 Copynumber: 18.6 Consensus size: 15
316835 TTAGCAAAGA
*
316845 TACTTTTGGCACAAG
1 TACTTTTGGCATAAG
* *
316860 TATTTTTGGCAAAAG
1 TACTTTTGGCATAAG
* * * *
316875 TACTTTTAGTAGAGG
1 TACTTTTGGCATAAG
*
316890 TAC--TTGGCACAAG
1 TACTTTTGGCATAAG
*
316903 TACTTTTGGCATATG
1 TACTTTTGGCATAAG
* * *
316918 TA-GTTTAGCACAAG
1 TACTTTTGGCATAAG
*
316932 TA--TTTGACATAAG
1 TACTTTTGGCATAAG
*
316945 TACTTTTAGCATAAG
1 TACTTTTGGCATAAG
*
316960 TACTTTTGGTATAAG
1 TACTTTTGGCATAAG
*
316975 TA-TTTTAGTCGAT--G
1 TACTTTT-GGC-ATAAG
* *
316989 TACTTTTGGCAGAGG
1 TACTTTTGGCATAAG
* *
317004 TACTTTAGTACAT-A-
1 TACTTTTG-GCATAAG
* *
317018 TACTTTTTGCATAGG
1 TACTTTTGGCATAAG
* *
317033 TA-TTTTAGCATAGG
1 TACTTTTGGCATAAG
* **
317047 T-TTTTTAACA-AAGG
1 TACTTTTGGCATAA-G
*
317061 TAC-TTTGGTATAAG
1 TACTTTTGGCATAAG
** *
317075 TACTTTTAACATAGG
1 TACTTTTGGCATAAG
* * *
317090 TATTTTTCGCACAAG
1 TACTTTTGGCATAAG
317105 TACTTTTGG
1 TACTTTTGG
317114 TATAGTATTT
Statistics
Matches: 183, Mismatches: 54, Indels: 34
0.68 0.20 0.13
Matches are distributed among these distances:
13 24 0.13
14 54 0.30
15 101 0.55
16 4 0.02
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (15 bp):
TACTTTTGGCATAAG
Found at i:317010 original size:29 final size:29
Alignment explanation
Indices: 316902--317040 Score: 104
Period size: 29 Copynumber: 4.8 Consensus size: 29
316892 CTTGGCACAA
* * * *
316902 GTACTTTTGGCATATGTAGTTTAGCACAA
1 GTACTTTTGGCATAGGTATTTTAGTACAT
* * * * *
316931 GTA--TTTGACATAAGTACTTTTAGCATAA
1 GTACTTTTGGCATAGGTA-TTTTAGTACAT
* *
316959 GTACTTTTGGTATAAGTATTTTAGT-CGAT
1 GTACTTTTGGCATAGGTATTTTAGTAC-AT
* *
316988 GTACTTTTGGCAGAGGTACTTTAGTACAT
1 GTACTTTTGGCATAGGTATTTTAGTACAT
* *
317017 ATACTTTTTGCATAGGTATTTTAG
1 GTACTTTTGGCATAGGTATTTTAG
317041 CATAGGTTTT
Statistics
Matches: 88, Mismatches: 17, Indels: 10
0.77 0.15 0.09
Matches are distributed among these distances:
27 11 0.12
28 12 0.14
29 53 0.60
30 12 0.14
ACGTcount: A:0.27, C:0.11, G:0.19, T:0.42
Consensus pattern (29 bp):
GTACTTTTGGCATAGGTATTTTAGTACAT
Found at i:317053 original size:14 final size:14
Alignment explanation
Indices: 317021--317053 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
317011 GTACATATAC
317021 TTTTT-GCATAGGT
1 TTTTTAGCATAGGT
*
317034 ATTTTAGCATAGGT
1 TTTTTAGCATAGGT
317048 TTTTTA
1 TTTTTA
317054 ACAAAGGTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.21, C:0.06, G:0.18, T:0.55
Consensus pattern (14 bp):
TTTTTAGCATAGGT
Found at i:317095 original size:14 final size:14
Alignment explanation
Indices: 317027--317095 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 14
317017 ATACTTTTTG
*
317027 CATAGGTATTTTAG
1 CATAGGTATTTTAA
*
317041 CATAGGTTTTTTAA
1 CATAGGTATTTTAA
* * **
317055 CAAAGGTACTTTGG
1 CATAGGTATTTTAA
* *
317069 TATAAGTACTTTTAA
1 CATAGGTA-TTTTAA
317084 CATAGGTATTTT
1 CATAGGTATTTT
317096 TCGCACAAGT
Statistics
Matches: 39, Mismatches: 15, Indels: 2
0.70 0.27 0.04
Matches are distributed among these distances:
14 30 0.77
15 9 0.23
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.43
Consensus pattern (14 bp):
CATAGGTATTTTAA
Found at i:319660 original size:229 final size:234
Alignment explanation
Indices: 319343--319923 Score: 659
Period size: 238 Copynumber: 2.5 Consensus size: 234
319333 ACTAAAAAGC
