Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold32
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: 5587194
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.26
Warning! 895791 characters in sequence are not A, C, G, or T
File 2 of 33
Found at i:156232 original size:129 final size:129
Alignment explanation
Indices: 156001--156325 Score: 501
Period size: 129 Copynumber: 2.5 Consensus size: 129
155991 TTCATCTCGA
*
156001 GGATACTCCAACCCCGGCTTTATTTCTAAAATATTAATTTTTCATCTCAGAGGATACTCCAACCC
1 GGATACTCCAACCCCGGCTTTATTTCTAAAATATTGATTTTTCATCTCAG-GGATACTCCAACCC
* * ***
156066 CGATTTTATTTTCAAAACATCAATTTTTCATAATCGAGGATACTCCAATCCCGTTATTTTTGAGG
65 CGATTTTATTTCCAAAACATCAATTTTTCATAATCGAGGATACTCAAATCCCGTTATTTCCAAGG
**
156131 GGATACTCCAACCCCAACTTTATTTCTAAAATATTGATTTTTCATCTCAGGGATACTCCAACCCC
1 GGATACTCCAACCCCGGCTTTATTTCTAAAATATTGATTTTTCATCTCAGGGATACTCCAACCCC
156196 GATTTTATTTCCAAAACATCAATTTTTCATAATCGAGGATACTCAAATCCCGTTATTTCCAAGG
66 GATTTTATTTCCAAAACATCAATTTTTCATAATCGAGGATACTCAAATCCCGTTATTTCCAAGG
* * * *
156260 GGATACTCCAACCCCGGTTTTATTTTTAAAATATTGATTTCTCA-CAAT-GGGGATACTCCAACC
1 GGATACTCCAACCCCGGCTTTATTTCTAAAATATTGATTTTTCATC--TCAGGGATACTCCAACC
156323 CCG
64 CCG
156326 TTATTTTGGC
Statistics
Matches: 179, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
128 1 0.01
129 130 0.73
130 48 0.27
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (129 bp):
GGATACTCCAACCCCGGCTTTATTTCTAAAATATTGATTTTTCATCTCAGGGATACTCCAACCCC
GATTTTATTTCCAAAACATCAATTTTTCATAATCGAGGATACTCAAATCCCGTTATTTCCAAGG
Found at i:156275 original size:79 final size:79
Alignment explanation
Indices: 156180--156437 Score: 320
Period size: 79 Copynumber: 3.3 Consensus size: 79
156170 TTTCATCTCA
* * * * * *
156180 GGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTCATAATCGAGGATACTCAAATC
1 GGGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCAACC
* *
156245 CCGTTATTTCCAAG
66 CCGTTATTTTCGAG
* * * * *
156259 GGGATACTCCAACCCCGGTTTTATTTTTAAAATATTGATTTCTCACAAT-GGGGATACTCCAACC
1 GGGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCAACC
* *
156323 CCGTTATTTTGGCG
66 CCGTTATTTTCGAG
* ** * * *
156337 GGGATACTCCAACTCCGACCTTATTTCTAAAGCTTCGATTTTTAACAATCGGGGATACTCCAACC
1 GGGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCAACC
156402 CCGTTATTTTCGAG
66 CCGTTATTTTCGAG
156416 GGGATACTCCAACCCCGATTTT
1 GGGATACTCCAACCCCGATTTT
156438 CTATAATCAG
Statistics
Matches: 147, Mismatches: 31, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
78 60 0.41
79 87 0.59
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.32
Consensus pattern (79 bp):
GGGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCAACC
CCGTTATTTTCGAG
Found at i:156427 original size:28 final size:28
Alignment explanation
Indices: 156387--156483 Score: 99
Period size: 28 Copynumber: 3.4 Consensus size: 28
156377 TTTAACAATC
156387 GGGGATACTCCAACCCCGTTATTTTCGA
1 GGGGATACTCCAACCCCGTTATTTTCGA
*
156415 GGGGATACTCCAACCCCGATTTTCTATAATC-A
1 GGGGATACTCCAACCCCG-TTAT-T-T--TCGA
* **
156447 -GGGATATTCCAACCATGTTATTTTCGA
1 GGGGATACTCCAACCCCGTTATTTTCGA
156474 GGGGATACTC
1 GGGGATACTC
156484 AATCCCGATT
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
26 2 0.04
27 1 0.02
28 27 0.48
29 4 0.07
30 4 0.07
31 15 0.27
32 1 0.02
33 2 0.04
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTTCGA
Found at i:156467 original size:59 final size:58
Alignment explanation
Indices: 156383--156495 Score: 172
Period size: 59 Copynumber: 1.9 Consensus size: 58
156373 GATTTTTAAC
* *
156383 AATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTCTAT
1 AATCAGGGATACTCCAACCACGTTATTTTCGAGGGGATACT-CAACCCCGATTTTCTAT
* * *
156442 AATCAGGGATATTCCAACCATGTTATTTTCGAGGGGATACTCAATCCCGATTTT
1 AATCAGGGATACTCCAACCACGTTATTTTCGAGGGGATACTCAACCCCGATTTT
156496 ATTTCTAGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
58 12 0.24
59 37 0.76
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.31
Consensus pattern (58 bp):
AATCAGGGATACTCCAACCACGTTATTTTCGAGGGGATACTCAACCCCGATTTTCTAT
Found at i:161330 original size:17 final size:17
Alignment explanation
Indices: 161310--161344 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
161300 ACATATGAAC
*
161310 ATAAAGTAAATAAAATA
1 ATAAAGGAAATAAAATA
*
161327 ATAAAGGCAATAAAATA
1 ATAAAGGAAATAAAATA
161344 A
1 A
161345 ACATGACAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.03, G:0.09, T:0.20
Consensus pattern (17 bp):
ATAAAGGAAATAAAATA
Found at i:161850 original size:22 final size:20
Alignment explanation
Indices: 161809--161875 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
161799 TTTTTATATG
*
161809 TTTTTCTTCTTTTTCTTTTT
1 TTTTTCTTCTTTGTCTTTTT
161829 TTTTTCTCTCTTCTGTC-TTTT
1 TTTTTCT-TCTT-TGTCTTTTT
* **
161850 TTTTCCTT-TTTCCCTTTTT
1 TTTTTCTTCTTTGTCTTTTT
161869 TTTTTCT
1 TTTTTCT
161876 CTAGAGCTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
18 2 0.05
19 12 0.31
20 8 0.21
21 14 0.36
22 3 0.08
ACGTcount: A:0.00, C:0.21, G:0.01, T:0.78
Consensus pattern (20 bp):
TTTTTCTTCTTTGTCTTTTT
Found at i:162229 original size:14 final size:14
Alignment explanation
Indices: 162212--162241 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
162202 AAATTTAATA
162212 TAAGATGTCCCATG
1 TAAGATGTCCCATG
162226 TAAGATGTCCCATG
1 TAAGATGTCCCATG
162240 TA
1 TA
162242 TTTATAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (14 bp):
TAAGATGTCCCATG
Found at i:163120 original size:20 final size:20
Alignment explanation
Indices: 163095--163155 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
163085 TTTATCAATT
163095 TTGATTAGATTTAACTTAAA
1 TTGATTAGATTTAACTTAAA
*
163115 TTGATTA-AGTTTAACTCAAA
1 TTGATTAGA-TTTAACTTAAA
*
163135 TTGATT-GAATTTAACCTAAA
1 TTGATTAG-ATTTAACTTAAA
163155 T
1 T
163156 CAATATTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 1 0.03
20 33 0.94
21 1 0.03
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (20 bp):
TTGATTAGATTTAACTTAAA
Found at i:164701 original size:19 final size:20
Alignment explanation
Indices: 164662--164705 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
164652 TTTAATTTTT
164662 ATATTTTAATTTGTAAAATA
1 ATATTTTAATTTGTAAAATA
*
164682 ATATTTTAATTT-TCAAATA
1 ATATTTTAATTTGTAAAATA
164701 A-ATTT
1 ATATTT
164706 AATATTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.17
19 7 0.30
20 12 0.52
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
ATATTTTAATTTGTAAAATA
Found at i:164712 original size:19 final size:19
Alignment explanation
Indices: 164662--164713 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
164652 TTTAATTTTT
* *
164662 ATATTTTAATTTGTAAAATA
1 ATATTTAAATTT-TCAAATA
*
164682 ATATTTTAATTTTCAAATA
1 ATATTTAAATTTTCAAATA
164701 A-ATTTAATATTTT
1 ATATTTAA-ATTTT
164714 ATATGTTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 5 0.17
19 12 0.41
20 12 0.41
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (19 bp):
ATATTTAAATTTTCAAATA
Found at i:164929 original size:24 final size:24
Alignment explanation
Indices: 164902--164955 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
164892 TGATTATTTT
**
164902 ATAATAAAATCAAATTTCAAATTA
1 ATAATAAAATCAAATGCCAAATTA
*
164926 ATAATAAAATTAAATGCCAAATTA
1 ATAATAAAATCAAATGCCAAATTA
164950 ATAATA
1 ATAATA
164956 TTATTTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.31
Consensus pattern (24 bp):
ATAATAAAATCAAATGCCAAATTA
Found at i:168706 original size:361 final size:361
Alignment explanation
Indices: 168042--168761 Score: 1431
Period size: 361 Copynumber: 2.0 Consensus size: 361
168032 GAAAGAAGTC
168042 ATTTGAACTGTTAGCTAATATCCTTTTAAGAATTTGAATTTAGGGCATTGTTACATAGGTTAAGA
1 ATTTGAACTGTTAGCTAATATCCTTTTAAGAATTTGAATTTAGGGCATTGTTACATAGGTTAAGA
168107 ATTCATCCTATGAAATAGAAACCATAACACATGAAGCATACACCCAAAATTGGTTGCATTCATCG
66 ATTCATCCTATGAAATAGAAACCATAACACATGAAGCATACACCCAAAATTGGTTGCATTCATCG
168172 GTTGAATACTCAGATGGGACAAATCCAAGAATAAAAATAAGATTAACTAGTTGTTTCTTTTATTA
131 GTTGAATACTCAGATGGGACAAATCCAAGAATAAAAATAAGATTAACTAGTTGTTTCTTTTATTA
*
168237 AAGAAATATGAAACACCACCAAGAGCTTTTTTGCTTGTGCAGTAGTATTATTAGAAGGAAAGCTG
196 AAGAAATATGAAACACCAACAAGAGCTTTTTTGCTTGTGCAGTAGTATTATTAGAAGGAAAGCTG
168302 AATTTGCAAATTAAATAACGCGCAAGGGAAATCTATTCTCCACGCCTTTTTTCTCTCTTTGTTCA
261 AATTTGCAAATTAAATAACGCGCAAGGGAAATCTATTCTCCACGCCTTTTTTCTCTCTTTGTTCA
168367 GTTCCATTATTCTCATAAAACAGAACCCTAATTTGA
326 GTTCCATTATTCTCATAAAACAGAACCCTAATTTGA
168403 ATTTGAACTGTTAGCTAATATCCTTTTAAGAATTTGAATTTAGGGCATTGTTACATAGGTTAAGA
1 ATTTGAACTGTTAGCTAATATCCTTTTAAGAATTTGAATTTAGGGCATTGTTACATAGGTTAAGA
168468 ATTCATCCTATGAAATAGAAACCATAACACATGAAGCATACACCCAAAATTGGTTGCATTCATCG
66 ATTCATCCTATGAAATAGAAACCATAACACATGAAGCATACACCCAAAATTGGTTGCATTCATCG
168533 GTTGAATACTCAGATGGGACAAATCCAAGAATAAAAATAAGATTAACTAGTTGTTTCTTTTATTA
131 GTTGAATACTCAGATGGGACAAATCCAAGAATAAAAATAAGATTAACTAGTTGTTTCTTTTATTA
168598 AAGAAATATGAAACACCAACAAGAGCTTTTTTGCTTGTGCAGTAGTATTATTAGAAGGAAAGCTG
196 AAGAAATATGAAACACCAACAAGAGCTTTTTTGCTTGTGCAGTAGTATTATTAGAAGGAAAGCTG
168663 AATTTGCAAATTAAATAACGCGCAAGGGAAATCTATTCTCCACGCCTTTTTTCTCTCTTTGTTCA
261 AATTTGCAAATTAAATAACGCGCAAGGGAAATCTATTCTCCACGCCTTTTTTCTCTCTTTGTTCA
168728 GTTCCATTATTCTCATAAAACAGAACCCTAATTT
326 GTTCCATTATTCTCATAAAACAGAACCCTAATTT
168762 TCTCTATGAT
Statistics
Matches: 358, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
361 358 1.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (361 bp):
ATTTGAACTGTTAGCTAATATCCTTTTAAGAATTTGAATTTAGGGCATTGTTACATAGGTTAAGA
ATTCATCCTATGAAATAGAAACCATAACACATGAAGCATACACCCAAAATTGGTTGCATTCATCG
GTTGAATACTCAGATGGGACAAATCCAAGAATAAAAATAAGATTAACTAGTTGTTTCTTTTATTA
AAGAAATATGAAACACCAACAAGAGCTTTTTTGCTTGTGCAGTAGTATTATTAGAAGGAAAGCTG
AATTTGCAAATTAAATAACGCGCAAGGGAAATCTATTCTCCACGCCTTTTTTCTCTCTTTGTTCA
GTTCCATTATTCTCATAAAACAGAACCCTAATTTGA
Found at i:169103 original size:5 final size:5
Alignment explanation
Indices: 169089--169118 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
169079 TCCAGATATG
*
169089 GAAAA TAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
169119 CGGAGAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (5 bp):
GAAAA
Found at i:169360 original size:15 final size:15
Alignment explanation
Indices: 169340--169368 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
169330 ATTTGGTCTG
169340 ATTTTTATTTTTTTT
1 ATTTTTATTTTTTTT
169355 ATTTTTATTTTTTT
1 ATTTTTATTTTTTT
169369 GTGATTTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (15 bp):
ATTTTTATTTTTTTT
Found at i:169495 original size:21 final size:20
Alignment explanation
Indices: 169469--169515 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
169459 ATTAATATAA
* *
169469 AAATAATATTTTAATATTTTT
1 AAATAATAATTT-ATATTTAT
169490 AAATAATAATTTATATTTAT
1 AAATAATAATTTATATTTAT
169510 AAATAA
1 AAATAA
169516 AAATAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATAATAATTTATATTTAT
Found at i:170323 original size:15 final size:15
Alignment explanation
Indices: 170305--170444 Score: 67
Period size: 15 Copynumber: 9.5 Consensus size: 15
170295 CACAGGTATC
*
170305 TTTGGCACAAGTACT
1 TTTGACACAAGTACT
*
170320 TTTGACACAGGTAC-
1 TTTGACACAAGTACT
* * * *
170334 GTTGATATAGGTACT
1 TTTGACACAAGTACT
*
170349 TTTGACACAAGTACC
1 TTTGACACAAGTACT
*
170364 TTT-AGCATAAGTAC-
1 TTTGA-CACAAGTACT
* * *
170378 TTTGATATAGGTACT
1 TTTGACACAAGTACT
*
170393 TTTAGTACA-AA-TACA
1 TTT-G-ACACAAGTACT
* *
170408 TTTAACATAAGTAC-
1 TTTGACACAAGTACT
*
170422 TTTGATACAAGTACCT
1 TTTGACACAAGTA-CT
170438 TTTGACA
1 TTTGACA
170445 GCAACGTTTC
Statistics
Matches: 94, Mismatches: 21, Indels: 19
0.70 0.16 0.14
Matches are distributed among these distances:
13 3 0.03
14 34 0.36
15 47 0.50
16 8 0.09
17 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (15 bp):
TTTGACACAAGTACT
Found at i:170338 original size:14 final size:15
Alignment explanation
Indices: 170294--170362 Score: 52
Period size: 15 Copynumber: 4.7 Consensus size: 15
170284 AGATATTTCT
170294 ACACAGGTATCT-TTG
1 ACACAGGTA-CTGTTG
* * *
170309 GCACAAGTACTTTTG
1 ACACAGGTACTGTTG
170324 ACACAGGTAC-GTTG
1 ACACAGGTACTGTTG
* * *
170338 ATATAGGTACTTTTG
1 ACACAGGTACTGTTG
*
170353 ACACAAGTAC
1 ACACAGGTAC
170363 CTTTAGCATA
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
14 13 0.32
15 28 0.68
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (15 bp):
ACACAGGTACTGTTG
Found at i:170358 original size:44 final size:44
Alignment explanation
Indices: 170305--170444 Score: 124
Period size: 44 Copynumber: 3.2 Consensus size: 44
170295 CACAGGTATC
* * *
170305 TTTGGCACAAGTA-CTTTTGACACAGGTACGTTGATATAGGTACT
1 TTTGACACAAGTACCTTTAG-CACAAGTACGTTGATATAGGTACT
* *
170349 TTTGACACAAGTACCTTTAGCATAAGTACTTTGATATAGGTACT
1 TTTGACACAAGTACCTTTAGCACAAGTACGTTGATATAGGTACT
* * * * * *
170393 TTTAGTACA-AA-TACATTTAACATAAGTACTTTGATACAAGTACCT
1 TTT-G-ACACAAGTACCTTTAGCACAAGTACGTTGATATAGGTA-CT
170438 TTTGACA
1 TTTGACA
170445 GCAACGTTTC
Statistics
Matches: 83, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
43 3 0.04
44 64 0.77
45 13 0.16
46 3 0.04
