Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008214.1 Hibiscus syriacus cultivar Beakdansim tig00110840_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2117680
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 11
Found at i:1205777 original size:27 final size:25
Alignment explanation
Indices: 1205737--1205792 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 25
1205727 TAAAAAATTA
*
1205737 TATTAACTTATTAAATATATTTTAT
1 TATTAACTTATTAAAAATATTTTAT
*
1205762 TATTAACTTAATTTAAAAATATTTTTT
1 TATTAACTT-A-TTAAAAATATTTTAT
1205789 TATT
1 TATT
1205793 TTTTATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 9 0.33
26 1 0.04
27 17 0.63
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (25 bp):
TATTAACTTATTAAAAATATTTTAT
Found at i:1205810 original size:27 final size:27
Alignment explanation
Indices: 1205749--1205818 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
1205739 TTAACTTATT
*
1205749 AAATATATTTTATTATTAACTTAATTTA
1 AAATATATTTTTTTATT-ACTTAATTTA
* *
1205777 AAA-ATATTTTTTTATT-TTTTATTTAA
1 AAATATATTTTTTTATTACTTAATTT-A
*
1205803 AAATATATATTTTTAT
1 AAATATATTTTTTTAT
1205819 GTTAAAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 6 0.17
26 4 0.11
27 23 0.64
28 3 0.08
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (27 bp):
AAATATATTTTTTTATTACTTAATTTA
Found at i:1207312 original size:3 final size:3
Alignment explanation
Indices: 1207306--1207357 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
1207296 TTCATCTAAA
*
1207306 TAT TAT T-T ATAT TAT TAT TAT TAT TAT AAT TAT TAT TAT TAT T-T
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1207350 TAT TAT TA
1 TAT TAT TA
1207358 ATAAATATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
2 3 0.07
3 40 0.91
4 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1207438 original size:18 final size:18
Alignment explanation
Indices: 1207417--1207452 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1207407 GACTCAACTG
1207417 GCCCAAACCCATCAGGAA
1 GCCCAAACCCATCAGGAA
*
1207435 GCCCAAACCTATCAGGAA
1 GCCCAAACCCATCAGGAA
1207453 ACCCTAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.36, G:0.17, T:0.08
Consensus pattern (18 bp):
GCCCAAACCCATCAGGAA
Found at i:1208866 original size:21 final size:23
Alignment explanation
Indices: 1208842--1208891 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
1208832 ATAAATAATA
1208842 ATTTATAT-ATATTTTTAA-A-TT
1 ATTTATATCATA-TTTTAATATTT
*
1208863 ATTTTTATCATATTTTAATATTT
1 ATTTATATCATATTTTAATATTT
1208886 ATTTAT
1 ATTTAT
1208892 TTTTCAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 13 0.54
22 4 0.17
23 7 0.29
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (23 bp):
ATTTATATCATATTTTAATATTT
Found at i:1220292 original size:13 final size:12
Alignment explanation
Indices: 1220268--1220348 Score: 55
Period size: 12 Copynumber: 6.8 Consensus size: 12
1220258 TATTATGCTT
1220268 GAAGAAAAAAAA
1 GAAGAAAAAAAA
*
1220280 GAAG-AACAAAA
1 GAAGAAAAAAAA
*
1220291 -AAGAAAAAAAT
1 GAAGAAAAAAAA
* *
1220302 GAGGAAAAAAGA
1 GAAGAAAAAAAA
1220314 -AAGAAAAAGGAAA
1 GAAGAAAAA--AAA
1220327 -AA-AAAGAGAAAA
1 GAAGAAA-A-AAAA
1220339 GAAGAAAAAA
1 GAAGAAAAAA
1220349 GAGGGGGTCA
Statistics
Matches: 53, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
10 3 0.06
11 18 0.34
12 20 0.38
13 8 0.15
14 4 0.08
ACGTcount: A:0.78, C:0.01, G:0.20, T:0.01
Consensus pattern (12 bp):
GAAGAAAAAAAA
Found at i:1220297 original size:22 final size:23
Alignment explanation
Indices: 1220269--1220321 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
1220259 ATTATGCTTG
*
1220269 AAGAAAAAAAAGAAGAACAAA-A
1 AAGAAAAAAAAGAAGAAAAAAGA
* *
1220291 AAGAAAAAAATGAGGAAAAAAGA
1 AAGAAAAAAAAGAAGAAAAAAGA
1220314 AAGAAAAA
1 AAGAAAAA
1220322 GGAAAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (23 bp):
AAGAAAAAAAAGAAGAAAAAAGA
Found at i:1220309 original size:18 final size:18
Alignment explanation
Indices: 1220287--1220350 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 18
1220277 AAAGAAGAAC
1220287 AAAAAAGAAA-AAAATGAGG
1 AAAAAAGAAAGAAAA--AGG
1220306 AAAAAAGAAAGAAAAAGG
1 AAAAAAGAAAGAAAAAGG
*
1220324 AAAAAA-AAGAGAAAAGAAG
1 AAAAAAGAA-AGAAAA-AGG
1220343 AAAAAAGA
1 AAAAAAGA
1220351 GGGGGTCAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
17 2 0.05
18 15 0.38
19 18 0.45
20 5 0.12
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (18 bp):
AAAAAAGAAAGAAAAAGG
Found at i:1220327 original size:30 final size:30
Alignment explanation
Indices: 1220276--1220345 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
1220266 TTGAAGAAAA
* *
1220276 AAAAGAAG-AACAAAAAAGAAAAAAATGAGG
1 AAAAGAAGAAAGAAAAAAGAAAAAAAAGA-G
*
1220306 AAAA-AAGAAAGAAAAAGGAAAAAAAAGAG
1 AAAAGAAGAAAGAAAAAAGAAAAAAAAGAG
1220335 AAAAGAAGAAA
1 AAAAGAAGAAA
1220346 AAAGAGGGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 8 0.23
30 27 0.77
ACGTcount: A:0.77, C:0.01, G:0.20, T:0.01
Consensus pattern (30 bp):
AAAAGAAGAAAGAAAAAAGAAAAAAAAGAG
Found at i:1220349 original size:10 final size:10
Alignment explanation
Indices: 1220269--1220350 Score: 68
Period size: 10 Copynumber: 8.4 Consensus size: 10
1220259 ATTATGCTTG
1220269 AAGAA-AAAA
1 AAGAAGAAAA
1220278 AAGAAGAACAA
1 AAGAAGAA-AA
1220289 AA-AAGAAAAA
1 AAGAAG-AAAA
*
1220299 AATGAGGAAAA
1 AA-GAAGAAAA
1220310 AAGAA-AGAAA
1 AAGAAGA-AAA
1220320 AAG--GAAAA
1 AAGAAGAAAA
*
1220328 AA-AAGAGAA
1 AAGAAGAAAA
1220337 AAGAAGAAAA
1 AAGAAGAAAA
1220347 AAGA
1 AAGA
1220351 GGGGGTCAAG
Statistics
Matches: 59, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
8 5 0.08
9 13 0.22
10 27 0.46
11 12 0.20
12 2 0.03
ACGTcount: A:0.78, C:0.01, G:0.20, T:0.01
Consensus pattern (10 bp):
AAGAAGAAAA
Found at i:1220746 original size:19 final size:20
Alignment explanation
Indices: 1220681--1220754 Score: 64
Period size: 19 Copynumber: 3.8 Consensus size: 20
1220671 ATTTATTAAT
*
1220681 AAATTCTAAGTTTATTTTCTCT
1 AAATTC-AAGTTTATTTTCT-A
* * *
1220703 AAATTCAATTTTATATT-TG
1 AAATTCAAGTTTATTTTCTA
*
1220722 AGATTCAA-TTTATTTTCTA
1 AAATTCAAGTTTATTTTCTA
1220741 AAATTCAA-TTTATT
1 AAATTCAAGTTTATT
1220755 CTTTTATTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
18 7 0.16
19 21 0.48
20 1 0.02
21 9 0.20
22 6 0.14
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.53
Consensus pattern (20 bp):
AAATTCAAGTTTATTTTCTA
Found at i:1221383 original size:114 final size:114
Alignment explanation
Indices: 1221048--1221385 Score: 532
Period size: 114 Copynumber: 3.0 Consensus size: 114
1221038 GTGCTACGTT
* *
1221048 CTCATAGTAGAAATAAGAAGACCCAATAACATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
*
1221113 ATTTGGTATGAACCCCAAAATCAATCATTAGATTTAAAAGATAAATTTG
66 ATTTGGTATGAACCCCAAAATCAATCATTAGATTTAAAAGATGAATTTG
*
1221162 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
*
1221227 ATTTGGTATGAACCCCAAAATCAATCATTAGATTTGAAAGATGAATTTG
66 ATTTGGTATGAACCCCAAAATCAATCATTAGATTTAAAAGATGAATTTG
* * *
1221276 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTTTTCTTTGAGTCATCTAATCTG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* * * * * * * *
1221341 GTTCGGTAAGAACCACAGAACCAATCATTGGAATTAAAAGATGAA
66 ATTTGGTATGAACCCCAAAATCAATCATTAGATTTAAAAGATGAA
1221386 CTGCATGATC
Statistics
Matches: 206, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 206 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.31
Consensus pattern (114 bp):
CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
ATTTGGTATGAACCCCAAAATCAATCATTAGATTTAAAAGATGAATTTG
Found at i:1222166 original size:113 final size:112
Alignment explanation
Indices: 1222033--1222645 Score: 658
Period size: 113 Copynumber: 5.4 Consensus size: 112
1222023 AGTTCATAAT
* * *
1222033 AAGAAGGAAGAATAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCACTTG
1 AAGAA-GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTG
1222098 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
65 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
* ** * *
1222146 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTG
1 AAGAA-GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTG
* * *
1222211 ATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCAT-
65 ATGGATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATC-TG
** * *
1222259 CTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAA-CTTTTACTCAAATCCATCACTTGA
1 AAGAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGA
*
1222323 TGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAA-AACTCATCTG
66 TGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
* ** * *
1222369 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTG
1 AAGAA-GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTG
* * *
1222434 ATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTG
65 ATGGATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTG
* ** * * *
1222482 AAGAAGAAGAAG--G-TCACAATGAGAAGAGCTTGTTCAACCTTTTGCAT-AATTCTATCAC-AG
1 AAGAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC-TCAAATCCATCACTTG
*
1222542 AAGGAGAAAAATTAGCATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT-
65 -ATG-G----A-T--CA--A-CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
* **
1222601 --GAAGAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTG
1 AAGAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
1222646 AATGACTCTA
Statistics
Matches: 424, Mismatches: 51, Indels: 43
0.82 0.10 0.08
Matches are distributed among these distances:
108 1 0.00
109 37 0.09
110 14 0.03
111 83 0.20
112 91 0.21
113 116 0.27
114 2 0.00
115 1 0.00
117 12 0.03
119 2 0.00
120 64 0.15
121 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (112 bp):
AAGAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGA
TGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
Found at i:1222436 original size:223 final size:222
Alignment explanation
Indices: 1222039--1222645 Score: 886
Period size: 223 Copynumber: 2.7 Consensus size: 222
1222029 TAATAAGAAG
*
1222039 GAAGAATAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCACTTGATGGAT
1 GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCACTTGATGGAT
*
1222104 CAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
66 CAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
1222169 TGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGA
131 TGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGA
1222234 GTTCATAATGAGAAGAACTCATCATCTGAA
196 GTTCATAATGAGAAGAA--C-TCATCTGAA
1222264 GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAA-CTTTTACTCAAATCCATCACTTGATGGAT
1 GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCACTTGATGGAT
1222328 CAGCTTTTCCAGAGAAAGTTCATAATGAGAA-AACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
66 CAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
1222392 TGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGA
131 TGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGA
1222457 GTTCATAATGAGAAGAACTCATCTGAA
196 GTTCATAATGAGAAGAACTCATCTGAA
** * ** * * * **
1222484 GAAGAAGAAGGTCACAATGAGAAGAGCTTGTTCAACCTTTTGCAT-AATTCTATCACAGAAGGAG
1 GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTAC-TCAAATCCATCAC-----TTG
*
1222548 AAAAATTAGCATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT---GAA-GAAGA
60 ----A-T-GGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
* **
1222609 AGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTG
119 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
1222646 AATGACTCTA
Statistics
Matches: 352, Mismatches: 16, Indels: 24
0.90 0.04 0.06
Matches are distributed among these distances:
220 39 0.11
221 16 0.05
222 1 0.00
223 115 0.33
224 59 0.17
225 34 0.10
226 1 0.00
229 39 0.11
230 4 0.01
231 1 0.00
232 34 0.10
233 9 0.03
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (222 bp):
GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCACTTGATGGAT
CAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
TGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGA
GTTCATAATGAGAAGAACTCATCTGAA
Found at i:1222611 original size:120 final size:118
Alignment explanation
Indices: 1222456--1222724 Score: 380
Period size: 120 Copynumber: 2.3 Consensus size: 118
1222446 TGCCAGGTAG
1222456 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGGTCACAATGAGAAGAGCTTGTTCAACC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGGTCACAATGAGAAGAGCTTGTTCAACC
* * * * **
1222521 TTTTGCATAATTCTATCACAGAAGGAGAA-AAATTAGCATCAGCTTTTCCAG-AGAA
66 TTTTGAATAACTCTATCACAGAAGGA-AATAAATCAACATCA---TCCCCAGCAGAA
*
1222576 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGGTCACAATGAGAAGAGCTTGTTCAACC
* * ** *
1222641 TTTTGAATGACTCTATCACATAAGGAAATAGGTCAACATCATCCCCAGCGGAA
66 TTTTGAATAACTCTATCACAGAAGGAAATAAATCAACATCATCCCCAGCAGAA
1222694 AGTTCATAATGAGAAGAACTCATCTGAAGAA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAA
1222725 AGAGAAGAAT
Statistics
Matches: 135, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
117 5 0.04
118 34 0.25
119 2 0.01
120 94 0.70
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (118 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGGTCACAATGAGAAGAGCTTGTTCAACC
TTTTGAATAACTCTATCACAGAAGGAAATAAATCAACATCATCCCCAGCAGAA
Found at i:1222912 original size:24 final size:26
Alignment explanation
Indices: 1222879--1222938 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 26
1222869 AATATTATTT
1222879 ATATTATTATTA-TTATTA-TAATAA
1 ATATTATTATTATTTATTATTAATAA
*
1222903 TTATTATTATTATTTTATTATTAATAA
1 ATATTATTATTA-TTTATTATTAATAA
1222930 ATATTATTA
1 ATATTATTA
1222939 CAGGCCCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 11 0.35
26 6 0.19
27 14 0.45
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
ATATTATTATTATTTATTATTAATAA
Found at i:1222938 original size:3 final size:3
Alignment explanation
Indices: 1222871--1222925 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
1222861 TTTATTTAAA
* *
1222871 TAT TAT T-T ATAT TAT TAT TAT TAT TAT AAT AAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1222916 T-T TAT TAT TA
1 TAT TAT TAT TA
1222926 ATAAATATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 3 0.06
3 43 0.91
4 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1224357 original size:28 final size:27
Alignment explanation
Indices: 1224283--1224358 Score: 64
Period size: 29 Copynumber: 2.7 Consensus size: 27
1224273 GTTCTAATTG
** *
1224283 TATTTTTATTATTGTT-TATTTATGTTT
1 TATTTTTATTATT-TTATATTTAAATAT
* *
1224310 TAATTTTACTTGTTTATATATTTAAATAT
1 TATTTTTA-TTATTT-TATATTTAAATAT
1224339 TATTTTTATTATTATTATAT
1 TATTTTTATTATT-TTATAT
1224359 AGTCATATAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
27 8 0.21
28 14 0.37
29 16 0.42
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.67
Consensus pattern (27 bp):
TATTTTTATTATTTTATATTTAAATAT
Found at i:1232453 original size:2 final size:2
Alignment explanation
Indices: 1232448--1232478 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1232438 ATAACAATGA
1232448 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1232479 AGAAAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1239498 original size:54 final size:54
Alignment explanation
Indices: 1239416--1239559 Score: 164
Period size: 54 Copynumber: 2.7 Consensus size: 54
1239406 ACGAACTAGA
* * * *
1239416 AAGTCGTGCCCACACTTTAACTAAAGACCTCTTCTGCGATAGCTTAGAATGAAT
1 AAGTCGTGCCCACGCCTTAACTGAAGACCTCTTCTGCGATAGCTCAGAATGAAT
* * * *
1239470 AAGTCGTGCCCACGCCTTAACTGAAGACCTTTTCTACTATAGCTCATAATGAAT
1 AAGTCGTGCCCACGCCTTAACTGAAGACCTCTTCTGCGATAGCTCAGAATGAAT
* * * *
1239524 AAGCCGTGCCCAAGCCTTATGCGGAA-ACCTCTTCTG
1 AAGTCGTGCCCACGCCTTA-ACTGAAGACCTCTTCTG
1239560 GTCTTTTCGT
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
54 71 0.95
55 4 0.05
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.27
Consensus pattern (54 bp):
AAGTCGTGCCCACGCCTTAACTGAAGACCTCTTCTGCGATAGCTCAGAATGAAT
Found at i:1240047 original size:25 final size:25
Alignment explanation
Indices: 1239999--1240088 Score: 89
Period size: 25 Copynumber: 3.7 Consensus size: 25
1239989 TATGGCACTA
* *
1239999 CGGTGC-AA-TTCTACGCGGTACTT
1 CGGTGCAAATTTCTACGTGGTCCTT
1240022 CGGTGCAAATTTCTACGTGGTCCTT
1 CGGTGCAAATTTCTACGTGGTCCTT
*
1240047 CGG-GACAAAATTCTACGTGG-CACTT
1 CGGTG-CAAATTTCTACGTGGTC-CTT
* *
1240072 TGGTGCAAATTTATACG
1 CGGTGCAAATTTCTACG
1240089 AGTTGTGGTG
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
23 6 0.11
24 4 0.07
25 45 0.80
26 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (25 bp):
CGGTGCAAATTTCTACGTGGTCCTT
Found at i:1250754 original size:22 final size:22
Alignment explanation
Indices: 1250726--1250769 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1250716 TTTTATAGAC
1250726 CCGAAATTTAAAAGCGAACCAT
1 CCGAAATTTAAAAGCGAACCAT
1250748 CCGAAATTTAAAAGCGAACCAT
1 CCGAAATTTAAAAGCGAACCAT
1250770 AAACGACGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.23, G:0.14, T:0.18
Consensus pattern (22 bp):
CCGAAATTTAAAAGCGAACCAT
Found at i:1251556 original size:70 final size:70
Alignment explanation
Indices: 1251475--1251613 Score: 242
Period size: 70 Copynumber: 2.0 Consensus size: 70
1251465 CGCATATATA
1251475 CAGAAATTGATAATACAATTTGACCAAACTCAAATTTGTTGGATTATAGATTGCAAAATTTGAAC
1 CAGAAATTGATAATACAATTTGACCAAACTCAAATTTGTTGGATTATAGATTGCAAAATTTGAAC
1251540 TTCTT
66 TTCTT
* * * *
1251545 CAGAAATTGATAATACAGTTTGACCGAACTCAATTTTGTTGGATTATAGATTGCAAAATTTGAGC
1 CAGAAATTGATAATACAATTTGACCAAACTCAAATTTGTTGGATTATAGATTGCAAAATTTGAAC
1251610 TTCT
66 TTCT
1251614 AAACTTAAAC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (70 bp):
CAGAAATTGATAATACAATTTGACCAAACTCAAATTTGTTGGATTATAGATTGCAAAATTTGAAC
TTCTT
Found at i:1253087 original size:27 final size:27
Alignment explanation
Indices: 1253057--1253124 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 27
1253047 TGCGAATGTT
*
1253057 TTATTTATTTAATTTTTTAGTATTACC
1 TTATTTATTTAATTTTTTAATATTACC
*
1253084 TTATTTATTTAATTTTTTAATATTACT
1 TTATTTATTTAATTTTTTAATATTACC
*
1253111 TTATAT-TTTAATTT
1 TTATTTATTTAATTT
1253125 GTATACCATT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
