Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008424.1 Hibiscus syriacus cultivar Beakdansim tig00111207_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: 4198033
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 16
Found at i:2328281 original size:17 final size:17
Alignment explanation
Indices: 2328256--2328288 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2328246 ATTTTCAAAG
*
2328256 TTTTCAGTTTTATTTTA
1 TTTTAAGTTTTATTTTA
2328273 TTTTAAGTTTTATTTT
1 TTTTAAGTTTTATTTT
2328289 TAAACATACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.03, G:0.06, T:0.73
Consensus pattern (17 bp):
TTTTAAGTTTTATTTTA
Found at i:2344365 original size:132 final size:132
Alignment explanation
Indices: 2344205--2345199 Score: 622
Period size: 132 Copynumber: 7.5 Consensus size: 132
2344195 TGAGATAAGA
* * * *
2344205 GAACAAGTAT-ACGTCGATTCAATGTTCCCTGAAGAATACTGGAATGAATCAATGTTTTCAGATC
1 GAACAAATATAAC-TCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAATGTTTTCAGATC
* * *
2344269 TGATCTACCCTGAAGAGCAGCAGGGTAGATCCCCTTTTTCTAGATTTGATCTTCCCTGAGGAGAA
65 TGATCTACCCTGAAGAGCAGCAGGGCAGATCCCCTTTTTCTAGATTTGATATTCCCTAAGGAGAA
2344334 GTG
130 GTG
* * * ** * * *
2344337 GAACAAGTTTAACTCGATTCAATCTTCCCTAAAGATTAGTGGAATAAATCAATGTTTCCATATCT
1 GAACAAATATAACTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAATGTTTTCAGATCT
* ** * * * * * * *
2344402 GATCTACCCTGAAGAG-TGGTGGAGCATAT-CCCTTTTTTTGGATTTGATCTTTCTTAAGGAGCA
66 GATCTACCCTGAAGAGCAGCAGG-GCAGATCCCCTTTTTCTAGATTTGATATTCCCTAAGGAGAA
2344465 GTG
130 GTG
* * * ** * *
2344468 GAACAAATCTATCTCGATTCAATCTTCTCTGAAGAACAGTGGGCTGAATCAACGTTTGCAGATCT
1 GAACAAATATAACTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAATGTTTTCAGATCT
* * * ** * * * * * * **
2344533 GATCTATCCTGAATAGCAACATAGCATATCCTCTTTTTCCATATTTGATATTCCGTAAGAATTAG
66 GATCTACCCTGAAGAGCAGCAGGGCAGATCCCCTTTTTCTAGATTTGATATTCCCTAAGGAGAAG
2344598 TG
131 TG
* * * * * * * * *
2344600 GAACAAATTTGACTCGATTTAATATTCCTTGAAGAGCAGTGCAATGAATCAACG-TTTCTAGATT
1 GAACAAATATAACTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAATGTTTTC-AGATC
** * * * *
2344664 TGATCTACCCTGAAGAGCAGCAAAGAAGATCCCATTTTT-TAAGATTTGATATTTCCTGAGGAGA
65 TGATCTACCCTGAAGAGCAGCAGGGCAGATCCCCTTTTTCT-AGATTTGATATTCCCTAAGGAGA
2344728 AGTG
129 AGTG
* * * * *
2344732 GAACAAATCTACCTCGATTCAATCTTCCCTAAAGAACAATGGAATGAATCAAT-ATTTCTAGATC
1 GAACAAATATAACTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAATGTTTTC-AGATC
* * * * * * * *
2344796 TAATCTACCCTGAAGAGAAG-TGGATCAGATCCCCTTTTTCTATATTTTATATTCCATAAGAAGA
65 TGATCTACCCTGAAGAGCAGCAGG-GCAGATCCCCTTTTTCTAGATTTGATATTCCCTAAGGAGA
2344860 AGTG
129 AGTG
* * * * * * *
2344864 GAACAAATAT-GCTTTGATT-ACATCTTCCCTGAAGAGCAGTTGAATGAATCAAAGTTTCCAGAC
1 GAACAAATATAAC-TCGATTCA-ATCTTCCCTGAAGAACAGTGGAATGAATCAATGTTTTCAGAT
* * * ** * * * * *
2344927 CTGATGTA-CCTGAAGAGCAGC-GGATCATATAACATCTTTTCCAGATTTGATCTT--ATATGAG
64 CTGATCTACCCTGAAGAGCAGCAGG-GCAGATCCCCT-TTTTCTAGATTTGATATTCCCTAAG-G
*
2344988 AAACAGTG
126 AGA-AGTG
* * * * * *
2344996 GAACAAATCT-GCATCGATTCAATCATTCCC-GAAGAATAGTAGAATTAATCAAT-ATTTCTAGA
1 GAACAAATATAAC-TCGATTCAATC-TTCCCTGAAGAACAGTGGAATGAATCAATGTTTTC-AGA
* * * * * * * ** * * *
2345058 TATGATCTACCCTAAAGAACAAC-GAAGCAAATCCCCTTTTTTCTATATAAGATCTTCCGTGAGG
63 TCTGATCTACCCTGAAGAGCAGCAG-GGCAGATCCCC-TTTTTCTAGATTTGATATTCCCTAAGG
*
2345122 AGCAGTG
126 AGAAGTG
* * * * * * * * * *
2345129 GTACAAATAT-ACTTTGAGTCAATCTACCCTGAAGATCAGTGGAGTGAATCAACGTTTCCAAATA
1 GAACAAATATAAC-TCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAATGTTTTCAGATC
2345193 TGATCTA
65 TGATCTA
2345200 TAAGAATCTC
Statistics
Matches: 659, Mismatches: 178, Indels: 51
0.74 0.20 0.06
Matches are distributed among these distances:
130 4 0.01
131 137 0.21
132 418 0.63
133 92 0.14
134 6 0.01
135 2 0.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (132 bp):
GAACAAATATAACTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAATGTTTTCAGATCT
GATCTACCCTGAAGAGCAGCAGGGCAGATCCCCTTTTTCTAGATTTGATATTCCCTAAGGAGAAG
TG
Found at i:2344835 original size:264 final size:262
Alignment explanation
Indices: 2344176--2345075 Score: 818
Period size: 264 Copynumber: 3.4 Consensus size: 262
2344166 TAATGTTTAC
* * * * * *
2344176 TTTTCAGATTTGATA-TTCTTGAGATAAG-AGAACAAGTATACGTCGATTCAATGTTCCCTGAAG
1 TTTTCAGATTTGATATTTCTTGAGAGAAGTGGAACAAATCTACCTCGATTCAATCTTCCCTGAAG
* * * * * *
2344239 AATACTGGAATGAATCAATGTTT-TCAGATCTGATCTACCCTGAAGAGCAGCAGGGT-AGATCCC
66 AACAGTGGAATGAATCAATATTTCT-AGATCTGATCTACCCTGAAGAGAAG-TGGATCAGATCCC
* * * * * * * *
2344302 CTTTTTCTAGATTTGATCTTCCCTGAGGAGAAGTGGAACAAGTTTAACTCGATTCAATCTTCCCT
129 CTTTTTCTATATTTGATATTCCATAAGAAGAAGTGGAACAAATTTGACTCGATTTAATCTTCCCT
* ** * * * ** *
2344367 AAAGATTAGTGGAATAAATCAATGTTTCCATATCTGATCTACCCTGAAGAGTGGTGGAGCATATC
194 GAAGAGCAGT-GAATGAATCAAAGTTTCCAGATCTGATCTACCCTGAAGAGCAGCGGAGCATATC
2344432 CC-TT
258 CCATT
** * * * * *
2344436 TTTTTGGATTTGATCTTTCTTAAGGAGCAGTGGAACAAATCTATCTCGATTCAATCTTCTCTGAA
1 TTTTCAGATTTGATATTTCTTGA-GAGAAGTGGAACAAATCTACCTCGATTCAATCTTCCCTGAA
** ** * * * * *
2344501 GAACAGTGGGCTGAATCAACGTTTGC-AGATCTGATCTATCCTGAATAGCAACAT--AGCATATC
65 GAACAGTGGAATGAATCAATATTT-CTAGATCTGATCTACCCTGAAGAG-AA-GTGGATCAGATC
* * * ** *
2344563 CTCTTTTTCCATATTTGATATTCCGTAAGAATTAGTGGAACAAATTTGACTCGATTTAATATTCC
127 CCCTTTTTCTATATTTGATATTCCATAAGAAGAAGTGGAACAAATTTGACTCGATTTAATCTTCC
* * * * ** * *
2344628 TTGAAGAGCAGTGCAATGAATCAACGTTTCTAGATTTGATCTACCCTGAAGAGCAGCAAAGAAGA
192 CTGAAGAGCAGTG-AATGAATCAAAGTTTCCAGATCTGATCTACCCTGAAGAGCAGCGGAGCATA
2344693 TCCCATT
256 TCCCATT
* * *
2344700 TTTTAAGATTTGATATTTCCTGAGGAGAAGTGGAACAAATCTACCTCGATTCAATCTTCCCTAAA
1 TTTTCAGATTTGATATTTCTTGA-GAGAAGTGGAACAAATCTACCTCGATTCAATCTTCCCTGAA
* *
2344765 GAACAATGGAATGAATCAATATTTCTAGATCTAATCTACCCTGAAGAGAAGTGGATCAGATCCCC
65 GAACAGTGGAATGAATCAATATTTCTAGATCTGATCTACCCTGAAGAGAAGTGGATCAGATCCCC
* * *
2344830 TTTTTCTATATTTTATATTCCATAAGAAGAAGTGGAACAAATATG-CTTTGA-TTACATCTTCCC
130 TTTTTCTATATTTGATATTCCATAAGAAGAAGTGGAACAAATTTGAC-TCGATTTA-ATCTTCCC
* * *
2344893 TGAAGAGCAGTTGAATGAATCAAAGTTTCCAGACCTGATGTA-CCTGAAGAGCAGCGGATCATAT
193 TGAAGAGCAG-TGAATGAATCAAAGTTTCCAGATCTGATCTACCCTGAAGAGCAGCGGAGCATAT
**
2344957 AACATCT
257 CCCAT-T
* * * * * *
2344964 TTTCCAGATTTGATCTTAT-ATGAGAAACAGTGGAACAAATCTGCATCGATTCAATCATTCCC-G
1 TTTTCAGATTTGATATT-TCTTGAGAGA-AGTGGAACAAATCTACCTCGATTCAATC-TTCCCTG
* * * * *
2345027 AAGAATAGTAGAATTAATCAATATTTCTAGATATGATCTACCCTAAAGA
63 AAGAACAGTGGAATGAATCAATATTTCTAGATCTGATCTACCCTGAAGA
2345076 ACAACGAAGC
Statistics
Matches: 508, Mismatches: 112, Indels: 36
0.77 0.17 0.05
Matches are distributed among these distances:
260 12 0.02
261 6 0.01
262 6 0.01
263 203 0.40
264 273 0.54
265 8 0.02
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (262 bp):
TTTTCAGATTTGATATTTCTTGAGAGAAGTGGAACAAATCTACCTCGATTCAATCTTCCCTGAAG
AACAGTGGAATGAATCAATATTTCTAGATCTGATCTACCCTGAAGAGAAGTGGATCAGATCCCCT
TTTTCTATATTTGATATTCCATAAGAAGAAGTGGAACAAATTTGACTCGATTTAATCTTCCCTGA
AGAGCAGTGAATGAATCAAAGTTTCCAGATCTGATCTACCCTGAAGAGCAGCGGAGCATATCCCA
TT
Found at i:2351398 original size:24 final size:24
Alignment explanation
Indices: 2351371--2351425 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
2351361 GATGAATTAA
2351371 GGATAAAGCCAATGCTTTTAGATC
1 GGATAAAGCCAATGCTTTTAGATC
2351395 GGATAAAGCCAATGCTTTTAGATC
1 GGATAAAGCCAATGCTTTTAGATC
2351419 GGATAAA
1 GGATAAA
2351426 AGAGCTACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (24 bp):
GGATAAAGCCAATGCTTTTAGATC
Found at i:2366517 original size:10 final size:10
Alignment explanation
Indices: 2366502--2366540 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
2366492 CTTGAAGAAG
2366502 AAAAAAAAGAA
1 AAAAAAAAG-A
2366513 AAAAAAAAGA
1 AAAAAAAAGA
**
2366523 GGAAAAAAGA
1 AAAAAAAAGA
2366533 AAAAAAAA
1 AAAAAAAA
2366541 ATGAATGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:2366527 original size:23 final size:21
Alignment explanation
Indices: 2366499--2366552 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 21
2366489 ATGCTTGAAG
2366499 AAGAA-AAAAAAGAAAAAAAA
1 AAGAAGAAAAAAGAAAAAAAA
*
2366519 AAGAGGAAAAAAGAAAAAAAA
1 AAGAAGAAAAAAGAAAAAAAA
2366540 AATGAATGAAAAA
1 AA-GAA-GAAAAA
2366553 TGATGAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 4 0.14
21 17 0.59
22 2 0.07
23 6 0.21
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (21 bp):
AAGAAGAAAAAAGAAAAAAAA
Found at i:2368359 original size:114 final size:113
Alignment explanation
Indices: 2368143--2368801 Score: 909
Period size: 114 Copynumber: 5.8 Consensus size: 113
2368133 ACAATTTTAG
* * **
2368143 GTAGAGTTCATAATGAGAAGAACTCATCTG-A-AA--AACAAGAAGTTCATAATGAGAAGAACAT
1 GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTT
*
2368204 GTTC-AACCTTTTGCTTGAATTCATCATTTGATGTATCAGCATTGCCA
66 GTTCAAACCTTTTGTTTGAATTCATCATTTGATGTATCAGCATTGCCA
2368251 TGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATT
1 -GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATT
* *
2368316 TGTTCAAACCTTTTGATTGAATTCATCATTTGATGTATTAGCATTGCCA
65 TGTTCAAACCTTTTGTTTGAATTCATCATTTGATGTATCAGCATTGCCA
2368365 GGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATT
1 -GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATT
2368430 TGTTCAAACCTTTTGTTTGAATTCATCATTTGATGTATCAGCATTGCCAA
65 TGTTCAAACCTTTTGTTTGAATTCATCATTTGATGTATCAGCATTGCC-A
*
2368480 GTAGAGTTCATAATGTGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTT
1 GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTT
* * * * * * *** *
2368545 GTTCAAACCTTTTTTTTTTGAATTCATCACTCGGTGGATTAATTTTTCCA
66 GTTCAAACC--TTTTGTTTGAATTCATCATTTGATGTATCAGCATTGCCA
* *
2368595 G-AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAATGAAGAAGAAATTCATAATGAGAAGAAT
1 GTAG--AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
* * * *** *
2368659 TTGTTCAAACCTTTTGTTTGAATTCATCACTCGATGGATCAATTTTTCCA
64 TTGTTCAAACCTTTTGTTTGAATTCATCATTTGATGTATCAGCATTGCCA
* * * *
2368709 G-AGAAAGTTCATAATAAGAAGAACTTATCTGAAAAAGGAAGAAGAAATTCATAATAAGAAGAAT
1 GTAG--AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
2368773 TTGTTCAAACCTTTTGTTTGAATTCATCA
64 TTGTTCAAACCTTTTGTTTGAATTCATCA
2368802 CTCGATGGAT
Statistics
Matches: 510, Mismatches: 30, Indels: 15
0.92 0.05 0.03
Matches are distributed among these distances:
109 30 0.06
110 1 0.00
111 2 0.00
113 28 0.05
114 351 0.69
115 3 0.01
116 95 0.19
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.31
Consensus pattern (113 bp):
GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTT
GTTCAAACCTTTTGTTTGAATTCATCATTTGATGTATCAGCATTGCCA
Found at i:2368720 original size:230 final size:226
Alignment explanation
Indices: 2368147--2369015 Score: 961
Period size: 230 Copynumber: 3.8 Consensus size: 226
2368137 TTTTAGGTAG
* * *
2368147 AGTTCATAATGAGAAGAACTCATCTG-A-AA--AACAAGAAGTTCATAATGAGAAGAACATGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC
* *
2368208 AACCTTTTGCTTGAATTCATCATTTGATGTATCAGCATTGCCATGTAG-AGTTCATAATGAGAAG
66 AACCTTTTGTTTGAATTCATCACTTGATGTATCAGCATTGCCA-G-AGAAGTTCATAATGAGAAG
*
2368272 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACCTTTTGATTGAA
129 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACCTTTTGTTTGAA
* * * *** * *
2368337 TTCATCATTTGATGTATTAGCATTGCCAG-GTAG
194 TTCATCACTCGATGGATTAATTTTTCCAGAG-AA
*
2368370 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC
* *
2368435 AAACCTTTTGTTTGAATTCATCATTTGATGTATCAGCATTGCCA-AGTAGAGTTCATAATGTGAA
66 -AACCTTTTGTTTGAATTCATCACTTGATGTATCAGCATTGCCAGAG-A-AGTTCATAATGAGAA
*
2368499 GAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACCTTTTTTTTTT
128 GAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACC--TTTTGTTT
*
2368564 GAATTCATCACTCGGTGGATTAATTTTTCCAGAGAA
191 GAATTCATCACTCGATGGATTAATTTTTCCAGAGAA
* * *
2368600 AGTTCATAATGAGAAGAACTTATCTGAAGAATGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC
* * *** * *
2368665 AAACCTTTTGTTTGAATTCATCACTCGATGGATCAATTTTTCCAGAGAAAGTTCATAATAAGAAG
66 -AACCTTTTGTTTGAATTCATCACTTGATGTATCAGCATTGCCAGAG-AAGTTCATAATGAGAAG
* * *
2368730 AACTTATCTGAAAAAGGAAGAAGAAATTCATAATAAGAAGAATTTGTTCAAACCTTTTGTTTGAA
129 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACCTTTTGTTTGAA
* * *
2368795 TTCATCACTCGATGGATCAATTTTTCCAAAAAA
194 TTCATCACTCGATGGATTAATTTTTCCAGAGAA
* * *
2368828 AGTTC---AT----A-AACTTATTTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC
* * * *
2368884 AACCTTTT-TTTG-ATTCTATCACATAAGGAGATAGATCAACATCAACATTTCCAGA-AGTGTTC
66 AACCTTTTGTTTGAATTC-ATCAC-T----TGAT-G-T----ATCAGCATTGCCAGAGA-AGTTC
* * * * *
2368946 ATAATGAGAAGAACACATCTGAAG-AGAAAGAAGAAGTTTATAATGAGAAGAACTTGTTC-AACC
118 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACC
2369009 TTTTGTT
183 TTTTGTT
2369016 ACATTACATC
Statistics
Matches: 566, Mismatches: 55, Indels: 48
0.85 0.08 0.07
Matches are distributed among these distances:
216 4 0.01
217 9 0.02
218 9 0.02
219 32 0.06
220 12 0.02
221 1 0.00
222 3 0.01
223 27 0.05
224 1 0.00
225 17 0.03
226 31 0.05
227 52 0.09
228 168 0.30
230 196 0.35
231 4 0.01
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (226 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC
AACCTTTTGTTTGAATTCATCACTTGATGTATCAGCATTGCCAGAGAAGTTCATAATGAGAAGAA
CTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACCTTTTGTTTGAATT
CATCACTCGATGGATTAATTTTTCCAGAGAA
Found at i:2368802 original size:114 final size:114
Alignment explanation
Indices: 2368147--2369015 Score: 904
Period size: 114 Copynumber: 7.7 Consensus size: 114
2368137 TTTTAGGTAG
* * **
2368147 AGTTCATAATGAGAAGAACTCATCTG-A-AA--AACAAGAAGTTCATAATGAGAAGAACATGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* * * * *
2368208 -AACCTTTTGCTTGAATTCATCATTTGATGTATCAGCATTGCCATGTAG--