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (44 bp):
TTTGACACAAGTACCTTTAGCACAAGTACGTTGATATAGGTACT
Found at i:170381 original size:29 final size:30
Alignment explanation
Indices: 170294--170397 Score: 95
Period size: 29 Copynumber: 3.5 Consensus size: 30
170284 AGATATTTCT
* * *
170294 ACACAGGTATCTTTGGCACAAGTACTTTTG
1 ACACAGGTACCTTTAGCATAAGTACTTTTG
* * * *
170324 ACACAGGTACGTTGA-TATAGGTACTTTTG
1 ACACAGGTACCTTTAGCATAAGTACTTTTG
*
170353 ACACAAGTACCTTTAGCATAAGTAC-TTTG
1 ACACAGGTACCTTTAGCATAAGTACTTTTG
* * *
170382 ATATAGGTACTTTTAG
1 ACACAGGTACCTTTAG
170398 TACAAATACA
Statistics
Matches: 57, Mismatches: 16, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
29 39 0.68
30 18 0.32
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (30 bp):
ACACAGGTACCTTTAGCATAAGTACTTTTG
Found at i:184215 original size:13 final size:13
Alignment explanation
Indices: 184197--184223 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
184187 GCATTATGCT
184197 TTGTATCGATACA
1 TTGTATCGATACA
184210 TTGTATCGATACA
1 TTGTATCGATACA
184223 T
1 T
184224 GTTCATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:187922 original size:118 final size:118
Alignment explanation
Indices: 187569--187945 Score: 479
Period size: 117 Copynumber: 3.2 Consensus size: 118
187559 GATAAGTATA
* * * *
187569 CTTTGGCCGCAACTATAATCGCTCATACATTGGCCTAAGTCATTTATTTGAAAAAAAAGTTGAAT
1 CTTTGGCCACAGCTATAATCGCTCATACATTAGCCTAAGTCATTTATTTG-AAAAAGAGTTGAAT
*
187634 AATTTGCTTCATTTAAGGTTGAGATACAATCTCAT-TAATGAAGTAGATAGTTTC
65 AATTTGCTTCATTTAAGGTTGAGATACAATCTC-TCTAATGAAGTAGATAGTTCC
* * * *
187688 TTTTGGCCGCAGCTATAATCGCTAATACATTAGCCTAAGTCATTTATTCGAAAAAG-GTTGAATA
1 CTTTGGCCACAGCTATAATCGCTCATACATTAGCCTAAGTCATTTATTTGAAAAAGAGTTGAATA
* * *
187752 ATTTGCTTCATTTAAGGTTGAGATATAATCTCCCTAACGAAGTAGATAGTTCC
66 ATTTGCTTCATTTAAGGTTGAGATACAATCTCTCTAATGAAGTAGATAGTTCC
* * * * * **
187805 CTTTGGGCATAGCTATAATCACTCATACATTTGTCTAAGTCACCTATTTGAAAAAGAGTTGAATA
1 CTTTGGCCACAGCTATAATCGCTCATACATTAGCCTAAGTCATTTATTTGAAAAAGAGTTGAATA
* * * * * *
187870 ATTTACTCCATTTAAAGTTGAGATACAATCTCTCTTATAAAGTAGATTGTTCC
66 ATTTGCTTCATTTAAGGTTGAGATACAATCTCTCTAATGAAGTAGATAGTTCC
* *
187923 CTCTGGCCACAACTATAATCGCT
1 CTTTGGCCACAGCTATAATCGCT
187946 TGTATCTTGG
Statistics
Matches: 221, Mismatches: 35, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
117 101 0.46
118 75 0.34
119 45 0.20
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (118 bp):
CTTTGGCCACAGCTATAATCGCTCATACATTAGCCTAAGTCATTTATTTGAAAAAGAGTTGAATA
ATTTGCTTCATTTAAGGTTGAGATACAATCTCTCTAATGAAGTAGATAGTTCC
Found at i:187977 original size:118 final size:117
Alignment explanation
Indices: 187569--188047 Score: 435
Period size: 117 Copynumber: 4.1 Consensus size: 117
187559 GATAAGTATA
* * * * * * *
187569 CTTTGGCCGCAACTATAATCGCTCATACATTGGCCTAAGTCATTTATTTGAAAAAAAAGTTGAAT
1 CTTTGGCCACAGCTATAATCGCTAATACATTAGCCTAAGTCACTTA-TT-CAAAAAAGGTTGAAT
* *
187634 AATTTGCTTCATTTAAGGTTGAGATACAATCTCAT-TAATGAAGTAGATAGTTTC
64 AATTTACTTCATTTAAGGTTGAGATACAATCTC-TCTAATGAAGTAGATAGTTCC
* * * *
187688 TTTTGGCCGCAGCTATAATCGCTAATACATTAGCCTAAGTCATTTATTCGAAAAAGGTTGAATAA
1 CTTTGGCCACAGCTATAATCGCTAATACATTAGCCTAAGTCACTTATTCAAAAAAGGTTGAATAA
* * * *
187753 TTTGCTTCATTTAAGGTTGAGATATAATCTCCCTAACGAAGTAGATAGTTCC
66 TTTACTTCATTTAAGGTTGAGATACAATCTCTCTAATGAAGTAGATAGTTCC
* * * * * * * **
187805 CTTTGGGCATAGCTATAATCACTCATACATTTGTCTAAGTCACCTATTTGAAAAAGAGTTGAATA
1 CTTTGGCCACAGCTATAATCGCTAATACATTAGCCTAAGTCACTTATTCAAAAAAG-GTTGAATA
* * * * *
187870 ATTTACTCCATTTAAAGTTGAGATACAATCTCTCTTATAAAGTAGATTGTTCC
65 ATTTACTTCATTTAAGGTTGAGATACAATCTCTCTAATGAAGTAGATAGTTCC
* * ** * * * *
187923 CTCTGGCCACAACTATAATCGCTTGTATC-TTGGCC-ATAGACACTTAATCAAAAAAGGTTGGAT
1 CTTTGGCCACAGCTATAATCGCTAATA-CATTAGCCTA-AGTCACTTATTCAAAAAAGGTTGAAT
* * * ** * *
187986 AATTTACTTTATTTTAGGTTGAAATTTAATCTC-CTTAATTGAAGTGGATGGTTCCC
64 AATTTACTTCATTTAAGGTTGAGATACAATCTCTC-TAA-TGAAGTAGATAGTT-CC
188042 CTTTGG
1 CTTTGG
188048 TCGTATTCTT
Statistics
Matches: 295, Mismatches: 58, Indels: 14
0.80 0.16 0.04
Matches are distributed among these distances:
116 1 0.00
117 141 0.48
118 103 0.35
119 50 0.17
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.36
Consensus pattern (117 bp):
CTTTGGCCACAGCTATAATCGCTAATACATTAGCCTAAGTCACTTATTCAAAAAAGGTTGAATAA
TTTACTTCATTTAAGGTTGAGATACAATCTCTCTAATGAAGTAGATAGTTCC
Found at i:188007 original size:235 final size:238
Alignment explanation
Indices: 187581--188047 Score: 559
Period size: 235 Copynumber: 2.0 Consensus size: 238
187571 TTGGCCGCAA
* ** * *
187581 CTATAATCGCTCATACATTGGCCTAAGTCATTTATTTGAAAAAAAAGTTGAATAATTTGCTTCAT
1 CTATAATCACTCATACATTGGCCTAAGTCACCTATTTGAAAAAAAAGTTGAATAATTTACTCCAT
* * * * * * *
187646 TTAAGGTTGAGATACAATCTCATTAATGAAGTAGATAGTTTCTTTTGGCCGCAGCTATAATCGCT
66 TTAAAGTTGAGATACAATCTCATTAATAAAGTAGATAGTTCCCTCTGGCCACAACTATAATCGCT
* * * * * *
187711 AATACATTAGCCTAAGTCATTTATTCGAAAAAGGTTGAATAATTTGCTTCATTTAAGGTTGAGAT
131 AATACATTAGCCTAAGACACTTAATCAAAAAAGGTTGAATAATTTACTTCATTTAAGGTTGAAAT
187776 ATAATCTCCCTAA-CGAAGTAGATAGTT-CCCTTTGGGCATAG
196 ATAATCTCCCTAATCGAAGTAGATAGTTCCCCTTTGGGCATAG
* * *
187817 CTATAATCACTCATACATTTGTCTAAGTCACCTATTTG-AAAAAGAGTTGAATAATTTACTCCAT
1 CTATAATCACTCATACATTGGCCTAAGTCACCTATTTGAAAAAAAAGTTGAATAATTTACTCCAT
* *
187881 TTAAAGTTGAGATACAATCTC-TCTTATAAAGTAGATTGTTCCCTCTGGCCACAACTATAATCGC
66 TTAAAGTTGAGATACAATCTCAT-TAATAAAGTAGATAGTTCCCTCTGGCCACAACTATAATCGC
** * * * *
187945 TTGTATC-TTGGCC-ATAGACACTTAATCAAAAAAGGTTGGATAATTTACTTTATTTTAGGTTGA
130 TAATA-CATTAGCCTA-AGACACTTAATCAAAAAAGGTTGAATAATTTACTTCATTTAAGGTTGA
* * * * *
188008 AATTTAATCTCCTTAATTGAAGTGGATGGTTCCCCTTTGG
193 AATATAATCTCCCTAATCGAAGTAGATAGTTCCCCTTTGG
188048 TCGTATTCTT
Statistics
Matches: 192, Mismatches: 34, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
234 2 0.01
235 137 0.71
236 45 0.23
237 8 0.04
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (238 bp):
CTATAATCACTCATACATTGGCCTAAGTCACCTATTTGAAAAAAAAGTTGAATAATTTACTCCAT
TTAAAGTTGAGATACAATCTCATTAATAAAGTAGATAGTTCCCTCTGGCCACAACTATAATCGCT
AATACATTAGCCTAAGACACTTAATCAAAAAAGGTTGAATAATTTACTTCATTTAAGGTTGAAAT
ATAATCTCCCTAATCGAAGTAGATAGTTCCCCTTTGGGCATAG
Found at i:188911 original size:24 final size:24
Alignment explanation
Indices: 188884--188959 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
188874 AATCCAAATG
*
188884 TGTTCCATGAGTCATGCAAAAAGA
1 TGTTCCATAAGTCATGCAAAAAGA
* * * *
188908 TGTTCCATAAGTTATGCCAAAGGT
1 TGTTCCATAAGTCATGCAAAAAGA
* *
188932 TGTTCCACAAGTCGTGCCAAAAA-A
1 TGTTCCATAAGTCATG-CAAAAAGA
188956 TGTT
1 TGTT
188960 TTAAGAGTTG
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
24 36 0.90
25 4 0.10
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (24 bp):
TGTTCCATAAGTCATGCAAAAAGA
Found at i:189749 original size:31 final size:30
Alignment explanation
Indices: 189697--189792 Score: 93
Period size: 36 Copynumber: 3.0 Consensus size: 30
189687 CCTTACAACA
* *
189697 CTATCTTTTGAAGACTAAGATAAAACCTCC
1 CTATCTTTTCAAGGCTAAGATAAAACCTCC
*
189727 CTATCTTTTCACAGGCTAAGATAGAACCTTTCTCC
1 CTATCTTTTCA-AGGCTAAGATA-AAAC---CTCC
*
189762 CTATCTTTTTCAAAGGCTAAGATAGAACCTC
1 CTATC-TTTTC-AAGGCTAAGATAAAACCTC
189793 TCAATCACTT
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
30 10 0.19
31 10 0.19
32 6 0.11
35 11 0.20
36 16 0.30
37 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.32
Consensus pattern (30 bp):
CTATCTTTTCAAGGCTAAGATAAAACCTCC
Found at i:189769 original size:35 final size:36
Alignment explanation
Indices: 189723--189791 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
189713 AAGATAAAAC
*
189723 CTCCCTATC-TTTTCACAGGCTAAGATAGAACCTTT
1 CTCCCTATCTTTTTCAAAGGCTAAGATAGAACCTTT
189758 CTCCCTATCTTTTTCAAAGGCTAAGATAGAACCT
1 CTCCCTATCTTTTTCAAAGGCTAAGATAGAACCT
189792 CTCAATCACT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 9 0.28
36 23 0.72
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.33
Consensus pattern (36 bp):
CTCCCTATCTTTTTCAAAGGCTAAGATAGAACCTTT
Found at i:190240 original size:20 final size:20
Alignment explanation
Indices: 190212--190249 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
190202 CCGTTGGGCT
190212 TAATATATTGATACAATTTA
1 TAATATATTGATACAATTTA
* *
190232 TAATGTATTTATACAATT
1 TAATATATTGATACAATT
190250 ATAGCCGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (20 bp):
TAATATATTGATACAATTTA
Found at i:191667 original size:21 final size:21
Alignment explanation
Indices: 191642--191698 Score: 89
Period size: 21 Copynumber: 2.7 Consensus size: 21
191632 AAAATTTCCA
*
191642 AATGTATCGATACATTTGTAGG
1 AATGTATCGATACATTCGT-GG
191664 -ATGTATCGATACATTCGTGG
1 AATGTATCGATACATTCGTGG
191684 AATGTATCGATACAT
1 AATGTATCGATACAT
191699 CCTACAAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 2 0.06
21 31 0.94
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTCGTGG
Found at i:191778 original size:19 final size:19
Alignment explanation
Indices: 191754--191821 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
191744 AATTCAACAA
191754 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
191773 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
191788 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
191805 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
191822 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:191793 original size:13 final size:13
Alignment explanation
Indices: 191775--191799 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
191765 ACATAAGTTT
191775 TGTATCGATACAA
1 TGTATCGATACAA
191788 TGTATCGATACA
1 TGTATCGATACA
191800 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:191797 original size:32 final size:32
Alignment explanation
Indices: 191756--191818 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
191746 TTCAACAATT
*
191756 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
191788 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
191819 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:191880 original size:13 final size:13
Alignment explanation
Indices: 191862--191888 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
191852 ATTTTTCTGT
191862 GTATCGATACATG
1 GTATCGATACATG
191875 GTATCGATACATG
1 GTATCGATACATG
191888 G
1 G
191889 ATCTTTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (13 bp):
GTATCGATACATG
Found at i:191884 original size:33 final size:33
Alignment explanation
Indices: 191842--191906 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
191832 TCAAGGAAAT
***
191842 GTATCGATACATTTTTCTGTGTATCGATACATG
1 GTATCGATACATGGATCTGTGTATCGATACATG
*
191875 GTATCGATACATGGATCTTTGTATCGATACAT
1 GTATCGATACATGGATCTGTGTATCGATACAT
191907 TTGGAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.40
Consensus pattern (33 bp):
GTATCGATACATGGATCTGTGTATCGATACATG
Found at i:194309 original size:51 final size:53
Alignment explanation
Indices: 194248--194581 Score: 203
Period size: 52 Copynumber: 6.3 Consensus size: 53
194238 AATTCTCCAC
* * * *
194248 AATCGAGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-TT-TTCTAT
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTCTTC-AT
*
194299 AATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCAT
1 AATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAATTTCTTCAT
* * * *** * * ***
194353 AATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAACCCCGTT-AT
1 AATCGGGGATACTCCAACTCCGATTTTAT-TTC-CAAAAACACCAATTTC-TTCAT
* * * * *
194406 -TTCCGAGGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAATTT-TTCCAC
1 AAT-C--GGGGATACTCCAACTCCGATTTTATTTC-CAAAAACACCAATTTCTT-CAT
* * *
194460 AATCGGGGATACTCCAA-TCCTGGTTTTATTTTC-AAAACGCCAATTTTCCTT--T
1 AATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAAACACCAA-TTT-CTTCAT
* *
194512 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTT-TTCAC
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTCTTCAT
*
194564 AATCGAGGATACTCCAAC
1 AATCGGGGATACTCCAAC
194582 CTCGTTATTT
Statistics
Matches: 217, Mismatches: 41, Indels: 49
0.71 0.13 0.16
Matches are distributed among these distances:
50 2 0.01
51 32 0.15
52 82 0.38
53 37 0.17
54 38 0.18
55 23 0.11
57 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (53 bp):
AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTCTTCAT
Found at i:194424 original size:28 final size:27
Alignment explanation
Indices: 194357--194425 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
194347 CTTCATAATC
**
194357 GGGGATACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCAGA
* *
194384 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTA-ATCAGA
194412 GGGGATACTCCAAC
1 GGGGATACTCCAAC
194426 TCCGGTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.25, C:0.32, G:0.22, T:0.22
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCAGA
Found at i:194565 original size:104 final size:103
Alignment explanation
Indices: 194245--194580 Score: 288
Period size: 104 Copynumber: 3.2 Consensus size: 103
194235 ATCAATTCTC
* * * *