26 8 0.21
27 30 0.79
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.66
Consensus pattern (27 bp):
TTATTTATTTAATTTTTTAATATTACC
Found at i:1255768 original size:3 final size:3
Alignment explanation
Indices: 1255760--1255823 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
1255750 AGAGTTTTAG
1255760 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1255808 TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC T
1255824 GTGTCTTCAG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:1257594 original size:21 final size:21
Alignment explanation
Indices: 1257526--1257670 Score: 85
Period size: 21 Copynumber: 6.7 Consensus size: 21
1257516 CCTTCAAGAC
**
1257526 ATATATGTAATCCTTTGGAAT
1 ATATATGTGGTCCTTTGGAAT
* * * * *
1257547 ATATATGCGGTTCTTCGGGAC
1 ATATATGTGGTCCTTTGGAAT
* *
1257568 ACATATTTGGTCCTTTGGAAT
1 ATATATGTGGTCCTTTGGAAT
*
1257589 ATATATGTGGTCCTTAAGGAGAT
1 ATATATGTGGTCCTT-TGGA-AT
* * *
1257612 TTCTATGTGGTCCTTCGGGACAT
1 ATATATGTGGTCCTT-TGGA-AT
* * *
1257635 TTCTACGTGGTCCTTT-GAGAT
1 ATATATGTGGTCCTTTGGA-AT
*
1257656 ATCTATGTGGTCCTT
1 ATATATGTGGTCCTT
1257671 CGGGACATTC
Statistics
Matches: 95, Mismatches: 27, Indels: 4
0.75 0.21 0.03
Matches are distributed among these distances:
21 58 0.61
22 3 0.03
23 34 0.36
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (21 bp):
ATATATGTGGTCCTTTGGAAT
Found at i:1257622 original size:23 final size:23
Alignment explanation
Indices: 1257592--1257695 Score: 108
Period size: 23 Copynumber: 4.7 Consensus size: 23
1257582 TTGGAATATA
** *
1257592 TATGTGGTCCTTAAGGAGATTTC
1 TATGTGGTCCTTCGGGACATTTC
1257615 TATGTGGTCCTTCGGGACATTTC
1 TATGTGGTCCTTCGGGACATTTC
* * * *
1257638 TACGTGGTCCTT--TGAGATATC
1 TATGTGGTCCTTCGGGACATTTC
1257659 TATGTGGTCCTTCGGGACA-TTC
1 TATGTGGTCCTTCGGGACATTTC
1257681 TATGTGG-CACTTCGG
1 TATGTGGTC-CTTCGG
1257696 TGTAATTATA
Statistics
Matches: 67, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
21 18 0.27
22 15 0.22
23 34 0.51
ACGTcount: A:0.16, C:0.19, G:0.27, T:0.38
Consensus pattern (23 bp):
TATGTGGTCCTTCGGGACATTTC
Found at i:1257624 original size:44 final size:44
Alignment explanation
Indices: 1257575--1257678 Score: 122
Period size: 44 Copynumber: 2.4 Consensus size: 44
1257565 GACACATATT
* * *
1257575 TGGTCCTT-TGGA-ATATATATGTGGTCCTTAAGGAGATTTCTATG
1 TGGTCCTTCGGGACATATATACGTGGTCCTT--GGAGATATCTATG
* * *
1257619 TGGTCCTTCGGGACATTTCTACGTGGTCCTTTGAGATATCTATG
1 TGGTCCTTCGGGACATATATACGTGGTCCTTGGAGATATCTATG
1257663 TGGTCCTTCGGGACAT
1 TGGTCCTTCGGGACAT
1257679 TCTATGTGGC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
44 35 0.67
45 3 0.06
46 14 0.27
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.38
Consensus pattern (44 bp):
TGGTCCTTCGGGACATATATACGTGGTCCTTGGAGATATCTATG
Found at i:1262525 original size:21 final size:21
Alignment explanation
Indices: 1262446--1262552 Score: 108
Period size: 21 Copynumber: 5.0 Consensus size: 21
1262436 GTCTTTTGAA
* *
1262446 ATATATATGTGGTCCTTAAGGAG
1 ATATCTATGTGGTCCTT-CGG-G
*
1262469 ATTTCTATGTGGT-CTTCGGG
1 ATATCTATGTGGTCCTTCGGG
* * *
1262489 ACATTTCTACGCGGTCCTTCGGG
1 --ATATCTATGTGGTCCTTCGGG
1262512 ATATCTATGTGGTCCTTCGGG
1 ATATCTATGTGGTCCTTCGGG
*
1262533 ATATCTATATGGTCCTTCGG
1 ATATCTATGTGGTCCTTCGG
1262553 TGCAATTATA
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
20 1 0.01
21 39 0.54
22 14 0.19
23 18 0.25
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (21 bp):
ATATCTATGTGGTCCTTCGGG
Found at i:1265732 original size:25 final size:24
Alignment explanation
Indices: 1265704--1265823 Score: 66
Period size: 25 Copynumber: 5.2 Consensus size: 24
1265694 TATATTTATC
1265704 ATTTATCCCATAAGCTCGTAAGCTT
1 ATTT-TCCCATAAGCTCGTAAGCTT
* *
1265729 ATTTTACCATTATA-CT--T--GC-C
1 ATTTTCCCA-TA-AGCTCGTAAGCTT
1265749 ATTTATCCCATAAGCTCGTAAGCTT
1 ATTT-TCCCATAAGCTCGTAAGCTT
*
1265774 ATTTTACCCATATA-CT--T-ACCTT
1 ATTTT-CCCATA-AGCTCGTAAGCTT
1265796 -TTGTT-CCATAAGCTCGTAAGCTT
1 ATT-TTCCCATAAGCTCGTAAGCTT
1265819 ATTTT
1 ATTTT
1265824 ACCAATATAC
Statistics
Matches: 72, Mismatches: 6, Indels: 36
0.63 0.05 0.32
Matches are distributed among these distances:
19 2 0.03
20 15 0.21
21 8 0.11
22 8 0.11
23 8 0.11
24 9 0.12
25 20 0.28
26 2 0.03
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42
Consensus pattern (24 bp):
ATTTTCCCATAAGCTCGTAAGCTT
Found at i:1265754 original size:45 final size:45
Alignment explanation
Indices: 1265690--1265939 Score: 378
Period size: 45 Copynumber: 5.6 Consensus size: 45
1265680 ACATGCATAT
* * *
1265690 CCAATATATTTATCATTTATCCCATAAGCTCGTAAGCTTATTTTA
1 CCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA
* * *
1265735 CCATTATACTTGCCATTTATCCCATAAGCTCGTAAGCTTATTTTA
1 CCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA
* * *
1265780 CCCATATACTTACCTTTTGTTCCATAAGCTCGTAAGCTTATTTTA
1 CCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA
1265825 CCAATATACTTACCA-TTATTCCATAAGCTCGTAAGCTTATTTTA
1 CCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA
*
1265869 CCAATATACTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTA
1 CCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA
* *
1265914 CCAATACACTTGCCA-TTATTCCATAA
1 CCAATATACTTACCATTTATTCCATAA
1265940 ACCATATTCC
Statistics
Matches: 187, Mismatches: 17, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
44 53 0.28
45 134 0.72
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.40
Consensus pattern (45 bp):
CCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA
Found at i:1265888 original size:89 final size:89
Alignment explanation
Indices: 1265690--1265939 Score: 401
Period size: 89 Copynumber: 2.8 Consensus size: 89
1265680 ACATGCATAT
* * * * *
1265690 CCAATATATTTATCATTTATCCCATAAGCTCGTAAGCTTATTTTACCATTATACTTGCCATTTAT
1 CCAATATACTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA-TTAT
*
1265755 CCCATAAGCTCGTAAGCTTATTTTA
65 TCCATAAGCTCGTAAGCTTATTTTA
* * *
1265780 CCCATATACTTACCTTTTGTTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTATT
1 CCAATATACTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCATTATT
1265845 CCATAAGCTCGTAAGCTTATTTTA
66 CCATAAGCTCGTAAGCTTATTTTA
*
1265869 CCAATATACTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTACCAATACACTTGCCATTATT
1 CCAATATACTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCATTATT
1265934 CCATAA
66 CCATAA
1265940 ACCATATTCC
Statistics
Matches: 147, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
89 95 0.65
90 52 0.35
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.40
Consensus pattern (89 bp):
CCAATATACTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCATTATT
CCATAAGCTCGTAAGCTTATTTTA
Found at i:1269774 original size:11 final size:11
Alignment explanation
Indices: 1269758--1269782 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1269748 TTTTAATAAT
1269758 TAAATATAACA
1 TAAATATAACA
1269769 TAAATATAACA
1 TAAATATAACA
1269780 TAA
1 TAA
1269783 TAAAAAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (11 bp):
TAAATATAACA
Found at i:1269848 original size:13 final size:12
Alignment explanation
Indices: 1269830--1269865 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
1269820 TCTACTTAGC
1269830 TTGATAGAAGAAA
1 TTGATAGAAG-AA
1269843 TTGATAGAATGAA
1 TTGATAGAA-GAA
1269856 TTGATAGAAG
1 TTGATAGAAG
1269866 TGAGAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 1 0.05
13 20 0.91
14 1 0.05
ACGTcount: A:0.47, C:0.00, G:0.25, T:0.28
Consensus pattern (12 bp):
TTGATAGAAGAA
Found at i:1270273 original size:14 final size:14
Alignment explanation
Indices: 1270254--1270283 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1270244 GGAGAAAAAA
1270254 AAACATTTGTAAAG
1 AAACATTTGTAAAG
*
1270268 AAACATTTGTAGAG
1 AAACATTTGTAAAG
1270282 AA
1 AA
1270284 GAGCAAGTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.27
Consensus pattern (14 bp):
AAACATTTGTAAAG
Found at i:1275997 original size:22 final size:23
Alignment explanation
Indices: 1275972--1276015 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
1275962 TAAGCACTAT
*
1275972 AAGAAAAGCAAATAA-GAACATA
1 AAGAAAAACAAATAAGGAACATA
1275994 AAGAAAAACAAATAAGGAACAT
1 AAGAAAAACAAATAAGGAACAT
1276016 TTTTATTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.68, C:0.09, G:0.14, T:0.09
Consensus pattern (23 bp):
AAGAAAAACAAATAAGGAACATA
Found at i:1279425 original size:23 final size:25
Alignment explanation
Indices: 1279386--1279443 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
1279376 TATAACCATT
1279386 TTTTAATAAAACAATTA-AATATT-A
1 TTTTAA-AAAACAATTATAATATTAA
* * *
1279410 TTTTAAAAAACGATTATGATTTTAA
1 TTTTAAAAAACAATTATAATATTAA
1279435 TTTTAAAAA
1 TTTTAAAAA
1279444 TTGATAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 9 0.31
24 10 0.34
25 10 0.34
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (25 bp):
TTTTAAAAAACAATTATAATATTAA
Found at i:1281900 original size:3 final size:3
Alignment explanation
Indices: 1281882--1281933 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
1281872 ATTTATATAT
* * *
