Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008005.1 Hibiscus syriacus cultivar Beakdansim tig00110467_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: 1778185
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 5 of 7
Found at i:1256537 original size:2 final size:2
Alignment explanation
Indices: 1256530--1256557 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1256520 AATTATCTTT
1256530 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1256558 AGTATATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1258688 original size:15 final size:15
Alignment explanation
Indices: 1258666--1258825 Score: 91
Period size: 15 Copynumber: 10.5 Consensus size: 15
1258656 GGCGGCTGTG
1258666 CCTTCTTCTCCTCTT
1 CCTTCTTCTCCTCTT
* * *
1258681 CTTTCTTCTCTTCCT
1 CCTTCTTCTCCTCTT
*
1258696 CCTTCTTC-CCTTCCT
1 CCTTCTTCTCC-TCTT
1258711 CCTTCTTC-CCTTCTT
1 CCTTCTTCTCC-TCTT
*
1258726 CCTTC-TCTCCCCCTT
1 CCTTCTTCT-CCTCTT
*
1258741 CCTTC-TCTCCCCCTT
1 CCTTCTTCT-CCTCTT
1258756 CCTTCTTTTCTCCTTCTT
1 CCTTC--TTCTCC-TCTT
*
1258774 TCTT-TTCTCCTTCTT
1 CCTTCTTCTCC-TCTT
*
1258789 TCTT-TTCTCCCTCTT
1 CCTTCTTCT-CCTCTT
* *
1258804 CTTTCTT-TGCTTCTT
1 CCTTCTTCT-CCTCTT
1258819 CCTTCTT
1 CCTTCTT
1258826 TGGCTCCTCT
Statistics
Matches: 122, Mismatches: 14, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
14 3 0.02
15 102 0.84
16 6 0.05
17 2 0.02
18 9 0.07
ACGTcount: A:0.00, C:0.44, G:0.01, T:0.55
Consensus pattern (15 bp):
CCTTCTTCTCCTCTT
Found at i:1258702 original size:30 final size:31
Alignment explanation
Indices: 1258666--1258843 Score: 102
Period size: 30 Copynumber: 5.8 Consensus size: 31
1258656 GGCGGCTGTG
1258666 CCTTCTTCT-CCTCTTCTTTCTTCTCTTCCT
1 CCTTCTTCTCCCTCTTCTTTCTTCTCTTCCT
* * * * *
1258696 CCTTCTTC-CCTTCCTCCTTCTTCCCTTCTT
1 CCTTCTTCTCCCTCTTCTTTCTTCTCTTCCT
* * **
1258726 CCTTC-TCTCCCCCTTCCTTC-TCTCCCCCTT
1 CCTTCTTCTCCCTCTTCTTTCTTCTCTTCC-T
* * *
1258756 CCTTCTTTTCTC-CTTCTTTCTTTTC-TCCTT
1 CCTTCTTCTCCCTCTTCTTTCTTCTCTTCC-T
* *
1258786 CTTTCTTTTCTCCCTCTTCTTTCTT-TGCTTCTT
1 CCTTC--TTCTCCCTCTTCTTTCTTCT-CTTCCT
** *
1258819 CCTTCTT-TGGCTCCTCTTTCTTCTC
1 CCTTCTTCTCCCTCTTCTTTCTTCTC
1258844 CGGTTCTTTT
Statistics
Matches: 112, Mismatches: 25, Indels: 22
0.70 0.16 0.14
Matches are distributed among these distances:
29 6 0.05
30 72 0.64
31 10 0.09
32 6 0.05
33 16 0.14
34 2 0.02
ACGTcount: A:0.00, C:0.44, G:0.02, T:0.54
Consensus pattern (31 bp):
CCTTCTTCTCCCTCTTCTTTCTTCTCTTCCT
Found at i:1258771 original size:48 final size:47
Alignment explanation
Indices: 1258703--1258824 Score: 122
Period size: 48 Copynumber: 2.6 Consensus size: 47
1258693 CCTCCTTCTT
*
1258703 CCCTTCCTCCTTCTTCCCTTCTTCCTTCTCTCCCCCTTCCTTCTCTCC
1 CCCTTCCTTCTT-TTCCCTTCTTCCTTCTCTCCCCCTTCCTTCTCTCC
* * ** * *
1258751 CCCTTCCTTCTTTTCTCCTTCTTTCTTTTCTCCTTCTTTCTTTTCTCC
1 CCCTTCCTTCTTTTC-CCTTCTTCCTTCTCTCCCCCTTCCTTCTCTCC
* * *
1258799 CTCTTCTTTC-TTT-GCTTCTTCCTTCT
1 CCCTTCCTTCTTTTCCCTTCTTCCTTCT
1258825 TTGGCTCCTC
Statistics
Matches: 61, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
45 10 0.16
47 6 0.10
48 45 0.74
ACGTcount: A:0.00, C:0.45, G:0.01, T:0.54
Consensus pattern (47 bp):
CCCTTCCTTCTTTTCCCTTCTTCCTTCTCTCCCCCTTCCTTCTCTCC
Found at i:1258806 original size:18 final size:15
Alignment explanation
Indices: 1258752--1258840 Score: 90
Period size: 15 Copynumber: 5.7 Consensus size: 15
1258742 CTTCTCTCCC
*
1258752 CCTTCCTTCTTTTCT
1 CCTTCTTTCTTTTCT
1258767 CCTTCTTTCTTTTCT
1 CCTTCTTTCTTTTCT
1258782 CCTTCTTTCTTTTCT
1 CCTTCTTTCTTTTCT
*
1258797 CCCTCTTCTTTCTTTGCT
1 --C-CTTCTTTCTTTTCT
* * *
1258815 TCTTCCTTCTTTGGCT
1 CCTTCTTTCTTT-TCT
1258831 CC-TCTTTCTT
1 CCTTCTTTCTT
1258841 CTCCGGTTCT
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
15 46 0.72
16 4 0.06
17 1 0.02
18 13 0.20
ACGTcount: A:0.00, C:0.36, G:0.03, T:0.61
Consensus pattern (15 bp):
CCTTCTTTCTTTTCT
Found at i:1258835 original size:33 final size:32
Alignment explanation
Indices: 1258752--1258836 Score: 102
Period size: 33 Copynumber: 2.7 Consensus size: 32
1258742 CTTCTCTCCC
*
1258752 CCTTCCTTCTTTTCT-C-CTTCTTTCTTTTCT
1 CCTTCCTTCTTTTCTCCTCTTCTTTCTTTGCT
*
1258782 CCTTCTTTCTTTTCTCCCTCTTCTTTCTTTGCT
1 CCTTCCTTCTTTTCT-CCTCTTCTTTCTTTGCT
* *
1258815 TCTTCCTTCTTTGGCTCCTCTT
1 CCTTCCTTCTTT-TCTCCTCTT
1258837 TCTTCTCCGG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
30 14 0.30
32 1 0.02
33 29 0.63
34 2 0.04
ACGTcount: A:0.00, C:0.36, G:0.04, T:0.60
Consensus pattern (32 bp):
CCTTCCTTCTTTTCTCCTCTTCTTTCTTTGCT
Found at i:1261676 original size:37 final size:38
Alignment explanation
Indices: 1261635--1261721 Score: 153
Period size: 37 Copynumber: 2.4 Consensus size: 38
1261625 GCCGAGAAAA
1261635 TAGGAAAT-TTGTTATTTTATTTTTTAATTTGTGTTTT
1 TAGGAAATATTGTTATTTTATTTTTTAATTTGTGTTTT
1261672 TAGG-AATATTGTTATTTTATTTTTTAATTTGTGTTTT
1 TAGGAAATATTGTTATTTTATTTTTTAATTTGTGTTTT
1261709 TAGG-AATATTGTT
1 TAGGAAATATTGTT
1261722 GTAATGTTGT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
36 3 0.06
37 46 0.94
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (38 bp):
TAGGAAATATTGTTATTTTATTTTTTAATTTGTGTTTT
Found at i:1261710 original size:20 final size:20
Alignment explanation
Indices: 1261640--1261703 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
1261630 GAAAATAGGA
1261640 AATTTGTTATTTTATTTTTT
1 AATTTGTTATTTTATTTTTT
**
1261660 AATTTGTGT-TTTTA----GG
1 AATTTGT-TATTTTATTTTTT
1261676 AATATTGTTATTTTATTTTTT
1 AAT-TTGTTATTTTATTTTTT
1261697 AATTTGT
1 AATTTGT
1261704 GTTTTTAGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
16 4 0.12
17 9 0.27
20 16 0.48
21 4 0.12
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (20 bp):
AATTTGTTATTTTATTTTTT
Found at i:1263288 original size:2 final size:2
Alignment explanation
Indices: 1263283--1263314 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1263273 CCCTTTTTTA
1263283 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
1263315 TCATTTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1264166 original size:11 final size:11
Alignment explanation
Indices: 1264152--1264403 Score: 100
Period size: 11 Copynumber: 22.0 Consensus size: 11
1264142 TAACGAAAAT
1264152 AAAAAAATAAA
1 AAAAAAATAAA
1264163 AAAAATGAGATAAA
1 AAAAA--A-ATAAA
1264177 AAATTTAAAA-AAA
1 AAA---AAAATAAA
*
1264190 TAAAAAAT-AA
1 AAAAAAATAAA
1264200 AAAAAAATAAA
1 AAAAAAATAAA
** *
1264211 GTAAAGATAAA
1 AAAAAAATAAA
**
1264222 AAATTAATAAA
1 AAAAAAATAAA
* *
1264233 ATAAAGATAAA
1 AAAAAAATAAA
1264244 AAATAAAATAAA
1 AAA-AAAATAAA
* *
1264256 TAAAAAGTAAA
1 AAAAAAATAAA
*
1264267 AATAAAAA-ACA
1 AA-AAAAATAAA
*
1264278 AAGAAAAT--A
1 AAAAAAATAAA
*
1264287 AATAAAATAAA
1 AAAAAAATAAA
* *
1264298 AAACATAATAAT
1 AAA-AAAATAAA
* *
1264310 AATATAATAAA
1 AAAAAAATAAA
* *
1264321 TAAATAATCATAGA
1 -AAA-AA-AATAAA
*
1264335 AATAAAATAAA
1 AAAAAAATAAA
* *
1264346 AAATAAAGAAA
1 AAAAAAATAAA
*
1264357 AAAAGAAAGAAA
1 AAAA-AAATAAA
*
1264369 GAAAGAAAATATA
1 -AAA-AAAATAAA
*
1264382 AAGAAAATAAA
1 AAAAAAATAAA
*
1264393 AAATAAATAAA
1 AAAAAAATAAA
1264404 GATAATGAAA
Statistics
Matches: 176, Mismatches: 45, Indels: 40
0.67 0.17 0.15
Matches are distributed among these distances:
9 8 0.05
10 17 0.10
11 83 0.47
12 34 0.19
13 17 0.10
14 14 0.08
15 1 0.01
17 2 0.01
ACGTcount: A:0.77, C:0.01, G:0.06, T:0.17
Consensus pattern (11 bp):
AAAAAAATAAA
Found at i:1264234 original size:44 final size:45
Alignment explanation
Indices: 1264150--1264268 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 45
1264140 AGTAACGAAA
* *
1264150 ATAAAAAAATAAAAAAAAT-GAGATAAAAAATTTAAAAAAATAAA-
1 ATAAAAAAA-AAAATAAATAAAGATAAAAAATTTAAAAAAATAAAG
*
1264194 A-AATAAAAAAAAATAAAGTAAAGATAAAAAA-TTAATAAAATAAAG
1 ATAA-AAAAAAAAATAAA-TAAAGATAAAAAATTTAAAAAAATAAAG
* *
1264239 ATAAAAAATAAAATAAATAAAAAGTAAAAA
1 ATAAAAAAAAAAATAAATAAAGA-TAAAAA
1264269 TAAAAAACAA
Statistics
Matches: 64, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
43 9 0.14
44 24 0.38
45 29 0.45
46 2 0.03
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (45 bp):
ATAAAAAAAAAAATAAATAAAGATAAAAAATTTAAAAAAATAAAG
Found at i:1264258 original size:4 final size:4
Alignment explanation
Indices: 1264182--1264403 Score: 62
Period size: 4 Copynumber: 56.0 Consensus size: 4
1264172 ATAAAAAATT
* *
1264182 TAAA AAAA TAAA -AAA TAAA -AAA -AAA TAAA GTAAAGA TAAA -AAA TTAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA -T-AA-A TAAA TAAA TAAA
*
1264229 TAAAA TAAAGA TAAA -AAA TAAAA TAAA TAAA -AAG T-AA -AAA TAAA
1 T-AAA T-AA-A TAAA TAAA T-AAA TAAA TAAA TAAA TAAA TAAA TAAA
* * *
1264273 -AAA CAAA GAAAA TAAA TAAAA TAAA -AAA CATAA T-AA T-AA TATAA
1 TAAA TAAA -TAAA TAAA T-AAA TAAA TAAA TA-AA TAAA TAAA TA-AA
* * * * *
1264317 TAAA TAAA T-AA TCATA GAAA TAAAA TAAA -AAA TAAA GAAA AAAA GAAA
1 TAAA TAAA TAAA T-AAA TAAA T-AAA TAAA TAAA TAAA TAAA TAAA TAAA
* * * * *
1264365 GAAA GAAA GAAA -ATA TAAA GAAAA TAAA -AAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA -TAAA TAAA TAAA TAAA TAAA
1264404 GATAATGAAA
Statistics
Matches: 171, Mismatches: 20, Indels: 54
0.70 0.08 0.22
Matches are distributed among these distances:
3 43 0.25
4 86 0.50
5 36 0.21
6 5 0.03
7 1 0.01
ACGTcount: A:0.77, C:0.01, G:0.05, T:0.17
Consensus pattern (4 bp):
TAAA
Found at i:1264327 original size:73 final size:77
Alignment explanation
Indices: 1264185--1264399 Score: 200
Period size: 73 Copynumber: 2.8 Consensus size: 77
1264175 AAAAATTTAA
* *
1264185 AAAAATAAAAAATAAAAAAAAATAAAGTAAAGATAAAAAATTAATAAAATAAAGATAAAAAATAA
1 AAAAATAAAAAA-AAAAGAAAATAAAGTAAAGATAAAAAAATAAT-AAATAAAGATAAAAAATAA
1264250 AATAA-ATAAAAAGT
64 AATAACATAAAAA-T
* * *
1264264 AAAAATAAAAAACAAAGAAAATAAA-TAAA-ATAAAAAACATAAT-AAT-AATATAATAAAT-AA
1 AAAAATAAAAAAAAAAGAAAATAAAGTAAAGATAAAAAA-ATAATAAATAAAGATAAAAAATAAA
*
1264324 ATAATCATAGAAAT
65 ATAA-CATAAAAAT
* * *
1264338 -AAAATAAAAAATAAAGAAAA-AAAG-AAAGA-AAGAAAGAAAATATAAAGAAA-ATAAAAAATA
1 AAAAATAAAAAAAAAAGAAAATAAAGTAAAGATAA-AAA-AATA-ATAAATAAAGATAAAAAATA
1264398 AA
63 AA
1264400 TAAAGATAAT
Statistics
Matches: 115, Mismatches: 10, Indels: 25
0.77 0.07 0.17
Matches are distributed among these distances:
72 8 0.07
73 31 0.27
74 14 0.12
75 19 0.17
76 12 0.10
77 8 0.07
78 11 0.10
79 12 0.10
ACGTcount: A:0.77, C:0.01, G:0.06, T:0.16
Consensus pattern (77 bp):
AAAAATAAAAAAAAAAGAAAATAAAGTAAAGATAAAAAAATAATAAATAAAGATAAAAAATAAAA
TAACATAAAAAT
Found at i:1264332 original size:28 final size:27
Alignment explanation
Indices: 1264266--1264352 Score: 83
Period size: 28 Copynumber: 3.3 Consensus size: 27
1264256 TAAAAAGTAA
*
1264266 AAATAAAAAACAAAG-AA-AATA-AAT
1 AAATAAAAAACATAGAAATAATATAAT
1264290 AAAATAAAAAACATA-ATAATAATATAAT