194245 CACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTT-CTATAATCGGGGAT
1 CACAATCGAGGATACTCCAA-TCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGAT
*
194309 ACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
65 ACTCCAACTCCGATTTTATTTCC-AAAAACACCAATTT-TT
* * * * * ** * * * ** * *
194350 CATAATCGGGGATACTCCAACCCCG-TTAATCATCGGGGATACTCCAA--CCCCGTTATTTCCGA
1 CACAATCGAGGATACTCCAATCCGGTTTTATTTTC---AAAACACCAATTTTCCTTTA-AT-C--
* * *
194412 GGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAATTTTT
59 GGGGATACTCCAACTCCGATTTTATTTC-CAAAAACACCAATTTTT
* *
194456 CCACAATCGGGGATACTCCAATCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGGGA
1 -CACAATCGAGGATACTCCAATCC-GGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGA
*
194521 TACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
64 TACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
194561 CACAATCGAGGATACTCCAA
1 CACAATCGAGGATACTCCAA
194581 CCTCGTTATT
Statistics
Matches: 175, Mismatches: 40, Indels: 33
0.71 0.16 0.13
Matches are distributed among these distances:
103 6 0.03
104 44 0.25
105 34 0.19
106 19 0.11
107 37 0.21
108 7 0.04
109 28 0.16
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (103 bp):
CACAATCGAGGATACTCCAATCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATA
CTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
Found at i:194601 original size:28 final size:28
Alignment explanation
Indices: 194565--194641 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
194555 ATTTTTCACA
* * *
194565 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
194593 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
194621 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
194642 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:194610 original size:212 final size:212
Alignment explanation
Indices: 194243--194648 Score: 629
Period size: 212 Copynumber: 1.9 Consensus size: 212
194233 TTATCAATTC
* *
194243 TCCACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
* * *
194308 TACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCATAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
* * *
194373 CGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACTCCGGTTTTATC
131 CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATC
194438 GCTAAAACACTAATTTT
196 GCTAAAACACTAATTTT
* * * *
194455 TCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGG
1 TCCACAATCGAGGATACTCCAACTCC-GATTTTATTTTCAAAACACCAATTTT-CTATAATCGGG
*
194519 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* *
194582 CTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
129 CCCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
194647 AT
193 AT
194649 TCCCAAAATA
Statistics
Matches: 176, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
211 30 0.17
212 111 0.63
213 35 0.20
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (212 bp):
TCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATC
GCTAAAACACTAATTTT
Found at i:194708 original size:107 final size:104
Alignment explanation
Indices: 194303--194720 Score: 337
Period size: 107 Copynumber: 3.9 Consensus size: 104
194293 TTCTATAATC
* * * * *
194303 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCATAATCGGGGATACTCC
1 GGGGATACTCCAACTCCGGTTTTA-TTCC-AAAAATACTAATTTC-TCACAATCGGGGATACTCC
**
194368 AACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGA
63 AACCCCGTT-ATTTTCGGGGATACTCCAACCCCGTTA-TTCCGA
* * *
194412 GGGGATACTCCAACTCCGGTTTTA-TCGCTAAAACACTAATTTTTCCACAATCGGGGATACTCCA
1 GGGGATACTCCAACTCCGGTTTTATTC-CAAAAATACTAATTTCT-CACAATCGGGGATACTCCA
** * * * ** * *
194476 ATCCTGGTTTTATTTTC---AAAACGCCAATTTTCCTTTAAT-C--
64 A-CCCCG--TTATTTTCGGGGATACTCCAA--CCCCGTTATTCCGA
* * * *
194516 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACTCCGGTTTTA-TTCCAAAAATACTAATTTCTCACAATCGGGGATACTCCAA
*
194581 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
65 CCCCGTTATTT--TCGGGGATACTCCAACCCCGTTA-TTCCGA
* * * * * * *
194624 GGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAAC
1 GGGGATACTCCAACTCCGGTTTTATTCCAAAAATACTAATTTCTCACAATCGGGGATACTCCAAC
*
194689 CCCGTTATTTTCGAAGGGATACTCCAATCCCG
66 CCCGTTATTTTCG--GGGATACTCCAACCCCG
194721 ATTTTTTTTT
Statistics
Matches: 246, Mismatches: 43, Indels: 42
0.74 0.13 0.13
Matches are distributed among these distances:
101 6 0.02
103 6 0.02
104 47 0.19
105 18 0.07
106 19 0.08
107 92 0.37
108 30 0.12
109 26 0.11
110 2 0.01
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (104 bp):
GGGGATACTCCAACTCCGGTTTTATTCCAAAAATACTAATTTCTCACAATCGGGGATACTCCAAC
CCCGTTATTTTCGGGGATACTCCAACCCCGTTATTCCGA
Found at i:194744 original size:79 final size:79
Alignment explanation
Indices: 194595--194797 Score: 230
Period size: 79 Copynumber: 2.6 Consensus size: 79
194585 GTTATTTCAT
* * * *
194595 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
* * *
194660 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * * ** *
194674 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGATTTTTTTTTC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAAT-A
194738 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* *
194753 CGGGGATACTCCAGCCCCGTTATTTTC-AAGGGAACACTCCAACCC
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACCC
194798 TGTCATTATC
Statistics
Matches: 104, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
78 8 0.08
79 96 0.92
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:195842 original size:28 final size:28
Alignment explanation
Indices: 195773--196390 Score: 619
Period size: 28 Copynumber: 21.5 Consensus size: 28
195763 CGTCGCGACA
* * *
195773 GTGGGCATTAAAAGGGTGCCACTGACTTGC
1 GTGGGCTTTGAAAGGATGCCACTGAC-T-C
195803 GTGGGCTTTGAAAGGATGCCACTGACTC
1 GTGGGCTTTGAAAGGATGCCACTGACTC
*
195831 GTGGGCTTTGAAA-GAGTGCCACTGACTT
1 GTGGGCTTTGAAAGGA-TGCCACTGACTC
195859 GTGGGCTTTGAAAGG-TGCCACTGACTC
1 GTGGGCTTTGAAAGGATGCCACTGACTC
*
195886 GTGGGCTTTGAAAAGG-TACCACTGACTC
1 GTGGGCTTTG-AAAGGATGCCACTGACTC
* *
195914 GTGGGC-TTGAAAGGGTGCCACTGACTT
1 GTGGGCTTTGAAAGGATGCCACTGACTC
195941 GTGGGCTTTGAAA-GAGTGCCACTGACTC
1 GTGGGCTTTGAAAGGA-TGCCACTGACTC
* *
195969 GTGGGCTTTGAAA-AAGTGCCACTAACTTGC
1 GTGGGCTTTGAAAGGA-TGCCACTGAC-T-C
*
195999 GTGGGCTTTGAAAGGAGTGCCACTGACTTGT
1 GTGGGCTTTGAAAGGA-TGCCACTGAC-T-C
*
196030 GTGGGCTTTGAAAAGG-TGCCACTAACTC
1 GTGGGCTTTG-AAAGGATGCCACTGACTC
*
196058 GTGGGCTTTGAAAGGATGCCACTGACTT
1 GTGGGCTTTGAAAGGATGCCACTGACTC
196086 GTGGGCTTTGAAA-GATGCCACTGACTC
1 GTGGGCTTTGAAAGGATGCCACTGACTC
*
196113 GTGGGCTTTGAAAAGG-TACCACTGACTC
1 GTGGGCTTTG-AAAGGATGCCACTGACTC
* *
196141 GTGGGC-TTGAAAGGGTGCCACTGACTT
1 GTGGGCTTTGAAAGGATGCCACTGACTC
196168 GTGGGCTTTGAAA-GAGTGCCACTGACTC
1 GTGGGCTTTGAAAGGA-TGCCACTGACTC
* * *
196196 GTGGGCTTTGAAAAGAGTGCCACTAACTT
1 GTGGGCTTTGAAAGGA-TGCCACTGACTC
* * *
196225 GTGGGCTTTAAAAGGGTGCCACTAACTTGC
1 GTGGGCTTTGAAAGGATGCCACTGAC-T-C
* *
196255 GTGGGCTTTGAAAGGGGTGCCACTGACTT
1 GTGGGCTTTGAAA-GGATGCCACTGACTC
* * *
196284 GTGGGCTTTGAAAGGGTGCCACCGACTTAT
1 GTGGGCTTTGAAAGGATGCCACTGAC-T-C
* * *
196314 GTGGGCTTTGAAAAGTGTTGCCACCGACTTGT
1 GTGGGCTTTG-AAAG-GATGCCACTGAC-T-C
* * *
196346 GTGGGCTTTGAAATGGGTTGCCACCGACTT
1 GTGGGCTTTGAAA--GGATGCCACTGACTC
196376 GTATGGGCTTTGAAA
1 G--TGGGCTTTGAAA
196391 TGGGTTGCCA
Statistics
Matches: 523, Mismatches: 37, Indels: 54
0.85 0.06 0.09
Matches are distributed among these distances:
26 10 0.02
27 91 0.17
28 206 0.39
29 46 0.09
30 72 0.14
31 44 0.08
32 53 0.10
33 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (28 bp):
GTGGGCTTTGAAAGGATGCCACTGACTC
Found at i:195893 original size:55 final size:55
Alignment explanation
Indices: 195773--196390 Score: 670
Period size: 55 Copynumber: 10.7 Consensus size: 55
195763 CGTCGCGACA
* * *
195773 GTGGGCATTAAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAGGATGCCACTGACTC
1 GTGGGCTTTGAAAGAGTGCCACTGACTT--GTGGGCTTTGAAAGG-TGCCACTGACTC
195831 GTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGTGCCACTGACTC
1 GTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGTGCCACTGACTC
* * *
195886 GTGGGCTTTGAAA-AGGTACCACTGACTCGTGGGC-TTGAAAGGGTGCCACTGACTT
1 GTGGGCTTTGAAAGA-GTGCCACTGACTTGTGGGCTTTGAAA-GGTGCCACTGACTC
* * *
195941 GTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAAGTGCCACTAACTTGC
1 GTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGTGCCACTGAC-T-C
*
195999 GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAAGGTGCCACTAACTC
1 GTGGGCTTTGAAA-GAGTGCCACTGAC-T-TGTGGGCTTTG-AAAGGTGCCACTGACTC
*
196058 GTGGGCTTTGAAAG-GATGCCACTGACTTGTGGGCTTTGAAAGATGCCACTGACTC
1 GTGGGCTTTGAAAGAG-TGCCACTGACTTGTGGGCTTTGAAAGGTGCCACTGACTC
* * *
196113 GTGGGCTTTGAAA-AGGTACCACTGACTCGTGGGC-TTGAAAGGGTGCCACTGACTT
1 GTGGGCTTTGAAAGA-GTGCCACTGACTTGTGGGCTTTGAAA-GGTGCCACTGACTC
* * *
196168 GTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGAGTGCCACTAACTT
1 GTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAG-GTGCCACTGACTC
* * * *
196225 GTGGGCTTTAAAAGGGTGCCACTAACTTGCGTGGGCTTTGAAAGGGGTGCCACTGACTT
1 GTGGGCTTTGAAAGAGTGCCACTGACTT--GTGGGCTTTGAAA--GGTGCCACTGACTC
* * * *
196284 GTGGGCTTTGAAAGGGTGCCACCGACTTATGTGGGCTTTGAAAAGTGTTGCCACCGACTTGT
1 GTGGGCTTTGAAAGAGTGCCACTGAC-T-TGTGGGCTTTG-AAAG-G-TGCCACTGAC-T-C
* *
196346 GTGGGCTTTGAAATGGGTTGCCACCGACTTGTATGGGCTTTGAAA
1 GTGGGCTTTGAAA-GAG-TGCCACTGACTTG--TGGGCTTTGAAA
196391 TGGGTTGCCA
Statistics
Matches: 498, Mismatches: 29, Indels: 61
0.85 0.05 0.10
Matches are distributed among these distances:
54 13 0.03
55 173 0.35
56 46 0.09
57 45 0.09
58 53 0.11
59 83 0.17
60 16 0.03
61 27 0.05
62 16 0.03
63 7 0.01
64 19 0.04
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (55 bp):
GTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGTGCCACTGACTC
Found at i:196183 original size:227 final size:225
Alignment explanation
Indices: 195773--196488 Score: 927
Period size: 227 Copynumber: 3.1 Consensus size: 225
195763 CGTCGCGACA
*
195773 GTGGGCATTAAAAGGGTGCCACTGACTTGCGTGGGCTTTG-AAAGGATGCCACTGACTCGTGGGC
1 GTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAAGG-TGCCACTGACTCGTGGGC
*
195837 TTTGAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAGGTGCCACTGACTCGTGGGCTTTGAAAAG
65 TTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAGATGCCACTGACTCGTGGGCTTTGAAAAG
195901 GTACCACTGACTCGTGGGCTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGA
129 GTACCACTGACTCGTGGGCTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGA
195966 CTCGTGGGCTTTGAAAA-AGTGCCACTAACTT
194 CTCGTGGGCTTTGAAAAGAGTGCCACTAACTT
* * *
195997 GCGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAAGGTGCCACTAACTCGTGG
1 --GTGGGCTTTAAAAGG-GTGCCACTGACTTGCGTGGGCTTTGAAAAGGTGCCACTGACTCGTGG
196062 GCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGATGCCACTGACTCGTGGGCTTTGAAAA
63 GCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGATGCCACTGACTCGTGGGCTTTGAAAA
196127 GGTACCACTGACTCGTGGGCTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTG
128 GGTACCACTGACTCGTGGGCTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTG
196192 ACTCGTGGGCTTTGAAAAGAGTGCCACTAACTT
193 ACTCGTGGGCTTTGAAAAGAGTGCCACTAACTT
* * *
196225 GTGGGCTTTAAAAGGGTGCCACTAACTTGCGTGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGC
1 GTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAA-AGGTGCCACTGACTCGTGGGC
* * * * *
196290 TTTGAAAGGGTGCCACCGACTTATGTGGGCTTTGAAAAGTGTTGCCACCGACTTGTGTGGGCTTT
65 TTTGAAAGGATGCCACTGAC-T-TGTGGGCTTTG-AAA--GATGCCACTGAC-T-CGTGGGCTTT
* * * * **
196355 GAAATGGGTTGCCACCGACTTGTATGGGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTG
123 GAAA-AGG-TACCACTGACTCG--TGGGC-TTGAAA-GGG-TGCCACTGAC-T-TGTGGGCTTTG
* * * * * * ** *
196420 AAATGGGTGCCACAGAGTTGT-GGATTTTAAAAGAGTGCCACGGAGTT
179 AAA-GAGTGCCACTGACTCGTGGGCTTTGAAAAGAGTGCCACTAACTT
**
196467 GTGGATTTTAAAAGGGTGCCAC
1 GTGGGCTTTAAAAGGGTGCCAC
196489 GGAGTTGTGG
Statistics
Matches: 435, Mismatches: 33, Indels: 28
0.88 0.07 0.06
Matches are distributed among these distances:
225 26 0.06
226 63 0.14
227 184 0.42
228 32 0.07
229 3 0.01
231 10 0.02
232 1 0.00
233 13 0.03
234 2 0.00
235 10 0.02
237 5 0.01
238 6 0.01
239 3 0.01
240 8 0.02
241 1 0.00
242 55 0.13
243 13 0.03
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (225 bp):
GTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAAGGTGCCACTGACTCGTGGGCT
TTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGATGCCACTGACTCGTGGGCTTTGAAAAGGT
ACCACTGACTCGTGGGCTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
CGTGGGCTTTGAAAAGAGTGCCACTAACTT
Found at i:196577 original size:27 final size:27
Alignment explanation
Indices: 196424--196998 Score: 907
Period size: 27 Copynumber: 21.0 Consensus size: 27
196414 GCTTTGAAAT
* *
196424 GGGTGCCACAGAGTTGTGGATTTTAAAA
1 GGGTGCCACGGAGTTGTGGA-CTTAAAA
* *
196452 GAGTGCCACGGAGTTGTGGATTTTAAAA
1 GGGTGCCACGGAGTTGTGGA-CTTAAAA
*
196480 GGGTGCCACGGAGTTGTGGATTTTAAAA
1 GGGTGCCACGGAGTTGTGGA-CTTAAAA
* *
196508 GGGTGCCACAGAGTTGTGGACTCAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