66 AAACCTTTTGTTTGAATTCATCACTCGATGGATCAACATTGCCA-G-AGAA
2368256 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* * * * * * *
2368321 AAACCTTTTGATTGAATTCATCATTTGATGTATTAGCATTGCCAG-GTAG
66 AAACCTTTTGTTTGAATTCATCACTCGATGGATCAACATTGCCAGAG-AA
2368370 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* * * * *
2368435 AAACCTTTTGTTTGAATTCATCATTTGATGTATCAGCATTGCCA-AGTAG
66 AAACCTTTTGTTTGAATTCATCACTCGATGGATCAACATTGCCAGAG-AA
*
2368484 AGTTCATAATGTGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* * * ** *
2368549 AAACCTTTTTTTTTTGAATTCATCACTCGGTGGATTAATTTTTCCAGAGAA
66 AAACC--TTTTGTTTGAATTCATCACTCGATGGATCAACATTGCCAGAGAA
* *
2368600 AGTTCATAATGAGAAGAACTTATCTGAAGAATGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
** *
2368665 AAACCTTTTGTTTGAATTCATCACTCGATGGATCAATTTTTCCAGAGAA
66 AAACCTTTTGTTTGAATTCATCACTCGATGGATCAACATTGCCAGAGAA
* * * *
2368714 AGTTCATAATAAGAAGAACTTATCTGAAAAAGGAAGAAGAAATTCATAATAAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
** * * *
2368779 AAACCTTTTGTTTGAATTCATCACTCGATGGATCAATTTTTCCAAAAAA
66 AAACCTTTTGTTTGAATTCATCACTCGATGGATCAACATTGCCAGAGAA
* * * *
2368828 AGTTC---AT----A-AACTTATTTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* * * *
2368884 -AACCTTTT-TTTG-ATTCTATCACATAAGGAGATAGATCAACATCAACATTTCCAGA-AG
66 AAACCTTTTGTTTGAATTC-ATCAC-T----CGAT-G-----GATCAACATTGCCAGAGAA
* * * * * *
2368941 TGTTCATAATGAGAAGAACACATCTGAAG-AGAAAGAAGAAGTTTATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
2369005 -AACCTTTTGTT
66 AAACCTTTTGTT
2369016 ACATTACATC
Statistics
Matches: 678, Mismatches: 49, Indels: 53
0.87 0.06 0.07
Matches are distributed among these distances:
102 4 0.01
103 9 0.01
104 9 0.01
105 32 0.05
106 11 0.02
107 1 0.00
108 3 0.00
109 27 0.04
110 1 0.00
111 5 0.01
113 34 0.05
114 387 0.57
116 99 0.15
117 2 0.00
120 1 0.00
121 51 0.08
122 2 0.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (114 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
AAACCTTTTGTTTGAATTCATCACTCGATGGATCAACATTGCCAGAGAA
Found at i:2369064 original size:344 final size:338
Alignment explanation
Indices: 2368160--2369080 Score: 823
Period size: 344 Copynumber: 2.7 Consensus size: 338
2368150 TCATAATGAG
* * * **
2368160 AAGAACTCATCTG-A-AA--AACAAGAAGTTCATAATGAGAAGAACATGTTC-AACCTTTTGCTT
1 AAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAAACCTTTTTTTT
* * * * * * *
2368220 GAATTCATCATTTGAT-GTATCAGCATTGCCATGTAG--AGTTCATAATGAGAAGAACTCATCTG
66 GAATTCATCACTCGGTAG-ATTAACATTTCCA-G-AGAAAGTTCATAATGAGAAGAACACATCTG
* * * *
2368282 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACCTTTTGATTGAATTCATCATTT
128 AAGAA-GAAGAAGAAATTCATAATGAGAAGAACTTGTTCAAACCTTTTGTTTGAATTCATCACTA
* * *** ** * * * * *
2368347 GATGTATTAGCATTG-CCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
192 GATGGATCAATTTTGAAAAAGAAGAGTTCATAATAAGAAGAACTTATCTGAAAAAGGAAGAAGAA
* * * * *
2368411 ATTCATAATGAGAAGAATTTGTTCAAACCTTTTGTTTGAATTCATCATTTGATGTATCAGCATTG
257 ATTCATAATAAGAAGAATTTGTTCAAACCTTTTGTTTGAATTCATCACTCGATGGATCAACATTG
** *
2368476 CCAAGTAGAGTTCATAATGT
322 CCAAAAAAAGTTC--AA-GT
*
2368496 GAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACCTTTTTTT
1 -AAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAAACC--TTTTT
* ** **
2368561 TTTGAATTCATCACTCGGTGGATTAATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTG
63 TTTGAATTCATCACTCGGTAGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACACATCTG
* *
2368626 AAGAATGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACCTTTTGTTTGAATTCATCACTC
128 AAGAA-GAAGAAGAAATTCATAATGAGAAGAACTTGTTCAAACCTTTTGTTTGAATTCATCACTA
*** *
2368691 GATGGATCAATTTTTCCAGAGAA-AGTTCATAATAAGAAGAACTTATCTGAAAAAGGAAGAAGAA
192 GATGGATCAATTTTGAAAAAGAAGAGTTCATAATAAGAAGAACTTATCTGAAAAAGGAAGAAGAA
** *
2368755 ATTCATAATAAGAAGAATTTGTTCAAACCTTTTGTTTGAATTCATCACTCGATGGATCAATTTTT
257 ATTCATAATAAGAAGAATTTGTTCAAACCTTTTGTTTGAATTCATCACTCGATGGATCAACATTG
2368820 CCAAAAAAAGTTC-A-T
322 CCAAAAAAAGTTCAAGT
* * *
2368835 -A-AACTTATTTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC-AACC-TTTTTTT
1 AAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAAACCTTTTTTTT
* **
2368895 G-ATTCTATCACATAAGGAGATAGATCAACATCAACATTTCCAGA-AGTGTTCATAATGAGAAGA
66 GAATTC-ATCAC-T--CG-G-TAGAT-----T-AACATTTCCAGAGAAAGTTCATAATGAGAAGA
* *
2368958 ACACATCTGAAG-AGAAAGAAGAAGTTTATAATGAGAAGAACTTGTTC-AACCTTTTG-TT-ACA
119 ACACATCTGAAGAAG-AAGAAGAAATTCATAATGAGAAGAACTTGTTCAAACCTTTTGTTTGA-A
*
2369019 TTACATCAC-AGAT-TATC-ATTCTCAGTGGAAAAATGGAAGAGTTCATAATAAGAAGAACTTAT
182 TT-CATCACTAGATGGATCAATT-T---T-GAAAAA--GAAGAGTTCATAATAAGAAGAACTTAT
2369081 TCAACATTGC
Statistics
Matches: 486, Mismatches: 64, Indels: 61
0.80 0.10 0.10
Matches are distributed among these distances:
330 4 0.01
331 13 0.03
332 1 0.00
334 5 0.01
335 34 0.07
336 18 0.04
337 19 0.04
338 9 0.02
339 19 0.04
340 31 0.06
341 59 0.12
342 16 0.03
343 4 0.01
344 250 0.51
345 4 0.01
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (338 bp):
AAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAAACCTTTTTTTT
GAATTCATCACTCGGTAGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACACATCTGAAG
AAGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAAACCTTTTGTTTGAATTCATCACTAGATG
GATCAATTTTGAAAAAGAAGAGTTCATAATAAGAAGAACTTATCTGAAAAAGGAAGAAGAAATTC
ATAATAAGAAGAATTTGTTCAAACCTTTTGTTTGAATTCATCACTCGATGGATCAACATTGCCAA
AAAAAGTTCAAGT
Found at i:2369319 original size:3 final size:3
Alignment explanation
Indices: 2369233--2369301 Score: 90
Period size: 3 Copynumber: 24.0 Consensus size: 3
2369223 ATTTTTTGAT
* *
2369233 TTA TTA TAA TTA TT- TTA TT- GTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
2369279 TTA TTA TT- TTA TTA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
2369302 AATAATAAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
2 5 0.09
3 52 0.91
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2376465 original size:14 final size:14
Alignment explanation
Indices: 2376446--2376472 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2376436 CAAATACAAT
2376446 AATATAATATTCCC
1 AATATAATATTCCC
2376460 AATATAATATTCC
1 AATATAATATTCC
2376473 ATGAACCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (14 bp):
AATATAATATTCCC
Found at i:2376711 original size:15 final size:15
Alignment explanation
Indices: 2376687--2376717 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2376677 GATTCCTTTT
2376687 AAATAAAAAAATATA
1 AAATAAAAAAATATA
*
2376702 AAATATAAAAATATA
1 AAATAAAAAAATATA
2376717 A
1 A
2376718 GAGAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATAAAAAAATATA
Found at i:2390246 original size:7 final size:8
Alignment explanation
Indices: 2390224--2390252 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
2390214 CTCAAAAAAA
2390224 TAATTTTT
1 TAATTTTT
2390232 TAATTTTT
1 TAATTTTT
2390240 TAATTTTT
1 TAATTTTT
2390248 TAATT
1 TAATT
2390253 AAATTATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
TAATTTTT
Found at i:2390851 original size:21 final size:21
Alignment explanation
Indices: 2390825--2390881 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
2390815 AAATGTGTAT
2390825 CGATGCACTGCTACAGTGCAC
1 CGATGCACTGCTACAGTGCAC
2390846 CGATGCACTGCTACAGTGCAC
1 CGATGCACTGCTACAGTGCAC
2390867 CGATGCACTGCTACA
1 CGATGCACTGCTACA
2390882 ATAACTGCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.25, C:0.33, G:0.23, T:0.19
Consensus pattern (21 bp):
CGATGCACTGCTACAGTGCAC
Found at i:2391245 original size:15 final size:16
Alignment explanation
Indices: 2391225--2391254 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2391215 CATGAATTTC
2391225 AATGTCA-AAAATCAA
1 AATGTCATAAAATCAA
2391240 AATGTCATAAAATCA
1 AATGTCATAAAATCA
2391255 TGTTACCAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.57, C:0.13, G:0.07, T:0.23
Consensus pattern (16 bp):
AATGTCATAAAATCAA
Found at i:2391400 original size:46 final size:46
Alignment explanation
Indices: 2391315--2391547 Score: 378
Period size: 46 Copynumber: 5.1 Consensus size: 46
2391305 ATAAAATTTC
* **
2391315 TTACCAATATACTTGTCATTT-ATCCCATAAGCTCGTAAGCTTATT
1 TTACCAAAATACTTACCATTTAATCCCATAAGCTCGTAAGCTTATT
2391360 TTACCAAAATACTTACCATTTAATCCCATAAGCTCGTAAGCTTATT
1 TTACCAAAATACTTACCATTTAATCCCATAAGCTCGTAAGCTTATT
** *
2391406 TTACCAAAATACTTATTATTTAATCTCATAAGCTCGTAAGCTTATT
1 TTACCAAAATACTTACCATTTAATCCCATAAGCTCGTAAGCTTATT
*
2391452 TTACCAAAATACTTACCATTTAATCCCATAGGCTCGTAAGCTTATT
1 TTACCAAAATACTTACCATTTAATCCCATAAGCTCGTAAGCTTATT
* *
2391498 TTACCAAAATATTTACCATTTAATCCCAGAAGCTCGTAAGCTTATT
1 TTACCAAAATACTTACCATTTAATCCCATAAGCTCGTAAGCTTATT
2391544 TTAC
1 TTAC
2391548 ATGGTTACTA
Statistics
Matches: 174, Mismatches: 13, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
45 18 0.10
46 156 0.90
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (46 bp):
TTACCAAAATACTTACCATTTAATCCCATAAGCTCGTAAGCTTATT
Found at i:2394866 original size:3 final size:3
Alignment explanation
Indices: 2394853--2395073 Score: 84
Period size: 3 Copynumber: 71.3 Consensus size: 3
2394843 TTTTTTCATG
* * * *
2394853 TTA TTA CTA TTA TTA CTA CTA CTTA TTA TTA TTA TATA ATA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA T-TA TTA TTA TTA
* * * *
2394899 TATA TTA TTTA CTA TTA TTA TATA ATA TTTA TTA TTA -TA TAA GTA TTCA
1 T-TA TTA -TTA TTA TTA TTA T-TA TTA -TTA TTA TTA TTA TTA TTA TT-A
* * *
2394948 -TA TTTA TT- TTA CTA TTA TTA TTA TTA TATG TTA TT- TT- TTA TTG
1 TTA -TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
*
2394991 TT- TTA TGTA -TA TTTA TTA TTAA TGTA ATA TTA TATA TTA TTA TGTA
1 TTA TTA T-TA TTA -TTA TTA TT-A T-TA TTA TTA T-TA TTA TTA T-TA
* * *
2395037 TTA TTA GTA TTTA CTA TTA -TA TTA ATA -TA TTTA TTA T
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA -TTA TTA T
2395074 ATGGGATTTG
Statistics
Matches: 166, Mismatches: 26, Indels: 52
0.68 0.11 0.21
Matches are distributed among these distances:
2 19 0.11
3 110 0.66
4 36 0.22
5 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:2394897 original size:10 final size:10
Alignment explanation
Indices: 2394882--2394950 Score: 56
Period size: 10 Copynumber: 6.8 Consensus size: 10
2394872 TACTTATTAT
2394882 TATTATATAA
1 TATTATATAA
2394892 TATTATAT-A
1 TATTATATAA
*
2394901 TATTATTTACTAT
1 TATTA--TA-TAA
2394914 TATTATATAA
1 TATTATATAA
2394924 TATT-TAT--
1 TATTATATAA
2394931 TATTATATAA
1 TATTATATAA
2394941 GTATTCATAT
1 -TATT-ATAT
2394951 TTATTTTACT
Statistics
Matches: 48, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
7 4 0.08
8 3 0.06
9 9 0.19
10 14 0.29
11 8 0.17
12 5 0.10
13 5 0.10
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (10 bp):
TATTATATAA
Found at i:2394897 original size:32 final size:31
Alignment explanation
Indices: 2394860--2394933 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 31
2394850 ATGTTATTAC
*
2394860 TATTATTACTACTACTTATTATTATTATATAA
1 TATTATTA-TACTACTTACTATTATTATATAA
* *
2394892 TATTATATATATTATTTACTATTATTATATAA
1 TATTAT-TATACTACTTACTATTATTATATAA
2394924 TATTTATTAT
1 TA-TTATTAT
2394934 TATATAAGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 31 0.84
33 6 0.16
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (31 bp):
TATTATTATACTACTTACTATTATTATATAA
Found at i:2398679 original size:21 final size:22
Alignment explanation
Indices: 2398655--2398699 Score: 56
Period size: 25 Copynumber: 2.0 Consensus size: 22
2398645 ATAATGATAA
2398655 AAAC-ATCAATTAATATATCCT
1 AAACAATCAATTAATATATCCT
2398676 AAACTTAAATCAATTAATATATCC
1 AAAC---AATCAATTAATATATCC
2398700 ATAACTGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.20
25 16 0.80
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (22 bp):
AAACAATCAATTAATATATCCT
Found at i:2398990 original size:2 final size:2
Alignment explanation
Indices: 2398985--2399059 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
2398975 TATGTGTGAC
2398985 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
2399027 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2399060 CACTGTGATA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2412047 original size:25 final size:25
Alignment explanation
Indices: 2412019--2412066 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2412009 TCAATCAGAA
2412019 CAAAAAGAAAAAAAAAAGAAAAAAG
1 CAAAAAGAAAAAAAAAAGAAAAAAG
* * *
2412044 CAAAGAGAAAAAACAAAGGAAAA
1 CAAAAAGAAAAAAAAAAGAAAAA
2412067 TTGAAGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (25 bp):
CAAAAAGAAAAAAAAAAGAAAAAAG
Found at i:2414259 original size:318 final size:314
Alignment explanation
Indices: 2413617--2414308 Score: 779
Period size: 318 Copynumber: 2.2 Consensus size: 314
2413607 ATCAAACTCA
*
2413617 AAGCAACATACAATACTTGGATTTCAACTTCATGGTGAAGGATATTCAAGTCAAGGCTCAACTTC
1 AAGCAACATACAATACTTGGATTTCAACTTCATGGCGAAGGATATTCAAGTCAAGGCTCAACTTC
* * *
2413682 ACAACGAATGGGTCATCCACGATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACGT
66 ACAACGAAGGGGCCATCCACGATTTCAACTCCACGACAAAGGATATCCAATTCAAAGCTCAACGT
*
2413747 CACGACGAAGGGGCTTTCCAGTTTCATTCAAAGCCAATTTCAACTTCACGGCGAAGGATATTGGA
131 CACGACGAAAGGGCTTTCCAG-TT-ATTCAAAGCCAATTTCAACTTCACGGCGAAGGATATTGGA
* * * *
2413812 ATCGAAACAATACAAGCTTGAATTTCAACTTCACGACGAAGAATATTCAAGTCAAGGTTCAACTT
194 AGCGAAACAATACAAACTTGAATTTCAACTTCACGACGAAGAATATCCAAGTCAAGGCTCAACTT
* *
2413877 CACGACGAAGGGACCATCCACGGTTTCAACTTCACGGCGAAGGGAATCGTGTCCAC
259 CACAACGAAGGGACCATCCACGATTTCAACTTCACGGCGAAGGGAATCGTGTCCAC
** * * *
2413933 CCGCAACATACGATACTTGGATTTCAACTTTA-GGACGAAGGATATTCAAGTCAAGGCTCAGCTT
1 AAGCAACATACAATACTTGGATTTCAACTTCATGG-CGAAGGATATTCAAGTCAAGGCTCAACTT
* ** *** * ** *
2413997 CACGACGAAGGGGCCATCTGCGATTTCAACTCCACGATGGAGGATATCGTGCCATTTGAGGCTCA
