Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008716.1 Hibiscus syriacus cultivar Beakdansim tig00111769_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5677467
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 24
Found at i:1731341 original size:20 final size:21
Alignment explanation
Indices: 1731316--1731367 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1731306 TTTTCCCAAT
*
1731316 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1731336 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1731357 TCGCAATGCGA
1 TCGCAATGCGA
1731368 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1731490 original size:20 final size:20
Alignment explanation
Indices: 1731356--1731489 Score: 153
Period size: 20 Copynumber: 6.7 Consensus size: 20
1731346 AATTGGGAAA
1731356 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
1731376 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
1731396 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
1731416 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
1731437 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
1731457 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* *
1731477 TTCGCAACGCGAT
1 ATCGCAATGCGAT
1731490 TTACATAGCG
Statistics
Matches: 101, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
19 2 0.02
20 84 0.83
21 13 0.13
22 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1732116 original size:33 final size:33
Alignment explanation
Indices: 1732074--1732161 Score: 158
Period size: 33 Copynumber: 2.6 Consensus size: 33
1732064 ATTGCAATTT
1732074 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
1732107 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1732140 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
1732162 ATTATCTCGT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 38 0.72
34 15 0.28
ACGTcount: A:0.11, C:0.27, G:0.23, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:1732163 original size:20 final size:20
Alignment explanation
Indices: 1732129--1732186 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1732119 GCGATTCTCT
**
1732129 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
1732149 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
1732169 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
1732187 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:1734012 original size:83 final size:83
Alignment explanation
Indices: 1733873--1734030 Score: 271
Period size: 83 Copynumber: 1.9 Consensus size: 83
1733863 TAGATTGCTT
* * * *
1733873 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTGTTCTTTATCACTGTGAAGTTAGT
1 AGTAAATTTATTCGATTCCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1733938 ATTTGTCTTTTGGTTGAA
66 ATTTGTCTTTTGGTTGAA
*
1733956 AGTAAATTTGTTCGATTCCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGATTCCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1734021 ATTTGTCTTT
66 ATTTGTCTTT
1734031 GTTTTATCTT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 70 1.00
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.44
Consensus pattern (83 bp):
AGTAAATTTATTCGATTCCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTTGGTTGAA
Found at i:1734479 original size:21 final size:21
Alignment explanation
Indices: 1734423--1734480 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 21
1734413 GAGAGTCTCA
1734423 TCCCACCATTCAAGAGGCTAC
1 TCCCACCATTCAAGAGGCTAC
** * * * * *
1734444 TGTCATCGTTGAAGAGGTTCC
1 TCCCACCATTCAAGAGGCTAC
1734465 TCCCACCATTCAAGAG
1 TCCCACCATTCAAGAG
1734481 CCCGATTCAC
Statistics
Matches: 25, Mismatches: 12, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (21 bp):
TCCCACCATTCAAGAGGCTAC
Found at i:1735230 original size:10 final size:10
Alignment explanation
Indices: 1735215--1735241 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1735205 TAATAAATAG
1735215 ACGAACATAA
1 ACGAACATAA
1735225 ACGAACATAA
1 ACGAACATAA
1735235 ACGAACA
1 ACGAACA
1735242 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.59, C:0.22, G:0.11, T:0.07
Consensus pattern (10 bp):
ACGAACATAA
Found at i:1735322 original size:10 final size:10
Alignment explanation
Indices: 1735307--1735381 Score: 70
Period size: 10 Copynumber: 7.7 Consensus size: 10
1735297 CATTTAATAA
1735307 ATAAACGAAC
1 ATAAACGAAC
1735317 ATAAACGAAC
1 ATAAACGAAC
1735327 ----ACGAAC
1 ATAAACGAAC
1735333 ATAAACGAAC
1 ATAAACGAAC
* *
1735343 ACAAAC-ATAA
1 ATAAACGA-AC
1735353 ATGAACACGAAC
1 AT-AA-ACGAAC
1735365 ATAAACGAAC
1 ATAAACGAAC
1735375 ATAAACG
1 ATAAACG
1735382 TTGGAGACCC
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
6 6 0.11
9 1 0.02
10 36 0.68
11 4 0.08
12 5 0.09
13 1 0.02
ACGTcount: A:0.59, C:0.21, G:0.11, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1735332 original size:16 final size:16
Alignment explanation
Indices: 1735311--1735375 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
1735301 TAATAAATAA
1735311 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1735327 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
1735343 ACAAACATAAATGAAC
1 ACGAACATAAACGAAC
1735359 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1735375 A
1 A
1735376 TAAACGTTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.58, C:0.23, G:0.11, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1736149 original size:24 final size:24
Alignment explanation
Indices: 1736109--1736183 Score: 93
Period size: 24 Copynumber: 3.1 Consensus size: 24
1736099 GATTGGGTTA
*
1736109 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
1736133 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
1736157 AACATAA-CTGAACGAACA-AAACCG
1 AACATAATC-GAACGAACATAAA-CG
1736181 AAC
1 AAC
1736184 GTTCACGAAC
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
23 7 0.15
24 40 0.85
ACGTcount: A:0.56, C:0.20, G:0.12, T:0.12
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:1736170 original size:14 final size:13
Alignment explanation
Indices: 1736109--1736174 Score: 54
Period size: 14 Copynumber: 5.3 Consensus size: 13
1736099 GATTGGGTTA
*
1736109 AACATAAATGAATG
1 AACAT-AATGAACG
1736123 AACAT-A--AACG
1 AACATAATGAACG
1736133 AACATAATCGAACG
1 AACATAAT-GAACG
1736147 AACAT-A--AACG
1 AACATAATGAACG
1736157 AACATAACTGAACG
1 AACATAA-TGAACG
1736171 AACA
1 AACA
1736175 AAACCGAACG
Statistics
Matches: 43, Mismatches: 1, Indels: 16
0.72 0.02 0.27
Matches are distributed among these distances:
10 17 0.40
11 2 0.05
12 1 0.02
13 1 0.02
14 22 0.51
ACGTcount: A:0.56, C:0.18, G:0.12, T:0.14
Consensus pattern (13 bp):
AACATAATGAACG
Found at i:1736193 original size:24 final size:23
Alignment explanation
Indices: 1736122--1736207 Score: 95
Period size: 24 Copynumber: 3.6 Consensus size: 23
1736112 ATAAATGAAT
1736122 GAACATAAACGAACATAATCGAAC
1 GAACATAAACGAACATAA-CGAAC
1736146 GAACATAAACGAACATAACTGAAC
1 GAACATAAACGAACATAAC-GAAC
* *
1736170 GAACA-AAACCGAACGTTCACGAAC
1 GAACATAAA-CGAAC-ATAACGAAC
1736194 GTAA-ATAAACGAAC
1 G-AACATAAACGAAC
1736208 GAGACCTATG
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
23 4 0.07
24 43 0.78
25 8 0.15
ACGTcount: A:0.52, C:0.22, G:0.14, T:0.12
Consensus pattern (23 bp):
GAACATAAACGAACATAACGAAC
Found at i:1737230 original size:33 final size:33
Alignment explanation
Indices: 1737185--1737274 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
1737175 AAAAAGTACT
1737185 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1737218 ATCGCAACGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1737251 ATCGCAATGCGAAATTAAATTCGC
1 ATCGCAATGCGAAATGAAAATCGC
1737275 GTTACGATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1737244 original size:19 final size:19
Alignment explanation
Indices: 1737185--1737245 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
1737175 AAAAAGTACT
*
1737185 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1737204 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
1737218 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1737237 ATCGCAACG
1 ATCGCAACG
1737246 AGTGAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1737301 original size:19 final size:19
Alignment explanation
Indices: 1737279--1737400 Score: 76
Period size: 19 Copynumber: 7.2 Consensus size: 19
1737269 ATTCGCGTTA
1737279 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTG
**
1737298 CGA--TTC-CCTCG--TTG
1 CGATTTTCATTTCGCATTG
1737312 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTG
* * *
1737331 CGA-----AATTAGCGTTG
1 CGATTTTCATTTCGCATTG
*
1737345 CGATTTTCATTTTGCATTG
1 CGATTTTCATTTCGCATTG
*
1737364 CGA--TTC-TCTCG--TTG
1 CGATTTTCATTTCGCATTG
1737378 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTG
1737397 CGAT
1 CGAT
1737401 AGTAATTTCC
Statistics
Matches: 75, Mismatches: 13, Indels: 30
0.64 0.11 0.25
Matches are distributed among these distances:
14 23 0.31
16 12 0.16
17 13 0.17
19 27 0.36
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (19 bp):