1281882 TAA TAG TAA AAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
*
1281928 AAA TAA
1 TAA TAA
1281934 ATAGAAAAGA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:1281912 original size:15 final size:16
Alignment explanation
Indices: 1281893--1281933 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
1281883 AATAGTAAAA
1281893 ATAATAATAATAATAG
1 ATAATAATAATAATAG
1281909 -TAATAATAATAATAG
1 ATAATAATAATAATAG
*
1281924 ATAAAAATAA
1 ATAATAATAA
1281934 ATAGAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (16 bp):
ATAATAATAATAATAG
Found at i:1282342 original size:134 final size:132
Alignment explanation
Indices: 1282154--1282415 Score: 362
Period size: 134 Copynumber: 2.0 Consensus size: 132
1282144 TGAAGAGTTA
** *
1282154 TGGCCATCTTTAGAGAAGTGATACTCGGTTCCTACGCGATGAGGACGGTTGGTTATCTAGGGGTG
1 TGGCCATCTTTAGAGAAGTGATACTCGGTTCCTACGCGATGAGGACGACTGGTTATCTAGGGGTA
* *
1282219 ACACGGCTCCTACATGATGAGGAGTTCTGGTCGGGGGATGACATGATTCCTACGTGATGAGGACG
66 ACACGGCTCCTACATGATGAGGAGGTCTGGTCGGGGGATGACACGATTCCTACGTGATGAGGACG
1282284 GC
131 GC
** ** * * **
1282286 TGGCCATCTTTAAGAGTGGTGATAACTCGGTTCCTACTTGATGAGGACGACTGGTTATTTATGTT
1 TGGCCATCTTT-AGAGAAGTGAT-ACTCGGTTCCTACGCGATGAGGACGACTGGTTATCTAGGGG
* * *
1282351 TAACACTGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCCTACGTGATGAGGA
64 TAACACGGCTCCTACATGATGAGGAGGTCTGGTCGGGGGATGACACGATTCCTACGTGATGAGGA
1282416 TATCTGGTCA
Statistics
Matches: 112, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
132 11 0.10
133 9 0.08
134 92 0.82
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.28
Consensus pattern (132 bp):
TGGCCATCTTTAGAGAAGTGATACTCGGTTCCTACGCGATGAGGACGACTGGTTATCTAGGGGTA
ACACGGCTCCTACATGATGAGGAGGTCTGGTCGGGGGATGACACGATTCCTACGTGATGAGGACG
GC
Found at i:1283385 original size:8 final size:7
Alignment explanation
Indices: 1283363--1283475 Score: 101
Period size: 7 Copynumber: 16.1 Consensus size: 7
1283353 CTCCTTTTAT
1283363 TTTTTTC
1 TTTTTTC
1283370 TTTCTTTTC
1 -TT-TTTTC
*
1283379 TCTTTT-
1 TTTTTTC
1283385 TTTTTTC
1 TTTTTTC
1283392 TTTTTTC
1 TTTTTTC
1283399 TTTTTTC
1 TTTTTTC
*
1283406 -TTCTTC
1 TTTTTTC
1283412 TTTTTTTC
1 -TTTTTTC
*
1283420 TTTTTCC
1 TTTTTTC
1283427 TTTTTTCC
1 TTTTTT-C
1283435 TTTTTTC
1 TTTTTTC
*
1283442 --TTCT-
1 TTTTTTC
1283446 TTTTTTC
1 TTTTTTC
1283453 TTTTTTC
1 TTTTTTC
*
1283460 ATTTTTCC
1 -TTTTTTC
1283468 TTTTTTC
1 TTTTTTC
1283475 T
1 T
1283476 CTTCTTCAAG
Statistics
Matches: 86, Mismatches: 10, Indels: 19
0.75 0.09 0.17
Matches are distributed among these distances:
5 3 0.03
6 13 0.15
7 44 0.51
8 21 0.24
9 5 0.06
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTTC
Found at i:1283443 original size:33 final size:32
Alignment explanation
Indices: 1283357--1283475 Score: 127
Period size: 33 Copynumber: 3.7 Consensus size: 32
1283347 TGAACCCTCC
* * * *
1283357 TTTTATTTTTTTCTTTCTT-TTCTCTTTTT-T
1 TTTTCTTTTTTCCTTTTTTCTTCTTTTTTTCT
1283387 TTTTCTTTTTT-CTTTTTTCTTCTTCTTTTTTTCT
1 TTTTCTTTTTTCCTTTTTTC-T--TCTTTTTTTCT
1283421 TTTTCCTTTTTTCCTTTTTTCTTCTTTTTTTCTT
1 TTTT-CTTTTTTCCTTTTTTCTTCTTTTTTTC-T
*
1283455 TTTTCATTTTTCCTTTTTTCT
1 TTTTCTTTTTTCCTTTTTTCT
1283476 CTTCTTCAAG
Statistics
Matches: 77, Mismatches: 4, Indels: 13
0.82 0.04 0.14
Matches are distributed among these distances:
29 6 0.08
30 10 0.13
31 1 0.01
33 34 0.44
34 10 0.13
35 8 0.10
36 8 0.10
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.81
Consensus pattern (32 bp):
TTTTCTTTTTTCCTTTTTTCTTCTTTTTTTCT
Found at i:1290573 original size:30 final size:30
Alignment explanation
Indices: 1290538--1290597 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1290528 AATGAATGCA
** * *
1290538 TATTGGTAATGTGTTATAAATTATGCATTT
1 TATTGGTAATGCATTATAAATGATGAATTT
*
1290568 TATTGGTGATGCATTATAAATGATGAATTT
1 TATTGGTAATGCATTATAAATGATGAATTT
1290598 ATTCATGCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.47
Consensus pattern (30 bp):
TATTGGTAATGCATTATAAATGATGAATTT
Found at i:1295792 original size:9 final size:10
Alignment explanation
Indices: 1295778--1295804 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1295768 TTTTCTCTCA
1295778 TTTTTTCTGT
1 TTTTTTCTGT
1295788 TTTTTTCTGT
1 TTTTTTCTGT
1295798 TTTTTTC
1 TTTTTTC
1295805 GTATCCCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.11, G:0.07, T:0.81
Consensus pattern (10 bp):
TTTTTTCTGT
Found at i:1296471 original size:3 final size:3
Alignment explanation
Indices: 1296453--1296501 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
1296443 ATTTATGTAT
* * *
1296453 TAA TAG TAA AAA TAA TAA TAA TAA TAA TAA TAA TAA TAGA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
1296499 TAA
1 TAA
1296502 ATATAAAAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:1301924 original size:20 final size:18
Alignment explanation
Indices: 1301899--1301944 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
1301889 TTTTTCTAAC
1301899 AATATATTAAGATTTTTATA
1 AATATATTAA-ATTTTT-TA
*
1301919 AATATATTCAATTTTTTA
1 AATATATTAAATTTTTTA
*
1301937 AAAATATT
1 AATATATT
1301945 TCAAAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.38
19 6 0.25
20 9 0.38
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
AATATATTAAATTTTTTA
Found at i:1301947 original size:19 final size:20
Alignment explanation
Indices: 1301889--1301948 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
1301879 ATATTATATT
*
1301889 TTTTTCTAACAATATATT-AA
1 TTTTT-TAAAAATATATTCAA
* *
1301909 GATTTTTATAAATATATTCAA
1 -TTTTTTAAAAATATATTCAA
1301930 TTTTTTAAAAATAT-TTCAA
1 TTTTTTAAAAATATATTCAA
1301949 AATTTTATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 5 0.15
20 22 0.67
21 6 0.18
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.50
Consensus pattern (20 bp):
TTTTTTAAAAATATATTCAA
Found at i:1301954 original size:20 final size:20
Alignment explanation
Indices: 1301899--1301955 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1301889 TTTTTCTAAC
*
1301899 AATATATT-AAGATTTTTATA
1 AATATATTCAA-ATTTTTAAA
*
1301919 AATATATTCAATTTTTTAAA
1 AATATATTCAAATTTTTAAA
*
1301939 AATAT-TTCAAAATTTTA
1 AATATATTCAAATTTTTA
1301956 TTTATTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 10 0.31
20 20 0.62
21 2 0.06
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (20 bp):
AATATATTCAAATTTTTAAA
Found at i:1306057 original size:35 final size:36
Alignment explanation
Indices: 1305998--1306099 Score: 109
Period size: 35 Copynumber: 2.9 Consensus size: 36
1305988 CGAAAGTGTT
* * *
1305998 GATGCTTCCTTTCTTTCACTTTGAATCGAAAATGCC
1 GATGCTTCATTCCGTTCACTTTGAATCGAAAATGCC
* * * * *
1306034 GATGTTTC-TTTCGTTC-TTCTTGAATCGAAAGTGTC
1 GATGCTTCATTCCGTTCACT-TTGAATCGAAAATGCC
1306069 GATGCTTCATTCCGTTCACTTTGAATCGAAA
1 GATGCTTCATTCCGTTCACTTTGAATCGAAA
1306100 GTGCTTATGC
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
34 1 0.02
35 28 0.51
36 25 0.45
37 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.40
Consensus pattern (36 bp):
GATGCTTCATTCCGTTCACTTTGAATCGAAAATGCC
Found at i:1306093 original size:36 final size:35
Alignment explanation
Indices: 1305982--1306119 Score: 136
Period size: 36 Copynumber: 3.9 Consensus size: 35
1305972 AGATGAACAA
* * *
1305982 TTGAGTCGAAAGTGTTGATGCTTCCTTTCTTTCACT
1 TTGAATCGAAAGTGTCGATGCTT-CTTTCGTTCACT
* * * *
1306018 TTGAATCGAAAATGCCGATGTTTCTTTCGTTC-TT
1 TTGAATCGAAAGTGTCGATGCTTCTTTCGTTCACT
*
1306052 CTTGAATCGAAAGTGTCGATGCTTCATTCCGTTCACT
1 -TTGAATCGAAAGTGTCGATGCTTC-TTTCGTTCACT
*
1306089 TTGAATCGAAAGTG-CTTATGCTTCCTTTCGT
1 TTGAATCGAAAGTGTC-GATGCTT-CTTTCGT
1306120 ACTTCTGATT
Statistics
Matches: 83, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
34 1 0.01
35 30 0.36
36 50 0.60
37 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (35 bp):
TTGAATCGAAAGTGTCGATGCTTCTTTCGTTCACT
Found at i:1309909 original size:30 final size:30
Alignment explanation
Indices: 1309875--1309937 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
1309865 CTTTCCTAAA
* *
1309875 TGTCTCCGATGATCTTCTTCCTTCCTTCTT
1 TGTCTCCGATAATCTTCTTCCATCCTTCTT
* *
1309905 TGTCTCTGATAATTTTCTTCCATCCTTCTT
1 TGTCTCCGATAATCTTCTTCCATCCTTCTT
1309935 TGT
1 TGT
1309938 ACTAGTCTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.10, C:0.29, G:0.10, T:0.52
Consensus pattern (30 bp):
TGTCTCCGATAATCTTCTTCCATCCTTCTT
Found at i:1310321 original size:24 final size:25
Alignment explanation
Indices: 1310284--1310332 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1310274 TAAAAACATG
*
1310284 TTAACTATTTAATTACAAATAAAAA
1 TTAACTATTGAATTACAAATAAAAA
* *
1310309 TTAA-TATTGAATTACCATTAAAAA
1 TTAACTATTGAATTACAAATAAAAA
1310333 AATATAGACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (25 bp):
TTAACTATTGAATTACAAATAAAAA
Found at i:1311261 original size:20 final size:20
Alignment explanation
Indices: 1311238--1311287 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1311228 GTTTCCAACT
*
1311238 TCGCAACGCAAATCTGTAAA
1 TCGCAACACAAATCTGTAAA
* *
1311258 TCGCAACACGAATTTGTAAA
1 TCGCAACACAAATCTGTAAA
1311278 TCGCAACACA
1 TCGCAACACA
