Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 128 of 344
Found at i:43309534 original size:43 final size:43
Alignment explanation
Indices: 43309472--43309574 Score: 179
Period size: 43 Copynumber: 2.4 Consensus size: 43
43309462 TTGGTTTTCA
*
43309472 GCACTAAGTGTGCGAGCAATAAGTGTTCACGATTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGATTGTGAGATTG
* *
43309515 GCACTAAGTGTGCGGGCAATAAGTGTTCATGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGATTGTGAGATTG
43309558 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
43309575 TTGAAATGCA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.24, C:0.15, G:0.34, T:0.27
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGATTGTGAGATTG
Found at i:43309591 original size:29 final size:30
Alignment explanation
Indices: 43309556--43309629 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
43309546 GTTGTGAGAT
** *
43309556 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGGAATTGAAAGTACA
* *
43309585 TGGCACTAAGTGT-CCGAATTTAAAGTACA
1 TGGCACTAAGTGTGCGGAATTGAAAGTACA
43309614 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
43309630 TGGTTGATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
28 7 0.19
29 29 0.78
30 1 0.03
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.26
Consensus pattern (30 bp):
TGGCACTAAGTGTGCGGAATTGAAAGTACA
Found at i:43309992 original size:40 final size:40
Alignment explanation
Indices: 43309944--43310179 Score: 330
Period size: 40 Copynumber: 5.9 Consensus size: 40
43309934 TTGAATGATG
43309944 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
43309984 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
*
43310024 TCCGGGCTAAGTCCCGAGGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
* * *
43310064 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
* * * * * * *
43310104 TCCGTGCTAA-ACTCCGAAGAGCATTCGTGCTGGTGTTATG
1 TCCGGGCTAAGTC-CCGAAGAGCATTCATGCTAGTGATGTA
* * *
43310144 TCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
43310180 CGTGTATTCG
Statistics
Matches: 177, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
40 176 0.99
41 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
Found at i:43313088 original size:27 final size:26
Alignment explanation
Indices: 43313057--43313234 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 26
43313047 TAAATTGTAC
43313057 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
43313084 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
43313110 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
43313138 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA--TTGACTATGT
* *
43313166 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* *
43313193 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* *
43313220 AGTACTGAGTGTGCG
1 AGCACTAAGTGTGCG
43313235 GGCTCAATAT
Statistics
Matches: 128, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
26 1 0.01
27 102 0.80
28 25 0.20
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:43313173 original size:82 final size:81
Alignment explanation
Indices: 43313058--43313213 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
43313048 AAATTGTACA
* *
43313058 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
43313122 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
43313139 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
43313204 TGCGAGTTGA
65 TGCGAATTGA
43313214 TTATATAGTA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.76
83 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:43321198 original size:27 final size:26
Alignment explanation
Indices: 43321167--43321344 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 26
43321157 TAAATTGTAC
43321167 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
43321194 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
43321220 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
43321248 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA--TTGACTATGT
* *
43321276 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* *
43321303 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
43321330 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
43321345 GGCTCAATAT
Statistics
Matches: 129, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
26 1 0.01
27 103 0.80
28 25 0.19
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:43321281 original size:82 final size:81
Alignment explanation
Indices: 43321168--43321323 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
43321158 AAATTGTACA
* *
43321168 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
43321232 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
43321249 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
43321314 TGCGAGTTGA
65 TGCGAATTGA
43321324 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.76
83 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:43321335 original size:82 final size:81
Alignment explanation
Indices: 43321164--43321344 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
43321154 GATTAAATTG
* *
43321164 TACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
43321229 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * * ** *
43321245 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
43321309 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
43321327 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
43321345 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:43321355 original size:27 final size:27
Alignment explanation
Indices: 43321249--43321355 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
43321239 TGACCATGCG
* * * *
43321249 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * **
43321277 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
43321304 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
43321331 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
43321356 CATTCGTGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 53 0.78
28 15 0.22
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:43325754 original size:47 final size:47
Alignment explanation
Indices: 43325059--43325725 Score: 1046
Period size: 47 Copynumber: 14.1 Consensus size: 47
43325049 GAAATGATAG
* * *
43325059 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTG--TATATGTGTGA
* * * * ** *
43325108 TAGGGCCTAATGGCCGATGTAATGAATGTGAAAGTGTATATACGTAA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
* * **
43325155 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
* *
43325202 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
*
43325249 TAAGGCCTAATAGCCGACATGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
*
43325296 TAGGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
*
43325343 TAGGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
43325390 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
* *
43325437 TAGGGCCTAATAGCCGAGGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
43325484 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
* * *
43325531 TAGGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATGTGTGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
*
43325578 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATGTGTGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
*
43325625 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
* * *
43325672 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
*
43325719 CAAGGCC
1 TAAGGCC
43325726 GAGTGGCCAA
Statistics
Matches: 589, Mismatches: 29, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
47 555 0.94
49 34 0.06
ACGTcount: A:0.31, C:0.10, G:0.30, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
Found at i:43325957 original size:37 final size:37
Alignment explanation
Indices: 43325888--43325966 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
43325878 CCGAGCTCTA
* * *
43325888 AAGACCCGATGACTACGTATGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTATGGAGATTATGTCCGGGT
* *
43325925 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTATGGAGATTATGTCCGGGT
43325962 AAGAC
1 AAGAC
43325967 TTCATAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTATGGAGATTATGTCCGGGT
Found at i:43340216 original size:25 final size:25
Alignment explanation
Indices: 43340188--43340265 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
43340178 CTCGGCCCTG
43340188 TCACATATATACACTTTCACATTCA
1 TCACATATATACACTTTCACATTCA
*** *** *
43340213 TCACAT-TGGCCA-TTAGGCCTT-A
1 TCACATATATACACTTTCACATTCA
43340235 TCACATATATACACTTTCACATTCA
1 TCACATATATACACTTTCACATTCA
43340260 TCACAT
1 TCACAT
43340266 CGGCCATTAG
Statistics
Matches: 36, Mismatches: 14, Indels: 6
0.64 0.25 0.11
Matches are distributed among these distances:
22 7 0.19
23 8 0.22
24 8 0.22
25 13 0.36
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (25 bp):
TCACATATATACACTTTCACATTCA
Found at i:43340405 original size:49 final size:47
Alignment explanation
Indices: 43340137--43340601 Score: 696
Period size: 47 Copynumber: 9.6 Consensus size: 47
43340127 CCCTTCGGGA
* * * * * *
43340137 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
43340184 CCTGTCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
43340231 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
43340278 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
43340325 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
43340372 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
43340421 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
43340470 CTTATCACATATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC------ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
43340523 CTTATCACATATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
43340574 CTTATCACATATATACACTTTCACATTC
1 CTTATCACATATATACACTTTCACATTC
43340602 CAATGAATAA
Statistics
Matches: 398, Mismatches: 14, Indels: 12
0.94 0.03 0.03
Matches are distributed among these distances:
47 204 0.51
49 96 0.24
51 49 0.12
53 49 0.12
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:43342210 original size:13 final size:13
Alignment explanation
Indices: 43342192--43342216 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43342182 TACTAAACTT
43342192 TCATGGATTCAAA
1 TCATGGATTCAAA
43342205 TCATGGATTCAA
1 TCATGGATTCAA
43342217 TATACCATTA
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):
TCATGGATTCAAA
Found at i:43344240 original size:40 final size:40
Alignment explanation
Indices: 43344196--43344465 Score: 387
Period size: 40 Copynumber: 6.8 Consensus size: 40
43344186 AGCATGATTA
* * * * * *
43344196 CTCTTCGGGACCTAGCCCAGATATAACACCAGCACAAATG
1 CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
** * *
43344236 CTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
* *
43344276 CTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
* *
43344316 CTCTTCGAGACTTAGCCTGGATACATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
43344356 CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
* *
43344396 CTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
*
43344436 CTCTTCGAGACTTAGCCCGGATACATCACT
1 CTCTTCGGGACTTAGCCCGGATACATCACT
43344466 CTCAATTCTC
Statistics
Matches: 205, Mismatches: 25, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 205 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (40 bp):
CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
Found at i:43344409 original size:120 final size:120
Alignment explanation
Indices: 43344196--43344465 Score: 432
Period size: 120 Copynumber: 2.2 Consensus size: 120
43344186 AGCATGATTA
* * * * * * ** *
43344196 CTCTTCGGGACCTAGCCCAGATATAACACCAGCACAAATGCTCTTCGGGGTTTAGCACGGATATA
1 CTCTTCGAGACTTAGCCCGGATACATCACTAGCACAAATGCTCTTCGGGACTTAGCACGGATACA
43344261 TCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATG
66 TCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATG
* * *
43344316 CTCTTCGAGACTTAGCCTGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACA
1 CTCTTCGAGACTTAGCCCGGATACATCACTAGCACAAATGCTCTTCGGGACTTAGCACGGATACA
43344381 TCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATG
66 TCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATG
43344436 CTCTTCGAGACTTAGCCCGGATACATCACT
1 CTCTTCGAGACTTAGCCCGGATACATCACT
43344466 CTCAATTCTC
Statistics
Matches: 137, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
120 137 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (120 bp):
CTCTTCGAGACTTAGCCCGGATACATCACTAGCACAAATGCTCTTCGGGACTTAGCACGGATACA
TCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATG
Found at i:43345995 original size:47 final size:47
Alignment explanation
Indices: 43345910--43346013 Score: 127
Period size: 47 Copynumber: 2.2 Consensus size: 47
43345900 CTTCGGGACT
* * * *
43345910 TATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCC
1 TATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCC
* * * * *
43345957 TGTCACATATATACATTTTCACATTCATCACATCGGCCATTAGGCCT
1 TATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCC
43346004 TATCACATAT
1 TATCACATAT
43346014 GTGACAGCCC
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.27, C:0.31, G:0.10, T:0.33
Consensus pattern (47 bp):
TATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCC
Found at i:43347679 original size:80 final size:79
Alignment explanation
Indices: 43347595--43347766 Score: 211
Period size: 79 Copynumber: 2.2 Consensus size: 79
43347585 GGACTAAGAT
*
43347595 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
43347659 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * * * *
43347675 CCGAAGGCATTCGTGCGAGTTATTAAATCTGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
43347740 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
43347754 CCGAAGGCATTTG
1 CCGAAGGCATTTG
43347767 AACGAGGAGC
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
79 38 0.49
80 37 0.47
81 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:43347752 original size:39 final size:39
Alignment explanation
Indices: 43347595--43347764 Score: 198
Period size: 40 Copynumber: 4.3 Consensus size: 39
43347585 GGACTAAGAT
* * *
43347595 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
1 CCGAAGGCA-TTGTGCGAGTTACTAAA-TCCGGGTTATGTC
* * *
43347635 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGG-CATTGTGCGAGTTACTAAATCCGGGTTATGTC
* *
43347675 CCGAAGGCATTCGTGCGAGTTATTAAATCTGGGTTATGTC
1 CCGAAGGCATT-GTGCGAGTTACTAAATCCGGGTTATGTC
* * *
43347715 CCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTATGTC
43347754 CCGAAGGCATT
1 CCGAAGGCATT
43347765 TGAACGAGGA
Statistics
Matches: 115, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
39 37 0.32
40 74 0.64
41 4 0.03
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTATGTC
Found at i:43363305 original size:50 final size:50
Alignment explanation
Indices: 43363182--43363457 Score: 301
Period size: 50 Copynumber: 5.5 Consensus size: 50
43363172 ACCGAAGCTC
* *
43363182 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
1 TCTGATACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
* * * * *
43363232 TCT-AGTGCATGCAT--TAGCTTGCACTTAGTACTACACATGGGACTTATCCA
1 TCTGA-TACA--CATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
** *
43363282 TCTGATACACATAGTAGCCTGCACTTAGTACTACACATGCGATCGAAGTTAA
1 TCTGATACACATAGTAGCCTGCACTTAGTACTACACATGCGA-CCTA-TCAA
* *
43363334 -CGGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
1 TCTGATACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
* * * *
43363383 TCT-AGTACACATAGTAGCCTGCACTTACTACTACACATGTGACCTAACCA
1 TCTGA-TACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
* *
43363433 TCTGATTCACGTAGTAGCCTGCACT
1 TCTGATACACATAGTAGCCTGCACT
43363458 GGAACTCTAT
Statistics
Matches: 188, Mismatches: 27, Indels: 22
0.79 0.11 0.09
Matches are distributed among these distances:
48 3 0.02
49 3 0.02
50 134 0.71
51 43 0.23
52 5 0.03
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (50 bp):
TCTGATACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
Found at i:43363370 original size:26 final size:26
Alignment explanation
Indices: 43363338--43363420 Score: 68
Period size: 26 Copynumber: 3.3 Consensus size: 26
43363328 AGTTAACGGG
43363338 TACACATAGTAGCCTGCACTTAGTAC
1 TACACATAGTAGCCTGCACTTAGTAC
* * *
43363364 TACACAT-G-CGACCTATCAATCTAG---
1 TACACATAGTAG-CCT-GCACT-TAGTAC
*
43363388 TACACATAGTAGCCTGCACTTACTAC
1 TACACATAGTAGCCTGCACTTAGTAC
43363414 TACACAT
1 TACACAT
43363421 GTGACCTAAC
Statistics
Matches: 42, Mismatches: 7, Indels: 16
0.65 0.11 0.25
Matches are distributed among these distances:
23 2 0.05
24 11 0.26
25 8 0.19
26 18 0.43
27 3 0.07
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.27
Consensus pattern (26 bp):
TACACATAGTAGCCTGCACTTAGTAC
Found at i:43363400 original size:101 final size:98
Alignment explanation
Indices: 43363186--43363426 Score: 288
Period size: 101 Copynumber: 2.4 Consensus size: 98
43363176 AAGCTCTCTG
* * * * *
43363186 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTAGTGCATGCATTAGCT
1 GTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATCAATCGAGTACA-GCATTAGCC
* * *
43363251 TGCACTTAGTACTACACATGGGACTTATCCATCT
65 TGCACTTAGTACTACACATGCGACCTATCAATCT
* * *
43363285 GATACACATAGTAGCCTGCACTTAGTACTACACATGCGATCGAAGTTAA-CGGGTACA-CATAGT
1 G-TACACATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-TCAATCGAGTACAGCAT--T
43363348 AGCCTGCACTTAGTACTACACATGCGACCTATCAATCT
61 AGCCTGCACTTAGTACTACACATGCGACCTATCAATCT
* *
43363386 AGTACACATAGTAGCCTGCACTTACTACTACACATGTGACC
1 -GTACACATAGTAGCCTGCACTTAGTACTACACATGCGACC
43363427 TAACCATCTG
Statistics
Matches: 122, Mismatches: 14, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
99 4 0.03
100 37 0.30
101 77 0.63
102 4 0.03
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (98 bp):
GTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATCAATCGAGTACAGCATTAGCCT
GCACTTAGTACTACACATGCGACCTATCAATCT
Found at i:43363448 original size:151 final size:150
Alignment explanation
Indices: 43363185--43363457 Score: 431
Period size: 151 Copynumber: 1.8 Consensus size: 150
43363175 GAAGCTCTCT
* *
43363185 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTAGTGCATGCATTAGC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTAGTACA-GCATTAGC
* * * *
43363250 TTGCACTTAGTACTACACATGGGACTTATCCATCTGATACACATAGTAGCCTGCACTTAGTACTA
65 CTGCACTTACTACTACACATGGGACCTAACCATCTGATACACATAGTAGCCTGCACTTAGTACTA
43363315 CACATGCGATCGAAGTTAACG
130 CACATGCGATCGAAGTTAACG
43363336 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTAGTACA-CATAGTAG
1 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTAGTACAGCAT--TAG
* * *
43363400 CCTGCACTTACTACTACACATGTGACCTAACCATCTGATTCACGTAGTAGCCTGCACT
64 CCTGCACTTACTACTACACATGGGACCTAACCATCTGATACACATAGTAGCCTGCACT
43363458 GGAACTCTAT
Statistics
Matches: 111, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
149 3 0.03
151 108 0.97
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (150 bp):
GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTAGTACAGCATTAGCC
TGCACTTACTACTACACATGGGACCTAACCATCTGATACACATAGTAGCCTGCACTTAGTACTAC
ACATGCGATCGAAGTTAACG
Found at i:43363921 original size:17 final size:18
Alignment explanation
Indices: 43363889--43363924 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
43363879 ATGGGCCAGG
*
43363889 ATGGGCCATGTGGGCCCA
1 ATGGGCCATATGGGCCCA
43363907 ATGGGCC-TATGGGCCCA
1 ATGGGCCATATGGGCCCA
43363924 A
1 A
43363925 GTGGATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.19, C:0.28, G:0.36, T:0.17
Consensus pattern (18 bp):
ATGGGCCATATGGGCCCA
Found at i:43364013 original size:27 final size:27
Alignment explanation
Indices: 43363983--43364063 Score: 99
Period size: 27 Copynumber: 3.0 Consensus size: 27
43363973 AATCTCATAT
* * *
43363983 CTGTAGGCTAGTACTACTGAAATACCC
1 CTGTAGGATAGAATTACTGAAATACCC
*
43364010 CTGTAGGATAGAATTACTGAAATGCCC
1 CTGTAGGATAGAATTACTGAAATACCC
* * *
43364037 TTGTAGGGTAGAATTATTGAAATACCC
1 CTGTAGGATAGAATTACTGAAATACCC
43364064 ATGGTTTACA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (27 bp):
CTGTAGGATAGAATTACTGAAATACCC
Found at i:43364096 original size:26 final size:27
Alignment explanation
Indices: 43364048--43364116 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 27
43364038 TGTAGGGTAG
* * *
43364048 AATTATTGAAATACCCATGGTTTACAA
1 AATTACTGAAATACCCATAGTTTAAAA
*
43364075 AATTACTG-AATACCCTTAGTTTAAAA
1 AATTACTGAAATACCCATAGTTTAAAA
**
43364101 AATTACCAAAATACCC
1 AATTACTGAAATACCC
43364117 TCGATTAGCA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 21 0.60
27 14 0.40
ACGTcount: A:0.43, C:0.19, G:0.07, T:0.30
Consensus pattern (27 bp):
AATTACTGAAATACCCATAGTTTAAAA
Found at i:43364129 original size:27 final size:27
Alignment explanation
Indices: 43364099--43364356 Score: 191
Period size: 27 Copynumber: 9.5 Consensus size: 27
43364089 CTTAGTTTAA
*
43364099 AAAATTACCAAAATACCCTCGA-TTAGC
1 AAAATTACCAAAATACCCTCGACTT-GT
* **
43364126 AAAATTACCAAAGTATCCCT-GGTTTGT
1 AAAATTACCAAAATA-CCCTCGACTTGT
* *
43364153 AAAATTACCAAAATACCCTAGATTTGT
1 AAAATTACCAAAATACCCTCGACTTGT
** * * * *
43364180 GGAATTACCGAAATACCCTTGACCTAT
1 AAAATTACCAAAATACCCTCGACTTGT
** *
43364207 AAAATTACTGAAATACCCTCGACCTGT
1 AAAATTACCAAAATACCCTCGACTTGT
* * *
43364234 AAAATTACCGAAATGCCCTCGACCTGT
1 AAAATTACCAAAATACCCTCGACTTGT
* * * *
43364261 AAAATTATCGAAACAACCTCGACTTGT
1 AAAATTACCAAAATACCCTCGACTTGT
* *
43364288 AAAATTACCAAAATACCC-CTGATTTGGA
1 AAAATTACCAAAATACCCTC-GACTT-GT
* * *
43364316 AAAATTACCGAAAA-ACCCTTGATTTGG
1 AAAATTACC-AAAATACCCTCGACTTGT
*
43364343 AAAATTACAAAAAT
1 AAAATTACCAAAAT
43364357 GCCCCTAATT
Statistics
Matches: 190, Mismatches: 33, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
26 9 0.05
27 152 0.80
28 25 0.13
29 4 0.02
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.26
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTCGACTTGT
Found at i:43364367 original size:27 final size:27
Alignment explanation
Indices: 43364288--43364367 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 27
43364278 CTCGACTTGT
*
43364288 AAAATTACCAAAATACCCCTGATTTGGA
1 AAAATTACAAAAAT-CCCCTGATTTGGA
*
43364316 AAAATTACCGAAAAA-CCCTTGATTTGG-
1 AAAATTA-C-AAAAATCCCCTGATTTGGA
*
43364343 AAAATTACAAAAATGCCCCTAATTT
1 AAAATTACAAAAAT-CCCCTGATTT
43364368 ACAAATTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
25 5 0.11
26 1 0.02
27 15 0.34
28 18 0.41
29 1 0.02
30 4 0.09
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.26
Consensus pattern (27 bp):
AAAATTACAAAAATCCCCTGATTTGGA
Found at i:43364427 original size:28 final size:26
Alignment explanation
Indices: 43364369--43364450 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 26
43364359 CCCTAATTTA
* *
43364369 CAAATTTATAGAAATATCCTTGACTTT-