65 CACAACGAAGGGGCCATCCACGATTTCAACTCCACGACAAAGGATATC---CAATTCAAAGCTCA
* * * *
2414062 ACTTCACGACGAAAGGGC-TTCCTAG-T-TTCAGAGCCAATTTCAACTTCACGGTGGAGGATATT
127 ACGTCACGACGAAAGGGCTTTCC-AGTTATTCAAAGCCAATTTCAACTTCACGGCGAAGGATATT
* * * * *
2414124 GGACGCGGAACAATACAACTTACTTGGATTTCAACTTCACGACGAATG-ATATCCAATTCCAGGC
191 GGAAGCGAAACAATACAA---ACTTGAATTTCAACTTCACGACGAA-GAATATCCAAGTCAAGGC
* * *
2414188 TCAACTTCACAACGAAGGGGCCA-CCTATGATTTCAACTTCACGGCGAAGGGAATCGTG-CACAT
252 TCAACTTCACAACGAAGGGACCATCC-ACGATTTCAACTTCACGGCGAAGGGAATCGTGTC-CAC
* * * * *
2414251 AAGCAACAT-CAATCTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAA
1 AAGCAACATACAA----TA-CTTGGATTTCAACTTCATGGCGAAGGATATTCAAGTCAA
2414309 AGAATGAGTG
Statistics
Matches: 313, Mismatches: 46, Indels: 28
0.81 0.12 0.07
Matches are distributed among these distances:
315 50 0.16
316 94 0.30
317 6 0.02
318 99 0.32
319 29 0.09
321 2 0.01
322 32 0.10
323 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (314 bp):
AAGCAACATACAATACTTGGATTTCAACTTCATGGCGAAGGATATTCAAGTCAAGGCTCAACTTC
ACAACGAAGGGGCCATCCACGATTTCAACTCCACGACAAAGGATATCCAATTCAAAGCTCAACGT
CACGACGAAAGGGCTTTCCAGTTATTCAAAGCCAATTTCAACTTCACGGCGAAGGATATTGGAAG
CGAAACAATACAAACTTGAATTTCAACTTCACGACGAAGAATATCCAAGTCAAGGCTCAACTTCA
CAACGAAGGGACCATCCACGATTTCAACTTCACGGCGAAGGGAATCGTGTCCAC
Found at i:2414291 original size:124 final size:122
Alignment explanation
Indices: 2414147--2414807 Score: 395
Period size: 124 Copynumber: 5.3 Consensus size: 122
2414137 TACAACTTAC
* *
2414147 TTGGATTTCAACTTCACGACGAATGATATCCAATTCCAGGCTCAACTTCACAACGAAGGGGCCAC
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCCAGGATCAACTTCACAACGAAGGGGCCAC
*
2414212 CTATGATTTCAACTTCACGGCGAAGGGAATCGTGCACATAAGCAACATCAATCTCTAGA
66 CCA-GATTTCAACTTCACGGCGAAGGGAATCGTGCAC-TAAGCAACATCAATCTCTAGA
* * ** *
2414271 TTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAATGAGTGTA-TGTCAATAAACTTT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTC-CAG---GA-TCAACT-TC-A-CAAC---
** *** * * * * *
2414335 CCAGTTTCAGACCCA-ATTTCAACTTCACGGCGGA-GGATAT--TGGACT-CGGAACAATACAA-
55 GAAGGGGC-CACCCAGATTTCAACTTCACGGCGAAGGGA-ATCGTGCACTAAGCAAC-AT-CAAT
*
2414394 CT-TA-C
116 CTCTAGA
** *
2414399 TTGGATTTCAACTTCACGTTGAAGGATATCCAATTCCAGGATCAACTTCACAACGAAGGGGCTAC
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCCAGGATCAACTTCACAACGAAGGGGCCAC
* * * * *
2414464 CCACGATTTCAACTTCACGTCGAAGGGAATCGTGTACGCAAACAACATCCATCTCTAGA
66 CCA-GATTTCAACTTCACGGCGAAGGGAATCGTGCAC-TAAGCAACATCAATCTCTAGA
* * * * * *
2414523 TTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAATGAGTGTCTGTCAATAAAATTTC
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTC-CAGGATCA---ACT-TC---ACAA---C
* *** * * * * *
2414588 -CAGTTTCAGACCCA-ATTTCAACTTCACGGCGGA-GGATAT--TGGACT-CGGAACAATACAA-
55 GAAGGGGC-CACCCAGATTTCAACTTCACGGCGAAGGGA-ATCGTGCACTAAGCAAC-AT-CAAT
*
2414646 CT-TACA
116 CTCTAGA
* *
2414652 -TGGATTTCAACTTCACGACGAAGGATATCCAATTTCAGGCTCAACTTCACAACGAAGGGGCCAC
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCCAGGATCAACTTCACAACGAAGGGGCCAC
* * * * * *
2414716 CCACGGTTTCAAATTCACGGCGAAGGGAATCGTGCACACAAACAACATCCATATCTAGA
66 CCA-GATTTCAACTTCACGGCGAAGGGAATCGTGCAC-TAAGCAACATCAATCTCTAGA
* *
2414775 TTAGATTTCAACTTCACAACGAAGGATATCCAA
1 TTGGATTTCAACTTCACGACGAAGGATATCCAA
2414808 CTTAAATAAG
Statistics
Matches: 396, Mismatches: 89, Indels: 104
0.67 0.15 0.18
Matches are distributed among these distances:
117 11 0.03
118 6 0.02
119 37 0.09
120 9 0.02
121 15 0.04
122 8 0.02
123 17 0.04
124 102 0.26
125 7 0.02
127 6 0.02
128 70 0.18
129 18 0.05
130 10 0.03
131 16 0.04
132 9 0.02
133 39 0.10
134 6 0.02
135 10 0.03
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (122 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAATTCCAGGATCAACTTCACAACGAAGGGGCCAC
CCAGATTTCAACTTCACGGCGAAGGGAATCGTGCACTAAGCAACATCAATCTCTAGA
Found at i:2414387 original size:252 final size:252
Alignment explanation
Indices: 2414080--2414996 Score: 1359
Period size: 252 Copynumber: 3.6 Consensus size: 252
2414070 ACGAAAGGGC
* * *
2414080 TTCCTAGTTTCAGAGCCAATTTCAACTTCACGGTGGAGGATATTGGACGCGGAACAATACAACTT
1 TTCC-AGTTTCAGACCCAATTTCAACTTCACGGCGGAGGATATTGGACTCGGAACAATACAACTT
*
2414145 ACTTGGATTTCAACTTCACGACGAATGATATCCAATTCCAGGCTCAACTTCACAACGAAGGGGCC
65 ACTTGGATTTCAACTTCACGACGAAGGATATCCAATTCCAGGCTCAACTTCACAACGAAGGGGCC
* * * * *
2414210 ACCTATGATTTCAACTTCACGGCGAAGGGAATCGTGCACATAAGCAACATCAATCTCTAGATTGG
130 ACCCACGATTTCAACTTCACGGCGAAGGGAATCGTGCACACAAACAACATCCATCTCTAGATTGG
*
2414275 ATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAATGAGTGTATGTCAATAAACT
195 ATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAATGAGTGTCTGTCAATAAACT
2414333 TTCCAGTTTCAGACCCAATTTCAACTTCACGGCGGAGGATATTGGACTCGGAACAATACAACTTA
1 TTCCAGTTTCAGACCCAATTTCAACTTCACGGCGGAGGATATTGGACTCGGAACAATACAACTTA
** * *
2414398 CTTGGATTTCAACTTCACGTTGAAGGATATCCAATTCCAGGATCAACTTCACAACGAAGGGGCTA
66 CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCCAGGCTCAACTTCACAACGAAGGGGCCA
* * *
2414463 CCCACGATTTCAACTTCACGTCGAAGGGAATCGTGTACGCAAACAACATCCATCTCTAGATTGGA
131 CCCACGATTTCAACTTCACGGCGAAGGGAATCGTGCACACAAACAACATCCATCTCTAGATTGGA
*
2414528 TTTCAACTTCACGACGAAGGATATCCAACTCAAAGAATGAGTGTCTGTCAATAAAAT
196 TTTCAACTTCACGACGAAGGATATCCAACTCAAAGAATGAGTGTCTGTCAATAAACT
2414585 TTCCAGTTTCAGACCCAATTTCAACTTCACGGCGGAGGATATTGGACTCGGAACAATACAACTTA
1 TTCCAGTTTCAGACCCAATTTCAACTTCACGGCGGAGGATATTGGACTCGGAACAATACAACTTA
* *
2414650 CATGGATTTCAACTTCACGACGAAGGATATCCAATTTCAGGCTCAACTTCACAACGAAGGGGCCA
66 CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCCAGGCTCAACTTCACAACGAAGGGGCCA
* * * *
2414715 CCCACGGTTTCAAATTCACGGCGAAGGGAATCGTGCACACAAACAACATCCATATCTAGATTAGA
131 CCCACGATTTCAACTTCACGGCGAAGGGAATCGTGCACACAAACAACATCCATCTCTAGATTGGA
* * * *
2414780 TTTCAACTTCACAACGAAGGATATCCAACTTAAATAAGGAGTGTCTG-CTAATAAACT
196 TTTCAACTTCACGACGAAGGATATCCAACTCAAAGAATGAGTGTCTGTC-AATAAACT
** * * * * * * ***
2414837 TTCCAGTTTCAGAGTCAATTTCAACTTCACAGTGAAAGATATTGGCCTCGAAACAACGGAACTTA
1 TTCCAGTTTCAGACCCAATTTCAACTTCACGGCGGAGGATATTGGACTCGGAACAATACAACTTA
** *
2414902 CATTGGATTTCAACTTCACGACGAAGGATATCCAATTCCAAGGCTCAACTTCATGACAAAGGGGC
66 C-TTGGATTTCAACTTCACGACGAAGGATATCCAATTCC-AGGCTCAACTTCACAACGAAGGGGC
*** * **
2414967 CATATACGATTCCAACTTCACTACGAAGGG
129 CACCCACGATTTCAACTTCACGGCGAAGGG
2414997 TATCATACCC
Statistics
Matches: 601, Mismatches: 60, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
251 1 0.00
252 517 0.86
253 39 0.06
254 44 0.07
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (252 bp):
TTCCAGTTTCAGACCCAATTTCAACTTCACGGCGGAGGATATTGGACTCGGAACAATACAACTTA
CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCCAGGCTCAACTTCACAACGAAGGGGCCA
CCCACGATTTCAACTTCACGGCGAAGGGAATCGTGCACACAAACAACATCCATCTCTAGATTGGA
TTTCAACTTCACGACGAAGGATATCCAACTCAAAGAATGAGTGTCTGTCAATAAACT
Found at i:2416797 original size:18 final size:17
Alignment explanation
Indices: 2416736--2416797 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 17
2416726 ATTGAGGCCT
*
2416736 TTTATTTTATTTATTTTAA
1 TTTA-TTTACTTATTTT-A
*
2416755 TTTATTTAGTTACTATTT-
1 TTTATTTACTTA-T-TTTA
2416773 TTTATTTACTTATTTTA
1 TTTATTTACTTATTTTA
2416790 TTTCATTT
1 TTT-ATTT
2416798 TGTATACACC
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
16 3 0.08
17 4 0.11
18 22 0.59
19 5 0.14
20 3 0.08
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.71
Consensus pattern (17 bp):
TTTATTTACTTATTTTA
Found at i:2418929 original size:32 final size:33
Alignment explanation
Indices: 2418867--2418935 Score: 81
Period size: 32 Copynumber: 2.1 Consensus size: 33
2418857 AATTAAACTG
*
2418867 AAATTAACCTGATCCAGAAGTAACTCGAACC-A
1 AAATTAACCTGATCCAGAAGCAACTCGAACCGA
*
2418899 AAATTAACCTGA-CCTGAAAGCAA-TCTGAACCGA
1 AAATTAACCTGATCCAG-AAGCAACTC-GAACCGA
2418932 AAAT
1 AAAT
2418936 AACTCGAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
31 5 0.16
32 22 0.69
33 5 0.16
ACGTcount: A:0.45, C:0.23, G:0.13, T:0.19
Consensus pattern (33 bp):
AAATTAACCTGATCCAGAAGCAACTCGAACCGA
Found at i:2419899 original size:2 final size:2
Alignment explanation
Indices: 2419892--2419925 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2419882 TTTGATAGAT
2419892 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2419926 TTATTTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2423497 original size:29 final size:30
Alignment explanation
Indices: 2423446--2423503 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
2423436 AATAACTTAT
2423446 TTGATTTAATTTTCGATTCT-AAAATTTAA
1 TTGATTTAATTTTCGATTCTAAAAATTTAA
2423475 TTGATTTAAATTTTC-AGTT-TAAAAATTTA
1 TTGATTT-AATTTTCGA-TTCTAAAAATTTA
2423504 GTTGGATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (30 bp):
TTGATTTAATTTTCGATTCTAAAAATTTAA
Found at i:2428675 original size:24 final size:24
Alignment explanation
Indices: 2428557--2428663 Score: 144
Period size: 24 Copynumber: 4.5 Consensus size: 24
2428547 TGATATGTTT
*
2428557 TGATACTTGACATGGATTCTGATC
1 TGATACTTGACATGGATTCTGATA
*
2428581 TGATA-TCTGACATGGATTCTGATC
1 TGATACT-TGACATGGATTCTGATA
* *
2428605 TTATACTTGACTTGGATTCTGATA
1 TGATACTTGACATGGATTCTGATA
* *
2428629 TGATACTTGACCTGGATTTTGATA
1 TGATACTTGACATGGATTCTGATA
2428653 TGATACTTGAC
1 TGATACTTGAC
2428664 GTGAATTATG
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
23 1 0.01
24 73 0.97
25 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (24 bp):
TGATACTTGACATGGATTCTGATA
Found at i:2428680 original size:24 final size:24
Alignment explanation
Indices: 2428555--2428680 Score: 139
Period size: 24 Copynumber: 5.2 Consensus size: 24
2428545 TTTGATATGT
2428555 TTTGATACTTGACATGGATTCTGA
1 TTTGATACTTGACATGGATTCTGA
*
2428579 TCTGATA-TCTGACATGGATTCTGA
1 TTTGATACT-TGACATGGATTCTGA
*
2428603 TCTT-ATACTTGACTTGGATTCTGA
1 T-TTGATACTTGACATGGATTCTGA
* * *
2428627 TATGATACTTGACCTGGATTTTGA
1 TTTGATACTTGACATGGATTCTGA
* * * *
2428651 TATGATACTTGACGTGAATTATGA
1 TTTGATACTTGACATGGATTCTGA
2428675 TTTGAT
1 TTTGAT
2428681 TTTTGATATA
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
23 2 0.02
24 84 0.95
25 2 0.02
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (24 bp):
TTTGATACTTGACATGGATTCTGA
Found at i:2433342 original size:48 final size:48
Alignment explanation
Indices: 2433267--2433384 Score: 175
Period size: 48 Copynumber: 2.4 Consensus size: 48
2433257 TTTTCGATTT
2433267 GATTTCTGATATGATACTTGACATGGATTCTGATCTGATA-TCTGACATG
1 GATTT-TGATATGATACTTGACATGGATTCTGATCTGATACT-TGACATG
* * * *
2433316 GATTTTGATCTTATACTTGACTTGGATTCTGATCTGATACTTGACCTG
1 GATTTTGATATGATACTTGACATGGATTCTGATCTGATACTTGACATG
2433364 GATTTTGATATGATACTTGAC
1 GATTTTGATATGATACTTGAC
2433385 GTGAATTATG
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
48 56 0.90
49 6 0.10
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (48 bp):
GATTTTGATATGATACTTGACATGGATTCTGATCTGATACTTGACATG
Found at i:2433396 original size:24 final size:24
Alignment explanation
Indices: 2433270--2433384 Score: 151
Period size: 24 Copynumber: 4.8 Consensus size: 24
2433260 TCGATTTGAT
*
2433270 TTCTGATATGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
2433294 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
* * *
2433318 TTTTGATCTTATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
*
2433342 TTCTGATCTGATACTTGACCTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
2433366 TTTTGATATGATACTTGAC
1 TTCTGATCTGATACTTGAC
2433385 GTGAATTATG
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
23 1 0.01
24 78 0.98
25 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:2435758 original size:8 final size:8
Alignment explanation
Indices: 2435747--2435773 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
2435737 TCATTCGTTA
2435747 GTTTGTTC
1 GTTTGTTC
2435755 GTTTGTTC
1 GTTTGTTC
2435763 GTTTGTTC
1 GTTTGTTC
2435771 GTT
1 GTT
2435774 CGTTAGTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.11, G:0.26, T:0.63
Consensus pattern (8 bp):
GTTTGTTC
Found at i:2436863 original size:85 final size:85
Alignment explanation
Indices: 2436694--2436864 Score: 227
Period size: 85 Copynumber: 2.0 Consensus size: 85
2436684 ATTTAGAGAT
* *
2436694 GATAATTTGACACAAATTCGATCCTATAACACGTGTTAGAGTTTCTAACCTGAATTTTATATTGA
1 GATAATTTGACACAAATTCAATCCTATAACACGTGTTAGAATTTCTAACCTGAATTTTATATTGA
*
2436759 TTTGGTCCTAAAAGTTTATA
66 TTTGGTCCAAAAAGTTTATA
* * * ** *
2436779 GATAATTTGACCCAAGTTTAATCCTATAATGCGTGTTAGAATTTGTAACCTGAATTTTATATTGA
1 GATAATTTGACACAAATTCAATCCTATAACACGTGTTAGAATTTCTAACCTGAATTTTATATTGA
* *
2436844 TTTAGTTCGAAAAAG-TTATA
66 TTT-GGTCCAAAAAGTTTATA
2436864 G
1 G
2436865 CAAAAACTTT
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
85 66 0.89
86 8 0.11
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.39
Consensus pattern (85 bp):
GATAATTTGACACAAATTCAATCCTATAACACGTGTTAGAATTTCTAACCTGAATTTTATATTGA
TTTGGTCCAAAAAGTTTATA
Found at i:2439985 original size:36 final size:36
Alignment explanation
Indices: 2439938--2440120 Score: 258
Period size: 36 Copynumber: 5.1 Consensus size: 36
2439928 GATCAGACTC
* **
2439938 AAGATTAATTTGCTTCACTACTCTTTTGCAAAGGCT
1 AAGATTAATTTGCTTCACTACTCTTCTGTGAAGGCT
* *
2439974 AAGATTAATTTGCTCCACTACTCTTCTGTGAAGACT
1 AAGATTAATTTGCTTCACTACTCTTCTGTGAAGGCT
* **
2440010 AAGATTGATTTATTTCACTACTCTTCTGTGAAGGCT
1 AAGATTAATTTGCTTCACTACTCTTCTGTGAAGGCT
* *
2440046 AAGATAAATTTGCTTCACTACTCTTATGTGAAGGCT
1 AAGATTAATTTGCTTCACTACTCTTCTGTGAAGGCT
* *
2440082 AATATTGATTTGCTTCACTACTCTTCTGTGAAGGCT
1 AAGATTAATTTGCTTCACTACTCTTCTGTGAAGGCT
2440118 AAG
1 AAG
2440121 TCCGGGATGG
Statistics
Matches: 127, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 127 1.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (36 bp):
AAGATTAATTTGCTTCACTACTCTTCTGTGAAGGCT