1 -AAATAAAAAACATAGA-AATAATATAAT
* * *
1264318 AAATAAATAATCATAGAAATAAAATAAA
1 AAATAAA-AAACATAGAAATAATATAAT
1264346 AAATAAA
1 AAATAAA
1264353 GAAAAAAAGA
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
25 13 0.25
26 2 0.04
27 11 0.21
28 25 0.48
29 1 0.02
ACGTcount: A:0.75, C:0.03, G:0.02, T:0.20
Consensus pattern (27 bp):
AAATAAAAAACATAGAAATAATATAAT
Found at i:1264363 original size:28 final size:27
Alignment explanation
Indices: 1264160--1264423 Score: 112
Period size: 29 Copynumber: 9.4 Consensus size: 27
1264150 ATAAAAAAAT
* *
1264160 AAAAAAAATGAGATAAAAAATTTAAA-AA
1 AAAAAAAATAAAATAAAAAA--TAAAGAA
*
1264188 AATAAAAAAT-AAA-AAAAAATAAAGTA
1 AA-AAAAAATAAAATAAAAAATAAAGAA
* * *
1264214 AAGATAAA-AAATTAATAAAATAAAGATA
1 AAAAAAAATAAAATAA-AAAATAAAGA-A
* *
1264242 AAAAATAAA-ATAAATAAAAAGTAAAAATA
1 AAAAA-AAATA-AAATAAAAAATAAAGA-A
*
1264271 AAAAACAAAGAAAATAAATAAAATAAA-AA
1 AAAAA-AAATAAAAT-AA-AAAATAAAGAA
* * * * *
1264300 ACATAATAATAATATAATAAATAAATAA
1 A-AAAAAAATAAAATAAAAAATAAAGAA
* * *
1264328 TCATAGAAATAAAATAAAAAATAAAGAA
1 -AAAAAAAATAAAATAAAAAATAAAGAA
* *
1264356 AAAAAGAAAGAAAGAAAGAAAATATAAAGAA
1 AAAAA-AAATAAA-ATA-AAAA-ATAAAGAA
* *
1264387 AATAAAAAAT-AAAT-AAAGATAATGAA
1 AA-AAAAAATAAAATAAAAAATAAAGAA
1264413 AATAAAAAATA
1 AA-AAAAAATA
1264424 TATATACATC
Statistics
Matches: 183, Mismatches: 33, Indels: 41
0.71 0.13 0.16
Matches are distributed among these distances:
25 10 0.05
26 22 0.12
27 27 0.15
28 39 0.21
29 44 0.24
30 18 0.10
31 20 0.11
32 3 0.02
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.17
Consensus pattern (27 bp):
AAAAAAAATAAAATAAAAAATAAAGAA
Found at i:1264384 original size:31 final size:31
Alignment explanation
Indices: 1264343--1264405 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
1264333 GAAATAAAAT
1264343 AAAAAATAAAGAAAA-AAAGAAAGAAAGAAAG
1 AAAAAATAAAGAAAATAAA-AAAGAAAGAAAG
* * *
1264374 AAAATATAAAGAAAATAAAAAATAAATAAAG
1 AAAAAATAAAGAAAATAAAAAAGAAAGAAAG
1264405 A
1 A
1264406 TAATGAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 25 0.89
32 3 0.11
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.10
Consensus pattern (31 bp):
AAAAAATAAAGAAAATAAAAAAGAAAGAAAG
Found at i:1264415 original size:26 final size:25
Alignment explanation
Indices: 1264186--1264300 Score: 81
Period size: 27 Copynumber: 4.4 Consensus size: 25
1264176 AAAATTTAAA
* *
1264186 AAAATAAAAAATAAAAAAAAATAAAG
1 AAAATAAAAAAT-AAATAAAATAATG
* *
1264212 TAAAGATAAAAAATTAATAAAATAAAG
1 -AAA-ATAAAAAATAAATAAAATAATG
* * *
1264239 ATAAAAAATAAAATAAATAAAA-AGTA
1 A-AAATAA-AAAATAAATAAAATAATG
* *
1264265 AAAATAAAAAACAAAGAAAATAAAT-
1 AAAATAAAAAATAAATAAAAT-AATG
1264290 AAAATAAAAAA
1 AAAATAAAAAA
1264301 CATAATAATA
Statistics
Matches: 72, Mismatches: 11, Indels: 12
0.76 0.12 0.13
Matches are distributed among these distances:
24 11 0.15
25 16 0.22
26 8 0.11
27 28 0.39
28 9 0.12
ACGTcount: A:0.79, C:0.01, G:0.04, T:0.16
Consensus pattern (25 bp):
AAAATAAAAAATAAATAAAATAATG
Found at i:1264888 original size:13 final size:12
Alignment explanation
Indices: 1264846--1264915 Score: 61
Period size: 12 Copynumber: 5.7 Consensus size: 12
1264836 TATTAGATAA
1264846 AAAATAAGAAAT-
1 AAAATAA-AAATG
* *
1264858 AAGATAAAAATT
1 AAAATAAAAATG
1264870 AAAATAAACAATG
1 AAAATAAA-AATG
*
1264883 AAAATAATAATG
1 AAAATAAAAATG
* *
1264895 AAAATAATAATA
1 AAAATAAAAATG
1264907 AATAATAAA
1 AA-AATAAA
1264916 TAAAGGATCA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
11 4 0.08
12 30 0.61
13 15 0.31
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.21
Consensus pattern (12 bp):
AAAATAAAAATG
Found at i:1265436 original size:39 final size:41
Alignment explanation
Indices: 1265380--1265458 Score: 94
Period size: 39 Copynumber: 2.0 Consensus size: 41
1265370 TATGTATATA
*
1265380 TTTTACTTTATTATTTATTAT-TAT-TA-TTTTTTGTTTTGT
1 TTTTACCTTATTATTTA-TATGTATATAGTTTTTTGTTTTGT
1265419 TTTTACCTTA-TATTTTATATGTATATATGTTTTTTGTTTT
1 TTTTACCTTATTA-TTTATATGTATATA-GTTTTTTGTTTT
1265459 TTACTTATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
38 5 0.15
39 16 0.47
40 2 0.06
42 11 0.32
ACGTcount: A:0.19, C:0.04, G:0.06, T:0.71
Consensus pattern (41 bp):
TTTTACCTTATTATTTATATGTATATAGTTTTTTGTTTTGT
Found at i:1265901 original size:33 final size:35
Alignment explanation
Indices: 1265833--1265901 Score: 81
Period size: 33 Copynumber: 2.0 Consensus size: 35
1265823 TATTATTTTT
* *
1265833 TGTTTTGTTTTTACCTTATATTTTATATGTATATA
1 TGTTTTGTTTTTACCTTATATTTTAAATATATATA
*
1265868 TGTTTT-TTTTTA-CTTATTTTATTAAATAT-TATA
1 TGTTTTGTTTTTACCTTATATT-TTAAATATATATA
1265901 T
1 T
1265902 TATATATACA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
33 12 0.40
34 12 0.40
35 6 0.20
ACGTcount: A:0.25, C:0.04, G:0.06, T:0.65
Consensus pattern (35 bp):
TGTTTTGTTTTTACCTTATATTTTAAATATATATA
Found at i:1266075 original size:20 final size:22
Alignment explanation
Indices: 1266050--1266097 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 22
1266040 TTTTTTTCCC
*
1266050 TATTTTTT-CCTATTA-TTAT-
1 TATTTTTTACCTAATAGTTATA
1266069 TATTTTTTACCTAATAGTTATA
1 TATTTTTTACCTAATAGTTATA
1266091 TATTTTT
1 TATTTTT
1266098 AGTTTTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 8 0.32
20 6 0.24
21 4 0.16
22 7 0.28
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65
Consensus pattern (22 bp):
TATTTTTTACCTAATAGTTATA
Found at i:1266098 original size:21 final size:19
Alignment explanation
Indices: 1266050--1266098 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
1266040 TTTTTTTCCC
* *
1266050 TATTTTTTCCTATTATTAT
1 TATTTTTACCTAATATTAT
1266069 TATTTTTTACCTAATAGTTAT
1 TA-TTTTTACCTAATA-TTAT
1266090 ATATTTTTA
1 -TATTTTTA
1266099 GTTTTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 2 0.08
20 11 0.44
21 10 0.40
22 2 0.08
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63
Consensus pattern (19 bp):
TATTTTTACCTAATATTAT
Found at i:1266136 original size:12 final size:12
Alignment explanation
Indices: 1266119--1266152 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
1266109 TTCATTATTA
1266119 TTATTTTCTTTT
1 TTATTTTCTTTT
1266131 TTA-TTTCTTTT
1 TTATTTTCTTTT
1266142 TTATTTT-TTTT
1 TTATTTTCTTTT
1266153 GTAGTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.85
Consensus pattern (12 bp):
TTATTTTCTTTT
Found at i:1266239 original size:23 final size:21
Alignment explanation
Indices: 1266207--1266332 Score: 82
Period size: 23 Copynumber: 5.9 Consensus size: 21
1266197 TTCTATTTCC
*
1266207 TTTATATTTATTTTGTTTCTTCA
1 TTTATTTTTATTTTGTTT-TT-A
1266230 TTTATTTTTATTTTGTTTTTA
1 TTTATTTTTATTTTGTTTTTA
* *
1266251 TTTATTTATTTATTATATTTTTA
1 TTTA-TT-TTTATTTTGTTTTTA
*
1266274 TTATGTTCTTTATTTT-TTTGTT-
1 TT-TATT-TTTATTTTGTTT-TTA
* **
1266296 TTT-TGTTT-TTTTACTTTTA
1 TTTATTTTTATTTTGTTTTTA
*
1266315 TTTA-TTTTATTTTATTTT
1 TTTATTTTTATTTTGTTTT
1266333 CTTATCTTTA
Statistics
Matches: 85, Mismatches: 10, Indels: 19
0.75 0.09 0.17
Matches are distributed among these distances:
18 6 0.07
19 11 0.13
20 9 0.11
21 6 0.07
22 9 0.11
23 43 0.51
24 1 0.01
ACGTcount: A:0.16, C:0.03, G:0.04, T:0.77
Consensus pattern (21 bp):
TTTATTTTTATTTTGTTTTTA
Found at i:1266248 original size:5 final size:5
Alignment explanation
Indices: 1266230--1266431 Score: 69
Period size: 5 Copynumber: 41.4 Consensus size: 5
1266220 TGTTTCTTCA
* * *
1266230 TTTATT TTTAT TTTGT TTT-T ATTTA- TTTA- TTTAT TATAT TTT-T ATTAT
1 TTTA-T TTTAT TTTAT TTTAT -TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
* *
1266278 GTT-C TTTAT TTT-T TTGT-T TTT-T GTTT-T TTTACT TTTA- TTTAT
1 TTTAT TTTAT TTTAT TT-TAT TTTAT -TTTAT TTTA-T TTTAT TTTAT
* * *
1266320 TTTAT TTTA- TTT-T CTTAT CTTTAT TTTAT TTATTT TTTAT CTTTAC
1 TTTAT TTTAT TTTAT TTTAT -TTTAT TTTAT TT-TAT TTTAT -TTTAT
* * *
1266366 TTTAT TTT-T TCATT-T TTTAT CTCTTTT TTTAA TTTA- TTT-T TTTCT
1 TTTAT TTTAT T--TTAT TTTAT -T-TTAT TTTAT TTTAT TTTAT TTTAT
*
1266411 TTTAT TTT-C TTTAT TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TT
1266432 ACTTTCATTA
Statistics
Matches: 153, Mismatches: 20, Indels: 47
0.70 0.09 0.21
Matches are distributed among these distances:
4 44 0.29
5 79 0.52
6 27 0.18
7 3 0.02
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:1266252 original size:34 final size:36
Alignment explanation
Indices: 1266213--1266289 Score: 97
Period size: 34 Copynumber: 2.2 Consensus size: 36
1266203 TTCCTTTATA
* * *
1266213 TTTATTTTGTTTCTTCATT-TATTTTTATTTTGTT-
1 TTTATTTTATTTATTCATTATATTTTTATTATGTTC
*
1266247 TTTA-TTTATTTATTTATTATATTTTTATTATGTTC
1 TTTATTTTATTTATTCATTATATTTTTATTATGTTC
1266282 TTTATTTT
1 TTTATTTT
1266290 TTTGTTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 11 0.31
34 18 0.50
35 4 0.11
36 3 0.08
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.75
Consensus pattern (36 bp):
TTTATTTTATTTATTCATTATATTTTTATTATGTTC
Found at i:1266300 original size:56 final size:54
Alignment explanation
Indices: 1266208--1266372 Score: 147
Period size: 56 Copynumber: 2.9 Consensus size: 54
1266198 TCTATTTCCT
* *
1266208 TTATA-TTTATTTTGTTTCTTCATTTATTTTTATTTTGTTTTTATTTATTTATTTA
1 TTATATTTTATTTTG-TTCTTTATTT-TTTTTTTTTTGTTTTTATTTATTTATTTA
*
1266263 TTATATTTTTATTATGTTCTTTATTTTTTTGTTTTTTG-TTTT-TTTACTTTTATTTA
1 TTATA-TTTTATTTTGTTCTTTATTTTTTT-TTTTTTGTTTTTATTTA--TTTATTTA
* * * *
1266319 TTTTATTTTATTTTCTTATCTTTATTTTATTTATTTTTTATCTTTACTTTATTT
1 TTATATTTTATTTT-GT-TCTTTATTTT-TTT-TTTTTTGTTTTTA-TTTATTT
1266373 TTTCATTTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 18
0.77 0.08 0.15
Matches are distributed among these distances:
54 4 0.04
55 21 0.23
56 28 0.31
57 18 0.20
58 9 0.10
59 6 0.07
61 4 0.04
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (54 bp):
TTATATTTTATTTTGTTCTTTATTTTTTTTTTTTTGTTTTTATTTATTTATTTA
Found at i:1266313 original size:9 final size:8
Alignment explanation
Indices: 1266230--1266432 Score: 94
Period size: 9 Copynumber: 23.5 Consensus size: 8
1266220 TGTTTCTTCA
1266230 TTTATTTT
1 TTTATTTT
1266238 TATT-TTGTT
1 T-TTATT-TT
*
1266247 TTTATTTA
1 TTTATTTT
1266255 TTTATTTAT
1 TTTATTT-T
*
1266264 TATATTTT
1 TTTATTTT
*
1266272 TATTATGTTC
1 T-TTAT-TTT
1266282 TTTATTTT
1 TTTATTTT
*
1266290 TTT-GTTT
1 TTTATTTT
*
1266297 TTTGTTTT
1 TTTATTTT
1266305 TTTACTTTT
1 TTTA-TTTT
1266314 ATTTATTTTAT
1 -TTTA-TTT-T
1266325 TTTATTTT
1 TTTATTTT
* *
1266333 CTTA--TC
1 TTTATTTT
1266339 TTTATTTT
1 TTTATTTT
1266347 ATTTA-TTT
1 -TTTATTTT
1266355 TTTATCTTT
1 TTTAT-TTT
1266364 ACTTTATTTT
1 --TTTATTTT
*
1266374 TTCATTTTT
1 TTTA-TTTT
*
1266383 TATCTCTTTT
1 T-T-TATTTT
1266393 TTTAATTTAT
1 TTT-ATTT-T
1266403 TTT-TTTCT
1 TTTATTT-T
1266411 TTTATTTT
1 TTTATTTT
1266419 CTTTATTTT
1 -TTTATTTT
1266428 ATTTA