1 CAAAATTATAGAAATA-CCTTG-GTTTG
43364396 CAAAAATTATAGAAATACCATTGGTTTG
1 C-AAAATTATAGAAATACC-TTGGTTTG
* *
43364424 CAAAATTATCGAAATACCCTTAGTTTG
1 CAAAATTATAGAAATA-CCTTGGTTTG
43364451 TATATTTACC
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
27 27 0.57
28 20 0.43
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (26 bp):
CAAAATTATAGAAATACCTTGGTTTG
Found at i:43364437 original size:27 final size:27
Alignment explanation
Indices: 43364398--43364450 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
43364388 TTGACTTTCA
*
43364398 AAAATTATAGAAATACCATTGGTTTGC
1 AAAATTATAGAAATACCATTAGTTTGC
* *
43364425 AAAATTATCGAAATACCCTTAGTTTG
1 AAAATTATAGAAATACCATTAGTTTG
43364451 TATATTTACC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (27 bp):
AAAATTATAGAAATACCATTAGTTTGC
Found at i:43364757 original size:41 final size:41
Alignment explanation
Indices: 43364712--43364829 Score: 157
Period size: 41 Copynumber: 2.9 Consensus size: 41
43364702 AGAAGAAATT
* *
43364712 GAGGATTGCATGGTTGCTTGACGACCGTGGATCCACCGATC
1 GAGGATCGCATGGTTGCTTGAAGACCGTGGATCCACCGATC
* * *
43364753 GAGGATCGCATGGTTG-TTTAATGACCGTGAATCCACCGATT
1 GAGGATCGCATGGTTGCTTGAA-GACCGTGGATCCACCGATC
* *
43364794 AAGGATCGCATGGTTGCTTGAAGACTGTGGATCCAC
1 GAGGATCGCATGGTTGCTTGAAGACCGTGGATCCAC
43364830 TGGTGGCTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
40 3 0.05
41 59 0.89
42 4 0.06
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (41 bp):
GAGGATCGCATGGTTGCTTGAAGACCGTGGATCCACCGATC
Found at i:43365014 original size:22 final size:22
Alignment explanation
Indices: 43364989--43365036 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
43364979 TGGCTTTGCA
43364989 CCAACCT-ACATATGGCTCTGTG
1 CCAACCTGA-ATATGGCTCTGTG
* *
43365011 CCAACCTGATTATGGCTGTGTG
1 CCAACCTGAATATGGCTCTGTG
43365033 CCAA
1 CCAA
43365037 ACGTATTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (22 bp):
CCAACCTGAATATGGCTCTGTG
Found at i:43367643 original size:27 final size:27
Alignment explanation
Indices: 43367579--43367635 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
43367569 GTAGGCTAGT
*
43367579 ATTACTGAAATGCCCCTGTAGGATAGA
1 ATTACTGAAATGCCCCTGGAGGATAGA
* * *
43367606 ATTACTGAAATGTCCTTGGAGGGTAGA
1 ATTACTGAAATGCCCCTGGAGGATAGA
43367633 ATT
1 ATT
43367636 GTTGAAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (27 bp):
ATTACTGAAATGCCCCTGGAGGATAGA
Found at i:43367677 original size:26 final size:26
Alignment explanation
Indices: 43367641--43367690 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
43367631 GAATTGTTGA
*
43367641 AATACCATTGGTTTTCAAAATTACTG
1 AATACCATTGGTTTACAAAATTACTG
*
43367667 AATACCCTTGGTTTACAAAATTAC
1 AATACCATTGGTTTACAAAATTAC
43367691 CAAAATACCC
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:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (26 bp):
AATACCATTGGTTTACAAAATTACTG
Found at i:43367750 original size:27 final size:26
Alignment explanation
Indices: 43367732--43367915 Score: 124
Period size: 27 Copynumber: 6.9 Consensus size: 26
43367722 ATGCCGCTGG
*
43367732 TTTGTAAAATTATCGAAATACCCCTAA
1 TTTGTAAAATTATCGAAATA-CCCTGA
*
43367759 TTTGT-GAATTATCGAAATACCCTCGA
1 TTTGTAAAATTATCGAAATACCCT-GA
**
43367785 CCTGTAAAATTATCGAAATACCCTCGA
1 TTTGTAAAATTATCGAAATACCCT-GA
** * * *
43367812 CCTGTGAAATTACCAAAATACCCTTGA
1 TTTGTAAAATTATCGAAATACCC-TGA
** * *
43367839 CCTGTAAAATTACCGAAA-ACCCTCGG
1 TTTGTAAAATTATCGAAATACCCT-GA
* *
43367865 CTTGTAAAATTA-CCAGAATACCCTTGA
1 TTTGTAAAATTATCGA-AATACCC-TGA
*
43367892 TTTAG-AAAATTATTGAAATACCCT
1 TTT-GTAAAATTATCGAAATACCCT
43367916 TAACTCAAAA
Statistics
Matches: 131, Mismatches: 17, Indels: 19
0.78 0.10 0.11
Matches are distributed among these distances:
25 7 0.05
26 36 0.27
27 84 0.64
28 4 0.03
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.29
Consensus pattern (26 bp):
TTTGTAAAATTATCGAAATACCCTGA
Found at i:43367796 original size:53 final size:55
Alignment explanation
Indices: 43367734--43367914 Score: 167
Period size: 53 Copynumber: 3.4 Consensus size: 55
43367724 GCCGCTGGTT
** * *
43367734 TGTAAAATTATCGAAATACCCCT-AATTTGTG-AATTATCGAAATACCCTCGACC
1 TGTAAAATTATCGAAATACCCCTCAACCTGTGAAATTACCAAAATACCCTCGACC
* *
43367787 TGTAAAATTATCGAAATA-CCCTCGACCTGTGAAATTACCAAAATACCCTTGACC
1 TGTAAAATTATCGAAATACCCCTCAACCTGTGAAATTACCAAAATACCCTCGACC
* ** * * * * **
43367841 TGTAAAATTACCGAAA-A-CCCTCGGCTTGTAAAATTACCAGAATACCCTTGATT
1 TGTAAAATTATCGAAATACCCCTCAACCTGTGAAATTACCAAAATACCCTCGACC
*
43367894 TAG-AAAATTATTGAAATACCC
1 T-GTAAAATTATCGAAATACCC
43367915 TTAACTCAAA
Statistics
Matches: 108, Mismatches: 15, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
52 4 0.04
53 66 0.61
54 36 0.33
55 2 0.02
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.28
Consensus pattern (55 bp):
TGTAAAATTATCGAAATACCCCTCAACCTGTGAAATTACCAAAATACCCTCGACC
Found at i:43367939 original size:54 final size:54
Alignment explanation
Indices: 43367818--43368025 Score: 163
Period size: 54 Copynumber: 3.9 Consensus size: 54
43367808 TCGACCTGTG
* ** * *** **
43367818 AAATTACCAAAATACCCTTGACCT-GTAAAATTACCGAAA-ACCCTCGGCTTGTA
1 AAATTACAAAAATACCCTTGATTTAG-AAAATTACTGAAATACCCTTAACTTCAA
* * *
43367871 AAATTACCAGAATACCCTTGATTTAGAAAATTATTGAAATACCCTTAAC-TCAAA
1 AAATTACAAAAATACCCTTGATTTAGAAAATTACTGAAATACCCTTAACTTC-AA
* * * * **
43367925 AAATTACAAAAATACCCCTAACTTACAAAATTACAAAAATACCCTTAACTTTCAA
1 AAATTACAAAAATACCCTTGATTTAGAAAATTACTGAAATACCCTTAAC-TTCAA
* * *
43367980 AAATTACAGAAATACCATTGGTTT-GAAATATTACTGAAATACCCTT
1 AAATTACAAAAATACCCTTGATTTAGAAA-ATTACTGAAATACCCTT
43368026 GGTTTGTAGA
Statistics
Matches: 121, Mismatches: 28, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
53 33 0.27
54 51 0.42
55 35 0.29
56 2 0.02
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.28
Consensus pattern (54 bp):
AAATTACAAAAATACCCTTGATTTAGAAAATTACTGAAATACCCTTAACTTCAA
Found at i:43367963 original size:28 final size:27
Alignment explanation
Indices: 43367870--43367995 Score: 126
Period size: 27 Copynumber: 4.6 Consensus size: 27
43367860 CTCGGCTTGT
* * * * *
43367870 AAAATTACCAGAATACCCTTGATTTAG
1 AAAATTACAAAAATACCCTTAACTTAC
*** * *
43367897 AAAATTATTGAAATACCCTTAACTCAA
1 AAAATTACAAAAATACCCTTAACTTAC
*
43367924 AAAATTACAAAAATACCCCTAACTTAC
1 AAAATTACAAAAATACCCTTAACTTAC
*
43367951 AAAATTACAAAAATACCCTTAACTTTC
1 AAAATTACAAAAATACCCTTAACTTAC
*
43367978 AAAAATTACAGAAATACC
1 -AAAATTACAAAAATACC
43367996 ATTGGTTTGA
Statistics
Matches: 81, Mismatches: 17, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
27 65 0.80
28 16 0.20
ACGTcount: A:0.49, C:0.21, G:0.04, T:0.26
Consensus pattern (27 bp):
AAAATTACAAAAATACCCTTAACTTAC
Found at i:43368336 original size:41 final size:41
Alignment explanation
Indices: 43368291--43368413 Score: 174
Period size: 41 Copynumber: 3.0 Consensus size: 41
43368281 GGAGGAAGAA
43368291 ATTGAGGATTGCATGGTTGCTTGACGATCGTGGATCCACCG
1 ATTGAGGATTGCATGGTTGCTTGACGATCGTGGATCCACCG
** * *
43368332 ATTGAGGATCACATGGTTACTTGACGATCGTGGATCCACCA
1 ATTGAGGATTGCATGGTTGCTTGACGATCGTGGATCCACCG
* * * *
43368373 ATTAAGGATTGTATGGTTGCTTAACGATCATGGATCCACCG
1 ATTGAGGATTGCATGGTTGCTTGACGATCGTGGATCCACCG
43368414 GTGGCTTTTA
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 70 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (41 bp):
ATTGAGGATTGCATGGTTGCTTGACGATCGTGGATCCACCG
Found at i:43368607 original size:22 final size:22
Alignment explanation
Indices: 43368555--43368619 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
43368545 GCCAATTATT
*
43368555 CTGATTATGGCTTTGCGCCAAC
1 CTGATTATGGCTTTGTGCCAAC
* *
43368577 CT-ACATATGGCTTTGTACCAAC
1 CTGA-TTATGGCTTTGTGCCAAC
*
43368599 CTGATTATGGCTGTGTGCCAA
1 CTGATTATGGCTTTGTGCCAA
43368620 ACGTATTTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.32
Consensus pattern (22 bp):
CTGATTATGGCTTTGTGCCAAC
Found at i:43369046 original size:27 final size:27
Alignment explanation
Indices: 43368988--43369046 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
43368978 TTTAGGCTAA
* * *
43368988 GCCCAATTGATTTTGTTATGGACTGTG
1 GCCCAAATGATATTGTAATGGACTGTG
* * *
43369015 ACCCAAATGATATTGTAATGGGCTTTG
1 GCCCAAATGATATTGTAATGGACTGTG
43369042 GCCCA
1 GCCCA
43369047 CGTATGCTCT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (27 bp):
GCCCAAATGATATTGTAATGGACTGTG
Found at i:43370785 original size:17 final size:18
Alignment explanation
Indices: 43370759--43370792 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
43370749 ATTCTTACAT
*
43370759 TTATTGAAACCT-TCCAC
1 TTATTCAAACCTATCCAC
43370776 TTATTCAAACCTATCCA
1 TTATTCAAACCTATCCA
43370793 ATCACTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.32, C:0.29, G:0.03, T:0.35
Consensus pattern (18 bp):
TTATTCAAACCTATCCAC
Found at i:43372114 original size:18 final size:18
Alignment explanation
Indices: 43372079--43372141 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
43372069 AAAAGAATGA
* *
43372079 GAAAAAGAAAAACAAAATC
1 GAAAAAGAAAAA-GAAATT
43372098 GAAAAAGAAAAAGAAATT
1 GAAAAAGAAAAAGAAATT
**
43372116 GATCAAG-AAAAGAAAATT
1 GAAAAAGAAAAAG-AAATT
43372134 GAAAAAGA
1 GAAAAAGA
43372142 GAGTGAGTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 5 0.14
18 19 0.53
19 12 0.33
ACGTcount: A:0.70, C:0.05, G:0.16, T:0.10
Consensus pattern (18 bp):
GAAAAAGAAAAAGAAATT
Found at i:43373527 original size:20 final size:20
Alignment explanation
Indices: 43373504--43373570 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
43373494 AGCTCTGTGT
43373504 AGCTCAACTCAGCTTATTTG
1 AGCTCAACTCAGCTTATTTG
** *
43373524 AGCTCATTTCAGCTTGTTTG
1 AGCTCAACTCAGCTTATTTG
* *
43373544 AGCTCAACCCAGCTTACTTTT
1 AGCTCAACTCAGCTTA-TTTG
43373565 AGCTCA
1 AGCTCA
43373571 TTCTTTATTT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
20 29 0.76
21 9 0.24
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.36
Consensus pattern (20 bp):
AGCTCAACTCAGCTTATTTG
Found at i:43374900 original size:414 final size:414
Alignment explanation
Indices: 43374130--43374958 Score: 1532
Period size: 414 Copynumber: 2.0 Consensus size: 414
43374120 GGCTATTTTA
43374130 TGTACATGTATTTGAATATTCATGGACCGTAATTAAGGAAGAACATGCATATGGACGTTTCATGC
1 TGTACATGTATTTGAATATTCATGGACCGTAATTAAGGAAGAACATGCATATGGACGTTTCATGC
43374195 ATGTATCATGCATATCCAAGTTGTCCATTCAAGTATTCAAGGTACATTAAAGCCTCATTCGGCCA
66 ATGTATCATGCATATCCAAGTTGTCCATTCAAGTATTCAAGGTACATTAAAGCCTCATTCGGCCA
43374260 AGGGAGATGTTGGAGTATTAGAGGGCTGCACATTCATGAACTATGGCTTTTCTTCTAGGCTAAGT
131 AGGGAGATGTTGGAGTATTAGAGGGCTGCACATTCATGAACTATGGCTTTTCTTCTAGGCTAAGT
*
43374325 ATGAATGAATGCATCAGGTGAAGCAACATGATGGTTCGGCCAATTCATTCACCATCTCTAAGCAT
196 ATGAATGAATGCACCAGGTGAAGCAACATGATGGTTCGGCCAATTCATTCACCATCTCTAAGCAT
* * *
43374390 GAACCGAATTTTAATGCTTTTGTGTGAATATGTTAAATACAAAAGTGAACAGAATTTAAGTAAGT
261 AAACCAAATTTTAATGCTTTTGTGTGAACATGTTAAATACAAAAGTGAACAGAATTTAAGTAAGT
**
43374455 GTGAACATCATAGATGCTGAATATCAATAGGCATCTTAGGCTTATAAATAGTTTGTTTATTTCTT
326 GTGAACATCATAGATGCCAAATATCAATAGGCATCTTAGGCTTATAAATAGTTTGTTTATTTCTT
*
43374520 TGTAAAAAGGCTTTTGCCAATTTG
391 TGTAAAAAGACTTTTGCCAATTTG
43374544 TGTACATGTATTTGAATATTCATGGACCGTAATTAAGGAAGAACATGCATATGGACGTTTCATGC
1 TGTACATGTATTTGAATATTCATGGACCGTAATTAAGGAAGAACATGCATATGGACGTTTCATGC
*
43374609 ATGTATCATGCATATCCAAGTTGTCCATTCAAGTATTCAAGGTACATTAAAGCCTCATTTGGCCA
66 ATGTATCATGCATATCCAAGTTGTCCATTCAAGTATTCAAGGTACATTAAAGCCTCATTCGGCCA
*
43374674 GGGGAGATGTTGGAGTATTAGAGGGCTGCACATTCATGAACTATGGCTTTTCTTCTAGGCTAAGT