Found at i:2440404 original size:61 final size:61
Alignment explanation
Indices: 2440225--2440441 Score: 285
Period size: 61 Copynumber: 3.6 Consensus size: 61
2440215 TGCAATATTG
*
2440225 ACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTATTGGAAGTCATAAATAACAAATGTTT
1 ACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTGGAAGTCATAAATAACAAATGTTT
** * *
2440286 ACTTCT-TTTTCGAGAAAGTCAAGGATTAACTCTACTGGAAGTCATAAATAACAAATGTTT
1 ACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTGGAAGTCATAAATAACAAATGTTT
** ** * *
2440346 ACTTCTCTTTTCGAGGAAGTCAAGGATTGACTCTACTGGGGTGTCAGAAATAAC-AATGTTG
1 ACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACT-GGAAGTCATAAATAACAAATGTTT
* **
2440407 ACTTCTCTTCACGAGGAATTCAAAAATTGACTCTA
1 ACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTA
2440442 GGAAACAAAA
Statistics
Matches: 138, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
60 55 0.40
61 70 0.51
62 13 0.09
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (61 bp):
ACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTGGAAGTCATAAATAACAAATGTTT
Found at i:2442018 original size:76 final size:76
Alignment explanation
Indices: 2441889--2442030 Score: 196
Period size: 76 Copynumber: 1.9 Consensus size: 76
2441879 AACAAAAATG
*
2441889 TCTTGCATTTTTTATATGATCTGAGATATGTGCCCCTTCCGAATAAGGCGATCATATTCTTCTTG
1 TCTTGCATTTTTTATATGATCTGAGATATGTGCCCCTTCCAAATAAGGCGATCATATTCTTCTTG
2441954 ACTAGTCGTAC
66 ACTAGTCGTAC
* * * * * * *
2441965 TCTTGCATTTTTTATATGCA-CTGGGATATGTGCCCTTTTCAAATAGGGTGATCATCTTCTTTTT
1 TCTTGCATTTTTTATATG-ATCTGAGATATGTGCCCCTTCCAAATAAGGCGATCATATTCTTCTT
2442029 GA
65 GA
2442031 TAGGTTGCTG
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
76 56 0.98
77 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.42
Consensus pattern (76 bp):
TCTTGCATTTTTTATATGATCTGAGATATGTGCCCCTTCCAAATAAGGCGATCATATTCTTCTTG
ACTAGTCGTAC
Found at i:2445588 original size:54 final size:54
Alignment explanation
Indices: 2445523--2446111 Score: 788
Period size: 54 Copynumber: 11.1 Consensus size: 54
2445513 GGCACAACGA
* ** *
2445523 GTGCAGCCTAAGAAATTCATAATGAGTTTATGAATTTTTGTATTTGCACTATGT
1 GTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGT
2445577 GTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGT
1 GTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGT
*
2445631 GTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTATGT
1 GTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGT
* *
2445685 GTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTAGCACTATGT
1 GTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGT
* *
2445739 GTGTAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTAGCACTATGT
1 GTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGT
**
2445793 GTGCAACCT----AA--C-T--T---TTTATGAATTTTTGTATTGGCACTATGT
1 GTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGT
* ** * *
2445835 GTACAATATAAGAAATTCATAATGAGTTTATGAATTTTCGTATGGGCACTATGT
1 GTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGT
* *
2445889 GTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGTCACTATGT
1 GTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGT
*
2445943 GTGCAACCTAAGAAATTCATAATGAGTTTATAAATTTCCGTATTGGCACTATGT
1 GTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGT
* * * **
2445997 GTGCAACCTGAGAAATTCATAATAAGTTTATGAATTTCTGTATTTACACTATGT
1 GTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGT
* * * * * * * **
2446051 GTGCAACCCCACGTAATTCATAATGAGTTTGTGAATTACTGCATTGGCACTACAT
1 GTGCAA-CCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGT
2446106 GTGCAA
1 GTGCAA
2446112 AACCATAGAA
Statistics
Matches: 477, Mismatches: 45, Indels: 25
0.87 0.08 0.05
Matches are distributed among these distances:
42 31 0.06
45 1 0.00
46 2 0.00
47 1 0.00
48 2 0.00
49 1 0.00
50 2 0.00
51 1 0.00
54 394 0.83
55 42 0.09
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (54 bp):
GTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGT
Found at i:2445953 original size:204 final size:204
Alignment explanation
Indices: 2445603--2446005 Score: 691
Period size: 204 Copynumber: 2.0 Consensus size: 204
2445593 TCATAATGAG
* *
2445603 TTTATGAATTTCCGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTT
1 TTTATGAATTTCCGTATTGGCACTATGTGTACAACATAAGAAATTCATAATGAGTTTATGAATTT
*
2445668 TCGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTAGCA
66 TCGTATGGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTAGCA
* *
2445733 CTATGTGTGTAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTAGCACTATGTGTGCA
131 CTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATAAATTTCCGTATTAGCACTATGTGTGCA
2445798 ACCTAACTT
196 ACCTAACTT
** *
2445807 TTTATGAATTTTTGTATTGGCACTATGTGTACAATATAAGAAATTCATAATGAGTTTATGAATTT
1 TTTATGAATTTCCGTATTGGCACTATGTGTACAACATAAGAAATTCATAATGAGTTTATGAATTT
* *
2445872 TCGTATGGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTTCGTATT-GTC
66 TCGTATGGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTAG-C
*
2445936 ACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATAAATTTCCGTATTGGCACTATGTGTGC
130 ACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATAAATTTCCGTATTAGCACTATGTGTGC
2446001 AACCT
195 AACCT
2446006 GAGAAATTCA
Statistics
Matches: 187, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
203 1 0.01
204 186 0.99
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (204 bp):
TTTATGAATTTCCGTATTGGCACTATGTGTACAACATAAGAAATTCATAATGAGTTTATGAATTT
TCGTATGGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTAGCA
CTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATAAATTTCCGTATTAGCACTATGTGTGCA
ACCTAACTT
Found at i:2446013 original size:258 final size:258
Alignment explanation
Indices: 2445549--2446058 Score: 878
Period size: 258 Copynumber: 2.0 Consensus size: 258
2445539 TCATAATGAG
* * *
2445549 TTTATGAATTTTTGTATTTGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTT
1 TTTATGAATTTTTGTATTGGCACTATGTGTACAACATAAGAAATTCATAATGAGTTTATGAATTT
*
2445614 CCGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCA
66 CCGTATGGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCA
* *
2445679 CTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTAGCACTATGTGTGTA
131 CTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATAAATTTCCGTATTAGCACTATGTGTGCA
*
2445744 ACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTA-TTAGCACTATGTGTGCAACCTAACTT
196 ACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTTA-CACTATGTGTGCAACCTAACTT
*
2445807 TTTATGAATTTTTGTATTGGCACTATGTGTACAATATAAGAAATTCATAATGAGTTTATGAATTT
1 TTTATGAATTTTTGTATTGGCACTATGTGTACAACATAAGAAATTCATAATGAGTTTATGAATTT
* *
2445872 TCGTATGGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGTCA
66 CCGTATGGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCA
* *
2445937 CTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATAAATTTCCGTATTGGCACTATGTGTGCA
131 CTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATAAATTTCCGTATTAGCACTATGTGTGCA
* *
2446002 ACCTGAGAAATTCATAATAAGTTTATGAATTTCTGTATTTACACTATGTGTGCAACC
196 ACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTTACACTATGTGTGCAACC
2446059 CCACGTAATT
Statistics
Matches: 237, Mismatches: 14, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
258 234 0.99
259 3 0.01
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (258 bp):
TTTATGAATTTTTGTATTGGCACTATGTGTACAACATAAGAAATTCATAATGAGTTTATGAATTT
CCGTATGGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCA
CTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATAAATTTCCGTATTAGCACTATGTGTGCA
ACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTTACACTATGTGTGCAACCTAACTT
Found at i:2446962 original size:19 final size:19
Alignment explanation
Indices: 2446938--2447027 Score: 180
Period size: 19 Copynumber: 4.7 Consensus size: 19
2446928 AATGCATTTT
2446938 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
2446957 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
2446976 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
2446995 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
2447014 ATGCATCGATGCAC
1 ATGCATCGATGCAC
2447028 TCAGGATTTA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 71 1.00
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (19 bp):
ATGCATCGATGCACATACC
Found at i:2447064 original size:65 final size:63
Alignment explanation
Indices: 2446994--2447136 Score: 191
Period size: 65 Copynumber: 2.2 Consensus size: 63
2446984 ATGCACATAC
* *
2446994 CATGCATCGATGCACATA-CCATGCATCGATGCACTCAGG-ATTTAATGAAAACATCGAATGCAT
1 CATGCATCGATGCACA-AGCCATGCATCGATACACTCAGGCATTT--TG-AAACATCGAATGCAG
2447057 TT
62 TT
*
2447059 GATGCATCGATGCACAAGCCATGCATCGATACACTCAGGCTATTTTGAAACATCGAATGCAGTT
1 CATGCATCGATGCACAAGCCATGCATCGATACACTCAGGC-ATTTTGAAACATCGAATGCAGTT
*
2447123 CATGCATTGATGCA
1 CATGCATCGATGCA
2447137 TCTTAGTGCA
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
64 29 0.41
65 37 0.53
67 4 0.06
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (63 bp):
CATGCATCGATGCACAAGCCATGCATCGATACACTCAGGCATTTTGAAACATCGAATGCAGTT
Found at i:2451146 original size:32 final size:33
Alignment explanation
Indices: 2451105--2451174 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 33
2451095 ATTAAAAGCT
* *
2451105 CGAACGATTAAATTTTCATTTT-CCAATACGTA
1 CGAAAGATTAAATTTTCATTTTGCAAATACGTA
2451137 CGAAAGATTAAATTTTCATTTTGCAAATACGTA
1 CGAAAGATTAAATTTTCATTTTGCAAATACGTA
2451170 CGAAA
1 CGAAA
2451175 ACAAACTTCG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 21 0.60
33 14 0.40
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (33 bp):
CGAAAGATTAAATTTTCATTTTGCAAATACGTA
Found at i:2451524 original size:16 final size:17
Alignment explanation
Indices: 2451498--2451529 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2451488 AAGTTTGTTT
2451498 ATTTATTTTCATTTTTC
1 ATTTATTTTCATTTTTC
2451515 ATTT-TTTTCATTTTT
1 ATTTATTTTCATTTTT
2451530 TTTGTTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (17 bp):
ATTTATTTTCATTTTTC
Found at i:2451540 original size:12 final size:12
Alignment explanation
Indices: 2451516--2451556 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
2451506 TCATTTTTCA
2451516 TTTTTTTCATTT
1 TTTTTTTCATTT
2451528 TTTTTGTTC-TTT
1 TTTTT-TTCATTT
2451540 TTTTTATTCATTT
1 TTTTT-TTCATTT
2451553 TTTT
1 TTTT
2451557 CTTCGTTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.07, C:0.07, G:0.02, T:0.83
Consensus pattern (12 bp):
TTTTTTTCATTT
Found at i:2451542 original size:21 final size:20
Alignment explanation
Indices: 2451509--2451576 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
2451499 TTTATTTTCA
2451509 TTTTTCATTTTTTTCATTTTT
1 TTTTTC-TTTTTTTCATTTTT
* *
2451530 TTTGTTCTTTTTTTTATTCATT
1 TTT-TTCTTTTTTTCATT-TTT
* *
2451552 TTTTTCTTCGTTTTCCTTTTT
1 TTTTTCTT-TTTTTCATTTTT
2451573 TTTT
1 TTTT
2451577 GAAAATTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 24 0.63
22 14 0.37
ACGTcount: A:0.06, C:0.12, G:0.03, T:0.79
Consensus pattern (20 bp):
TTTTTCTTTTTTTCATTTTT
Found at i:2451565 original size:25 final size:24
Alignment explanation
Indices: 2451516--2451565 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2451506 TCATTTTTCA
*
2451516 TTTTTTTCATTTTTTTTGTTCTTT
1 TTTTTTTCATTTTTTTTCTTCTTT
*
2451540 TTTTTATTCA-TTTTTTTCTTCGTT
1 TTTTT-TTCATTTTTTTTCTTCTTT
2451564 TT
1 TT
2451566 CCTTTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.06, C:0.10, G:0.04, T:0.80
Consensus pattern (24 bp):
TTTTTTTCATTTTTTTTCTTCTTT
Found at i:2452274 original size:259 final size:256
Alignment explanation
Indices: 2451721--2452369 Score: 781
Period size: 258 Copynumber: 2.5 Consensus size: 256
2451711 GAATGATTTA
* * * * *
2451721 AATTTTGGAAATAGTTTATTGGGTAAGAAACTTTGAAAATTGTTTATTTCTTTTCAAAAATTTCA
1 AATTTTGAAAATAGTTTATTGGGTAAGAAACTTTGGAAATCGTTTCTTACTTTTCAAAAATTTCA
* * *
2451786 TTTTTTGAAAATATCAAATGAGAAACTTTGAAAATCGATTTCTAATTTTTCACAAACATCATATG
66 TTTTCTGAAAATATTAAATGAGAAACTTTGAAAATCGATTTCTAATTTTTCTC-AA-ATCATATG
* * * *
2451851 AAAGA-ATCTTGCCCGAAGGTCTTATAGATGACCCGAATGAATTATCATCTTACTCGAAAGACTA
129 AAA-ACACCTTGCCCGAAGATCTTACAGATGACCCGAAAGAATTATCATCTTACTCGAAAGACTA
* * * * *
2451915 ACAATGACCCGAAAGATTTAATCATCATGCTTGAAAGATTTATTGAGGGACCGAAGGAGTTACC
193 ACAATGACCAGAAAGATTTAATCATCATGCTTGAAAGACTTACTGAGGGACCAAAGGACTTACC
* * *
2451979 AATTTT-AGAAATAGTCTACT-GGTAACAAACTTTGGAAATCGATTTCTTACTTTTTCAAAAATT
1 AATTTTGA-AAATAGTTTATTGGGTAAGAAACTTTGGAAATCG-TTTCTTAC-TTTTCAAAAATT
* * * * *
2452042 TCATTTTCTGAAAATATTAAATGAGAAATTTTGAAAATCGCTTCCTCATTTTTCTCAAATCATAG
63 TCATTTTCTGAAAATATTAAATGAGAAACTTTGAAAATCGATTTCTAATTTTTCTCAAATCATAT
* * * *
2452107 GAAAACACCTTGCCTGAAGATCTTACAGATGGCCCGAAAGACTTATCATCTTGCTCGAAAGACTA
128 GAAAACACCTTGCCCGAAGATCTTACAGATGACCCGAAAGAATTATCATCTTACTCGAAAGACTA
* * * * *
2452172 ACATATGACCATAAGGATTTAATCATCATGCTTGAAAGACTTACTGATGGCCCAAATGACTTACC
193 ACA-ATGACCAGAAAGATTTAATCATCATGCTTGAAAGACTTACTGAGGGACCAAAGGACTTACC
* * **
2452237 AATTTTGAAAAAAGTTTATTGGGTAAGAAAATTTGGAAATCGTTTTCTTACTTTTCAAAAA--AA
1 AATTTTGAAAATAGTTTATTGGGTAAGAAACTTTGGAAATCG-TTTCTTACTTTTCAAAAATTTC
** * *
2452300 ATAATCTAAAAATCA-TAAATGAGAAACTTTGAAAATCGATTTCTTATTTTT-TACAAATCATAT
65 ATTTTCTGAAAAT-ATTAAATGAGAAACTTTGAAAATCGATTTCTAATTTTTCT-CAAATCATAT
2452363 GAAAACA
128 GAAAACA
2452370 TCTTAATGGT
Statistics
Matches: 332, Mismatches: 50, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
255 1 0.00
256 59 0.18
257 83 0.25
258 100 0.30
259 89 0.27
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.34
Consensus pattern (256 bp):
AATTTTGAAAATAGTTTATTGGGTAAGAAACTTTGGAAATCGTTTCTTACTTTTCAAAAATTTCA
TTTTCTGAAAATATTAAATGAGAAACTTTGAAAATCGATTTCTAATTTTTCTCAAATCATATGAA