1311288 GAAGTCAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.40, C:0.26, G:0.14, T:0.20
Consensus pattern (20 bp):
TCGCAACACAAATCTGTAAA
Found at i:1311334 original size:40 final size:40
Alignment explanation
Indices: 1311289--1311391 Score: 127
Period size: 40 Copynumber: 2.5 Consensus size: 40
1311279 CGCAACACAG
* *
1311289 AAGTCAAATTTGCAACGCGATAGTCAAATTCACAACGCGAT
1 AAGTCAAATTCGCAACGCGAAAGTCAAATTCACAACGC-AT
* * *
1311330 -AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCAT
1 AAGTCAAATTCGCAACGCGAAAGTCAAATTCACAACGCAT
*
1311369 AATTTCAAATTCGCAACGCGAAA
1 AA-GTCAAATTCGCAACGCGAAA
1311392 CACAATATTA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
39 2 0.04
40 33 0.63
41 17 0.33
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (40 bp):
AAGTCAAATTCGCAACGCGAAAGTCAAATTCACAACGCAT
Found at i:1311378 original size:21 final size:20
Alignment explanation
Indices: 1311278--1311387 Score: 112
Period size: 20 Copynumber: 5.5 Consensus size: 20
1311268 AATTTGTAAA
* *
1311278 TCGCAACACAGAAGTCAAAT
1 TCGCAACGCAAAAGTCAAAT
* * *
1311298 TTGCAACGCGATAGTCAAAT
1 TCGCAACGCAAAAGTCAAAT
* * *
1311318 TCACAACGCGATAGTCAAAT
1 TCGCAACGCAAAAGTCAAAT
*
1311338 TCGCAACACAAAAGTCAAAT
1 TCGCAACGCAAAAGTCAAAT
**
1311358 TCGCAACGCATAATTTCAAAT
1 TCGCAACGCA-AAAGTCAAAT
1311379 TCGCAACGC
1 TCGCAACGC
1311388 GAAACACAAT
Statistics
Matches: 75, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
20 58 0.77
21 17 0.23
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.20
Consensus pattern (20 bp):
TCGCAACGCAAAAGTCAAAT
Found at i:1311411 original size:26 final size:26
Alignment explanation
Indices: 1311375--1311442 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
1311365 GCATAATTTC
*
1311375 AAATTCGCAACGCGAAACACAATATT
1 AAATTCGCAACGCAAAACACAATATT
*
1311401 AATTTCGCAACGCAAAACACAATATT
1 AAATTCGCAACGCAAAACACAATATT
*
1311427 AAATTCGCAACACAAA
1 AAATTCGCAACGCAAA
1311443 TGTAAACAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.49, C:0.24, G:0.09, T:0.19
Consensus pattern (26 bp):
AAATTCGCAACGCAAAACACAATATT
Found at i:1311571 original size:22 final size:22
Alignment explanation
Indices: 1311520--1311577 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
1311510 TCACTCTCTA
*
1311520 CGGCGACATCCGTCCCCATCTC
1 CGGCGAAATCCGTCCCCATCTC
* ** *
1311542 TGAAGAAATCTGTCCCCATCTC
1 CGGCGAAATCCGTCCCCATCTC
1311564 CGGCGAAATCCGTC
1 CGGCGAAATCCGTC
1311578 TATCTCTATC
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.21, C:0.40, G:0.19, T:0.21
Consensus pattern (22 bp):
CGGCGAAATCCGTCCCCATCTC
Found at i:1313719 original size:21 final size:21
Alignment explanation
Indices: 1313695--1313744 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
1313685 GTTAGGGGAG
*
1313695 TTACGTGATGAGGTCGGTGCT
1 TTACGTGATGAGGTCGGTACT
*
1313716 TTACGTCATGAGGTCGGTACT
1 TTACGTGATGAGGTCGGTACT
1313737 TTACGTGA
1 TTACGTGA
1313745 AGATAATGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.18, C:0.16, G:0.32, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCGGTACT
Found at i:1313802 original size:62 final size:63
Alignment explanation
Indices: 1313696--1313854 Score: 146
Period size: 62 Copynumber: 2.5 Consensus size: 63
1313686 TTAGGGGAGT
*** * * ** * *
1313696 TACGTGATGAGGTCGGTGCTTTACGTCATGAGGTCGG-TACTTTACGTGAAGATAATGGTGC-A
1 TACGTGATGAGGTATCTACTTTACGTGATGAGGT-GGATTTTTTACGCGAAGACAATGGTGCGA
* * *
1313758 TGACGTGATGAGGT-TC-ATCTTTACGTGGTGAGGTGGATTTTTTACGCGATGACAATGGTGCGC
1 T-ACGTGATGAGGTATCTA-CTTTACGTGATGAGGTGGATTTTTTACGCGAAGACAATGGTGCGA
*
1313821 TACGTGGTGAGGTATCTACTTTACGTGATGAGGT
1 TACGTGATGAGGTATCTACTTTACGTGATGAGGT
1313855 TGCGCTCTAT
Statistics
Matches: 78, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
61 2 0.03
62 45 0.58
63 30 0.38
64 1 0.01
ACGTcount: A:0.21, C:0.14, G:0.33, T:0.33
Consensus pattern (63 bp):
TACGTGATGAGGTATCTACTTTACGTGATGAGGTGGATTTTTTACGCGAAGACAATGGTGCGA
Found at i:1314209 original size:21 final size:21
Alignment explanation
Indices: 1314153--1314203 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
1314143 CCTATCATCA
1314153 TTCAAGAGGTGCCTCCTATCG
1 TTCAAGAGGTGCCTCCTATCG
* *
1314174 TTCAAGAGATGCCTCCTTTCG
1 TTCAAGAGGTGCCTCCTATCG
1314195 TTCAAGAGG
1 TTCAAGAGG
1314204 CCCCTCTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.29
Consensus pattern (21 bp):
TTCAAGAGGTGCCTCCTATCG
Found at i:1314239 original size:42 final size:42
Alignment explanation
Indices: 1314193--1314286 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 42
1314183 TGCCTCCTTT
*
1314193 CGTTCAAGAGGCCCCTCTCATC-ATCGAAGAAGCCTCTCCCAC
1 CGTTCAAGAGGCCCCTCTCATCGATC-AAGAAGCCTCGCCCAC
* * * *
1314235 CGTTCAAGAGGCCCCTGTCATCGTTCAAGAGGTCTCGCCCAC
1 CGTTCAAGAGGCCCCTCTCATCGATCAAGAAGCCTCGCCCAC
1314277 CGTTCAAGAG
1 CGTTCAAGAG
1314287 CCCGATTCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 44 0.96
43 2 0.04
ACGTcount: A:0.22, C:0.36, G:0.21, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTCTCATCGATCAAGAAGCCTCGCCCAC
Found at i:1314259 original size:21 final size:21
Alignment explanation
Indices: 1314192--1314266 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
1314182 ATGCCTCCTT
1314192 TCGTTCAAGAGGCCCCTCTCA
1 TCGTTCAAGAGGCCCCTCTCA
* * * *
1314213 TC-ATCGAAGAAGCCTCTCCCA
1 TCGTTC-AAGAGGCCCCTCTCA
* *
1314234 CCGTTCAAGAGGCCCCTGTCA
1 TCGTTCAAGAGGCCCCTCTCA
1314255 TCGTTCAAGAGG
1 TCGTTCAAGAGG
1314267 TCTCGCCCAC
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
20 2 0.05
21 37 0.90
22 2 0.05
ACGTcount: A:0.23, C:0.35, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGTTCAAGAGGCCCCTCTCA
Found at i:1314280 original size:21 final size:22
Alignment explanation
Indices: 1314230--1314286 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
1314220 AGAAGCCTCT
1314230 CCCACCGTTCAAGAGGCCCCTG
1 CCCACCGTTCAAGAGGCCCCTG
* * * *
1314252 -TCATCGTTCAAGAGGTCTC-G
1 CCCACCGTTCAAGAGGCCCCTG
1314272 CCCACCGTTCAAGAG
1 CCCACCGTTCAAGAG
1314287 CCCGATTCAT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.21, C:0.37, G:0.23, T:0.19
Consensus pattern (22 bp):
CCCACCGTTCAAGAGGCCCCTG
Found at i:1315667 original size:69 final size:67
Alignment explanation
Indices: 1315587--1315753 Score: 211
Period size: 66 Copynumber: 2.5 Consensus size: 67
1315577 TGGGGTGCAC
* *
1315587 TTTTTTCCTTGTTTAATTGAATTT-TACATTGAAAGTTGATTTGTTTAA-TTGATGAAG-AAATA
1 TTTTTTGCTTGTTTAATTGAATTTGT--A---AAAGTTGAGTTGTTTAATTTGATG-AGTAAATA
1315649 AGAATTA-
60 AGAATTAT
*
1315656 TTTTTTGCTTGTTTAATTG-ATTTGTAAAAGTTGAGTTGTTTAATTTGATGTGTAAATAAGAATT
1 TTTTTTGCTTGTTTAATTGAATTTGTAAAAGTTGAGTTGTTTAATTTGATGAGTAAATAAGAATT
1315720 AT
66 AT
1315722 TTTTTTGCTTGTTTAATTG-ATTTGTAAAAGTT
1 TTTTTTGCTTGTTTAATTGAATTTGTAAAAGTT
1315754 CATTTGTTGT
Statistics
Matches: 91, Mismatches: 3, Indels: 11
0.87 0.03 0.10
Matches are distributed among these distances:
64 17 0.19
65 18 0.20
66 32 0.35
67 1 0.01
68 4 0.04
69 19 0.21
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.51
Consensus pattern (67 bp):
TTTTTTGCTTGTTTAATTGAATTTGTAAAAGTTGAGTTGTTTAATTTGATGAGTAAATAAGAATT
AT
Found at i:1315761 original size:66 final size:64
Alignment explanation
Indices: 1315618--1315761 Score: 227
Period size: 66 Copynumber: 2.2 Consensus size: 64
1315608 TTTTACATTG
1315618 AAAGTTGATTTGTTTAATTGATGAAGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAAGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTGTA
* *
1315682 AAAGTTGAGTTGTTTAATTTGATG-TGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTG
1 AAAGTTGATTTGTTTAA-TTGATGAAG-AAATAAGAATTA-TTTTTTGCTTGTTTAATTGATTTG
1315746 TA
63 TA
*
1315748 AAAGTTCATTTGTT
1 AAAGTTGATTTGTT
1315762 GTTTTAAATT
Statistics
Matches: 73, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
64 17 0.23
65 18 0.25
66 38 0.52
ACGTcount: A:0.31, C:0.02, G:0.17, T:0.50
Consensus pattern (64 bp):
AAAGTTGATTTGTTTAATTGATGAAGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTGTA
Found at i:1315839 original size:20 final size:20
Alignment explanation
Indices: 1315814--1315859 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1315804 TATTGAAGGT
1315814 AAATTCGCAACGCGAAAGTC
1 AAATTCGCAACGCGAAAGTC
*
1315834 AAATTCGCAATGCGAAAGTC
1 AAATTCGCAACGCGAAAGTC
1315854 AAATTC
1 AAATTC
1315860 ACGTTGCGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAGTC
Found at i:1315907 original size:20 final size:20
Alignment explanation
Indices: 1315882--1315921 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1315872 TCGGTTTGCG
1315882 ATTTCGCGTTGCAAATTTGA
1 ATTTCGCGTTGCAAATTTGA
*
1315902 ATTTCGCGTTGCGAATTTGA
1 ATTTCGCGTTGCAAATTTGA
1315922 CTATCGCAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.40
Consensus pattern (20 bp):
ATTTCGCGTTGCAAATTTGA
Found at i:1315928 original size:20 final size:20
Alignment explanation
Indices: 1315885--1315928 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1315875 GTTTGCGATT
*
1315885 TCGCGTTGCAAATTTGAATT
1 TCGCGTTGCAAATTTGAATA
* *
1315905 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCAAATTTGAATA
1315925 TCGC
1 TCGC