131 AGGGAGATGTTGGAGTATTAGAGGGCTGCACATTCATGAACTATGGCTTTTCTTCTAGGCTAAGT
* *
43374739 ATGAATGAATGCACCAGGTGAAGCAACATGATGGTTTGGCCAATTTATTCACCATCTCTAAGCAT
196 ATGAATGAATGCACCAGGTGAAGCAACATGATGGTTCGGCCAATTCATTCACCATCTCTAAGCAT
* * *
43374804 AAACCAAATTTTAATGTTTTTGTGTGAACATGTTAAATACAAATGTGAACAGAATTTAAGTTAGT
261 AAACCAAATTTTAATGCTTTTGTGTGAACATGTTAAATACAAAAGTGAACAGAATTTAAGTAAGT
43374869 GTGAACATCATAGATGCCAAATATCAATAGGCATCTTAGGCTTATAAATAGTTTGTTTATTTCTT
326 GTGAACATCATAGATGCCAAATATCAATAGGCATCTTAGGCTTATAAATAGTTTGTTTATTTCTT
43374934 TGTAAAAAGACTTTTGCCAATTTG
391 TGTAAAAAGACTTTTGCCAATTTG
43374958 T
1 T
43374959 TAATGAACAT
Statistics
Matches: 401, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
414 401 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (414 bp):
TGTACATGTATTTGAATATTCATGGACCGTAATTAAGGAAGAACATGCATATGGACGTTTCATGC
ATGTATCATGCATATCCAAGTTGTCCATTCAAGTATTCAAGGTACATTAAAGCCTCATTCGGCCA
AGGGAGATGTTGGAGTATTAGAGGGCTGCACATTCATGAACTATGGCTTTTCTTCTAGGCTAAGT
ATGAATGAATGCACCAGGTGAAGCAACATGATGGTTCGGCCAATTCATTCACCATCTCTAAGCAT
AAACCAAATTTTAATGCTTTTGTGTGAACATGTTAAATACAAAAGTGAACAGAATTTAAGTAAGT
GTGAACATCATAGATGCCAAATATCAATAGGCATCTTAGGCTTATAAATAGTTTGTTTATTTCTT
TGTAAAAAGACTTTTGCCAATTTG
Found at i:43375305 original size:17 final size:18
Alignment explanation
Indices: 43375283--43375319 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
43375273 ACTATTCTTA
*
43375283 CACTTATTGAAACCT-TC
1 CACTTATTCAAACCTATC
43375300 CACTTATTCAAACCTATC
1 CACTTATTCAAACCTATC
43375318 CA
1 CA
43375320 ATCACTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.32, C:0.32, G:0.03, T:0.32
Consensus pattern (18 bp):
CACTTATTCAAACCTATC
Found at i:43379011 original size:37 final size:37
Alignment explanation
Indices: 43378961--43379039 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
43378951 TTATTACGAA
* * *
43378961 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
43378998 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
43379035 GTCTT
1 GTCTT
43379040 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:43379245 original size:47 final size:47
Alignment explanation
Indices: 43379158--43379699 Score: 823
Period size: 47 Copynumber: 11.4 Consensus size: 47
43379148 CCTTTCGGGA
* * * * * * *
43379158 CTTATCACATTTATGCACTTTCACATCCATTACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
43379205 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
43379252 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
43379299 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
43379346 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTTGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
43379393 CTTATCACACATATACACTTTCACATTCATCACGTCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
43379440 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
43379487 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
43379534 CTTATTACATATATACATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTA-T-CACATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGC
43379585 CTTATCACATATACATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
43379634 CTTATTACATACATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
43379681 CTTATCACATATATACACT
1 CTTATCACATATATACACT
43379700 CTCTCGGCTG
Statistics
Matches: 462, Mismatches: 29, Indels: 8
0.93 0.06 0.02
Matches are distributed among these distances:
47 364 0.79
48 1 0.00
49 58 0.13
50 1 0.00
51 38 0.08
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:43383300 original size:40 final size:40
Alignment explanation
Indices: 43383230--43383386 Score: 242
Period size: 40 Copynumber: 3.9 Consensus size: 40
43383220 CGAATACACG
* * ** * * *
43383230 TCACCAGCATGATTGCTCTTCGGGGTTTAGCACAGATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
*
43383270 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
43383310 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
43383350 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
43383387 TTAGTAACTC
Statistics
Matches: 108, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 108 1.00
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
Found at i:43383411 original size:40 final size:40
Alignment explanation
Indices: 43383243--43383465 Score: 238
Period size: 40 Copynumber: 5.6 Consensus size: 40
43383233 CCAGCATGAT
** * * *
43383243 TGCTCTTCGGGGTTTAGCACAGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
43383283 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
43383323 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
** * * *
43383363 TGCTCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACCAA
1 TGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCACGAA
* **
43383404 TGC-CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCAC-AA
1 TGCTCTTCGGGA-CTTAGCCCGGATA-CATCAC-TAGCACGAA
*
43383444 AGC-CTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGGACTTAGCCCGGA
43383466 CATCATTCAA
Statistics
Matches: 158, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
39 3 0.02
40 135 0.85
41 20 0.13
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:43383810 original size:29 final size:29
Alignment explanation
Indices: 43383771--43383849 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
43383761 CTTAATAATC
*
43383771 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
43383801 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
43383830 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
43383850 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:43385796 original size:37 final size:37
Alignment explanation
Indices: 43385746--43385824 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
43385736 TTATTACGAA
* * *
43385746 GTCTTACCCGGACATAATCTCCACACGA-AGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACAC-ATAGTCATCGG
43385783 GTCTTACCCGGACAAAATCCCCACACATAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACATAGTCATCGG
43385820 GTCTT
1 GTCTT
43385825 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 1 0.03
37 37 0.97
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACATAGTCATCGG
Found at i:43386028 original size:47 final size:47
Alignment explanation
Indices: 43385943--43386484 Score: 787
Period size: 47 Copynumber: 11.4 Consensus size: 47
43385933 CCTTTCGGGA
* * * * * * * *
43385943 CTTATCACATTTATGCACTTTCACATCCATTACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
43385990 CCTGTCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
43386037 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
43386084 CTTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
43386131 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTTGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
43386178 CTTATCACACATATACACTTTCACATTCATCACGTCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
43386225 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
43386272 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
43386319 CTTATTACATATATACATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTA-T-CACATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGC
43386370 CTTATCACATATACATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
43386419 CTTATTACATACATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
43386466 CTTATCACATATATACACT
1 CTTATCACATATATACACT
43386485 CTCTTGGCTG
Statistics
Matches: 457, Mismatches: 34, Indels: 8
0.92 0.07 0.02
Matches are distributed among these distances:
47 359 0.79
48 1 0.00
49 58 0.13
50 1 0.00
51 38 0.08
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:43388964 original size:79 final size:81
Alignment explanation
Indices: 43388828--43389012 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
43388818 TTGAATGATG
* *
43388828 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
43388892 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
43388907 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
43388969 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
43388987 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
43389013 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:43389026 original size:40 final size:40
Alignment explanation
Indices: 43388829--43389012 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
43388819 TGAATGATGT
* * * *
43388829 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
43388869 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
43388909 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
43388947 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
43388988 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
43389013 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:43389034 original size:79 final size:79
Alignment explanation
Indices: 43388881--43389045 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
43388871 GGACTAAGAT
* * **
43388881 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
43388946 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
43388960 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
43389023 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
43389039 CCGAAGG
1 CCGAAGG
43389046 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:43404783 original size:47 final size:47
Alignment explanation
Indices: 43404702--43405199 Score: 712
Period size: 47 Copynumber: 10.6 Consensus size: 47
43404692 TAATTGAATA
*
43404702 AATGTGAA-AGTGTATATGTGTGAATAGGGCCGAATGGCCAATGTGATG
1 AATGTGAACA-TGTATATGTGTG-ATAAGGCCGAATGGCCAATGTGATG
* * *
43404750 AATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
*
43404797 AATGTGAACACGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* * *
43404844 AAAGTGAACATGTGTATGTGTGATAGGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* * *
43404891 AATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
*
43404938 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* *
43404985 AAAGTGAACACGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* *
43405032 AAAGTGAACATGTATATGTGTGATAAAGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* * * *
43405079 AAAGTGAACAGGTGTATGTGTGATAAGGCCGAGTGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* * * * *
43405126 AATGTGAGCATGTGTATGTGAGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
**
43405173 AATGTGAA-AGTGTATAAATGTGATAAG
1 AATGTGAACA-TGTATATGTGTGATAAG
43405200 TCCCGAAGGG
Statistics
Matches: 405, Mismatches: 43, Indels: 5
0.89 0.09 0.01
Matches are distributed among these distances:
46 1 0.00
47 386 0.95
48 17 0.04
49 1 0.00
ACGTcount: A:0.33, C:0.11, G:0.31, T:0.26
Consensus pattern (47 bp):
AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:43405374 original size:37 final size:37
Alignment explanation
Indices: 43405318--43405397 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
43405308 CCGGGCTATA
* * *
43405318 AAGACCCGATGACTGCGTGTGG-GAATTTTGTCCGGGT
1 AAGACTCGATAACTGCGTGTGGAG-ATTATGTCCGGGT
*
43405355 AAGACTCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACTCGATAACTGCGTGTGGAGATTATGTCCGGGT
43405392 AAGACT
1 AAGACT
43405398 TCGTAATAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (37 bp):
AAGACTCGATAACTGCGTGTGGAGATTATGTCCGGGT
Found at i:43417440 original size:27 final size:26
Alignment explanation
Indices: 43417392--43417451 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