196535 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
196563 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
196590 GGGTTCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
196617 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
196644 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
196671 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
196698 GGGTGCCACGGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
196725 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
196753 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
196780 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
196808 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
196835 GGGTGCCACGGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
196862 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
196890 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
196917 GAGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
196944 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
196971 GGGTGCCACGGAGTTGTGGGCTTTAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
196998 G
1 G
196999 AGGTCACACT
Statistics
Matches: 511, Mismatches: 32, Indels: 9
0.93 0.06 0.02
Matches are distributed among these distances:
27 341 0.67
28 170 0.33
ACGTcount: A:0.28, C:0.14, G:0.35, T:0.23
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:196769 original size:273 final size:274
Alignment explanation
Indices: 196424--196989 Score: 931
Period size: 273 Copynumber: 2.1 Consensus size: 274
196414 GCTTTGAAAT
* * * *
196424 GGGTGCCACAGAGTTGTGGATTTTAAAAGAGTGCCACGGAGTTGTGGATTTTAAAAGGGTGCCAC
1 GGGTGCCACGGAGTTGTGGATCTAAAAAGAGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCAC
* * * *
196489 GGAGTTGTGGATTTTAAAAG-GGTGCCACAGAGTTGTGGACTCAAAAGAGATGCCACGGAGTTAT
66 AGAGTTGTGGA-CTTAAAAGAGATGCCACAGAGTTATGGACTCAAAAG-GATGCCACGGAGTTAT
*
196553 GGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG-TTCCACGGAGTTGTGGACTTAAAA
129 GGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAA
* *
196617 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAG
194 GGGTGCCACGGAGTTGTGGACTTAAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACAG
196682 AGTTGTGGACTTAAAA
259 AGTTGTGGACTTAAAA
*
196698 GGGTGCCACGGAGTTGTGGA-CTAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCAC
1 GGGTGCCACGGAGTTGTGGATCTAAAAAGAGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCAC
* * * *
196762 AGAGTTGTGGACTTAAAAGAGATGCCACGGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGG
66 AGAGTTGTGGACTTAAAAGAGATGCCACAGAGTTATGGACTCAAAAGGATGCCACGGAGTTATGG
*
196827 ACTTAAAAGGGTGCCACGGAGTTGTGGTCTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGG
131 ACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGG
*
196892 GTGCCACGGAGTTGTGGACTTAAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
196 GTGCCACGGAGTTGTGGACTTAAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACAGAG
196957 TTGTGGACTTAAAA
261 TTGTGGACTTAAAA
196971 GGGTGCCACGGAGTTGTGG
1 GGGTGCCACGGAGTTGTGG
196990 GCTTTAAAGA
Statistics
Matches: 272, Mismatches: 18, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
272 60 0.22
273 193 0.71
274 19 0.07
ACGTcount: A:0.28, C:0.14, G:0.35, T:0.23
Consensus pattern (274 bp):
GGGTGCCACGGAGTTGTGGATCTAAAAAGAGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCAC
AGAGTTGTGGACTTAAAAGAGATGCCACAGAGTTATGGACTCAAAAGGATGCCACGGAGTTATGG
ACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGG
GTGCCACGGAGTTGTGGACTTAAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACAGAG
TTGTGGACTTAAAA
Found at i:205348 original size:20 final size:19
Alignment explanation
Indices: 205323--205393 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
205313 AGACATAATG
205323 TATCGATACATTGTAGAATA
1 TATCGATACATTGTA-AATA
* * *
205343 TATCGATACATTCATACATG
1 TATCGATACATT-GTAAATA
* *
205363 TATCGATATATTGAAAAATA
1 TATCGATACATTG-TAAATA
205383 TATCGATACAT
1 TATCGATACAT
205394 CAAGGTAAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 38 0.95
21 2 0.05
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (19 bp):
TATCGATACATTGTAAATA
Found at i:205383 original size:40 final size:39
Alignment explanation
Indices: 205316--205393 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
205306 GGTAAAAAGA
* *
205316 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
*
205355 CATACATGTATCGATATATTGAAAAATATATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
205394 CAAGGTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:208859 original size:45 final size:45
Alignment explanation
Indices: 208810--208896 Score: 122
Period size: 45 Copynumber: 1.9 Consensus size: 45
208800 TATCCCACGA
* * *
208810 ATATTACCTCGCAAATACTA-CTTAGCTTTGAATAATACCTTGTGG
1 ATATTACCTCGCAAATAATATCGT-GCATTGAATAATACCTTGTGG
*
208855 ATATTACCTCGCGAATAATATCGTGCATTGAATAATACCTTG
1 ATATTACCTCGCAAATAATATCGTGCATTGAATAATACCTTG
208897 CAAATAATGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 35 0.95
46 2 0.05
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (45 bp):
ATATTACCTCGCAAATAATATCGTGCATTGAATAATACCTTGTGG
Found at i:209494 original size:15 final size:15
Alignment explanation
Indices: 209459--209556 Score: 67
Period size: 15 Copynumber: 6.7 Consensus size: 15
209449 ACTTTTGTAC
* *
209459 AAGTGCCTTTAGCAT
1 AAGTACCTTTGGCAT
* * *
209474 AGGTACCTTTGACAC
1 AAGTACCTTTGGCAT
209489 AAGTA-CTTTGGCA-
1 AAGTACCTTTGGCAT
* *
209502 CAGATA-CTTCGGCAT
1 AAG-TACCTTTGGCAT
*
209517 AAGTAGCTTTGGCAT
1 AAGTACCTTTGGCAT
* *
209532 AAGTACCTTCGACAT
1 AAGTACCTTTGGCAT
*
209547 AGGTACCTTT
1 AAGTACCTTT
209557 TGGTAGCAAT
Statistics
Matches: 64, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
13 2 0.03
14 18 0.28
15 44 0.69
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (15 bp):
AAGTACCTTTGGCAT
Found at i:209503 original size:14 final size:14
Alignment explanation
Indices: 209480--209537 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
209470 GCATAGGTAC
*
209480 CTTTGACACAAGTA
1 CTTTGGCACAAGTA
209494 CTTTGGCAC-AGATA
1 CTTTGGCACAAG-TA
* *
209508 CTTCGGCATAAGTA
1 CTTTGGCACAAGTA
*
209522 GCTTTGGCATAAGTA
1 -CTTTGGCACAAGTA
209537 C
1 C
209538 CTTCGACATA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
13 2 0.05
14 20 0.54
15 15 0.41
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (14 bp):
CTTTGGCACAAGTA
Found at i:212200 original size:19 final size:20
Alignment explanation
Indices: 212176--212226 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
212166 ATAATTCTTT
*
212176 ATGTATCGATACAATG-AGC
1 ATGTATCGATACAATGCAAC
* *
212195 ATGTATCGATACATTGCAAT
1 ATGTATCGATACAATGCAAC
212215 ATGTATCGATAC
1 ATGTATCGATAC
212227 TTCTGGGCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGCAAC
Found at i:212921 original size:17 final size:17
Alignment explanation
Indices: 212901--212934 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
212891 CCTTTTTTGT
212901 TATCTCTCCCCAAAAAA
1 TATCTCTCCCCAAAAAA
212918 TATCTCTCCCCAAAAAA
1 TATCTCTCCCCAAAAAA
212935 ACTTTCTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.24
Consensus pattern (17 bp):
TATCTCTCCCCAAAAAA
Found at i:214923 original size:20 final size:20
Alignment explanation
Indices: 214898--214951 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
214888 GGTTTTTTAG
*
214898 ATGTATTGATACATCATTCA
1 ATGTATCGATACATCATTCA
214918 ATGTATCGATACATCATTCA
1 ATGTATCGATACATCATTCA
214938 ATGTATCGATACAT
1 ATGTATCGATACAT
214952 TTAGAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATCATTCA
Found at i:221892 original size:51 final size:52
Alignment explanation
Indices: 221816--221943 Score: 231
Period size: 51 Copynumber: 2.5 Consensus size: 52
221806 CGAAATATGA
221816 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACAT-TGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
221867 AAATTTGCCTGTACGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
221919 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
221944 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
51 44 0.61
52 28 0.39
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:221970 original size:13 final size:13
Alignment explanation
Indices: 221952--221976 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
221942 CAAAGATCAG
221952 TGTATCGATACAA
1 TGTATCGATACAA
221965 TGTATCGATACA
1 TGTATCGATACA
221977 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:222059 original size:32 final size:32
Alignment explanation
Indices: 222023--222093 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
222013 GGCTTCGTAG
*
222023 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCAATACAACACTTATGTAT
* *
222055 CGATACATTGTATCAATACAACATTTTTGTAT
1 CGATACATTGTATCAATACAACACTTATGTAT
222087 CGATACA
1 CGATACA
222094 AATCGTTGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.35
Consensus pattern (32 bp):
CGATACATTGTATCAATACAACACTTATGTAT
Found at i:224296 original size:33 final size:32
Alignment explanation
Indices: 224236--224297 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
224226 CAATTCTTTA
* *
224236 TGTATCGATACAATGAGCATGTATCGATAGAT
1 TGTATCGATACAAAGAACATGTATCGATAGAT
*
224268 TGTATCGATACAAAGCAATATGTATCGATA
1 TGTATCGATACAAAG-AACATGTATCGATA
224298 CTTCTGGGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 14 0.54
33 12 0.46
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (32 bp):
TGTATCGATACAAAGAACATGTATCGATAGAT
Found at i:224673 original size:3 final size:3
Alignment explanation
Indices: 224658--224708 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
224648 TTGGAAATGC
*
224658 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
224706 TTA
1 TTA
224709 AATATAAGAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:338890 original size:76 final size:78
Alignment explanation
Indices: 338796--338945 Score: 223
Period size: 79 Copynumber: 1.9 Consensus size: 78
338786 TGATTATGAG
* * * * *
338796 AATAACGGGGTTGGAGTATCCCCGATGA-AG-AATTGATGTTTTGGAAATAAAACCGGGGTTGGA
1 AATAACGGGGATGGAGTATCCCCGATGAGAGAAATTAATATTTTAGAAATAAAAACGGGGTTGGA
338859 GTATCCCCTCGAA
66 GTATCCCCTCGAA
*
338872 AATAACGGGGATGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAAACGGGGTTGG
1 AATAACGGGGATGGAGTATCCCCGATGA-GAGAAATTAATATTTTAGAAATAAAAACGGGGTTGG
338937 AGTATCCCC
65 AGTATCCCC
338946 GATGATGAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
76 26 0.40
78 2 0.03
79 37 0.57
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (78 bp):
AATAACGGGGATGGAGTATCCCCGATGAGAGAAATTAATATTTTAGAAATAAAAACGGGGTTGGA
GTATCCCCTCGAA
Found at i:339155 original size:153 final size:153
Alignment explanation
Indices: 338877--339164 Score: 359
Period size: 153 Copynumber: 1.9 Consensus size: 153
338867 TCGAAAATAA
* *
338877 CGGGGATGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAAACGGGGTTGGAGTAT
1 CGGGGATGGAGTATCCCCGATTATGAGAAATTAATATTTGAGAAATAAAAACGGAGTTGGAGTAT
* * * *
338942 CCCCGATGATGAAAAATTAGTATTTTGGAAATACAATCGGAGTTGGAGTATCCCCGATTATAG-A
66 CCCCGATGATGAAAAATTAATATTTTAGAAATAAAACCGGAGTTGGAGTATCCCCGATTAT-GCA
339006 AAATTGGTGTTTTGAAAATAAAAC
130 AAATTGGTGTTTTGAAAATAAAAC
* * ** * *
339030 CGGGGTTGGAGTATCCCCGATTGTG-GAAAATTGGTGTTCTGAG-AATAAAATCGGAGTTGGAGT
1 CGGGGATGGAGTATCCCCGATTATGAG-AAATTAATATT-TGAGAAATAAAAACGGAGTTGGAGT
* * * * *
339093 GTCCCCGATTG-TGGAAAATTAATGTTTTAGAAGTAAAACCGGGGTTGGAGTATCCCCGATTATG
64 ATCCCCGA-TGATGAAAAATTAATATTTTAGAAATAAAACCGGAGTTGGAGTATCCCCGATTATG
339157 CAAAATTG
128 CAAAATTG
339165 AGAAAACTTG
Statistics
Matches: 114, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
152 2 0.02
153 107 0.94
154 5 0.04
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (153 bp):
CGGGGATGGAGTATCCCCGATTATGAGAAATTAATATTTGAGAAATAAAAACGGAGTTGGAGTAT
CCCCGATGATGAAAAATTAATATTTTAGAAATAAAACCGGAGTTGGAGTATCCCCGATTATGCAA
AATTGGTGTTTTGAAAATAAAAC
Found at i:339162 original size:51 final size:50
Alignment explanation
Indices: 338877--339163 Score: 308
Period size: 51 Copynumber: 5.6 Consensus size: 50
338867 TCGAAAATAA
* * * *
338877 CGGGGATGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAAA
1 CGGGGTTGGAGTATCCCCGATTATGA-AAATTAGTGTTTTAGAAATAAAAC
* * * * *
338928 CGGGGTTGGAGTATCCCCGATGATGAAAAATTAGTATTTTGGAAATACAAT
1 CGGGGTTGGAGTATCCCCGATTATG-AAAATTAGTGTTTTAGAAATAAAAC
* *
338979 CGGAGTTGGAGTATCCCCGATTATAGAAAATTGGTGTTTT-GAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTAT-GAAAATTAGTGTTTTAG-AAATAAAAC
* * * *
339030 CGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTCT-GAGAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTAT-GAAAATTAGTGTTTTAGA-AATAAAAC
* * * * *
339081 CGGAGTTGGAGTGTCCCCGATTGTGGAAAATTAATGTTTTAGAAGTAAAAC
1 CGGGGTTGGAGTATCCCCGATTAT-GAAAATTAGTGTTTTAGAAATAAAAC
339132 CGGGGTTGGAGTATCCCCGATTATGCAAAATT
1 CGGGGTTGGAGTATCCCCGATTATG-AAAATT
339164 GAGAAAACTT
Statistics
Matches: 203, Mismatches: 27, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
50 3 0.01
51 196 0.97
52 4 0.02