1315929 AACGCTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.36
Consensus pattern (20 bp):
TCGCGTTGCAAATTTGAATA
Found at i:1317257 original size:18 final size:18
Alignment explanation
Indices: 1317234--1317270 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1317224 CGAAATTTAT
1317234 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1317252 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1317270 A
1 A
1317271 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1317691 original size:21 final size:22
Alignment explanation
Indices: 1317656--1317700 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
1317646 TTCCAAATAA
*
1317656 TGTACCCATAACAATGTTCAAT
1 TGTACCCACAACAATGTTCAAT
*
1317678 TGTA-CCACAACAATGTTTAAT
1 TGTACCCACAACAATGTTCAAT
1317699 TG
1 TG
1317701 ATTTGTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (22 bp):
TGTACCCACAACAATGTTCAAT
Found at i:1317782 original size:22 final size:20
Alignment explanation
Indices: 1317754--1317810 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
1317744 AAACCTGTTG
1317754 AAGGTAAACTTTCGCAACGCGA
1 AAGGTAAA--TTCGCAACGCGA
*
1317776 AAGGTAAATTCACAACGCGA
1 AAGGTAAATTCGCAACGCGA
1317796 AA-GTAAAATTCGCAA
1 AAGGT-AAATTCGCAA
1317811 TGCGGAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.06
20 22 0.69
22 8 0.25
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.18
Consensus pattern (20 bp):
AAGGTAAATTCGCAACGCGA
Found at i:1317880 original size:14 final size:14
Alignment explanation
Indices: 1317858--1317896 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1317848 GAAAGTCAAA
1317858 TTCGCTTTGCGATT
1 TTCGCTTTGCGATT
*
1317872 TTCGGTTTGCGATT
1 TTCGCTTTGCGATT
*
1317886 TT-GCATTGCGA
1 TTCGCTTTGCGA
1317897 ATTTAACTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.10, C:0.18, G:0.26, T:0.46
Consensus pattern (14 bp):
TTCGCTTTGCGATT
Found at i:1321606 original size:40 final size:40
Alignment explanation
Indices: 1321512--1321609 Score: 118
Period size: 36 Copynumber: 2.6 Consensus size: 40
1321502 TGCGAATTTG
*
1321512 AAATTCAT-TTGCGAATTTGACTTTGTGTTGCGAATTGAC
1 AAATTCGTGTTGCGAATTTGACTTTGTGTTGCGAATTGAC
* *
1321551 ----TCGCGTTGCGAATTTGACTTCTGTGTTGC-AATTTAC
1 AAATTCGTGTTGCGAATTTGACTT-TGTGTTGCGAATTGAC
1321587 AAATTCGTGTTGCGAATTTGACT
1 AAATTCGTGTTGCGAATTTGACT
1321610 ATCGCGTTGT
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
35 2 0.04
36 21 0.43
37 8 0.16
40 18 0.37
ACGTcount: A:0.22, C:0.15, G:0.21, T:0.41
Consensus pattern (40 bp):
AAATTCGTGTTGCGAATTTGACTTTGTGTTGCGAATTGAC
Found at i:1321618 original size:20 final size:19
Alignment explanation
Indices: 1321457--1321640 Score: 148
Period size: 19 Copynumber: 9.6 Consensus size: 19
1321447 ACGAAATTAA
*
1321457 TTCGTGTTGCGAATTTGAAA
1 TTCGTGTTGCGAATTTG-AC
* *
1321477 TTC-AGTTGCGAATTTGAAA
1 TTCGTGTTGCGAATTTG-AC
** *
1321496 TTC-AATTGCGAATTTGAAA
1 TTCGTGTTGCGAATTTG-AC
*
1321515 TTCAT-TTGCGAATTTGAC
1 TTCGTGTTGCGAATTTGAC
*
1321533 TTTGTGTTGCGAA-TTGAC
1 TTCGTGTTGCGAATTTGAC
*
1321551 -TCGCGTTGCGAATTTGAC
1 TTCGTGTTGCGAATTTGAC
1321569 TTCTGTGTTGC-AATTT-AC
1 TTC-GTGTTGCGAATTTGAC
1321587 AAATTCGTGTTGCGAATTTGAC
1 ---TTCGTGTTGCGAATTTGAC
* *
1321609 TATCGCGTTGTGAATTTGAC
1 T-TCGTGTTGCGAATTTGAC
1321629 TTCGTGTTGCGA
1 TTCGTGTTGCGA
1321641 TTTACAGATT
Statistics
Matches: 140, Mismatches: 13, Indels: 23
0.80 0.07 0.13
Matches are distributed among these distances:
17 10 0.07
18 16 0.11
19 71 0.51
20 33 0.24
21 8 0.06
22 2 0.01
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.40
Consensus pattern (19 bp):
TTCGTGTTGCGAATTTGAC
Found at i:1321624 original size:60 final size:56
Alignment explanation
Indices: 1321536--1321652 Score: 171
Period size: 60 Copynumber: 2.0 Consensus size: 56
1321526 ATTTGACTTT
1321536 GTGTTGCGAATTGACTCGCGTTGCGAATTTGACTTCTGTGTTGCAATTTACAAATTC
1 GTGTTGCGAATTGACTCGCGTTGCGAATTTGACTTC-GTGTTGCAATTTACAAATTC
* * *
1321593 GTGTTGCGAATTTGACTATCGCGTTGTGAATTTGACTTCGTGTTGCGATTTACAGATTC
1 GTGTTGCGAA-TTGAC--TCGCGTTGCGAATTTGACTTCGTGTTGCAATTTACAAATTC
1321652 G
1 G
1321653 CATTGTGAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
57 10 0.19
58 5 0.09
59 19 0.35
60 20 0.37
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (56 bp):
GTGTTGCGAATTGACTCGCGTTGCGAATTTGACTTCGTGTTGCAATTTACAAATTC
Found at i:1322633 original size:2 final size:2
Alignment explanation
Indices: 1322626--1322660 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1322616 AATAAGAATA
1322626 AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1322661 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1322648 original size:17 final size:17
Alignment explanation
Indices: 1322626--1322658 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1322616 AATAAGAATA
1322626 ATATATATATATATATT
1 ATATATATATATATATT
1322643 ATATATATATATATAT
1 ATATATATATATATAT
1322659 ATGTGTGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATATATATATATATT
Found at i:1322665 original size:2 final size:2
Alignment explanation
Indices: 1322660--1322689 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1322650 TATATATATA
1322660 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1322690 GTGGAAAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1323069 original size:16 final size:15
Alignment explanation
Indices: 1323034--1323080 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 15
1323024 TTTATGTTGT
1323034 AGTGGTTTAAGGTTTTA
1 AGTGGTTTAAGG--TTA
*
1323051 AGTGATTTTAAGGTTA
1 AGTG-GTTTAAGGTTA
1323067 AGTGGTTTAAGGTT
1 AGTGGTTTAAGGTT
1323081 TGTTTAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 9 0.33
16 7 0.26
17 4 0.15
18 7 0.26
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.45
Consensus pattern (15 bp):
AGTGGTTTAAGGTTA
Found at i:1323107 original size:19 final size:22
Alignment explanation
Indices: 1323078--1323122 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
1323068 GTGGTTTAAG
1323078 GTTTGTTT-AAATGAT-TTAGT
1 GTTTGTTTAAAATGATATTAGT
*
1323098 GTTT-TTTAAAATTATATTAGT
1 GTTTGTTTAAAATGATATTAGT
1323119 GTTT
1 GTTT
1323123 ATTTTAAGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 10 0.45
21 9 0.41
ACGTcount: A:0.27, C:0.00, G:0.16, T:0.58
Consensus pattern (22 bp):
GTTTGTTTAAAATGATATTAGT
Found at i:1324782 original size:27 final size:28
Alignment explanation
Indices: 1324730--1324784 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 28
1324720 ATGTATGAAG
*
1324730 ATCGTTGTATCTTGTTAGTTCTTATATC
1 ATCGTTGTATCTTGTTAGTTCCTATATC
1324758 ATCGTTGTATC-TGTTAGTTCCTATATC
1 ATCGTTGTATCTTGTTAGTTCCTATATC
1324785 TTATTCTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 15 0.58
28 11 0.42
ACGTcount: A:0.18, C:0.16, G:0.15, T:0.51
Consensus pattern (28 bp):
ATCGTTGTATCTTGTTAGTTCCTATATC
Found at i:1329813 original size:27 final size:27
Alignment explanation
Indices: 1329775--1329833 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
1329765 AAAACAGTGT
1329775 TGAATGCTTCAGCACAGAAGTACATTC
1 TGAATGCTTCAGCACAGAAGTACATTC
1329802 TGAATGCTTCAGCACAGAAGTACATTC
1 TGAATGCTTCAGCACAGAAGTACATTC
1329829 TGAAT
1 TGAAT
1329834 ACATTCTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (27 bp):
TGAATGCTTCAGCACAGAAGTACATTC
Found at i:1329874 original size:32 final size:31
Alignment explanation
Indices: 1329833--1329942 Score: 165
Period size: 32 Copynumber: 3.6 Consensus size: 31
1329823 ACATTCTGAA
1329833 TACATTCTGAATGCTTCAGTTCAGCACAGAAG
1 TACATTCTGAATG-TTCAGTTCAGCACAGAAG
1329865 TACATTCTGAATGCTTCAGTTCAGCACAGAAG
1 TACATTCTGAATG-TTCAGTTCAGCACAGAAG
1329897 TACATTCTGAATG---A-TTCAGCACAGAAG
1 TACATTCTGAATGTTCAGTTCAGCACAGAAG
1329924 TACATTCTGAATGATTCAG
1 TACATTCTGAATG-TTCAG
1329943 AGCCAGTAAA
Statistics
Matches: 73, Mismatches: 0, Indels: 10
0.88 0.00 0.12
Matches are distributed among these distances:
27 26 0.36
28 1 0.01
31 1 0.01
32 45 0.62
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (31 bp):
TACATTCTGAATGTTCAGTTCAGCACAGAAG
Found at i:1329922 original size:27 final size:27
Alignment explanation
Indices: 1329852--1329942 Score: 137
Period size: 27 Copynumber: 3.2 Consensus size: 27
1329842 AATGCTTCAG
1329852 TTCAGCACAGAAGTACATTCTGAATGCTTCA
1 TTCAGCACAGAAGTACATTCTGAATG----A
1329883 GTTCAGCACAGAAGTACATTCTGAATGA
1 -TTCAGCACAGAAGTACATTCTGAATGA
1329911 TTCAGCACAGAAGTACATTCTGAATGA
1 TTCAGCACAGAAGTACATTCTGAATGA
1329938 TTCAG
1 TTCAG
1329943 AGCCAGTAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
27 32 0.54
28 1 0.02
32 26 0.44
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (27 bp):
TTCAGCACAGAAGTACATTCTGAATGA
Found at i:1338711 original size:16 final size:16
Alignment explanation
Indices: 1338675--1338715 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1338665 AATTTCATCC
1338675 TTATA-TTATATAATA
1 TTATATTTATATAATA
1338690 TATATATTTATTATAA-A
1 T-TATATTTA-TATAATA
1338707 TTATATTTA
1 TTATATTTA
1338716 CATTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 12 0.52
17 5 0.22
18 5 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATATTTATATAATA
Found at i:1339717 original size:20 final size:19
Alignment explanation
Indices: 1339682--1339722 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
1339672 TAATTATCTT
1339682 TTTATATTACATTATAATA
1 TTTATATTACATTATAATA
* *
1339701 TTTATATATATATTATATTA
1 TTTATAT-TACATTATAATA
1339721 TT
1 TT
1339723 ATTAGTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTATATTACATTATAATA
Found at i:1339804 original size:18 final size:17
Alignment explanation
Indices: 1339783--1339826 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 17
1339773 CTTATACGTT
1339783 TTATTATATATATATATA
1 TTATTAT-TATATATATA
*
1339801 TTATTATTGT-TAT-TA
1 TTATTATTATATATATA
1339816 TTATTATTATA
1 TTATTATTATA
1339827 CGTATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 11 0.48
16 3 0.13
17 2 0.09
18 7 0.30
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
TTATTATTATATATATA
Found at i:1339805 original size:3 final size:3
Alignment explanation
Indices: 1339783--1339825 Score: 50
Period size: 3 Copynumber: 13.3 Consensus size: 3
1339773 CTTATACGTT
*
1339783 TTA TTA TATA TATA TATA TTA TTA TTG TTA TTA TTA TTA TTA T
1 TTA TTA T-TA T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TTA T
1339826 ACGTATATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 26 0.70
4 11 0.30
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1339826 original size:48 final size:51
Alignment explanation
Indices: 1339741--1339851 Score: 124
Period size: 46 Copynumber: 2.2 Consensus size: 51
1339731 TTTACACTCG
*
1339741 TATATATGTATTATTAGTATAGTATTATGTCACTTATACGTTTTATTATATATA
1 TATATAT-TATTATTAGTATAGTATTATGTCACTTATACG-TATA-TATATATA
* *
1339795 TATATATTATTATT-GT-TATTATTAT-T-A-TTATACGTATATATATGTA
1 TATATATTATTATTAGTATAGTATTATGTCACTTATACGTATATATATATA
*
1339841 TATATTTTATT
1 TATATATTATT
1339852 TCTTTTTATA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
46 17 0.32
47 3 0.06
48 7 0.13
49 1 0.02
50 1 0.02
51 8 0.15
52 2 0.04
53 7 0.13
54 7 0.13
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (51 bp):
TATATATTATTATTAGTATAGTATTATGTCACTTATACGTATATATATATA
Found at i:1339906 original size:18 final size:18
Alignment explanation
Indices: 1339883--1339942 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 18
1339873 TTTTTATTTT
1339883 TATTATTATTATTCTTTA
1 TATTATTATTATTCTTTA
** * *
1339901 TATTATCCTTATTATTTC
1 TATTATTATTATTCTTTA
*
1339919 TATTATTACTATTCTTTA
1 TATTATTATTATTCTTTA
1339937 T-TTATT
1 TATTATT
1339943 CATGTAATTA
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
17 5 0.15
18 28 0.85
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTATTATTATTCTTTA
Found at i:1351190 original size:59 final size:59
Alignment explanation
Indices: 1351096--1351209 Score: 156
Period size: 59 Copynumber: 1.9 Consensus size: 59
1351086 AATACTTCGC
* ** *
1351096 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGAAAAAAAAAAAAAAAAAAAAAAACT
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAAAAAAAAAAAAAAAAAACT
* * * *
1351155 TTAGGGTGAAAACCCGAAAGGGCACCCTAAATTGAAAAAGAAAAAAGAGAAAAAA
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAAAAAAAAAAAAAAAA
1351210 GAAGAGAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 47 1.00
ACGTcount: A:0.55, C:0.12, G:0.20, T:0.12
Consensus pattern (59 bp):
TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAAAAAAAAAAAAAAAAAACT
Found at i:1352999 original size:105 final size:105
Alignment explanation
Indices: 1351951--1352979 Score: 2006
Period size: 105 Copynumber: 9.8 Consensus size: 105
1351941 GGTTTTACCC
*
1351951 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1352016 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
*
1352056 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1352121 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
1352161 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1352226 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
1352266 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1352331 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
1352371 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1352436 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
1352476 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1352541 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
1352581 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1352646 CGAAGGGACCGCTGGTTGTCACC-AACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
1352685 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1352750 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
1352790 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1352855 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
* * *
1352895 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAGGTTCAACTTCATGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1352960 CGAAGGGACCGCTGGTTGTC
66 CGAAGGGACCGCTGGTTGTC
1352980 GATAAACAAT
Statistics
Matches: 919, Mismatches: 4, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
104 104 0.11
105 815 0.89
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (105 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
Found at i:1353085 original size:20 final size:20
Alignment explanation
Indices: 1353060--1353101 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1353050 CCAGAACTCT
1353060 GAGTTCGACTTCAACTTCAC
1 GAGTTCGACTTCAACTTCAC
* *
1353080 GAGTTCGATTTCAATTTCAC
1 GAGTTCGACTTCAACTTCAC
1353100 GA
1 GA
1353102 CGAAGGATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (20 bp):
GAGTTCGACTTCAACTTCAC
Found at i:1353351 original size:16 final size:16
Alignment explanation
Indices: 1353315--1353355 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1353305 AATTTCATCC
1353315 TTATA-TTATATAATA
1 TTATATTTATATAATA
1353330 TATATATTTATTATAA-A
1 T-TATATTTA-TATAATA
1353347 TTATATTTA
1 TTATATTTA
1353356 CATTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 12 0.52
17 5 0.22
18 5 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATATTTATATAATA
Found at i:1354363 original size:20 final size:19
Alignment explanation
Indices: 1354324--1354364 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
1354314 TAATTATCTT
1354324 TTTATATTACATTATAATA
1 TTTATATTACATTATAATA
* *
1354343 TTTATATATATATTATTATA
1 TTTATAT-TACATTATAATA
1354363 TT
1 TT
1354365 ATTAGTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTATATTACATTATAATA
Found at i:1354463 original size:31 final size:32
Alignment explanation
Indices: 1354425--1354486 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
1354415 CTTATACGTT
*
1354425 TTATTATATATATATAT-TAT-TATTGTTATTA
1 TTATTATACATATATATGTATATATT-TTATTA
*
1354456 TTATTATACGTATATATGTATATATTTTATT
1 TTATTATACATATATATGTATATATTTTATT
1354487 TCTTTTATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 15 0.56
32 8 0.30
33 4 0.15
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.60
Consensus pattern (32 bp):
TTATTATACATATATATGTATATATTTTATTA
Found at i:1354539 original size:18 final size:18
Alignment explanation
Indices: 1354516--1354575 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 18
1354506 ATTTTTATTT
1354516 TATTATTATTATTCTTTA
1 TATTATTATTATTCTTTA
** * *
1354534 TATTATCCTTATTATTTC
1 TATTATTATTATTCTTTA
*
1354552 TATTATTACTATTCTTTA
1 TATTATTATTATTCTTTA
1354570 T-TTATT
1 TATTATT
1354576 CATGTAATTA
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
17 5 0.15
18 28 0.85
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTATTATTATTCTTTA
Found at i:1356683 original size:18 final size:17
Alignment explanation
Indices: 1356660--1356693 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1356650 CCGCTACTAG
1356660 TGAACCGGTCAGAATCGC
1 TGAACCGGTCA-AATCGC
*
1356678 TGAACCGTTCAAATCG
1 TGAACCGGTCAAATCG
1356694 GACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.26, G:0.24, T:0.21
Consensus pattern (17 bp):
TGAACCGGTCAAATCGC
Found at i:1358920 original size:31 final size:31
Alignment explanation
Indices: 1358882--1358962 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
1358872 CAAATTTTTT
* * *
1358882 TTGTTCATATACGTTCATTAAGGAATATAAC
1 TTGTTCATTTTCGTTCATTAAGAAATATAAC
*
1358913 TTGTTCATTTTCGTTCATTAAGAAATATAGC
1 TTGTTCATTTTCGTTCATTAAGAAATATAAC
1358944 TTGTTCATTTTCGTTCATT
1 TTGTTCATTTTCGTTCATT
1358963 TAAATGATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.47
Consensus pattern (31 bp):
TTGTTCATTTTCGTTCATTAAGAAATATAAC
Found at i:1359001 original size:14 final size:14
Alignment explanation
Indices: 1358982--1359012 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1358972 AACGAACGTA
1358982 AACGAACACAAACG
1 AACGAACACAAACG
*
1358996 AACGAACATAAACG
1 AACGAACACAAACG
1359010 AAC
1 AAC
1359013 ATAATAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.26, G:0.13, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:1359029 original size:23 final size:23
Alignment explanation
Indices: 1358969--1359066 Score: 101
Period size: 23 Copynumber: 4.3 Consensus size: 23
1358959 CATTTAAATG