43417382 GCGAAGCTGC
*
43417392 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
43417419 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
43417445 CAGATAT
1 CAGATAT
43417452 ATATATATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:43417540 original size:27 final size:26
Alignment explanation
Indices: 43417493--43417543 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
43417483 CGAGGCTGCT
*
43417493 AGATATTGTGACGAAGTCACCAGAAC
1 AGATATTGTGACGAAGCCACCAGAAC
* *
43417519 AGATATATGTGGCGAGGCCACCAGA
1 AGATAT-TGTGACGAAGCCACCAGA
43417544 TTACAGCGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.18
Consensus pattern (26 bp):
AGATATTGTGACGAAGCCACCAGAAC
Found at i:43418226 original size:27 final size:27
Alignment explanation
Indices: 43418196--43418314 Score: 148
Period size: 27 Copynumber: 4.4 Consensus size: 27
43418186 GGGGCAAAAT
* * *
43418196 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
43418223 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
43418250 GGTATTTATACCCTACAAGGGTATTTA
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
43418277 GGTAATTCTATCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
43418304 GGTAATTCTAC
1 GGTAATTCTAC
43418315 AACTTATCCA
Statistics
Matches: 77, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 77 1.00
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:43419316 original size:31 final size:31
Alignment explanation
Indices: 43419273--43419336 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
43419263 CCTTTTCATA
43419273 TTTCATAATTCATAACACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
* **
43419304 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
43419335 TT
1 TT
43419337 ACGGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCATAATTCATAACACTGGGCCGAAGCCT
Found at i:43419575 original size:24 final size:24
Alignment explanation
Indices: 43419542--43419694 Score: 247
Period size: 24 Copynumber: 6.4 Consensus size: 24
43419532 CTAGAGGCCT
43419542 AGCCTCTTTTAATAACTGGGGCA-A
1 AGCC-CTTTTAATAACTGGGGCATA
43419566 AGCCCTTTTTAATAACTGGGGCATA
1 AGCCC-TTTTAATAACTGGGGCATA
43419591 AGCCC-TTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
43419614 AGCCCTTTTAATAATTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
43419638 AGCCCTTTTAATAACTGGGGTATA
1 AGCCCTTTTAATAACTGGGGCATA
*
43419662 AGCCCTTTTAATAATTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
43419686 AGCCCTTTT
1 AGCCCTTTT
43419695 GCACTTCCTC
Statistics
Matches: 121, Mismatches: 5, Indels: 6
0.92 0.04 0.05
Matches are distributed among these distances:
23 24 0.20
24 91 0.75
25 6 0.05
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:43419765 original size:9 final size:9
Alignment explanation
Indices: 43419751--43419827 Score: 64
Period size: 9 Copynumber: 7.9 Consensus size: 9
43419741 ATCTCGTGTG
43419751 CATATCATA
1 CATATCATA
*
43419760 CATATCATGTG
1 CATATCA--TA
43419771 CATATCATA
1 CATATCATA
* *
43419780 CATGTCATCTG
1 CATATCA--TA
43419791 CATATCATA
1 CATATCATA
*
43419800 CATATCATGTG
1 CATATCA--TA
43419811 CATATCATA
1 CATATCATA
43419820 CATATCAT
1 CATATCAT
43419828 GTTTATCAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
9 31 0.57
11 23 0.43
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:43419770 original size:20 final size:20
Alignment explanation
Indices: 43419747--43419829 Score: 148
Period size: 20 Copynumber: 4.2 Consensus size: 20
43419737 GAACATCTCG
43419747 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
43419767 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
*
43419787 TCTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
43419807 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
43419827 TGT
1 TGT
43419830 TTATCAAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:43419894 original size:25 final size:25
Alignment explanation
Indices: 43419866--43419913 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
43419856 ATATATAAAC
* *
43419866 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAATGGTCATTTTTA
43419891 CCTAGGGGCAAAATGGTCATTTT
1 CCTAGGGGCAAAATGGTCATTTT
43419914 CATATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAATGGTCATTTTTA
Found at i:43442691 original size:40 final size:40
Alignment explanation
Indices: 43442601--43442821 Score: 245
Period size: 40 Copynumber: 5.5 Consensus size: 40
43442591 CTCAAGTAAT
* * * *
43442601 CTTCGGGATTTAG-CCAGATATA-ACTACTAGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* *
43442639 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
43442679 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * * *
43442719 CTTCGGGTCCTAGCCCGGATATAG-CAACTCGCACGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * *
43442759 CTTC-GGATCTTAGTCCGGTTATAGTCACCTAGCACAAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCA-CTAGCACAAATGC
43442800 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
43442822 CATTCGAATA
Statistics
Matches: 152, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
38 11 0.07
39 18 0.12
40 93 0.61
41 27 0.18
42 3 0.02
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:43446143 original size:40 final size:40
Alignment explanation
Indices: 43446000--43446143 Score: 191
Period size: 40 Copynumber: 3.6 Consensus size: 40
43445990 CGGATGATAA
* * * * *
43446000 CCGGGCTAAGTCCTGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTA-TAT
* *
43446040 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
*
43446080 TCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
*
43446120 CCGGGCTATGTCCCGAAGGCATTG
1 CCGGGCTAAGTCCCGAAGGCATTG
43446144 AGCAAGTAGT
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
39 1 0.01
40 92 0.99
ACGTcount: A:0.21, C:0.24, G:0.30, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
Found at i:43455362 original size:40 final size:40
Alignment explanation
Indices: 43455316--43455500 Score: 214
Period size: 40 Copynumber: 4.6 Consensus size: 40
43455306 TTTGCACAAG
* *
43455316 GCCTTCGGGTCTTAGCCCAGATATAGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * *
43455356 GCCTTCGGGACTTAGCCCAGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
43455396 GCCTTCGGGTCTTAGCCCGGATATAG-CAACT--CACAGGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACA--AAT
* * * * *
43455436 GCCTTCGGATCTTAGTCCGGTTATAGTCACCAAGCACAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCA-CTAGCACAAAT
*
43455477 GCCTTCGGGGCTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
43455501 CATTCGAATA
Statistics
Matches: 123, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
38 4 0.03
39 1 0.01
40 90 0.73
41 24 0.20
43 4 0.03
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:43458169 original size:15 final size:16
Alignment explanation
Indices: 43458142--43458171 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
43458132 AGGAGAAAAA
43458142 AGAAAGAAAAGGAGAG
1 AGAAAGAAAAGGAGAG
43458158 AGAAAG-AAAGGAGA
1 AGAAAGAAAAGGAGA
43458172 AAGGGGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (16 bp):
AGAAAGAAAAGGAGAG
Found at i:43458205 original size:23 final size:21
Alignment explanation
Indices: 43458132--43458209 Score: 72
Period size: 23 Copynumber: 3.6 Consensus size: 21
43458122 AAAGGAATAG
43458132 AGGAGAA-AAAAGAAAG-AAA
1 AGGAGAAGAAAAGAAAGAAAA
*
43458151 AGGAG-AGAGAAAGAAAGGAGAA
1 AGGAGAAGA-AAAGAAA-GAAAA
*
43458173 AGGGGAAAGAAAAGAAAGAAAAA
1 AGGAG-AAGAAAAGAAAG-AAAA
43458196 ATGGAGAAGAAAAG
1 A-GGAGAAGAAAAG
43458210 GGTGGCTGGT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
18 1 0.02
19 6 0.13
20 7 0.15
21 1 0.02
22 7 0.15
23 19 0.40
24 6 0.13
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.01
Consensus pattern (21 bp):
AGGAGAAGAAAAGAAAGAAAA
Found at i:43459170 original size:42 final size:42
Alignment explanation
Indices: 43459101--43459194 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
43459091 CGGTTCCAAG
* * *
43459101 CATGCCCCTGTCTCCATCTCGTGGGTGTTACACGACCTAGGA
1 CATGCCCGTGTCTCCATCTCGTAGGTGTCACACGACCTAGGA
* * *
43459143 CATGCCCGTGTCTCCAT-TCTGTAGGTGTCGCAGGGCCTAGGA
1 CATGCCCGTGTCTCCATCTC-GTAGGTGTCACACGACCTAGGA
*
43459185 CATGCTCGTG
1 CATGCCCGTG
43459195 GGTCCAGGCC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 2 0.05
42 42 0.95
ACGTcount: A:0.15, C:0.31, G:0.28, T:0.27
Consensus pattern (42 bp):
CATGCCCGTGTCTCCATCTCGTAGGTGTCACACGACCTAGGA
Found at i:43464036 original size:13 final size:13
Alignment explanation
Indices: 43464018--43464046 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
43464008 GAACCTGTAG
43464018 CCAAAGTGGTAAC
1 CCAAAGTGGTAAC
43464031 CCAAAGTGGTAAC
1 CCAAAGTGGTAAC
43464044 CCA
1 CCA
43464047 TGGTAAGGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.28, G:0.21, T:0.14
Consensus pattern (13 bp):
CCAAAGTGGTAAC
Found at i:43467014 original size:26 final size:26
Alignment explanation
Indices: 43466978--43467029 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
43466968 TTTGTATATT
43466978 AGATTTGTAAAAATGATTGAGTTAAG
1 AGATTTGTAAAAATGATTGAGTTAAG
43467004 AGATTTGTAAAAATGATTGAGTTAAG
1 AGATTTGTAAAAATGATTGAGTTAAG
43467030 TTGAAAGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (26 bp):
AGATTTGTAAAAATGATTGAGTTAAG
Found at i:43470840 original size:131 final size:131
Alignment explanation
Indices: 43470606--43470867 Score: 515
Period size: 131 Copynumber: 2.0 Consensus size: 131
43470596 TTCCAGCCTA
43470606 GTATTCAGATGGCACCCTAAGAAGTCTTGTATGGTCGTAGGTGTCGTACTCTTCTATGTTGGACA
1 GTATTCAGATGGCACCCTAAGAAGTCTTGTATGGTCGTAGGTGTCGTACTCTTCTATGTTGGACA
43470671 AAATTAAGTGAACGCTAGATATTGGGTCCTGAACTGGTTTCTGAAACTGAGAGCACTATGAAAGT
66 AAATTAAGTGAACGCTAGATATTGGGTCCTGAACTGGTTTCTGAAACTGAGAGCACTATGAAAGT
43470736 G
131 G
43470737 GTATTCAGATGGCACCCTAAGAAGTCTTGTATGGTCGTAGGTGTCGTACTCTTCTATGTTGGACA
1 GTATTCAGATGGCACCCTAAGAAGTCTTGTATGGTCGTAGGTGTCGTACTCTTCTATGTTGGACA
*
43470802 AAATTAAGTGAACGCTAGATATTGGGTCCTGAGCTGGTTTCTGAAACTGAGAGCACTATGAAAGT
66 AAATTAAGTGAACGCTAGATATTGGGTCCTGAACTGGTTTCTGAAACTGAGAGCACTATGAAAGT
43470867 G
131 G
43470868 ATTCGTGAGC
Statistics
Matches: 130, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
131 130 1.00
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (131 bp):
GTATTCAGATGGCACCCTAAGAAGTCTTGTATGGTCGTAGGTGTCGTACTCTTCTATGTTGGACA
AAATTAAGTGAACGCTAGATATTGGGTCCTGAACTGGTTTCTGAAACTGAGAGCACTATGAAAGT
G
Found at i:43471767 original size:14 final size:13
Alignment explanation
Indices: 43471748--43471799 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
43471738 TGACATGTTC
43471748 TTCTTTCCTTTTCT
1 TTCTTT-CTTTTCT
* *
43471762 TTCTTTTTATTTTT
1 TTCTTTCT-TTTCT
43471776 TTCTTTTCTTTTCT
1 TTC-TTTCTTTTCT
43471790 TTC-TTCTTTT
1 TTCTTTCTTTT
43471800 TACTGCTTCG
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
12 7 0.22
13 1 0.03
14 20 0.62
15 4 0.12
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (13 bp):
TTCTTTCTTTTCT
Found at i:43485500 original size:28 final size:28
Alignment explanation
Indices: 43485450--43485506 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
43485440 TAGTTGGGCT
* *
43485450 TGATGGGCCATATGAATGTGATTAGGCC
1 TGATGGGCCATATGAACGAGATTAGGCC
* *
43485478 TGATGGGCCATGTGAACGAGATTGGGCC
1 TGATGGGCCATATGAACGAGATTAGGCC
43485506 T
1 T
43485507 AAAGGGGCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.23, C:0.16, G:0.35, T:0.26