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (50 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAATTAGTGTTTTAGAAATAAAAC
Found at i:339164 original size:102 final size:101
Alignment explanation
Indices: 338883--339164 Score: 370
Period size: 102 Copynumber: 2.8 Consensus size: 101
338873 ATAACGGGGA
* *
338883 TGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAAACGGGGTTGGAGTATCCCCGA
1 TGGAGTATCCCCGATTATGA-AAATTAATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCGA
* * * *
338948 TGATGAAAAATTAGTATTTTGGAAATACAATCGGAGT
65 TTATGAAAAATTGGTATTCTGGAAATAAAATCGGAGT
**
338985 TGGAGTATCCCCGATTATAGAAAATTGGTGTTTT-GAAAATAAAACCGGGGTTGGAGTATCCCCG
1 TGGAGTATCCCCGATTAT-GAAAATTAATGTTTTAG-AAATAAAACCGGGGTTGGAGTATCCCCG
* * *
339049 ATTGTGGAAAATTGGTGTTCT-GAGAATAAAATCGGAGT
64 ATTATGAAAAATTGGTATTCTGGA-AATAAAATCGGAGT
* * *
339087 TGGAGTGTCCCCGATTGTGGAAAATTAATGTTTTAGAAGTAAAACCGGGGTTGGAGTATCCCCGA
1 TGGAGTATCCCCGATTAT-GAAAATTAATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCGA
*
339152 TTATGCAAAATTG
65 TTATGAAAAATTG
339165 AGAAAACTTG
Statistics
Matches: 157, Mismatches: 19, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
101 3 0.02
102 151 0.96
103 3 0.02
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (101 bp):
TGGAGTATCCCCGATTATGAAAATTAATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCGAT
TATGAAAAATTGGTATTCTGGAAATAAAATCGGAGT
Found at i:341543 original size:13 final size:13
Alignment explanation
Indices: 341525--341550 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
341515 ACAAAGATCC
341525 ATGTATCGATACA
1 ATGTATCGATACA
341538 ATGTATCGATACA
1 ATGTATCGATACA
341551 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:341546 original size:33 final size:33
Alignment explanation
Indices: 341504--341570 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
341494 AAAATTTCCA
***
341504 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
341537 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
341570 A
1 A
341571 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:341614 original size:19 final size:18
Alignment explanation
Indices: 341590--341657 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
341580 CAGTAGCTAA
341590 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
341609 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
341624 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
*
341641 TTACGTATCGATACAAA
1 TTATGTATCGATACAAA
341658 TTGTTGAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.10
19 24 0.57
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:341630 original size:13 final size:13
Alignment explanation
Indices: 341612--341636 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
341602 ACAATACTTA
341612 TGTATCGATACAT
1 TGTATCGATACAT
341625 TGTATCGATACA
1 TGTATCGATACA
341637 AAACTTACGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:341634 original size:32 final size:32
Alignment explanation
Indices: 341593--341655 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
341583 TAGCTAATTA
* *
341593 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTACGTATCGATACAT
341625 TGTATCGATACAAAACTTACGTATCGATACA
1 TGTATCGATACAAAACTTACGTATCGATACA
341656 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (32 bp):
TGTATCGATACAAAACTTACGTATCGATACAT
Found at i:341737 original size:21 final size:21
Alignment explanation
Indices: 341713--341769 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
341703 CATTTGTAGG
341713 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
341734 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
341755 ATGTATCGATACATT
1 ATGTATCGATACATT
341770 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:341780 original size:1 final size:1
Alignment explanation
Indices: 341774--341805 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
341764 TACATTTAAA
341774 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
341806 CAAACACTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:342485 original size:55 final size:55
Alignment explanation
Indices: 342401--343078 Score: 1025
Period size: 55 Copynumber: 12.3 Consensus size: 55
342391 ATAAGTTGTA
* * ** * *
342401 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
342456 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCCACTTGTGTGGGCTTTGAAAAGTG
1 TCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
342511 TCCTGCTCTTTGGGGAAT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
342566 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
342621 TCCTGTTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
342676 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
342731 TCCTGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
342786 TCCTGCTCTTTGAGGACTGGACAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGA-AAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
342841 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
342896 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
342951 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
343006 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAACGTG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
343061 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
343079 AAAAAGCGGA
Statistics
Matches: 586, Mismatches: 23, Indels: 28
0.92 0.04 0.04
Matches are distributed among these distances:
53 2 0.00
54 15 0.03
55 551 0.94
56 16 0.03
57 2 0.00
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:342785 original size:29 final size:29
Alignment explanation
Indices: 342697--342785 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
342687 GAGGACTGAA
342697 AGGTGCCACCAACTTGTGTGGGCTTTAAG
1 AGGTGCCACCAACTTGTGTGGGCTTTAAG
** * *
342726 AGGTGTCCTGC-TCTT-TG-GGGAC-TGAA-
1 AGGTG-CCACCAACTTGTGTGGG-CTTTAAG
342752 AGGTGCCACCAACTTGTGTGGGCTTTAAG
1 AGGTGCCACCAACTTGTGTGGGCTTTAAG
342781 AGGTG
1 AGGTG
342786 TCCTGCTCTT
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
25 3 0.07
26 8 0.18
27 9 0.20
28 9 0.20
29 13 0.29
30 3 0.07
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (29 bp):
AGGTGCCACCAACTTGTGTGGGCTTTAAG
Found at i:344112 original size:13 final size:13
Alignment explanation
Indices: 344094--344119 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
344084 ACAAAGATCC
344094 ATGTATCGATACA
1 ATGTATCGATACA
344107 ATGTATCGATACA
1 ATGTATCGATACA
344120 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:344115 original size:33 final size:33
Alignment explanation
Indices: 344073--344139 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
344063 AAAATTTCCA
***
344073 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
344106 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
344139 A
1 A
344140 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:344183 original size:19 final size:18
Alignment explanation
Indices: 344159--344226 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
344149 CAGTAGCTAA
344159 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
344178 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
344193 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
*
344210 TTACGTATCGATACAAA
1 TTATGTATCGATACAAA
344227 TTGTTGAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.10
19 24 0.57
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:344199 original size:13 final size:13
Alignment explanation
Indices: 344181--344205 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
344171 ACAATACTTA
344181 TGTATCGATACAT
1 TGTATCGATACAT
344194 TGTATCGATACA
1 TGTATCGATACA
344206 AAACTTACGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:344203 original size:32 final size:32
Alignment explanation
Indices: 344162--344224 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
344152 TAGCTAATTA
* *
344162 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTACGTATCGATACAT
344194 TGTATCGATACAAAACTTACGTATCGATACA
1 TGTATCGATACAAAACTTACGTATCGATACA
344225 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (32 bp):
TGTATCGATACAAAACTTACGTATCGATACAT
Found at i:344306 original size:21 final size:21
Alignment explanation
Indices: 344282--344338 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
344272 CATTTGTAGG
344282 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
344303 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
344324 ATGTATCGATACATT
1 ATGTATCGATACATT
344339 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:344349 original size:1 final size:1
Alignment explanation
Indices: 344343--344369 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
344333 TACATTTAAA
344343 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
344370 CAAACACTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:344630 original size:49 final size:49
Alignment explanation
Indices: 344566--345944 Score: 711
Period size: 48 Copynumber: 30.8 Consensus size: 49
344556 GTCTACAGTG
* ** * *
344566 CCAATATGCTAATTCAAGGCCAGCGATACCGGACTTAAAGACGAAGATA
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* * * *
344615 CCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATAACAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG---ACAAAGGTA
*
344667 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTT--AG----A-GTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* * * * *
344709 GCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGCA
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* * *
344758 TCAATATGCCGATTCAAGGCCAGCGATATTGGACTT------AAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* * * * * *
344801 CGAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAC-ACGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* * * * *
344849 CCAATATGCTAATTCAAAGCCAACGATATTGGGCTT--------A--TG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* * * * *
344888 CCAATGTGCTGATTCAAGGCCAACGA-CTTGGTCTTAAAGAC-AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* *
344935 CCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT--------A--TG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* * * *
344974 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGCA
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* ** * *
345023 CCAATATGCTGATTCAAGGTCAATGATATTGGACTT------AAAGTTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* * * * * *
345066 CCAATGTGTTGATTCAAGGCCAGCAACATTGGTCTTAAAGAC-AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* *
345114 CCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT--------A--TG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* * * *
345153 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAC-AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* * *
345201 CCAATATGCTGATTCAAGGCCAGCAATATTGGGCTT--------A--TG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* * * *
345240 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAC-AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* *
345288 CCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT--------A--TG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* * * *
345327 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGCA
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
** * *
345376 CCAATATGCTGATTCAAGGCCAATGATATTGGACTT------AAAGTTT
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* * * * * *
345419 CCAATGTGTTGATTCAAGGCCAGCAACATTGGTCTTAAAGAC-AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* *
345467 CCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT--------A--TG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* * * *
345506 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAC-AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* * *
345554 CCAATATGCTGATTCAAGGCC-GCAATATTGGGCTT-------ATGG--
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* * * *
345593 -CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGCA
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* * * *
345641 GCAATATGCTGATTCAAAGCCAGTGATATTGGACTT------AAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* * * * * *
345684 CCAATGTGCTGATTCAAGGCTAGCGACATTGGCCTTAAAGA-TAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* * *
345732 CCAATATGCTAATTCAAGGCCAGCGATATTGGGCTT--------A--TG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* * * *
345771 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAC-AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* * * *
345819 CCAATATGCTGATTCAAGGCTAGCAATATTGGGCTT--------A--TG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* * * * *
345858 CCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGAC-AAGGTC
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
* *
345906 CCAATATGCTGGTTCAAGGCCAGCGATTTTGGACTTAAA
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
345945 AGAAGATGCC
Statistics
Matches: 1040, Mismatches: 171, Indels: 239