CGATTTTCATTTCGCATTG
Found at i:1737321 original size:33 final size:32
Alignment explanation
Indices: 1737274--1737400 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
1737264 ATTAAATTCG
*
1737274 CGTTACGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
1737307 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
1737340 CGTTGCGATTTTCATTTTGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
1737373 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1737401 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1737354 original size:66 final size:66
Alignment explanation
Indices: 1737267--1737399 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
1737257 ATGCGAAATT
*
1737267 AAATTCGCGTTACGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTACGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1737332 G
66 G
* * *
1737333 AAATTAGCGTTGCGATTTTCATTTTGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTACGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1737398 G
66 G
1737399 A
1 A
1737400 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTACGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:1739708 original size:12 final size:12
Alignment explanation
Indices: 1739691--1739715 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1739681 TCTTCGGGGA
1739691 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1739703 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1739715 C
1 C
1739716 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1739924 original size:24 final size:24
Alignment explanation
Indices: 1739890--1739943 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1739880 CTGAAACATC
* *
1739890 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
1739914 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
1739938 ATCAAA
1 ATCAAA
1739944 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:1741026 original size:20 final size:20
Alignment explanation
Indices: 1741001--1741058 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
1740991 ATTCATTTGA
1741001 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1741021 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
1741041 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
1741059 CGCAATGCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1741118 original size:19 final size:19
Alignment explanation
Indices: 1741077--1741144 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
1741067 AAAATGAAAA
1741077 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
*
1741093 TCG--TTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
1741110 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1741129 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
1741145 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.22
16 3 0.07
17 3 0.07
19 29 0.64
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1741286 original size:14 final size:14
Alignment explanation
Indices: 1741267--1741303 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1741257 CATCAATTAA
1741267 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1741281 ACAAATCATCTTTT
1 ACAAATCAACATTT
1741295 ACAAATCAA
1 ACAAATCAA
1741304 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1743192 original size:20 final size:19
Alignment explanation
Indices: 1743169--1743236 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
1743159 GAAACTTAAA
1743169 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
1743189 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
1743209 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
1743228 ATCGCAACG
1 ATCGCAACG
1743237 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.34
20 26 0.63
21 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1743244 original size:14 final size:14
Alignment explanation
Indices: 1743225--1743282 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1743215 ATGCGAAATG
1743225 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
1743239 AAAATCGCAATGCAAA
1 AAAATCGCAA--CGAC
1743255 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1743271 AAAATCGCAACG
1 AAAATCGCAACG
1743283 TGAAACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 21 0.58
16 6 0.17
18 9 0.25
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1743267 original size:32 final size:33
Alignment explanation
Indices: 1743209--1743280 Score: 128
Period size: 32 Copynumber: 2.2 Consensus size: 33
1743199 GGAAATGGCT
*
1743209 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCAAAATGAAAATCGCAACGACAAA
1743242 ATCGCAATGCAAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCAAAATGAAAATCGCAACGACAAA
1743274 ATCGCAA
1 ATCGCAA
1743281 CGTGAAACAC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 23 0.61
33 15 0.39
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCAAAATGAAAATCGCAACGACAAA
Found at i:1743335 original size:14 final size:14
Alignment explanation
Indices: 1743316--1743373 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1743306 TTTCATTTCG
1743316 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1743330 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1743346 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1743362 CGTTGCGATTTT
1 CGTTGCGATTTT
1743374 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1743380 original size:33 final size:33
Alignment explanation
Indices: 1743299--1743389 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
1743289 ACAAATCGCA
*
1743299 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1743332 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1743364 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1743390 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1743930 original size:18 final size:18
Alignment explanation
Indices: 1743904--1743948 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1743894 GTCGATCAGA
*
1743904 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1743922 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1743940 TGATGGCTC
1 TGATGGCTC
1743949 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1745293 original size:20 final size:20
Alignment explanation
Indices: 1745268--1745305 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1745258 AATAGTTTCT
1745268 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
1745288 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
1745306 GCGAGTTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1745619 original size:22 final size:22
Alignment explanation
Indices: 1745589--1745632 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1745579 GATGGAGATA
*
1745589 GACGGATTTCGCCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
*
1745611 GACGAATTTCGTCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
1745633 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGAATTTCGCCGGAGATGGG
Found at i:1745846 original size:20 final size:20
Alignment explanation
Indices: 1745821--1745872 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1745811 ATTATGTATT
1745821 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
*
1745841 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
*
1745861 ATCTCGTTGCGA
1 ATCGCGTTGCGA
1745873 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:1745906 original size:20 final size:19
Alignment explanation
Indices: 1745800--1745914 Score: 77
Period size: 20 Copynumber: 5.7 Consensus size: 19
1745790 CGCTTTGAAA
*
1745800 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGA-TA-GTAGT
* * *
1745821 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGT-AGT
* *
1745841 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGT-AGT
* * * *
1745861 ATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGA--TAGTAGT
1745882 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGT-AGT
1745902 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1745915 TTTCCCAATT
Statistics
Matches: 77, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
19 5 0.06
20 47 0.61
21 23 0.30
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (19 bp):
ATCGCATTGCGATAGTAGT
Found at i:1745933 original size:41 final size:41
Alignment explanation
Indices: 1745841--1745935 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 41
1745831 GAAAGTCAGA
* * * * ** *
1745841 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
*
1745882 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAAT
1745924 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
1745936 TTACTTATTC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 42 0.95
42 2 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
Found at i:1747473 original size:4 final size:4
Alignment explanation
Indices: 1747464--1747516 Score: 71
Period size: 4 Copynumber: 14.5 Consensus size: 4
1747454 TGGTTCAAGA
1747464 AAAG AAAG AAAG AAAG -AAG AAAG -AAG AAAG -AAG AAAG -AAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