AACACCTTGCCCGAAGATCTTACAGATGACCCGAAAGAATTATCATCTTACTCGAAAGACTAACA
ATGACCAGAAAGATTTAATCATCATGCTTGAAAGACTTACTGAGGGACCAAAGGACTTACC
Found at i:2453661 original size:2 final size:2
Alignment explanation
Indices: 2453654--2453717 Score: 85
Period size: 2 Copynumber: 32.0 Consensus size: 2
2453644 AGTAAATCAA
* * *
2453654 AT AT AT AT AT AT AT AT AT -T AT TT TT CAA AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT
2453696 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
2453718 GTGTGTGTGT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2460042 original size:16 final size:16
Alignment explanation
Indices: 2460021--2460053 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2460011 AATTCTTGTA
2460021 AACACCTACCTTAGAG
1 AACACCTACCTTAGAG
2460037 AACACCTACCTTAGAG
1 AACACCTACCTTAGAG
2460053 A
1 A
2460054 GGTTTTCTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.30, G:0.12, T:0.18
Consensus pattern (16 bp):
AACACCTACCTTAGAG
Found at i:2460540 original size:15 final size:16
Alignment explanation
Indices: 2460516--2460550 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2460506 AGTGCCTATT
*
2460516 ACATTGAAGATTCA-A
1 ACATTCAAGATTCACA
2460531 ACATTCAAGATTCACA
1 ACATTCAAGATTCACA
2460547 ACAT
1 ACAT
2460551 GTTAACAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.46, C:0.20, G:0.09, T:0.26
Consensus pattern (16 bp):
ACATTCAAGATTCACA
Found at i:2467549 original size:2 final size:2
Alignment explanation
Indices: 2467542--2467593 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
2467532 GAGTTAAAAC
2467542 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2467584 AT AT AT AT AT
1 AT AT AT AT AT
2467594 GCACACTCGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2483061 original size:90 final size:90
Alignment explanation
Indices: 2482905--2483082 Score: 284
Period size: 90 Copynumber: 2.0 Consensus size: 90
2482895 CCTAACACAC
* * *
2482905 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTTTTATTATTTCAAATTAATTAAATATAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATATAT
* *
2482970 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
* * *
2482995 CCTTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTGTTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATATAT
2483060 ATTTAATTAATTGAAATTAAATA
66 ATTTAATTAATTGAAATTAAATA
2483083 TTCGAGATTA
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATATAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:2489800 original size:29 final size:29
Alignment explanation
Indices: 2489768--2489847 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 29
2489758 GAAGTTTTTA
* * *
2489768 CTTTCATTTTAATTTGTAAAAAGATTTGT
1 CTTTAATTGTAATTTATAAAAAGATTTGT
* * *
2489797 CTTTTTATTGTAAATTATAAAAATATTTGT
1 C-TTTAATTGTAATTTATAAAAAGATTTGT
*
2489827 CCTTAATTGTAATTTATAAAA
1 CTTTAATTGTAATTTATAAAA
2489848 TAATTTTTCA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 18 0.43
30 24 0.57
ACGTcount: A:0.36, C:0.06, G:0.07, T:0.50
Consensus pattern (29 bp):
CTTTAATTGTAATTTATAAAAAGATTTGT
Found at i:2489853 original size:29 final size:29
Alignment explanation
Indices: 2489777--2489882 Score: 90
Period size: 29 Copynumber: 3.6 Consensus size: 29
2489767 ACTTTCATTT
* **
2489777 TAATTTGTAAAAAGATTTGTCTTTTTATTG
1 TAATTTATAAAAAGATTTGTC-ACTTATTG
* *
2489807 TAAATTATAAAAATATTTGTC-CTTAATTG
1 TAATTTATAAAAAGATTTGTCACTT-ATTG
* * *
2489836 TAATTTATAAAATA-ATTTTTCACCTATTA
1 TAATTTATAAAA-AGATTTGTCACTTATTG
*
2489865 TAATTTATAAAAAAATTT
1 TAATTTATAAAAAGATTT
2489883 ATCTATATTA
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
28 3 0.05
29 40 0.62
30 21 0.33
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.48
Consensus pattern (29 bp):
TAATTTATAAAAAGATTTGTCACTTATTG
Found at i:2489928 original size:31 final size:28
Alignment explanation
Indices: 2489860--2489929 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 28
2489850 ATTTTTCACC
*
2489860 TATTATAATTTATAAAAAAATTTATCTA
1 TATTATAATTTAAAAAAAAATTTATCTA
*
2489888 TATTATAATTTACAAAAAAAGATTTATCCTC
1 TATTATAATTTA-AAAAAAA-ATTTAT-CTA
*
2489919 TGTTATAATTT
1 TATTATAATTT
2489930 TTCACCTTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 12 0.33
29 6 0.17
30 6 0.17
31 12 0.33
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (28 bp):
TATTATAATTTAAAAAAAAATTTATCTA
Found at i:2490547 original size:353 final size:351
Alignment explanation
Indices: 2490001--2490699 Score: 1281
Period size: 353 Copynumber: 2.0 Consensus size: 351
2489991 AGAGGTGTCG
2490001 GTCCATTTCATAGGCTCTGCCTTTTGTGTTCCCTATTTCTTGTATTGATTTGTCTGGGTTGGCTT
1 GTCCATTTCATAGGCTCTGCCTTTTGTGTTCCCTATTTCTTGTATTGATTTGTCTGGGTTGGCTT
*
2490066 ATTTTCGAACTGCCGAGGGATTGTTGTAGGGATGGGGATGGATTGTGTGATGTATGTTTCTGTGT
66 ATTTTCGAACTGCCGAGGGATTGTTGTAGGGATGGGGATGGATTGTGTGATATATGTTTCTGTGT
* * *
2490131 TTGTTGATCTTACCACCTCAAGGTACACTTTTTTTCTTCCGTTTAAGATTAGAGAGGTTTTTTAA
131 TTGTTGATCTTACCACCTCAAGGTACACTCTTTTTCCTCCATTTAAGATTAGAGAGGTTTTTTAA
*
2490196 TGAGATTCTTGAAGTGGTTTGCTTTCTATTCTTTTTTAATACAAAGTACCATCTTTCAAAAAAAA
196 TGAGATCCTTGAAGTGGTTTGCTTTCTATTCTTTTTTAATACAAAGTACCATCTTTC-AAAAAAA
*
2490261 TAATTTATTGTGCTATAAATCTAGACGTAATTTCATGAAATTATAATATTTTTTAAAAAGTTAAA
260 TAATTTATTGTGCTATAAATCTAGACGTAATTTCATGAAATTATAATATTTTTTAAAAAGAT-AA
2490326 TAAAAAATTATGACAATTTTATTGATTT
324 TAAAAAATTATGACAATTTTATTGATTT
*
2490354 GTCCATTTCATAGGTTCTGCCTTTTGTGTTCCCTATTTCTTGTATTGATTTGTCTGGGTTGGCTT
1 GTCCATTTCATAGGCTCTGCCTTTTGTGTTCCCTATTTCTTGTATTGATTTGTCTGGGTTGGCTT
*
2490419 ATTTTCGAACTGTCGAGGGATTGTTGTAGGGATGGGGATGGATTGTGTGATATATGTTTCTGTGT
66 ATTTTCGAACTGCCGAGGGATTGTTGTAGGGATGGGGATGGATTGTGTGATATATGTTTCTGTGT
*
2490484 TTGTTGATCTTACCACCTCAAGGTACACTCTTTTTCCTCCATTTAAGATTAGGGAGGTTTTTTAA
131 TTGTTGATCTTACCACCTCAAGGTACACTCTTTTTCCTCCATTTAAGATTAGAGAGGTTTTTTAA
* *
2490549 TGAGATCCTTGAGGTGGTTTGCTTTGTATTCTTTTTTAATACAAAGTACCATCTTTCAAAAAAAT
196 TGAGATCCTTGAAGTGGTTTGCTTTCTATTCTTTTTTAATACAAAGTACCATCTTTCAAAAAAAT
2490614 AATTTATTGTGCTATAAATCTAGACGTAATTTCATGAAATTATAATATTTTTTAAAAAGATAATA
261 AATTTATTGTGCTATAAATCTAGACGTAATTTCATGAAATTATAATATTTTTTAAAAAGATAATA
2490679 AAAAATTATGACAATTTTATT
326 AAAAATTATGACAATTTTATT
2490700 TTTGTCATCA
Statistics
Matches: 335, Mismatches: 11, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
351 25 0.07
352 68 0.20
353 242 0.72
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.43
Consensus pattern (351 bp):
GTCCATTTCATAGGCTCTGCCTTTTGTGTTCCCTATTTCTTGTATTGATTTGTCTGGGTTGGCTT
ATTTTCGAACTGCCGAGGGATTGTTGTAGGGATGGGGATGGATTGTGTGATATATGTTTCTGTGT
TTGTTGATCTTACCACCTCAAGGTACACTCTTTTTCCTCCATTTAAGATTAGAGAGGTTTTTTAA
TGAGATCCTTGAAGTGGTTTGCTTTCTATTCTTTTTTAATACAAAGTACCATCTTTCAAAAAAAT
AATTTATTGTGCTATAAATCTAGACGTAATTTCATGAAATTATAATATTTTTTAAAAAGATAATA
AAAAATTATGACAATTTTATTGATTT
Found at i:2495124 original size:22 final size:22
Alignment explanation
Indices: 2495099--2495148 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2495089 TAACGGGCGT
*
2495099 TCAATGGT-TGGTCAACGCCCGG
1 TCAATGGTCTGGTCAACG-ACGG
* *
2495121 TCAAAGTTCTGGTCAACGACGG
1 TCAATGGTCTGGTCAACGACGG
2495143 TCAATG
1 TCAATG
2495149 ACGGTCAACG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (22 bp):
TCAATGGTCTGGTCAACGACGG
Found at i:2497338 original size:48 final size:48
Alignment explanation
Indices: 2497255--2497365 Score: 132
Period size: 48 Copynumber: 2.3 Consensus size: 48
2497245 ATAAACGGAG
* * * *
2497255 ATATCAAAAATCAAAACAGAATTCAGATTAGATATCATAACAGAATCC
1 ATATCAGAAATCAGAACAGAATCCAGATCAGATATCATAACAGAATCC
* * * **
2497303 ATATCAGAAATCAGAACAGAATCCAGGTCATATATCATAACATAATTT
1 ATATCAGAAATCAGAACAGAATCCAGATCAGATATCATAACAGAATCC
*
2497351 AAATCAGAAATCAGA
1 ATATCAGAAATCAGA
2497366 TAAAACATTC
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.50, C:0.16, G:0.10, T:0.23
Consensus pattern (48 bp):
ATATCAGAAATCAGAACAGAATCCAGATCAGATATCATAACAGAATCC
Found at i:2497339 original size:24 final size:24
Alignment explanation
Indices: 2497264--2497344 Score: 90
Period size: 24 Copynumber: 3.4 Consensus size: 24
2497254 GATATCAAAA
* * *
2497264 ATCAAAACAGAATTCAGATTAGAT
1 ATCATAACAGAATCCAGATCAGAT
* *
2497288 ATCATAACAGAATCCATATCAGAA
1 ATCATAACAGAATCCAGATCAGAT
* * *
2497312 ATCAGAACAGAATCCAGGTCATAT
1 ATCATAACAGAATCCAGATCAGAT
2497336 ATCATAACA
1 ATCATAACA
2497345 TAATTTAAAT
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.48, C:0.19, G:0.11, T:0.22
Consensus pattern (24 bp):
ATCATAACAGAATCCAGATCAGAT
Found at i:2506474 original size:21 final size:21
Alignment explanation
Indices: 2506450--2506489 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2506440 TTTTCAAAGG
2506450 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
**
2506471 CATGCGTCGATGCATCAAT
1 CATGCACCGATGCATCAAT
2506490 GAATAAGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:2506539 original size:19 final size:19
Alignment explanation
Indices: 2506515--2506553 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2506505 TCAAATGCAT
2506515 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
2506534 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
2506553 T
1 T
2506554 GATTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:2506632 original size:64 final size:63
Alignment explanation
Indices: 2506450--2506652 Score: 176
Period size: 64 Copynumber: 3.1 Consensus size: 63
2506440 TTTTCAAAGG
* * ** * * * *
2506450 CATGCACCGATGCATCAATACCATGCGTCGATGCATCAATGAATAAGTTGAAACATCAAATGCAT
1 CATGCATCGATGCA-CAAT-CCATGCATCGATGCA-CGCTGATTTA-TTAAAACATCGAATGCAT
*
2506515 TC
62 TT
* ** *
2506517 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGATTTAATTAAAACATCGAATGCATTT
1 CATGCATCGATGCACAATCCATGCATCGATGCACGCTGATTT-ATTAAAACATCGAATGCATTT
* * *
2506581 GATGCATCGATGCACAATCCATGCATCGATGCACCGGGCT-ATTT-TTCAAACATCGAATGCACT
1 CATGCATCGATGCACAATCCATGCATCGATGCA-C--GCTGATTTATTAAAACATCGAATGCATT
2506644 T
63 T
2506645 CATGCATC
1 CATGCATC
2506653 CGTGCACTCT
Statistics
Matches: 114, Mismatches: 18, Indels: 11
0.80 0.13 0.08
Matches are distributed among these distances:
64 76 0.67
65 16 0.14
66 6 0.05
67 16 0.14
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (63 bp):
CATGCATCGATGCACAATCCATGCATCGATGCACGCTGATTTATTAAAACATCGAATGCATTT
Found at i:2509222 original size:49 final size:50
Alignment explanation
Indices: 2509166--2509269 Score: 142
Period size: 50 Copynumber: 2.1 Consensus size: 50
2509156 CAAATTATTT
*
2509166 ATATTTTAATTAA-TGTTATTGGATTGTT-TAGTTCAAAATGTATAAGTTA
1 ATATTTTAATTAATTGTTATTGAATT-TTGTAGTTCAAAATGTATAAGTTA
* * *
2509215 ATATTTTAATTAATTTTTATTGAATTTTGTAGTTGAAAATGTATAATTTA
1 ATATTTTAATTAATTGTTATTGAATTTTGTAGTTCAAAATGTATAAGTTA
2509265 A-ATTT
1 ATATTT
2509270 AATACATTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
49 19 0.39
50 30 0.61
ACGTcount: A:0.36, C:0.01, G:0.12, T:0.52
Consensus pattern (50 bp):
ATATTTTAATTAATTGTTATTGAATTTTGTAGTTCAAAATGTATAAGTTA
Found at i:2509626 original size:29 final size:29
Alignment explanation
Indices: 2509584--2509643 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
2509574 CAACATAAAA
*
2509584 AATATATATTATTGTGTGTGTAGTAATAC
1 AATATATATTATTGTGTGTCTAGTAATAC
2509613 AATATATATTATTGTGTGTCTAGTAATAC
1 AATATATATTATTGTGTGTCTAGTAATAC
2509642 AA
1 AA
2509644 ATTGTGAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.43
Consensus pattern (29 bp):
AATATATATTATTGTGTGTCTAGTAATAC
Found at i:2511649 original size:43 final size:42
Alignment explanation
Indices: 2511602--2511937 Score: 144
Period size: 43 Copynumber: 7.8 Consensus size: 42
2511592 AAAAATGATT
* *
2511602 AAATTATGGGCTTAAATTATAAAAGTAAAAAATATGATTGAAA
1 AAATTA-GGGCATCAATTATAAAAGTAAAAAATATGATTGAAA
* * * *
2511645 AAATTAGTGGCCTCAATTTTAAAGGTAAAAAGTGA-GATT-AAA
1 AAATTAG-GGCATCAATTATAAAAGTAAAAAAT-ATGATTGAAA
* * *
2511687 AAATTTAAGGGAATCAATTTTAAAGGT---AAATAGTGAATT-AAA
1 AAA-TT-AGGGCATCAATTATAAAAGTAAAAAATA-TG-ATTGAAA
* * * *
2511729 AAATTAGAGGTC-TTAATTATAAAGGTAAAAAGTGTGATTGAAAA
1 AAATTAG-GG-CATCAATTATAAAAGTAAAAAATATGATTG-AAA
2511773 AAATTAGGGTCATCAATTATAAATA-TAAAAAAGTGA-GATTG-AA
1 AAATTAGGG-CATCAATTATAAA-AGTAAAAAA-T-ATGATTGAAA
* * *
2511816 AAATTAATGGTC-TCAATTAT-AAAGATAAAAATTGTGATT-ACAA
1 AAATT-A-GGGCATCAATTATAAAAG-TAAAAAATATGATTGA-AA
* * **
2511859 AAATTAGGGGCCTCAATTGTAAATA-TAAAAAATAAAATTGAAGA
1 AAATTA-GGGCATCAATTATAAA-AGTAAAAAATATGATTGAA-A
* ** *
2511903 AAATGAAATG-ACTCAATTATAAAAATAAAAAATAT
1 AAAT-TAGGGCA-TCAATTATAAAAGTAAAAAATAT
2511938 AATAGAGAAA
Statistics
Matches: 227, Mismatches: 33, Indels: 65
0.70 0.10 0.20
Matches are distributed among these distances:
39 1 0.00
40 5 0.02
41 18 0.08
42 30 0.13
43 101 0.44
44 62 0.27
45 10 0.04
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.29
Consensus pattern (42 bp):
AAATTAGGGCATCAATTATAAAAGTAAAAAATATGATTGAAA
Found at i:2511906 original size:87 final size:85
Alignment explanation
Indices: 2511602--2511933 Score: 280
Period size: 87 Copynumber: 3.9 Consensus size: 85
2511592 AAAAATGATT
* * * ** * * *
2511602 AAATTATGGGCTTAAATTATAAA-AGTAAAAAATATGATTGAAAAAATTAGTGGCCTCAATTTTA
1 AAATTAGGGGCATCAATTATAAATA-TAAAAAATAAAATTGAAAAAATTAATGGTCTCAATTATA
* *
2511666 AAGGTAAAAAGTGAGATTAAA
65 AAGATAAAAAGTGTGATTAAA
* * * ** * * * *
2511687 AAATTTAAGGGAATCAATTTTAAAGGTAAATAGT-GAATT-AAAAAATTAGA-GGTCTTAATTAT
1 AAA-TTAGGGGCATCAATTATAAATATAAAAAATAAAATTGAAAAAATTA-ATGGTCTCAATTAT
*
2511749 AAAGGTAAAAAGTGTGATTGAAAA
64 AAAGATAAAAAGTGTGATT--AAA
* * *
2511773 AAATTAGGGTCATCAATTATAAATATAAAAAAGTGAGATTG-AAAAATTAATGGTCTCAATTATA
1 AAATTAGGGGCATCAATTATAAATATAAAAAA-TAAAATTGAAAAAATTAATGGTCTCAATTATA
*
2511837 AAGATAAAAATTGTGATTACAA
65 AAGATAAAAAGTGTGATTA-AA
* * * *
2511859 AAATTAGGGGCCTCAATTGTAAATATAAAAAATAAAATTGAAGAAAATGAAAT-GACTCAATTAT