Consensus pattern (28 bp):
TGATGGGCCATATGAACGAGATTAGGCC
Found at i:43485853 original size:27 final size:28
Alignment explanation
Indices: 43485823--43486056 Score: 215
Period size: 27 Copynumber: 8.7 Consensus size: 28
43485813 TAATAAAGAG
43485823 AAATTACTAG-AATACCCTCGATTTGTA
1 AAATTACTAGAAATACCCTCGATTTGTA
*
43485850 AAATTA-TCGAAATA-CCTGCGATTTGTA
1 AAATTACTAGAAATACCCT-CGATTTGTA
* * *
43485877 TAATTA-TCGAAACACCCTCGATTTGTA
1 AAATTACTAGAAATACCCTCGATTTGTA
* *
43485904 AAATTA-TAGAAATACCCTTGATTTGAA
1 AAATTACTAGAAATACCCTCGATTTGTA
*
43485931 AAATTAC-CGAAATACCCTCGATTTGTA
1 AAATTACTAGAAATACCCTCGATTTGTA
* *
43485958 AAATTACT-GAAATACCTTTGATTTGTA
1 AAATTACTAGAAATACCCTCGATTTGTA
* * *
43485985 AAATTAC-CGAAAAACCC-CCATTTTGTA
1 AAATTACTAGAAATACCCTCGA-TTTGTA
* *
43486012 AAATTA-TCA-AAATACCCTTG-TAGTGTA
1 AAATTACT-AGAAATACCCTCGAT-TTGTA
43486039 AAATTACTA-AAATACCCT
1 AAATTACTAGAAATACCCT
43486057 TGTAGTGTAA
Statistics
Matches: 173, Mismatches: 22, Indels: 24
0.79 0.10 0.11
Matches are distributed among these distances:
26 7 0.04
27 162 0.94
28 4 0.02
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.32
Consensus pattern (28 bp):
AAATTACTAGAAATACCCTCGATTTGTA
Found at i:43485906 original size:54 final size:53
Alignment explanation
Indices: 43485836--43486045 Score: 246
Period size: 54 Copynumber: 3.9 Consensus size: 53
43485826 TTACTAGAAT
* * * *
43485836 ACCCTCGATTTGTAAAATTATCGAAATACCTGCGATTTGTATAATTATCGAAAC
1 ACCCTCGATTTGTAAAATTATCGAAATACCT-TGATTTGTAAAATTACCGAAAA
* * *
43485890 ACCCTCGATTTGTAAAATTATAGAAATACCCTTGATTTGAAAAATTACCGAAAT
1 ACCCTCGATTTGTAAAATTATCGAAATA-CCTTGATTTGTAAAATTACCGAAAA
43485944 ACCCTCGATTTGTAAAATTA-CTGAAATACCTTTGATTTGTAAAATTACCGAAAA
1 ACCCTCGATTTGTAAAATTATC-GAAATACC-TTGATTTGTAAAATTACCGAAAA
* * *
43485998 ACCC-CCATTTTGTAAAATTATCAAAATACCCTTG-TAGTGTAAAATTAC
1 ACCCTCGA-TTTGTAAAATTATCGAAATA-CCTTGAT-TTGTAAAATTAC
43486046 TAAAATACCC
Statistics
Matches: 137, Mismatches: 12, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
53 5 0.04
54 126 0.92
55 6 0.04
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (53 bp):
ACCCTCGATTTGTAAAATTATCGAAATACCTTGATTTGTAAAATTACCGAAAA
Found at i:43486080 original size:27 final size:27
Alignment explanation
Indices: 43486008--43486099 Score: 96
Period size: 27 Copynumber: 3.4 Consensus size: 27
43485998 ACCCCCATTT
* *
43486008 TGTAAAATTATCAAAATACCCTTGTAG
1 TGTAAAATGACCAAAATACCCTTGTAG
* *
43486035 TGTAAAATTACTAAAATACCCTTGTAG
1 TGTAAAATGACCAAAATACCCTTGTAG
* * * *
43486062 TGTAAAATGACCGACATACCCCTATAAG
1 TGTAAAATGACCAAAATACCCTTGT-AG
43486090 -GTAAAATGAC
1 TGTAAAATGAC
43486100 TGTTTTACCC
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
27 54 0.96
28 2 0.04
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.28
Consensus pattern (27 bp):
TGTAAAATGACCAAAATACCCTTGTAG
Found at i:43491529 original size:349 final size:349
Alignment explanation
Indices: 43490741--43491779 Score: 1999
Period size: 348 Copynumber: 3.0 Consensus size: 349
43490731 ATGTGGATTC
* * *
43490741 AATTTTTATGCACACGATTTGTTCTTGCATTGAATGTGTCTAATGTTAATAGTTTCTAAGCAATT
1 AATTTTTATGCACACGAGTTGTTCTTGCTTTGAGTGTGTCTAATGTTAATAGTTTCTAAGCAATT
*
43490806 TTGCTTTATGCTATTTTGCAAAAAAAATAGATATGCATCGGGAAATGTCTTTACCAAAATATGCA
66 TTGCTTTATGCTATTTTGCAAAAAAAATAGATATGCATCGGGAAATGTATTTACCAAAATATGCA
43490871 TAGATGCATCAGTGGCCAAAAAGTGGGAGTTTTCTTTCCCCACTTACTGACGTCTTTATGCAAAA
131 TAGATGCATCAGTGGCCAAAAAGTGGGAGTTTTCTTTCCCCACTTACTGACGTCTTTATGCAAAA
* *
43490936 AAGTTGGTGTTCCAATGGCATCCACAAAACAATCAATGAATCCATCTCGAAGTATCATCGATGAC
196 AAGTTGGTGTTCCAATGGCATCCACAAAACAATCAATGAAGCCATCCCGAAGTATCATCGATGAC
43491001 ACTTTTTTTTCACAATACATTGAACTTCGAGCAAAATAGATAAATGAATGGAAGAAATGCCAACA
261 ACTTTTTTTTCACAATACATTGAACTTCGAGCAAAATAGATAAATGAATGGAAGAAATGCCAACA
43491066 AGAGGCGACAGTAATCTTGCTTTG
326 AGAGGCGACAGTAATCTTGCTTTG
43491090 AATTTTTATGCACACGAGTTGTTCTTGCTTTGAGTGTGTCTAATGTTAATAGTTTCTAAGCAATT
1 AATTTTTATGCACACGAGTTGTTCTTGCTTTGAGTGTGTCTAATGTTAATAGTTTCTAAGCAATT
43491155 TTGCTTTATGCTATTTTGCAAAAAAAATAGATATGCATCGGGAAATGTATTTACCAAAATATGCA
66 TTGCTTTATGCTATTTTGCAAAAAAAATAGATATGCATCGGGAAATGTATTTACCAAAATATGCA
43491220 TAGATGCATCAGTGGCCAAAAAGTGGGAGTTTTCTTTCCCCACTTACTGACGTCTTTATGCAAAA
131 TAGATGCATCAGTGGCCAAAAAGTGGGAGTTTTCTTTCCCCACTTACTGACGTCTTTATGCAAAA
*
43491285 AAGTTGGTGTTCCAATGGCATCCACAAAACAATCAATGAAGCCATCCCGAAGTATCAGCGATGAC
196 AAGTTGGTGTTCCAATGGCATCCACAAAACAATCAATGAAGCCATCCCGAAGTATCATCGATGAC
43491350 AC-TTTTTTTCACAATACATTGAACTTCGAGCAAAATAGATAAATGAATGGAAGAAATGCCAACA
261 ACTTTTTTTTCACAATACATTGAACTTCGAGCAAAATAGATAAATGAATGGAAGAAATGCCAACA
43491414 AGAGGCGACAGTAATCTTGCTTTG
326 AGAGGCGACAGTAATCTTGCTTTG
43491438 AATTTTTATGCACACGAGTTGTTCTTGCTTTGAGTGTGTCTAATGTTAATAGTTTCTAAGCAATT
1 AATTTTTATGCACACGAGTTGTTCTTGCTTTGAGTGTGTCTAATGTTAATAGTTTCTAAGCAATT
*
43491503 TTGCTTTATGCTATTTTGCAAAAAAAATAGATATGCATCGGGAAATGTATTTACCAAAATATGCG
66 TTGCTTTATGCTATTTTGCAAAAAAAATAGATATGCATCGGGAAATGTATTTACCAAAATATGCA
43491568 TAGATGCATCAGTGGCCAAAAAGTGGGAGTTTTCTTTCCCCACTTACTGACGTCTTTATGCAAAA
131 TAGATGCATCAGTGGCCAAAAAGTGGGAGTTTTCTTTCCCCACTTACTGACGTCTTTATGCAAAA
43491633 AAGTTGGTGTTCCAATGGCATCCACAAAACAATCAATGAAGCCATCCCGAAGTATCATCGATGAC
196 AAGTTGGTGTTCCAATGGCATCCACAAAACAATCAATGAAGCCATCCCGAAGTATCATCGATGAC
43491698 ACTTTTTTTTCACAATACATTGAACTTCGAGCAAAATAGATAAATGAATGGAAGAAATGCCAACA
261 ACTTTTTTTTCACAATACATTGAACTTCGAGCAAAATAGATAAATGAATGGAAGAAATGCCAACA
43491763 AGAGGCGACAGTAATCT
326 AGAGGCGACAGTAATCT
43491780 CGACTTTGTC
Statistics
Matches: 680, Mismatches: 9, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
348 346 0.51
349 334 0.49
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Consensus pattern (349 bp):
AATTTTTATGCACACGAGTTGTTCTTGCTTTGAGTGTGTCTAATGTTAATAGTTTCTAAGCAATT
TTGCTTTATGCTATTTTGCAAAAAAAATAGATATGCATCGGGAAATGTATTTACCAAAATATGCA
TAGATGCATCAGTGGCCAAAAAGTGGGAGTTTTCTTTCCCCACTTACTGACGTCTTTATGCAAAA
AAGTTGGTGTTCCAATGGCATCCACAAAACAATCAATGAAGCCATCCCGAAGTATCATCGATGAC
ACTTTTTTTTCACAATACATTGAACTTCGAGCAAAATAGATAAATGAATGGAAGAAATGCCAACA
AGAGGCGACAGTAATCTTGCTTTG
Found at i:43492239 original size:7 final size:7
Alignment explanation
Indices: 43492227--43492252 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
43492217 TCTAGATGAA
43492227 TTGGGCT
1 TTGGGCT
43492234 TTGGGCT
1 TTGGGCT
43492241 TTGGGCT
1 TTGGGCT
43492248 TTGGG
1 TTGGG
43492253 TTTCATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.46, T:0.42
Consensus pattern (7 bp):
TTGGGCT
Found at i:43493505 original size:16 final size:16
Alignment explanation
Indices: 43493484--43493517 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
43493474 TCGGCAAATC
*
43493484 CCAAAATGCCGAAAAG
1 CCAAAATGCCAAAAAG
43493500 CCAAAATGCCAAAAAG
1 CCAAAATGCCAAAAAG
43493516 CC
1 CC
43493518 GAAAGTTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.29, G:0.15, T:0.06
Consensus pattern (16 bp):
CCAAAATGCCAAAAAG
Found at i:43495715 original size:14 final size:14
Alignment explanation
Indices: 43495698--43495728 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
43495688 ACAAAGTTCC
43495698 TTTTATTTTTGTTAT
1 TTTTATTTTT-TTAT
43495713 TTTTATTTTTTTAT
1 TTTTATTTTTTTAT
43495727 TT
1 TT
43495729 ACAAAAACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.84
Consensus pattern (14 bp):
TTTTATTTTTTTAT
Found at i:43497291 original size:41 final size:40
Alignment explanation
Indices: 43497246--43497453 Score: 136
Period size: 41 Copynumber: 5.1 Consensus size: 40
43497236 GTGTAAATAG
* * *
43497246 GGGCACATTTGTGCTATTCAAGGGTACTGAAGTACAAACAA
1 GGGCACGTATGTGCTATTCAAGGGTAC-AAAGTACAAACAA
* *
43497287 GGGCACGTATGTG-TAATTCAAGGGTAACAAAGTATAAACAG
1 GGGCACGTATGTGCT-ATTCAAGGGT-ACAAAGTACAAACAA
* * * *
43497328 GGGCACGTATGTGCGATTCAGGGGTACCAAAGTA-TAACTA
1 GGGCACGTATGTGCTATTCAAGGGTA-CAAAGTACAAACAA
* * * * * *
43497368 GGTGCACGTATGTACAATT-TAGGG-ACCGAAGTACAAATAG
1 GG-GCACGTATGTGCTATTCAAGGGTA-CAAAGTACAAACAA
** * * * *
43497408 GGGCGTGTATGTGCAATTTAGGGGTACCAAAGTACAAACAT
1 GGGCACGTATGTGCTATTCAAGGGTA-CAAAGTACAAACAA
43497449 GGGCA
1 GGGCA
43497454 TGCATTTAGG
Statistics
Matches: 131, Mismatches: 28, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
39 21 0.16
40 17 0.13
41 91 0.69
42 2 0.02
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.23
Consensus pattern (40 bp):
GGGCACGTATGTGCTATTCAAGGGTACAAAGTACAAACAA
Found at i:43497466 original size:34 final size:34
Alignment explanation
Indices: 43497423--43497487 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
43497413 TGTATGTGCA
43497423 ATTTAGGGGTACCAAAGTACAAACATGGGCATGC
1 ATTTAGGGGTACCAAAGTACAAACATGGGCATGC
*
43497457 ATTTAGGGGTACTAAAGTACAAACATGGGCA
1 ATTTAGGGGTACCAAAGTACAAACATGGGCA
43497488 CGTATATGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (34 bp):
ATTTAGGGGTACCAAAGTACAAACATGGGCATGC
Found at i:43497509 original size:41 final size:41
Alignment explanation
Indices: 43497457--43497548 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 41
43497447 ATGGGCATGC
* *
43497457 ATTTAGGGGTACTAAAGTACAAACATGGGCACGTATATGCA
1 ATTTAGGGGTACCAAAGTACAAACATGGGCACGTATGTGCA
* * * *
43497498 ATTTAGGGGTACCGAAGTACAAACA-GGGGATTGTATATGCA
1 ATTTAGGGGTACCAAAGTACAAACATGGGCA-CGTATGTGCA
*
43497539 ATTCAGGGGT
1 ATTTAGGGGT
43497549 TAACTAACTA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
40 4 0.09
41 41 0.91
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.25
Consensus pattern (41 bp):
ATTTAGGGGTACCAAAGTACAAACATGGGCACGTATGTGCA
Found at i:43503453 original size:49 final size:49
Alignment explanation
Indices: 43503390--43503561 Score: 170
Period size: 49 Copynumber: 3.5 Consensus size: 49
43503380 CAAAGTCGAT
* *
43503390 GCCATGTCCCAGACAGGTCTTAAACTGACTTTCATATATCGAGGCCGAG
1 GCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGGCCAAG
* * * * * * *
43503439 GCCGTGTCCTAGACAGGTCTTACACTGGCTCTCATCTATC-AGTGTCAAT
1 GCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAG-GCCAAG
* * ** *
43503488 GCCATGTCCCAGACAGGTCTTACACT-AGCTTGCATATCTCGAGGCTGAT
1 GCCATGTCCCAGACAGGTCTTACACTGA-CTTTCATATATCGAGGCCAAG
*
43503537 G-CATGTCCCAGACATGTCTTACACT
1 GCCATGTCCCAGACAGGTCTTACACT
43503562 AGCTCTCGTC
Statistics
Matches: 100, Mismatches: 20, Indels: 7
0.79 0.16 0.06
Matches are distributed among these distances:
48 25 0.25
49 73 0.73
50 2 0.02
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.27
Consensus pattern (49 bp):
GCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGGCCAAG
Found at i:43503504 original size:98 final size:96
Alignment explanation
Indices: 43503336--43503568 Score: 281
Period size: 98 Copynumber: 2.4 Consensus size: 96
43503326 AGGGTAAAAT
* ** *
43503336 GCCGATGCCATGTCCCAGACATGGTCTTACAGTGGCTAGCACATCAAAGTCGATGCCATGTCCCA
1 GCCGATGCCATGTCCCAGACA-GGTCTTACACTGGCTCTCACATCAAAGTCAATGCCATGTCCCA
*
43503401 GACAGGTCTTAAACT-GACTTTCATATATCGAG
65 GACAGGTCTTAAACTAG-CTTGCATATATCGAG
* * * **
43503433 GCCGAGGCCGTGTCCTAGACAGGTCTTACACTGGCTCTCATCTATCAGTGTCAATGCCATGTCCC
1 GCCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCA-C-ATCAAAGTCAATGCCATGTCCC
* *
43503498 AGACAGGTCTTACACTAGCTTGCATATCTCGAG
64 AGACAGGTCTTAAACTAGCTTGCATATATCGAG
* * *
43503531 GCTGATG-CATGTCCCAGACATGTCTTACACTAGCTCTC
1 GCCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTC
43503569 GTCTCAACAC
Statistics
Matches: 115, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
96 16 0.14
97 46 0.40
98 52 0.45
99 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (96 bp):
GCCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCACATCAAAGTCAATGCCATGTCCCAG
ACAGGTCTTAAACTAGCTTGCATATATCGAG
Found at i:43507605 original size:21 final size:21
Alignment explanation
Indices: 43507558--43507599 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
43507548 AAGAAGTTGA
43507558 TAATTTGTTATATTATATATG
1 TAATTTGTTATATTATATATG
*
43507579 TAATTTGTTTTTATTATATAT
1 TAATTTG-TTATATTATATAT
43507600 TGATTTATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (21 bp):
TAATTTGTTATATTATATATG
Found at i:43507612 original size:22 final size:23
Alignment explanation
Indices: 43507563--43507613 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
43507553 GTTGATAATT
* *
43507563 TGTTATATTATATATGTAATTTG
1 TGTTTTATTATATATGTAATTTA
*
43507586 T-TTTTATTATATAT-TGATTTA
1 TGTTTTATTATATATGTAATTTA
43507607 TGTTTTA
1 TGTTTTA
43507614 AACTATGTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 6 0.25
22 17 0.71
23 1 0.04
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (23 bp):
TGTTTTATTATATATGTAATTTA
Found at i:43515378 original size:93 final size:93
Alignment explanation
Indices: 43515219--43515389 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
43515209 GCCCATAAGT
* *
43515219 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
43515284 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* *
43515312 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
43515377 CGAGTTCGGATGC
66 CGAGTTCGGATGC
43515390 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:43515386 original size:46 final size:46
Alignment explanation
Indices: 43515211--43515386 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
43515201 TGTAACCCGC
* * * *
43515211 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
* *
43515257 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCAT
* * *
43515307 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
43515350 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
43515387 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
44 1 0.01
45 2 0.02
46 64 0.59
47 29 0.27
48 2 0.02
49 1 0.01
50 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:43519526 original size:9 final size:9
Alignment explanation
Indices: 43519514--43519570 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
43519504 TTTGATAAAC
43519514 ATGATATGT
1 ATGATATGT
*
43519523 ATGATATGCAC
1 ATGATATG--T
*
43519534 ATGACATGT
1 ATGATATGT
*
43519543 ATGATATGCAC
1 ATGATATG--T
43519554 ATGATATGT
1 ATGATATGT
43519563 ATGATATG
1 ATGATATG
43519571 CACATGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:43519537 original size:20 final size:20
Alignment explanation
Indices: 43519512--43519582 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
43519502 ATTTTGATAA
43519512 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
43519532 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
43519552 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
43519572 ACATGAGATGT
1 ACATGATATGT
43519583 TCATAAATAC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:43519559 original size:11 final size:11
Alignment explanation
Indices: 43519523--43519577 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
43519513 CATGATATGT
43519523 ATGATATGCAC
1 ATGATATGCAC
* *
43519534 ATGACATG--T
1 ATGATATGCAC
43519543 ATGATATGCAC
1 ATGATATGCAC
*
43519554 ATGATATG--T
1 ATGATATGCAC
43519563 ATGATATGCAC
1 ATGATATGCAC
43519574 ATGA
1 ATGA
43519578 GATGTTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:43519683 original size:24 final size:24
Alignment explanation
Indices: 43519628--43519792 Score: 239
Period size: 24 Copynumber: 6.9 Consensus size: 24
43519618 GAGGAAGTGC
43519628 AAAGGGCTTATGCCCCAGTTATT-
1 AAAGGGCTTATGCCCCAGTTATTA
43519651 AAAGGGCTTATGCCCCAGTTATTA
1 AAAGGGCTTATGCCCCAGTTATTA
*
43519675 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTATTA
43519699 AAAGGGCTTATGCCCCAGTTATT-
1 AAAGGGCTTATGCCCCAGTTATTA
43519722 AAAGGGCTTATGCCCCAGTTATTAA
1 AAAGGGCTTATGCCCCAGTTATT-A
* *
43519747 AAAGGGCTT-TGCCTCAGTTACTA
1 AAAGGGCTTATGCCCCAGTTATTA
*
43519770 AAAGAGGC-TAGGCCTCCAGTTAT
1 AAAG-GGCTTATGCC-CCAGTTAT
43519793 ATGATAAAGC
Statistics
Matches: 129, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
23 52 0.40
24 62 0.48
25 15 0.12
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (24 bp):
AAAGGGCTTATGCCCCAGTTATTA
Found at i:43519726 original size:47 final size:46
Alignment explanation
Indices: 43519628--43519793 Score: 219
Period size: 47 Copynumber: 3.5 Consensus size: 46
43519618 GAGGAAGTGC
*
43519628 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
43519674 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATT
* *
43519722 AAAGGGCTTATGCCCCAGTTATTAAAAAGGGCTT-TGCCTCAGTTACTA
1 AAAGGGCTTATGCCCCAGTTA-T-AAAAGGGCTTATGCCCCAGTTA-TT
*
43519770 AAAGAGGC-TAGGCCTCCAGTTATA
1 AAAG-GGCTTATGCC-CCAGTTATA
43519794 TGATAAAGCA
Statistics
Matches: 109, Mismatches: 5, Indels: 10
0.88 0.04 0.08
Matches are distributed among these distances:
47 54 0.50
48 45 0.41
49 10 0.09
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.28
Consensus pattern (46 bp):
AAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
Found at i:43519744 original size:71 final size:71
Alignment explanation
Indices: 43519628--43519792 Score: 255
Period size: 71 Copynumber: 2.3 Consensus size: 71
43519618 GAGGAAGTGC
43519628 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT-AAAAGGGCTTATGCCCCA
1 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAAAGGGCTT-TGCCCCA
43519692 GTTA-TCA
65 GTTACT-A
*
43519699 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAAAGGGCTTTGCCTCAG
1 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAAAGGGCTTTGCCCCAG
43519764 TTACTA
66 TTACTA
*
43519770 AAAGAGGC-TAGGCCTCCAGTTAT
1 AAAG-GGCTTATGCC-CCAGTTAT
43519793 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 2, Indels: 7
0.91 0.02 0.07
Matches are distributed among these distances:
71 66 0.75
72 22 0.25
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (71 bp):
AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAAAGGGCTTTGCCCCAG
TTACTA
Found at i:43521496 original size:22 final size:22
Alignment explanation
Indices: 43521448--43521497 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
43521438 AGTTGATAAT
*
43521448 TTTTTATTATATATGTAATTTG
1 TTTTTATTATATATGTAATTTA
*
43521470 TTTTTATTATATAT-TGATTTA
1 TTTTTATTATATATGTAATTTA
43521491 TGTTTTA
1 T-TTTTA
43521498 AACTATGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (22 bp):
TTTTTATTATATATGTAATTTA
Found at i:43523332 original size:49 final size:49
Alignment explanation
Indices: 43523269--43523547 Score: 211
Period size: 49 Copynumber: 5.6 Consensus size: 49
43523259 CTGGTACGCA
*
43523269 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACCATCTGATACACG
* *
43523318 TAGTAGCCTACACTTAGTACTACATACAT--GACCTAACCATTTGATACACG
1 TAGTAGCCTGCACTTAGTACTAC--ACATGCGACC-AACCATCTGATACACG
* *** * *** * * * *
43523368 TAGTAGCTTGCACTTAGTACTACACACATGATCGAAGTTGTCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-CCATCTGATACACG
* * * * *
43523419 TAGTAGCCTGCGCTTAGTACTACACATGCGACCTACTATATGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACCATCTGATACACG
* * * * * * *
43523468 TAGGAGCCTGCACTTTGTACTACACACGTGACCTAAAACCATCTTAAACACA
1 TAGTAGCCTGCACTTAGTACTACACATGCGACC---AACCATCTGATACACG
* *
43523520 TAGTAGCCTTCACATAGTACTACACATG
1 TAGTAGCCTGCACTTAGTACTACACATG
43523548 TGTTCTCACA
Statistics
Matches: 175, Mismatches: 45, Indels: 17
0.74 0.19 0.07
Matches are distributed among these distances:
48 3 0.02
49 62 0.35
50 41 0.23
51 37 0.21
52 32 0.18
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAACCATCTGATACACG
Found at i:43523545 original size:150 final size:149
Alignment explanation
Indices: 43523261--43523547 Score: 391
Period size: 150 Copynumber: 1.9 Consensus size: 149
43523251 GAAGCTATCT
* *
43523261 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCTGATACACGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATATGATACACGTAGGAGCC
* * * *
43523326 TACACTTAGTACTACATACATGACCTAACCATTTGATACACGTAGTAGCTTGCACTTAGTACTAC
66 TACACTTAGTACTACACACATGACCTAACCATTTGAAACACATAGTAGCTTGCACATAGTACTA-
43523391 ACACATGATCGAAGTTGTCG
130 ACACATGATCGAAGTTGTCG
* * * *
43523411 GGTACGCATAGTAGCCTGCGCTTAGTACTACACATGCGACCTACTATATGGTACACGTAGGAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATATGATACACGTAGGAGCC
* * *
43523476 TGCACTTTGTACTACACACGTGACCTAAAACCATCTT-AAACACATAGTAGCCTT-CACATAGTA
66 TACACTTAGTACTACACACATGACCT--AACCAT-TTGAAACACATAGTAG-CTTGCACATAGTA
43523539 CT-ACACATG
127 CTAACACATG
43523548 TGTTCTCACA
Statistics
Matches: 120, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
150 88 0.73
152 27 0.22
153 5 0.04
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.25
Consensus pattern (149 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATATGATACACGTAGGAGCC
TACACTTAGTACTACACACATGACCTAACCATTTGAAACACATAGTAGCTTGCACATAGTACTAA
CACATGATCGAAGTTGTCG
Found at i:43524299 original size:16 final size:17
Alignment explanation
Indices: 43524278--43524316 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
43524268 TCTATAATGC
43524278 CCCAAAAATATCGAAA-
1 CCCAAAAATATCGAAAT
* *
43524294 CCCAAAAATCTTGAAAT
1 CCCAAAAATATCGAAAT
43524311 CCCAAA
1 CCCAAA
43524317 CTTTCTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.51, C:0.28, G:0.05, T:0.15
Consensus pattern (17 bp):
CCCAAAAATATCGAAAT
Found at i:43525615 original size:16 final size:16
Alignment explanation
Indices: 43525596--43525647 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
43525586 CCAAAAAGCT
*
43525596 GAAATACCGAAAAGTC
1 GAAATGCCGAAAAGTC
*
43525612 GAAATGTCGAAAAGTC
1 GAAATGCCGAAAAGTC
* * *
43525628 AAAATGCCAAAAAGCC
1 GAAATGCCGAAAAGTC
43525644 GAAA
1 GAAA
43525648 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.52, C:0.17, G:0.19, T:0.12
Consensus pattern (16 bp):
GAAATGCCGAAAAGTC
Found at i:43543130 original size:16 final size:16
Alignment explanation
Indices: 43543092--43543130 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
43543082 TTTTTCAAAG
43543092 TTACAAAACTGTTGTA
1 TTACAAAACTGTTGTA
* * *
43543108 GTCCAAAACTGTTTTA
1 TTACAAAACTGTTGTA
43543124 TTACAAA
1 TTACAAA
43543131 TTTCACTCTT
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (16 bp):
TTACAAAACTGTTGTA
Found at i:43543420 original size:49 final size:49
Alignment explanation
Indices: 43543354--43543627 Score: 262
Period size: 49 Copynumber: 5.5 Consensus size: 49
43543344 GTACGTATAA
* * * *
43543354 TAGCCTGCACTTAGTACTGCACATGCGACCAACAATCTGGTACACGTAG
1 TAGCCTGCACTTAGTACTACACACGTGACCAACCATCTGGTACACGTAG
* *
43543403 TAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAA
1 TAGCCTGCACTTAGTACTACACACGTGACC-AACCATCTGGTACACGTAG
* * *** * * *
43543453 TAGGCTGCACTTAGTACTACACACGTGATCGAAGTTGTCGGGTACGCATAG
1 TAGCCTGCACTTAGTACTACACACGTGA-CCAA-CCATCTGGTACACGTAG
* * * * * * *
43543504 TAGCCTGCAATTAGTACTACACATGCGACCTACTATATGGTACATGTAG
1 TAGCCTGCACTTAGTACTACACACGTGACCAACCATCTGGTACACGTAG
* *
43543553 TAGCCTGCACTTAGTACTACACACGTGACCTAAAACCATCTTAG-ACACATAG
1 TAGCCTGCACTTAGTACTACACACGTGACC---AACCATC-TGGTACACGTAG
*
43543605 TAGCCTGCACATAGTACTACACA
1 TAGCCTGCACTTAGTACTACACA
43543628 TGTGTTCTTA
Statistics
Matches: 179, Mismatches: 39, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