1747508 -AAG AAAG AA
1 AAAG AAAG AA
1747517 GGTTTCTGGT
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
3 15 0.34
4 29 0.66
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:1747485 original size:7 final size:7
Alignment explanation
Indices: 1747465--1747517 Score: 97
Period size: 7 Copynumber: 7.4 Consensus size: 7
1747455 GGTTCAAGAA
1747465 AAGAAAG
1 AAGAAAG
1747472 AAAGAAAG
1 -AAGAAAG
1747480 AAGAAAG
1 AAGAAAG
1747487 AAGAAAG
1 AAGAAAG
1747494 AAGAAAG
1 AAGAAAG
1747501 AAGAAAG
1 AAGAAAG
1747508 AAGAAAG
1 AAGAAAG
1747515 AAG
1 AAG
1747518 GTTTCTGGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
7 38 0.84
8 7 0.16
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (7 bp):
AAGAAAG
Found at i:1748765 original size:24 final size:24
Alignment explanation
Indices: 1748719--1748765 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1748709 TTTTATAAAT
* *
1748719 ATAATTTTTTAATTAAAAGTTTTA
1 ATAATTTTTTAATAAAAAATTTTA
1748743 ATAATTTTTTAA-AAAAATATTTT
1 ATAATTTTTTAATAAAAA-ATTTT
1748766 TTTAATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
ATAATTTTTTAATAAAAAATTTTA
Found at i:1750948 original size:107 final size:107
Alignment explanation
Indices: 1750752--1750949 Score: 317
Period size: 107 Copynumber: 1.9 Consensus size: 107
1750742 TATATATATA
* * *
1750752 TATATATATAAAAGTGACGGAATTTGGTGATAGAGTTTGGGGACTTTGTTTAAATCTTTAAAAAG
1 TATATATATAAAAGTGACGGAACTTGATGATAGAGTTTGGGGACATTGTTTAAATCTTTAAAAAG
* * **
1750817 TTTAGATGTTTATATTAATTTTTTTTTAAATTGAGTTAAATT
66 TTTAGAAGTTTAGATTAAAATTTTTTTAAATTGAGTTAAATT
1750859 TATATATATAAAAGT-AGCGGAACTTGATGATAGAGTTTGGGGACATTGTTTAAATCTTTAAAAA
1 TATATATATAAAAGTGA-CGGAACTTGATGATAGAGTTTGGGGACATTGTTTAAATCTTTAAAAA
1750923 GTTTAGAAGTTTAGATTAAAATTTTTT
65 GTTTAGAAGTTTAGATTAAAATTTTTT
1750950 AAAAATTTTG
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
106 1 0.01
107 82 0.99
ACGTcount: A:0.35, C:0.04, G:0.18, T:0.43
Consensus pattern (107 bp):
TATATATATAAAAGTGACGGAACTTGATGATAGAGTTTGGGGACATTGTTTAAATCTTTAAAAAG
TTTAGAAGTTTAGATTAAAATTTTTTTAAATTGAGTTAAATT
Found at i:1761674 original size:16 final size:16
Alignment explanation
Indices: 1761655--1761687 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1761645 CCGAGAGGAC
1761655 TTGAAATGGTGAGGGG
1 TTGAAATGGTGAGGGG
1761671 TTGAAATGGTGAGGGG
1 TTGAAATGGTGAGGGG
1761687 T
1 T
1761688 AGCAAGACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.48, T:0.27
Consensus pattern (16 bp):
TTGAAATGGTGAGGGG
Found at i:1764002 original size:2 final size:2
Alignment explanation
Indices: 1763966--1763990 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1763956 TTATGTATTC
1763966 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1763991 TTAAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1765774 original size:17 final size:17
Alignment explanation
Indices: 1765752--1765785 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1765742 AGTTTCTATC
1765752 TTTTTTTT-AATAAATA
1 TTTTTTTTAAATAAATA
1765768 TTTTTTTTAAATAAATA
1 TTTTTTTTAAATAAATA
1765785 T
1 T
1765786 ATAAATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTTTTTAAATAAATA
Found at i:1767778 original size:57 final size:60
Alignment explanation
Indices: 1767658--1767779 Score: 160
Period size: 60 Copynumber: 2.1 Consensus size: 60
1767648 TAAAATATAC
* * * *
1767658 AAATGATCCCTTAATTATAGAATGTTATTTTGTTGAGTCTCTCAATTTTTAAAAGTTACA
1 AAATGATCCCTTAATTATAGAATATTATTCTGTTGAGTCTCTCAACTATTAAAAGTTACA
* * *
1767718 AAATGATCCCTTGATTATAGGATATT-TTCT-TTGAGTCTC-CAACTATTAGAAGTTACA
1 AAATGATCCCTTAATTATAGAATATTATTCTGTTGAGTCTCTCAACTATTAAAAGTTACA
1767775 AAATG
1 AAATG
1767780 GTCACTCGAC
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
57 20 0.36
58 9 0.16
59 3 0.05
60 23 0.42
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (60 bp):
AAATGATCCCTTAATTATAGAATATTATTCTGTTGAGTCTCTCAACTATTAAAAGTTACA
Found at i:1774858 original size:16 final size:15
Alignment explanation
Indices: 1774832--1774867 Score: 63
Period size: 16 Copynumber: 2.3 Consensus size: 15
1774822 AAGTTCAAAT
1774832 GAAAAATGATAAACA
1 GAAAAATGATAAACA
1774847 GAAAAGATGATAAACA
1 GAAAA-ATGATAAACA
1774863 GAAAA
1 GAAAA
1774868 TAGAAGATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.67, C:0.06, G:0.17, T:0.11
Consensus pattern (15 bp):
GAAAAATGATAAACA
Found at i:1780548 original size:2 final size:2
Alignment explanation
Indices: 1780543--1780585 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
1780533 ATTAATCTAG
1780543 AT AT AT CAT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1780585 A
1 A
1780586 AAAGTAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1780569 original size:21 final size:21
Alignment explanation
Indices: 1780543--1780585 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1780533 ATTAATCTAG
*
1780543 ATATATCATATATATATATAT
1 ATATATAATATATATATATAT
1780564 ATATATAATATATATATATAT
1 ATATATAATATATATATATAT
1780585 A
1 A
1780586 AAAGTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATATAATATATATATATAT
Found at i:1784380 original size:32 final size:32
Alignment explanation
Indices: 1784318--1784382 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
1784308 GTGACCAAAA
* * *
1784318 TTTAAAAAATTATAGTTTAGACCTTTAAATTT
1 TTTAAAAAATTATAGTTTACACCCTAAAATTT
*
1784350 TTTAAAAATATT-TAGTTTACCCCCTAAAATTT
1 TTTAAAAA-ATTATAGTTTACACCCTAAAATTT
1784382 T
1 T
1784383 AGAAATTTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 25 0.89
33 3 0.11
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (32 bp):
TTTAAAAAATTATAGTTTACACCCTAAAATTT
Found at i:1786395 original size:156 final size:156
Alignment explanation
Indices: 1786201--1786573 Score: 484
Period size: 156 Copynumber: 2.4 Consensus size: 156
1786191 TGATTTAGTC
* *
1786201 TCAT-ATTTCATTATTCTTTCAATTCA-TCTTTTATTTTAAGTCCGTTTTTATCAAATTTGAACC
1 TCATAATTTCCTTATT-TTTCAATTCATTC-TTTATTTTAAGTCCGTTTTTAACAAATTTGAACC
* *
1786264 ACATACTCCTAAACCATTGTAGAATATGTATGTACTTTCAATTCCTCTTTTTTATAACAAATTT-
64 ACATACTCCAAAACCATTGTAGAATATCTATGTACTTTCAATTCCTCTTTTTTATAA-AAATTTA
* * *
1786328 TCTATTTTTTAATTTAGTCTCTCAATTTT
128 TCTATTTTTCAATTTAATCCCTCAATTTT
* * ** *
1786357 TTATAATTT-CTTTTTTTTCAAATTCATTCTTTATTTTAAGTCTATTTTTAACAATTTTGAACCA
1 TCATAATTTCCTTATTTTTC-AATTCATTCTTTATTTTAAGTCCGTTTTTAACAAATTTGAACCA
* * *** *
1786421 CATGCTCCAAAACCATTTTAGAATATCTATGTACTTTCAATTCCTCTTTTTTATAATTTTTTATT
65 CATACTCCAAAACCATTGTAGAATATCTATGTACTTTCAATTCCTCTTTTTTATAAAAATTTATC
1786486 TATTTTTCAATTTAATCCCTCAATTTT
130 TATTTTTCAATTTAATCCCTCAATTTT
* * *
1786513 TCATAATTTCCTTATTTCTCCAATTCATCCTTTATTTTAAGTCCGTTTTTACCAAATTTGA
1 TCATAATTTCCTTATTT-TTCAATTCATTCTTTATTTTAAGTCCGTTTTTAACAAATTTGA
1786574 GCTACATGCT
Statistics
Matches: 185, Mismatches: 26, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
155 7 0.04
156 129 0.70
157 47 0.25
158 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.04, T:0.51
Consensus pattern (156 bp):
TCATAATTTCCTTATTTTTCAATTCATTCTTTATTTTAAGTCCGTTTTTAACAAATTTGAACCAC
ATACTCCAAAACCATTGTAGAATATCTATGTACTTTCAATTCCTCTTTTTTATAAAAATTTATCT
ATTTTTCAATTTAATCCCTCAATTTT
Found at i:1786617 original size:157 final size:156
Alignment explanation
Indices: 1786220--1786619 Score: 473
Period size: 156 Copynumber: 2.6 Consensus size: 156
1786210 ATTATTCTTT
* * * * *
1786220 CAATTCATCTTTTATTTTAAGTCCGTTTTTATCAAATTTGAACCACATACTCCTAAACCATTGTA
1 CAATTCATCCTTTATTTTAAGTCCGTTTTTAACAAATTTGAACCACATGCTCATAAACCATTATA
* * * *
1786285 GAATATGTATGTACTTTCAATTCCTCTTTTTTATAACAAATTTTCTATTTTTTAATTTAGTCTCT
66 GAATATCTATGTACTTTCAATTCCTCTTTTTTATAACAAATTTTCTATTTTTCAATTTAATCCCT
* * *
1786350 CAATTTTTTATAATTTCTTTTTTTTC
131 CAATTTTTCATAATTTCTTATTTCTC
* * ** * *
1786376 AAATTCATTCTTTATTTTAAGTCTATTTTTAACAATTTTGAACCACATGCTCCA-AAACCATTTT
1 CAATTCATCCTTTATTTTAAGTCCGTTTTTAACAAATTTGAACCACATGCT-CATAAACCATTAT
*** *
1786440 AGAATATCTATGTACTTTCAATTCCTCTTTTTTATAA-TTTTTTATTTATTTTTCAATTTAATCC
65 AGAATATCTATGTACTTTCAATTCCTCTTTTTTATAACAAATTT-TCTATTTTTCAATTTAATCC
1786504 CTCAATTTTTCATAATTTCCTTATTTCTC
129 CTCAATTTTTCATAATTT-CTTATTTCTC
* * * * * ** *
1786533 CAATTCATCCTTTATTTTAAGTCCGTTTTTACCAAATTTGAGCTACATGCTTATATACCACAATG
1 CAATTCATCCTTTATTTTAAGTCCGTTTTTAACAAATTTGAACCACATGCTCATAAACCATTATA
1786598 GAATATCTATGTAAC-TTCAATT
66 GAATATCTATGT-ACTTTCAATT
1786620 ATTAATTTTT
Statistics
Matches: 204, Mismatches: 35, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
155 3 0.01
156 122 0.60
157 77 0.38
158 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.49
Consensus pattern (156 bp):
CAATTCATCCTTTATTTTAAGTCCGTTTTTAACAAATTTGAACCACATGCTCATAAACCATTATA
GAATATCTATGTACTTTCAATTCCTCTTTTTTATAACAAATTTTCTATTTTTCAATTTAATCCCT
CAATTTTTCATAATTTCTTATTTCTC
Found at i:1788431 original size:26 final size:26
Alignment explanation
Indices: 1788402--1788451 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
1788392 AATATTTAGG
*
1788402 CTGCACAATTTATCCATCAATAAAGT
1 CTGCAAAATTTATCCATCAATAAAGT