* *
319343 AATTTTATTTCAAAAAAAAAAAGTTAGCTCAAGAGGTTTATTAGAAC-TGCATTATATATTTTAA
1 AATTTTATTTC--AAAAAAAAAGTT---T-AAGAGATTTATTTGAACTTG-ATTATATATTTTAA
*
319407 AAATTATATAAAATATACATAATATTAGTATTTGATAATTAGT-GATGAAAA-TTTTTT-A-CAA
59 AAATTATATAAAATATATATAATATTAGTATTTGATAATTAGTAG-T-AAAATTTTTTTAATCAA
* *
319468 ACAG-A-TTAAATTAATGTGCTATGTATTTTA-TTTTTA-T-TTTTAATTAATTTTTTATTAAAT
122 A-AGAATTTAAATTAATGTACCATGTATTTTATTTTTTATTATTTTAATTAATTTTTTATTAAAT
* *
319528 TTAAACA-CTAAACTGTCATAAATGATGCTATAAAGATTTAATGGAAAAT
186 TTAAACACCT-AACTATCATAAATGATGCTATAAAGATTTAATAGAAAAT
* *
319577 AATTTTATTTCAAAAAAAAATGTTTAAGAGATTGATTTGAACTTGATTATATATTTTAAGAATTA
1 AATTTTATTTCAAAAAAAAA-GTTTAAGAGATTTATTTGAACTTGATTATATATTTTAAAAATTA
*
319642 TATAAAATATATATAATATTAGTATTTAATAATTAGTAGTAAAATTTTTTTAATTTCAAAAGTAA
65 TATAAAATATATATAATATTAGTATTTGATAATTAGTAGTAAAATTTTTTTAA--TCAAAAG-AA
*
319707 TTTAAATTAATTTACCATGTATTTTATTTTTTATTTTTAATTTTAATTAATTTTTTATTAAATTT
127 TTTAAATTAATGTACCATGTATTTTATTTTTTA---TT-ATTTTAATTAATTTTTTATTAAATTT
* * * * * *
319772 AAACACCTGATTATCATCAATGATGTTGTAAATATTTAATAGAAAAT
188 AAACACCTAACTATCATAAATGATGCTATAAAGATTTAATAGAAAAT
* * *
319819 AAATTTATTT---AAAAAAAGTTTAAAAGATTTATTTGAACTTAATTATATATTTTAAAAATTAT
1 AATTTTATTTCAAAAAAAAAGTTTAAGAGATTTATTTGAACTTGATTATATATTTTAAAAATTAT
* * * * * *
319881 ATAAAATGTGTATAATATTAATATTTGGTAATTAATAATAAAA
66 ATAAAATATATATAATATTAGTATTTGATAATTAGTAGTAAAA
319924 AATTAAATTA
Statistics
Matches: 299, Mismatches: 29, Indels: 34
0.83 0.08 0.09
Matches are distributed among these distances:
228 4 0.01
229 75 0.25
230 5 0.02
232 11 0.04
233 7 0.02
234 12 0.04
235 22 0.07
236 6 0.02
238 77 0.26
239 7 0.02
240 1 0.00
242 70 0.23
243 2 0.01
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.44
Consensus pattern (234 bp):
AATTTTATTTCAAAAAAAAAGTTTAAGAGATTTATTTGAACTTGATTATATATTTTAAAAATTAT
ATAAAATATATATAATATTAGTATTTGATAATTAGTAGTAAAATTTTTTTAATCAAAAGAATTTA
AATTAATGTACCATGTATTTTATTTTTTATTATTTTAATTAATTTTTTATTAAATTTAAACACCT
AACTATCATAAATGATGCTATAAAGATTTAATAGAAAAT
Found at i:325258 original size:2 final size:2
Alignment explanation
Indices: 325251--325282 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
325241 AGCTGGCAAC
325251 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
325283 TGGCTCAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:327091 original size:22 final size:22
Alignment explanation
Indices: 327063--327130 Score: 118
Period size: 22 Copynumber: 3.1 Consensus size: 22
327053 AGCTTGGTTG
327063 ATAACTAATATGTTAAGCTGAT
1 ATAACTAATATGTTAAGCTGAT
*
327085 ATAACTAATATATTAAGCTGAT
1 ATAACTAATATGTTAAGCTGAT
*
327107 ATAACTAATATGTTATGCTGAT
1 ATAACTAATATGTTAAGCTGAT
327129 AT
1 AT
327131 GTTCTTGTGT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (22 bp):
ATAACTAATATGTTAAGCTGAT
Found at i:335747 original size:15 final size:15
Alignment explanation
Indices: 335727--335756 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
335717 ATCCCTTGCT
335727 AGGTGGTATACTGCC
1 AGGTGGTATACTGCC
*
335742 AGGTGGTATCCTGCC
1 AGGTGGTATACTGCC
335757 TAGGCTAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.23, G:0.33, T:0.27
Consensus pattern (15 bp):
AGGTGGTATACTGCC
Found at i:336032 original size:9 final size:9
Alignment explanation