0.72 0.12 0.16
Matches are distributed among these distances:
38 26 0.03
39 278 0.27
41 10 0.01
42 35 0.03
43 135 0.13
44 2 0.00
45 1 0.00
46 8 0.01
47 39 0.04
48 308 0.30
49 157 0.15
50 2 0.00
52 39 0.04
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (49 bp):
CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAAGGTA
Found at i:344903 original size:39 final size:40
Alignment explanation
Indices: 344847--345895 Score: 545
Period size: 39 Copynumber: 24.0 Consensus size: 40
344837 AAAGACACGG
* * * *
344847 TGCCAATATGCTAATTCAAAGCCAACGATATTGGGCTT-A
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAA
* * *
344886 TGCCAATGTGCTGATTCAAGGCCAACGA-CTTGGTCTTAAAGACAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT------AA
*
344931 GGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT-A
1 --TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAA
* *
344972 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT-------AA
* * ** *
345019 GGCACCAATATGCTGATTCAAGGTCAATGATATTGGACTTAAA
1 TG--CCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT-AA
* * * *
345062 GTTGCCAATGTGTTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAA
1 --TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT------AA
*
345110 GGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT-A
1 --TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAA
* *
345151 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT------AA
* *
345197 GGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTT-A
1 --TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAA
* *
345238 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT------AA
*
345284 GGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT-A
1 --TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAA
* *
345325 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT-------AA
* ** *
345372 GGCACCAATATGCTGATTCAAGGCCAATGATATTGGACTTAAA
1 TG--CCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT-AA
* * * * *
345415 GTTTCCAATGTGTTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAA
1 --TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT------AA
*
345463 GGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT-A
1 --TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAA
* *
345504 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT------AA
* *
345550 GGTGCCAATATGCTGATTCAAGGCC-GCAATATTGGGCTT-A
1 --TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAA
* * *
345590 TGGCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT-------AA
* * * *
345637 GGCAGCAATATGCTGATTCAAAGCCAGTGATATTGGACTTAAA
1 TGC--CAATATGCTGATTCAAGGCCAGCGATATTGGTCTT-AA
* * * *
345680 GGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGCCTTAAAGATAA
1 --TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTC-T-----TAA
* *
345728 GGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGGCTT-A
1 --TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAA
* *
345769 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT------AA
* * *
345815 GGTGCCAATATGCTGATTCAAGGCTAGCAATATTGGGCTT-A
1 --TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAA
* * *
345856 TGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAA
345896 AGACAAGGTC
Statistics
Matches: 791, Mismatches: 119, Indels: 199
0.71 0.11 0.18
Matches are distributed among these distances:
38 28 0.04
39 278 0.35
40 2 0.00
41 7 0.01
42 1 0.00
43 93 0.12
44 1 0.00
45 4 0.01
46 4 0.01
47 44 0.06
48 237 0.30
49 92 0.12
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.26
Consensus pattern (40 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAA
Found at i:345182 original size:87 final size:87
Alignment explanation
Indices: 344615--345942 Score: 1944
Period size: 87 Copynumber: 15.0 Consensus size: 87
344605 GACGAAGATA
* *
344615 CCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATAACAAAGGTGCCAATATGCTGAT
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAG---AC-AAGGTGCCAATATGCTGAT
*
344680 TCAAGGCCAGCGATATTGGACTTAGAGTG
62 TCAAGGCCAGCGATATTGGGCTT--A-TG
* * *
344709 GCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAG-GCATCAATATGCCGATTC
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGC--CAATATGCTGATTC
*
344773 AAGGCCAGCGATATTGGACTTAAAGGTG
64 AAGGCCAGCGATATTGGGCTT--A--TG
* * *
344801 CGAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACACGGTGCCAATATGCTAATTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
* *
344866 AGCCAACGATATTGGGCTTATG
66 GGCCAGCGATATTGGGCTTATG
*
344888 CCAATGTGCTGATTCAAGGCCAACGAC-TTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
344952 GGCCAGCGATATTGGGCTTATG
66 GGCCAGCGATATTGGGCTTATG
**
344974 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGCACCAATATGCTGATTCA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAC-AAGGTGCCAATATGCTGATTCA
* ** *
345039 AGGTCAATGATATTGGACTTAAAGTTG
65 AGGCCAGCGATATTGGGCTT--A--TG
* *
345066 CCAATGTGTTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
345131 GGCCAGCGATATTGGGCTTATG
66 GGCCAGCGATATTGGGCTTATG
345153 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
*
345218 GGCCAGCAATATTGGGCTTATG
66 GGCCAGCGATATTGGGCTTATG
345240 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
345305 GGCCAGCGATATTGGGCTTATG
66 GGCCAGCGATATTGGGCTTATG
**
345327 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGCACCAATATGCTGATTCA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAC-AAGGTGCCAATATGCTGATTCA
** * *
345392 AGGCCAATGATATTGGACTTAAAGTTT
65 AGGCCAGCGATATTGGGCTT--A--TG
* *
345419 CCAATGTGTTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
345484 GGCCAGCGATATTGGGCTTATG
66 GGCCAGCGATATTGGGCTTATG
345506 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
*
345571 GGCC-GCAATATTGGGCTTATG
66 GGCCAGCGATATTGGGCTTATG
* *
345592 GCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAG-GCAGCAATATGCTGATTC
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGC--CAATATGCTGATTC
* * *
345656 AAAGCCAGTGATATTGGACTTAAAGGTG
64 AAGGCCAGCGATATTGGGCTT--A--TG
* * * *
345684 CCAATGTGCTGATTCAAGGCTAGCGACATTGGCCTTAAAGATAAGGTGCCAATATGCTAATTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
345749 GGCCAGCGATATTGGGCTTATG
66 GGCCAGCGATATTGGGCTTATG
345771 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
* *
345836 GGCTAGCAATATTGGGCTTATG
66 GGCCAGCGATATTGGGCTTATG
* * *
345858 CCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAAGGTCCCAATATGCTGGTTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
* *
345923 GGCCAGCGATTTTGGACTTA
66 GGCCAGCGATATTGGGCTTA
345943 AAAGAAGATG
Statistics
Matches: 1126, Mismatches: 85, Indels: 53
0.89 0.07 0.04
Matches are distributed among these distances:
85 2 0.00
86 141 0.13
87 503 0.45
88 84 0.07
89 6 0.01
90 6 0.01
91 172 0.15
92 171 0.15
93 4 0.00
94 37 0.03
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (87 bp):
CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
GGCCAGCGATATTGGGCTTATG
Found at i:345889 original size:618 final size:619
Alignment explanation
Indices: 344615--345942 Score: 2255
Period size: 618 Copynumber: 2.1 Consensus size: 619
344605 GACGAAGATA
* *
344615 CCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATAACAAAGGTGCCAATATGCTGAT
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAG---AC-AAGGTGCCAATATGCTGAT
*
344680 TCAAGGCCAGCGATATTGGACTTAGAGTGGCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT
62 TCAAGGCCAGCGATATTGGACTT--AGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT
* * *
344745 AAAGACAAAGGCATCAATATGCCGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCGAATGTGC
125 AAAGACAAAGGCACCAATATGCCGATTCAAGGCCAACGATATTGGACTTAAAGGTGCCAATGTGC
* *
344810 TGATTCAAGGCCAGCGACATTGGTCTTAAAGACACGGTGCCAATATGCTAATTCAAAGCCAACGA
190 TGATTCAAGGCCAGCAACATTGGTCTTAAAGACAAGGTGCCAATATGCTAATTCAAAGCCAACGA
344875 TATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAACGACTTGGTCTTAAAGACAAGGTGCCAAT
255 TATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAACGACTTGGTCTTAAAGACAAGGTGCCAAT
*
344940 ATGCTGATTCAAGGCCAGCGATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTG
320 ATGCTGATTCAAGGCCAGCAATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTG
* * *
345005 GTCTTAAAGACAAAGGCACCAATATGCTGATTCAAGGTCAATGATATTGGACTTAAAGTTGCCAA
385 GTCTTAAAGACAAAGGCACCAATATGCTGATTCAAAGCCAATGATATTGGACTTAAAGGTGCCAA
* * *
345070 TGTGTTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCC
450 TGTGCTGATTCAAGGCCAGCAACATTGGCCTTAAAGACAAGGTGCCAATATGCTAATTCAAGGCC
345135 AGCGATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGT
515 AGCGATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGT
345200 GCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTTATG
580 GCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTTATG
345240 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
*
345305 GGCCAGCGATATTGGGCTTA-TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAC
66 GGCCAGCGATATTGGACTTAGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAC
* * * * *
345369 AAAGGCACCAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGTTTCCAATGTGTTGATTC
131 AAAGGCACCAATATGCCGATTCAAGGCCAACGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
* * *
345434 AAGGCCAGCAACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGG
196 AAGGCCAGCAACATTGGTCTTAAAGACAAGGTGCCAATATGCTAATTCAAAGCCAACGATATTGG
*
345499 GCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCT
261 GCTTATGCCAATGTGCTGATTCAAGGCCAACGAC-TTGGTCTTAAAGACAAGGTGCCAATATGCT
*
345564 GATTCAAGGCC-GCAATATTGGGCTTATGGCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT
325 GATTCAAGGCCAGCAATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT
* *
345628 AAAGACAAAGGCAGCAATATGCTGATTCAAAGCCAGTGATATTGGACTTAAAGGTGCCAATGTGC
390 AAAGACAAAGGCACCAATATGCTGATTCAAAGCCAATGATATTGGACTTAAAGGTGCCAATGTGC
* * *
345693 TGATTCAAGGCTAGCGACATTGGCCTTAAAGATAAGGTGCCAATATGCTAATTCAAGGCCAGCGA
455 TGATTCAAGGCCAGCAACATTGGCCTTAAAGACAAGGTGCCAATATGCTAATTCAAGGCCAGCGA
345758 TATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAA
520 TATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAA
*
345823 TATGCTGATTCAAGGCTAGCAATATTGGGCTTATG
585 TATGCTGATTCAAGGCCAGCAATATTGGGCTTATG
* * *
345858 CCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAAGGTCCCAATATGCTGGTTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
*
345923 GGCCAGCGATTTTGGACTTA
66 GGCCAGCGATATTGGACTTA
345943 AAAGAAGATG
Statistics
Matches: 665, Mismatches: 37, Indels: 9
0.94 0.05 0.01
Matches are distributed among these distances:
618 542 0.82
619 42 0.06
621 41 0.06
622 2 0.00
625 38 0.06
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (619 bp):
CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
GGCCAGCGATATTGGACTTAGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAC
AAAGGCACCAATATGCCGATTCAAGGCCAACGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
AAGGCCAGCAACATTGGTCTTAAAGACAAGGTGCCAATATGCTAATTCAAAGCCAACGATATTGG
GCTTATGCCAATGTGCTGATTCAAGGCCAACGACTTGGTCTTAAAGACAAGGTGCCAATATGCTG
ATTCAAGGCCAGCAATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA
AAGACAAAGGCACCAATATGCTGATTCAAAGCCAATGATATTGGACTTAAAGGTGCCAATGTGCT
GATTCAAGGCCAGCAACATTGGCCTTAAAGACAAGGTGCCAATATGCTAATTCAAGGCCAGCGAT
ATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAAT
ATGCTGATTCAAGGCCAGCAATATTGGGCTTATG
Found at i:345943 original size:265 final size:263
Alignment explanation
Indices: 344615--345944 Score: 1949
Period size: 265 Copynumber: 5.0 Consensus size: 263
344605 GACGAAGATA
* *
344615 CCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATAACAAAGGTGCCAATATGCTGAT
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAG---AC-AAGGTGCCAATATGCTGAT
* *
344680 TCAAGGCCAGCGATATTGGACTTAGAGTGGCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT
62 TCAAGGCCAGCGATATTGGGCTT--A-TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT
* * * * *
344745 AAAGACAAAG-GCATCAATATGCCGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCGAATGTG
124 AAAGACAAGGTGC--CAATATGCTGATTCAAGGCCAGCAATATTGGGCTT--A--TGCCAATGTG
* * * * *
344809 CTGATTCAAGGCCAGCGACATTGGTCTTAAAGACACGGTGCCAATATGCTAATTCAAAGCCAACG
183 CTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTCCCAATATGCTGATTCAAGGCCAGCG
*
344874 ATATTGGGCTT--ATG
248 ATATTGGACTTAAATG
*
344888 CCAATGTGCTGATTCAAGGCCAACGAC-TTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
344952 GGCCAGCGATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACA
66 GGCCAGCGATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAC-
** * *** * *
345017 AAGGCACCAATATGCTGATTCAAGGTCAATGATATTGGACTTAAAGTTGCCAATGTGTTGATTCA
130 AAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTT--A--TGCCAATGTGCTGATTCA
* * *
345082 AGGCCAGCAACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGG
191 AGGCCAGCGACATTGGTCTTAAAGACAAGGTCCCAATATGCTGATTCAAGGCCAGCGATATTGGA
345147 CTT--ATG
256 CTTAAATG
345153 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