*
1788428 CTGCAAAATTTATTCATCAATAAA
1 CTGCAAAATTTATCCATCAATAAA
1788452 ACATTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.42, C:0.20, G:0.06, T:0.32
Consensus pattern (26 bp):
CTGCAAAATTTATCCATCAATAAAGT
Found at i:1788835 original size:23 final size:24
Alignment explanation
Indices: 1788800--1788844 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
1788790 AATTCGCCGA
* *
1788800 GAAATTTATATTT-TAGTCAATTT
1 GAAATTCACATTTGTAGTCAATTT
*
1788823 GAAATTCACATTTGTATTCAAT
1 GAAATTCACATTTGTAGTCAAT
1788845 ATTTATATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.47
Consensus pattern (24 bp):
GAAATTCACATTTGTAGTCAATTT
Found at i:1793914 original size:22 final size:22
Alignment explanation
Indices: 1793867--1793957 Score: 82
Period size: 22 Copynumber: 4.1 Consensus size: 22
1793857 ATCCAAAAAC
**
1793867 AATATTATTTAAAATAAATACTT
1 AATATTATTT-AAATAAATAAAT
*
1793890 AATATTATTTCAATAAATAAAT
1 AATATTATTTAAATAAATAAAT
*
1793912 AATATAATTTTAAA-AAATAAAT
1 AATATTA-TTTAAATAAATAAAT
1793934 AA-A-TATTTAAAATAAA-ATAAT
1 AATATTATTT-AAATAAATA-AAT
1793955 AAT
1 AAT
1793958 TTAATAAAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
19 3 0.05
20 5 0.09
21 9 0.16
22 25 0.44
23 15 0.26
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
AATATTATTTAAATAAATAAAT
Found at i:1793955 original size:17 final size:17
Alignment explanation
Indices: 1793908--1793961 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
1793898 TTCAATAAAT
*
1793908 AAATAATATAAT-TTTA
1 AAATAAAATAATATTTA
*
1793924 AAAAATAAATAAATATTTA
1 AAATA-AAAT-AATATTTA
1793943 AAATAAAATAATAATTTA
1 AAATAAAATAAT-ATTTA
1793961 A
1 A
1793962 TAAAATTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 4 0.13
17 6 0.19
18 13 0.42
19 8 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATAAAATAATATTTA
Found at i:1793960 original size:18 final size:19
Alignment explanation
Indices: 1793904--1793967 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 19
1793894 TTATTTCAAT
1793904 AAATAAATAATATAATTTTAAA
1 AAATAAAT-A-ATAA-TTTAAA
1793926 AAATAAATAA-ATATTTAAA
1 AAATAAATAATA-ATTTAAA
*
1793945 ATA-AAATAATAATTTAATA
1 AAATAAATAATAATTTAA-A
1793964 AAAT
1 AAAT
1793968 TTTATAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
18 12 0.33
19 13 0.36
20 2 0.06
21 1 0.03
22 8 0.22
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AAATAAATAATAATTTAAA
Found at i:1794765 original size:32 final size:31
Alignment explanation
Indices: 1794729--1794796 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 31
1794719 TTTATATTTC
*
1794729 ATAAAAATACAAAATAATTAACACCAATATTA
1 ATAAAAAGACAAAATAATTAACACCAATA-TA
* * **
1794761 ATAAAAAGATAAATTAATTAACATTAATATA
1 ATAAAAAGACAAAATAATTAACACCAATATA
1794792 ATAAA
1 ATAAA
1794797 TTTCTCATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
31 7 0.23
32 24 0.77
ACGTcount: A:0.63, C:0.07, G:0.01, T:0.28
Consensus pattern (31 bp):
ATAAAAAGACAAAATAATTAACACCAATATA
Found at i:1796618 original size:15 final size:15
Alignment explanation
Indices: 1796600--1796638 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
1796590 TAATTGTTAG
1796600 GATCATTTTCAGCCA
1 GATCATTTTCAGCCA
1796615 GATCATTTTCAGCCA
1 GATCATTTTCAGCCA
*
1796630 TATCATTTT
1 GATCATTTT
1796639 GATGTTACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.41
Consensus pattern (15 bp):
GATCATTTTCAGCCA
Found at i:1803274 original size:24 final size:24
Alignment explanation
Indices: 1803244--1803315 Score: 94
Period size: 24 Copynumber: 3.0 Consensus size: 24
1803234 GTAAACAGAG
1803244 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAAAACAGAATTC
* *
1803268 ATATCAGATATCAGAACAGAA-TC
1 ATATCAGAAATCAAAACAGAATTC
*
1803291 AAGATCAG-AATCAAAACAGAATTC
1 -ATATCAGAAATCAAAACAGAATTC
1803315 A
1 A
1803316 GGTAACGTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
23 14 0.34
24 27 0.66
ACGTcount: A:0.53, C:0.17, G:0.11, T:0.19
Consensus pattern (24 bp):
ATATCAGAAATCAAAACAGAATTC
Found at i:1803287 original size:12 final size:11
Alignment explanation
Indices: 1803252--1803312 Score: 50
Period size: 12 Copynumber: 5.3 Consensus size: 11
1803242 AGATATCAGA
*
1803252 AATCAAAACAG
1 AATCAGAACAG
* *
1803263 AATTCATATCAG
1 AA-TCAGAACAG
1803275 ATATCAGAACAG
1 A-ATCAGAACAG
*
1803287 AATCAAGATCAG
1 AATC-AGAACAG
*
1803299 AATCAAAACAG
1 AATCAGAACAG
1803310 AAT
1 AAT
1803313 TCAGGTAACG
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
11 13 0.32
12 26 0.65
13 1 0.03
ACGTcount: A:0.54, C:0.16, G:0.11, T:0.18
Consensus pattern (11 bp):
AATCAGAACAG
Found at i:1805079 original size:23 final size:23
Alignment explanation
Indices: 1805039--1805088 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1805029 AATGGTCAAT
*
1805039 GGGTCGGGTCAACAGGTC-GTGTC
1 GGGTCGGGTAAACAGGTCAG-GTC
**
1805062 GGGTCGGGTAAATGGGTCAGGTC
1 GGGTCGGGTAAACAGGTCAGGTC
1805085 GGGT
1 GGGT
1805089 TATGACCGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.14, C:0.16, G:0.48, T:0.22
Consensus pattern (23 bp):
GGGTCGGGTAAACAGGTCAGGTC
Found at i:1820001 original size:13 final size:13
Alignment explanation
Indices: 1819983--1820007 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1819973 ATGAACTTCT
1819983 TTCCTTGCTCAAA
1 TTCCTTGCTCAAA
1819996 TTCCTTGCTCAA
1 TTCCTTGCTCAA
1820008 GAATAGTTAC
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:0.20, C:0.32, G:0.08, T:0.40
Consensus pattern (13 bp):
TTCCTTGCTCAAA
Found at i:1820762 original size:49 final size:49
Alignment explanation
Indices: 1820706--1820814 Score: 155
Period size: 49 Copynumber: 2.2 Consensus size: 49
1820696 CCTTTATGCT
* * *
1820706 GTTCCATTATGCTCGACATGCTTTTGCCAGTTGTTAGTATTTTAACGCC
1 GTTCCATTATGCTCGACATGCTTTTGCCAGTCGTTAGTATTCTAACGAC
* * * *
1820755 GTTCCATTACGCTCGACATGTTTTTGCCAGTCGTTGGTATTCTAACGAT
1 GTTCCATTATGCTCGACATGCTTTTGCCAGTCGTTAGTATTCTAACGAC
1820804 GTTCCATTATG
1 GTTCCATTATG
1820815 TTTGTTTGGC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.18, C:0.22, G:0.19, T:0.40
Consensus pattern (49 bp):
GTTCCATTATGCTCGACATGCTTTTGCCAGTCGTTAGTATTCTAACGAC
Found at i:1825972 original size:3 final size:3
Alignment explanation
Indices: 1825964--1826029 Score: 89
Period size: 3 Copynumber: 22.3 Consensus size: 3
1825954 ATTTTATTTA
* * *
1825964 TAT TAT TAT TAT TAT TAT TAT TAT TAT AAT TAT AAT TAT AAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1826012 TAT TAT TAA TA- TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
1826030 TAATATTACA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1825972 original size:12 final size:12
Alignment explanation
Indices: 1825957--1826037 Score: 50
Period size: 12 Copynumber: 7.0 Consensus size: 12
1825947 CATTTTCATT
1825957 TTATTTATATTA
1 TTATTTATATTA
1825969 TTA--T-TATTA
1 TTATTTATATTA
1825978 TTA-TTATTATTA
1 TTATTTA-TATTA
*
1825990 -TAATTATAATTA
1 TTATTTAT-ATTA
*
1826002 -TAATTATTATTA
1 TTATTTA-TATTA
*
1826014 TTATTAATA-TA
1 TTATTTATATTA
1826025 TTATTTAATATTA
1 TTATTT-ATATTA
1826038 CAAGCCCAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
9 8 0.14
10 2 0.04
11 10 0.18
12 30 0.53
13 7 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTATTTATATTA
Found at i:1826518 original size:15 final size:15
Alignment explanation
Indices: 1826498--1826539 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
1826488 ACAACTCAGC
1826498 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
1826513 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
*
1826528 AAAGAAGAGAAA
1 AAAGAAAAGAAA
1826540 CTTACTGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:1826523 original size:20 final size:20
Alignment explanation
Indices: 1826498--1826539 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1826488 ACAACTCAGC
*
1826498 AAAGAAACAGAAAAGAA-AGA
1 AAAGAAAAAG-AAAGAAGAGA
1826518 AAAGAAAAAGAAAGAAGAGA
1 AAAGAAAAAGAAAGAAGAGA
1826538 AA
1 AA
1826540 CTTACTGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAGAAAGAAGAGA
Found at i:1827609 original size:109 final size:107
Alignment explanation
Indices: 1827414--1827630 Score: 242
Period size: 109 Copynumber: 2.0 Consensus size: 107
1827404 ATATAATAAA
* * * *
1827414 TAATAATTAATTTTTTTAAATAAATTATTTTAATATTTATTTTTCAATATCGAAGAAAAGGACAG
1 TAATAATTAATTTTTTAAAATAAATTAATTTAATATTTATTTATCAATATCAAAGAAAAGGACAG
* * * * *
1827479 TCTTAATACAACTGGATGTCCTATTCTGGTATTTTAAA-ATT
66 TCTTAAGACAACTAGAAGTCCTATTATGATATTTTAAATATT
*
1827520 TAATAATTAATTTTTTAAAATATTATTTAATTTAA-ATTAATATTTATCAATATCAAAGAAAA-G
1 TAATAATTAATTTTTTAAAATA--AATTAATTTAATATT--TATTTATCAATATCAAAGAAAAGG
* * * *
1827583 AGCTGTCTTAAGGCACCTAGAAGTCCTTTTATGATATTTTAAATATT
62 A-CAGTCTTAAGACAACTAGAAGTCCTATTATGATATTTTAAATATT
1827630 T
1 T
1827631 TTTATAATTT
Statistics
Matches: 91, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
106 21 0.23
107 3 0.03
108 11 0.12
109 52 0.57
110 4 0.04
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.44
Consensus pattern (107 bp):
TAATAATTAATTTTTTAAAATAAATTAATTTAATATTTATTTATCAATATCAAAGAAAAGGACAG