Indices: 336020--336064 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
336010 ACATGACATG
336020 ACACGATTA
1 ACACGATTA
336029 ACACGATTA
1 ACACGATTA
*
336038 ACACAATTA
1 ACACGATTA
336047 ACACAGA-TA
1 ACAC-GATTA
*
336056 ACATGATTA
1 ACACGATTA
336065 GGACACGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
8 2 0.06
9 28 0.90
10 1 0.03
ACGTcount: A:0.49, C:0.20, G:0.09, T:0.22
Consensus pattern (9 bp):
ACACGATTA
Found at i:339362 original size:27 final size:29
Alignment explanation
Indices: 339332--339386 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 29
339322 AGTAATTTAA
339332 TTAAA-AAAATTAAATA-TTAA-AAAAATG
1 TTAAACAAAA-TAAATATTTAATAAAAATG
*
339359 TTAAACATAATAAATATTTAATAAAAAT
1 TTAAACAAAATAAATATTTAATAAAAAT
339387 AGACATTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 11 0.46
28 7 0.29
29 6 0.25
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (29 bp):
TTAAACAAAATAAATATTTAATAAAAATG
Found at i:340627 original size:13 final size:13
Alignment explanation
Indices: 340609--340633 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
340599 TACTTATTTG
340609 ATTTTTAAAATTA
1 ATTTTTAAAATTA
340622 ATTTTTAAAATT
1 ATTTTTAAAATT
340634 TTTTATATTT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTTTTAAAATTA
Found at i:345376 original size:70 final size:70
Alignment explanation
Indices: 345219--345497 Score: 236
Period size: 70 Copynumber: 4.0 Consensus size: 70
345209 AGTTGTCCAG
* * * * ** * * * * * * *
345219 TCATCTCCATGTCAGCCAACTAGAATTTGCCACGTATCATCATTGCTATGTCATCACCCAATCAG
1 TCATCGCCATGTCAGCCAACCAAAATCTATCACGTGTCATCACTGCCACGTCATCACCTAGTCAA
*
345284 CATAG
66 CATAA
* ** * * * * *
345289 TCATCACCACATCAGCCAACCATAA-CCAGTCGCGTGTCATCGCTGCCACATCATCACCTAGTCA
1 TCATCGCCATGTCAGCCAACCAAAATCTA-TCACGTGTCATCACTGCCACGTCATCACCTAGTCA
345353 ACATAA
65 ACATAA
* * ** ** *
345359 TCATCGCCATGTTAGCCAACCAAAATCTATCACGTGCCATCTTTGCCACGTCATCACAAAGTCAG
1 TCATCGCCATGTCAGCCAACCAAAATCTATCACGTGTCATCACTGCCACGTCATCACCTAGTCAA
*
345424 CATAG
66 CATAA
* * * *
345429 TCATTGCCATGTCAGCCAACCAAAATCTACCACGTGTCATCACAGCCACGTCATCGCCTAGTCAA
1 TCATCGCCATGTCAGCCAACCAAAATCTATCACGTGTCATCACTGCCACGTCATCACCTAGTCAA
345494 CATA
66 CATA
345498 TTTTTCTTTA
Statistics
Matches: 161, Mismatches: 46, Indels: 4
0.76 0.22 0.02
Matches are distributed among these distances:
70 159 0.99
71 2 0.01
ACGTcount: A:0.30, C:0.33, G:0.13, T:0.24
Consensus pattern (70 bp):
TCATCGCCATGTCAGCCAACCAAAATCTATCACGTGTCATCACTGCCACGTCATCACCTAGTCAA
CATAA
Found at i:345617 original size:56 final size:57
Alignment explanation
Indices: 345557--345683 Score: 134
Period size: 56 Copynumber: 2.2 Consensus size: 57
345547 ACCCTTACAG
* *
345557 TTTTTAAAATTTTAAATTAACCCTTA-ACTT-CAAAAATTTCATACT-AACCCTAATAT
1 TTTTTAAAATTTCAAATTAACCCTTATACTTCCAAAAATTACA-ACTAAACCCTAA-AT
* * * * * * *
345613 TTTTTCAAATTACATATTAACTCTTATACTTCCTAAAATTACACCTAAACCTTAAAT
1 TTTTTAAAATTTCAAATTAACCCTTATACTTCCAAAAATTACAACTAAACCCTAAAT
345670 TTTTTAAAATTTCA
1 TTTTTAAAATTTCA
345684 TTTTGACTCC
Statistics
Matches: 57, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
56 21 0.37
57 20 0.35
58 16 0.28
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.43
Consensus pattern (57 bp):
TTTTTAAAATTTCAAATTAACCCTTATACTTCCAAAAATTACAACTAAACCCTAAAT
Done.