49 64 0.36
50 47 0.26
51 34 0.19
52 32 0.18
53 2 0.01
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (49 bp):
TAGCCTGCACTTAGTACTACACACGTGACCAACCATCTGGTACACGTAG
Found at i:43543604 original size:101 final size:100
Alignment explanation
Indices: 43543351--43543629 Score: 287
Period size: 101 Copynumber: 2.8 Consensus size: 100
43543341 TTTGTACGTA
* * * * *
43543351 TAATAGCCTGCACTTAGTACTGCACATGCGACC-AACAATCTGGTACACGTAGTAGCCTGCACTT
1 TAATAGCCTGCACTTAGTACTACACACGTGACCAAACAATCTGGTACACATAGTAGCCTGCAATT
* * *
43543415 AGTACTACACACGTGACCTAACCATCTGATACACG
66 AGTACTACACATGCGACCTAACCATATGATACACG
* * **** * *
43543450 TAATAGGCTGCACTTAGTACTACACACGTGATCGAAGTTGTCGGGTACGCATAGTAGCCTGCAAT
1 TAATAGCCTGCACTTAGTACTACACACGTGA-CCAAACAATCTGGTACACATAGTAGCCTGCAAT
* * *
43543515 TAGTACTACACATGCGACCT-ACTATATGGTACATG
65 TAGTACTACACATGCGACCTAACCATATGATACACG
* * *
43543550 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAAAACCATCTTAG-ACACATAGTAGCCTGCA
1 TAATAGCCTGCACTTAGTACTACACACGTGACC--AAACAATC-TGGTACACATAGTAGCCTGCA
43543614 CA-TAGTACTACACATG
63 -ATTAGTACTACACATG
43543630 TGTTCTTACA
Statistics
Matches: 145, Mismatches: 29, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
99 28 0.19
100 41 0.28
101 74 0.51
102 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (100 bp):
TAATAGCCTGCACTTAGTACTACACACGTGACCAAACAATCTGGTACACATAGTAGCCTGCAATT
AGTACTACACATGCGACCTAACCATATGATACACG
Found at i:43552975 original size:47 final size:48
Alignment explanation
Indices: 43552902--43553117 Score: 214
Period size: 46 Copynumber: 4.6 Consensus size: 48
43552892 AGTAAGGTGT
* * * * *
43552902 CGATGCCATGTCCTAGACACGATCTTACTCTAGCTCACATCTC-AAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATCTCGAAGC
* *
43552949 CAATGCCATGTCCCAGACATGGTCTTACACT-GACT-ATCATCTCGTAGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAG-CTCA-CATCTCGAAGC
* * * *
43552997 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACTTCTCGAGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATCTCGAAGC
* * *
43553043 CGATG-CATGTCCTAGACAT-GTCTTACACTAGCCCTCATCTC-AATGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATCTCGAA-GC
*
43553089 CGATGCCATGTCCCAAACATGGTCTTACA
1 CGATGCCATGTCCCAGACATGGTCTTACA
43553118 TTGGCTCTCA
Statistics
Matches: 141, Mismatches: 20, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
45 1 0.01
46 64 0.45
47 62 0.44
48 14 0.10
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.27
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATCTCGAAGC
Found at i:43553038 original size:46 final size:47
Alignment explanation
Indices: 43552902--43553123 Score: 186
Period size: 47 Copynumber: 4.7 Consensus size: 47
43552892 AGTAAGGTGT
* * * * * * * *
43552902 CGATGCCATGTCCTAGACACGATCTTACTCTAGCTCACATCTC-AAGT
1 CGATG-CATGTCCCAGACATGGTCTTACACTGGCTTACATCTCGAGGC
* *
43552949 CAATGCCATGTCCCAGACATGGTCTTACACTGAC-TATCATCTCGTA-GC
1 CGATG-CATGTCCCAGACATGGTCTTACACTGGCTTA-CATCTCG-AGGC
*
43552997 CGATGCATGTCCCAGACAT-GTCTTACACTGGCTTACTTCTCGAGGC
1 CGATGCATGTCCCAGACATGGTCTTACACTGGCTTACATCTCGAGGC
* * * * *
43553043 CGATGCATGTCCTAGACAT-GTCTTACACTAGCCCT-CATCTCAATGC
1 CGATGCATGTCCCAGACATGGTCTTACACT-GGCTTACATCTCGAGGC
* *
43553089 CGATGCCATGTCCCAAACATGGTCTTACATTGGCT
1 CGATG-CATGTCCCAGACATGGTCTTACACTGGCT
43553124 CTCATAATAT
Statistics
Matches: 144, Mismatches: 23, Indels: 16
0.79 0.13 0.09
Matches are distributed among these distances:
45 1 0.01
46 62 0.43
47 66 0.46
48 14 0.10
49 1 0.01
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (47 bp):
CGATGCATGTCCCAGACATGGTCTTACACTGGCTTACATCTCGAGGC
Found at i:43559467 original size:11 final size:11
Alignment explanation
Indices: 43559451--43559476 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
43559441 CGAAGCCCAC
43559451 ATCACAATAAT
1 ATCACAATAAT
43559462 ATCACAATAAT
1 ATCACAATAAT
43559473 ATCA
1 ATCA
43559477 TACATGCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (11 bp):
ATCACAATAAT
Found at i:43559911 original size:27 final size:27
Alignment explanation
Indices: 43559867--43560009 Score: 137
Period size: 27 Copynumber: 5.3 Consensus size: 27
43559857 CAAAATAGTC
* * * * *
43559867 ATTTTACCCTATAGGGGTATGTCGGTC
1 ATTTTACACTACAAGGGTATTTCGGTA
43559894 ATTTTACACTACAAGGGTATTTCGGTA
1 ATTTTACACTACAAGGGTATTTCGGTA
*
43559921 ATTTTACACTACAAGGGTATTTCGATA
1 ATTTTACACTACAAGGGTATTTCGGTA
* * * *
43559948 ATTTTACA-AATCGAGGGTGTTTCGATA
1 ATTTTACACTA-CAAGGGTATTTCGGTA
* **
43559975 ATTTTACA-AATCAAGGGTATTTTAGTA
1 ATTTTACACTA-CAAGGGTATTTCGGTA
43560002 ATTTTACA
1 ATTTTACA
43560010 AATCGATGGT
Statistics
Matches: 101, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
26 1 0.01
27 100 0.99
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.38
Consensus pattern (27 bp):
ATTTTACACTACAAGGGTATTTCGGTA
Found at i:43560298 original size:27 final size:27
Alignment explanation
Indices: 43559907--43560301 Score: 422
Period size: 27 Copynumber: 14.7 Consensus size: 27
43559897 TTACACTACA
* * *
43559907 AGGGTATTTCGGTAATTTTAC-ACTACA
1 AGGGTATTTCGATAATTTTACAAAT-CG
43559934 AGGGTATTTCGATAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* *
43559961 AGGGTGTTTCGATAATTTTACAAATCA
1 AGGGTATTTCGATAATTTTACAAATCG
*
43559988 AGGGTATTT-TAGTAATTTTACAAATCG
1 AGGGTATTTCGA-TAATTTTACAAATCG
* * *
43560015 ATGGTATTTCGAAAATTTTACAAATTG
1 AGGGTATTTCGATAATTTTACAAATCG
* **
43560042 AGGGTGTTTCGGCAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
*
43560069 AGGGTGTTTCGATAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* * * *
43560096 AGGGTGTTTCGGTAATTTCACAAATTG
1 AGGGTATTTCGATAATTTTACAAATCG
* * *
43560123 GGGGTATTTTGATAATTTTACAAATTG
1 AGGGTATTTCGATAATTTTACAAATCG
* * *
43560150 AGGGTATTT-TAGTAATTTCAC-AATCA
1 AGGGTATTTCGA-TAATTTTACAAATCG
* * *
43560176 AGGGTATTTTGGTAATTTTACAAAT-T
1 AGGGTATTTCGATAATTTTACAAATCG
*
43560202 AGGGGTATTTCAATAATTTTACAAATCG
1 A-GGGTATTTCGATAATTTTACAAATCG
* * * *
43560230 AGGGTATTTTGGTAATTTTATAAACCG
1 AGGGTATTTCGATAATTTTACAAATCG
*
43560257 AGGGTACTTCGATAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
*
43560284 AGGGTATTTCAATAATTT
1 AGGGTATTTCGATAATTT
43560302 CTCTTTATTA
Statistics
Matches: 308, Mismatches: 52, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
26 23 0.07
27 281 0.91
28 4 0.01
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.39
Consensus pattern (27 bp):
AGGGTATTTCGATAATTTTACAAATCG
Found at i:43560659 original size:28 final size:28
Alignment explanation
Indices: 43560607--43560680 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
43560597 CTTATTCATT
* * *
43560607 TGGCCCATTTAGGCCAAATCTCATTCACA
1 TGGCCCA-TCAGGCCCAATCACATTCACA
*
43560636 TGGCCCATCAGGCCCAATCACATTCATA
1 TGGCCCATCAGGCCCAATCACATTCACA
43560664 TGGCCCATCAGGCCCAA
1 TGGCCCATCAGGCCCAA
43560681 CTATTTCCCA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 34 0.83
29 7 0.17
ACGTcount: A:0.27, C:0.35, G:0.16, T:0.22
Consensus pattern (28 bp):
TGGCCCATCAGGCCCAATCACATTCACA
Found at i:43569463 original size:47 final size:46
Alignment explanation
Indices: 43569403--43569565 Score: 176
Period size: 47 Copynumber: 3.5 Consensus size: 46
43569393 AATGTCCGAA
43569403 CTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCATCTGAG
1 CTCGTTGAGTTGAGTCCGAGTTC-AGAGATGTAACTAGGCATCTGAG
* * * *
43569450 CTCGTTGAGTTGAGTCCGAGTTCACTTATGATGCGAA-T--G--TCCGAA
1 CTCGTTGAGTTGAGTCCGAGTTCA--GA-GATG-TAACTAGGCATCTGAG
43569495 CTCGTTGAGTTGAGTCCGAGTTCAAGAGATGTAACTAGGCAT-TCGAG
1 CTCGTTGAGTTGAGTCCGAGTTC-AGAGATGTAACTAGGCATCT-GAG
*
43569542 CTTGTTGAGTTGAGTCCGAGTTCA
1 CTCGTTGAGTTGAGTCCGAGTTCA
43569566 CTTGTGGATG
Statistics
Matches: 96, Mismatches: 9, Indels: 23
0.75 0.07 0.18
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
44 1 0.01
45 28 0.29
46 3 0.03
47 49 0.51
48 1 0.01
49 5 0.05
50 2 0.02
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (46 bp):
CTCGTTGAGTTGAGTCCGAGTTCAGAGATGTAACTAGGCATCTGAG
Found at i:43569512 original size:92 final size:93
Alignment explanation
Indices: 43569347--43569611 Score: 435
Period size: 92 Copynumber: 2.9 Consensus size: 93
43569337 AGGATATTTG
* *
43569347 GGCATTCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATTCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
43569412 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
43569440 GGCA-TCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTAT-GATGCGAATGTCCGAACTCGTTGA
1 GGCATTC-GAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGA
*
43569503 GTTGAGTCCGAGTTCAAGAGATGTAACTA
65 GTTGAGTCCGAGTTCGAGAGATGTAACTA
* * * * *
43569532 GGCATTCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTGTGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATTCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
43569597 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
43569612 CTTATGGGCG
Statistics
Matches: 160, Mismatches: 9, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
92 88 0.55
93 72 0.45
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (93 bp):
GGCATTCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:43582694 original size:2 final size:2
Alignment explanation
Indices: 43582687--43582712 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
43582677 TGCTAGAGAA
43582687 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
43582713 ATATTTCAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:43588443 original size:6 final size:6
Alignment explanation
Indices: 43588424--43588490 Score: 62
Period size: 6 Copynumber: 11.2 Consensus size: 6
43588414 TTTACAGCCG
* * * * * * *
43588424 TTATCA TTACTA TTATTA TTATTA TAATTA TTCTTA TTCTTA TTCTTC
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA
*
43588472 TTATTA TTATTA CTATTA T
1 TTATTA TTATTA TTATTA T
43588491 CATCTTCTTT
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.61
Consensus pattern (6 bp):
TTATTA
Found at i:43588446 original size:9 final size:9
Alignment explanation
Indices: 43588424--43588490 Score: 62
Period size: 9 Copynumber: 7.4 Consensus size: 9
43588414 TTTACAGCCG
*
43588424 TTATCATTA
1 TTATTATTA
*
43588433 CTATTATTA
1 TTATTATTA
*
43588442 TTATTATAA
1 TTATTATTA
*
43588451 TTATTCTTA
1 TTATTATTA
* *
43588460 TTCTTATTC
1 TTATTATTA
*
43588469 TTCTTATTA
1 TTATTATTA
*
43588478 TTATTACTA
1 TTATTATTA
43588487 TTAT
1 TTAT
43588491 CATCTTCTTT
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 46 1.00
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.61
Consensus pattern (9 bp):
TTATTATTA
Found at i:43593503 original size:14 final size:16
Alignment explanation
Indices: 43593480--43593512 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
43593470 TAAATCACGA
43593480 AAATTCCACACAT-AT
1 AAATTCCACACATAAT
43593495 AAATT-CACACATAAT
1 AAATTCCACACATAAT
43593510 AAA
1 AAA
43593513 CACTGAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATTCCACACATAAT
Found at i:43593930 original size:22 final size:22
Alignment explanation
Indices: 43593898--43593966 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
43593888 TATGCACTAT
43593898 TAAACAGAGAGCACAAATGTGC
1 TAAACAGAGAGCACAAATGTGC
*
43593920 TAAACAAAGAGCACAAATGTGC
1 TAAACAGAGAGCACAAATGTGC
* *
43593942 TAAACAGAGAGCACTAACGTGC
1 TAAACAGAGAGCACAAATGTGC
43593964 TAA
1 TAA
43593967 TTATCAGAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.14
Consensus pattern (22 bp):
TAAACAGAGAGCACAAATGTGC
Done.