TCTTAAGACAACTAGAAGTCCTATTATGATATTTTAAATATT
Found at i:1839972 original size:16 final size:16
Alignment explanation
Indices: 1839953--1839987 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1839943 GTTTTCAATA
*
1839953 TGACATGTTATGAACC
1 TGACATGTTATCAACC
*
1839969 TGACATGTTTTCAACC
1 TGACATGTTATCAACC
1839985 TGA
1 TGA
1839988 TCTGTAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (16 bp):
TGACATGTTATCAACC
Found at i:1840041 original size:16 final size:16
Alignment explanation
Indices: 1840022--1840064 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
1840012 TGACATGATA
*
1840022 TGATATTTATCTAACT
1 TGATATTTACCTAACT
1840038 TGATATTTACCTAACT
1 TGATATTTACCTAACT
1840054 T-ATATATTACC
1 TGATAT-TTACC
1840065 ATTGATGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.33, C:0.16, G:0.05, T:0.47
Consensus pattern (16 bp):
TGATATTTACCTAACT
Found at i:1842887 original size:6 final size:6
Alignment explanation
Indices: 1842876--1842916 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
1842866 TGCATTCTCG
1842876 CAGGCA CAGGCA CAGGCA CAGGCA CAGGCA CAGGCA CAGGC
1 CAGGCA CAGGCA CAGGCA CAGGCA CAGGCA CAGGCA CAGGC
1842917 TCAACTAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.32, C:0.34, G:0.34, T:0.00
Consensus pattern (6 bp):
CAGGCA
Found at i:1844843 original size:46 final size:47
Alignment explanation
Indices: 1844792--1844899 Score: 130
Period size: 46 Copynumber: 2.3 Consensus size: 47
1844782 CGCCTCCCGG
1844792 AAGTGATGCTCCAGGAAG-CACATGAATCATGT-AAACCACCTGCTGC
1 AAGTGATGCTCCAGGAAGCCA-ATGAATCATGTGAAACCACCTGCTGC
* * * * *
1844838 AAGTGATGTTTCTGGAAGCCAATGAATCATGTGAAGCCACCTGCTGG
1 AAGTGATGCTCCAGGAAGCCAATGAATCATGTGAAACCACCTGCTGC
* *
1844885 AATTGATTCTCCAGG
1 AAGTGATGCTCCAGG
1844900 GAGAACAAGA
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
46 26 0.52
47 24 0.48
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (47 bp):
AAGTGATGCTCCAGGAAGCCAATGAATCATGTGAAACCACCTGCTGC
Found at i:1845679 original size:16 final size:16
Alignment explanation
Indices: 1845658--1845697 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1845648 TGAACGATGT
1845658 ATAGTGAC-GAAAATCG
1 ATAGTGACTG-AAATCG
*
1845674 ATAGTGACTGAAATTG
1 ATAGTGACTGAAATCG
1845690 ATAGTGAC
1 ATAGTGAC
1845698 ATGTGACGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 21 0.95
17 1 0.05
ACGTcount: A:0.40, C:0.10, G:0.25, T:0.25
Consensus pattern (16 bp):
ATAGTGACTGAAATCG
Found at i:1845773 original size:45 final size:44
Alignment explanation
Indices: 1845722--1845808 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 44
1845712 AGGGACAATT
* *
1845722 AACTATGTAAATTTTAGCTAAATTTAAGATCAAATTGATATTTAA
1 AACTATGTAAACTTTAACTAAA-TTAAGATCAAATTGATATTTAA
* * * *
1845767 AACTATGTAAACTTTAATTGAATTAAGTTGAAATTGATATTT
1 AACTATGTAAACTTTAACTAAATTAAGATCAAATTGATATTT
1845809 GAACTTTAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 18 0.50
45 18 0.50
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (44 bp):
AACTATGTAAACTTTAACTAAATTAAGATCAAATTGATATTTAA
Found at i:1845814 original size:34 final size:35
Alignment explanation
Indices: 1845776--1845843 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
1845766 AAACTATGTA
1845776 AACTTTAATT-GAATTAAGTTGAAATTGATATTTG
1 AACTTTAATTGGAATTAAGTTGAAATTGATATTTG
*
1845810 AACTTTAATTGGATTTAAGTTGAAATTGATATTT
1 AACTTTAATTGGAATTAAGTTGAAATTGATATTT
1845844 ATATAAAGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 10 0.31
35 22 0.69
ACGTcount: A:0.37, C:0.03, G:0.15, T:0.46
Consensus pattern (35 bp):
AACTTTAATTGGAATTAAGTTGAAATTGATATTTG
Found at i:1848021 original size:16 final size:15
Alignment explanation
Indices: 1847991--1848026 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
1847981 CCCTATTGTC
1847991 TATATTTTTTATAGA
1 TATATTTTTTATAGA
*
1848006 TATATTTTTATCTAGA
1 TATATTTTT-TATAGA
1848022 TATAT
1 TATAT
1848027 CTTAAATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (15 bp):
TATATTTTTTATAGA
Found at i:1852784 original size:49 final size:49
Alignment explanation
Indices: 1852727--1852825 Score: 148
Period size: 49 Copynumber: 2.0 Consensus size: 49
1852717 AAGATTAAAA
*
1852727 AAATTTAAC-CACAATTTAAGATGTGACAGA-CGATACAAAACTGATTGCT
1 AAATTTAACTC-CAATTTAAGATGTGACAGATC-ATACAAAACTAATTGCT
*
1852776 AAATTTAACTCCAATTTGAGATGTGACAGATCATACAAAACTAATTGCT
1 AAATTTAACTCCAATTTAAGATGTGACAGATCATACAAAACTAATTGCT
1852825 A
1 A
1852826 TGAAAACAGT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
49 44 0.96
50 2 0.04
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.28
Consensus pattern (49 bp):
AAATTTAACTCCAATTTAAGATGTGACAGATCATACAAAACTAATTGCT
Found at i:1853515 original size:21 final size:21
Alignment explanation
Indices: 1853473--1853516 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1853463 AATAATGACT
* * * *
1853473 TTTGTTTCATTTGTTTGTTTG
1 TTTGTTCCATTAGTTAGATTG
1853494 TTTGTTCCATTAGTTAGATTG
1 TTTGTTCCATTAGTTAGATTG
1853515 TT
1 TT
1853517 GTTTGTGGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.11, C:0.07, G:0.18, T:0.64
Consensus pattern (21 bp):
TTTGTTCCATTAGTTAGATTG
Found at i:1854336 original size:28 final size:28
Alignment explanation
Indices: 1854273--1854343 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
1854263 TTTAGACGGC
*
1854273 AGAGTCGACCATATATCAATCATACAAT
1 AGAGTCGACCATATATCAATCAGACAAT
* * * ***
1854301 ATAATCGACCATATATCAATTAGGTGAT
1 AGAGTCGACCATATATCAATCAGACAAT
*
1854329 AGAGTCGATCATATA
1 AGAGTCGACCATATA
1854344 ATAAAACTAA
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (28 bp):
AGAGTCGACCATATATCAATCAGACAAT
Found at i:1855796 original size:31 final size:31
Alignment explanation
Indices: 1855760--1855824 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
1855750 AAAAAATCTT
*
1855760 ATAAATGAGTAAATTATAGTTGTTTAATGTC
1 ATAAATGAATAAATTATAGTTGTTTAATGTC
1855791 ATAAATGAATAAATTATAGTTGTTTAATGTC
1 ATAAATGAATAAATTATAGTTGTTTAATGTC
1855822 ATA
1 ATA
1855825 TATATGTTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.42, C:0.03, G:0.14, T:0.42
Consensus pattern (31 bp):
ATAAATGAATAAATTATAGTTGTTTAATGTC
Found at i:1856008 original size:16 final size:17
Alignment explanation
Indices: 1855987--1856029 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1855977 CATCATCATC
1855987 TAAATATAAAAAGTA-A
1 TAAATATAAAAAGTATA
*
1856003 TAAATATTAAAAATTATA
1 TAAATA-TAAAAAGTATA
*
1856021 AAAATATAA
1 TAAATATAA
1856030 TAATATAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 6 0.26
17 11 0.48
18 6 0.26
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (17 bp):
TAAATATAAAAAGTATA
Found at i:1856028 original size:8 final size:8
Alignment explanation
Indices: 1855988--1856038 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
1855978 ATCATCATCT
1855988 AAATATAA
1 AAATATAA
*
1855996 AAAGTA-AT
1 AAA-TATAA
1856004 AAATATTAA
1 AAATA-TAA
1856013 AAATTATAA
1 AAA-TATAA
1856022 AAATATAA
1 AAATATAA
*
1856030 TAATATAA
1 AAATATAA
1856038 A
1 A
1856039 CTACATAACT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
7 2 0.06
8 19 0.54
9 12 0.34
10 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (8 bp):
AAATATAA
Found at i:1856804 original size:35 final size:36
Alignment explanation
Indices: 1856730--1856805 Score: 91
Period size: 35 Copynumber: 2.1 Consensus size: 36
1856720 TAGATCGACT
*
1856730 TAAAATGTAAAAAAATTAAATTATATAATCCAAACA
1 TAAAATGTAAAAAAATTAAATTATATAATCCAAAAA
* * * **
1856766 TAAAAT-TTAAAAAGTTAAATTATATTATTTAAAAA
1 TAAAATGTAAAAAAATTAAATTATATAATCCAAAAA
1856801 TAAAA
1 TAAAA
1856806 ATATAAAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
35 28 0.82
36 6 0.18
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.33
Consensus pattern (36 bp):
TAAAATGTAAAAAAATTAAATTATATAATCCAAAAA
Found at i:1856832 original size:9 final size:7
Alignment explanation
Indices: 1856797--1856827 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
1856787 ATATTATTTA
1856797 AAAATA-
1 AAAATAT
1856803 AAAATAT
1 AAAATAT
1856810 AAAATAT
1 AAAATAT
1856817 AAAATAT
1 AAAATAT
1856824 AAAA
1 AAAA
1856828 AATATTACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAATAT
Found at i:1859323 original size:37 final size:36
Alignment explanation
Indices: 1859268--1859386 Score: 188
Period size: 35 Copynumber: 3.3 Consensus size: 36
1859258 TCTCATTATC
*
1859268 ATTTTTC-AACAAACATTTACCAAACTTTGAAAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTG-AAAACT
*
1859304 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
1859340 A-TTTTCAAAGAAACATTTACCAAACTTTGAAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
1859375 ATTTTTTCAAAG
1 A-TTTTTCAAAG
1859387 TTGGTTGCCA
Statistics
Matches: 77, Mismatches: 3, Indels: 5
0.91 0.04 0.06
Matches are distributed among these distances:
35 34 0.44
36 13 0.17
37 30 0.39
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.34
Consensus pattern (36 bp):
ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