*
345218 GGCCAGCAATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACA
66 GGCCAGCGATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACA
*
345283 AGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTATGCCAATGTGCTGATTCAAGGCC
131 AGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTTATGCCAATGTGCTGATTCAAGGCC
**
345348 AGCGACATTGGTCTTAAAGACAAAGG-CACCAATATGCTGATTCAAGGCCAATGATATTGGACTT
196 AGCGACATTGGTCTTAAAGAC-AAGGTC-CCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
*
345412 AAAGTTT
259 AAA--TG
* *
345419 CCAATGTGTTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
345484 GGCCAGCGATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACA
66 GGCCAGCGATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACA
*
345549 AGGTGCCAATATGCTGATTCAAGGCC-GCAATATTGGGCTTATGGCAATGTGCTGATTCAAGGCC
131 AGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTTATGCCAATGTGCTGATTCAAGGCC
* * *
345613 AGCGACATTGGTCTTAAAGACAAAGG-CAGCAATATGCTGATTCAAAGCCAGTGATATTGGACTT
196 AGCGACATTGGTCTTAAAGAC-AAGGTC-CCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
345677 AAAGGTG
259 AAA--TG
* * * *
345684 CCAATGTGCTGATTCAAGGCTAGCGACATTGGCCTTAAAGATAAGGTGCCAATATGCTAATTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
345749 GGCCAGCGATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACA
66 GGCCAGCGATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACA
*
345814 AGGTGCCAATATGCTGATTCAAGGCTAGCAATATTGGGCTTATGCCAATGTGCTGATTCAAGGCC
131 AGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTTATGCCAATGTGCTGATTCAAGGCC
* * *
345879 AGCAACATTGGTCTTAAAGACAAGGTCCCAATATGCTGGTTCAAGGCCAGCGATTTTGGACTTAA
196 AGCGACATTGGTCTTAAAGACAAGGTCCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA
345944 A
261 A
345945 AGAAGATGCC
Statistics
Matches: 988, Mismatches: 58, Indels: 30
0.92 0.05 0.03
Matches are distributed among these distances:
261 42 0.04
262 37 0.04
263 1 0.00
264 1 0.00
265 511 0.52
266 316 0.32
267 1 0.00
268 41 0.04
269 2 0.00
272 11 0.01
273 25 0.03
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (263 bp):
CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
GGCCAGCGATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACA
AGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTTATGCCAATGTGCTGATTCAAGGCC
AGCGACATTGGTCTTAAAGACAAGGTCCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA
ATG
Found at i:346057 original size:33 final size:33
Alignment explanation
Indices: 346020--346340 Score: 235
Period size: 33 Copynumber: 10.4 Consensus size: 33
346010 TGCCACTTAC
*
346020 TTGTGGGCTTAAAAAGAGAAAGATGCCACGGAG
1 TTGTGGACTTAAAAAGAGAAAGATGCCACGGAG
*
346053 TTGTGGACTT-AAAAG-G---G-TGCCACGGAA
1 TTGTGGACTTAAAAAGAGAAAGATGCCACGGAG
* *
346080 TTGTGGACTTAAAAGGA-AAAGGTGCCACGGAG
1 TTGTGGACTTAAAAAGAGAAAGATGCCACGGAG
* *
346112 TTGTGGACTTAAAAGGA-AAAAAGTGCCACGGAG
1 TTGTGGACTTAAAAAGAGAAAGA-TGCCACGGAG
* * *
346145 TTGTGGACTTAAAAGGAAAAAGATGCCATGGAG
1 TTGTGGACTTAAAAAGAGAAAGATGCCACGGAG
* *
346178 TTGTGGACTTAAAAGGAAAAAGATGCCACGGA-
1 TTGTGGACTTAAAAAGAGAAAGATGCCACGGAG
* * * **
346210 TGTGTGCACTT-AAAAGGGACAAGGTGCCATAGAG
1 T-TGTGGACTTAAAAAGAGA-AAGATGCCACGGAG
*
346244 TTGTGGACTT--AAA-AG---GATGCCATGGAG
1 TTGTGGACTTAAAAAGAGAAAGATGCCACGGAG
* *
346271 TTGTGGGCTT-TAAA-AG--AG-TGCCACGGAG
1 TTGTGGACTTAAAAAGAGAAAGATGCCACGGAG
* * *
346299 TTGTGGGCTT-TAAA-AG--AG-TGCCACGGGG
1 TTGTGGACTTAAAAAGAGAAAGATGCCACGGAG
346327 TTGTGGACTTAAAA
1 TTGTGGACTTAAAA
346341 GGATGCCATG
Statistics
Matches: 249, Mismatches: 25, Indels: 32
0.81 0.08 0.10
Matches are distributed among these distances:
27 38 0.15
28 55 0.22
29 3 0.01
31 3 0.01
32 43 0.17
33 102 0.41
34 5 0.02
ACGTcount: A:0.33, C:0.12, G:0.32, T:0.22
Consensus pattern (33 bp):
TTGTGGACTTAAAAAGAGAAAGATGCCACGGAG
Found at i:346193 original size:66 final size:64
Alignment explanation
Indices: 346069--346260 Score: 278
Period size: 66 Copynumber: 2.9 Consensus size: 64
346059 ACTTAAAAGG
*
346069 GTGCCACGGAATTGTGGACTTAAAAGGAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAA
1 GTGCCACGG-ATTGTGGACTTAAAAGGAAAAGGTGCCATGGAGTTGTGGACTTAAAAGGAAAAAA
*
346134 GTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGATGCCATGGAGTTGTGGACTTAAAAGG-AAAA
1 GTGCCACGGA-TTGTGGACTTAAAAGG-AAAAGGTGCCATGGAGTTGTGGACTTAAAAGGAAAAA
346198 A
64 A
* * *
346199 GATGCCACGGATGTGTGCACTTAAAAGGGACAAGGTGCCATAGAGTTGTGGACTTAAAAGGA
1 G-TGCCACGGAT-TGTGGACTTAAAA-GGAAAAGGTGCCATGGAGTTGTGGACTTAAAAGGA
346261 TGCCATGGAG
Statistics
Matches: 115, Mismatches: 6, Indels: 10
0.88 0.05 0.08
Matches are distributed among these distances:
64 1 0.01
65 32 0.28
66 80 0.70
67 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.31, T:0.20
Consensus pattern (64 bp):
GTGCCACGGATTGTGGACTTAAAAGGAAAAGGTGCCATGGAGTTGTGGACTTAAAAGGAAAAAA
Found at i:346223 original size:99 final size:93
Alignment explanation
Indices: 346038--346359 Score: 296
Period size: 99 Copynumber: 3.5 Consensus size: 93
346028 TTAAAAAGAG
*
346038 AAAGATGCCACGGAGTTGTGGACTTAAAAGG-GTGCCACGGAATTGTGGACTTAAAAGGAAAAGG
1 AAAG-TGCCACGGAGTTGTGGACTTAAAAGGAGTGCCACGGAATTGTGGACTTAAAAGGAAAAGA
*
346102 TGCCACGGAGTTGTGGACTTAAAAGGAAA
65 TGCCACGGAGTTGTGCACTTAAAAGGAAA
* *
346131 AAAGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGATGCCATGGAGTTGTGGACTTAAAAGGAA
1 AAAGTGCCACGGAGTTGTGGACTTAAAAGG----AG-TGCCACGGAATTGTGGACTTAAAAGG-A
* *
346196 AAAGATGCCACGGA-TGTGTGCACTTAAAAGGGAC
60 AAAGATGCCACGGAGT-TGTGCACTTAAAAGGAAA
* ** * * *
346230 AAGGTGCCATAGAGTTGTGGACTTAAAAGGA-TGCCATGGAGTTGTGGGCTTTAAAA-G---AG-
1 AAAGTGCCACGGAGTTGTGGACTTAAAAGGAGTGCCACGGAATTGTGGAC-TTAAAAGGAAAAGA
**
346289 TGCCACGGAGTTGTGGGCTTTAAAA-G---
65 TGCCACGGAGTTGTGCAC-TTAAAAGGAAA
* * *
346315 --AGTGCCACGGGGTTGTGGACTTAAAAGGA-TGCCATGGAGTTGTGG
1 AAAGTGCCACGGAGTTGTGGACTTAAAAGGAGTGCCACGGAATTGTGG
346360 GCTTTGGGAC
Statistics
Matches: 202, Mismatches: 16, Indels: 32
0.81 0.06 0.13
Matches are distributed among these distances:
83 41 0.20
88 15 0.07
89 9 0.04
92 26 0.13
93 22 0.11
94 6 0.03
95 1 0.00
97 1 0.00
98 25 0.12
99 56 0.28
ACGTcount: A:0.32, C:0.13, G:0.33, T:0.22
Consensus pattern (93 bp):
AAAGTGCCACGGAGTTGTGGACTTAAAAGGAGTGCCACGGAATTGTGGACTTAAAAGGAAAAGAT
GCCACGGAGTTGTGCACTTAAAAGGAAA
Found at i:346284 original size:28 final size:28
Alignment explanation
Indices: 346230--346364 Score: 163
Period size: 28 Copynumber: 4.9 Consensus size: 28
346220 TAAAAGGGAC
* *
346230 AAGG-TGCCATAGAGTTGTGGAC-TTAA
1 AAGGATGCCATGGAGTTGTGGGCTTTAA
346256 AAGGATGCCATGGAGTTGTGGGCTTTAA
1 AAGGATGCCATGGAGTTGTGGGCTTTAA
*
346284 AA-GAGTGCCACGGAGTTGTGGGCTTTAA
1 AAGGA-TGCCATGGAGTTGTGGGCTTTAA
* * *
346312 AA-GAGTGCCACGGGGTTGTGGAC-TTAA
1 AAGGA-TGCCATGGAGTTGTGGGCTTTAA
346339 AAGGATGCCATGGAGTTGTGGGCTTT
1 AAGGATGCCATGGAGTTGTGGGCTTT
346365 GGGACAAAAT
Statistics
Matches: 96, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.04
27 39 0.41
28 53 0.55
ACGTcount: A:0.25, C:0.13, G:0.36, T:0.27
Consensus pattern (28 bp):
AAGGATGCCATGGAGTTGTGGGCTTTAA
Found at i:346360 original size:55 final size:56
Alignment explanation
Indices: 346230--346364 Score: 163
Period size: 55 Copynumber: 2.5 Consensus size: 56
346220 TAAAAGGGAC
* * * *
346230 AAGG-TGCCATAGAGTTGTGGAC-TTAAAAGGATGCCATGGAGTTGTGGGCTTTAA
1 AAGGATGCCATGGAGTTGTGGGCTTTAAAAGGATGCCACGGAGTTGTGGACTTTAA
* *
346284 AA-GAGTGCCACGGAGTTGTGGGCTTTAAAA-GAGTGCCACGGGGTTGTGGAC-TTAA
1 AAGGA-TGCCATGGAGTTGTGGGCTTTAAAAGGA-TGCCACGGAGTTGTGGACTTTAA
346339 AAGGATGCCATGGAGTTGTGGGCTTT
1 AAGGATGCCATGGAGTTGTGGGCTTT
346365 GGGACAAAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
53 1 0.01
54 2 0.03
55 43 0.62
56 23 0.33
ACGTcount: A:0.25, C:0.13, G:0.36, T:0.27
Consensus pattern (56 bp):
AAGGATGCCATGGAGTTGTGGGCTTTAAAAGGATGCCACGGAGTTGTGGACTTTAA
Found at i:346393 original size:30 final size:31
Alignment explanation
Indices: 346372--346431 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
346362 TTTGGGACAA
346372 AATGCCACTGAGTCGTAGGCTTTGAGAAGAG
1 AATGCCACTGAGTCGTAGGCTTTGAGAAGAG
* *
346403 ATTGCCACTGAGTCGT-GGACTTTAAGAAG
1 AATGCCACTGAGTCGTAGG-CTTTGAGAAG
346432 GTACTTGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (31 bp):
AATGCCACTGAGTCGTAGGCTTTGAGAAGAG
Found at i:347737 original size:21 final size:21
Alignment explanation
Indices: 347710--347751 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
347700 CTTTGCACTT
*
347710 TTTTTTTGTGTTTTTTGTTTTG
1 TTTTTTTGT-TGTTTTGTTTTG
347732 TTTTTTTGTTGTTTTGTTTT
1 TTTTTTTGTTGTTTTGTTTT
347752 TTTGTGTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (21 bp):
TTTTTTTGTTGTTTTGTTTTG
Found at i:347738 original size:8 final size:8
Alignment explanation
Indices: 347710--347756 Score: 55
Period size: 8 Copynumber: 6.1 Consensus size: 8
347700 CTTTGCACTT
347710 TTTTTTTG
1 TTTTTTTG
347718 TGTTTTTTG
1 T-TTTTTTG
347727 ---TTTTG
1 TTTTTTTG
347732 TTTTTTTG
1 TTTTTTTG
*
347740 TTGTTTTG
1 TTTTTTTG
347748 TTTTTTTG
1 TTTTTTTG
347756 T
1 T
347757 GTTTGTACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
5 5 0.15
8 21 0.64
9 7 0.21
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (8 bp):
TTTTTTTG
Found at i:347768 original size:16 final size:14
Alignment explanation
Indices: 347714--347762 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 14
347704 GCACTTTTTT
347714 TTTGTGTTTTTTGT-
1 TTTGT-TTTTTTGTG
347728 TTTGTTTTTTTGTTG
1 TTTGTTTTTTTG-TG
347743 TTTTGTTTTTTTGTG
1 -TTTGTTTTTTTGTG
347758 TTTGT
1 TTTGT
347763 ACTTTTAAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.22
14 11 0.34
15 2 0.06
16 12 0.38
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (14 bp):
TTTGTTTTTTTGTG
Found at i:350575 original size:9 final size:9
Alignment explanation
Indices: 350536--350576 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
350526 GAGGGTAAAG
350536 AATGATCAA
1 AATGATCAA
*
350545 AATCATCAA
1 AATGATCAA
*
350554 AATCATCAA
1 AATGATCAA
350563 AATGATCAA
1 AATGATCAA
350572 AATGA
1 AATGA
350577 CTGAAGGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (9 bp):
AATGATCAA
Found at i:351612 original size:19 final size:19
Alignment explanation
Indices: 351588--351701 Score: 117
Period size: 19 Copynumber: 6.6 Consensus size: 19
351578 AGCGATACAT
* *
351588 TGTATCGATACAAAACTAA
1 TGTATCGATACAACACTTA
351607 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
351620 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
351639 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
351658 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
*
351671 TGTGTCGATACAACACTTA
1 TGTATCGATACAACACTTA
351690 TGTATCGATACA
1 TGTATCGATACA
351702 GTTACTGTTT
Statistics
Matches: 79, Mismatches: 4, Indels: 24
0.74 0.04 0.22
Matches are distributed among these distances:
13 17 0.22
14 1 0.01
16 11 0.14
18 2 0.03
19 48 0.61
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:351621 original size:32 final size:32
Alignment explanation
Indices: 351580--351650 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
351570 AGCTTCGTAG
351580 CGATACATTGTATCGATACAAAACTAATGTAT
1 CGATACATTGTATCGATACAAAACTAATGTAT
* *
351612 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTAATGTAT
351644 CGATACA
1 CGATACA
351651 ACACTTATGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTAATGTAT
Found at i:351625 original size:13 final size:13
Alignment explanation
Indices: 351607--351631 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
351597 ACAAAACTAA
351607 TGTATCGATACAT
1 TGTATCGATACAT
351620 TGTATCGATACA
1 TGTATCGATACA
351632 ACACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:351664 original size:51 final size:51
Alignment explanation
Indices: 351588--351701 Score: 201
Period size: 51 Copynumber: 2.2 Consensus size: 51
351578 AGCGATACAT
351588 TGTATCGATACAAAACTAATGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACAAAACTAATGTATCGATACATTGTATCGATACAACACTTA
* * *
351639 TGTATCGATACAACACTTATGTATCGATACATTGTGTCGATACAACACTTA
1 TGTATCGATACAAAACTAATGTATCGATACATTGTATCGATACAACACTTA
351690 TGTATCGATACA
1 TGTATCGATACA
351702 GTTACTGTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.32
Consensus pattern (51 bp):
TGTATCGATACAAAACTAATGTATCGATACATTGTATCGATACAACACTTA
Found at i:358163 original size:13 final size:13
Alignment explanation
Indices: 358145--358170 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
358135 ACATTTGGTC
358145 ATGTATCGATACA
1 ATGTATCGATACA
358158 ATGTATCGATACA
1 ATGTATCGATACA
358171 TCTTGTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:358165 original size:33 final size:32
Alignment explanation
Indices: 358123--358190 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
358113 CGTTACAAGC
358123 CAATGTATCGATACAT-TTGGTCATGTATCGATA
1 CAATGTATCGATACATCTT-GT-ATGTATCGATA
358156 CAATGTATCGATACATCTTGTATGTATCGATA
1 CAATGTATCGATACATCTTGTATGTATCGATA
358188 CAA
1 CAA
358191 ACAGTTAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 14 0.41
33 18 0.53
34 2 0.06