1 AAATTAGGGGCATCAATTATAAATATAAAAAATAAAATTGAA-AAAAT-TAATGGTCTCAATTAT
*
2511923 AAAAATAAAAA
64 AAAGATAAAAA
2511934 ATATAATAGA
Statistics
Matches: 198, Mismatches: 36, Indels: 24
0.77 0.14 0.09
Matches are distributed among these distances:
84 36 0.18
85 34 0.17
86 61 0.31
87 64 0.32
88 3 0.02
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.29
Consensus pattern (85 bp):
AAATTAGGGGCATCAATTATAAATATAAAAAATAAAATTGAAAAAATTAATGGTCTCAATTATAA
AGATAAAAAGTGTGATTAAA
Found at i:2511949 original size:87 final size:86
Alignment explanation
Indices: 2511771--2511941 Score: 195
Period size: 86 Copynumber: 2.0 Consensus size: 86
2511761 TGTGATTGAA
* * * * *
2511771 AAAAATTAGGGTCATCAATTATAAATATAAAAAAGTGAGATTGAAAAATTAATGGTCTCAATTAT
1 AAAAATTAGGGGCATCAATTATAAATATAAAAAAGTAAAATTGAAAAATAAATGGACTCAATTAT
* * * *
2511836 AAAGATAAAAATTGTGATTAC
66 AAAAATAAAAAATATGAATAC
* *
2511857 AAAAATTAGGGGCCTCAATTGTAAATATAAAAAA-TAAAATTGAAGAAAATGAAAT-GACTCAAT
1 AAAAATTAGGGGCATCAATTATAAATATAAAAAAGTAAAATTG-A-AAAAT-AAATGGACTCAAT
2511920 TATAAAAATAAAAAATAT-AATA
63 TATAAAAATAAAAAATATGAATA
2511942 GAGAAAATAA
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
85 6 0.08
86 35 0.49
87 27 0.38
88 3 0.04
ACGTcount: A:0.54, C:0.06, G:0.12, T:0.27
Consensus pattern (86 bp):
AAAAATTAGGGGCATCAATTATAAATATAAAAAAGTAAAATTGAAAAATAAATGGACTCAATTAT
AAAAATAAAAAATATGAATAC
Found at i:2515131 original size:73 final size:73
Alignment explanation
Indices: 2515012--2515156 Score: 200
Period size: 73 Copynumber: 2.0 Consensus size: 73
2515002 TCTTTTTCCT
* * * *
2515012 CTTTCAAGATTACCGCAAAAATTCATCCAAGAGAAAATCTTTTCAAAGTTTCATCTTCAAAGTTT
1 CTTTCAAGATTACAGCAAAAACTCATCCAAGAGAAAATCTGTTCAAAATTTCATCTTCAAAGTTT
2515077 CAAGATTC
66 CAAGATTC
* * ** *
2515085 CTTTCAAGATTACATCAAAAACTCATTCAAGAGAAGCTCTGTTCAAAATTTCATCTTTAAAGTTT
1 CTTTCAAGATTACAGCAAAAACTCATCCAAGAGAAAATCTGTTCAAAATTTCATCTTCAAAGTTT
*
2515150 CTAGATT
66 CAAGATT
2515157 ACGTCAAAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
73 62 1.00
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (73 bp):
CTTTCAAGATTACAGCAAAAACTCATCCAAGAGAAAATCTGTTCAAAATTTCATCTTCAAAGTTT
CAAGATTC
Found at i:2516352 original size:63 final size:63
Alignment explanation
Indices: 2516205--2516367 Score: 179
Period size: 63 Copynumber: 2.5 Consensus size: 63
2516195 ACTCCAACTA
* *
2516205 AATATCTTTTAATATTCAAATTTAAACAGATAATATTATCTTTTAATTTGAAATATCCAAAAGAT
1 AATATCTTTTAATATTCAAATTTAAATAG---ATATTA-CTTTTAATTTGAAAGATCCAAAAGAT
*
2516270 TT
62 AT
* *
2516272 AA-ACTCCTTTTATTATTCAAATTTAAATAGATATTA-TTTTAATTTGAAAGATTC-AAAGTATA
1 AATA-T-CTTTTAATATTCAAATTTAAATAGATATTACTTTTAATTTGAAAGATCCAAAAG-ATA
2516334 T
63 T
*
2516335 AATTATCTTTTAATATTCAAAGTTAAATAGATA
1 AA-TATCTTTTAATATTCAAATTTAAATAGATA
2516368 ATAAATATCT
Statistics
Matches: 84, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
62 4 0.05
63 46 0.55
64 1 0.01
65 7 0.08
66 1 0.01
67 3 0.04
68 22 0.26
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.44
Consensus pattern (63 bp):
AATATCTTTTAATATTCAAATTTAAATAGATATTACTTTTAATTTGAAAGATCCAAAAGATAT
Found at i:2519911 original size:63 final size:66
Alignment explanation
Indices: 2519770--2519935 Score: 173
Period size: 63 Copynumber: 2.5 Consensus size: 66
2519760 ATTCCAACTA
*
2519770 AATATCTTTTAATATTCAAATTTAAACAGATAATATTATGTTTTAATTTGAAATATCCAAAAGAT
1 AATATCTTTTAATATTCAAATTTAAACAGATAATATTA-GTTTTAATTTAAAATATCCAAAAGAT
*
2519835 TT
65 AT
* * *
2519837 AA-ACTCCTTTTATTATTCAAATTT-AA-ATA-AATATTA-TTTTAATTTAAAATATTC-AAAGT
1 AATA-T-CTTTTAATATTCAAATTTAAACAGATAATATTAGTTTTAATTTAAAATATCCAAAAG-
2519896 ATAT
63 ATAT
** *
2519900 AATTATCTTTTAATATTCAAAACTAAATAGATAATA
1 AA-TATCTTTTAATATTCAAATTTAAACAGATAATA
2519936 AATACCTATT
Statistics
Matches: 82, Mismatches: 9, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
62 4 0.05
63 36 0.44
64 3 0.04
65 10 0.12
66 7 0.09
67 5 0.06
68 17 0.21
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (66 bp):
AATATCTTTTAATATTCAAATTTAAACAGATAATATTAGTTTTAATTTAAAATATCCAAAAGATA
T
Found at i:2522700 original size:21 final size:20
Alignment explanation
Indices: 2522663--2522702 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2522653 TTAATTAAAA
* *
2522663 TTAAAAATTAAATTTGTTTT
1 TTAAAAATAAAAATTGTTTT
2522683 TTAAAAATAAAAAATTGTTT
1 TTAAAAAT-AAAAATTGTTT
2522703 CGACAGTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
TTAAAAATAAAAATTGTTTT
Found at i:2525913 original size:18 final size:18
Alignment explanation
Indices: 2525873--2525935 Score: 74
Period size: 18 Copynumber: 3.4 Consensus size: 18
2525863 CCTAGCATCA
2525873 TGCATTTACATTTTCTGCAT
1 TGCATTTAC-TTTTC-GCAT
*
2525893 TGCATTTACTTTTCACAT
1 TGCATTTACTTTTCGCAT
*
2525911 TGCATTTTA-TTTTTGCAT
1 TGCA-TTTACTTTTCGCAT
2525929 TGCATTT
1 TGCATTT
2525936 TATTAATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
17 3 0.08
18 18 0.46
19 9 0.23
20 9 0.23
ACGTcount: A:0.19, C:0.17, G:0.10, T:0.54
Consensus pattern (18 bp):
TGCATTTACTTTTCGCAT
Found at i:2527752 original size:13 final size:13
Alignment explanation
Indices: 2527736--2527768 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
2527726 TATGACGCGT
2527736 ATTTATGACACAC
1 ATTTATGACACAC
2527749 ATTTATGACACAC
1 ATTTATGACACAC
2527762 ATTTATG
1 ATTTATG
2527769 GCGTTCATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (13 bp):
ATTTATGACACAC
Found at i:2527900 original size:85 final size:85
Alignment explanation
Indices: 2527749--2527908 Score: 198
Period size: 85 Copynumber: 1.9 Consensus size: 85
2527739 TATGACACAC
* * * ** *
2527749 ATTTATGACACACATTTATGGCGTTCATTGAGCGTCATTGAAGCCCCCGTCATAAATCTGCTTGA
1 ATTTATGACACACATGTATGACGTTCATTGAGCGTCATTGAAGCACCCGTCATAAATAAGCATGA
2527814 CACACATTTGCGTGTCATAA
66 CACACATTTGCGTGTCATAA
* * * *
2527834 ATTTATGACACGCATGTATGAC-TTACATTGCGTGTCATTGAAGCACCCGTCATACATGAAG-AT
1 ATTTATGACACACATGTATGACGTT-CATTGAGCGTCATTGAAGCACCCGTCATAAAT-AAGCAT
2527897 GACACACATTTG
64 GACACACATTTG
2527909 TATGACTTAC
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
84 2 0.03
85 60 0.95
86 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (85 bp):
ATTTATGACACACATGTATGACGTTCATTGAGCGTCATTGAAGCACCCGTCATAAATAAGCATGA
CACACATTTGCGTGTCATAA
Found at i:2532434 original size:12 final size:12
Alignment explanation
Indices: 2532417--2532441 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2532407 GCATCGATGC
2532417 ACTGCTACAGTA
1 ACTGCTACAGTA
2532429 ACTGCTACAGTA
1 ACTGCTACAGTA
2532441 A
1 A
2532442 TTTTAACATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (12 bp):
ACTGCTACAGTA
Found at i:2532857 original size:21 final size:21
Alignment explanation
Indices: 2532832--2532901 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
2532822 ATACTTACCA
2532832 TTATTCCATAAGCTCGTTAGC
1 TTATTCCATAAGCTCGTTAGC
** ** *
2532853 TTATTTTATCAATATAC-TTACC
1 TTATTCCAT-AAGCT-CGTTAGC
*
2532875 ATTATTCCATAAGCTCGTAAGC
1 -TTATTCCATAAGCTCGTTAGC
2532897 TTATT
1 TTATT
2532902 TTACCAATAT
Statistics
Matches: 34, Mismatches: 11, Indels: 8
0.64 0.21 0.15
Matches are distributed among these distances:
21 13 0.38
22 13 0.38
23 8 0.24
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.43
Consensus pattern (21 bp):
TTATTCCATAAGCTCGTTAGC
Found at i:2532945 original size:21 final size:21
Alignment explanation
Indices: 2532920--2532989 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
2532910 ATACTTACCA
2532920 TTATTCCATAAGCTCGTAAGC
1 TTATTCCATAAGCTCGTAAGC
**
2532941 TTATTTTACCAATACA-CT--TACCC
1 TTA--TT-CC-ATA-AGCTCGTAAGC
2532964 TTATTCCATAAGCTCGTAAGC
1 TTATTCCATAAGCTCGTAAGC
2532985 TTATT
1 TTATT
2532990 TTACCAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 16
0.65 0.07 0.28
Matches are distributed among these distances:
18 1 0.03
19 5 0.14
20 2 0.05
21 13 0.35
23 8 0.22
24 2 0.05
25 5 0.14
26 1 0.03
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.39
Consensus pattern (21 bp):
TTATTCCATAAGCTCGTAAGC
Found at i:2533064 original size:44 final size:44
Alignment explanation
Indices: 2532766--2533063 Score: 517
Period size: 44 Copynumber: 6.8 Consensus size: 44
2532756 ATATATCCAA
*
2532766 TATTTTCCCAATATACTTACCATTATTCCATAAGCTCGTAAGCT
1 TATTTTACCAATATACTTACCATTATTCCATAAGCTCGTAAGCT
*
2532810 TATTTTACCAATATACTTACCATTATTCCATAAGCTCGTTAGCT
1 TATTTTACCAATATACTTACCATTATTCCATAAGCTCGTAAGCT
*
2532854 TATTTTATCAATATACTTACCATTATTCCATAAGCTCGTAAGCT
1 TATTTTACCAATATACTTACCATTATTCCATAAGCTCGTAAGCT
2532898 TATTTTACCAATATACTTACCATTATTCCATAAGCTCGTAAGCT
1 TATTTTACCAATATACTTACCATTATTCCATAAGCTCGTAAGCT
* *
2532942 TATTTTACCAATACACTTACCCTTATTCCATAAGCTCGTAAGCT
1 TATTTTACCAATATACTTACCATTATTCCATAAGCTCGTAAGCT
* *
2532986 TATTTTACCAATATACTTATCC-TTATTCCATAAGATCGTAAACT
1 TATTTTACCAATATACTTA-CCATTATTCCATAAGCTCGTAAGCT
2533030 TATTTTACCAATATACTTACCATTATTCCATAAG
1 TATTTTACCAATATACTTACCATTATTCCATAAG
2533064 AAATTTGTAC
Statistics
Matches: 242, Mismatches: 10, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
43 2 0.01
44 238 0.98
45 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.40
Consensus pattern (44 bp):
TATTTTACCAATATACTTACCATTATTCCATAAGCTCGTAAGCT
Found at i:2533319 original size:59 final size:59
Alignment explanation
Indices: 2533079--2533702 Score: 502
Period size: 59 Copynumber: 10.6 Consensus size: 59
2533069 TGTACAATTC
* * * * * * * * *
2533079 GTATAATTTCCTTATAATATTAGCACTCTCAGTGCTCTATCTGGAATAT-CATATACTTA
1 GTATGATTTCCTTATCATTTTAGCACACTTAGTGCTCCATATGGAA-ATCCATACACTCA
* ** ** * *
2533138 ATATGATTTCCTCCTCATTTTAGCACACGAAGTGC-CC-TATGCAAGAATCCATAC-CATTA
1 GTATGATTTCCTTATCATTTTAGCACACTTAGTGCTCCATATG-GA-AATCCATACAC-TCA
* * * ** * *
2533197 GTCTGA-TTCTTTTAACATTTTTAG--CACTTAAAGC-CCTATATGAAAATCCATACTA-TTA
1 GTATGATTTC-CTTATCA-TTTTAGCACACTTAGTGCTCC-ATATGGAAATCCATAC-ACTCA
* * * * *** *
2533255 GTATGATTTCCTTATCCTTGTAGAACCCTTAGTGCTTTTTCTGGAAATCCATACACTCA
1 GTATGATTTCCTTATCATTTTAGCACACTTAGTGCTCCATATGGAAATCCATACACTCA
* * * * * * *
2533314 ATATGATTCCCTTACCATTTTAGCACA-TATAATGC-CCTATCTGGAAATCCATATATTCA
1 GTATGATTTCCTTATCATTTTAGCACACT-TAGTGCTCC-ATATGGAAATCCATACACTCA
* * *
2533373 ATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTTA
1 GTATGATTTCCTTATCATTTTAGCACACTTAGTGCTCCATATGGAAATCCATACACTCA
* * * * *
2533432 GTATGATTTCCTTATCTTTTTAGCACA-TATAATGC-CCTATCTGGAAATCCATATATTCA
1 GTATGATTTCCTTATCATTTTAGCACACT-TAGTGCTCC-ATATGGAAATCCATACACTCA
* * *
2533491 ATATGATTTCCTTATCATTTTAGCACACTTAGTGCTCCATATGGAAATCTAGACACTCA
1 GTATGATTTCCTTATCATTTTAGCACACTTAGTGCTCCATATGGAAATCCATACACTCA
* * * * *
2533550 GTATGATTTCTTTATCTTTTTAGCACACTCAGTTCTCCATATGGAAATTCATACACTCA
1 GTATGATTTCCTTATCATTTTAGCACACTTAGTGCTCCATATGGAAATCCATACACTCA
* * * *
2533609 GTATGATTTCCTTATCATTTTAGCACACTCAGTACTCCCTATGGAAATTCATACACTCA
1 GTATGATTTCCTTATCATTTTAGCACACTTAGTGCTCCATATGGAAATCCATACACTCA
*
2533668 GTATGATTTCTTTATCATTTTAGCACA-TATAGTGC
1 GTATGATTTCCTTATCATTTTAGCACACT-TAGTGC
2533703 CATTTGGTAA
Statistics
Matches: 452, Mismatches: 89, Indels: 48
0.77 0.15 0.08
Matches are distributed among these distances:
57 8 0.02
58 43 0.10
59 385 0.85
60 16 0.04
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (59 bp):
GTATGATTTCCTTATCATTTTAGCACACTTAGTGCTCCATATGGAAATCCATACACTCA
Found at i:2533383 original size:118 final size:118
Alignment explanation
Indices: 2533079--2533703 Score: 599
Period size: 118 Copynumber: 5.3 Consensus size: 118
2533069 TGTACAATTC
* * * * * * *
2533079 GTATAATTTCCTTATAATATTAGCAC-TCTCAGTGCTCTATCTGGAATAT-CATATACTT-AATA
1 GTATGATTTCCTTATCATTTTAGCACATAT-AATGCCCTATATGGAA-ATCCATATA-TTCAATA
** ** * *
2533141 TGATTTCCTCCTCATTTTAGCACACGAAGTGC-CC-TATGCAAGAATCCATAC-CATTA
63 TGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATG-GA-AATCCATACAC-TCA
* * * * * *
2533197 GTCTGA-TTCTTTTAACATTTTTAGCAC-T-TAAAGCCCTATATGAAAATCCATACTATT-AGTA
1 GTATGATTTC-CTTATCA-TTTTAGCACATATAATGCCCTATATGGAAATCCATA-TATTCAATA
* * * * * *** *
2533258 TGATTTCCTTATCCTTGTAGAACCCTTAGTGCTTTTTCTGGAAATCCATACACTCA
63 TGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCA
* * * *
2533314 ATATGATTCCCTTACCATTTTAGCACATATAATGCCCTATCTGGAAATCCATATATTCAATATGA
1 GTATGATTTCCTTATCATTTTAGCACATATAATGCCCTATATGGAAATCCATATATTCAATATGA
*
2533379 TTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTTA
66 TTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCA
* *
2533432 GTATGATTTCCTTATCTTTTTAGCACATATAATGCCCTATCTGGAAATCCATATATTCAATATGA
1 GTATGATTTCCTTATCATTTTAGCACATATAATGCCCTATATGGAAATCCATATATTCAATATGA
* * *
2533497 TTTCCTTATCATTTTAGCACACTTAGTGCTCCATATGGAAATCTAGACACTCA
66 TTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCA
* * * * * * * * *
2533550 GTATGATTTCTTTATCTTTTTAGCACACT-CAGTTCTCC-ATATGGAAATTCATACACTCAGTAT
1 GTATGATTTCCTTATCATTTTAGCACA-TATAATGC-CCTATATGGAAATCCATATATTCAATAT
* * *
2533613 GATTTCCTTATCATTTTAGCACACTCAGTACTCCCTATGGAAATTCATACACTCA
64 GATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCA
* *
2533668 GTATGATTTCTTTATCATTTTAGCACATATAGTGCC
1 GTATGATTTCCTTATCATTTTAGCACATATAATGCC
2533704 ATTTGGTAAT
Statistics
Matches: 423, Mismatches: 70, Indels: 29
0.81 0.13 0.06
Matches are distributed among these distances:
116 11 0.03
117 74 0.17
118 323 0.76
119 15 0.04
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (118 bp):
GTATGATTTCCTTATCATTTTAGCACATATAATGCCCTATATGGAAATCCATATATTCAATATGA
TTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCA
Found at i:2533478 original size:177 final size:176
Alignment explanation
Indices: 2533234--2533703 Score: 556
Period size: 177 Copynumber: 2.7 Consensus size: 176
2533224 TTAAAGCCCT
* * * * * * ** *
2533234 ATATGAAAATCCATACTA-TTAGTATGATTTCCTTATCCTTGTAGAACCCT-TAGTGCTTTTTCT