Found at i:1863972 original size:35 final size:35
Alignment explanation
Indices: 1863884--1863993 Score: 150
Period size: 35 Copynumber: 3.1 Consensus size: 35
1863874 CCATTATCAT
* * *
1863884 TTTTC-AACAAACATCTACCAAACTTTGAAAAACTA
1 TTTTCAAAGAAACATTTACCAAACTTTG-AAAACCA
1863919 TCTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 T-TTTCAAAGAAACATTTACCAAACTTTGAAAACCA
* *
1863955 TTTTCAAAGAAATATTTACTAAACTTTGAAAACCA
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1863990 TTTT
1 TTTT
1863994 AACAATACTT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
35 37 0.54
36 11 0.16
37 20 0.29
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.33
Consensus pattern (35 bp):
TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
Found at i:1870279 original size:21 final size:21
Alignment explanation
Indices: 1870255--1870297 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1870245 TATTTGAATT
*
1870255 AATTAATATATA-CTAAACATA
1 AATTAATAAATATC-AAACATA
*
1870276 AATTTATAAATATCAAACATA
1 AATTAATAAATATCAAACATA
1870297 A
1 A
1870298 TATCAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (21 bp):
AATTAATAAATATCAAACATA
Found at i:1878336 original size:29 final size:29
Alignment explanation
Indices: 1878275--1878340 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
1878265 GGATTTGATG
* **
1878275 TTGAACATGTGAATCCCACATGGTGCTTC
1 TTGAACTTGTGAATCCCACATGGAACTTC
* * *
1878304 TTGAACTTGTGGATCTCACATGGAACTTT
1 TTGAACTTGTGAATCCCACATGGAACTTC
1878333 TTGAACTT
1 TTGAACTT
1878341 ATTATTGTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (29 bp):
TTGAACTTGTGAATCCCACATGGAACTTC
Found at i:1880717 original size:20 final size:20
Alignment explanation
Indices: 1880688--1880726 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1880678 TTTTGAAAAG
*
1880688 TCAACAGTCAAAGTTAACAA
1 TCAACAGTCAAAGTCAACAA
*
1880708 TCAACGGTCAAAGTCAACA
1 TCAACAGTCAAAGTCAACA
1880727 GTCGATGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.23, G:0.13, T:0.18
Consensus pattern (20 bp):
TCAACAGTCAAAGTCAACAA
Found at i:1904828 original size:30 final size:30
Alignment explanation
Indices: 1904792--1904848 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
1904782 TAATGATTAA
*
1904792 TTAAACTTTAGATAAATACCTTTTTGAACT
1 TTAAACTTTAAATAAATACCTTTTTGAACT
*
1904822 TTAAACTTTAAATAAATATCTTTTTGA
1 TTAAACTTTAAATAAATACCTTTTTGA
1904849 CCTTAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.46
Consensus pattern (30 bp):
TTAAACTTTAAATAAATACCTTTTTGAACT
Found at i:1904855 original size:29 final size:30
Alignment explanation
Indices: 1904792--1904855 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
1904782 TAATGATTAA
* *
1904792 TTAAACTTTAGATAAATACCTTTTTGAACT
1 TTAAACTTTAAATAAATACCTTTTTGAACC
*
1904822 TTAAACTTTAAATAAATATCTTTTTG-ACC
1 TTAAACTTTAAATAAATACCTTTTTGAACC
1904851 TTAAA
1 TTAAA
1904856 TTCTTGATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (30 bp):
TTAAACTTTAAATAAATACCTTTTTGAACC
Found at i:1916094 original size:36 final size:35
Alignment explanation
Indices: 1916017--1916114 Score: 124
Period size: 36 Copynumber: 2.8 Consensus size: 35
1916007 TAACACAATA
* *
1916017 TCAATTACATTTTAAACCCCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCAAAAATACT
*
1916052 TCAATTACATTCTAAACCTCAAATTACAAAAATACT
1 TCAATTACATTCTAAACCCCAAATT-CAAAAATACT
* * **
1916088 TTAATTACATGCCCAACCCCAAATTCA
1 TCAATTACATTCTAAACCCCAAATTCA
1916115 TAATACATTC
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
35 25 0.46
36 29 0.54
ACGTcount: A:0.43, C:0.27, G:0.01, T:0.30
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATTCAAAAATACT
Found at i:1916729 original size:147 final size:148
Alignment explanation
Indices: 1916547--1916838 Score: 496
Period size: 147 Copynumber: 2.0 Consensus size: 148
1916537 AAACTATTTA
* *
1916547 AATTAGAATCAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAATAGAAACTCAAA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAATAGAAACTCAAA
1916612 AAATCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCG-AAAAATTTCGAGTAAACT
66 AAATCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTAAACT
1916676 ATTTTATAAACTGAACTG
131 ATTTTATAAACTGAACTG
* **
1916694 AATTATAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAATAGAAACTTGAA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAATAGAAACTCAAA
* * *
1916759 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGATTCAACT
66 AAATCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTAAACT
*
1916824 ATTTTATAAATTGAA
131 ATTTTATAAACTGAA
1916839 TTGAGTATTT
Statistics
Matches: 135, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
147 105 0.78
148 30 0.22
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.37
Consensus pattern (148 bp):
AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAATAGAAACTCAAA
AAATCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTAAACT
ATTTTATAAACTGAACTG
Found at i:1917049 original size:35 final size:35
Alignment explanation
Indices: 1916994--1917089 Score: 122
Period size: 35 Copynumber: 2.7 Consensus size: 35
1916984 AATGAATTAT
* * * * *
1916994 GAATTTGGGGTTGAGTATGTAATTGGAGTATTTTG
1 GAATTTGAGGTTTAGAATGTAATTGAAGCATTTTG
1917029 GAATTTGAGGTTTAGAATGTAATTGAAGCATTTTG
1 GAATTTGAGGTTTAGAATGTAATTGAAGCATTTTG
*
1917064 G-ATTTTAGGGTTTAGAATGTAATTGA
1 GAATTTGA-GGTTTAGAATGTAATTGA
1917090 TGATTGTATT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
34 5 0.09
35 49 0.91
ACGTcount: A:0.28, C:0.01, G:0.29, T:0.42
Consensus pattern (35 bp):
GAATTTGAGGTTTAGAATGTAATTGAAGCATTTTG
Found at i:1925773 original size:68 final size:68
Alignment explanation
Indices: 1925660--1925996 Score: 439
Period size: 68 Copynumber: 5.0 Consensus size: 68
1925650 TAGGGATTGT
* * * * *
1925660 TTTAGGGTAAATTACCTAATTTGGTCATTTATATATTATTTAATTTATGCTTTGGTCACTTGATT
1 TTTAGGGTAAACTACCT-ATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATT
1925725 ATTA
65 ATTA
* *
1925729 TTTAGGGTAAACTACCTATTTAGTCACTTATATATTATCTAATTTATGTTTTGGTTACTCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
*
1925794 TCA
66 TTA
1925797 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
1925862 TTA
66 TTA
* * * * * ** * **
1925865 TTTATGGTAAACTACGTATTTTGTTACTTATATATTATCTAATATAAT-TCAT-AT-A-TATATT
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAAT-TTATGTTTTGGTCACTCGATT
*
1925926 TTTA
65 ATTA
* *
1925930 TTTAGGGTAAACTACCTATTTGTTCACTTATATATTATCTAATTTATGTTTTGGTCGCTCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
1925995 TT
66 TT
1925997 TTTTCTTCAA
Statistics
Matches: 228, Mismatches: 35, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
64 3 0.01
65 47 0.21
66 2 0.01
67 1 0.00
68 156 0.68
69 19 0.08
ACGTcount: A:0.28, C:0.11, G:0.12, T:0.49
Consensus pattern (68 bp):
TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
TTA
Found at i:1925853 original size:31 final size:31
Alignment explanation
Indices: 1925679--1925855 Score: 84
Period size: 31 Copynumber: 5.3 Consensus size: 31
1925669 AATTACCTAA
* * *
1925679 TTTGGTCATTTATATATTATTTAATTTATGC
1 TTTGGTCACTTATATATTATCTAATTTATGT
** ** **
1925710 TTTGGTCACTTGATTATTATTTAGGGTAAACTACCT
1 TTTGGTCACTT-A-TA-TA-TTA-TCTAATTTATGT
*
1925746 ATTTAGTCACTTATATATTATCTAATTTATGT
1 -TTTGGTCACTTATATATTATCTAATTTATGT
* * ** ** **
1925778 TTTGGTTACTCGATTATCATTTAGGGTAAACTACCT
1 TTTGGTCACT-TA-TAT-A-TTA-TCTAATTTATGT
1925814 ATTTGGTCACTTATATATTATCTAATTTATGT
1 -TTTGGTCACTTATATATTATCTAATTTATGT
1925846 TTTGGTCACT
1 TTTGGTCACT
1925856 CGATTATTAT
Statistics
Matches: 102, Mismatches: 32, Indels: 24
0.65 0.20 0.15
Matches are distributed among these distances:
31 28 0.27
32 14 0.14
33 11 0.11
34 6 0.06
35 11 0.11
36 13 0.13
37 19 0.19
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.50
Consensus pattern (31 bp):
TTTGGTCACTTATATATTATCTAATTTATGT
Found at i:1936047 original size:15 final size:16
Alignment explanation
Indices: 1936011--1936048 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1936001 AGAGTCTCTA
1936011 AATCATTCAACATTTG
1 AATCATTCAACATTTG
* *
1936027 AATCATTCAGCGTTT-
1 AATCATTCAACATTTG
1936042 AATCATT
1 AATCATT
1936049 TTGAAGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.39
Consensus pattern (16 bp):
AATCATTCAACATTTG
Found at i:1958079 original size:8 final size:8
Alignment explanation
Indices: 1958066--1958347 Score: 438
Period size: 8 Copynumber: 35.2 Consensus size: 8
1958056 CGCATATCAA
1958066 ATACATAC
1 ATACATAC
1958074 ATACATAC
1 ATACATAC
1958082 ATACATAC
1 ATACATAC
1958090 ATACATAC
1 ATACATAC
1958098 ATACATAC
1 ATACATAC
1958106 ATACATAC
1 ATACATAC
1958114 ATACATAC
1 ATACATAC
1958122 ATACATAC
1 ATACATAC
1958130 ATACATAC
1 ATACATAC
1958138 ATACATAC
1 ATACATAC
1958146 ATACATAC
1 ATACATAC
1958154 ATACATAC
1 ATACATAC
1958162 ATACATAC
1 ATACATAC
1958170 ATACATAC
1 ATACATAC
**
1958178 ACGCATAC
1 ATACATAC
1958186 ATACATAC
1 ATACATAC
**
1958194 ACGCATAC
1 ATACATAC
1958202 ATACATAC
1 ATACATAC
*
1958210 ACACATAC
1 ATACATAC
*