1 -TTTA
1266433 CTTTCATTAC
Statistics
Matches: 151, Mismatches: 20, Indels: 47
0.69 0.09 0.22
Matches are distributed among these distances:
6 4 0.03
7 10 0.07
8 46 0.30
9 58 0.38
10 27 0.18
11 6 0.04
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (8 bp):
TTTATTTT
Found at i:1266319 original size:33 final size:32
Alignment explanation
Indices: 1266282--1266431 Score: 92
Period size: 33 Copynumber: 4.9 Consensus size: 32
1266272 TATTATGTTC
* * *
1266282 TTTATTTTTTTGTTTTTTGTT-TTTTTACTTTTA
1 TTTATTTTTTT-TATTTTCTTATCTTTA-TTTTA
1266315 TTTATTTTATTTTATTTTCTTATCTTTATTTTA
1 TTTATTTT-TTTTATTTTCTTATCTTTATTTTA
*
1266348 TTTA--TTTTTTA-TCT-TTA-CTTTATTTT-
1 TTTATTTTTTTTATTTTCTTATCTTTATTTTA
* * * *
1266374 TTCA--TTTTTTA-TCTCTT-TTTTTAATTTA
1 TTTATTTTTTTTATTTTCTTATCTTTATTTTA
1266402 TTT-TTTTCTTTTATTTTCTTTAT-TTTATTT
1 TTTATTTT-TTTTATTTTC-TTATCTTTATTT
1266432 ACTTTCATTA
Statistics
Matches: 96, Mismatches: 10, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
26 13 0.14
27 18 0.19
28 5 0.05
29 4 0.04
30 10 0.10
31 5 0.05
32 8 0.08
33 25 0.26
34 8 0.08
ACGTcount: A:0.14, C:0.07, G:0.01, T:0.78
Consensus pattern (32 bp):
TTTATTTTTTTTATTTTCTTATCTTTATTTTA
Found at i:1266356 original size:50 final size:51
Alignment explanation
Indices: 1266302--1266431 Score: 155
Period size: 50 Copynumber: 2.6 Consensus size: 51
1266292 TGTTTTTTGT
1266302 TTTTTTACTTTTATTTATTTTATTTTATTTTCTTATCT-TTATTTT-ATTTA
1 TTTTTTACTTTTATTTATTTTATTTTATTTT-TTATCTCTTATTTTAATTTA
* *
1266352 TTTTTTA-TCTTTACTTTA-TTT-TTTCATTTTTTATCTCTTTTTTTAATTTA
1 TTTTTTACT-TTTA-TTTATTTTATTTTATTTTTTATCTCTTATTTTAATTTA
*
1266402 TTTTTTTCTTTTATTT-TCTTTATTTTATTT
1 TTTTTTACTTTTATTTAT-TTTATTTTATTT
1266432 ACTTTCATTA
Statistics
Matches: 68, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
48 6 0.09
49 18 0.26
50 32 0.47
51 12 0.18
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (51 bp):
TTTTTTACTTTTATTTATTTTATTTTATTTTTTATCTCTTATTTTAATTTA
Found at i:1266357 original size:11 final size:11
Alignment explanation
Indices: 1266127--1266407 Score: 91
Period size: 11 Copynumber: 24.5 Consensus size: 11
1266117 TATTATTTTC
*
1266127 TTTTTTATTTC
1 TTTTTTATTTA
1266138 TTTTTTATTT-
1 TTTTTTATTTA
1266148 TTTTTGTAGTTTTA
1 TTTTT-TA--TTTA
*
1266162 TATTTATATTTA
1 T-TTTTTATTTA
* *
1266174 TATTTTCTTTA
1 TTTTTTATTTA
* * *
1266185 -TCTTGACTTA
1 TTTTTTATTTA
* *
1266195 TTTTCTATTTC
1 TTTTTTATTTA
* *
1266206 CTTTATATTTA
1 TTTTTTATTTA
1266217 TTTTGTT-TCTTCA
1 TTTT-TTAT-TT-A
*
1266230 TTTATT-TTTA
1 TTTTTTATTTA
1266240 TTTTGTT-TTTA
1 TTTT-TTATTTA
1266251 TTTATTTATTTA
1 TTT-TTTATTTA
*
1266263 TTATATT-TTTA
1 TT-TTTTATTTA
* *
1266274 TTATGTTCTTTA
1 TT-TTTTATTTA
*
1266286 TTTTTT-TGTTT
1 TTTTTTAT-TTA
*
1266297 TTTGTTTTTTTA
1 TTT-TTTATTTA
*
1266309 -CTTTTATTTA
1 TTTTTTATTTA
*
1266319 TTTTAT-TTTA
1 TTTTTTATTTA
1266329 TTTTCTTATCTT-
1 TTTT-TTAT-TTA
*
1266341 TATTTTATTTA
1 TTTTTTATTTA
1266352 TTTTTTATCTTTA
1 TTTTTTA--TTTA
1266365 CTTTATTT-TTTCA
1 -TTT-TTTATTT-A
1266378 TTTTTTATCTCT-
1 TTTTTTAT-T-TA
1266390 TTTTTTAATTTA
1 TTTTTT-ATTTA
1266402 TTTTTT
1 TTTTTT
1266408 TCTTTTATTT
Statistics
Matches: 205, Mismatches: 33, Indels: 63
0.68 0.11 0.21
Matches are distributed among these distances:
10 32 0.16
11 86 0.42
12 55 0.27
13 19 0.09
14 7 0.03
15 6 0.03
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.75
Consensus pattern (11 bp):
TTTTTTATTTA
Found at i:1266405 original size:13 final size:13
Alignment explanation
Indices: 1266230--1266431 Score: 100
Period size: 14 Copynumber: 13.9 Consensus size: 13
1266220 TGTTTCTTCA
1266230 TTTATTTTTATTTT
1 TTTA-TTTTATTTT
* *
1266244 GTTTTTATTTATTTA
1 -TTTAT-TTTATTTT
*
1266259 TTTATTATATTTT
1 TTTATTTTATTTT
1266272 TATTATGTTCTTTATTTTT
1 T-TTA---T-TTTA-TTTT
* *
1266291 TTGTTTTTTGTTTT
1 TT-TATTTTATTTT
1266305 TTTACTTTTATTTAT
1 TTTA-TTTTATTT-T
1266320 TTTATTTTATTTT
1 TTTATTTTATTTT
*
1266333 CTTATCTTTATTTT
1 TTTAT-TTTATTTT
1266347 ATTTATTTTTTATCTTT
1 -TTTA--TTTTAT-TTT
*
1266364 ACTTTATTTTTTCATTT
1 --TTTATTTTAT--TTT
* *
1266381 TTTA-TCTCTTTT
1 TTTATTTTATTTT
*
1266393 TTTAATTTATTTT
1 TTTATTTTATTTT
*
1266406 TTTCTTTTATTTT
1 TTTATTTTATTTT
1266419 CTTTATTTTATTT
1 -TTTATTTTATTT
1266432 ACTTTCATTA
Statistics
Matches: 146, Mismatches: 22, Indels: 39
0.71 0.11 0.19
Matches are distributed among these distances:
12 7 0.05
13 30 0.21
14 51 0.35
15 25 0.17
16 11 0.08
17 8 0.05
18 8 0.05
19 6 0.04
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.77
Consensus pattern (13 bp):
TTTATTTTATTTT
Found at i:1266405 original size:22 final size:23
Alignment explanation
Indices: 1266380--1266429 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
1266370 TTTTTTCATT
1266380 TTTTATCTCTTTT-TTTAATTTA
1 TTTTATCTCTTTTATTTAATTTA
* **
1266402 TTTT-TTTCTTTTATTTTCTTTA
1 TTTTATCTCTTTTATTTAATTTA
1266424 TTTTAT
1 TTTTAT
1266430 TTACTTTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 7 0.30
22 15 0.65
23 1 0.04
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTATCTCTTTTATTTAATTTA
Found at i:1277248 original size:21 final size:21
Alignment explanation
Indices: 1277222--1277289 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
1277212 TCAATATTAC
*
1277222 AATAATATTCTTATTTTAATA
1 AATAATATTATTATTTTAATA
* *
1277243 AAT-A-ATTAATATAATTAATAA
1 AATAATATTATTAT-TTTAAT-A
*
1277264 AATAATATTTTTATTTTAATA
1 AATAATATTATTATTTTAATA
1277285 AATAA
1 AATAA
1277290 CTGATATAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
19 6 0.16
20 6 0.16
21 13 0.35
22 6 0.16
23 6 0.16
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (21 bp):
AATAATATTATTATTTTAATA
Found at i:1277318 original size:37 final size:41
Alignment explanation
Indices: 1277222--1277323 Score: 115
Period size: 42 Copynumber: 2.6 Consensus size: 41
1277212 TCAATATTAC
*
1277222 AATAATAT-TCTTATTTTAATAAATAATTAATATAATTAATAA
1 AATAATATGT-TTATTTTAATAAATAACTAATATAATT-ATAA
* * *
1277264 AATAATATTTTTATTTTAATAAATAACTGATATAATT-TAT
1 AATAATATGTTTATTTTAATAAATAACTAATATAATTATAA
1277304 AA-AAT-TGTTT-TTTTAATAAA
1 AATAATATGTTTATTTTAATAAA
1277324 ATATAATAGT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
37 10 0.18
38 4 0.07
39 3 0.05
40 4 0.07
42 33 0.60
43 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (41 bp):
AATAATATGTTTATTTTAATAAATAACTAATATAATTATAA
Found at i:1277318 original size:42 final size:42
Alignment explanation
Indices: 1277222--1277308 Score: 138
Period size: 42 Copynumber: 2.1 Consensus size: 42
1277212 TCAATATTAC
* *
1277222 AATAATATTCTTATTTTAATAAATAATTAATATAATTAATAA
1 AATAATATTTTTATTTTAATAAATAACTAATATAATTAATAA
* *
1277264 AATAATATTTTTATTTTAATAAATAACTGATATAATTTATAA
1 AATAATATTTTTATTTTAATAAATAACTAATATAATTAATAA
1277306 AAT
1 AAT
1277309 TGTTTTTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (42 bp):
AATAATATTTTTATTTTAATAAATAACTAATATAATTAATAA
Found at i:1277394 original size:13 final size:14
Alignment explanation
Indices: 1277355--1277386 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1277345 TATTTATAGA
1277355 ATTTTAGAAATAAT
1 ATTTTAGAAATAAT
*
1277369 ATTTTAGTAATAAT
1 ATTTTAGAAATAAT
1277383 ATTT
1 ATTT
1277387 ACAAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (14 bp):
ATTTTAGAAATAAT
Found at i:1279363 original size:40 final size:39
Alignment explanation
Indices: 1279269--1279420 Score: 162
Period size: 39 Copynumber: 4.1 Consensus size: 39
1279259 TTGCAAATGG
* *
1279269 TTTTTGAAAACATATATAGTATATAGTTTTAAAAACATT
1 TTTTTGAAAACTTATATAATATATAGTTTTAAAAACATT
1279308 TTTTTGTAAAA-TTATATAATATATAGTTTTAAAAACATTT
1 TTTTTG-AAAACTTATATAATATATAGTTTTAAAAACA-TT
*
1279348 TTTTTGAAAACTTATAT-A-ATAT--TTTAAAAAACA--
1 TTTTTGAAAACTTATATAATATATAGTTTTAAAAACATT
* * *
1279381 -TTTTGGAAAC-TATGTAATATATAGTTTTGAAAAC-TT
1 TTTTTGAAAACTTATATAATATATAGTTTTAAAAACATT
1279417 TTTT
1 TTTT
1279421 AAAGTATATA
Statistics
Matches: 96, Mismatches: 7, Indels: 22
0.77 0.06 0.18
Matches are distributed among these distances:
31 4 0.04
32 10 0.10
33 4 0.04
35 8 0.08
36 10 0.10
37 3 0.03
38 4 0.04
39 35 0.36
40 18 0.19
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (39 bp):
TTTTTGAAAACTTATATAATATATAGTTTTAAAAACATT
Found at i:1279491 original size:5 final size:5
Alignment explanation
Indices: 1279481--1279505 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1279471 TTGTATCATA
1279481 TTATT TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT
1279506 AATTTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:1295475 original size:19 final size:19
Alignment explanation
Indices: 1295451--1295504 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
1295441 CGAAACCGGT
*
1295451 TTTTTTGGTTCGGTTCGGG
1 TTTTTTGGTTCGGTTCGGA
**
1295470 TTTTTT--AACGGTTCGGA
1 TTTTTTGGTTCGGTTCGGA
*
1295487 TTTTTCGGTTCGGTTCGG
1 TTTTTTGGTTCGGTTCGG
1295505 TTCGGTTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
17 13 0.48
19 14 0.52
ACGTcount: A:0.06, C:0.13, G:0.31, T:0.50
Consensus pattern (19 bp):
TTTTTTGGTTCGGTTCGGA
Found at i:1298191 original size:39 final size:38
Alignment explanation
Indices: 1298103--1298192 Score: 96
Period size: 38 Copynumber: 2.4 Consensus size: 38
1298093 TAAATTCAAC
* *
1298103 CTTAAAAT-AAATTCAAATACTTAAATATCAAAATAAA
1 CTTAAAATAAAATTCAAATACCTAAATATCAAAAGAAA
* *
1298140 CTTTAAAA-AAAATTTAAATACCTAATTTATC-AAAGAAA
1 C-TTAAAATAAAATTCAAATACCTAA-ATATCAAAAGAAA
1298178 CTTAAATATAAAATT
1 CTTAAA-ATAAAATT
1298193 AAACCTAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
37 6 0.14
38 28 0.64
39 10 0.23
ACGTcount: A:0.57, C:0.10, G:0.01, T:0.32
Consensus pattern (38 bp):
CTTAAAATAAAATTCAAATACCTAAATATCAAAAGAAA
Found at i:1302127 original size:91 final size:91
Alignment explanation
Indices: 1302001--1302208 Score: 326
Period size: 91 Copynumber: 2.3 Consensus size: 91
1301991 TTGTTGGTAG
* * *
1302001 TAACTATGATAAATAGCATAAAATGTACTTGATTACTTTGGTTACTAATGAGGAGCATGTATTTG
1 TAACTATGATAAATAGCATAAAATGTACCTGATTACTTTGGTTACTAATGAGAAGCACGTATTTG
* *
1302066 TTAATTGTTATTAGTCCAACTGATTA
66 TTAATTATTATTAGTCCAACTGATGA
* *
1302092 TAATTATGATAAATAGCATAACATGTACCTGATTACTTTGGTTACTAATGAGAAGCACGTATTTG
1 TAACTATGATAAATAGCATAAAATGTACCTGATTACTTTGGTTACTAATGAGAAGCACGTATTTG
1302157 TTAATTATTATTAGTCCAACTGATGA
66 TTAATTATTATTAGTCCAACTGATGA
* * *
1302183 TAACTATGATATATAGAATAATATGT
1 TAACTATGATAAATAGCATAAAATGT
1302209 GATTACTTGG
Statistics
Matches: 106, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 106 1.00
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (91 bp):
TAACTATGATAAATAGCATAAAATGTACCTGATTACTTTGGTTACTAATGAGAAGCACGTATTTG
TTAATTATTATTAGTCCAACTGATGA
Found at i:1312627 original size:22 final size:22
Alignment explanation