* *
1358969 ATAAACGAACGTAAACGAACACA
1 ATAAACGAACATAAACAAACACA
* *
1358992 A-ACGAACGAACATAAACGAACATA
1 ATA--AACGAACATAAACAAACACA
*
1359016 ATAAATGAACATAAACAAACACA
1 ATAAACGAACATAAACAAACACA
*
1359039 ATAAACGAACA-ACACAAACACA
1 ATAAACGAACATAAACAAACACA
*
1359061 AAAAAC
1 ATAAAC
1359067 AAACTTATTC
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
22 16 0.25
23 28 0.44
24 19 0.30
25 1 0.02
ACGTcount: A:0.62, C:0.21, G:0.08, T:0.08
Consensus pattern (23 bp):
ATAAACGAACATAAACAAACACA
Found at i:1368333 original size:2 final size:2
Alignment explanation
Indices: 1368326--1368350 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1368316 AAGGTTAGTT
1368326 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1368351 TAAAATAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1369251 original size:16 final size:15
Alignment explanation
Indices: 1369226--1369255 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1369216 TTAATAAGTT
1369226 TTATATTTTTATATC
1 TTATATTTTTATATC
1369241 TTATATGTTTTATAT
1 TTATAT-TTTTATAT
1369256 TTCGGTACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (15 bp):
TTATATTTTTATATC
Found at i:1372895 original size:20 final size:19
Alignment explanation
Indices: 1372855--1372893 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1372845 AAAAAATATT
*
1372855 ATAATCGAAATTATAAAAA
1 ATAATCGAAAATATAAAAA
*
1372874 ATAATCTAAAATATAAAAA
1 ATAATCGAAAATATAAAAA
1372893 A
1 A
1372894 ATTAAAATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.26
Consensus pattern (19 bp):
ATAATCGAAAATATAAAAA
Found at i:1372901 original size:16 final size:18
Alignment explanation
Indices: 1372855--1372902 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
1372845 AAAAAATATT
* *
1372855 ATAATCGAAATTATAAAAA
1 ATAATCTAAAATAT-AAAA
1372874 ATAATCTAAAATATAAAA
1 ATAATCTAAAATATAAAA
1372892 A-AAT-TAAAATA
1 ATAATCTAAAATA
1372903 CTCTGTCCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 7 0.26
17 3 0.11
18 5 0.19
19 12 0.44
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (18 bp):
ATAATCTAAAATATAAAA
Found at i:1373785 original size:23 final size:23
Alignment explanation
Indices: 1373759--1373810 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
1373749 AATATGTAGT
1373759 AATTTTTGTACGCTTAAAGAATA
1 AATTTTTGTACGCTTAAAGAATA
* *
1373782 AATTTTTGTACGTTTATAGAATA
1 AATTTTTGTACGCTTAAAGAATA
1373805 AATTTT
1 AATTTT
1373811 ATAAATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.46
Consensus pattern (23 bp):
AATTTTTGTACGCTTAAAGAATA
Found at i:1374117 original size:18 final size:17
Alignment explanation
Indices: 1374093--1374136 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
1374083 TTTGAAAGAT
1374093 AATAATATTAATTAAAA
1 AATAATATTAATTAAAA
1374110 ATATAATA--AATTAAAA
1 A-ATAATATTAATTAAAA
1374126 AACTAATATTA
1 AA-TAATATTA
1374137 TATTTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
15 1 0.04
16 14 0.61
17 1 0.04
18 7 0.30
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
AATAATATTAATTAAAA
Found at i:1376698 original size:20 final size:21
Alignment explanation
Indices: 1376652--1376704 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
1376642 TTTTAATTAA
1376652 ATATTTAACATAAAATAATATT
1 ATATTTAA-ATAAAATAATATT
*
1376674 ATATTTAAA-AAATTAATAATT
1 ATATTTAAATAAAATAAT-ATT
1376695 -TATTCTAAAT
1 ATATT-TAAAT
1376705 TTCAAATTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 11 0.41
21 8 0.30
22 8 0.30
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (21 bp):
ATATTTAAATAAAATAATATT
Found at i:1378150 original size:19 final size:19
Alignment explanation
Indices: 1378103--1378152 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
1378093 AACATGTTTT
* * * *
1378103 TATGAATAGCACTATATTG
1 TATGAATAGTATTATACTA
1378122 TATGAATAGTATTATACTA
1 TATGAATAGTATTATACTA
1378141 TATGAATAGTAT
1 TATGAATAGTAT
1378153 CGATACTGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.40
Consensus pattern (19 bp):
TATGAATAGTATTATACTA
Found at i:1378168 original size:20 final size:20
Alignment explanation
Indices: 1378145--1378182 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1378135 ATACTATATG
*
1378145 AATAGTATCGATACTGTGCA
1 AATAGTACCGATACTGTGCA
1378165 AATAGTACCGATACTGTG
1 AATAGTACCGATACTGTG
1378183 TGAACAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (20 bp):
AATAGTACCGATACTGTGCA
Found at i:1378191 original size:20 final size:20
Alignment explanation
Indices: 1378143--1378191 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1378133 TTATACTATA
*
1378143 TGAATAGTATCGATACTGTG
1 TGAATAGTACCGATACTGTG
**
1378163 CAAATAGTACCGATACTGTG
1 TGAATAGTACCGATACTGTG
*
1378183 TGAACAGTA
1 TGAATAGTA
1378192 ATGAATAGTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (20 bp):
TGAATAGTACCGATACTGTG
Found at i:1383199 original size:19 final size:20
Alignment explanation
Indices: 1383175--1383225 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1383165 AAAATATTTT
1383175 TATAAATAGTACT-ATACTG
1 TATAAATAGTACTAATACTG
*
1383194 TATAAATAGTATTAATACTG
1 TATAAATAGTACTAATACTG
*
1383214 TGTAAATAGTAC
1 TATAAATAGTAC
1383226 CGATACTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (20 bp):
TATAAATAGTACTAATACTG
Found at i:1383231 original size:20 final size:19
Alignment explanation
Indices: 1383177--1383236 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 19
1383167 AATATTTTTA
* *
1383177 TAAATAGTACTATACTGTA
1 TAAATAGTACAATACTGTG
*
1383196 TAAATAGTATTAATACTGTG
1 TAAATAGTA-CAATACTGTG
*
1383216 TAAATAGTACCGATACTGTG
1 TAAATAGTA-CAATACTGTG
1383236 T
1 T
1383237 GAACAGTAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 9 0.26
20 25 0.74
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (19 bp):
TAAATAGTACAATACTGTG
Found at i:1383982 original size:32 final size:32
Alignment explanation
Indices: 1383927--1384033 Score: 112
Period size: 33 Copynumber: 3.4 Consensus size: 32
1383917 GTTTATAAGA
*
1383927 ACATAGGTAAT--TGTCCATATGTCCCGAAGG
1 ACATAGGTAATCATATCCATATGTCCCGAAGG
* * *
1383957 ATATAGGTAATCATATTCATATGTCCCCGAAAG
1 ACATAGGTAATCATATCCATATGT-CCCGAAGG
* * *
1383990 ACATAAGTAATCTTGTCCATATGTCCCGAAAGG
1 ACATAGGTAATCATATCCATATGTCCCG-AAGG
1384023 -CATAGGTAATC
1 ACATAGGTAATC
1384034 CTCGACTCTT
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
30 10 0.16
32 23 0.37
33 29 0.47
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (32 bp):
ACATAGGTAATCATATCCATATGTCCCGAAGG
Found at i:1384000 original size:33 final size:32
Alignment explanation
Indices: 1383927--1384033 Score: 119
Period size: 32 Copynumber: 3.4 Consensus size: 32
1383917 GTTTATAAGA
* *
1383927 ACATAGGTAAT--TGTCCATATGTCCCGAAGG
1 ACATAGGTAATCATATCCATATGTCCCGAAAG
* *
1383957 ATATAGGTAATCATATTCATATGTCCCCGAAAG
1 ACATAGGTAATCATATCCATATGT-CCCGAAAG
* * *
1383990 ACATAAGTAATCTTGTCCATATGTCCCGAAAG
1 ACATAGGTAATCATATCCATATGTCCCGAAAG
*
1384022 GCATAGGTAATC
1 ACATAGGTAATC
1384034 CTCGACTCTT
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
30 10 0.16
32 27 0.43
33 26 0.41
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (32 bp):
ACATAGGTAATCATATCCATATGTCCCGAAAG
Found at i:1384264 original size:2 final size:2
Alignment explanation
Indices: 1384259--1384291 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1384249 CTTATATAAC
1384259 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1384292 TATCTCTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1388141 original size:22 final size:22
Alignment explanation
Indices: 1388116--1388171 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
1388106 AAATTAAGTA
*
1388116 AAAACATTACAAACTAAAT-AAT
1 AAAACATTA-AAAATAAATAAAT
* *
1388138 AAAACAATAAAAATAATTAAAT
1 AAAACATTAAAAATAAATAAAT
1388160 ATAAACATTAAA
1 A-AAACATTAAA
1388172 TACAAACGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 7 0.25
22 12 0.43
23 9 0.32
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (22 bp):
AAAACATTAAAAATAAATAAAT
Found at i:1390651 original size:17 final size:17
Alignment explanation
Indices: 1390629--1390665 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
1390619 TTGAAGAGTT
1390629 ATAGTGAGATATTAAAG
1 ATAGTGAGATATTAAAG
1390646 ATAGTGAGATATTAAAG
1 ATAGTGAGATATTAAAG
1390663 ATA
1 ATA
1390666 ATGAAGTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.30
Consensus pattern (17 bp):
ATAGTGAGATATTAAAG
Found at i:1391428 original size:2 final size:2
Alignment explanation
Indices: 1391421--1391447 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1391411 AGTACATCTT
1391421 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1391448 GAAATATGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1391807 original size:21 final size:21
Alignment explanation
Indices: 1391774--1391813 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1391764 TTCTACGTGG
*
1391774 TCCTTCGGGACATATATGTAA
1 TCCTTCGGAACATATATGTAA
*
1391795 TCCTTTGGAACATATATGT
1 TCCTTCGGAACATATATGT
1391814 GGTACTTCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
TCCTTCGGAACATATATGTAA
Done.