1958218 ATACACAC
1 ATACATAC
*
1958226 ATACACAC
1 ATACATAC
1958234 ATACATAC
1 ATACATAC
*
1958242 ACACATAC
1 ATACATAC
*
1958250 ACACATAC
1 ATACATAC
*
1958258 ATACACAC
1 ATACATAC
1958266 ATACATAC
1 ATACATAC
*
1958274 ACACATAC
1 ATACATAC
*
1958282 ACACATAC
1 ATACATAC
*
1958290 ATACACAC
1 ATACATAC
*
1958298 ATACACAC
1 ATACATAC
1958306 ATACATAC
1 ATACATAC
1958314 ATACATAC
1 ATACATAC
1958322 ATACATAC
1 ATACATAC
1958330 ATACATAC
1 ATACATAC
1958338 ATACATAC
1 ATACATAC
1958346 AT
1 AT
1958348 GCGTATGTAT
Statistics
Matches: 254, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 254 1.00
ACGTcount: A:0.49, C:0.29, G:0.01, T:0.21
Consensus pattern (8 bp):
ATACATAC
Found at i:1958083 original size:12 final size:12
Alignment explanation
Indices: 1958066--1958347 Score: 438
Period size: 12 Copynumber: 23.5 Consensus size: 12
1958056 CGCATATCAA
1958066 ATACATACATAC
1 ATACATACATAC
1958078 ATACATACATAC
1 ATACATACATAC
1958090 ATACATACATAC
1 ATACATACATAC
1958102 ATACATACATAC
1 ATACATACATAC
1958114 ATACATACATAC
1 ATACATACATAC
1958126 ATACATACATAC
1 ATACATACATAC
1958138 ATACATACATAC
1 ATACATACATAC
1958150 ATACATACATAC
1 ATACATACATAC
1958162 ATACATACATAC
1 ATACATACATAC
**
1958174 ATACACGCATAC
1 ATACATACATAC
**
1958186 ATACATACACGC
1 ATACATACATAC
1958198 ATACATACATAC
1 ATACATACATAC
*
1958210 ACACATACATAC
1 ATACATACATAC
* *
1958222 ACACATACACAC
1 ATACATACATAC
*
1958234 ATACATACACAC
1 ATACATACATAC
*
1958246 ATACACACATAC
1 ATACATACATAC
*
1958258 ATACACACATAC
1 ATACATACATAC
*
1958270 ATACACACATAC
1 ATACATACATAC
*
1958282 ACACATACATAC
1 ATACATACATAC
* *
1958294 ACACATACACAC
1 ATACATACATAC
1958306 ATACATACATAC
1 ATACATACATAC
1958318 ATACATACATAC
1 ATACATACATAC
1958330 ATACATACATAC
1 ATACATACATAC
1958342 ATACAT
1 ATACAT
1958348 GCGTATGTAT
Statistics
Matches: 252, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 252 1.00
ACGTcount: A:0.49, C:0.29, G:0.01, T:0.21
Consensus pattern (12 bp):
ATACATACATAC
Found at i:1958091 original size:20 final size:20
Alignment explanation
Indices: 1958066--1958347 Score: 438
Period size: 20 Copynumber: 14.1 Consensus size: 20
1958056 CGCATATCAA
1958066 ATACATACATACATACATAC
1 ATACATACATACATACATAC
1958086 ATACATACATACATACATAC
1 ATACATACATACATACATAC
1958106 ATACATACATACATACATAC
1 ATACATACATACATACATAC
1958126 ATACATACATACATACATAC
1 ATACATACATACATACATAC
1958146 ATACATACATACATACATAC
1 ATACATACATACATACATAC
**
1958166 ATACATACATACACGCATAC
1 ATACATACATACATACATAC
**
1958186 ATACATACACGCATACATAC
1 ATACATACATACATACATAC
* *
1958206 ATACACACATACATACACAC
1 ATACATACATACATACATAC
* *
1958226 ATACACACATACATACACAC
1 ATACATACATACATACATAC
* *
1958246 ATACACACATACATACACAC
1 ATACATACATACATACATAC
* *
1958266 ATACATACACACATACACAC
1 ATACATACATACATACATAC
* *
1958286 ATACATACACACATACACAC
1 ATACATACATACATACATAC
1958306 ATACATACATACATACATAC
1 ATACATACATACATACATAC
1958326 ATACATACATACATACATAC
1 ATACATACATACATACATAC
1958346 AT
1 AT
1958348 GCGTATGTAT
Statistics
Matches: 248, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 248 1.00
ACGTcount: A:0.49, C:0.29, G:0.01, T:0.21
Consensus pattern (20 bp):
ATACATACATACATACATAC
Found at i:1966172 original size:21 final size:20
Alignment explanation
Indices: 1966148--1966186 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1966138 GGATGGTGAT
1966148 TTTGGGTTGGTGTTAGGTTAG
1 TTTGGGTTGG-GTTAGGTTAG
*
1966169 TTTGGGTTGGGTTGGGTT
1 TTTGGGTTGGGTTAGGTT
1966187 GGGAGCTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.05, C:0.00, G:0.46, T:0.49
Consensus pattern (20 bp):
TTTGGGTTGGGTTAGGTTAG
Found at i:1981222 original size:43 final size:40
Alignment explanation
Indices: 1981146--1981441 Score: 175
Period size: 43 Copynumber: 7.2 Consensus size: 40
1981136 AATAGAGACA
* *
1981146 TCAATTATAAAGGTAAAAGTGAGATTAAAAAAATTAGGAGCT
1 TCAATTAT-AAGGTAAAAGTGAGATTGAAAAAATTAGG-GCC
*
1981188 TCAATTATAATGGTAGAACGTGAGATTGAAAAAATTATGGGCC
1 TCAATTATAA-GGTA-AAAGTGAGATTGAAAAAATTA-GGGCC
* *
1981231 TCAATTATGAAGGTAAAAGGTGGGTTTGAAAAAAATTAGAGG--
1 TCAATTAT-AAGGTAAAA-GTGAGATTG-AAAAAATTAG-GGCC
* * **
1981273 -C---T-T-A---AAAAGTGAAATTAAAAAAATTAAGGGTT
1 TCAATTATAAGGTAAAAGTGAGATTGAAAAAATT-AGGGCC
* *
1981305 TTAATTATAAAGGTAGAAAGTGAGATTGAGAAAATTAGGGCC
1 TCAATTAT-AAGGTA-AAAGTGAGATTGAAAAAATTAGGGCC
* * *
1981347 TCAATTATAAAGGTAAAAAGTGAGGTTGAAAAAAATTAAGGCA
1 TCAATTAT-AAGGT-AAAAGTGAGATTG-AAAAAATTAGGGCC
** * *
1981390 TCAATTATAAATATAAAAGGTGGGATTG-AAAAATTAAGAGCC
1 TCAATTAT-AAGGTAAAA-GTGAGATTGAAAAAATT-AGGGCC
*
1981432 TCAAATATAA
1 TCAATTATAA
1981442 AACTAAAAAA
Statistics
Matches: 200, Mismatches: 29, Indels: 51
0.71 0.10 0.18
Matches are distributed among these distances:
30 10 0.05
31 7 0.04
32 4 0.02
35 1 0.00
36 1 0.00
37 2 0.01
38 1 0.00
39 1 0.00
41 12 0.06
42 57 0.28
43 89 0.44
44 15 0.08
ACGTcount: A:0.47, C:0.05, G:0.21, T:0.26
Consensus pattern (40 bp):
TCAATTATAAGGTAAAAGTGAGATTGAAAAAATTAGGGCC
Found at i:1981311 original size:117 final size:115
Alignment explanation
Indices: 1981160--1981388 Score: 336
Period size: 117 Copynumber: 2.0 Consensus size: 115
1981150 TTATAAAGGT
* * *
1981160 AAAAGTGAGATTAAAAAAATTAGGAGCTTCAATTATAATGGTAGAACGTGAGATTGAAAAAATTA
1 AAAAGTGAAATTAAAAAAATTAGGAGCTTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAATTA
* *
1981225 TGGGCCTCAATTATGAAGGTAAAAGGTG-GGTTTGAAAAAAATTAGAGGCTTA
66 -GGGCCTCAATTATAAAGGTAAAAAGTGAGG-TTGAAAAAAATTA-AGGCTTA
* * *
1981277 AAAAGTGAAATTAAAAAAATTAAGG-GTTTTAATTATAAAGGTAGAAAGTGAGATTGAGAAAATT
1 AAAAGTGAAATTAAAAAAATT-AGGAGCTTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAATT
1981341 AGGGCCTCAATTATAAAGGTAAAAAGTGAGGTTGAAAAAAATTAAGGC
65 AGGGCCTCAATTATAAAGGTAAAAAGTGAGGTTGAAAAAAATTAAGGC
1981389 ATCAATTATA
Statistics
Matches: 102, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
115 4 0.04
116 38 0.37
117 57 0.56
118 3 0.03
ACGTcount: A:0.46, C:0.05, G:0.23, T:0.26
Consensus pattern (115 bp):
AAAAGTGAAATTAAAAAAATTAGGAGCTTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAATTA
GGGCCTCAATTATAAAGGTAAAAAGTGAGGTTGAAAAAAATTAAGGCTTA
Found at i:1981396 original size:85 final size:85
Alignment explanation
Indices: 1981275--1981442 Score: 198
Period size: 85 Copynumber: 2.0 Consensus size: 85
1981265 ATTAGAGGCT
** * *
1981275 TAAAAAGTGAAATTAAAAAAATTAAGGGTTTTAATTATAAAGGTAGAAA-GTGAGATTGAGAAAA
1 TAAAAAGTGAAATTAAAAAAATTAAGGGCATCAATTATAAAGATA-AAAGGTGAGATTGA-AAAA
* *
1981339 TT-AGGGCCTCAATTATAAAGG
64 TTAAGAGCCTCAAATATAAAGG
** * *
1981360 TAAAAAGTGAGGTTGAAAAAAATTAA-GGCATCAATTATAAATATAAAAGGTGGGATTGAAAAAT
1 TAAAAAGTGAAATT-AAAAAAATTAAGGGCATCAATTATAAAGATAAAAGGTGAGATTGAAAAAT
1981424 TAAGAGCCTCAAATATAAA
65 TAAGAGCCTCAAATATAAA
1981443 ACTAAAAAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
84 9 0.13
85 50 0.71
86 11 0.16
ACGTcount: A:0.50, C:0.05, G:0.20, T:0.26
Consensus pattern (85 bp):
TAAAAAGTGAAATTAAAAAAATTAAGGGCATCAATTATAAAGATAAAAGGTGAGATTGAAAAATT
AAGAGCCTCAAATATAAAGG
Found at i:1981449 original size:42 final size:41
Alignment explanation
Indices: 1981307--1981450 Score: 132
Period size: 42 Copynumber: 3.4 Consensus size: 41
1981297 TAAGGGTTTT
* * *
1981307 AATTATAAAGGTAGAAAGTGA-GATTGAGAAAATTAGGGCCTC
1 AATTATAAA-ATAAAAAGTGAGGATTGA-AAAATTAAGGCCTC
* *
1981349 AATTATAAAGGTAAAAAGTGAGG-TTGAAAAAAATTAAGGCATC
1 AATTATAAA-ATAAAAAGTGAGGATTG--AAAAATTAAGGCCTC
*
1981392 AATTATAAATATAAAAGGTG-GGATTGAAAAATTAAGAGCCTC
1 AATTATAAA-ATAAAAAGTGAGGATTGAAAAATTAAG-GCCTC
*
1981434 AAATATAAAACTAAAAA
1 AATTATAAAA-TAAAAA
1981451 AATAGAGGCC
Statistics
Matches: 87, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
41 11 0.13
42 42 0.48
43 33 0.38
44 1 0.01
ACGTcount: A:0.51, C:0.06, G:0.19, T:0.24
Consensus pattern (41 bp):
AATTATAAAATAAAAAGTGAGGATTGAAAAATTAAGGCCTC
Found at i:1981452 original size:159 final size:158
Alignment explanation
Indices: 1981148--1981452 Score: 375
Period size: 159 Copynumber: 1.9 Consensus size: 158
1981138 TAGAGACATC
* * * *
1981148 AATTATAAAGGTAAAAGTGAGATTAAAAAAATTAGGAGCTTCAATTATAATGGTAGAACGTGAGA
1 AATTATAAAGGTAAAAGTGAGATTAAAAAAATTAGGAGCCTCAATTATAAAGGTAAAAAGTGAGA
* * * * * * *
1981213 TTGAAAAAATTATGGGCCTCAATTATGAAGGTAAAAGGTGGGTTTGAAAAAAATTAGAGGCTTAA
66 TTGAAAAAATTATAGGCATCAATTATAAAGATAAAAGGTGGGATTG-AAAAAATTAGAGCCTCAA
* *
1981278 AAAGTGAAATTAAAAAAATTAAGGGTTTT
130 AAAGTAAAATAAAAAAAATTAAGGGTTTT
* *
1981307 AATTATAAAGGTAGAAAGTGAGATTGAGAAAATTAGG-GCCTCAATTATAAAGGTAAAAAGTGAG
1 AATTATAAAGGTA-AAAGTGAGATTAAAAAAATTAGGAGCCTCAATTATAAAGGTAAAAAGTGAG
* *
1981371 GTTGAAAAAAATTA-AGGCATCAATTATAAATATAAAAGGTGGGATTG-AAAAATTAAGAGCCTC
65 ATTG-AAAAAATTATAGGCATCAATTATAAAGATAAAAGGTGGGATTGAAAAAATT-AGAGCCTC
*
1981434 AAATA-TAAAACTAAAAAAA
128 AAAAAGTAAAA-TAAAAAAA
1981453 TAGAGGCCTC
Statistics
Matches: 124, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
157 11 0.09
158 17 0.14
159 66 0.53
160 30 0.24
ACGTcount: A:0.49, C:0.05, G:0.21, T:0.26
Consensus pattern (158 bp):
AATTATAAAGGTAAAAGTGAGATTAAAAAAATTAGGAGCCTCAATTATAAAGGTAAAAAGTGAGA