Indices: 1312602--1312671 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 22
1312592 TTACTCTTAT
1312602 TATTTTTAAACATATTCTTTTA
1 TATTTTTAAACATATTCTTTTA
* *
1312624 TATTTTGTCAATAT-TTCTTTTA
1 TATTTT-TAAACATATTCTTTTA
*
1312646 GTATTTGTAAACATATT-TATTTA
1 -TATTTTTAAACATATTCT-TTTA
1312669 TAT
1 TAT
1312672 ATTCATTGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
22 23 0.59
23 16 0.41
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (22 bp):
TATTTTTAAACATATTCTTTTA
Found at i:1314026 original size:25 final size:24
Alignment explanation
Indices: 1313998--1314046 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
1313988 AATTTTAAGA
1313998 ATTTTATATAATAATTAGTTTATAT
1 ATTTTATATAATAATTA-TTTATAT
* * *
1314023 ATTTTATTTTATTATTATTTATAT
1 ATTTTATATAATAATTATTTATAT
1314047 TTACCCATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
ATTTTATATAATAATTATTTATAT
Found at i:1316977 original size:38 final size:38
Alignment explanation
Indices: 1316935--1317008 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
1316925 TGATTAACTC
*
1316935 ATATATCGTAAAC-ATTATATATATATCACATATAATCA
1 ATATATCATAAACAATT-TATATATATCACATATAATCA
* * *
1316973 ATATATTATAAACAATTTATATGTATCATATATAAT
1 ATATATCATAAACAATTTATATATATCACATATAAT
1317009 ACAAAGATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 28 0.90
39 3 0.10
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (38 bp):
ATATATCATAAACAATTTATATATATCACATATAATCA
Found at i:1322296 original size:23 final size:23
Alignment explanation
Indices: 1322252--1322296 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1322242 AACATATTAA
**
1322252 GTAGCGCTTATATAATGTAATAT
1 GTAGCGCTTATATAATAAAATAT
*
1322275 GTAGCGCTTATTTAATAAAATA
1 GTAGCGCTTATATAATAAAATA
1322297 GGTTAATTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (23 bp):
GTAGCGCTTATATAATAAAATAT
Found at i:1322433 original size:23 final size:23
Alignment explanation
Indices: 1322398--1322457 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
1322388 ATTAAGCACA
*
1322398 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
*
1322421 ATAACGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
* *
1322444 ATAATAAAATAGGT
1 ATAACATAATAGGT
1322458 TAATTATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1322511 original size:158 final size:158
Alignment explanation
Indices: 1322218--1322751 Score: 834
Period size: 158 Copynumber: 3.4 Consensus size: 158
1322208 ATATCATTTA
* ** * * *
1322218 ACTGAAAATATTATCAAATACAATAACATATTAAGTAGCGCTTATATAATGTAATATGTAGCGCT
1 ACTGGAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAACGTAATAGGTAGCGCT
* * * * *
1322283 TATTTAATAAAATAGGTTAATTACTTAATTTGTTATTATAACATATTAGTTAAACACCTAAAATA
66 TATATAATAAAATAGGTTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAAAATG
*
1322348 TTACCAAGGATAACATAACCGGTTAATT
131 TTACCAATGATAACATAACCGGTTAATT
*
1322376 ACTGGAAATATTATTAAGCACAATAACATATTAGGTAGCGCTTATATAACGTAATAGGTAGCGCT
1 ACTGGAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAACGTAATAGGTAGCGCT
*
1322441 TATATAATAAAATAGGTTAATTATTTAATTTGTTATTACAACATATTAGGTAAACGCCTAAAATG
66 TATATAATAAAATAGGTTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAAAATG
1322506 TTACCAATGATAACATAACCGGTTAATT
131 TTACCAATGATAACATAACCGGTTAATT
* * * * *
1322534 ACTGTAAATATTATCAAGCTCAATAACATATTAGGTGGCGCTCATATAACGTAATAAGTAGCGCT
1 ACTGGAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAACGTAATAGGTAGCGCT
* *
1322599 TATATAATAAAATATGTTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCTTAAAATG
66 TATATAATAAAATAGGTTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAAAATG
1322664 TTACCAATGATAACATAACCGGTTAATT
131 TTACCAATGATAACATAACCGGTTAATT
* * * **
1322692 ACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGATTATATAACAAAATAGGTA
1 ACTGGAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAACGTAATAGGTA
1322752 ATTACTTAAA
Statistics
Matches: 343, Mismatches: 33, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
158 343 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.34
Consensus pattern (158 bp):
ACTGGAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAACGTAATAGGTAGCGCT
TATATAATAAAATAGGTTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAAAATG
TTACCAATGATAACATAACCGGTTAATT
Found at i:1323005 original size:75 final size:75
Alignment explanation
Indices: 1322815--1323064 Score: 377
Period size: 75 Copynumber: 3.4 Consensus size: 75
1322805 CAAAATTTAA
* * *
1322815 ACTACTTATTACATTAAAATACCTACCGG-TTTTTT-AAGGTTGTTAATAATGTAAACGGT--AA
1 ACTACCTATTACATTAAAATACCTACCGGTTTTTTTGAATGTTGCTAATAATGTAAACGGTAAAA
1322876 AAAAATAGGC
66 AAAAATAGGC
* *
1322886 GCTACCTATTACATTAAAATACCTATCGGTTTTTTTGAATGTTGCTAATAATGTAAACGGTAAAA
1 ACTACCTATTACATTAAAATACCTACCGGTTTTTTTGAATGTTGCTAATAATGTAAACGGTAAAA
*
1322951 AAAAATA-GT
66 AAAAATAGGC
1322960 ACTACCTATTACATTAAAATACCTACCGGTTTTTTTTGAATGTTGCTAATAATGTAAACGAG-AA
1 ACTACCTATTACATTAAAATACCTACCGG-TTTTTTTGAATGTTGCTAATAATGTAAACG-GTAA
1323024 AAAAAAATAGGC
64 AAAAAAATAGGC
*
1323036 ACTACCTATTACATTAAACTACCTACCGG
1 ACTACCTATTACATTAAAATACCTACCGG
1323065 ATATGTTGAA
Statistics
Matches: 162, Mismatches: 10, Indels: 9
0.90 0.06 0.05
Matches are distributed among these distances:
71 26 0.16
72 6 0.04
73 22 0.14
74 28 0.17
75 50 0.31
76 30 0.19
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (75 bp):
ACTACCTATTACATTAAAATACCTACCGGTTTTTTTGAATGTTGCTAATAATGTAAACGGTAAAA
AAAAATAGGC
Found at i:1323342 original size:112 final size:112
Alignment explanation
Indices: 1323144--1323569 Score: 665
Period size: 112 Copynumber: 3.8 Consensus size: 112
1323134 TAGCACCTAT
* * *
1323144 AAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAAGATGTAAAAATATGATAAA
1 AAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
* * *
1323209 ACCAGTTTCATTATGATAAAACCGGTAAAGAGCTACCTAATATGTTG
66 ACCAATTTCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTG
1323256 AAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
1 AAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
1323321 ACCAATTTCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTG
66 ACCAATTTCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTG
* * * *
1323368 AAAGTATCGATACTTTATAAAAATATATCAATACTTTATAATATAACATGTAAAAATATGACAAA
1 AAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
* * *
1323433 ACCAATTTTATTATGACAAAACTGGTAAAGAACTACCTGATATGTTG
66 ACCAATTTCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTG
*
1323480 AAAATATCGAT-CTTTTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGAC
1 AAAGTATCGATAC---TTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGAC
** *
1323544 AAAATTAGTTTCATTATGACAAAACC
63 AAAACCAATTTCATTATGACAAAACC
1323570 AGTTTCATTA
Statistics
Matches: 288, Mismatches: 23, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
111 1 0.00
112 221 0.77
114 66 0.23
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (112 bp):
AAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
ACCAATTTCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTG
Found at i:1323563 original size:20 final size:20
Alignment explanation
Indices: 1323538--1323588 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1323528 CAGGTAAAAA
**
1323538 TATGACAAAATTAGTTTCAT
1 TATGACAAAACCAGTTTCAT
1323558 TATGACAAAACCAGTTTCAT
1 TATGACAAAACCAGTTTCAT
1323578 TATGACAAAAC
1 TATGACAAAAC
1323589 TGGTAAAGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (20 bp):
TATGACAAAACCAGTTTCAT
Found at i:1323582 original size:134 final size:134
Alignment explanation
Indices: 1323424--1323700 Score: 455
Period size: 134 Copynumber: 2.1 Consensus size: 134
1323414 CATGTAAAAA
* *
1323424 TATGACAAAACCAATTTTATTATGACAAAACTGGTAAAGAACTACCTGATATGTTGAAAATATCG
1 TATGACAAAACCAATTTCATTATGACAAAACTGGTAAAGAACTACCTGATATGTTGAAAATATAG
* * **
1323489 ATCTTTTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAATTAGTT
66 ATATTTTTTATAAAAATGTATCGATACTTTACAATATAACAAGTAAAAATATGACAAAACCAGTT
1323554 TCAT
131 TCAT
* * * *
1323558 TATGACAAAACCAGTTTCATTATGACAAAACTGGTAAAGAGCTACCTGATATGTTGAAAGTATAT
1 TATGACAAAACCAATTTCATTATGACAAAACTGGTAAAGAACTACCTGATATGTTGAAAATATAG
1323623 ATATTTTTTATAAAAATGTATCGATACTTTACAATATAACAAGTAAAAATATGACAAAACCAGTT
66 ATATTTTTTATAAAAATGTATCGATACTTTACAATATAACAAGTAAAAATATGACAAAACCAGTT
*
1323688 TTAT
131 TCAT
1323692 TATGACAAA
1 TATGACAAA
1323701 TCCGATAAAG
Statistics
Matches: 132, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
134 132 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (134 bp):
TATGACAAAACCAATTTCATTATGACAAAACTGGTAAAGAACTACCTGATATGTTGAAAATATAG
ATATTTTTTATAAAAATGTATCGATACTTTACAATATAACAAGTAAAAATATGACAAAACCAGTT
TCAT
Found at i:1341714 original size:21 final size:21
Alignment explanation
Indices: 1341650--1341718 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
1341640 GTGCGGCGGT
* *
1341650 GGACGGTGGTCGGAAGACGGC
1 GGACGATGGTCGGAGGACGGC
* * *
1341671 GAACGGTGGTTGGAGGACGGC
1 GGACGATGGTCGGAGGACGGC
1341692 GGACGATGGTCGGAGGACGGC
1 GGACGATGGTCGGAGGACGGC
1341713 GGACGA
1 GGACGA
1341719 CAAGCGACTG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.20, C:0.17, G:0.52, T:0.10
Consensus pattern (21 bp):
GGACGATGGTCGGAGGACGGC
Found at i:1347043 original size:35 final size:36
Alignment explanation
Indices: 1346988--1347057 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 36
1346978 ACCTAATTCA
* *
1346988 AATAATTATTATAATTTCTCTCTCTATACATATATG
1 AATAATTATTATAATGTCTCTCTATATACATATATG
* *
1347024 AATAATTA-TATAATGTCTCTTTATATATATATAT
1 AATAATTATTATAATGTCTCTCTATATACATATAT
1347058 ATATTATTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 22 0.73
36 8 0.27
ACGTcount: A:0.39, C:0.10, G:0.03, T:0.49
Consensus pattern (36 bp):
AATAATTATTATAATGTCTCTCTATATACATATATG
Found at i:1352504 original size:23 final size:23
Alignment explanation
Indices: 1352486--1352545 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
1352476 CTCGTATAAA
1352486 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
1352509 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
1352532 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
1352546 ATATAATGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.32, G:0.27, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:1353144 original size:13 final size:12
Alignment explanation
Indices: 1353126--1353158 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
1353116 TAGCTTAGTC
1353126 TTTCTTTCTTTCT
1 TTTCTTTCTTT-T
1353139 TTTCTTTCTTTT
1 TTTCTTTCTTTT
1353151 TTT-TTTCT
1 TTTCTTTCT
1353159 CATGGGGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.25
12 4 0.20
13 11 0.55