1 ATATGGAAATCCATAC-ACTTAGTATGATTTCCTTATCATTTTAGCA-CATATAATGCCCTATCT
* * * *
2533297 GGAAATCCATACACTCAATATGATTCCCTTACCATTTTAGCACATATAATGCCCTATCTGGAAAT
64 GGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACATATAGTGCCC-ATATGGAAAT
* * *
2533362 CCATATATTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCC
128 CCAGACACTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCC
*
2533411 ATATGGAAATCCATACACTTAGTATGATTTCCTTATCTTTTTAGCACATATAATGCCCTATCTGG
1 ATATGGAAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACATATAATGCCCTATCTGG
* *
2533476 AAATCCATATATTCAATATGATTTCCTTATCATTTTAGCACACT-TAGTGCTCCATATGGAAATC
66 AAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACA-TATAGTGC-CCATATGGAAATC
* * * * *
2533540 TAGACACTCAGTATGATTTCTTTATCTTTTTAGCACACTCAGTTCTCC
129 CAGACACTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCC
* * *
2533588 ATATGGAAATTCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTACT-CCCTA--
1 ATATGGAAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACA-T-A-TAATGCCCTATC
* * *
2533650 TGGAAATTCATACACTCAGTATGATTTCTTTATCATTTTAGCACATATAGTGCC
63 TGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACATATAGTGCC
2533704 ATTTGGTAAT
Statistics
Matches: 253, Mismatches: 32, Indels: 17
0.84 0.11 0.06
Matches are distributed among these distances:
176 5 0.02
177 235 0.93
178 4 0.02
179 6 0.02
180 3 0.01
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (176 bp):
ATATGGAAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACATATAATGCCCTATCTGG
AAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACATATAGTGCCCATATGGAAATCCA
GACACTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCC
Found at i:2537154 original size:16 final size:16
Alignment explanation
Indices: 2537133--2537167 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2537123 TGTAAAACAA
2537133 TTGGAATGCAGAAGAG
1 TTGGAATGCAGAAGAG
2537149 TTGGAATGCAGAAGAG
1 TTGGAATGCAGAAGAG
2537165 TTG
1 TTG
2537168 CTTGTAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.34, C:0.06, G:0.37, T:0.23
Consensus pattern (16 bp):
TTGGAATGCAGAAGAG
Found at i:2540883 original size:20 final size:20
Alignment explanation
Indices: 2540866--2540941 Score: 62
Period size: 23 Copynumber: 3.5 Consensus size: 20
2540856 TGAAAAGGGG
*
2540866 AAAAAATAAAAAAAAAGGAA
1 AAAAAAGAAAAAAAAAGGAA
*
2540886 AAAAAAGAAAAAAGAAGAATGAA
1 AAAAAAG-AAAAA-AA-AAGGAA
* *
2540909 AAAAGAAGAATGAAAAAAGAAGA
1 AAAA-AAGAA-AAAAAAAGGA-A
2540932 AAAAAAGAAA
1 AAAAAAGAAA
2540942 GATGAAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
20 6 0.14
21 5 0.11
22 10 0.23
23 18 0.41
24 5 0.11
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (20 bp):
AAAAAAGAAAAAAAAAGGAA
Found at i:2540885 original size:18 final size:17
Alignment explanation
Indices: 2540864--2540899 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2540854 AATGAAAAGG
2540864 GGAAAAAATAAAAAAAAA
1 GGAAAAAA-AAAAAAAAA
*
2540882 GGAAAAAAAAGAAAAAA
1 GGAAAAAAAAAAAAAAA
2540899 G
1 G
2540900 AAGAATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.03
Consensus pattern (17 bp):
GGAAAAAAAAAAAAAAA
Found at i:2540887 original size:9 final size:9
Alignment explanation
Indices: 2540865--2540941 Score: 54
Period size: 9 Copynumber: 8.4 Consensus size: 9
2540855 ATGAAAAGGG
2540865 GAAAAAATAA
1 GAAAAAA-AA
*
2540875 -AAAAAAAG
1 GAAAAAAAA
2540883 GAAAAAAAA
1 GAAAAAAAA
2540892 GAAAAAAGAA
1 GAAAAAA-AA
2540902 GAATGAAAAAA
1 GAA--AAAAAA
* *
2540913 G--AAGAAT
1 GAAAAAAAA
2540920 GAAAAAAGAA
1 GAAAAAA-AA
2540930 G-AAAAAAA
1 GAAAAAAAA
2540938 GAAA
1 GAAA
2540942 GATGAAAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 17
0.70 0.08 0.22
Matches are distributed among these distances:
7 5 0.09
8 4 0.08
9 30 0.57
10 7 0.13
11 3 0.06
12 4 0.08
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:2540896 original size:7 final size:7
Alignment explanation
Indices: 2540865--2540943 Score: 56
Period size: 7 Copynumber: 11.3 Consensus size: 7
2540855 ATGAAAAGGG
2540865 GAAAAAA
1 GAAAAAA
*
2540872 TAAAAAA
1 GAAAAAA
*
2540879 -AAAGGAA
1 GAAA-AAA
2540886 -AAAAAA
1 GAAAAAA
2540892 GAAAAAA
1 GAAAAAA
* *
2540899 GAAGAAT
1 GAAAAAA
2540906 GAAAAAA
1 GAAAAAA
* *
2540913 GAAGAAT
1 GAAAAAA
2540920 GAAAAAA
1 GAAAAAA
2540927 GAAGAAAA
1 GAA-AAAA
2540935 -AAAGAAA
1 GAAA-AAA
2540942 GA
1 GA
2540944 TGAAAAAAAT
Statistics
Matches: 56, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
6 6 0.11
7 45 0.80
8 5 0.09
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (7 bp):
GAAAAAA
Found at i:2540909 original size:14 final size:14
Alignment explanation
Indices: 2540892--2540951 Score: 83
Period size: 14 Copynumber: 4.5 Consensus size: 14
2540882 GGAAAAAAAA
2540892 GAAAAAAGAAGAAT
1 GAAAAAAGAAGAAT
2540906 GAAAAAAGAAGAAT
1 GAAAAAAGAAGAAT
2540920 GAAAAAAGAAG-A-
1 GAAAAAAGAAGAAT
2540932 -AAAAAAGAA-AGAT
1 GAAAAAAGAAGA-AT
2540945 GAAAAAA
1 GAAAAAA
2540952 ATAAATAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.21
12 1 0.02
13 1 0.02
14 31 0.74
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (14 bp):
GAAAAAAGAAGAAT
Found at i:2540935 original size:25 final size:24
Alignment explanation
Indices: 2540873--2540951 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 24
2540863 GGGAAAAAAT
*
2540873 AAAAAAAAAGGAAAAAA-AAGAA--
1 AAAAAAGAA-GAAAAAAGAAGAATG
2540895 AAAAGAAGAATGAAAAAAGAAGAATG
1 AAAA-AAGAA-GAAAAAAGAAGAATG
2540921 AAAAAAGAAGAAAAAAAGAA-AGATG
1 AAAAAAGAAG-AAAAAAGAAGA-ATG
2540946 AAAAAA
1 AAAAAA
2540952 ATAAATAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
22 4 0.08
23 11 0.22
24 7 0.14
25 23 0.47
26 4 0.08
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (24 bp):
AAAAAAGAAGAAAAAAGAAGAATG
Found at i:2540939 original size:11 final size:10
Alignment explanation
Indices: 2540866--2540941 Score: 62
Period size: 11 Copynumber: 7.0 Consensus size: 10
2540856 TGAAAAGGGG
*
2540866 AAAAAATAAA
1 AAAAAAGAAA
*
2540876 AAAAAAGGAA
1 AAAAAAGAAA
2540886 AAAAAAGAAAA
1 AAAAAAG-AAA
2540897 AAGAAGAATGAAA
1 AA-AA-AA-GAAA
* *
2540910 AAAGAAGAATG
1 AAAAAAGAA-A
2540921 AAAAAAGAAGA
1 AAAAAAGAA-A
2540932 AAAAAAGAAA
1 AAAAAAGAAA
2540942 GATGAAAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
10 19 0.36
11 23 0.43
12 3 0.06
13 7 0.13
14 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:2542409 original size:15 final size:16
Alignment explanation
Indices: 2542385--2542419 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2542375 AAAGAATAAA
*
2542385 AAAATTAAAAAA-AAG
1 AAAATGAAAAAAGAAG
2542400 AAAATGAAAAAAGAAG
1 AAAATGAAAAAAGAAG
2542416 AAAA
1 AAAA
2542420 AAAGAAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (16 bp):
AAAATGAAAAAAGAAG
Found at i:2542410 original size:25 final size:24
Alignment explanation
Indices: 2542382--2542452 Score: 72
Period size: 25 Copynumber: 2.9 Consensus size: 24
2542372 GAAAAAGAAT
*
2542382 AAAAAAATTAAAAAAAAGAAA-ATG
1 AAAAAAA-AAAAAAAAAGAAAGATG
*
2542406 AAAAAAGAAGAAAAAAAGAAAGATG
1 AAAAAA-AAAAAAAAAAGAAAGATG
* *
2542431 AAAAAAATAAATAAATAGAAAG
1 AAAAAAA-AAAAAAAAAGAAAG
2542453 GGGGTTCAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
24 18 0.46
25 21 0.54
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (24 bp):
AAAAAAAAAAAAAAAAGAAAGATG
Found at i:2543966 original size:132 final size:133
Alignment explanation
Indices: 2543769--2544206 Score: 496
Period size: 132 Copynumber: 3.3 Consensus size: 133
2543759 GATAATGAAA
* * * * *
2543769 TGAATCAACGTTTACAGATCTGATCTACCCTGAGGAGCAG-TGAAGCAGATCC-CCTTATTTCAG
1 TGAATCAACGTTTCCAGATCTGATCTACCCTGAAGAGTAGCAGAATCAGATCCTCCTT-TTTCAG
* * * * * *
2543832 ATTTGATATTCCCTGAGGAACAGTAGAATAAATCTACCTTGATTCAATATACCCTGAATAGCAGT
65 ATTTGATATTCCCTGAGGAGCAGTAGAACAAATCTACCTCGATTCAATATTCCCTAAAGAGCAGT
2543897 AGAG
130 AGAG
* * * * *
2543901 TGAATCAATGTTTTCAGATTTGATCTACCCAGAAGAGTAGCAG-ATCAGATCCTTCTTTTTCAGA
1 TGAATCAACGTTTCCAGATCTGATCTACCCTGAAGAGTAGCAGAATCAGATCCTCCTTTTTCAGA
* * * * * * *
2543965 TTTGATCTTCCCTGAGGAGTAGTAGAACAAGTATACCTCGATTGAATTTTCCCTAAAGATCAGTA
66 TTTGATATTCCCTGAGGAGCAGTAGAACAAATCTACCTCGATTCAATATTCCCTAAAGAGCAGTA
2544030 GAG
131 GAG
* *
2544033 TGAATCAAC-TTTCCAAATCTGATCTACCCTGAAGAGTAGC-GAAGT-AGATCACTCCTTTTTTA
1 TGAATCAACGTTTCCAGATCTGATCTACCCTGAAGAGTAGCAGAA-TCAGATC-CTCCTTTTTCA
* * *
2544095 GATTTGATATTCCC-GAAGGAGCAGTGGAACAAATCTCCCTCGATTCAATCTTCCCTAAAGAGCA
64 GATTTGATATTCCCTG-AGGAGCAGTAGAACAAATCTACCTCGATTCAATATTCCCTAAAGAGCA
2544159 GT-GAAG
128 GTAG-AG
* * *
2544165 TGAATAAACATTTCCAGATCTGATCTACCCTGAAGAATAGCA
1 TGAATCAACGTTTCCAGATCTGATCTACCCTGAAGAGTAGCA
2544207 TAGCAAATCT
Statistics
Matches: 256, Mismatches: 41, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
130 1 0.00
131 35 0.14
132 187 0.73
133 33 0.13
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (133 bp):
TGAATCAACGTTTCCAGATCTGATCTACCCTGAAGAGTAGCAGAATCAGATCCTCCTTTTTCAGA
TTTGATATTCCCTGAGGAGCAGTAGAACAAATCTACCTCGATTCAATATTCCCTAAAGAGCAGTA
GAG
Found at i:2544431 original size:19 final size:19
Alignment explanation
Indices: 2544379--2544444 Score: 55
Period size: 22 Copynumber: 3.2 Consensus size: 19
2544369 TAAATAATAA
2544379 TATTTTTA-ATTATTATTAT
1 TATTTTTATA-TATTATTAT
2544398 TATTATTTAACTATATTAGTT-T
1 TATT-TTT-A-TATATTA-TTAT
2544420 TATTTTTATATATTTATTTAT
1 TATTTTTATATA-TTA-TTAT
2544441 TATT
1 TATT
2544445 ATTTTTATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
19 8 0.21
20 9 0.23
21 9 0.23
22 10 0.26
23 3 0.08
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TATTTTTATATATTATTAT
Found at i:2544437 original size:14 final size:14
Alignment explanation
Indices: 2544394--2544448 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
2544384 TTAATTATTA
*
2544394 TTATTATTATTTAA
1 TTATTATTATTTAT
*
2544408 CTA-TATTAGTTTTAT
1 TTATTATTA--TTTAT
2544423 TT-TTATATATTTAT
1 TTATTAT-TATTTAT
2544437 TTATTATTATTT
1 TTATTATTATTT
2544449 TTATTACAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
13 5 0.15
14 14 0.42
15 12 0.36
16 2 0.06
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (14 bp):
TTATTATTATTTAT
Found at i:2548249 original size:21 final size:21
Alignment explanation
Indices: 2548220--2548267 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
2548210 CTTTCTCAAT
*
2548220 GCTTAGGAGTGGGAGGAAAGC
1 GCTTGGGAGTGGGAGGAAAGC
2548241 GCTTGGGAGTGGGAGGAAAGC
1 GCTTGGGAGTGGGAGGAAAGC
*
2548262 ACTTGG
1 GCTTGG
2548268 AACATTCGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.25, C:0.10, G:0.48, T:0.17
Consensus pattern (21 bp):
GCTTGGGAGTGGGAGGAAAGC
Found at i:2553034 original size:19 final size:18
Alignment explanation
Indices: 2552990--2553040 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 18
2552980 AGGGAAAATA
2552990 TTATTTTTGA-TTTATTCC
1 TTATTTTT-ATTTTATTCC
2553008 TT-TATTTTATTTTATTTCC
1 TTAT-TTTTATTTTA-TTCC
2553027 TTATTTTTACTTTT
1 TTATTTTTA-TTTT
2553041 CTCTTTTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
17 2 0.07
18 10 0.36
19 11 0.39
20 5 0.18
ACGTcount: A:0.16, C:0.10, G:0.02, T:0.73
Consensus pattern (18 bp):
TTATTTTTATTTTATTCC
Found at i:2557716 original size:23 final size:23
Alignment explanation
Indices: 2557681--2557728 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
2557671 ATCAAGTACA
*
2557681 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
2557704 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
2557727 AT
1 AT
2557729 TAACATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:2558641 original size:182 final size:182
Alignment explanation
Indices: 2558331--2559323 Score: 1538
Period size: 182 Copynumber: 5.5 Consensus size: 182
2558321 TTTTTACTAT
* *
2558331 CGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTATCTGTTATATTGTTATGTATCGATAC
1 CGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
* * *
2558396 ATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCTAAAAGTGT
66 ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
2558461 CGATACTTATAATAAAGTATCGACACTTTCAACATATTCGGTAGCTCTTTAC
131 CGATACTTATAATAAAGTATCGACACTTTCAACATATTCGGTAGCTCTTTAC
* * * *
2558513 CGATTTTGTCATTTTGAGACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATAT
1 CGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
2558578 ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
66 ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
*
2558643 CAATACTTATAATAAAGTATCGACACTTTCAACATA-TCTGGTAGCTCTTTAC
131 CGATACTTATAATAAAGTATCGACACTTTCAACATATTC-GGTAGCTCTTTAC
* * *
2558695 CGGTTTTGTCATTTCGAGACCGGTTTTGTTATATTTTTACCTGTTATATTGTTATAGATCGATAC
1 CGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
* * *
2558760 ATTTTTATAAAGTATCGACATTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAGTGT
66 ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
* *
2558825 CGATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCTATTTAC
131 CGATACTTATAATAAAGTATCGACACTTTCAACATATTCGGTAGCTCTTTAC
* *
2558877 CGGTTTTGTCATTTTGAGA-CTAGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATA
1 CGGTTTTGTCATTTCGAGACCGA-TTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATA
*
2558941 CATTTTTATAAAGTATCGACACTTTAATAGCGCTATAA---CTTCTCTTTTAAATTCCAAAAGTG
65 CATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTG
* *
2559003 TTGATACTTATAATAAAGTATCGACACTTTCAAGATA-TCTGGTAGCTCTTTAC
130 TCGATACTTATAATAAAGTATCGACACTTTCAACATATTC-GGTAGCTCTTTAC
2559056 CGGTTTTGTCATTTCGAGACC-AGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATA
1 CGGTTTTGTCATTTCGAGACCGA-TTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATA
2559120 CATTTTTATAAAGTATCGACACTTTATTAGCGCTATAA---CTTCTCTTTTAAATTCCAAAAGTG
65 CATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTG
* * * * *