TTGAAAAAATTATAGGCATCAATTATAAAGATAAAAGGTGGGATTGAAAAAATTAGAGCCTCAAA
AAGTAAAATAAAAAAAATTAAGGGTTTT
Found at i:1989514 original size:23 final size:23
Alignment explanation
Indices: 1989453--1989516 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
1989443 TAAGAATTAT
*
1989453 TGTCTTTATGACACATTTATCTC
1 TGTCTTTATGGCACATTTATCTC
* *
1989476 -ATCTTTTATGGAACATTTATCTC
1 TGTC-TTTATGGCACATTTATCTC
*
1989499 TGTCTTTGTGGCACATTT
1 TGTCTTTATGGCACATTT
1989517 TTTTTTACCT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
22 2 0.06
23 29 0.88
24 2 0.06
ACGTcount: A:0.20, C:0.19, G:0.12, T:0.48
Consensus pattern (23 bp):
TGTCTTTATGGCACATTTATCTC
Found at i:1991095 original size:9 final size:9
Alignment explanation
Indices: 1991083--1991108 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1991073 TTTAATATAT
1991083 AATAATAAG
1 AATAATAAG
1991092 AATAATAAG
1 AATAATAAG
1991101 AATAATAA
1 AATAATAA
1991109 TAAATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (9 bp):
AATAATAAG
Found at i:1999697 original size:130 final size:130
Alignment explanation
Indices: 1999552--1999799 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
1999542 TATTTATATA
*
1999552 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* ** *
1999617 TTAGCACACGATCATGACACGTGTCATTGGTGACATGTGTTACCACCTAATTATTTATATATGCT
66 TTAACACACGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
1999682 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * * *
1999747 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACACGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
1999800 GAAGAAAATT
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACACGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:1999830 original size:130 final size:129
Alignment explanation
Indices: 1999566--1999830 Score: 291
Period size: 130 Copynumber: 2.0 Consensus size: 129
1999556 ATTTGGTCCT
* *
1999566 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACACGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACACGATCA
** * *** * * **** *
1999631 TGACACGTGTCATTGGTGACATGTGTTACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
*
1999696 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACACGATCA
* * * * *
1999761 TGATATGTGTTATTGGTGACACATGTCACCTCCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
1999825 -A
128 CA
1999826 AAATT
1 AAATT
1999831 TGGGTCTTGG
Statistics
Matches: 111, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
130 98 0.88
132 8 0.07
133 5 0.05
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.35
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACACGATCA
TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:2000160 original size:28 final size:27
Alignment explanation
Indices: 2000129--2000191 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
2000119 AGTTGATACA
*
2000129 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
2000157 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
2000185 ATATTTT
1 ATATTTT
2000192 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:2000297 original size:17 final size:17
Alignment explanation
Indices: 2000271--2000303 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2000261 ATTTCTTATT
2000271 AAAAATAAAT-ATTCAA
1 AAAAATAAATGATTCAA
2000287 AAAATATAAATGATTCA
1 AAAA-ATAAATGATTCA
2000304 TACATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (17 bp):
AAAAATAAATGATTCAA
Found at i:2000450 original size:21 final size:21
Alignment explanation
Indices: 2000426--2000468 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2000416 TATTAACTTA
2000426 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
2000447 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
2000468 A
1 A
2000469 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:2000486 original size:35 final size:35
Alignment explanation
Indices: 2000437--2000522 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
2000427 ATTGAAGTAT
** * *
2000437 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
2000472 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
2000507 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
2000523 TGAATGTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:2011148 original size:26 final size:28
Alignment explanation
Indices: 2011100--2011162 Score: 85
Period size: 26 Copynumber: 2.3 Consensus size: 28
2011090 AGTTTTTAAA
* *
2011100 AAATTATATTAAAAATTTAAAAGGTATG
1 AAATTATATAAAAAAATTAAAAGGTATG
*
2011128 AAATTATA-AAAAAAATT-AAAGGTGTG
1 AAATTATATAAAAAAATTAAAAGGTATG
2011154 AAATTATAT
1 AAATTATAT
2011163 CATCAATAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 16 0.52
27 7 0.23
28 8 0.26
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (28 bp):
AAATTATATAAAAAAATTAAAAGGTATG
Found at i:2015915 original size:25 final size:23
Alignment explanation
Indices: 2015864--2015920 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 23
2015854 ATAACTAGGT
*
2015864 TATTTATATTATAAACTAAAAATTA
1 TATTTA-ATT-TAAACCAAAAATTA
2015889 TATATTAATTTAAACCAATAAATTA
1 TAT-TTAATTTAAACCAA-AAATTA
2015914 TATTTAA
1 TATTTAA
2015921 AGTACTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 11 0.38
25 15 0.52
26 3 0.10
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (23 bp):
TATTTAATTTAAACCAAAAATTA
Found at i:2036477 original size:26 final size:28
Alignment explanation
Indices: 2036429--2036491 Score: 85
Period size: 26 Copynumber: 2.3 Consensus size: 28
2036419 AGTTTTTAAA
* *
2036429 AAATTATATTAAAAATTTAAAAGGTATG
1 AAATTATATAAAAAAATTAAAAGGTATG
*
2036457 AAATTATA-AAAAAAATT-AAAGGTGTG
1 AAATTATATAAAAAAATTAAAAGGTATG
2036483 AAATTATAT
1 AAATTATAT
2036492 CATCAATAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 16 0.52
27 7 0.23
28 8 0.26
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (28 bp):
AAATTATATAAAAAAATTAAAAGGTATG
Found at i:2041209 original size:25 final size:23
Alignment explanation
Indices: 2041158--2041214 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 23
2041148 ATAACTAGGT
*
2041158 TATTTATATTATAAACTAAAAATTA
1 TATTTA-ATT-TAAACCAAAAATTA
2041183 TATATTAATTTAAACCAATAAATTA
1 TAT-TTAATTTAAACCAA-AAATTA
2041208 TATTTAA
1 TATTTAA
2041215 AGTACTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 11 0.38
25 15 0.52
26 3 0.10
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (23 bp):
TATTTAATTTAAACCAAAAATTA
Found at i:2048621 original size:2 final size:2
Alignment explanation
Indices: 2048616--2048650 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2048606 CCCCAAAAAA
2048616 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2048651 ATTTTCCATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2049025 original size:30 final size:31
Alignment explanation
Indices: 2048991--2049048 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
2048981 GGTAAATTAC
*
2048991 ATATTT-AGTACATAAACTATTAGTTTTGAT
1 ATATTTAAGTACATAAACTATTAATTTTGAT
* *
2049021 ATATTTAAGTACCTAAACTTTTAATTTT
1 ATATTTAAGTACATAAACTATTAATTTT
2049049 TTCAAAACGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 6 0.25
31 18 0.75
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.48
Consensus pattern (31 bp):
ATATTTAAGTACATAAACTATTAATTTTGAT
Found at i:2064356 original size:13 final size:13
Alignment explanation
Indices: 2064338--2064363 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2064328 AAGATCTTTT
2064338 TGATTCTTACTAA
1 TGATTCTTACTAA
2064351 TGATTCTTACTAA
1 TGATTCTTACTAA
2064364 CGTAAATTGA
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:0.08, T:0.46
Consensus pattern (13 bp):
TGATTCTTACTAA
Found at i:2070027 original size:33 final size:33
Alignment explanation
Indices: 2069985--2070049 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2069975 AATTACATCA
2069985 GACCCACAATGAA-GTAC-AGCTGAAAGGCATTTT
1 GACCCACAAT-AAGGTACAAG-TGAAAGGCATTTT
2070018 GACCCACAATAAGGTACAAGTGAAAGGCATTT
1 GACCCACAATAAGGTACAAGTGAAAGGCATTT
2070050 GAAGAAACCA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 2 0.07
33 26 0.87
34 2 0.07
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (33 bp):
GACCCACAATAAGGTACAAGTGAAAGGCATTTT
Found at i:2071935 original size:21 final size:20
Alignment explanation
Indices: 2071898--2071937 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2071888 GTTGTCCCAT
* *
2071898 TATGTGTTGCTGCTGTTGTG
1 TATGTGTGGCTGATGTTGTG
2071918 TATGTGTAGGCTGATGTTGT
1 TATGTGT-GGCTGATGTTGT
2071938 TGCTGAGGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.10, C:0.07, G:0.35, T:0.47
Consensus pattern (20 bp):
TATGTGTGGCTGATGTTGTG
Found at i:2074727 original size:19 final size:19
Alignment explanation
Indices: 2074683--2074720 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2074673 AGTGTCGAAA
2074683 CCAAGTCGTTTTCGAGAAT
1 CCAAGTCGTTTTCGAGAAT
2074702 CCAAGTCGTTTTCGAGAAT
1 CCAAGTCGTTTTCGAGAAT
2074721 GGAAGTCTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (19 bp):
CCAAGTCGTTTTCGAGAAT
Done.