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTCTTTCTTTT
Found at i:1353146 original size:17 final size:15
Alignment explanation
Indices: 1353124--1353158 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
1353114 TATAGCTTAG
1353124 TCTTTCTTTCTTTCTTT
1 TCTTTCTTT-TTT-TTT
1353141 TCTTTCTTTTTTTTT
1 TCTTTCTTTTTTTTT
1353156 TCT
1 TCT
1353159 CATGGGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 3 0.17
17 9 0.50
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TCTTTCTTTTTTTTT
Found at i:1353271 original size:66 final size:66
Alignment explanation
Indices: 1353162--1353311 Score: 264
Period size: 66 Copynumber: 2.3 Consensus size: 66
1353152 TTTTTCTCAT
* *
1353162 GGGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAATTCATATTCGTT
1 GGGGGTATCGGTT-CCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAAATCATATTCGTT
1353227 GA
65 GA
*
1353229 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATCATATTCGTTG
1 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAAATCATATTCGTTG
1353294 A
66 A
1353295 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
1353312 TTGAATGGGT
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
66 68 0.85
67 12 0.15
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.29
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAAATCATATTCGTTG
A
Found at i:1360055 original size:19 final size:20
Alignment explanation
Indices: 1360018--1360055 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1360008 TTTTTTCTCA
*
1360018 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
1360038 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
1360056 ACTAGCATTC
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:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:1360127 original size:66 final size:66
Alignment explanation
Indices: 1360019--1360167 Score: 271
Period size: 66 Copynumber: 2.3 Consensus size: 66
1360009 TTTTTCTCAT
* *
1360019 GGGGGAATCGGTTCCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAATTCATATTCGTTG
1 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAAATCATATTCGTTG
1360084 A
66 A
*
1360085 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATCATATTCGTTG
1 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAAATCATATTCGTTG
1360150 A
66 A
1360151 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
1360168 TTGAATGGGT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 80 1.00
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.29
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAAATCATATTCGTTG
A
Found at i:1369795 original size:47 final size:44
Alignment explanation
Indices: 1369743--1369876 Score: 150
Period size: 40 Copynumber: 3.0 Consensus size: 44
1369733 ACCACAACAG
1369743 CAGCACCCACATCACCAGCCATCCGTCATATGGCTCAATGGGAGAGT
1 CAGCACCCACATC-CCAGCCAT--GTCATATGGCTCAATGGGAGAGT
* *
1369790 CAGCACTCACAT--C-TCCAT-TCATATGGCTCAATGGGAGAGT
1 CAGCACCCACATCCCAGCCATGTCATATGGCTCAATGGGAGAGT
* *
1369830 CAGCACCCACATCTCCAGTCATTGGTCATATGGCTCAAAGGGAGAGT
1 CAGCACCCACATC-CCAGCCA-T-GTCATATGGCTCAATGGGAGAGT
1369877 GCTAGACTGC
Statistics
Matches: 74, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
40 33 0.45
43 5 0.07
44 3 0.04
45 1 0.01
47 32 0.43
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (44 bp):
CAGCACCCACATCCCAGCCATGTCATATGGCTCAATGGGAGAGT
Found at i:1369823 original size:40 final size:40
Alignment explanation
Indices: 1369767--1369851 Score: 152
Period size: 40 Copynumber: 2.1 Consensus size: 40
1369757 CCAGCCATCC
*
1369767 GTCATATGGCTCAATGGGAGAGTCAGCACTCACATCTCCA
1 GTCATATGGCTCAATGGGAGAGTCAGCACCCACATCTCCA
*
1369807 TTCATATGGCTCAATGGGAGAGTCAGCACCCACATCTCCA
1 GTCATATGGCTCAATGGGAGAGTCAGCACCCACATCTCCA
1369847 GTCAT
1 GTCAT
1369852 TGGTCATATG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
GTCATATGGCTCAATGGGAGAGTCAGCACCCACATCTCCA
Found at i:1389797 original size:17 final size:18
Alignment explanation
Indices: 1389754--1389794 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1389744 AAATTATATT
1389754 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
1389771 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
1389789 ATTAAA
1 AGTAAA
1389795 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:1391706 original size:18 final size:18
Alignment explanation
Indices: 1391679--1391714 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1391669 TTATTCTGAT
* *
1391679 TATTTTATTTTATATTGA
1 TATTTCATTTTAAATTGA
1391697 TATTTCATTTTAAATTGA
1 TATTTCATTTTAAATTGA
1391715 AAAACAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.61
Consensus pattern (18 bp):
TATTTCATTTTAAATTGA
Found at i:1392156 original size:13 final size:14
Alignment explanation
Indices: 1392138--1392169 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
1392128 GAAAGTTTAT
1392138 TTTTTTTCAATTC-
1 TTTTTTTCAATTCA
1392151 TTTTTTTCAATTCA
1 TTTTTTTCAATTCA
1392165 TTTTT
1 TTTTT
1392170 AGTCATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTTTCAATTCA
Found at i:1394794 original size:78 final size:77
Alignment explanation
Indices: 1394665--1394873 Score: 233
Period size: 78 Copynumber: 2.7 Consensus size: 77
1394655 CACATCAATA
* *
1394665 TTTCATCACCCACATTAACGGTTATTAATAGAGAGTAACCAATTTGTTATAAATT-ATTA-TCGT
1 TTTCATCACCCACATTAACGATTATTAACAGAGAGTAACCAATTTGTTATAAATTGA-TAGT-GT
*
1394728 TAGTGACCGATTTG
64 CAGTGACCGATTTG
*** * * *
1394742 TTTTCATCACCCTTGTTAACGATTATTAACAGATAGTGACCGATTTGTTATAAATTGATAGTGTC
1 -TTTCATCACCCACATTAACGATTATTAACAGAGAGTAACCAATTTGTTATAAATTGATAGTGTC
1394807 AGTGACCGATTTG
65 AGTGACCGATTTG
* * ** * *
1394820 TTTCTATCACCCATAATAACGCCTATTAACAAAGAGTAACTAATTTGTTATAAA
1 TTTC-ATCACCCACATTAACGATTATTAACAGAGAGTAACCAATTTGTTATAAA
1394874 CCGATAACGT
Statistics
Matches: 109, Mismatches: 19, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
77 4 0.04
78 103 0.94
79 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (77 bp):
TTTCATCACCCACATTAACGATTATTAACAGAGAGTAACCAATTTGTTATAAATTGATAGTGTCA
GTGACCGATTTG
Found at i:1395042 original size:15 final size:15
Alignment explanation
Indices: 1395022--1395050 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1395012 AAGATGTTAT
1395022 TTTTCAAAATTAATA
1 TTTTCAAAATTAATA
1395037 TTTTCAAAATTAAT
1 TTTTCAAAATTAAT
1395051 TTAAAATATA
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:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTTCAAAATTAATA
Found at i:1395877 original size:24 final size:26
Alignment explanation
Indices: 1395843--1395890 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
1395833 ATGGTTATTT
1395843 AAAAATAATAATA-A-TTTATTTTTAA
1 AAAAATAATAA-AGATTTTATTTTTAA
1395868 AAAAAT-ATAAAGATTTTATTTTT
1 AAAAATAATAAAGATTTTATTTTT
1395891 TTATAAGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 1 0.05
24 5 0.24
25 15 0.71
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
AAAAATAATAAAGATTTTATTTTTAA
Found at i:1396502 original size:18 final size:18
Alignment explanation
Indices: 1396479--1396513 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1396469 AGATAAAAAC
*
1396479 AAAAAATATATCACAAAG
1 AAAAAAAATATCACAAAG
*
1396497 AAAAAAAATATTACAAA
1 AAAAAAAATATCACAAA
1396514 CATAATTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.09, G:0.03, T:0.17
Consensus pattern (18 bp):
AAAAAAAATATCACAAAG
Found at i:1401821 original size:61 final size:61
Alignment explanation
Indices: 1401744--1401888 Score: 202
Period size: 61 Copynumber: 2.4 Consensus size: 61
1401734 AGAACGCTTC
* * *
1401744 CATTTTGGTCACCCAACTTTTGAAACTTGA-ACTACAATCATCTAACTTTTACGGGTGCTCG
1 CATTTTGGTCACCCAACTTTTAAAACTT-ACACTACAATCATCTAACTTTTACGGGTACTCA
* * * * *
1401805 TATTTTGGTCATCCAACTTTTAAAACTTACACTACAGTCATCTAACTTTTAGGGGTACTTA
1 CATTTTGGTCACCCAACTTTTAAAACTTACACTACAATCATCTAACTTTTACGGGTACTCA
1401866 CATTTTGGTCACCCAACTTTTAA
1 CATTTTGGTCACCCAACTTTTAA
1401889 TCATTTACAG
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
60 1 0.01
61 72 0.99
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (61 bp):
CATTTTGGTCACCCAACTTTTAAAACTTACACTACAATCATCTAACTTTTACGGGTACTCA
Found at i:1417911 original size:8 final size:7
Alignment explanation
Indices: 1417898--1417960 Score: 71
Period size: 7 Copynumber: 9.4 Consensus size: 7
1417888 AATAAGAAGC
1417898 AAAAAAGG
1 AAAAAA-G
1417906 AAAAAAG
1 AAAAAAG
1417913 --AAAAG
1 AAAAAAG
1417918 AAAAAAG
1 AAAAAAG
*
1417925 AAAAAAC
1 AAAAAAG
1417932 AAAAAA-
1 AAAAAAG
1417938 AAAAAA-
1 AAAAAAG
*
1417944 ACAAAAG
1 AAAAAAG
1417951 AAAAAAG
1 AAAAAAG
1417958 AAA
1 AAA
1417961 GAACAAAGAT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
5 5 0.10
6 11 0.22
7 27 0.55
8 6 0.12
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:1417923 original size:14 final size:13
Alignment explanation
Indices: 1417906--1417956 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
1417896 GCAAAAAAGG
* *
1417906 AAAAAAGAAAAGA
1 AAAAAAAAAAACA
1417919 AAAAAGAAAAAACAA
1 AAAAA-AAAAAAC-A
1417934 AAAAAAAAAAACA
1 AAAAAAAAAAACA
*
1417947 AAAGAAAAAA
1 AAAAAAAAAA
1417957 GAAAGAACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
13 15 0.45
14 12 0.36
15 6 0.18
ACGTcount: A:0.88, C:0.04, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAACA
Found at i:1417955 original size:19 final size:19
Alignment explanation
Indices: 1417898--1417967 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
1417888 AATAAGAAGC
*
1417898 AAAAAAGGAA-AAAAGAAA
1 AAAAAAAGAACAAAAGAAA
*
1417916 AGAAAAAAGAA-AAAACAAA
1 A-AAAAAAGAACAAAAGAAA
*
1417935 AAAAAAAAAACAAAAGAAA
1 AAAAAAAGAACAAAAGAAA
*
1417954 AAAGAAAGAACAAA
1 AAAAAAAGAACAAA
1417968 GATCAAAAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
18 9 0.20
19 35 0.80
ACGTcount: A:0.84, C:0.04, G:0.11, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAACAAAAGAAA
Found at i:1417966 original size:33 final size:34
Alignment explanation
Indices: 1417891--1417967 Score: 111
Period size: 33 Copynumber: 2.3 Consensus size: 34
1417881 AATATTCAAT
* *
1417891 AAGAAGCAAAAAAGGAAAAAAGAAAAGAAAAAAGA
1 AAGAA-CAAAAAAGAAAAAAACAAAAGAAAAAAGA
*
1417926 AAAAACAAAAAA-AAAAAAACAAAAGAAAAAAGA
1 AAGAACAAAAAAGAAAAAAACAAAAGAAAAAAGA
1417959 AAGAACAAA
1 AAGAACAAA
1417968 GATCAAAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
33 27 0.71
34 7 0.18
35 4 0.11
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (34 bp):
AAGAACAAAAAAGAAAAAAACAAAAGAAAAAAGA
Found at i:1417974 original size:26 final size:27
Alignment explanation
Indices: 1417925--1417981 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 27
1417915 AAGAAAAAAG
1417925 AAAAAACAAAAAAAAAAAAAC-AAAAG
1 AAAAAACAAAAAAAAAAAAACAAAAAG