2559182 TCGATACTTTTTATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTAC
130 TCGATACTTATAATAAAGTATCGACACTTTCAACATATTCGGTAGCTCTTTAC
* ** * * * * * * *
2559235 CTGTTTTGTCATTTATAGAGCGGTTTTCTCATTTTTTTACCTATTATATTATTATTGATCGATAC
1 CGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
2559300 ATTTTTATAAAGTATCGACACTTT
66 ATTTTTATAAAGTATCGACACTTT
2559324 CAATATATCC
Statistics
Matches: 749, Mismatches: 55, Indels: 17
0.91 0.07 0.02
Matches are distributed among these distances:
178 1 0.00
179 314 0.42
180 2 0.00
181 3 0.00
182 428 0.57
183 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (182 bp):
CGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
CGATACTTATAATAAAGTATCGACACTTTCAACATATTCGGTAGCTCTTTAC
Found at i:2559437 original size:111 final size:111
Alignment explanation
Indices: 2559182--2559543 Score: 591
Period size: 112 Copynumber: 3.3 Consensus size: 111
2559172 TCCAAAAGTG
* *
2559182 TCGATAC-TTTTTATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCA
1 TCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCA
* * * * *
2559246 TTTATAGAGCGGTTTTCTCATTTTTTTACCTATTATATTATTATTGA
66 TTTATAGACCGGTTTTATCA-TTTTTTACCTGTTATATTGTTATGGA
*
2559293 TCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACATGTTTTGTCA
1 TCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCA
2559358 TTTATAGACCGGTTTTATCATTTTTTACCTGTTATATTGTTATGGA
66 TTTATAGACCGGTTTTATCATTTTTTACCTGTTATATTGTTATGGA
2559404 TCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCA
1 TCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCA
*
2559469 TTTATAGACCGGTTTTGTCATTTTCTTACCTGTTATATTGTTATGGA
66 TTTATAGACCGGTTTTATCATTTT-TTACCTGTTATATTGTTATGGA
* * *
2559516 TCAATATATTTTTATAAAATATCGACAC
1 TCGATACATTTTTATAAAGTATCGACAC
2559544 AAATCGACAA
Statistics
Matches: 236, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
111 117 0.50
112 119 0.50
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.44
Consensus pattern (111 bp):
TCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCA
TTTATAGACCGGTTTTATCATTTTTTACCTGTTATATTGTTATGGA
Found at i:2560130 original size:42 final size:42
Alignment explanation
Indices: 2560059--2560194 Score: 143
Period size: 42 Copynumber: 3.2 Consensus size: 42
2560049 TAGGGACTTA
* * * *
2560059 AATTATAAAAAT-AAAAGTTAGATTGAAAAAATCAAAAGCTTC
1 AATTATAAAGATAAAAAGTGAGATTAAAAAAAT-TAAAGCTTC
** *
2560101 AATTATAAAGATAAAAAGTGA-ACTT-AAAAAATTAGGGATTTC
1 AATTATAAAGATAAAAAGTGAGA-TTAAAAAAATTAAAG-CTTC
*
2560143 AGTTATAAAGATAAAAAGTGAGATTAAAAAAATTAAAGCGTTC
1 AATTATAAAGATAAAAAGTGAGATTAAAAAAATTAAAGC-TTC
2560186 AATTATAAA
1 AATTATAAA
2560195 ATATTAAAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
41 2 0.03
42 44 0.57
43 31 0.40
ACGTcount: A:0.55, C:0.05, G:0.12, T:0.27
Consensus pattern (42 bp):
AATTATAAAGATAAAAAGTGAGATTAAAAAAATTAAAGCTTC
Found at i:2560201 original size:32 final size:32
Alignment explanation
Indices: 2560165--2560226 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
2560155 AAAAAGTGAG
*
2560165 ATTAAAAAAATTAAAGCGT-TCAATTATAAAAT
1 ATTAAAAAAATTAAAG-GTCTCAAATATAAAAT
*
2560197 ATTAAAAAAATTAGAGGTCTCAAATATAAA
1 ATTAAAAAAATTAAAGGTCTCAAATATAAA
2560227 TGTAATACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 2 0.07
32 25 0.93
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.29
Consensus pattern (32 bp):
ATTAAAAAAATTAAAGGTCTCAAATATAAAAT
Found at i:2561658 original size:18 final size:19
Alignment explanation
Indices: 2561620--2561659 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2561610 GAAACCGAGA
*
2561620 CTTTAACAAATAAAATAAT
1 CTTTAACAAAAAAAATAAT
*
2561639 CTTTATCAAAAAAAAT-AT
1 CTTTAACAAAAAAAATAAT
2561657 CTT
1 CTT
2561660 GAAATAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (19 bp):
CTTTAACAAAAAAAATAAT
Found at i:2564883 original size:3 final size:3
Alignment explanation
Indices: 2564870--2564980 Score: 63
Period size: 3 Copynumber: 38.7 Consensus size: 3
2564860 ATTGTTTTAC
* * ** *
2564870 TAT TA- TAT TAT TAT TAG TAC TA- TAT TA- TAT TAT TAT TGC TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
2564915 CAT TAT TAT TA- TGT TA- TAT TAC TAT TAT TAA TAT TA- TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
2564960 TACT TAC TAT TAG TAT TAT TA
1 TA-T TAT TAT TAT TAT TAT TA
2564981 CTGTCAATGA
Statistics
Matches: 79, Mismatches: 22, Indels: 14
0.69 0.19 0.12
Matches are distributed among these distances:
2 11 0.14
3 65 0.82
4 3 0.04
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:2564941 original size:22 final size:21
Alignment explanation
Indices: 2564870--2564961 Score: 70
Period size: 22 Copynumber: 4.5 Consensus size: 21
2564860 ATTGTTTTAC
2564870 TATTATATTATTATTA-GTACTA
1 TATTATATTATTATTATGT--TA
*
2564892 TATTATATTATTA-T-TGCTA
1 TATTATATTATTATTATGTTA
* *
2564911 T-TAACATTATTATTATGTTA
1 TATTATATTATTATTATGTTA
*
2564931 TATTACTATTATTA--ATATTA
1 TATTA-TATTATTATTATGTTA
2564951 TATTATCATTA
1 TATTAT-ATTA
2564962 CTTACTATTA
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
18 9 0.16
19 5 0.09
20 19 0.33
21 4 0.07
22 20 0.35
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.55
Consensus pattern (21 bp):
TATTATATTATTATTATGTTA
Found at i:2565114 original size:3 final size:3
Alignment explanation
Indices: 2565108--2565273 Score: 54
Period size: 3 Copynumber: 55.0 Consensus size: 3
2565098 CGTGTACTAC
* * * *
2565108 TAT TAT TAT TGT TAA TAT TAT TAA TAT T-T TAC TAT T-T CTA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
* * * * * *
2565151 TAT CAT TACT TCAC TATT TAT TGT TAT TA- TAT TAT TAT TAC TA- AAG
1 TAT TAT TA-T T-AT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * *
2565197 TAG TAT TAG TAT TAT TGGT GAG TAT TAT TAT TAT TAT TAG TAG TAG
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
2565243 TAG TAT TAT CACT TAT TAT TTT TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
2565274 ATACTACTAT
Statistics
Matches: 120, Mismatches: 32, Indels: 22
0.69 0.18 0.13
Matches are distributed among these distances:
2 8 0.07
3 103 0.86
4 8 0.07
5 1 0.01
ACGTcount: A:0.31, C:0.05, G:0.08, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:2576626 original size:17 final size:17
Alignment explanation
Indices: 2576575--2576628 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 17
2576565 GCAATACATC
2576575 ACTTGGTTGATATATAA
1 ACTTGGTTGATATATAA
* **
2576592 ACTTGATCCAT-T-TAA
1 ACTTGGTTGATATATAA
2576607 ACTTGGTTGATATATAA
1 ACTTGGTTGATATATAA
2576624 ACTTG
1 ACTTG
2576629 TTATCAAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 11 0.38
16 2 0.07
17 16 0.55
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (17 bp):
ACTTGGTTGATATATAA
Found at i:2578537 original size:16 final size:16
Alignment explanation
Indices: 2578516--2578590 Score: 62
Period size: 16 Copynumber: 4.4 Consensus size: 16
2578506 ATAGGAGAAA
2578516 GGAAAAAAAAGAAAAT
1 GGAAAAAAAAGAAAAT
*
2578532 GGAAAAAGAAGAAAAT
1 GGAAAAAAAAGAAAAT
* *
2578548 AAAGAAAAAAAATGAAAAA
1 --GGAAAAAAAA-GAAAAT
*
2578567 GAACAAAAAAAGAATAA-
1 GGA-AAAAAAAGAA-AAT
2578584 GGAAAAA
1 GGAAAAA
2578591 GGAGGGTTCA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
16 19 0.40
17 6 0.13
18 17 0.36
19 5 0.11
ACGTcount: A:0.76, C:0.01, G:0.17, T:0.05
Consensus pattern (16 bp):
GGAAAAAAAAGAAAAT
Found at i:2578567 original size:28 final size:29
Alignment explanation
Indices: 2578518--2578589 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 29
2578508 AGGAGAAAGG
*
2578518 AAAA-AAAAGAAAATGGAAAAAGAAGAAA
1 AAAAGAAAAGAAAATGGAAAAAGAACAAA
2578546 ATAAAGAAAA-AAAAT-GAAAAAGAACAAA
1 A-AAAGAAAAGAAAATGGAAAAAGAACAAA
2578574 AAAAGAATAAGGAAAA
1 AAAAGAA-AA-GAAAA
2578590 AGGAGGGTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
27 6 0.16
28 16 0.42
29 8 0.21
30 8 0.21
ACGTcount: A:0.78, C:0.01, G:0.15, T:0.06
Consensus pattern (29 bp):
AAAAGAAAAGAAAATGGAAAAAGAACAAA
Found at i:2582680 original size:101 final size:101
Alignment explanation
Indices: 2582429--2582728 Score: 287
Period size: 101 Copynumber: 2.9 Consensus size: 101
2582419 TCACAAAAGG
* * * * * **
2582429 GGTGGATCAACATTTCTAGAAGAGTTCATAATAAGAAGAACTCACCCC-AAGGAAAAAGTTTGTA
1 GGTGGATCGACATTTCCAGAAGAGTTCTTAACAAGAAAAACTCACCCCGAA-GAAAAAGTTCATA
* * * * * * *
2582493 ATGAGAAGAGCTTATTTGATTCCTTTCGAGTCCAAGTAGAAGGA
65 ATGAGAAGAAC--A--T-ATCCCTTTCAAAT-CTA-TCGTAGGA
* * ** * *
2582537 GGTGGATCGACCTTTTCAGAAGAGTTCTTAATGAGAAAAACTCTCCCCGAAGAAAAATTTCATAA
1 GGTGGATCGACATTTCCAGAAGAGTTCTTAACAAGAAAAACTCACCCCGAAGAAAAAGTTCATAA
2582602 TGAGAAGAACATATCCCTTTCAAATCTATCGTAGGA
66 TGAGAAGAACATATCCCTTTCAAATCTATCGTAGGA
* * * *
2582638 TGTGGGTCGACATTTCCAGAAGAGTTCTTAACAATAAGAACTCACCCCGAAGAAAAAGTTCATAA
1 GGTGGATCGACATTTCCAGAAGAGTTCTTAACAAGAAAAACTCACCCCGAAGAAAAAGTTCATAA
* *
2582703 TTAGAAGAACTTATCCCTTTCAAATC
66 TGAGAAGAACATATCCCTTTCAAATC
2582729 CATCACATAA
Statistics
Matches: 161, Mismatches: 30, Indels: 9
0.81 0.15 0.05
Matches are distributed among these distances:
101 85 0.53
102 2 0.01
103 10 0.06
104 1 0.01
106 1 0.01
108 60 0.37
109 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (101 bp):
GGTGGATCGACATTTCCAGAAGAGTTCTTAACAAGAAAAACTCACCCCGAAGAAAAAGTTCATAA
TGAGAAGAACATATCCCTTTCAAATCTATCGTAGGA
Found at i:2585053 original size:103 final size:103
Alignment explanation
Indices: 2584879--2585068 Score: 290
Period size: 103 Copynumber: 1.8 Consensus size: 103
2584869 ATTGTTTTTT
* *
2584879 TACGAAGGGAGTTAGACCATCACTCCTACCATCCCACACTCTAGATGAAAGGGAGCATACATTCC
1 TACGAAGGGAGTCAGACCATCACACCTACCATCCCACACTCTAGATGAAAGGGAGCATACATTCC
* *
2584944 ATCCCCAAGCTAGTCAGGTAGATTTTTTTTTGTTCTGC
66 ACCCCCAAGCTAGTCAAGTAGATTTTTTTTTGTTCTGC
* * * ** *
2584982 TACGAAGGGAGTCAGCCCATCACACCTACCATCCCATACTCTAGGTGAAAGGTTGCATACCTTCC
1 TACGAAGGGAGTCAGACCATCACACCTACCATCCCACACTCTAGATGAAAGGGAGCATACATTCC
2585047 ACCCCCAAGCTAGTCAAGTAGA
66 ACCCCCAAGCTAGTCAAGTAGA
2585069 GTCATCCTGT
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
103 77 1.00
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.24
Consensus pattern (103 bp):
TACGAAGGGAGTCAGACCATCACACCTACCATCCCACACTCTAGATGAAAGGGAGCATACATTCC
ACCCCCAAGCTAGTCAAGTAGATTTTTTTTTGTTCTGC
Found at i:2593456 original size:39 final size:39
Alignment explanation
Indices: 2593363--2593458 Score: 183
Period size: 39 Copynumber: 2.5 Consensus size: 39
2593353 AATAGAGAAG
*
2593363 AGTTCATAATGAGAAAAACTCGTCCTAAGAAGAGTAAAA
1 AGTTCATAATGAGAAGAACTCGTCCTAAGAAGAGTAAAA
2593402 AGTTCATAATGAGAAGAACTCGTCCTAAGAAGAGTAAAA
1 AGTTCATAATGAGAAGAACTCGTCCTAAGAAGAGTAAAA
2593441 AGTTCATAATGAGAAGAA
1 AGTTCATAATGAGAAGAA
2593459 TTTGGAGATC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.48, C:0.11, G:0.20, T:0.21
Consensus pattern (39 bp):
AGTTCATAATGAGAAGAACTCGTCCTAAGAAGAGTAAAA
Found at i:2593672 original size:22 final size:21
Alignment explanation
Indices: 2593647--2593714 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 21
2593637 ATAATATAGG
* *
2593647 TATTGTTTTACTATTATATTAT
1 TATTGTATTA-TATCATATTAT
2593669 TATTAGTATTATATCATATTAT
1 TATT-GTATTATATCATATTAT
2593691 TATTGCTATTA-A-CATTATTAT
1 TATTG-TATTATATCA-TATTAT
2593712 TAT
1 TAT
2593715 GTTAAATTAC
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
20 2 0.05
21 11 0.27
22 23 0.56
23 5 0.12
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.57
Consensus pattern (21 bp):
TATTGTATTATATCATATTAT
Found at i:2593678 original size:6 final size:5
Alignment explanation
Indices: 2593658--2593745 Score: 52
Period size: 5 Copynumber: 16.4 Consensus size: 5
2593648 ATTGTTTTAC
* * *
2593658 TATTA TATTA TTATTA GTATTA TATCA TATTA TTATTGC TATTAA CATTA
1 TATTA TATTA -TATTA -TATTA TATTA TATTA -TATT-A TATT-A TATTA
* * *
2593708 TTATTA TGTTA AATTA CTATTA T-TAA TATTA TATTA TA
1 -TATTA TATTA TATTA -TATTA TATTA TATTA TATTA TA
2593746 ATTACTTACT
Statistics
Matches: 63, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
4 3 0.05
5 31 0.49
6 29 0.46
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (5 bp):
TATTA
Found at i:2593688 original size:19 final size:17
Alignment explanation
Indices: 2593658--2593692 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
2593648 ATTGTTTTAC
2593658 TATTATATTATTATTAG
1 TATTATATTATTATTAG
2593675 TATTATATCATATTATTA
1 TATTATAT--TATTATTA
2593693 TTGCTATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (17 bp):
TATTATATTATTATTAG
Found at i:2595009 original size:2 final size:2
Alignment explanation
Indices: 2595002--2595034 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2594992 ATCCTAACCC
2595002 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2595035 TTCCTCCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2597557 original size:27 final size:27
Alignment explanation
Indices: 2597527--2597578 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2597517 TTGAAAATAA
2597527 AAATGAATA-AATAATTATTAAAAAATT
1 AAATGAA-ACAATAATTATTAAAAAATT
* *
2597554 AAATTAAACTATAATTATTAAAAAA
1 AAATGAAACAATAATTATTAAAAAA
2597579 ATCATTACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 1 0.05
27 21 0.95
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (27 bp):
AAATGAAACAATAATTATTAAAAAATT
Found at i:2598609 original size:29 final size:29
Alignment explanation
Indices: 2598551--2598611 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
2598541 AATGGTATTA
* *
2598551 AAATGTAAATAAATAATGTAAAGGTGCTG
1 AAATGAAAATAAATAATGTAAAGGTACTG
2598580 AAATGAAAATAAAATAAAT-TAAA-GTACTG
1 AAATGAAAAT-AAAT-AATGTAAAGGTACTG
2598609 AAA
1 AAA
2598612 CTAAAATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 17 0.61
30 8 0.29
31 3 0.11
ACGTcount: A:0.57, C:0.03, G:0.15, T:0.25
Consensus pattern (29 bp):
AAATGAAAATAAATAATGTAAAGGTACTG
Done.