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATCTTGTATGTATCGATA
Found at i:359392 original size:20 final size:19
Alignment explanation
Indices: 359337--359392 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
359327 AAAACCCTTA
*
359337 AAAGTATCGATACATAATTC
1 AAAGTATCGATACAT-GTTC
359357 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
359377 AATGTATCGATACATG
1 AAAGTATCGATACATG
359393 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:359486 original size:20 final size:20
Alignment explanation
Indices: 359443--359494 Score: 88
Period size: 19 Copynumber: 2.6 Consensus size: 20
359433 GTAGCCAAAC
*
359443 TTGTATCGATACACAAAATA
1 TTGTATCGATACACAAAAAA
359463 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
359482 TTGTATCGATACA
1 TTGTATCGATACA
359495 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:361715 original size:21 final size:21
Alignment explanation
Indices: 361682--361731 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
361672 TTGCAAGTTG
*
361682 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
361704 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
361725 AAATAAA
1 AAATAAA
361732 AATTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:363549 original size:15 final size:15
Alignment explanation
Indices: 363529--363559 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
363519 TAAAAATATC
*
363529 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
363544 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
363559 C
1 C
363560 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:365658 original size:13 final size:13
Alignment explanation
Indices: 365640--365677 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
365630 CATTTTTCTT
365640 TGTATCGATACAA
1 TGTATCGATACAA
*
365653 TGTATCGATACAC
1 TGTATCGATACAA
365666 TGTATCGATACA
1 TGTATCGATACA
365678 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:365832 original size:20 final size:20
Alignment explanation
Indices: 365789--365834 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
365779 AAATCTTTTG
365789 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
365810 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
365830 CAAAA
1 CAAAA
365835 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:368164 original size:20 final size:19
Alignment explanation
Indices: 368109--368164 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
368099 AAAACCCTTA
*
368109 AAAGTATCGATACATAATTC
1 AAAGTATCGATACAT-GTTC
368129 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
368149 AATGTATCGATACATG
1 AAAGTATCGATACATG
368165 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:368258 original size:20 final size:20
Alignment explanation
Indices: 368215--368266 Score: 88
Period size: 19 Copynumber: 2.6 Consensus size: 20
368205 GTAGCCAAAC
*
368215 TTGTATCGATACACAAAATA
1 TTGTATCGATACACAAAAAA
368235 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
368254 TTGTATCGATACA
1 TTGTATCGATACA
368267 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:370718 original size:13 final size:13
Alignment explanation
Indices: 370700--370738 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
370690 ATAAACCTTT
*
370700 TGTATCGATACAC
1 TGTATCGATACAA
370713 TGTATCGATACAA
1 TGTATCGATACAA
370726 TGTATCGATACAA
1 TGTATCGATACAA
370739 AGAATGCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:376131 original size:13 final size:13
Alignment explanation
Indices: 376113--376138 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
376103 ACATTTGGTC
376113 ATGTATCGATACA
1 ATGTATCGATACA
376126 ATGTATCGATACA
1 ATGTATCGATACA
376139 TCTTGTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:376154 original size:32 final size:33
Alignment explanation
Indices: 376091--376158 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
376081 CGTTACAAGC
*
376091 CAATGTATTGATACATTTGGTCATGTATCGATA
1 CAATGTATCGATACATTTGGTCATGTATCGATA
376124 CAATGTATCGATACATCTT-GT-ATGTATCGATA
1 CAATGTATCGATACAT-TTGGTCATGTATCGATA
376156 CAA
1 CAA
376159 ACAGTTAAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 14 0.42
33 17 0.52
34 2 0.06
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (33 bp):
CAATGTATCGATACATTTGGTCATGTATCGATA
Found at i:378630 original size:19 final size:19
Alignment explanation
Indices: 378587--378642 Score: 94
Period size: 19 Copynumber: 2.9 Consensus size: 19
378577 TTGCCAGTTT
378587 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-TGAG
*
378607 TATGTATCGATACAATGAG
1 CATGTATCGATACAATGAG
378626 CATGTATCGATACAATG
1 CATGTATCGATACAATG
378643 TATCAATACT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 20 0.59
20 14 0.41
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAG
Found at i:379346 original size:13 final size:13
Alignment explanation
Indices: 379328--379353 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
379318 ACATATTGCT
379328 TTGTATTGATACA
1 TTGTATTGATACA
379341 TTGTATTGATACA
1 TTGTATTGATACA
379354 AGATCTTGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
TTGTATTGATACA
Found at i:379902 original size:23 final size:23
Alignment explanation
Indices: 379875--379918 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
379865 GCATTCAACC
*
379875 TTGGGTTATAATCTCTT-AAGAAT
1 TTGGGGTATAAT-TCTTGAAGAAT
379898 TTGGGGTATAATTCTTGAAGA
1 TTGGGGTATAATTCTTGAAGA
379919 GATTGAGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.41
Consensus pattern (23 bp):
TTGGGGTATAATTCTTGAAGAAT
Found at i:387577 original size:97 final size:96
Alignment explanation
Indices: 387450--387691 Score: 326
Period size: 97 Copynumber: 2.5 Consensus size: 96
387440 TTTTTATTGG
* *
387450 AAAA-CGAGGTTGAAGTATCCCCTCGGAGGAATGGGGTTAGAGTGTCCCCAATAATGACAATTTA
1 AAAAGCGAGGTTGGAGTATCCCCTCGGAGGAATGGGGTT-GAGTGTCCCCAATAATGACAATGTA
387514 AGTGAGAATAAAATTTAAACTTTGATGCGTTT
65 AGTGAGAATAAAATTTAAACTTTGATGCGTTT
* * * **
387546 AAAAGCGAGGTTGGAGTCTCCCTTCGGAGGAATGGGGTTGAAGTGTCCCCGATGGTGACAATGTA
1 AAAAGCGAGGTTGGAGTATCCCCTCGGAGGAATGGGGTTG-AGTGTCCCCAATAATGACAATGTA
* *
387611 AGTGAGAATAAGATTTAAACTTTGATGTGTTT
65 AGTGAGAATAAAATTTAAACTTTGATGCGTTT
* * *
387643 AAAAGC-AGGGTTGGAGTATCCCCTCGGAAGAATAGGGTTGGAGTATCCC
1 AAAAGCGA-GGTTGGAGTATCCCCTCGGAGGAATGGGGTT-GAGTGTCCC
387692 TGATAAATAA
Statistics
Matches: 128, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
96 6 0.05
97 121 0.95
98 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.27
Consensus pattern (96 bp):
AAAAGCGAGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGAGTGTCCCCAATAATGACAATGTAA
GTGAGAATAAAATTTAAACTTTGATGCGTTT
Found at i:389270 original size:2 final size:2
Alignment explanation
Indices: 389263--389296 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
389253 ACTTGAAAAC
389263 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
389297 GCTGATATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:389444 original size:18 final size:16
Alignment explanation
Indices: 389408--389456 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
389398 TTTTTTCTAC
389408 CTCTTTGTTTCTATTTCTT
1 CTCTTT-TTTCT-TTTC-T
389427 CTCTTTTTTC-TTTCT
1 CTCTTTTTTCTTTTCT
389442 CTTCTTTTTTCTTTT
1 C-TCTTTTTTCTTTT
389457 TTTTAGTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 2 0.07
16 13 0.46
17 3 0.11
18 4 0.14
19 6 0.21
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.73
Consensus pattern (16 bp):
CTCTTTTTTCTTTTCT
Found at i:393262 original size:136 final size:137
Alignment explanation
Indices: 393008--393280 Score: 401
Period size: 136 Copynumber: 2.0 Consensus size: 137
392998 ACCTAAGACT
* *
393008 CAATTTTTAAAAAATTACTAAAATAGCTTTAAGGTATACCTTTGACATGAAAGTATCTTGGTAAC
1 CAATTTCTAAAAAATTACTAAAATAGCTTTAAGGTATACCTTTGACATGAAAGTATCTTGATAAC
* * *
393073 CCTAAAAAACTCTAAAATGAGTGAAACTATCCTGAATATGCACCTTTGGCATAATAGCATCCCGA
66 CCTAAAAAACTCTAAAATGAGTGAAACTATCCTAAATATGCACCTTTGACATAAAAGCATCCCGA
393138 TGGTAAC
131 TGGTAAC
*
393145 CAATTTCT-AAAAATTACTAAAAT-GCCTTTAAGGTATACCTTTGACATGAAAGTATTTTGATAA
1 CAATTTCTAAAAAATTACTAAAATAG-CTTTAAGGTATACCTTTGACATGAAAGTATCTTGATAA
* * *
393208 CCCTAAAAGACTTTAAAATG-GAT-AAACCTATCCTAAATATGCACCTTTGACATAAAAGCATCT
65 CCCTAAAAAACTCTAAAATGAG-TGAAA-CTATCCTAAATATGCACCTTTGACATAAAAGCATCC
*
393271 CGGTGGTAAC
128 CGATGGTAAC
393281 TATAGACACA
Statistics
Matches: 123, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
135 5 0.04
136 111 0.90
137 7 0.06
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (137 bp):
CAATTTCTAAAAAATTACTAAAATAGCTTTAAGGTATACCTTTGACATGAAAGTATCTTGATAAC
CCTAAAAAACTCTAAAATGAGTGAAACTATCCTAAATATGCACCTTTGACATAAAAGCATCCCGA
TGGTAAC
Found at i:397012 original size:78 final size:79
Alignment explanation
Indices: 396752--397128 Score: 397
Period size: 79 Copynumber: 4.8 Consensus size: 79
396742 ACAGCGGGGC
* *
396752 TGGAGTATCCCTGATTATGAAAAATTGGTGTTCTGAAAATAAAATCGGGGTTGGAGTATCCCCTC
1 TGGAGTATCCCTGATTATGAAAAATCGGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCTC
396817 GAAAATAAC-AGGGT
66 GAAAATAACGA-GGT
* * * *
396831 TGGAGCATCCCTGGTTAT-AGGAAATCAGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCT
1 TGGAGTATCCCTGATTATGA-AAAATCGGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCT
* *
396895 CGAAAGTAACAAGGT
65 CGAAAATAACGAGGT
* *
396910 TGGAGTATCCCTGATTAT-AGAAAATCGGTGTTTTGAAAATAAAATCAGGGTT-GAGCATCCCCT
1 TGGAGTATCCCTGATTATGA-AAAATCGGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCT
396973 CGAAAATAACGAGGT
65 CGAAAATAACGAGGT
* * * ** ** ** * * *
396988 TAGAGTATCCCCGATTGTGAAAAATCAATGCATT-AGAAATAAGGTCGGGGTCGGAGTATCCTCG
1 TGGAGTATCCCTGATTATGAAAAATCGGTGTTTTGA-AAATAAAATCGGGGTTGGAGTATCCCCT
*
397052 CG-AAATAACGGGGT
65 CGAAAATAACGAGGT
** * * * ** *
397066 TGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTGGAAATAAAATTAGGGTTAGAGTATCCCC
1 TGGAGTATCCCTGATTATGAAAAATCGGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCC
397129 GATTGTGAGA
Statistics
Matches: 247, Mismatches: 45, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
77 1 0.00
78 119 0.48
79 126 0.51
80 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (79 bp):
TGGAGTATCCCTGATTATGAAAAATCGGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCTC
GAAAATAACGAGGT
Found at i:397046 original size:157 final size:157
Alignment explanation
Indices: 396752--397128 Score: 440
Period size: 157 Copynumber: 2.4 Consensus size: 157
396742 ACAGCGGGGC
* * *
396752 TGGAGTATCCCTGATTATGAAAAATTGGTGTTCTGAAAATAAAATCGGGGTTGGAGTATCCCCTC
1 TGGAGTATCCCTGATTATGAAAAATTGGTGTTTTGAAAATAAAATCAGGGTTAGAGTATCCCCTC
* * * * * * *
396817 GAAAATAACAGGGTTGGAGCATCCCTGGTTATAGGAAATCAGTGTTTTGAAAATAAAATCGGGGT
66 GAAAATAACAGGGTTAGAGCATCCCCGATTATAGAAAATCAATGATTAGAAAATAAAATCGGGGT
* *
396882 TGGAGTATCCCCTCGAAAGTAACAAGGT
131 CGGAGTATCCCCGCGAAA-TAACAAGGT
* *
396910 TGGAGTATCCCTGATTAT-AGAAAATCGGTGTTTTGAAAATAAAATCAGGGTT-GAGCATCCCCT
1 TGGAGTATCCCTGATTATGA-AAAATTGGTGTTTTGAAAATAAAATCAGGGTTAGAGTATCCCCT
* * **
396973 CGAAAATAAC-GAGGTTAGAGTATCCCCGATTGT-GAAAAATCAATGCATTAG-AAATAAGGTCG
65 CGAAAATAACAG-GGTTAGAGCATCCCCGATTATAG-AAAATCAATG-ATTAGAAAATAAAATCG
* **
397035 GGGTCGGAGTATCCTCGCGAAATAACGGGGT
127 GGGTCGGAGTATCCCCGCGAAATAACAAGGT
** * * *
397066 TGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTGGAAATAAAATTAGGGTTAGAGTATCCCC
1 TGGAGTATCCCTGATTATGAAAAATTGGTGTTTTGAAAATAAAATCAGGGTTAGAGTATCCCC
397129 GATTGTGAGA
Statistics
Matches: 186, Mismatches: 27, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
156 53 0.28
157 83 0.45
158 50 0.27
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (157 bp):
TGGAGTATCCCTGATTATGAAAAATTGGTGTTTTGAAAATAAAATCAGGGTTAGAGTATCCCCTC
GAAAATAACAGGGTTAGAGCATCCCCGATTATAGAAAATCAATGATTAGAAAATAAAATCGGGGT
CGGAGTATCCCCGCGAAATAACAAGGT
Found at i:397142 original size:129 final size:130
Alignment explanation
Indices: 396985--397271 Score: 384
Period size: 129 Copynumber: 2.2 Consensus size: 130
396975 AAAATAACGA
* * *
396985 GGTTAGAGTATCCCCGATTGTGAAAAATCAATGCATTAGAAATAAGGTCGGGGTCGGAGTATCCT
1 GGTTAGAGTATCCCCGATTGTGAAAAATCAATACATTAGAAATAAAGCCGGGGTCGGAGTATCCT
* * **
397050 CGCG-AAATAACGGGG-TTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTGGAAATAAAATTA
66 CGCGAAAATAA-GGGGATTGGAGTATCCCCAATTATGAAAAATTGATGTTTTGGAAATAAAACCA
397113 G
130 G
* ** * *
397114 GGTTAGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATGCT
1 GGTTAGAGTATCCCCGATTGTGAAAAATCAATACATTAGAAATAAAGCCGGGGTCGGAGTATCCT
** * *
397179 CTTGAAAATAAGGGGATTGGAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAACCGG
66 CGCGAAAATAAGGGGATTGGAGTATCCCCAATTATGAAAAATTGATGTTTTGGAAATAAAACCAG
397244 GGTTAGAGTATCCCCG--TGATGAAAAATC
1 GGTTAGAGTATCCCCGATTG-TGAAAAATC
397272 TAGAAATTTA
Statistics
Matches: 138, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
128 2 0.01
129 71 0.51
130 65 0.47
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (130 bp):
GGTTAGAGTATCCCCGATTGTGAAAAATCAATACATTAGAAATAAAGCCGGGGTCGGAGTATCCT
CGCGAAAATAAGGGGATTGGAGTATCCCCAATTATGAAAAATTGATGTTTTGGAAATAAAACCAG
Done.