* * * * *
1417951 AAAAAAGAAAGAACAAAGATCAAAAAG
1 AAAAAACAAAAAAAAAAAAACAAAAAG
1417978 AAAA
1 AAAA
1417982 GGGGACAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 16 0.64
27 9 0.36
ACGTcount: A:0.82, C:0.07, G:0.09, T:0.02
Consensus pattern (27 bp):
AAAAAACAAAAAAAAAAAAACAAAAAG
Found at i:1418616 original size:22 final size:22
Alignment explanation
Indices: 1418588--1418638 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1418578 CCCCATCAAT
1418588 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
1418610 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
1418632 CCTTTGA
1 CCTTTGA
1418639 CAAAACACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:1419619 original size:37 final size:37
Alignment explanation
Indices: 1419576--1419855 Score: 147
Period size: 37 Copynumber: 8.0 Consensus size: 37
1419566 CCTTGAAATG
*
1419576 AATTTTGTCTCTTTTGAGACAGTTTCTCTTGAAACAA
1 AATTTTGTCTCCTTTGAGACAGTTTCTCTTGAAACAA
1419613 AATTTTGTCTCCTTTGAGACAGTTTCTCTTGAAACATA
1 AATTTTGTCTCCTTTGAGACAGTTTCTCTTGAAACA-A
* ** * * * **
1419651 AA--------CATTAAAAACA-CTTCCCTTGAAA-TG
1 AATTTTGTCTCCTTTGAGACAGTTTCTCTTGAAACAA
*
1419678 AATTTTGTCT-CTCTTGAGACCGTTTCTCTTGAAACAA
1 AATTTTGTCTCCT-TTGAGACAGTTTCTCTTGAAACAA
* *
1419715 AATTTTGTCTCCCTTGAGACAGTTTTCTCTTGAAGCATA
1 AATTTTGTCTCCTTTGAGACAG-TTTCTCTTGAAACA-A
* * **
1419754 AA---------CATTGAAAACA-TTTCTCTTGAAA-TG
1 AATTTTGTCTCCTTTG-AGACAGTTTCTCTTGAAACAA
* *
1419781 AATTTCGTCT-CTCTTGAGACAGTTTCCCTTGAAACAA
1 AATTTTGTCTCCT-TTGAGACAGTTTCTCTTGAAACAA
* *
1419818 AATTTTATCTCCATTGAGACAGTTTTTCTCTTGAAACA
1 AATTTTGTCTCCTTTGAGACAG--TTTCTCTTGAAACA
1419856 TGAACGTTGA
Statistics
Matches: 178, Mismatches: 35, Indels: 58
0.66 0.13 0.21
Matches are distributed among these distances:
27 4 0.02
29 21 0.12
30 11 0.06
31 4 0.02
34 1 0.01
35 9 0.05
36 24 0.13
37 70 0.39
38 18 0.10
39 16 0.09
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (37 bp):
AATTTTGTCTCCTTTGAGACAGTTTCTCTTGAAACAA
Found at i:1419695 original size:102 final size:103
Alignment explanation
Indices: 1419514--1419929 Score: 647
Period size: 102 Copynumber: 4.0 Consensus size: 103
1419504 CGTGCTCACC
1419514 TTTGTCTCCCTTGAGACAG-TTTCTCTTGAAACATAAACATTAAAAACACTTCCCTTGAAATGAA
1 TTTGTCTCCCTTGAGACAGTTTTCTCTTGAAACATAAACATTAAAAACACTTCCCTTGAAATGAA
* *
1419578 TTTTGTCTCTTTTGAGACAGTTTCTCTTGAAACAAAAT
66 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
*
1419616 TTTGTCTCCTTTGAGACAG-TTTCTCTTGAAACATAAACATTAAAAACACTTCCCTTGAAATGAA
1 TTTGTCTCCCTTGAGACAGTTTTCTCTTGAAACATAAACATTAAAAACACTTCCCTTGAAATGAA
* *
1419680 TTTTGTCTCTCTTGAGACCGTTTCTCTTGAAACAAAAT
66 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
* * * *
1419718 TTTGTCTCCCTTGAGACAGTTTTCTCTTGAAGCATAAACATTGAAAACATTTCTCTTGAAATGAA
1 TTTGTCTCCCTTGAGACAGTTTTCTCTTGAAACATAAACATTAAAAACACTTCCCTTGAAATGAA
*
1419783 TTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
66 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
* * * * * *
1419821 TTTATCTCCATTGAGACAGTTTTTCTCTTGAAACATGAACGTTGAAAACATTTCCCTTGAAATGA
1 TTTGTCTCCCTTGAGACAG-TTTTCTCTTGAAACATAAACATTAAAAACACTTCCCTTGAAATGA
*
1419886 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAAT
65 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
1419925 CTTTG
1 -TTTG
1419930 AATATGTTTT
Statistics
Matches: 291, Mismatches: 20, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
102 117 0.40
103 93 0.32
104 78 0.27
105 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.38
Consensus pattern (103 bp):
TTTGTCTCCCTTGAGACAGTTTTCTCTTGAAACATAAACATTAAAAACACTTCCCTTGAAATGAA
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
Found at i:1420102 original size:36 final size:34
Alignment explanation
Indices: 1420052--1420140 Score: 126
Period size: 34 Copynumber: 2.6 Consensus size: 34
1420042 TTCTTGAAAC
1420052 AAAAT-TTTCTCTTGAAACATAAAAAGAAACCTCTG
1 AAAATGTTTCTCTTGAAACA-AAAAA-AAACCTCTG
* * *
1420087 AAATTGTTTCACTTGAAACAAAAAAAAACCTTTG
1 AAAATGTTTCTCTTGAAACAAAAAAAAACCTCTG
1420121 AAAATGTTTCTCTTGAAACA
1 AAAATGTTTCTCTTGAAACA
1420141 CAAAGCCTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
34 26 0.54
35 9 0.19
36 13 0.27
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.30
Consensus pattern (34 bp):
AAAATGTTTCTCTTGAAACAAAAAAAAACCTCTG
Found at i:1433438 original size:15 final size:15
Alignment explanation
Indices: 1433403--1433436 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1433393 TAATTTCAGT
*
1433403 AATTTAAATTTATGC
1 AATTTAAATTTATAC
1433418 AATTTAAATTT-TAC
1 AATTTAAATTTATAC
1433432 AATTT
1 AATTT
1433437 TATTTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (15 bp):
AATTTAAATTTATAC
Found at i:1447486 original size:20 final size:20
Alignment explanation
Indices: 1447454--1447502 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1447444 TTCACGGAAT
*
1447454 GTAA-ATTATCAGTGGAAAC
1 GTAAGATTACCAGTGGAAAC
* *
1447473 GTAAGATTACCAGTGGGAAT
1 GTAAGATTACCAGTGGAAAC
1447493 GTAAGATTAC
1 GTAAGATTAC
1447503 TAAGGGAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (20 bp):
GTAAGATTACCAGTGGAAAC
Found at i:1447511 original size:19 final size:20
Alignment explanation
Indices: 1447449--1447511 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
1447439 TTTGATTCAC
* *
1447449 GGAATGTAA-ATTATCAGTG
1 GGAATGTAAGATTACCAGAG
* * *
1447468 GAAACGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGAG
*
1447488 GGAATGTAAGATTACTA-AG
1 GGAATGTAAGATTACCAGAG
1447507 GGAAT
1 GGAAT
1447512 AAGATTATTG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 13 0.36
20 23 0.64
ACGTcount: A:0.40, C:0.08, G:0.27, T:0.25
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGAG
Found at i:1451767 original size:18 final size:21
Alignment explanation
Indices: 1451746--1451784 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
1451736 GTAAGGTAAA
1451746 ATTT-TTTTAT-TAT-ATTAT
1 ATTTATTTTATATATAATTAT
1451764 ATTTATTTTATATATAATTAT
1 ATTTATTTTATATATAATTAT
1451785 TTGAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 6 0.33
20 3 0.17
21 5 0.28
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTTATTTTATATATAATTAT
Found at i:1451924 original size:19 final size:19
Alignment explanation
Indices: 1451900--1451936 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1451890 AAATTATATT
1451900 TTTATATTATTTTGAAATG
1 TTTATATTATTTTGAAATG
1451919 TTTATATTATTTTGAAAT
1 TTTATATTATTTTGAAAT
1451937 TTTTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.59
Consensus pattern (19 bp):
TTTATATTATTTTGAAATG
Found at i:1458789 original size:34 final size:34
Alignment explanation
Indices: 1458709--1458793 Score: 86
Period size: 34 Copynumber: 2.5 Consensus size: 34
1458699 GCCTTTCATT
1458709 TTATAACTACAA-AAAA-AATAAAAAGTTAATATA
1 TTATAA-TACAATAAAATAATAAAAAGTTAATATA
* * ** *
1458742 ATAAAATTTAATAAAATAATAAAATA-TTAATTTA
1 TTATAATACAATAAAATAATAAAA-AGTTAATATA
1458776 TTATAATACAATAAAATA
1 TTATAATACAATAAAATA
1458794 TTTTTACATT
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
32 3 0.08
33 8 0.20
34 28 0.70
35 1 0.03
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (34 bp):
TTATAATACAATAAAATAATAAAAAGTTAATATA
Found at i:1466488 original size:23 final size:23
Alignment explanation
Indices: 1466462--1466509 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1466452 ATAAAGTACA
*
1466462 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
1466485 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1466508 AT
1 AT
1466510 TTACGTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1467166 original size:335 final size:335
Alignment explanation
Indices: 1466549--1467191 Score: 1200
Period size: 335 Copynumber: 1.9 Consensus size: 335
1466539 TTATACCGAT
1466549 AGCATTACAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAAGA
1 AGCATTACAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAAGA
*
1466614 TCGATATTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTC
66 TCGATATTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAACAGTGTTTCATGTTTTC
**
1466679 CACCTACAATATTAATTTAATAATTTCATTTGTACAAAAAATAATTTGATTGTTTTGATATTTTA
131 CACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATAATTTGATTGTTTTGATATTTTA
1466744 TAAAATATTATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATT
196 TAAAATATTATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATT
1466809 AGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTT
261 AGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTT
1466874 TTCCACAGTG
326 TTCCACAGTG
* *
1466884 AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
1 AGCATTACAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAAGA
1466949 TCGATACTTT-TTTTAAAAGTTATGTAATTTATGTTTCAA-TTTTTTTAACAGTGTTTCATGTTT
66 TCGATA-TTTCTTTT-AAAGTTATGTAATTTATGTTTCAATTTTTTTTAACAGTGTTTCATGTTT
*
1467012 TCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTT
129 TCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATAATTTGATTGTTTTGATATTT
1467077 TATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCA
194 TATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCA
1467142 TTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGAT
259 TTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGAT
1467192 GTATATACCT
Statistics
Matches: 300, Mismatches: 6, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
335 273 0.91
336 27 0.09
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (335 bp):
AGCATTACAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAAGA
TCGATATTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAACAGTGTTTCATGTTTTC
CACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATAATTTGATTGTTTTGATATTTTA
TAAAATATTATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATT
AGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTT
TTCCACAGTG
Found at i:1467247 original size:25 final size:25
Alignment explanation
Indices: 1467190--1467255 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
1467180 CACTCAAAAG
*
1467190 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
1467215 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
1467240 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
1467256 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:1469184 original size:183 final size:183
Alignment explanation
Indices: 1468871--1469945 Score: 1898
Period size: 183 Copynumber: 5.9 Consensus size: 183
1468861 CTTAAAATTA
* *
1468871 TCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAA
1 TCGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAA
*
1468936 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAATCGGTATATTTATACCGGT
66 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGT
*
1469001 TATATTACAAAATTATCTATTATATTATAAATCTGGGTTCCGATGTGTAAATG
131 TATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATG
1469054 TCGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAA
1 TCGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAA
* * * *
1469119 TATTATAAAGTGTTGAGATAGGTTGTAGACCTATTCGCGCATAAAACCGGTTTATTTATACCGGT
66 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGT
1469184 TATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATG
131 TATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATG
*
1469237 TCGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGAAACAA
1 TCGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAA
*
1469302 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCACATAAAACCGGTATATTTATACCGGT
66 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGT
* * *
1469367 TATATTATAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATG
131 TATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATG
*
1469420 TCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAA
1 TCGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAA
*
1469485 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGAT
66 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGT
1469550 TATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATG
131 TATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATG
1469603 TCGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAA
1 TCGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAA
* * * * * *
1469668 TATTATAAAGTGTTGAGATAGGTTGTAGACATATTCGCGCATAAAACCGATATATTTATACCAGT
66 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGT
1469733 TATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATG
131 TATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATG
1469786 TCGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAA
1 TCGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAA
* *
1469851 TATTAAAAAGTGTGGATATAGGTTGTAGACCTATTCACGCATAAAACCGGTATATTTATACCGGT
66 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGT
* * * **
1469916 TATATTGCAAATTTACCTATTTTATTATAA
131 TATATTACAAAATTATCTATTACATTATAA
1469946 TATGTTGAAA
Statistics
Matches: 848, Mismatches: 44, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
183 848 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (183 bp):
TCGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAA
TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGT
TATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATG
Found at i:1471375 original size:3 final size:3
Alignment explanation
Indices: 1471367--1471420 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
1471357 ACTTGTTTGG
* * *
1471367 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC ATC GTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
*
1471415 TTC ATC
1 ATC ATC
1471421 GTCAGCTTCA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.26, C:0.33, G:0.04, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:1471384 original size:12 final size:12
Alignment explanation
Indices: 1471367--1471424 Score: 80
Period size: 12 Copynumber: 4.8 Consensus size: 12
1471357 ACTTGTTTGG
* *
1471367 ATCATCATCTTC
1 ATCATCGTCATC
*
1471379 ATCATCATCATC
1 ATCATCGTCATC
1471391 ATCATCGTCATC
1 ATCATCGTCATC
1471403 ATCATCGTCATC
1 ATCATCGTCATC
*
1471415 TTCATCGTCA
1 ATCATCGTCA
1471425 GCTTCATCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.26, C:0.33, G:0.05, T:0.36
Consensus pattern (12 bp):
ATCATCGTCATC
Found at i:1471390 original size:18 final size:18
Alignment explanation
Indices: 1471367--1471435 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
1471357 ACTTGTTTGG
* *
1471367 ATCATCATCTTCATCATC
1 ATCATCATCATCTTCATC
*
1471385 ATCATCATCATCGTCATC
1 ATCATCATCATCTTCATC
*
1471403 ATCATCGTCATCTTCATC
1 ATCATCATCATCTTCATC
* * *
1471421 GTCAGCTTCATCTTC
1 ATCATCATCATCTTC
1471436 TGTGACCGCT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.38
Consensus pattern (18 bp):
ATCATCATCATCTTCATC
Found at i:1471429 original size:12 final size:12
Alignment explanation
Indices: 1471380--1471432 Score: 70
Period size: 12 Copynumber: 4.4 Consensus size: 12
1471370 ATCATCTTCA
* *
1471380 TCATCATCATCA
1 TCATCGTCATCT
*
1471392 TCATCGTCATCA
1 TCATCGTCATCT
1471404 TCATCGTCATCT
1 TCATCGTCATCT
*
1471416 TCATCGTCAGCT
1 TCATCGTCATCT
1471428 TCATC
1 TCATC
1471433 TTCTGTGACC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.23, C:0.34, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:1473226 original size:15 final size:15
Alignment explanation
Indices: 1473189--1473226 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1473179 ATATTACATT
*
1473189 ATACTTTTGGGTTCG
1 ATACTTTTGGGATCG
1473204 ATGA-TTTTGGGATCG
1 AT-ACTTTTGGGATCG
1473219 ATACTTTT
1 ATACTTTT
1473227 TATATATGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
14 1 0.05
15 18 0.90
16 1 0.05
ACGTcount: A:0.18, C:0.11, G:0.24, T:0.47
Consensus pattern (15 bp):
ATACTTTTGGGATCG
Found at i:1473228 original size:199 final size:199
Alignment explanation
Indices: 1472889--1474258 Score: 2589
Period size: 199 Copynumber: 6.9 Consensus size: 199
1472879 TTTAAATTAG
*
1472889 TATCGACACAAACTATATTAGTGTCGACACATT-TTTAGACATATTCTCTCATAAAACCGGTAAA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1472953 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1473018 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
1473083 CAAA
196 CAAA
1473087 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1473152 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
1473217 CGATACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
1473282 CAAA
196 CAAA
***
1473286 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1473351 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
1473416 CGACAATTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
1473481 CAAA
196 CAAA
1473485 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1473550 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1473615 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
1473680 CAAA
196 CAAA
***
1473684 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
1473749 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAATTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1473814 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
1473879 CAAA
196 CAAA
***
1473883 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1473948 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
1474013 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCATGTTTTCCATTCATTCTAGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
1474078 CAAA
196 CAAA
1474082 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1474147 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1474212 CGACACTTTGTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
131 CGACACTTT-TTATATATGGATCGACACTTTATGGGTGCACCCTGTT
1474259 GGCCATATTG
Statistics
Matches: 1148, Mismatches: 22, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
198 33 0.03
199 1079 0.94
200 36 0.03
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.36
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
CAAA
Found at i:1474423 original size:19 final size:19
Alignment explanation
Indices: 1474377--1474425 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1474367 TTATATTCAC
*
1474377 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
1474396 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1474415 ATACAAAATTA
1 ATACAAAATTA
1474426 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1476258 original size:33 final size:33
Alignment explanation
Indices: 1476221--1476286 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1476211 CATCTTAATA
* *
1476221 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCATTCACCACT
* *
1476254 TCACCCCTCAACACCTCTACTTCATTCACCACT
1 TCACCCCTCAACACCCCAACTTCATTCACCACT
1476287 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.48, G:0.00, T:0.27
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCATTCACCACT
Found at i:1476360 original size:21 final size:21
Alignment explanation
Indices: 1476320--1476384 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
1476310 CCCCTTATGC
* *
1476320 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
1476341 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
1476362 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
1476383 CT
1 CT
1476385 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:1478629 original size:17 final size:18
Alignment explanation
Indices: 1478607--1478649 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
1478597 ATATATCCGG
1478607 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
1478624 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
1478644 TATCAT
1 TATCAT
1478650 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:1478667 original size:20 final size:19
Alignment explanation
Indices: 1478612--1478658 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1478602 TCCGGTATCA
1478612 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
1478631 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
1478652 TTTTACC
1 TTTTACC
1478659 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:1478806 original size:20 final size:20
Alignment explanation
Indices: 1478780--1478825 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
1478770 CACTTTTAAA
1478780 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
1478799 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
1478820 TTTACC
1 TTTACC
1478826 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:1478923 original size:21 final size:20
Alignment explanation
Indices: 1478899--1478937 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1478889 GCTTTTAAAG
1478899 TTATGTAATTTATGTTTCAAT
1 TTATGTAA-TTATGTTTCAAT
* *
1478920 TTATTTAATTGTGTTTCA
1 TTATGTAATTATGTTTCA
1478938 TGTTTTCCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.26, C:0.05, G:0.10, T:0.59
Consensus pattern (20 bp):
TTATGTAATTATGTTTCAAT
Found at i:1480408 original size:24 final size:25
Alignment explanation
Indices: 1480381--1480433 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
1480371 ACCTCACTCT
*
1480381 TAATTA-GTATTAAAAATTATAATA
1 TAATTATGTATTAAAAAATATAATA
*
1480405 TAATTATTTATTAAAAAATATAATA
1 TAATTATGTATTAAAAAATATAATA
1480430 -AATT
1 TAATT
1480434 TAATAACTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
TAATTATGTATTAAAAAATATAATA
Found at i:1483858 original size:6 final size:6
Alignment explanation
Indices: 1483847--1483989 Score: 286
Period size: 6 Copynumber: 23.8 Consensus size: 6
1483837 TTATTACTTA
1483847 TAATTG TAATTG TAATTG TAATTG TAATTG TAATTG TAATTG TAATTG
1 TAATTG TAATTG TAATTG TAATTG TAATTG TAATTG TAATTG TAATTG
1483895 TAATTG TAATTG TAATTG TAATTG TAATTG TAATTG TAATTG TAATTG
1 TAATTG TAATTG TAATTG TAATTG TAATTG TAATTG TAATTG TAATTG
1483943 TAATTG TAATTG TAATTG TAATTG TAATTG TAATTG TAATTG TAATT
1 TAATTG TAATTG TAATTG TAATTG TAATTG TAATTG TAATTG TAATT
1483990 ATAAAGATGT
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 137 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
TAATTG
Found at i:1488439 original size:46 final size:46
Alignment explanation
Indices: 1488368--1488459 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
1488358 GATTTAGAAG
* *
1488368 TTAGTTTAGATTTAAACTTGTTTCCATTGTTGTCGTTTCTGCTGGT
1 TTAGTTTAGATTTAAACTTGCTTCCATTGCTGTCGTTTCTGCTGGT
1488414 TTAGTTTAGATTTAAACTTGCTTCCATTGCTGTCGTTTCTGCTGGT
1 TTAGTTTAGATTTAAACTTGCTTCCATTGCTGTCGTTTCTGCTGGT
1488460 GTTTTTAAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.15, C:0.15, G:0.20, T:0.50
Consensus pattern (46 bp):
TTAGTTTAGATTTAAACTTGCTTCCATTGCTGTCGTTTCTGCTGGT
Found at i:1495219 original size:14 final size:14
Alignment explanation
Indices: 1495200--1495230 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1495190 CATACATTTT
*
1495200 AAAAATTATAAACG
1 AAAAATTACAAACG
1495214 AAAAATTACAAACG
1 AAAAATTACAAACG
1495228 AAA
1 AAA
1495231 GAAGAGAAAT
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:0.68, C:0.10, G:0.06, T:0.16
Consensus pattern (14 bp):
AAAAATTACAAACG
Found at i:1495858 original size:15 final size:15
Alignment explanation
Indices: 1495835--1495872 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
1495825 ATATTTTTTT
1495835 TATAA-TTATTAATA
1 TATAATTTATTAATA
*
1495849 TATAATTTATTAATT
1 TATAATTTATTAATA
1495864 TA-AATTTAT
1 TATAATTTAT
1495873 ATAAAGATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATAATTTATTAATA
Found at i:1504418 original size:55 final size:54
Alignment explanation
Indices: 1504360--1504860 Score: 336
Period size: 51 Copynumber: 9.6 Consensus size: 54
1504350 TGACGAGCAT
*
1504360 GCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTC-ATAAAACGTGTCT
1 GCTCCCTATTCCTTCAGAG-AGTATAAGACTCGAACAATCTTCAAT-AAACG-GTCC
* * * * * *
1504415 GCTCTCTATTCATTCAGAGAGTATAATATTTGAACAATCTTTAATAAACGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGGTCC
* * *
1504469 GCTCTCTCTTCCTTCAGAGAGTAT-AGAACTCGAAAAATCTTCAATAAACAGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAATAAAC-GGTCC
* * * ** *
1504524 GCTCCCTATTCTTTCAGGGAGTATAGGACT----CAATCTTCAACGAACTAGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAC-GGTCC
* * ** *
1504575 GCTCCCTATTCTTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAC-GGTCC
* * ** *
1504626 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAC-GGTCC
* * ** *
1504677 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAC-GGTCC
* * ** *
1504728 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAC-GGTCC
* * * *
1504779 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAATGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAC-GGTCC
* *
1504830 GCTCCCTATTCATTCAGAGAGTATAGGACTC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTC
1504861 AATCTTCAAC
Statistics
Matches: 412, Mismatches: 28, Indels: 15
0.91 0.06 0.03
Matches are distributed among these distances:
51 297 0.72
53 1 0.00
54 43 0.10
55 67 0.16
56 4 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.30
Consensus pattern (54 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGGTCC
Found at i:1504580 original size:51 final size:51
Alignment explanation
Indices: 1504465--1504874 Score: 667
Period size: 51 Copynumber: 8.0 Consensus size: 51
1504455 TTAATAAACG
* * * * ** **
1504465 GTCCGCTCTCTCTTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACAG
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTC----AATCTTCAACGAACTT
* * *
1504520 GTCCGCTCCCTATTCTTTCAGGGAGTATAGGACTCAATCTTCAACGAACTA
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
1504571 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1504622 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1504673 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1504724 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
1504775 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAATGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1504826 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAAC
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAAC
1504875 GAATTTGCTT
Statistics
Matches: 341, Mismatches: 14, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
51 311 0.91
55 30 0.09
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (51 bp):
GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
Found at i:1506206 original size:14 final size:14
Alignment explanation
Indices: 1506187--1506221 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1506177 TGAACCCTCC
*
1506187 TTTTATTTCTCTTT
1 TTTTATTTCTCTCT
*
1506201 TTTTATTTTTCTCT
1 TTTTATTTCTCTCT
1506215 TTTTATT
1 TTTTATT
1506222 CCTTTTTCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTATTTCTCTCT
Found at i:1506279 original size:17 final size:17
Alignment explanation
Indices: 1506253--1506292 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1506243 TCTTTTTTTC
1506253 TTTTCGTTTTCCATCATT
1 TTTTCGTTTTCC-TCATT
* *
1506271 TTTTCTTTTTTCTCATT
1 TTTTCGTTTTCCTCATT
1506288 TTTTC
1 TTTTC
1506293 TTCTTTTCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.07, C:0.20, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTTCGTTTTCCTCATT
Found at i:1506280 original size:18 final size:17
Alignment explanation
Indices: 1506253--1506313 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
1506243 TCTTTTTTTC
*
1506253 TTTTCGTTTTCCATCATT
1 TTTTCTTTTTCC-TCATT
*
1506271 TTTTCTTTTTTCTCATT
1 TTTTCTTTTTCCTCATT
* *
1506288 TTTTCTTCTTTTCTCTTT
1 TTTTCTT-TTTCCTCATT
1506306 TATTTCTT
1 T-TTTCTT
1506314 CTTCAAGCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
17 12 0.32
18 20 0.53
19 6 0.16
ACGTcount: A:0.07, C:0.20, G:0.02, T:0.72
Consensus pattern (17 bp):
TTTTCTTTTTCCTCATT
Found at i:1506311 original size:19 final size:18
Alignment explanation
Indices: 1506266--1506316 Score: 77
Period size: 17 Copynumber: 2.8 Consensus size: 18
1506256 TCGTTTTCCA
1506266 TCATTTTTTCTT-TTTTC
1 TCATTTTTTCTTCTTTTC
1506283 TCATTTTTTCTTCTTTTC
1 TCATTTTTTCTTCTTTTC
*
1506301 TCTTTTATTTCTTCTT
1 TCATTT-TTTCTTCTT
1506317 CAAGCAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 12 0.39
18 10 0.32
19 9 0.29
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.75
Consensus pattern (18 bp):
TCATTTTTTCTTCTTTTC
Found at i:1516015 original size:45 final size:46
Alignment explanation
Indices: 1515955--1516093 Score: 174
Period size: 45 Copynumber: 2.9 Consensus size: 46
1515945 ACAAAAGAAT
1515955 CCTAACCGCATGATATCTAATTCGCATGCTTGTTC-AAAAAATAAA
1 CCTAACCGCATGATATCTAATTCGCATGCTTGTTCAAAAAAATAAA
* *
1516000 CCTAACCGCATGATATCTAGTTCGCATGCATTTATTCAAAAAAAAAAATAAA
1 CCTAACCGCATGATATCTAATTCGCATGC--TTGTTC----AAAAAAATAAA
*
1516052 CCTAACCACATGATATCT-ATTCGCATGCTTGTTCGAAAAAAA
1 CCTAACCGCATGATATCTAATTCGCATGCTTGTTC-AAAAAAA
1516094 AATGAATCAA
Statistics
Matches: 81, Mismatches: 6, Indels: 13
0.81 0.06 0.13
Matches are distributed among these distances:
45 28 0.35
46 7 0.09
47 5 0.06
49 5 0.06
51 9 0.11
52 27 0.33
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.28
Consensus pattern (46 bp):
CCTAACCGCATGATATCTAATTCGCATGCTTGTTCAAAAAAATAAA
Found at i:1516064 original size:52 final size:49
Alignment explanation
Indices: 1515955--1516095 Score: 166
Period size: 52 Copynumber: 2.9 Consensus size: 49
1515945 ACAAAAGAAT
* *
1515955 CCTAACCGCATGATATCTAATTCGCATGCTTGTTC-----AAAAAATAAA
1 CCTAACCACATGATATCT-ATTCGCATGCTTATTCAAAAAAAAAAATAAA
*
1516000 CCTAACCGCATGATATCTAGTTCGCATGCATTTATTCAAAAAAAAAAATAAA
1 CCTAACCACATGATATCTA-TTCGCATGC--TTATTCAAAAAAAAAAATAAA
* *
1516052 CCTAACCACATGATATCTATTCGCATGCTTGTTCGAAAAAAAAA
1 CCTAACCACATGATATCTATTCGCATGCTTATTCAAAAAAAAAA
1516096 TGAATCAAAA
Statistics
Matches: 84, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
44 1 0.01
45 27 0.32
47 5 0.06
49 14 0.17
51 9 0.11
52 28 0.33
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (49 bp):
CCTAACCACATGATATCTATTCGCATGCTTATTCAAAAAAAAAAATAAA
Found at i:1521395 original size:3 final size:3
Alignment explanation
Indices: 1521387--1521430 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
1521377 TTAATAGAAT
* *
1521387 TAA TAA TAA TTAA TAA TAA TAA TAA TAAA TAA TTA TTA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
1521431 CATATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 31 0.84
4 6 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1521399 original size:10 final size:10
Alignment explanation
Indices: 1521384--1521419 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
1521374 TTTTTAATAG
1521384 AATTAATAAT
1 AATTAATAAT
1521394 AATTAATAAT
1 AATTAATAAT
1521404 AA-TAATAAT
1 AATTAATAAT
*
1521413 AAATAAT
1 AATTAAT
1521420 TATTATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AATTAATAAT
Found at i:1521401 original size:19 final size:17
Alignment explanation
Indices: 1521377--1521418 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
1521367 GAAAAAATTT
1521377 TTAATAGAATTAATAATAA
1 TTAATA-AA-TAATAATAA
1521396 TTAAT-AATAATAATAA
1 TTAATAAATAATAATAA
*
1521412 TAAATAA
1 TTAATAA
1521419 TTATTATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 13 0.62
17 3 0.14
19 5 0.24
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
TTAATAAATAATAATAA
Found at i:1521408 original size:16 final size:16
Alignment explanation
Indices: 1521387--1521430 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
1521377 TTAATAGAAT
*
1521387 TAATAATAATTAATAA
1 TAATAATAATAAATAA
1521403 TAATAATAATAAATAA
1 TAATAATAATAAATAA
* *
1521419 TTATTATAATAA
1 TAATAATAATAA
1521431 CATATATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATAATAATAAATAA
Found at i:1521419 original size:19 final size:19
Alignment explanation
Indices: 1521387--1521430 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1521377 TTAATAGAAT
*
1521387 TAATAATAATTAATAATAA
1 TAATAATAAATAATAATAA
* *
1521406 TAATAATAAATAATTATTA
1 TAATAATAAATAATAATAA
1521425 TAATAA
1 TAATAA
1521431 CATATATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAATAATAAATAATAATAA
Done.